Staining in Microscopy Related Topics

Topics Related to Staining from Wikipedia

PDF generated using the open source mwlib toolkit. See http://code.pediapress.com/ for more information. PDF generated at: Sun, 08 Jul 2012 12:54:42 UTC

Contents
Articles
Amino acid Bacteria Bacteriology Biochemistry Biological membrane Blood Blood cell Bone Bone marrow Carbohydrate Cell (biology) Cell biology Cell membrane Cell nucleus Cell wall Cellular microbiology Collagen Connective tissue Copolymer Cytoplasm DNA Fecal fat test Flow cytometry Glucose Glycogen Glycoprotein Histology Immunohistochemistry Immunology Lipid Lipopolysaccharide Metabolism Microbial ecology Microbial genetics 1 16 40 40 49 51 67 68 79 84 91 101 105 112 128 135 136 148 150 154 156 180 181 188 197 201 205 211 216 221 232 237 256 258

Microbiology Mitochondrion Molecular microbiology Morphology (biology) Mucin Mycology Myofibril Nerve Nissl body Nucleic acid Organelle Parasitology Peptidoglycan Plant Polymer Polysaccharide Prion Protein Proteoglycan Red blood cell RNA Starch Tissue (biology) Virology Virus

258 264 282 286 288 290 293 296 298 299 303 309 312 315 332 343 350 364 378 380 391 400 408 414 421

References
Article Sources and Contributors Image Sources, Licenses and Contributors 449 463

Article Licenses
License 470

Amino acid

1

Amino acid
Amino acids (  /əˈmiːnoʊ/, /əˈmaɪnoʊ/, or /ˈæmɪnoʊ/) are molecules containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen. They are particularly important in biochemistry, where the term usually refers to alpha-amino acids. An alpha-amino acid has the generic formula H2NCHRCOOH, where R is an organic substituent;[1] the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (the α–carbon). Other types of amino acid exist when the amino group is attached to a different carbon atom; for example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the amino group attaches is separated from the carboxylate group by two other carbon atoms. The various alpha-amino acids differ in which side-chain (R-group) is attached to their alpha carbon, and can vary in size from just one hydrogen atom in glycine to a large heterocyclic group in tryptophan. Amino acids serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids can be linked together in varying sequences to form a vast variety of proteins.[2] Twenty amino acids are naturally incorporated into polypeptides and are called proteinogenic or standard amino acids. These 20 are encoded by the universal genetic code. Nine standard amino acids are called "essential" for humans because they cannot be created from other compounds by the human body, and so must be taken in as food.
The generic structure of an alpha amino acid in its unionized form

The 21 amino acids found in eukaryotes, grouped according to their side-chains' pKas and charge at physiological pH 7.4

Amino acids are important in nutrition and are commonly used in nutrition supplements, fertilizers, food technology and industry. In industry, applications include the production of biodegradable plastics, drugs, and chiral catalysts.

History
The first few amino acids were discovered in the early 19th century. In 1806, the French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, the

Amino acid first amino acid to be discovered.[3][4] Another amino acid that was discovered in the early 19th century was cystine, in 1810,[5] although its monomer, cysteine, was discovered much later, in 1884.[4][6] Glycine and leucine were also discovered around this time, in 1820.[7] Usage of the term amino acid in the English language is from 1898.[8] Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister proposed that proteins are the result of the formation of bonds between the amino group of one amino acid with the carboxyl group of another in a linear structure which Fischer termed peptide.[9]

2

General structure
Further information: Proteinogenic amino acid In the structure shown at the top of the page, R represents a side-chain specific to each amino acid. The carbon atom next to the carboxyl group is called the α–carbon and amino acids with a side-chain bonded to this carbon are referred to as alpha amino acids. These are the most common form found in nature. In the alpha amino acids, the α–carbon is a chiral carbon atom, with the exception of glycine.[10] In amino acids that have a carbon chain attached to the α–carbon (such as lysine, shown to the right) the carbons are labeled in order as α, β, γ, δ, and so on.[11] In some amino acids, the amine group is attached to the β or γ-carbon, and these are therefore referred to as beta or gamma amino acids. Amino acids are usually classified by the properties of their side-chain into four groups. The side-chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side-chain is polar or a hydrophobe if it is nonpolar.[10] The chemical structures of the 22 standard amino acids, along with their chemical properties, are described more fully in the article on these proteinogenic amino acids.

Lysine with the carbon atoms in the side-chain labeled

The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side-chains that are non-linear; these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side-group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position.[10] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group,[12] although it is still classed as an amino acid in the current biochemical nomenclature,[13] and may also be called an "N-alkylated alpha-amino acid".[14]

Isomerism
Of the standard α-amino acids, all but glycine can exist in either of two optical isomers, called L or D amino acids, which are mirror images of each other (see also Chirality). While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome, D-amino acids are found in some proteins produced by enzyme posttranslational modifications after translation and translocation to the endoplasmic reticulum, as in exotic sea-dwelling organisms such as The two optical isomers of alanine, D-Alanine cone snails.[15] They are also abundant components of the and L-Alanine peptidoglycan cell walls of bacteria,[16] and D-serine may act as a neurotransmitter in the brain.[17] The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can, in theory, be synthesized (D-glyceraldehyde is dextrorotary; L-glyceraldehyde is levorotatory). In alternative fashion, the (S) and (R) designators are used to indicate

Amino acid the absolute stereochemistry. Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral.[18] Cysteine is unusual since it has a sulfur atom at the second position in its side-chain, which has a larger atomic mass than the groups attached to the first carbon, which is attached to the α-carbon in the other standard amino acids, thus the (R) instead of (S).

3

Zwitterions
The amine and carboxylic acid functional groups found in amino acids allow them to have amphiprotic properties.[10] Carboxylic acid groups (−CO2H) can be deprotonated to become negative carboxylates (−CO2− ), and α-amino groups (NH2−) can be protonated to become positive + α-ammonium groups ( NH3−). At pH An amino acid in its (1) unionized and (2) zwitterionic forms values greater than the pKa of the carboxylic acid group (mean for the 20 common amino acids is about 2.2, see the table of amino acid structures above), the negative carboxylate ion predominates. At pH values lower than the pKa of the α-ammonium group (mean for the 20 common α-amino acids is about 9.4), the nitrogen is predominantly protonated as a positively charged α-ammonium group. Thus, at pH between 2.2 and 9.4, the predominant form adopted by α-amino acids contains a negative carboxylate and a positive α-ammonium group, as shown in structure (2) on the right, so has net zero charge. This molecular state is known as a zwitterion, from the German Zwitter meaning hermaphrodite or hybrid.[19] Below pH 2.2, the predominant form will have a neutral carboxylic acid group and a positive α-ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral α-amino group (net charge −1). The fully neutral form (structure (1) on the right) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 107). Amino acids also exist as zwitterions in the solid phase, and crystallize with salt-like properties unlike typical organic acids or amines.

Isoelectric point
At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.[20] This pH is known as the isoelectric point pI, so pI = ½(pKa1 + pKa2). The individual amino acids all have slightly different pKa values, so have different isoelectric points. For amino acids with charged side-chains, the pKa of the side-chain is involved. Thus for Asp, Glu with negative side-chains, pI = ½(pKa1 + pKaR), where pKaR is the side-chain pKa. Cysteine also has potentially negative side-chain with pKaR = 8.14, so pI should be calculated as for Asp and Glu, even though the side-chain is not significantly charged at neutral pH. For His, Lys, and Arg with positive side-chains, pI = ½(pKaR + pKa2). Amino acids have zero mobility in electrophoresis at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isolectric point and some amino acids (in particular, with non-polar side-chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.

Amino acid

4

Occurrence and functions in biochemistry
Standard amino acids
Amino acids are the structural units that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a A polypeptide is an unbranched chain of amino acids. growing protein chain by a ribozyme that is [21] called a ribosome. The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism's genes. Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids.[10] Of these, 20 are encoded by the universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon.[22] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG, which is normally a stop codon in other organisms.[23] This UAG codon is followed by a PYLIS downstream sequence.[24]

Non-standard amino acids
Aside from the 22 standard amino acids, there are many other amino acids that are called non-proteinogenic or non-standard. Those either are not found in proteins (for example carnitine, GABA), or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine). Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. These modifications are often essential for the The amino acid selenocysteine function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations,[25] and the hydroxylation of proline is critical for maintaining connective tissues.[26] Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue.[27] Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.[28]

Amino acid

5

Some nonstandard amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).[29] A β-alanine and its α-alanine isomer rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A.[30]

In human nutrition
Further information: Protein in nutrition and Amino acid synthesis When taken up into the human body from the diet, the 22 standard amino acids either are used to synthesize proteins and other biomolecules or are oxidized to urea and carbon dioxide as a source of energy.[31] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.[32] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.[33] Pyrrolysine trait is restricted to several microbes, and only one organism has both Pyl and Sec. Of the 22 standard amino acids, 9 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.[34] In addition, cysteine, taurine, tyrosine, and arginine are semiessential amino-acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.[35][36] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.
Essential Histidine Isoleucine Leucine Lysine Methionine Nonessential Alanine Arginine* Asparagine Aspartic acid Cysteine*

Phenylalanine Glutamic acid Threonine Tryptophan Valine Glutamine* Glycine Ornithine* Proline* Selenocysteine* Serine* Taurine* Tyrosine*

(*) Essential only in certain cases.[37][38]

Amino acid

6

Non-protein functions
Further information: Amino acid neurotransmitter In humans, non-protein amino acids also have important roles as metabolic intermediates, such as in the biosynthesis of the neurotransmitter gamma-aminobutyric acid. Many amino acids are used to synthesize other molecules, for example: • • • • • • • Tryptophan is a precursor of the neurotransmitter serotonin.[39] Tyrosine is a precursor of the neurotransmitter dopamine. Glycine is a precursor of porphyrins such as heme.[40] Arginine is a precursor of nitric oxide.[41] Ornithine and S-adenosylmethionine are precursors of polyamines.[42] Aspartate, glycine, and glutamine are precursors of nucleotides.[43] Phenylalanine is a precursor of various phenylpropanoids, which are important in plant metabolism.

However, not all of the functions of other abundant non-standard amino acids are known. For example, taurine is a major amino acid in muscle and brain tissues, but, although many functions have been proposed, its precise role in the body has not been determined.[44] Some non-standard amino acids are used as defenses against herbivores in plants.[45] For example canavanine is an analogue of arginine that is found in many legumes,[46] and in particularly large amounts in Canavalia gladiata (sword bean).[47] This amino acid protects the plants from predators such as insects and can cause illness in people if some types of legumes are eaten without processing.[48] The non-protein amino acid mimosine is found in other species of legume, particularly Leucaena leucocephala.[49] This compound is an analogue of tyrosine and can poison animals that graze on these plants.

Uses in technology
Amino acids are used for a variety of applications in industry, but their main use is as additives to animal feed. This is necessary, since many of the bulk components of these feeds, such as soybeans, either have low levels or lack some of the essential amino acids: Lysine, methionine, threonine, and tryptophan are most important in the production of these feeds.[50] In this industry, amino acids are also used to chelate metal cations in order to improve the absorption of minerals from supplements, which may be required to improve the health or production of these animals.[51] The food industry is also a major consumer of amino acids, in particular, glutamic acid, which is used as a flavor enhancer,[52] and Aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener.[53] Similar technology to that used for animal nutrition is employed in the human nutrition industry to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation.[54] The chelating ability of amino acids has been used in fertilizers for agriculture to facilitate the delivery of minerals to plants in order to correct mineral deficiencies, such as iron chlorosis. These fertilizers are also used to prevent deficiencies from occurring and improving the overall health of the plants.[55] The remaining production of amino acids is used in the synthesis of drugs and cosmetics.[50]

Amino acid

7

Amino acid derivative 5-HTP (5-hydroxytryptophan) L-DOPA (L-dihydroxyphenylalanine) Eflornithine

Pharmaceutical application Experimental treatment for depression. Treatment for Parkinsonism. [57] [58] [56]

Drug that inhibits ornithine decarboxylase and is used in the treatment of sleeping sickness.

Expanded genetic code
Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins.[59][60]

Chemical building blocks
Further information: Asymmetric synthesis Amino acids are important as low-cost feedstocks. These compounds are used in chiral pool synthesis as enantiomerically-pure building blocks.[61] Amino acids have been investigated as precursors chiral catalysts, e.g., for asymmetric hydrogenation reactions, although no commercial applications exist.[62]

Biodegradable plastics
Further information: Biodegradable plastic and Biopolymer Amino acids are under development as components of a range of biodegradable polymers. These materials have applications as environmentally friendly packaging and in medicine in drug delivery and the construction of prosthetic implants. These polymers include polypeptides, polyamides, polyesters, polysulfides, and polyurethanes with amino acids either forming part of their main chains or bonded as side-chains. These modifications alter the physical properties and reactivities of the polymers.[63] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.[64] Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradeable anti-scaling agent and a corrosion inhibitor.[65][66] In addition, the aromatic amino acid tyrosine is being developed as a possible replacement for toxic phenols such as bisphenol A in the manufacture of polycarbonates.[67]

Reactions
As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group.[68] The combination of these functional groups allow amino acids to be effective polydentate ligands for metal-amino acid chelates.[69] The multiple side-chains of amino acids can also undergo chemical reactions.[70] The types of these reactions are determined by the groups on these side-chains and are, therefore, different between the various types of amino acid.

Amino acid

8

Chemical synthesis
Several methods exist to synthesize amino acids. One of the oldest methods begins with the bromination at the α-carbon of a carboxylic acid. The Strecker amino acid synthesis Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid.[71] In alternative fashion, the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia, this produces an α-amino nitrile as an intermediate. Hydrolysis of the nitrile in acid then yields a α-amino acid.[72] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, while substituting primary and secondary amines will yield substituted amino acids.[73] Likewise, using ketones, instead of aldehydes, gives α,α-disubstituted amino [74] acids. The classical synthesis gives racemic mixtures of α-amino acids as products, but several alternative procedures using asymmetric auxiliaries [75] or asymmetric catalysts [76][77] have been developed.[78] At the current time, the most-adopted method is an automated synthesis on a solid support (e.g., polystyrene beads), using protecting groups (e.g., Fmoc and t-Boc) and activating groups (e.g., DCC and DIC).

Peptide bond formation
As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[79] This The condensation of two amino acids to form a peptide bond aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.[80] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving towards their C-terminus. However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids.[81] In the first step gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side-chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione.[82]

Amino acid In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.[83] The ability to easily synthesize vast numbers of different peptides by varying the types and order of amino acids (using combinatorial chemistry) has made peptide synthesis particularly important in creating libraries of peptides for use in drug discovery through high-throughput screening.[84]

9

Biosynthesis
In plants, nitrogen is first assimilated into organic compounds in the form of glutamate, formed from alpha-ketoglutarate and ammonia in the mitochondrion. In order to form other amino acids, the plant uses transaminases to move the amino group to another alpha-keto carboxylic acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate.[85] Other organisms use transaminases for amino acid synthesis, too. Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine,[44] while hydroxyproline is made by a posttranslational modification of proline.[86] Microorganisms and plants can synthesize many uncommon amino acids. For example, some microbes make 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidic lantibiotics such as alamethicin.[87] While in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene.[88]

Catabolism
Degradation of an amino acid often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia.[90] After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle, as detailed in image at right.

Catabolism of proteinogenic amino acids. Amino acids can be classified according [89] to the properties of their main products as either of the following: Glucogenic, with the products having the ability to form glucose by gluconeogenesisKetogenic, with the products not having the ability to form glucose. These products may still be used for ketogenesis or lipid synthesis.Amino acids catabolized into both glucogenic and ketogenic products.

Physicochemical properties of amino acids

Amino acid The 20 amino acids encoded directly by the genetic code can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups.[10] These properties are important for protein structure and protein–protein interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side-chains are exposed to the aqueous solvent. The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between these two extremes, some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. There are different hydrophobicity scales of amino acid residues.[91] Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteine residues, proline that forms a cycle to the polypeptide backbone, and glycine that is more flexible than other amino acids. Many proteins undergo a range of posttranslational modifications, when additional chemical groups are attached to the amino acids in proteins. Some modifications can produce hydrophobic lipoproteins,[92] or hydrophilic glycoproteins.[93] These type of modification allow the reversible targeting of a protein to a membrane. For example, the addition and removal of the fatty acid palmitic acid to cysteine residues in some signaling proteins causes the proteins to attach and then detach from cell membranes.[94]

10

Table of standard amino acid abbreviations and properties
Amino Acid 3-Letter [95] 1-Letter [95] Side-chain [95] polarity nonpolar polar polar polar polar polar polar nonpolar polar Side-chain charge [95] (pH 7.4) neutral positive neutral negative neutral negative neutral neutral positive(10%) neutral(90%) neutral neutral positive neutral neutral neutral neutral neutral neutral Hydropathy [96] index 1.8 −4.5 −3.5 −3.5 2.5 −3.5 −3.5 −0.4 −3.2 211 5.9 250 0.3 Absorbance [97] λmax(nm) ε at λmax (x10−3 [97] M−1 cm−1)

Alanine Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine

Ala Arg Asn Asp Cys Glu Gln Gly His

A R N D C E Q G H

Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan

Ile Leu Lys Met Phe Pro Ser Thr Trp

I L K M F P S T W

nonpolar nonpolar polar nonpolar nonpolar nonpolar polar polar nonpolar

4.5 3.8 −3.9 1.9 2.8 −1.6 −0.8 −0.7 −0.9 280, 219 5.6, 47.0 257, 206, 188 0.2, 9.3, 60.0

Amino acid

11
Tyr Val Y V polar nonpolar neutral neutral −1.3 4.2 274, 222, 193 1.4, 8.0, 48.0

Tyrosine Valine

In addition, there are two additional amino acids that are incorporated by overriding stop codons:
21st and 22nd amino acids 3-Letter 1-Letter Selenocysteine Pyrrolysine Sec Pyl U O

In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue.
Ambiguous Amino Acids Asparagine or aspartic acid Glutamine or glutamic acid Leucine or Isoleucine Unspecified or unknown amino acid 3-Letter 1-Letter Asx Glx Xle Xaa B Z J X

Unk is sometimes used instead of Xaa, but is less standard. In addition, many non-standard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and MG132, are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz-Phe-boroLeu, and MG132 is Z-Leu-Leu-Leu-al. To aid in the analysis of protein structure, photocrosslinking amino acid analogues are available. These include photoleucine (pLeu) and photomethionine (pMet).[98]

References and notes
[1] Proline is an exception to this general formula. It lacks the NH2 group because of the cyclization of the side-chain and is known as an imino acid; it falls under the category of special structured amino acids. [2] "The Structures of Life" (http:/ / publications. nigms. nih. gov/ structlife/ chapter1. html). National Institute of General Medical Sciences. . Retrieved 2008-05-20. [3] Vauquelin LN, Robiquet PJ (1806). "The discovery of a new plant principle in Asparagus sativus". Annales de Chimie 57: 88–93. [4] Anfinsen CB, Edsall JT, Richards FM (1972). Advances in Protein Chemistry. New York: Academic Press. pp. 99, 103. ISBN 978-0-12-034226-6. [5] Wollaston WH (1810). "On cystic oxide, a new species of urinary calculus". Philosophical Transactions of the Royal Society of London 100 (0): 223–30. doi:10.1098/rstl.1810.0015. [6] Baumann E (1884). "Über cystin und cystein" (http:/ / vlp. mpiwg-berlin. mpg. de/ library/ data/ lit16533). Z Physiol Chemie 8 (4): 299–305. Archived (http:/ / web. archive. org/ web/ 20110314075450/ http:/ / vlp. mpiwg-berlin. mpg. de/ library/ data/ lit16533) from the original on 14 March 2011. . Retrieved 28 March 2011. [7] Braconnot HM (1820). "Sur la conversion des matières animales en nouvelles substances par le moyen de l'acide sulfurique". Ann Chim Phys Ser 2 13: 113–25. [8] "etymonline.com entry for amino" (http:/ / www. etymonline. com/ index. php?term=amino). www.etymonline.com. . Retrieved 2010-07-19. [9] Joseph S. Fruton (1990). "Chapter 5- Emil Fischer and Franz Hofmeister". Contrasts in Scientific Style: Research Groups in the Chemical and Biochemical Sciences,. 191. American Philosophical Society. pp. 163–165. ISBN 0-87169-191-4. [10] Creighton, Thomas H. (1993). "Chapter 1". Proteins: structures and molecular properties. San Francisco: W. H. Freeman. ISBN 978-0-7167-7030-5. [11] "Nomenclature and Symbolism for Amino Acids and Peptides" (http:/ / www. chem. qmul. ac. uk/ iupac/ AminoAcid/ AA1n2. html). IUPAC-IUB Joint Commission on Biochemical Nomenclature. 1983. Archived (http:/ / web. archive. org/ web/ 20081009023202/ http:/ / www. chem. qmul. ac. uk/ iupac/ AminoAcid/ AA1n2. html) from the original on 9 October 2008. . Retrieved 2008-11-17. [12] Jodidi, S. L. (1926-03-01). "The Formol Titration of Certain Amino Acids". Journal of the American Chemical Society 48 (3): 751–753. doi:10.1021/ja01414a033. [13] Liebecq, Claude, ed. (1992). Biochemical Nomenclature and Related Documents (2nd ed.). Portland Press. pp. 39–69. ISBN 978-1-85578-005-7.

Amino acid
[14] Smith, Anthony D. (1997). Oxford dictionary of biochemistry and molecular biology. Oxford: Oxford University Press. pp. 535. ISBN 978-0-19-854768-6. OCLC 37616711. [15] Pisarewicz K, Mora D, Pflueger FC, Fields GB, Marí F (May 2005). "Polypeptide chains containing D-gamma-hydroxyvaline". Journal of the American Chemical Society 127 (17): 6207–15. doi:10.1021/ja050088m. PMID 15853325. [16] van Heijenoort J (March 2001). "Formation of the glycan chains in the synthesis of bacterial peptidoglycan". Glycobiology 11 (3): 25R–36R. doi:10.1093/glycob/11.3.25R. PMID 11320055. [17] Wolosker H, Dumin E, Balan L, Foltyn VN (July 2008). "D-amino acids in the brain: D-serine in neurotransmission and neurodegeneration". The FEBS Journal 275 (14): 3514–26. doi:10.1111/j.1742-4658.2008.06515.x. PMID 18564180. [18] Hatem, Salama Mohamed Ali (2006). "Gas chromatographic determination of Amino Acid Enantiomers in tobacco and bottled wines" (http:/ / geb. uni-giessen. de/ geb/ volltexte/ 2006/ 3038/ index. html). University of Giessen. . Retrieved 2008-11-17. [19] Simmons, William J.; Gerhard Meisenberg (2006). Principles of medical biochemistry. Mosby Elsevier. p. 19. ISBN 0-323-02942-6. [20] Fennema OR. Food Chemistry 3rd Ed. CRC Press. pp. 327–8. ISBN 0-8247-9691-8. [21] Rodnina MV, Beringer M, Wintermeyer W (January 2007). "How ribosomes make peptide bonds". Trends in Biochemical Sciences 32 (1): 20–6. doi:10.1016/j.tibs.2006.11.007. PMID 17157507. [22] Driscoll DM, Copeland PR (2003). "Mechanism and regulation of selenoprotein synthesis". Annual Review of Nutrition 23 (1): 17–40. doi:10.1146/annurev.nutr.23.011702.073318. PMID 12524431. [23] Krzycki JA (December 2005). "The direct genetic encoding of pyrrolysine". Current Opinion in Microbiology 8 (6): 706–12. doi:10.1016/j.mib.2005.10.009. PMID 16256420. [24] Théobald-Dietrich A, Giegé R, Rudinger-Thirion J (2005). "Evidence for the existence in mRNAs of a hairpin element responsible for ribosome dependent pyrrolysine insertion into proteins". Biochimie 87 (9–10): 813–7. doi:10.1016/j.biochi.2005.03.006. PMID 16164991. [25] Vermeer C (March 1990). "Gamma-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase". The Biochemical Journal 266 (3): 625–36. PMC 1131186. PMID 2183788. [26] Bhattacharjee A, Bansal M (March 2005). "Collagen structure: the Madras triple helix and the current scenario". IUBMB Life 57 (3): 161–72. doi:10.1080/15216540500090710. PMID 16036578. [27] Park MH (February 2006). "The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)". Journal of Biochemistry 139 (2): 161–9. doi:10.1093/jb/mvj034. PMC 2494880. PMID 16452303. [28] Blenis J, Resh MD (December 1993). "Subcellular localization specified by protein acylation and phosphorylation". Current Opinion in Cell Biology 5 (6): 984–9. doi:10.1016/0955-0674(93)90081-Z. PMID 8129952. [29] Curis E, Nicolis I, Moinard C et al. (November 2005). "Almost all about citrulline in mammals". Amino Acids 29 (3): 177–205. doi:10.1007/s00726-005-0235-4. PMID 16082501. [30] Coxon KM, Chakauya E, Ottenhof HH et al. (August 2005). "Pantothenate biosynthesis in higher plants". Biochemical Society Transactions 33 (Pt 4): 743–6. doi:10.1042/BST0330743. PMID 16042590. [31] Sakami W, Harrington H (1963). "Amino acid metabolism". Annual Review of Biochemistry 32 (1): 355–98. doi:10.1146/annurev.bi.32.070163.002035. PMID 14144484. [32] Brosnan JT (April 2000). "Glutamate, at the interface between amino acid and carbohydrate metabolism" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=10736367). The Journal of Nutrition 130 (4S Suppl): 988S–90S. PMID 10736367. . [33] Young VR, Ajami AM (September 2001). "Glutamine: the emperor or his clothes?" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=11533293). The Journal of Nutrition 131 (9 Suppl): 2449S–59S; discussion 2486S–7S. PMID 11533293. . [34] Young VR (August 1994). "Adult amino acid requirements: the case for a major revision in current recommendations" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=8064412). The Journal of Nutrition 124 (8 Suppl): 1517S–1523S. PMID 8064412. . [35] Imura K, Okada A (January 1998). "Amino acid metabolism in pediatric patients". Nutrition 14 (1): 143–8. doi:10.1016/S0899-9007(97)00230-X. PMID 9437700. [36] Lourenço R, Camilo ME (2002). "Taurine: a conditionally essential amino acid in humans? An overview in health and disease". Nutrición Hospitalaria 17 (6): 262–70. PMID 12514918. [37] Fürst P, Stehle P (June 2004). "What are the essential elements needed for the determination of amino acid requirements in humans?" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=15173430). The Journal of Nutrition 134 (6 Suppl): 1558S–1565S. PMID 15173430. . [38] Reeds PJ (July 2000). "Dispensable and indispensable amino acids for humans" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=10867060). The Journal of Nutrition 130 (7): 1835S–40S. PMID 10867060. . [39] Savelieva KV, Zhao S, Pogorelov VM et al. (2008). Bartolomucci, Alessandro. ed. "Genetic disruption of both tryptophan hydroxylase genes dramatically reduces serotonin and affects behavior in models sensitive to antidepressants". PloS ONE 3 (10): e3301. Bibcode 2008PLoSO...3.3301S. doi:10.1371/journal.pone.0003301. PMC 2565062. PMID 18923670. [40] Shemin D, Rittenberg D (1 December 1946). "The biological utilization of glycine for the synthesis of the protoporphyrin of hemoglobin" (http:/ / www. jbc. org/ cgi/ reprint/ 166/ 2/ 621). Journal of Biological Chemistry 166 (2): 621–5. PMID 20276176. . [41] Tejero J, Biswas A, Wang ZQ et al. (November 2008). "Stabilization and characterization of a heme-oxy reaction intermediate in inducible nitric-oxide synthase". The Journal of Biological Chemistry 283 (48): 33498–507. doi:10.1074/jbc.M806122200. PMC 2586280. PMID 18815130. [42] Rodríguez-Caso C, Montañez R, Cascante M, Sánchez-Jiménez F, Medina MA (August 2006). "Mathematical modeling of polyamine metabolism in mammals". The Journal of Biological Chemistry 281 (31): 21799–812. doi:10.1074/jbc.M602756200. PMID 16709566.

12

Amino acid
[43] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). Biochemistry. San Francisco: W.H. Freeman. pp. 693–8. ISBN 0-7167-4684-0. [44] Brosnan JT, Brosnan ME (June 2006). "The sulfur-containing amino acids: an overview" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=16702333). The Journal of Nutrition 136 (6 Suppl): 1636S–1640S. PMID 16702333. . [45] Hylin, John W. (1969). "Toxic peptides and amino acids in foods and feeds". Journal of Agricultural and Food Chemistry 17 (3): 492–6. doi:10.1021/jf60163a003. [46] Turner, B. L.; Harborne, J. B. (1967). "Distribution of canavanine in the plant kingdom". Phytochemistry 6 (6): 863–66. doi:10.1016/S0031-9422(00)86033-1. [47] Ekanayake S, Skog K, Asp NG (May 2007). "Canavanine content in sword beans (Canavalia gladiata): analysis and effect of processing". Food and Chemical Toxicology 45 (5): 797–803. doi:10.1016/j.fct.2006.10.030. PMID 17187914. [48] Rosenthal GA (2001). "L-Canavanine: a higher plant insecticidal allelochemical". Amino Acids 21 (3): 319–30. doi:10.1007/s007260170017. PMID 11764412. [49] Hammond AC (May 1995). "Leucaena toxicosis and its control in ruminants" (http:/ / jas. fass. org/ cgi/ pmidlookup?view=long& pmid=7665380). Journal of Animal Science 73 (5): 1487–92. PMID 7665380. . [50] Leuchtenberger W, Huthmacher K, Drauz K (November 2005). "Biotechnological production of amino acids and derivatives: current status and prospects". Applied Microbiology and Biotechnology 69 (1): 1–8. doi:10.1007/s00253-005-0155-y. PMID 16195792. [51] Ashmead, H. DeWayne (1993). The Role of Amino Acid Chelates in Animal Nutrition. Westwood: Noyes Publications. [52] Garattini S (April 2000). "Glutamic acid, twenty years later" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=10736350). The Journal of Nutrition 130 (4S Suppl): 901S–9S. PMID 10736350. . [53] Stegink LD (July 1987). "The aspartame story: a model for the clinical testing of a food additive" (http:/ / www. ajcn. org/ cgi/ pmidlookup?view=long& pmid=3300262). The American Journal of Clinical Nutrition 46 (1 Suppl): 204–15. PMID 3300262. . [54] Albion Laboratories, Inc.. "Albion Ferrochel Website" (http:/ / www. albionferrochel. com). . Retrieved Cited: July 12, 2011. [55] Ashmead, H. DeWayne (1986). Foliar Feeding of Plants with Amino Acid Chelates. Park Ridge: Noyes Publications. [56] Turner EH, Loftis JM, Blackwell AD (March 2006). "Serotonin a la carte: supplementation with the serotonin precursor 5-hydroxytryptophan". Pharmacology & Therapeutics 109 (3): 325–38. doi:10.1016/j.pharmthera.2005.06.004. PMID 16023217. [57] Kostrzewa RM, Nowak P, Kostrzewa JP, Kostrzewa RA, Brus R (March 2005). "Peculiarities of L: -DOPA treatment of Parkinson's disease". Amino Acids 28 (2): 157–64. doi:10.1007/s00726-005-0162-4. PMID 15750845. [58] Heby O, Persson L, Rentala M (August 2007). "Targeting the polyamine biosynthetic enzymes: a promising approach to therapy of African sleeping sickness, Chagas' disease, and leishmaniasis". Amino Acids 33 (2): 359–66. doi:10.1007/s00726-007-0537-9. PMID 17610127. [59] Xie J, Schultz PG (December 2005). "Adding amino acids to the genetic repertoire". Curr Opin Chem Biol 9 (6): 548–54. doi:10.1016/j.cbpa.2005.10.011. PMID 16260173. [60] Wang Q, Parrish AR, Wang L (March 2009). "Expanding the genetic code for biological studies". Chem. Biol. 16 (3): 323–36. doi:10.1016/j.chembiol.2009.03.001. PMC 2696486. PMID 19318213. [61] Hanessian, S. (1993). "Reflections on the total synthesis of natural products: Art, craft, logic, and the chiron approach". Pure and Applied Chemistry 65 (6): 1189–204. doi:10.1351/pac199365061189. [62] Blaser, Hans Ulrich (1992). "The chiral pool as a source of enantioselective catalysts and auxiliaries". Chemical Reviews 92 (5): 935–52. doi:10.1021/cr00013a009. [63] Sanda, Fumio; Endo, Takeshi (1999). "Feature Article Syntheses and functions of polymers based on amino acids". Macromolecular Chemistry and Physics 200 (12): 2651–61. doi:10.1002/(SICI)1521-3935(19991201)200:12<2651::AID-MACP2651>3.0.CO;2-P. [64] Gross, R. A.; Kalra, B. (2002). "Biodegradable Polymers for the Environment" (http:/ / www. sciencemag. org/ cgi/ content/ abstract/ 297/ 5582/ 803). Science 297 (5582): 803–807. Bibcode 2002Sci...297..803G. doi:10.1126/science.297.5582.803. PMID 12161646. . [65] Low, K. C.; Wheeler, A. P.; Koskan, L. P. (1996). Commercial poly(aspartic acid) and Its Uses. Advances in Chemistry Series. 248. Washington, D.C.: American Chemical Society. [66] Thombre, S.M.; Sarwade, B.D. (2005). "Synthesis and Biodegradability of Polyaspartic Acid: A Critical Review" (http:/ / www. informaworld. com/ index/ 718581646. pdf). Journal of Macromolecular Science, Part A 42 (9): 1299–1315. doi:10.1080/10601320500189604. . [67] Bourke, S. L.; Kohn, J. (2003). "Polymers derived from the amino acid l-tyrosine: polycarbonates, polyarylates and copolymers with poly(ethylene glycol)" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0169409X03000383). Advanced Drug Delivery Reviews 55 (4): 447–466. doi:10.1016/S0169-409X(03)00038-3. PMID 12706045. . [68] Elmore, Donald Trevor; Barrett, G. C. (1998). Amino acids and peptides. Cambridge, UK: Cambridge University Press. pp. 48–60. ISBN 0-521-46827-2. [69] Konar, Sanjit; et al. (2010). "Structural determination and characterization of copper and zinc bis-glycinates with X-ray crystallography and mass spectrometry". Journal of Coordination Chemistry 63 (19). [70] Gutteridge A, Thornton JM (November 2005). "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences 30 (11): 622–9. doi:10.1016/j.tibs.2005.09.006. PMID 16214343. [71] McMurry, John (1996). Organic chemistry. Pacific Grove, CA, USA: Brooks/Cole. p. 1064. ISBN 0-534-23832-7. [72] Strecker, Adolph (1850). "Ueber die künstliche Bildung der Milchsäure und einen neuen, dem Glycocoll homologen Körper". Justus Liebigs Annalen der Chemie 75 (1): 27–45. doi:10.1002/jlac.18500750103.

13

Amino acid
[73] Strecker, Adolph (1854). "Ueber einen neuen aus Aldehyd — Ammoniak und Blausäure entstehenden Körper". Justus Liebigs Annalen der Chemie 91 (3): 349–51. doi:10.1002/jlac.18540910309. [74] Masumoto S, Usuda H, Suzuki M, Kanai M, Shibasaki M (May 2003). "Catalytic enantioselective Strecker reaction of ketoimines". Journal of the American Chemical Society 125 (19): 5634–5. doi:10.1021/ja034980. PMID 12733893. [75] Davis, F. A.; Reddy, Rajarathnam E.; Portonovo, Padma S. (1994). "Asymmetric strecker synthesis using enantiopure sulfinimines: A convenient synthesis of α-amino acids". Tetrahedron Letters 35 (50): 9351. doi:10.1016/S0040-4039(00)78540-6. [76] Ishitani, Haruro; Komiyama, Susumu; Hasegawa, Yoshiki; Kobayashi, Shū (2000). "Catalytic Asymmetric Strecker Synthesis. Preparation of Enantiomerically Pure α-Amino Acid Derivatives from Aldimines and Tributyltin Cyanide or Achiral Aldehydes, Amines, and Hydrogen Cyanide Using a Chiral Zirconium Catalyst". Journal of the American Chemical Society 122 (5): 762–6. doi:10.1021/ja9935207. [77] Huang, Jinkun; Corey, E. J. (2004). "A New Chiral Catalyst for the Enantioselective Strecker Synthesis of α-Amino Acids". Orgic Letters 62 (6): 5027–9. doi:10.1021/ol047698w. PMID 15606127. [78] Duthaler, Rudolf O. (1994). "Recent developments in the stereoselective synthesis of α-aminoacids". Tetrahedron 50 (6): 1539–1650. doi:10.1016/S0040-4020(01)80840-1. [79] Ibba M, Söll D (May 2001). "The renaissance of aminoacyl-tRNA synthesis" (http:/ / www. nature. com/ embor/ journal/ v2/ n5/ full/ embor420. html). EMBO Reports 2 (5): 382–7. doi:10.1093/embo-reports/kve095 (inactive 2010-02-18). PMC 1083889. PMID 11375928. . [80] Lengyel P, Söll D (June 1969). "Mechanism of protein biosynthesis" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=4896351). Bacteriological Reviews 33 (2): 264–301. PMC 378322. PMID 4896351. . [81] Wu G, Fang YZ, Yang S, Lupton JR, Turner ND (March 2004). "Glutathione metabolism and its implications for health" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=14988435). The Journal of Nutrition 134 (3): 489–92. PMID 14988435. . [82] Meister A (November 1988). "Glutathione metabolism and its selective modification" (http:/ / www. jbc. org/ cgi/ pmidlookup?view=long& pmid=3053703). The Journal of Biological Chemistry 263 (33): 17205–8. PMID 3053703. . [83] Carpino, Louis A. (1992). "1-Hydroxy-7-azabenzotriazole. An efficient peptide coupling additive". Journal of the American Chemical Society 115 (10): 4397–8. doi:10.1021/ja00063a082. [84] Marasco D, Perretta G, Sabatella M, Ruvo M (October 2008). "Past and future perspectives of synthetic peptide libraries". Current Protein & Peptide Science 9 (5): 447–67. doi:10.2174/138920308785915209. PMID 18855697. [85] Jones, Russell Celyn; Buchanan, Bob B.; Gruissem, Wilhelm (2000). Biochemistry & molecular biology of plants. Rockville, Md: American Society of Plant Physiologists. pp. 371–2. ISBN 0-943088-39-9. [86] Kivirikko KI, Pihlajaniemi T (1998). "Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases". Advances in Enzymology and Related Areas of Molecular Biology 72: 325–98. PMID 9559057. [87] Whitmore L, Wallace BA (May 2004). "Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation". European Biophysics Journal 33 (3): 233–7. doi:10.1007/s00249-003-0348-1. PMID 14534753. [88] Alexander L, Grierson D (October 2002). "Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening". Journal of Experimental Botany 53 (377): 2039–55. doi:10.1093/jxb/erf072. PMID 12324528. [89] Stipanuk, M. H. (2006). Biochemical, physiological, & molecular aspects of human nutrition (2 ed.): Saunders Elsevier. [90] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). Biochemistry. San Francisco: W.H. Freeman. pp. 639–49. ISBN 0-7167-4684-0. [91] Urry, Dan W. (2004). "The change in Gibbs free energy for hydrophobic association: Derivation and evaluation by means of inverse temperature transitions". Chemical Physics Letters 399 (1–3): 177–83. doi:10.1016/S0009-2614(04)01565-9. [92] Magee T, Seabra MC (April 2005). "Fatty acylation and prenylation of proteins: what's hot in fat". Current Opinion in Cell Biology 17 (2): 190–6. doi:10.1016/j.ceb.2005.02.003. PMID 15780596. [93] Pilobello KT, Mahal LK (June 2007). "Deciphering the glycocode: the complexity and analytical challenge of glycomics". Current Opinion in Chemical Biology 11 (3): 300–5. doi:10.1016/j.cbpa.2007.05.002. PMID 17500024. [94] Smotrys JE, Linder ME (2004). "Palmitoylation of intracellular signaling proteins: regulation and function". Annual Review of Biochemistry 73 (1): 559–87. doi:10.1146/annurev.biochem.73.011303.073954. PMID 15189153. [95] Hausman, Robert E.; Cooper, Geoffrey M. (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p. 51. ISBN 0-87893-214-3. [96] Kyte J, Doolittle RF (May 1982). "A simple method for displaying the hydropathic character of a protein". Journal of Molecular Biology 157 (1): 105–32. doi:10.1016/0022-2836(82)90515-0. PMID 7108955. [97] Freifelder, D. (1983). Physical Biochemistry (2nd ed.). W. H. Freeman and Company. ISBN 0-7167-1315-2. [98] Suchanek M, Radzikowska A, Thiele C (April 2005). "Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells". Nature Methods 2 (4): 261–7. doi:10.1038/nmeth752. PMID 15782218.

14

Amino acid

15

Further reading
• Doolittle, Russell F. (1989). "Redundancies in protein sequences". In Fasman, G.D.. Predictions of Protein Structure and the Principles of Protein Conformation. New York: Plenum Press. pp. 599–623. ISBN 978-0-306-43131-9. LCCN 89008555. • Nelson, David L.; Cox, Michael M. (2000). Lehninger Principles of Biochemistry (3rd ed.). Worth Publishers. ISBN 978-1-57259-153-0. LCCN 99049137. • Meierhenrich, Uwe (2008) (PDF, 11.2 MB). Amino acids and the asymmetry of life (http://rogov.zwz.ru/ Macroevolution/amino.pdf). Berlin: Springer Verlag. ISBN 978-3-540-76885-2. LCCN 2008930865. • Morelli, Robert J. (1952). Studies of amino acid absorption from the small intestine. San Francisco.

External links
• The origin of the single-letter code for the amino acids (http://www.biology.arizona.edu/biochemistry/ problem_sets/aa/Dayhoff.html)

Bacteria

16

Bacteria
Bacteria

Scanning electron micrograph of Escherichia coli bacilli

Scientific classification Domain: Bacteria Phyla[1] Gram positive / no outer membrane Actinobacteria (high-G+C) Firmicutes (low-G+C) Tenericutes (no wall) • Gram negative / outer membrane present Aquificae Deinococcus-Thermus Fibrobacteres–Chlorobi/Bacteroidetes (FCB group) Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes–Verrucomicrobia/Chlamydiae (PVC group) Proteobacteria Spirochaetes Synergistetes • Unknown / ungrouped Acidobacteria Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Dictyoglomi Thermodesulfobacteria Thermotogae

Bacteria (English pronunciation: /bækˈtɪəriə/ ( listen); singular: bacterium) are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria are present in most habitats on Earth, growing in soil, acidic hot springs, radioactive waste,[2] water, and deep in the Earth's crust, as well as in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualism in the digestive tracts of humans, termites and cockroaches. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (5×1030) bacteria on Earth,[3] forming a biomass that exceeds that of all plants and animals.[4] Bacteria are vital in recycling nutrients, with many steps in nutrient cycles depending on these

Bacteria organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. In the biological communities surrounding hydrothermal vents and cold seeps, bacteria provide the nutrients needed to sustain life by converting dissolved compounds such as hydrogen sulphide and methane. Most bacteria have not been characterised, and only about half of the phyla of bacteria have species that can be grown in the laboratory.[5] The study of bacteria is known as bacteriology, a branch of microbiology. There are approximately ten times as many bacterial cells in the human flora as there are human cells in the body, with large numbers of bacteria on the skin and as gut flora.[6] The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, and a few are beneficial. However, a few species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa.[7] In developed countries, antibiotics are used to treat bacterial infections and in agriculture, so antibiotic resistance is becoming common. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector,[8] as well as in biotechnology, and the manufacture of antibiotics and other chemicals.[9] Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved independently from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.[10]

17

Etymology
The word bacteria is the plural of the New Latin bacterium, which is the latinisation of the Greek βακτήριον (baktērion),[11] the diminutive of βακτηρία (baktēria), meaning "staff, cane",[12] because the first ones to be discovered were rod-shaped.[13]

History of bacteriology
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design.[14] He called them "animalcules" and published his observations in a series of letters to the Royal Society.[15][16][17] The name Bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1828.[18] In fact, Bacterium was a genus that contained non-spore-forming rod-shaped bacteria,[19] as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835.[20] Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary Robert Koch, Pasteur was an early advocate of Antonie van Leeuwenhoek, the first the germ theory of disease.[21] Robert Koch was a pioneer in medical microbiologist and the first person to observe microbiology and worked on cholera, anthrax and tuberculosis. In his bacteria using a microscope. research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905.[22] In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today.[23]

Bacteria Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.[24] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum — the spirochaete that causes syphilis — into compounds that selectively killed the pathogen.[25] Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain.[26] A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria.[27] This new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system.[28]

18

Origin and early evolution
The ancestors of modern bacteria were single-celled microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life.[29][30] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.[31] Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.[32][33] This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later on, some eukaryotes that already contained mitochondria also engulfed cyanobacterial-like organisms. This led to the formation of chloroplasts in algae and plants. There are also some algae that originated from even later endosymbiotic events. Here, eukaryotes engulfed a eukaryotic algae that developed into a "second-generation" plastid.[34][35] This is known as secondary endosymbiosis.

Bacteria

19

Morphology
Further information: Bacterial cellular morphologies Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species — for example, Thiomargarita namibiensis and Epulopiscium fishelsoni — are up to half a millimetre long and are visible to the unaided eye;[36] E. fishelsoni reaches 0.7 mm.[37] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.[38] Some bacteria may be even smaller, but these ultramicrobacteria are not [39] well-studied.
Bacteria display many cell morphologies and arrangements Most bacterial species are either spherical, called cocci (sing. coccus, from Greek κόκκος-kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Elongation is associated with swimming.[40] Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; others, can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of species even have tetrahedral or cuboidal shapes.[41] More recently, bacteria were discovered deep under the Earth's crust that grow as long rods with a star-shaped cross-section. The large surface area to volume ratio of this morphology may give these bacteria an advantage in nutrient-poor environments.[42] This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.[43][44]

Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells. Certain types, such as species of the genus Nocardia, even form complex, branched filaments, similar in appearance to fungal mycelia.[45]
A biofilm of thermophilic bacteria in the outflow of Mickey Hot Springs, Oregon, approximately 20 mm thick.

Bacteria

20

Bacteria often attach to surfaces and form dense aggregations called biofilms or bacterial mats. These films can range from a few micrometers in thickness to up to half a meter in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients.[46][47] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.[48] Biofilms are also important in medicine, as The range of sizes shown by prokaryotes, relative these structures are often present during chronic bacterial infections or to those of other organisms and biomolecules in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria.[49] Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.[50] In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of multicellular organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and differentiate into a specialised dormant state called myxospores, which are more resistant to drying and other adverse environmental conditions than are ordinary cells.[51]

Cellular structure
Intracellular structures
The bacterial cell is surrounded by a lipid membrane, or cell membrane, which encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. As they are prokaryotes, bacteria do not tend to have membrane-bound organelles in their cytoplasm and thus contain few large intracellular structures. They consequently lack a true nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells, such as the Golgi apparatus and Structure and contents of a typical Gram positive endoplasmic reticulum.[52] Bacteria were once seen as simple bags of bacterial cell [53][54] cytoplasm, but elements such as prokaryotic cytoskeleton, and the localization of proteins to specific locations within the cytoplasm[53] have been found to show levels of complexity. These subcellular compartments have been called "bacterial hyperstructures".[55] Micro-compartments such as carboxysome[56] provides a further level of organization, which are compartments within bacteria that are surrounded by polyhedral protein shells, rather than by lipid membranes.[57] These "polyhedral organelles" localize and compartmentalize bacterial metabolism, a function performed by the membrane-bound organelles in eukaryotes.[58][59] Many important biochemical reactions, such as energy generation, occur by concentration gradients across membranes, a potential difference also found in a battery. The general lack of internal membranes in bacteria means reactions such as electron transport occur across the cell membrane between the cytoplasm and the periplasmic space.[60] However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell

Bacteria with layers of light-gathering membrane.[61] These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria.[62] Other proteins import nutrients across the cell membrane, or to expel undesired molecules from the cytoplasm. Most bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid.[64] The nucleoid contains the chromosome with associated proteins and RNA. The order Planctomycetes are an exception to the general absence of internal Carboxysomes are protein-enclosed bacterial organelles. Top left is an electron membranes in bacteria, because they microscope image of carboxysomes in Halothiobacillus neapolitanus, below is an image have a double membrane around their of purified carboxysomes. On the right is a model of their structure. Scale bars are [63] 100 nm. nucleoids and contain other membrane-bound cellular [65] structures. Like all living organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from those of eukaryotes and Archaea.[66] Some bacteria produce intracellular nutrient storage granules, such as glycogen,[67] polyphosphate,[68] sulfur[69] or polyhydroxyalkanoates.[70] These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vesicles, which they use to regulate their buoyancy – allowing them to move up or down into water layers with different light intensities and nutrient levels.[71]

21

Extracellular structures
In most bacteria a cell wall is present on the outside of the cytoplasmic membrane. A common bacterial cell wall material is peptidoglycan (called murein in older sources), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids.[72] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.[73] The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.[73] There are broadly speaking two different types of cell wall in bacteria, called Gram-positive and Gram-negative. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.[74] Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.[75] These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.[76] In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of the cell.[77] This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have

Bacteria diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus.[78] Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.[79] Fimbriae are fine filaments of protein, just 2–10 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in Helicobacter pylori electron micrograph, attachment to solid surfaces or to other cells and are essential for the showing multiple flagella on the cell surface virulence of some bacterial pathogens.[80] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation (see bacterial genetics, below).[81] Capsules or slime layers are produced by many bacteria to surround their cells, and vary in structural complexity: ranging from a disorganised slime layer of extra-cellular polymer, to a highly structured capsule or glycocalyx. These structures can protect cells from engulfment by eukaryotic cells, such as macrophages.[82] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.[83] The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.[84]

22

Endospores
Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter and Heliobacterium, can form highly resistant, dormant structures called endospores.[85] In almost all cases, one endospore is formed and this is not a reproductive process, although Anaerobacter can make up to seven endospores in a single cell.[86] Endospores have a central core of cytoplasm containing DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat. Endospores show no detectable metabolism and can survive extreme cerebrospinal fluid physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure and desiccation.[87] In this dormant state, these organisms may remain viable for millions of years,[88][89] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.[90] According to scientist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth — and we know they're very hardened to radiation."[91] Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus.[92]
Bacillus anthracis (stained purple) growing in

Bacteria

23

Metabolism
Bacteria exhibit an extremely wide variety of metabolic types.[93] The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications.[94] Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the kind of energy used for growth, the source of carbon, and the electron donors used for growth. An additional criterion of respiratory microorganisms are the electron acceptors used for aerobic or anaerobic respiration.[95]

Nutritional types in bacterial metabolism
Nutritional type Phototrophs Source of energy Sunlight Source of carbon Examples

Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs) Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs) Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs)

Cyanobacteria, Green sulfur bacteria, Chloroflexi, or Purple bacteria Thermodesulfobacteria, Hydrogenophilaceae, or Nitrospirae Bacillus, Clostridium or Enterobacteriaceae

Lithotrophs

Inorganic compounds Organic compounds

Organotrophs

Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide. Heterotrophic bacteria include parasitic types. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many chemolithotrophic species, such as nitrifying or sulfur-oxidising bacteria.[96] Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or based on chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration). Finally, bacteria are further divided into lithotrophs that use inorganic electron donors and organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g. carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the reduced substrate and transferring them to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to synthesise ATP and Filaments of photosynthetic cyanobacteria drive metabolism. In aerobic organisms, oxygen is used as the electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of denitrification, sulfate reduction and acetogenesis, respectively. Another way of life of chemotrophs in the absence of possible electron acceptors is fermentation, where the electrons taken from the reduced substrates are transferred to oxidised intermediates to generate reduced fermentation products (e.g. lactate, ethanol, hydrogen, butyric acid). Fermentation is possible, because the energy content of the substrates is higher than that of the products, which allows the organisms to synthesise ATP and drive their metabolism.[97][98] These processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment.[99] Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting

Bacteria metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves. Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron and other reduced metal ions, and several reduced sulfur compounds. Unusually, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.[100] In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic. In addition to fixing carbon dioxide in photosynthesis, some bacteria also fix nitrogen gas (nitrogen fixation) using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of nearly all the metabolic types listed above, but is not universal.[101] Regardless of the type of metabolic process they employ, the majority of bacteria are only able to take in raw materials in the form of relatively small molecules, which enter the cell by diffusion or through molecular channels in cell membranes. The Planctomycetes are the exception (as they are in possessing membranes around their nuclear material). It has recently been shown that Gemmata obscuriglobus is able to take in large molecules via a process that in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external items.[37][102]

24

Growth and reproduction
Unlike in multicellular organisms, increases in cell size (cell growth and reproduction by cell division) are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.[103] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.[104] In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

Many bacteria reproduce through binary fission

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as agar plates are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.[106] Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer.[107] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.[108] In
A colony of Escherichia [105] coli

nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses.[48] These relationships can be essential for growth of a particular organism

Bacteria or group of organisms (syntrophy).[109] Bacterial growth follows three phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced.[110] The second phase of growth is the logarithmic phase (log phase), also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The final phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport.[111]

25

Genetics
Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii,[112] to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum.[113] Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome.[114] The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much more rare than in eukaryotes.[115] Bacteria may also contain plasmids, which are small extra-chromosomal DNAs that may contain genes for antibiotic resistance or virulence factors. Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clonal). However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.[116] Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.[117] Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment, in a process called transformation. Genes can also be transferred by the process of transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. The third method of gene transfer is bacterial conjugation, where DNA is transferred through direct cell contact. This gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.[118] Gene transfer is particularly important in antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.[119]

Bacteriophages
Bacteriophages are viruses that infect bacteria. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. A bacteriophage can contain genes that contribute to its host's phenotype: for example, in the evolution of Escherichia coli O157:H7 and Clostridium botulinum, the toxin genes in an integrated phage converted a harmless ancestral bacterium into a lethal pathogen.[120] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA,[121] and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference.[122][123] This CRISPR system provides bacteria with acquired immunity to infection.

Bacteria

26

Behavior
Secretion
Bacteria frequently secrete chemicals into their environment in order to modify it favorably. The secretions are often proteins and may act as enzymes that digest some form of food in the environment.

Bioluminescence
A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals.[124] – see Milky seas effect

Multicellularity
(See also: Prokaryote#Sociality) Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell communication, and engaging in coordinated multicellular behavior.[125][126] The communal benefits of multicellular cooperation include a cellular division of labor, accessing resources that cannot effectively be utilized by single cells, collectively defending against antagonists, and optimizing population survival by differentiating into distinct cell types.[125] For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species.[126] One type of inter-cellular communication by a molecular signal is called quorum sensing, which serves the purpose of determining whether there is a local population density that is sufficiently high that it is productive to invest in processes that are only successful if large numbers of similar organisms behave similarly, as in excreting digestive enzymes or emitting light. Quorum sensing allows bacteria to coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population.[127]

Bacteria

27

Movement
Many bacteria can move using a variety of mechanisms: flagella are used for swimming through water; bacterial gliding and twitching motility move bacteria across surfaces; and changes of buoyancy allow vertical motion.[128] Swimming bacteria frequently move near 10 body lengths per second and a few as fast as 100. This makes them at least as fast as fish, on a relative scale.[129] In twitching motility, bacterial use their type IV pili as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 pN).[130] Flagella are semi-rigid cylindrical structures that are rotated and function much like the propeller on a ship. Objects as small as bacteria operate a low Reynolds number and cylindrical forms are more efficient than the flat, paddle-like, forms appropriate at human size scale.[131]

Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The bacterial flagella is the best-understood motility structure in any organism and is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.[128] The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power.[132] This motor drives the motion of the filament, which acts as a propeller. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk.[133] (See external links below for link to videos.) The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.[128] Motile bacteria are attracted or repelled by certain stimuli in behaviors called taxes: these include chemotaxis, phototaxis, energy taxis and magnetotaxis.[134][135][136] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.[51] The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media. Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerization at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.[137]

Flagellum of Gram-negative Bacteria. The base drives the rotation of the hook and filament.

Bacteria

28

Classification and identification
Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, fatty acids, pigments, antigens and quinones.[106] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as Streptococcus mutans visualized with a Gram lateral gene transfer between unrelated species.[138] Due to lateral gene stain transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.[139] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,[140] and Bergey's Manual of Systematic Bacteriology.[141] The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor.[10] The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiolology.[142] However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field.[5][143] For example, a few biologists argue that the Archaea and Eukaryotes evolved from Gram-positive bacteria.[144] Identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria.

Bacteria

29

The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls.[74] The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some Phylogenetic tree showing the diversity of bacteria, compared to other organisms are best identified by stains organisms.Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science 311 (5765): other than the Gram stain, particularly 1283–7. Bibcode 2006Sci...311.1283C. doi:10.1126/science.1123061. PMID 16513982.  mycobacteria or Nocardia, which show Eukaryotes are colored red, archaea green and bacteria blue. acid-fastness on Ziehl–Neelsen or similar stains.[145] Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology. Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms.[106][146] Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns such as (aerobic or anaerobic growth, patterns of hemolysis) and staining. As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.[147] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.[148] However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea.[149] but attempts to estimate the true level of bacterial diversity have ranged from 107 to 109 total species – and even these diverse estimates may be off by many orders of magnitude.[150][151]

Bacteria

30

Interactions with other organisms
Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odor.

Predators
Some species of bacteria kill and then consume other microorganisms, these species called predatory bacteria.[152] These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter.[153] Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirococcus, or invade another cell and multiply inside the cytosol, such as Daptobacter.[154] These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms.[155]

Mutualists
Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids such as butyric acid or propionic acid and produce hydrogen, and methanogenic Archaea that consume hydrogen.[156] The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow. In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds.[157] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates.[158][159][160] The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.[161]

Pathogens
If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.

Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

Bacteria Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death.[162] Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease.[163] Finally, some species such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.[164][165] Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic [168] ribosome. Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations.[169] Infections can be [166][167] Overview of bacterial infections and main species involved. prevented by antiseptic measures such as sterilizing the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilized to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.

31

Significance in technology and industry
Bacteria, often lactic acid bacteria such as Lactobacillus and Lactococcus, in combination with yeasts and molds, have been used for thousands of years in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yogurt.[170][171] The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills.[172] Fertilizer was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic

Bacteria wastes.[173] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.[174] Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide.[175] Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects.[176][177] Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms.[178] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.[179][180] This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.[181][182]

32

References
[1] "Bacteria (eubacteria)" (http:/ / www. ncbi. nlm. nih. gov/ Taxonomy/ Browser/ wwwtax. cgi?mode=Undef& id=2& lvl=3& lin=f& keep=1& srchmode=1& unlock). Taxonomy Browser. . Retrieved 2008-09-10. [2] Fredrickson JK, Zachara JM, Balkwill DL et al. (2004). "Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state". Applied and Environmental Microbiology 70 (7): 4230–41. doi:10.1128/AEM.70.7.4230-4241.2004. PMC 444790. PMID 15240306. [3] Whitman WB, Coleman DC, Wiebe WJ (1998). "Prokaryotes: the unseen majority". Proceedings of the National Academy of Sciences of the United States of America 95 (12): 6578–83. doi:10.1073/pnas.95.12.6578. PMC 33863. PMID 9618454. [4] C.Michael Hogan. 2010. Bacteria. Encyclopedia of Earth. eds. Sidney Draggan and C.J.Cleveland, National Council for Science and the Environment, Washington DC (http:/ / www. eoearth. org/ article/ Bacteria?topic=49480) [5] Rappé MS, Giovannoni SJ (2003). "The uncultured microbial majority". Annual Review of Microbiology 57: 369–94. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284. [6] Sears CL (2005). "A dynamic partnership: celebrating our gut flora". Anaerobe 11 (5): 247–51. doi:10.1016/j.anaerobe.2005.05.001. PMID 16701579. [7] "2002 WHO mortality data" (http:/ / www. who. int/ healthinfo/ bodgbd2002revised/ en/ index. html). . Retrieved 2007-01-20. [8] http:/ / www. sciencedaily. com/ releases/ 2010/ 09/ 100901191137. htm [9] Ishige T, Honda K, Shimizu S (2005). "Whole organism biocatalysis". Current Opinion in Chemical Biology 9 (2): 174–80. doi:10.1016/j.cbpa.2005.02.001. PMID 15811802. [10] Woese CR, Kandler O, Wheelis ML (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–9. Bibcode 1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. [11] βακτήριον (http:/ / www. perseus. tufts. edu/ hopper/ text?doc=Perseus:text:1999. 04. 0057:entry=bakth/ rion), Henry George Liddell, Robert Scott, A Greek-English Lexicon, on Perseus [12] βακτηρία (http:/ / www. perseus. tufts. edu/ hopper/ text?doc=Perseus:text:1999. 04. 0057:entry=bakthri/ a), Henry George Liddell, Robert Scott, A Greek-English Lexicon, on Perseus [13] bacterium (http:/ / oxforddictionaries. com/ view/ entry/ m_en_gb0055310#dws-m_en_gb-m-en_gb-msdict-00002–034344), on Oxford Dictionaries [14] Porter JR (1976). "Antony van Leeuwenhoek: tercentenary of his discovery of bacteria". Bacteriological Reviews 40 (2): 260–9. PMC 413956. PMID 786250. [15] van Leeuwenhoek A (1684). "An abstract of a letter from Mr. Anthony Leevvenhoek at Delft, dated Sep. 17, 1683, Containing Some Microscopical Observations, about Animals in the Scurf of the Teeth, the Substance Call'd Worms in the Nose, the Cuticula Consisting of Scales" (http:/ / www. journals. royalsoc. ac. uk/ content/ 120136/ ?k=Sep. + 17,+ 1683). Philosophical Transactions (1683–1775) 14 (155–166): 568–574. doi:10.1098/rstl.1684.0030. . Retrieved 2007-08-19. [16] van Leeuwenhoek A (1700). "Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs" (http:/ / www. journals. royalsoc. ac. uk/ link. asp?id=4j53731651310230). Philosophical Transactions (1683–1775) 22 (260–276): 509–518. doi:10.1098/rstl.1700.0013. . Retrieved 2007-08-19.

Bacteria
[17] van Leeuwenhoek A (1702). "Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them" (http:/ / www. journals. royalsoc. ac. uk/ link. asp?id=fl73121jk4150280). Philosophical Transactions (1683–1775) 23 (277–288): 1304–11. doi:10.1098/rstl.1702.0042. . Retrieved 2007-08-19. [18] Ehrenberg's Symbolae Physioe. Animalia evertebrata. Decas prima. Berlin, 1828. [19] Breed, R.; Conn, H. (1936). "The Status of the Generic Term Bacterium Ehrenberg 1828". Journal of bacteriology 31 (5): 517–518. PMC 543738. PMID 16559906. [20] EHRENBERG (C.G.): Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes. Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833-1835, 1835, pp. 143-336. [21] "Pasteur's Papers on the Germ Theory" (http:/ / biotech. law. lsu. edu/ cphl/ history/ articles/ pasteur. htm#paperII). LSU Law Center's Medical and Public Health Law Site, Historic Public Health Articles. . Retrieved 2006-11-23. [22] "The Nobel Prize in Physiology or Medicine 1905" (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1905/ ). Nobelprize.org. . Retrieved 2006-11-22. [23] O'Brien S, Goedert J (1996). "HIV causes AIDS: Koch's postulates fulfilled". Curr Opin Immunol 8 (5): 613–8. doi:10.1016/S0952-7915(96)80075-6. PMID 8902385. [24] Thurston A (2000). "Of blood, inflammation and gunshot wounds: the history of the control of sepsis". Aust N Z J Surg 70 (12): 855–61. doi:10.1046/j.1440-1622.2000.01983.x. PMID 11167573. [25] Schwartz R (2004). "Paul Ehrlich's magic bullets". N Engl J Med 350 (11): 1079–80. doi:10.1056/NEJMp048021. PMID 15014180. [26] "Biography of Paul Ehrlich" (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1908/ ehrlich-bio. html). Nobelprize.org. . Retrieved 2006-11-26. [27] Woese C, Fox G (1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proc Natl Acad Sci USA 74 (11): 5088–90. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744. [28] Woese CR, Kandler O, Wheelis ML (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America 87 (12): 4576–9. Bibcode 1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744. [29] Schopf J (1994). "Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic". Proc Natl Acad Sci USA 91 (15): 6735–42. Bibcode 1994PNAS...91.6735S. doi:10.1073/pnas.91.15.6735. PMC 44277. PMID 8041691. [30] DeLong E, Pace N (2001). "Environmental diversity of bacteria and archaea". Syst Biol 50 (4): 470–8. doi:10.1080/106351501750435040. PMID 12116647. [31] Brown JR, Doolittle WF (1997). "Archaea and the prokaryote-to-eukaryote transition". Microbiology and Molecular Biology Reviews 61 (4): 456–502. PMC 232621. PMID 9409149. [32] Poole A, Penny D (2007). "Evaluating hypotheses for the origin of eukaryotes". BioEssays 29 (1): 74–84. doi:10.1002/bies.20516. PMID 17187354. [33] Dyall S, Brown M, Johnson P (2004). "Ancient invasions: from endosymbionts to organelles". Science 304 (5668): 253–7. doi:10.1126/science.1094884. PMID 15073369. [34] Lang B, Gray M, Burger G (1999). "Mitochondrial genome evolution and the origin of eukaryotes". Annu Rev Genet 33: 351–97. doi:10.1146/annurev.genet.33.1.351. PMID 10690412. [35] McFadden G (1999). "Endosymbiosis and evolution of the plant cell". Curr Opin Plant Biol 2 (6): 513–9. doi:10.1016/S1369-5266(99)00025-4. PMID 10607659. [36] Schulz H, Jorgensen B (2001). "Big bacteria". Annu Rev Microbiol 55: 105–37. doi:10.1146/annurev.micro.55.1.105. PMID 11544351. [37] Williams, Caroline (2011). "Who are you calling simple?". New Scientist 211 (2821): 38–41. doi:10.1016/S0262-4079(11)61709-0. [38] Robertson J, Gomersall M, Gill P. (1975). "Mycoplasma hominis: growth, reproduction, and isolation of small viable cells". J Bacteriol. 124 (2): 1007–18. PMC 235991. PMID 1102522. [39] Velimirov, B. (2001). "Nanobacteria, Ultramicrobacteria and Starvation Forms: A Search for the Smallest Metabolizing Bacterium". Microbes and Environments 16 (2): 67–77. doi:10.1264/jsme2.2001.67. [40] Dusenbery, David B. (2009). Living at Micro Scale, pp.20–25. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6. [41] Fritz I, Strömpl C, Abraham W (2004). "Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov" (http:/ / ijs. sgmjournals. org/ cgi/ content/ full/ 54/ 3/ 651). Int J Syst Evol Microbiol 54 (Pt 3): 651–7. doi:10.1099/ijs.0.02746-0. PMID 15143003. . [42] Wanger, G; Onstott, TC; Southam, G (2008). "Stars of the terrestrial deep subsurface: A novel 'star-shaped' bacterial morphotype from a South African platinum mine". Geobiology 6 (3): 325–30. doi:10.1111/j.1472-4669.2008.00163.x. PMID 18498531. [43] Cabeen M, Jacobs-Wagner C (2005). "Bacterial cell shape". Nat Rev Microbiol 3 (8): 601–10. doi:10.1038/nrmicro1205. PMID 16012516. [44] Young K (2006). "The selective value of bacterial shape". Microbiol Mol Biol Rev 70 (3): 660–703. doi:10.1128/MMBR.00001-06. PMC 1594593. PMID 16959965. [45] Douwes K, Schmalzbauer E, Linde H, Reisberger E, Fleischer K, Lehn N, Landthaler M, Vogt T (2003). "Branched filaments no fungus, ovoid bodies no bacteria: Two unusual cases of mycetoma". J Am Acad Dermatol 49 (2 Suppl Case Reports): S170–3. doi:10.1067/mjd.2003.302. PMID 12894113. [46] Donlan R (2002). "Biofilms: microbial life on surfaces". Emerg Infect Dis 8 (9): 881–90. PMC 2732559. PMID 12194761. [47] Branda S, Vik S, Friedman L, Kolter R (2005). "Biofilms: the matrix revisited". Trends Microbiol 13 (1): 20–6. doi:10.1016/j.tim.2004.11.006. PMID 15639628.

33

Bacteria
[48] Davey M, O'toole G (2000). "Microbial biofilms: from ecology to molecular genetics". Microbiol Mol Biol Rev 64 (4): 847–67. doi:10.1128/MMBR.64.4.847-867.2000. PMC 99016. PMID 11104821. [49] Donlan RM, Costerton JW (2002). "Biofilms: survival mechanisms of clinically relevant microorganisms". Clin Microbiol Rev 15 (2): 167–93. doi:10.1128/CMR.15.2.167-193.2002. PMC 118068. PMID 11932229. [50] Shimkets L (1999). "Intercellular signaling during fruiting-body development of Myxococcus xanthus". Annu Rev Microbiol 53: 525–49. doi:10.1146/annurev.micro.53.1.525. PMID 10547700. [51] Kaiser D (2004). "Signaling in myxobacteria". Annu Rev Microbiol 58: 75–98. doi:10.1146/annurev.micro.58.030603.123620. PMID 15487930. [52] Berg JM, Tymoczko JL Stryer L (2002). Molecular Cell Biology (5th ed.). WH Freeman. ISBN 0-7167-4955-6. [53] Gitai Z (2005). "The new bacterial cell biology: moving parts and subcellular architecture". Cell 120 (5): 577–86. doi:10.1016/j.cell.2005.02.026. PMID 15766522. [54] Shih YL, Rothfield L (2006). "The bacterial cytoskeleton". Microbiology and Molecular Biology Reviews 70 (3): 729–54. doi:10.1128/MMBR.00017-06. PMC 1594594. PMID 16959967. [55] Norris V, den Blaauwen T, Cabin-Flaman A et al. (2007). "Functional taxonomy of bacterial hyperstructures". Microbiology and Molecular Biology Reviews 71 (1): 230–53. doi:10.1128/MMBR.00035-06. PMC 1847379. PMID 17347523. [56] Kerfeld CA, Sawaya MR, Tanaka S et al. (2005). "Protein structures forming the shell of primitive bacterial organelles". Science 309 (5736): 936–8. doi:10.1126/science.1113397. PMID 16081736. [57] Bobik, T. A. (2007). "Bacterial Microcompartments" (http:/ / www. asm. org/ ASM/ files/ ccLibraryFiles/ Filename/ 000000002765/ znw00107000025. pdf). Microbe (Am Soc Microbiol) 2: 25–31. . [58] Bobik, TA (2006). "Polyhedral organelles compartmenting bacterial metabolic processes". Applied Microbiology and Biotechnology 70 (5): 517–25. doi:10.1007/s00253-005-0295-0. PMID 16525780. [59] Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM (2008). "Protein-based organelles in bacteria: carboxysomes and related microcompartments". Nat. Rev. Microbiol. 6 (9): 681–91. doi:10.1038/nrmicro1913. PMID 18679172. [60] Harold FM (1972). "Conservation and transformation of energy by bacterial membranes". Bacteriological Reviews 36 (2): 172–230. PMC 408323. PMID 4261111. [61] Bryant, DA; Frigaard, NU (2006). "Prokaryotic photosynthesis and phototrophy illuminated". Trends Microbiol. 14 (11): 488–96. doi:10.1016/j.tim.2006.09.001. PMID 16997562. [62] Psencík J, Ikonen TP, Laurinmäki P et al. (2004). "Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria". Biophys. J. 87 (2): 1165–72. doi:10.1529/biophysj.104.040956. PMC 1304455. PMID 15298919. [63] Tanaka S, Kerfeld CA, Sawaya MR et al. (2008). "Atomic-level models of the bacterial carboxysome shell". Science 319 (5866): 1083–6. doi:10.1126/science.1151458. PMID 18292340. [64] Thanbichler M, Wang S, Shapiro L (2005). "The bacterial nucleoid: a highly organized and dynamic structure". J Cell Biochem 96 (3): 506–21. doi:10.1002/jcb.20519. PMID 15988757. [65] Fuerst J (2005). "Intracellular compartmentation in planctomycetes". Annu Rev Microbiol 59: 299–328. doi:10.1146/annurev.micro.59.030804.121258. PMID 15910279. [66] Poehlsgaard J, Douthwaite S (2005). "The bacterial ribosome as a target for antibiotics". Nat Rev Microbiol 3 (11): 870–81. doi:10.1038/nrmicro1265. PMID 16261170. [67] Yeo M, Chater K (2005). "The interplay of glycogen metabolism and differentiation provides an insight into the developmental biology of Streptomyces coelicolor" (http:/ / mic. sgmjournals. org/ cgi/ content/ full/ 151/ 3/ 855?view=long& pmid=15758231). Microbiology 151 (Pt 3): 855–61. doi:10.1099/mic.0.27428-0. PMID 15758231. . [68] Shiba T, Tsutsumi K, Ishige K, Noguchi T (2000). "Inorganic polyphosphate and polyphosphate kinase: their novel biological functions and applications" (http:/ / protein. bio. msu. ru/ biokhimiya/ contents/ v65/ full/ 65030375. html). Biochemistry (Mosc) 65 (3): 315–23. PMID 10739474. . [69] Brune DC (1995). "Isolation and characterization of sulfur globule proteins from Chromatium vinosum and Thiocapsa roseopersicina". Archives of Microbiology 163 (6): 391–9. doi:10.1007/BF00272127. PMID 7575095. [70] Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S (2005). "Ecological and agricultural significance of bacterial polyhydroxyalkanoates". Critical Reviews in Microbiology 31 (2): 55–67. doi:10.1080/10408410590899228. PMID 15986831. [71] Walsby AE (1994). "Gas vesicles". Microbiological Reviews 58 (1): 94–144. PMC 372955. PMID 8177173. [72] van Heijenoort J (2001). "Formation of the glycan chains in the synthesis of bacterial peptidoglycan". Glycobiology 11 (3): 25R–36R. doi:10.1093/glycob/11.3.25R. PMID 11320055. [73] Koch A (2003). "Bacterial wall as target for attack: past, present, and future research". Clin Microbiol Rev 16 (4): 673–87. doi:10.1128/CMR.16.4.673-687.2003. PMC 207114. PMID 14557293. [74] Gram, HC (1884). "Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten". Fortschr. Med. 2: 185–189. [75] Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era" (http:/ / genomebiology. com/ 1465-6906/ 3/ REVIEWS0003). Genome Biology 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374. . [76] Walsh F, Amyes S (2004). "Microbiology and drug resistance mechanisms of fully resistant pathogens". Curr Opin Microbiol 7 (5): 439–44. doi:10.1016/j.mib.2004.08.007. PMID 15451497. [77] Engelhardt H, Peters J (1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions". J Struct Biol 124 (2–3): 276–302. doi:10.1006/jsbi.1998.4070. PMID 10049812.

34

Bacteria
[78] Beveridge T, Pouwels P, Sára M, Kotiranta A, Lounatmaa K, Kari K, Kerosuo E, Haapasalo M, Egelseer E, Schocher I, Sleytr U, Morelli L, Callegari M, Nomellini J, Bingle W, Smit J, Leibovitz E, Lemaire M, Miras I, Salamitou S, Béguin P, Ohayon H, Gounon P, Matuschek M, Koval S (1997). "Functions of S-layers". FEMS Microbiol Rev 20 (1–2): 99–149. doi:10.1016/S0168-6445(97)00043-0. PMID 9276929. [79] Kojima S, Blair D (2004). "The bacterial flagellar motor: structure and function of a complex molecular machine". Int Rev Cytol. International Review of Cytology 233: 93–134. doi:10.1016/S0074-7696(04)33003-2. ISBN 978-0-12-364637-8. PMID 15037363. [80] Beachey E (1981). "Bacterial adherence: adhesin-receptor interactions mediating the attachment of bacteria to mucosal surface". J Infect Dis 143 (3): 325–45. doi:10.1093/infdis/143.3.325. PMID 7014727. [81] Silverman P (1997). "Towards a structural biology of bacterial conjugation". Mol Microbiol 23 (3): 423–9. doi:10.1046/j.1365-2958.1997.2411604.x. PMID 9044277. [82] Stokes R, Norris-Jones R, Brooks D, Beveridge T, Doxsee D, Thorson L (2004). "The glycan-rich outer layer of the cell wall of Mycobacterium tuberculosis acts as an antiphagocytic capsule limiting the association of the bacterium with macrophages". Infect Immun 72 (10): 5676–86. doi:10.1128/IAI.72.10.5676-5686.2004. PMC 517526. PMID 15385466. [83] Daffé M, Etienne G (1999). "The capsule of Mycobacterium tuberculosis and its implications for pathogenicity". Tuber Lung Dis 79 (3): 153–69. doi:10.1054/tuld.1998.0200. PMID 10656114. [84] Finlay BB, Falkow S (1997). "Common themes in microbial pathogenicity revisited". Microbiology and Molecular Biology Reviews 61 (2): 136–69. PMC 232605. PMID 9184008. [85] Nicholson WL, Munakata N, Horneck G, Melosh HJ, Setlow P (2000). "Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments". Microbiology and Molecular Biology Reviews 64 (3): 548–72. doi:10.1128/MMBR.64.3.548-572.2000. PMC 99004. PMID 10974126. [86] Siunov A, Nikitin D, Suzina N, Dmitriev V, Kuzmin N, Duda V (1999). "Phylogenetic status of Anaerobacter polyendosporus, an anaerobic, polysporogenic bacterium" (http:/ / ijs. sgmjournals. org/ cgi/ reprint/ 49/ 3/ 1119. pdf). Int J Syst Bacteriol 49 (3): 1119–24. PMID 10425769. . [87] Nicholson W, Fajardo-Cavazos P, Rebeil R, Slieman T, Riesenman P, Law J, Xue Y (2002). "Bacterial endospores and their significance in stress resistance". Antonie Van Leeuwenhoek 81 (1–4): 27–32. doi:10.1023/A:1020561122764. PMID 12448702. [88] Vreeland R, Rosenzweig W, Powers D (2000). "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal". Nature 407 (6806): 897–900. doi:10.1038/35038060. PMID 11057666. [89] Cano R, Borucki M (1995). "Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber". Science 268 (5213): 1060–4. doi:10.1126/science.7538699. PMID 7538699. [90] Nicholson W, Schuerger A, Setlow P (2005). "The solar UV environment and bacterial spore UV resistance: considerations for Earth-to-Mars transport by natural processes and human spaceflight". Mutat Res 571 (1–2): 249–64. doi:10.1016/j.mrfmmm.2004.10.012. PMID 15748651. [91] BBC Staff (23 August 2011). "Impacts 'more likely' to have spread life from Earth" (http:/ / www. bbc. co. uk/ news/ science-environment-14637109). BBC. . Retrieved 2011-08-24. [92] Hatheway CL (1990). "Toxigenic clostridia". Clinical Microbiology Reviews 3 (1): 66–98. PMC 358141. PMID 2404569. [93] Nealson K (1999). "Post-Viking microbiology: new approaches, new data, new insights". Orig Life Evol Biosph 29 (1): 73–93. doi:10.1023/A:1006515817767. PMID 11536899. [94] Xu J (2006). "Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances". Mol Ecol 15 (7): 1713–31. doi:10.1111/j.1365-294X.2006.02882.x. PMID 16689892. [95] Zillig W (1991). "Comparative biochemistry of Archaea and Bacteria". Curr Opin Genet Dev 1 (4): 544–51. doi:10.1016/S0959-437X(05)80206-0. PMID 1822288. [96] Hellingwerf K, Crielaard W, Hoff W, Matthijs H, Mur L, van Rotterdam B (1994). "Photobiology of bacteria". Antonie Van Leeuwenhoek 65 (4): 331–47. doi:10.1007/BF00872217. PMID 7832590. [97] Zumft W (1 December 1997). "Cell biology and molecular basis of denitrification". Microbiol Mol Biol Rev 61 (4): 533–616. PMC 232623. PMID 9409151. [98] Drake H, Daniel S, Küsel K, Matthies C, Kuhner C, Braus-Stromeyer S (1997). "Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?". BioFactors 6 (1): 13–24. doi:10.1002/biof.5520060103. PMID 9233536. [99] Morel, FMM; Kraepiel AML, Amyot M (1998). "The chemical cycle and bioaccumulation of mercury". Annual Review of Ecological Systems 29: 543–566. doi:10.1146/annurev.ecolsys.29.1.543. [100] Dalton H (2005). "The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria" (http:/ / www. journals. royalsoc. ac. uk/ content/ yl6umjthf30e4a59/ ). Philos Trans R Soc Lond B Biol Sci 360 (1458): 1207–22. doi:10.1098/rstb.2005.1657. PMC 1569495. PMID 16147517. . [101] Zehr J, Jenkins B, Short S, Steward G (2003). "Nitrogenase gene diversity and microbial community structure: a cross-system comparison". Environ Microbiol 5 (7): 539–54. doi:10.1046/j.1462-2920.2003.00451.x. PMID 12823187. [102] Lonhienne, Thierry G. A.; Sagulenko, Evgeny; Webb, Richard I.; Lee, Kuo-Chang; Franke, Josef; Devos, Damien P.; Nouwens, Amanda; Carroll, Bernard J. et al. (2010). "Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus". Proceedings of the National Academy of Sciences 107 (29): 12883–12888. doi:10.1073/pnas.1001085107. [103] Koch A (2002). "Control of the bacterial cell cycle by cytoplasmic growth". Crit Rev Microbiol 28 (1): 61–77. doi:10.1080/1040-840291046696. PMID 12003041.

35

Bacteria
[104] Eagon RG (1962). "Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes". Journal of Bacteriology 83 (4): 736–7. PMC 279347. PMID 13888946. [105] Stewart EJ, Madden R, Paul G, Taddei F (2005). "Aging and death in an organism that reproduces by morphologically symmetric division". PLoS Biol. 3 (2): e45. doi:10.1371/journal.pbio.0030045. PMC 546039. PMID 15685293. [106] Thomson R, Bertram H (2001). "Laboratory diagnosis of central nervous system infections". Infectious Disease Clinics of North America 15 (4): 1047–71. doi:10.1016/S0891-5520(05)70186-0. PMID 11780267. [107] Paerl H, Fulton R, Moisander P, Dyble J (2001). "Harmful freshwater algal blooms, with an emphasis on cyanobacteria". ScientificWorldJournal 1: 76–113. doi:10.1100/tsw.2001.16. PMID 12805693. [108] Challis G, Hopwood D (2003). "Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species". Proc Natl Acad Sci USA 100 Suppl 2 (90002): 14555–61. doi:10.1073/pnas.1934677100. PMC 304118. PMID 12970466. [109] Kooijman S, Auger P, Poggiale J, Kooi B (2003). "Quantitative steps in symbiogenesis and the evolution of homeostasis". Biol Rev Camb Philos Soc 78 (3): 435–63. doi:10.1017/S1464793102006127. PMID 14558592. [110] Prats C, López D, Giró A, Ferrer J, Valls J (2006). "Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase". J Theor Biol 241 (4): 939–53. doi:10.1016/j.jtbi.2006.01.029. PMID 16524598. [111] Hecker M, Völker U (2001). "General stress response of Bacillus subtilis and other bacteria". Adv Microb Physiol. Advances in Microbial Physiology 44: 35–91. doi:10.1016/S0065-2911(01)44011-2. ISBN 978-0-12-027744-5. PMID 11407115. [112] Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar H, Moran N, Hattori M (2006). "The 160-kilobase genome of the bacterial endosymbiont Carsonella". Science 314 (5797): 267. doi:10.1126/science.1134196. PMID 17038615. [113] Pradella S, Hans A, Spröer C, Reichenbach H, Gerth K, Beyer S (2002). "Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56". Arch Microbiol 178 (6): 484–92. doi:10.1007/s00203-002-0479-2. PMID 12420170. [114] Hinnebusch J, Tilly K (1993). "Linear plasmids and chromosomes in bacteria". Mol Microbiol 10 (5): 917–22. doi:10.1111/j.1365-2958.1993.tb00963.x. PMID 7934868. [115] Belfort M, Reaban ME, Coetzee T, Dalgaard JZ (1 July 1995). "Prokaryotic introns and inteins: a panoply of form and function". J. Bacteriol. 177 (14): 3897–903. PMC 177115. PMID 7608058. [116] Denamur E, Matic I (2006). "Evolution of mutation rates in bacteria". Mol Microbiol 60 (4): 820–7. doi:10.1111/j.1365-2958.2006.05150.x. PMID 16677295. [117] Wright B (2004). "Stress-directed adaptive mutations and evolution". Mol Microbiol 52 (3): 643–50. doi:10.1111/j.1365-2958.2004.04012.x. PMID 15101972. [118] Davison J (1999). "Genetic exchange between bacteria in the environment". Plasmid 42 (2): 73–91. doi:10.1006/plas.1999.1421. PMID 10489325. [119] Hastings P, Rosenberg S, Slack A (2004). "Antibiotic-induced lateral transfer of antibiotic resistance". Trends Microbiol 12 (9): 401–4. doi:10.1016/j.tim.2004.07.003. PMID 15337159. [120] Brüssow H, Canchaya C, Hardt WD (2004). "Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion". Microbiology and Molecular Biology Reviews 68 (3): 560–602. doi:10.1128/MMBR.68.3.560-602.2004. PMC 515249. PMID 15353570. [121] Bickle TA, Krüger DH (1 June 1993). "Biology of DNA restriction". Microbiol. Rev. 57 (2): 434–50. PMC 372918. PMID 8336674. [122] Barrangou R, Fremaux C, Deveau H et al. (2007). "CRISPR provides acquired resistance against viruses in prokaryotes". Science 315 (5819): 1709–12. doi:10.1126/science.1138140. PMID 17379808. [123] Brouns SJ, Jore MM, Lundgren M et al. (2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes". Science 321 (5891): 960–4. doi:10.1126/science.1159689. PMID 18703739. [124] Dusenbery, David B. (1996). Life at Small Scale. Scientific American Library. ISBN 0-7167-5060-0. [125] Shapiro JA (1998). "Thinking about bacterial populations as multicellular organisms" (http:/ / www. sci. uidaho. edu/ newton/ math501/ Sp05/ Shapiro. pdf). Annu. Rev. Microbiol. 52: 81–104. doi:10.1146/annurev.micro.52.1.81. PMID 9891794. . [126] Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995). "Microbial biofilms". Annu. Rev. Microbiol. 49: 711–45. doi:10.1146/annurev.mi.49.100195.003431. PMID 8561477. [127] Miller, M. B.; Bassler, B. L. (2001). "Quorumsensing Inbacteria". Annual Review of Microbiology 55: 165–199. doi:10.1146/annurev.micro.55.1.165. PMID 11544353. [128] Bardy S, Ng S, Jarrell K (2003). "Prokaryotic motility structures". Microbiology 149 (Pt 2): 295–304. doi:10.1099/mic.0.25948-0. PMID 12624192. [129] Dusenbery, David B. (2009). Living at Micro Scale, p. 136. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6. [130] Merz A, So M, Sheetz M (2000). "Pilus retraction powers bacterial twitching motility". Nature 407 (6800): 98–102. doi:10.1038/35024105. PMID 10993081. [131] Dusenbery, David B. (2009). Living at Micro Scale, Chapter 13. Harvard University Press, Cambridge, Mass. ISBN 978-0-674-03116-6. [132] Macnab RM (1 December 1999). "The bacterial flagellum: reversible rotary propellor and type III export apparatus". J. Bacteriol. 181 (23): 7149–53. PMC 103673. PMID 10572114. [133] Wu M, Roberts J, Kim S, Koch D, DeLisa M (2006). "Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique". Appl Environ Microbiol 72 (7): 4987–94. doi:10.1128/AEM.00158-06. PMC 1489374. PMID 16820497.

36

Bacteria
[134] Lux R, Shi W (2004). "Chemotaxis-guided movements in bacteria". Crit Rev Oral Biol Med 15 (4): 207–20. doi:10.1177/154411130401500404. PMID 15284186. [135] Schweinitzer T, Josenhans C. (2010). "Bacterial energy taxis: a global strategy?". Arch Microbiol 192 (7): 507–20. doi:10.1007/s00203-010-0575-7. PMC 2886117. PMID 20411245. [136] Frankel R, Bazylinski D, Johnson M, Taylor B (1997). "Magneto-aerotaxis in marine coccoid bacteria". Biophys J 73 (2): 994–1000. Bibcode 1997BpJ....73..994F. doi:10.1016/S0006-3495(97)78132-3. PMC 1180996. PMID 9251816. [137] Goldberg MB (2001). "Actin-based motility of intracellular microbial pathogens". Microbiol Mol Biol Rev 65 (4): 595–626, table of contents. doi:10.1128/MMBR.65.4.595-626.2001. PMC 99042. PMID 11729265. [138] Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbo CL, Case RJ, Doolittle WF (2003). "Lateral gene transfer and the origins of prokaryotic groups". Annu Rev Genet 37: 283–328. doi:10.1146/annurev.genet.37.050503.084247. PMID 14616063. [139] Olsen GJ, Woese CR, Overbeek R (1994). "The winds of (evolutionary) change: breathing new life into microbiology". Journal of Bacteriology 176 (1): 1–6. PMC 205007. PMID 8282683. [140] "IJSEM – Home" (http:/ / ijs. sgmjournals. org/ ). Ijs.sgmjournals.org. 2011-10-28. . Retrieved 2011-11-04. [141] "Bergey's Manual Trust" (http:/ / www. bergeys. org/ ). Bergeys.org. . Retrieved 2011-11-04. [142] Gupta R (2000). "The natural evolutionary relationships among prokaryotes". Crit Rev Microbiol 26 (2): 111–31. doi:10.1080/10408410091154219. PMID 10890353. [143] Doolittle RF (2005). "Evolutionary aspects of whole-genome biology". Curr Opin Struct Biol 15 (3): 248–53. doi:10.1016/j.sbi.2005.04.001. PMID 15963888. [144] Cavalier-Smith T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". Int J Syst Evol Microbiol 52 (Pt 1): 7–76. PMID 11837318. [145] Woods GL, Walker DH (1996). "Detection of infection or infectious agents by use of cytologic and histologic stains". Clinical Microbiology Reviews 9 (3): 382–404. PMC 172900. PMID 8809467. [146] Weinstein M (1994). "Clinical importance of blood cultures". Clin Lab Med 14 (1): 9–16. PMID 8181237. [147] Louie M, Louie L, Simor AE (8 August 2000). "The role of DNA amplification technology in the diagnosis of infectious diseases" (http:/ / www. cmaj. ca/ cgi/ content/ full/ 163/ 3/ 301). CMAJ 163 (3): 301–9. PMC 80298. PMID 10951731. . [148] Oliver J (2005). "The viable but nonculturable state in bacteria" (http:/ / www. msk. or. kr/ jsp/ view_old_journalD. jsp?paperSeq=2134). J Microbiol 43 Spec No: 93–100. PMID 15765062. . [149] Euzéby JP (8 December 2011). "Number of published names" (http:/ / www. bacterio. cict. fr/ number. html). List of Prokaryotic names with Standing in Nomenclature. . Retrieved 10 December 2011. [150] Curtis TP, Sloan WT, Scannell JW (2002). "Estimating prokaryotic diversity and its limits". Proceedings of the National Academy of Sciences of the United States of America 99 (16): 10494–9. doi:10.1073/pnas.142680199. PMC 124953. PMID 12097644. [151] Schloss PD, Handelsman J (2004). "Status of the microbial census". Microbiology and Molecular Biology Reviews 68 (4): 686–91. doi:10.1128/MMBR.68.4.686-691.2004. PMC 539005. PMID 15590780. [152] Martin MO (2002). "Predatory prokaryotes: an emerging research opportunity". Journal of Microbiology and Biotechnology 4 (5): 467–77. PMID 12432957. [153] Velicer GJ, Stredwick KL (2002). "Experimental social evolution with Myxococcus xanthus". Antonie Van Leeuwenhoek 81 (1–4): 155–64. doi:10.1023/A:1020546130033. PMID 12448714. [154] Guerrero R, Pedros-Alio C, Esteve I, Mas J, Chase D, Margulis L (1986). "Predatory prokaryotes: predation and primary consumption evolved in bacteria". Proc. Natl. Acad. Sci. U.S.A. 83 (7): 2138–42. doi:10.1073/pnas.83.7.2138. PMC 323246. PMID 11542073. [155] Velicer, GJ; Mendes-Soares, H (2009). "Bacterial predators". Current Biology 19 (2): R55–6. doi:10.1016/j.cub.2008.10.043. PMID 19174136. [156] Stams A, de Bok F, Plugge C, van Eekert M, Dolfing J, Schraa G (2006). "Exocellular electron transfer in anaerobic microbial communities". Environ Microbiol 8 (3): 371–82. doi:10.1111/j.1462-2920.2006.00989.x. PMID 16478444. [157] Barea J, Pozo M, Azcón R, Azcón-Aguilar C (2005). "Microbial co-operation in the rhizosphere". J Exp Bot 56 (417): 1761–78. doi:10.1093/jxb/eri197. PMID 15911555. [158] O'Hara A, Shanahan F (2006). "The gut flora as a forgotten organ". EMBO Rep 7 (7): 688–93. doi:10.1038/sj.embor.7400731. PMC 1500832. PMID 16819463. [159] Zoetendal E, Vaughan E, de Vos W (2006). "A microbial world within us". Mol Microbiol 59 (6): 1639–50. doi:10.1111/j.1365-2958.2006.05056.x. PMID 16553872. [160] Gorbach S (1990). "Lactic acid bacteria and human health". Ann Med 22 (1): 37–41. doi:10.3109/07853899009147239. PMID 2109988. [161] Salminen S, Gueimonde M, Isolauri E (1 May 2005). "Probiotics that modify disease risk". J Nutr 135 (5): 1294–8. PMID 15867327. [162] Fish D (2002). "Optimal antimicrobial therapy for sepsis". Am J Health Syst Pharm 59 Suppl 1: S13–9. PMID 11885408. [163] Belland R, Ouellette S, Gieffers J, Byrne G (2004). "Chlamydia pneumoniae and atherosclerosis". Cell Microbiol 6 (2): 117–27. doi:10.1046/j.1462-5822.2003.00352.x. PMID 14706098. [164] Heise ER (1982). "Diseases associated with immunosuppression". Environmental Health Perspectives 43: 9–19. doi:10.2307/3429162. JSTOR 3429162. PMC 1568899. PMID 7037390. [165] Saiman L (2004). "Microbiology of early CF lung disease". Paediatric Respiratory Reviews 5 Suppl A: S367–9. doi:10.1016/S1526-0542(04)90065-6. PMID 14980298.

37

Bacteria
[166] Fisher, Bruce; Harvey, Richard P.; Champe, Pamela C. (2007). Lippincott's Illustrated Reviews: Microbiology (Lippincott's Illustrated Reviews Series). Hagerstwon, MD: Lippincott Williams & Wilkins. pp. Chapter 33, pages 367–392. ISBN 0-7817-8215-5. [167] LEF.org > Bacterial Infections (http:/ / www. lef. org/ protocols/ infections/ bacterial_infection_01. htm) Updated: 01/19/2006. Retrieved on April 11, 2009 [168] Yonath A, Bashan A (2004). "Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics". Annu Rev Microbiol 58: 233–51. doi:10.1146/annurev.micro.58.030603.123822. PMID 15487937. [169] Khachatourians GG (1998). "Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria". CMAJ 159 (9): 1129–36. PMC 1229782. PMID 9835883. [170] Johnson M, Lucey J (2006). "Major technological advances and trends in cheese". J Dairy Sci 89 (4): 1174–8. doi:10.3168/jds.S0022-0302(06)72186-5. PMID 16537950. [171] Hagedorn S, Kaphammer B (1994). "Microbial biocatalysis in the generation of flavor and fragrance chemicals". Annu. Rev. Microbiol. 48: 773–800. doi:10.1146/annurev.mi.48.100194.004013. PMID 7826026. [172] Cohen Y (2002). "Bioremediation of oil by marine microbial mats". Int Microbiol 5 (4): 189–93. doi:10.1007/s10123-002-0089-5. PMID 12497184. [173] Neves LC, Miyamura TT, Moraes DA, Penna TC, Converti A (2006). "Biofiltration methods for the removal of phenolic residues". Appl. Biochem. Biotechnol. 129–132: 130–52. doi:10.1385/ABAB:129:1:130. PMID 16915636. [174] Liese A, Filho M (1999). "Production of fine chemicals using biocatalysis". Curr Opin Biotechnol 10 (6): 595–603. doi:10.1016/S0958-1669(99)00040-3. PMID 10600695. [175] Aronson AI, Shai Y (2001). "Why Bacillus thuringiensis insecticidal toxins are so effective: unique features of their mode of action". FEMS Microbiol. Lett. 195 (1): 1–8. doi:10.1111/j.1574-6968.2001.tb10489.x. PMID 11166987. [176] Bozsik A (2006). "Susceptibility of adult Coccinella septempunctata (Coleoptera: Coccinellidae) to insecticides with different modes of action". Pest Manag Sci 62 (7): 651–4. doi:10.1002/ps.1221. PMID 16649191. [177] Chattopadhyay A, Bhatnagar N, Bhatnagar R (2004). "Bacterial insecticidal toxins". Crit Rev Microbiol 30 (1): 33–54. doi:10.1080/10408410490270712. PMID 15116762. [178] Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome" (http:/ / genomebiology. com/ 1465-6906/ 2/ RESEARCH0035). Genome Biology 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9-research0035. PMC 56896. PMID 11574054. . [179] Almaas E, Kovács B, Vicsek T, Oltvai Z, Barabási A (2004). "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature 427 (6977): 839–43. doi:10.1038/nature02289. PMID 14985762. [180] Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54. PMC 193654. PMID 12952533. [181] Walsh G (2005). "Therapeutic insulins and their large-scale manufacture". Appl Microbiol Biotechnol 67 (2): 151–9. doi:10.1007/s00253-004-1809-x. PMID 15580495. [182] Graumann K, Premstaller A (2006). "Manufacturing of recombinant therapeutic proteins in microbial systems". Biotechnol J 1 (2): 164–86. doi:10.1002/biot.200500051. PMID 16892246.

38

Further reading
• Alcamo IE (2001). Fundamentals of microbiology. Boston: Jones and Bartlett. ISBN 0-7637-1067-9. • Atlas RM (1995). Principles of microbiology. St. Louis: Mosby. ISBN 0-8016-7790-4. • Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed.). Englewood Cliffs, N.J: Prentice Hall. ISBN 0-13-144329-1. • Holt JC, Bergey DH (1994). Bergey's manual of determinative bacteriology (9th ed.). Baltimore: Williams & Wilkins. ISBN 0-683-00603-7. • Hugenholtz P, Goebel BM, Pace NR (15 September 1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity" (http://jb.asm.org/cgi/content/full/180/18/ 4765?view=full&pmid=9733676). J Bacteriol 180 (18): 4765–74. PMC 107498. PMID 9733676. • Funke BR, Tortora GJ, Case CL (2004). Microbiology: an introduction (8th ed.). San Francisco: Benjamin Cummings. ISBN 0-8053-7614-3. • Shively, Jessup M. (2006). Complex Intracellular Structures in Prokaryotes (Microbiology Monographs). Berlin: Springer. ISBN 3-540-32524-7.

Bacteria

39

External links
• MicrobeWiki (http://microbewiki.kenyon.edu/index.php/MicrobeWiki), an extensive wiki about bacteria (http://microbewiki.kenyon.edu/index.php/Microbial_Biorealm) and viruses (http://microbewiki.kenyon. edu/index.php/Viral_Biorealm) • Bacteria that affect crops and other plants (http://www.ncppb.com) • Bacterial Nomenclature Up-To-Date from DSMZ (http://www.dsmz.de/bactnom/bactname.htm) • Genera of the domain Bacteria (http://www.bacterio.cict.fr/eubacteria.html) – list of Prokaryotic names with Standing in Nomenclature • The largest bacteria (http://www.sciencenews.org/pages/sn_arc99/4_17_99/fob5.htm) • Tree of Life: Eubacteria (http://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth) • Videos (http://www.rowland.harvard.edu/labs/bacteria/index_movies.html) of bacteria swimming and tumbling, use of optical tweezers and other videos. • Planet of the Bacteria (http://www.stephenjaygould.org/library/gould_bacteria.html) by Stephen Jay Gould • On-line text book on bacteriology (http://www.textbookofbacteriology.net/) • Animated guide to bacterial cell structure. (http://www.blackwellpublishing.com/trun/artwork/Animations/ Overview/overview.html) • Bacteria Make Major Evolutionary Shift in the Lab (http://www.newscientist.com/channel/life/ dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html) • Online collaboration for bacterial taxonomy. (http://esciencenews.com/articles/2009/02/19/online. collaboration.identifies.bacteria) • PATRIC (http://patricbrc.org/), a Bioinformatics Resource Center for bacterial pathogens, funded by NIAID (http://www.niaid.nih.gov/) • Bacterial Chemotaxis Interactive Simulator (http://wormweb.org/bacteriachemo) – A web-app that uses several simple algorithms to simulate bacterial chemotaxis. • Cell-Cell Communication in Bacteria (http://ascb.org/ibioseminars/Bassler/Bassler1.cfm) on-line lecture by Bonnie Bassler, and TED: Discovering bacteria's amazing communication system (http://www.ted.com/index. php/talks/bonnie_bassler_on_how_bacteria_communicate.html)

Bacteriology

40

Bacteriology
Bacteriology is the study of bacteria. This subdivision of microbiology involves the identification, classification, and characterization of bacterial species.[1] A person who studies bacteriology is a bacteriologist.

Bacteriology and microbiology
Because of the similarity of thinking and working with microorganisms other than bacteria, such as protozoa, fungi, and viruses, there has been a tendency for the field of bacteriology to extend as microbiology.[2] The terms were formerly often used interchangeably.[3] However, bacteriology can be classified as a distinct science.

References
[1] Wassenaar, T. M.. "Bacteriology: the study of bacteria" (http:/ / www. bacteriamuseum. org/ cms/ bacteria/ bacteriology-the-study-of-bacteria. html). www.mmgc.eu. . Retrieved 18 June 2011. [2] Ward J. MacNeal; Herbert Upham Williams (1914). Pathogenic micro-organisms; a text-book of microbiology for physicians and students of medicine (http:/ / books. google. com/ books?id=ijQRAAAAYAAJ& pg=PA1). P. Blakiston's sons & co.. pp. 1–. . Retrieved 18 June 2011. [3] Jeanne Stove Poindexter (30 November 1986). Methods and special applications in bacterial ecology (http:/ / books. google. com/ books?id=BYGRgeBChYYC& pg=PA87). Springer. p. 87. ISBN 978-0-306-42346-8. . Retrieved 18 June 2011.

Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. The laws of biochemistry govern all living organisms and living processes. By controlling information flow through biochemical signalling and the flow of chemical energy through metabolism, biochemical processes give rise to the complexity of life. Much of biochemistry deals with the structures, functions and interactions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules —although increasingly processes rather than individual molecules are the main focus. Among the vast number of different biomolecules, many are complex and large molecules (called biopolymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types.[1] For example, a protein is a polymer whose subunits are selected from a set of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions. The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the genetic code (DNA, RNA), protein synthesis, cell membrane transport and signal transduction. Over the last 40 years biochemistry has become so successful at explaining living processes that now almost all areas of the life sciences from botany to medicine are engaged in biochemical research. Today the main focus of pure biochemistry is in understanding how biological molecules give rise to the processes that occur within living cells, which in turn relates greatly to the study and understanding of whole organisms.

Biochemistry

41

History
It once was generally believed that life and its materials had some essential property or substance distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life. Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.[2][3] The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to have been first used in 1882, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German chemist. Previous to this Gerty Cori and Carl Cori jointly won the time, this area would have been referred to as physiological chemistry. Nobel Prize in 1947 for their discovery of Since then, biochemistry has advanced, especially since the mid-20th the Cori cycle at RPMI. century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy, and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle). Another significant historic event in biochemistry is the discovery of the gene and its role in the transfer of information in the cell. This part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to growth of forensic science. More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression.

Starting materials: the chemical elements of life
Around two dozen of the 94 naturally-occurring chemical elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life (exceptions being selenium and iodine), while a few common ones (aluminum and titanium) are not used. Most organisms share element needs, but there are a few differences between plants and animals. For example ocean algae use bromine but land plants and animals seem to need none. All animals require sodium, but some plants do not. Plants need boron and silicon, but animals may not (or may need ultra-small amounts). Just six elements—carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus—make up almost 99% of the mass of a human body (see composition of the human body for a complete list). In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more.[4]

Biochemistry

42

Biomolecules
The four main classes of molecules in biochemistry are carbohydrates, lipids, proteins, and nucleic acids. Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create large macromolecules, which are known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis. Different macromolecules can assemble in larger complexes, often needed for biological activity.

Carbohydrates
Carbohydrates are made from monomers called monosaccharides. Some of these monosaccharides include glucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4). When two monosaccharides undergo dehydration synthesis, water is produced, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides' hydroxyl group.
A molecule of sucrose (glucose + fructose), a disaccharide.

Lipids
Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain). Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g., in parenteral infusions) or else as drug carrier components (e.g., in a liposome or transfersome).

A triglyceride with a glycerol molecule on the left and three fatty acids coming off it.

Proteins
Proteins are very large molecules – macro-biopolymers – made from monomers called amino acids. There are 20 standard amino acids, each containing a carboxyl group, an amino group, and a side-chain (known as an "R" group). The "R" group is what makes each amino acid different, and the properties of the side-chains greatly influence the overall three-dimensional conformation of a protein. When amino acids combine, they form a special bond called a peptide bond through dehydration synthesis, and become a polypeptide, or protein.

In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like Sequence Alignments and Structural Alignments are powerful tools that help scientists identify homologies between related molecules.

The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.

The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

Biochemistry

43

Nucleic acids
Nucleic acids are the molecules that make up DNA, an extremely important substance that all cellular organisms use to store their genetic information. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Their monomers are called nucleotides. The most common nucleotides are adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil; Thymine binds only with adenine; and cytosine and guanine can bind only with each other.

Carbohydrates
The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.

The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together.

Monosaccharides
The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar commonly associated with the sweet taste of fruits.[5][a] Some carbohydrates (especially after condensation to oligo- and polysaccharides) contain less carbon Glucose relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e.g. glucose) and ketoses (having a keto group in their chain; e.g. fructose). Both aldoses and ketoses occur in an equilibrium (starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxyl groups of the sugar chain with the carbon of the aldehyde or keto group to form a hemiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.

Disaccharides
Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H2O is then released as a molecule of water, hence the term dehydration. The new molecule, consisting of two monosaccharides, is called a disaccharide and is conjoined together by a glycosidic or ether bond. The reverse reaction can also

Sucrose: ordinary table sugar and probably the most familiar carbohydrate.

Biochemistry occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance. Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom that can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side-chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

44

Oligosaccharides and polysaccharides
When a few (around three to six) monosaccharides are joined together, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers.

Cellulose as polymer of β-D-glucose

• Cellulose is made by plants and is an important structural component of their cell walls. Humans can neither manufacture nor digest it. • Glycogen, on the other hand, is an animal carbohydrate; humans and other animals use it as a form of energy storage.

Use of carbohydrates as an energy source
Glucose is the major energy source in most life forms. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides. Glycolysis (anaerobic) Glucose is mainly metabolized by a very important ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents in the form of converting NAD+ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e.g., in humans) or to ethanol plus carbon dioxide (e.g., in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.

Biochemistry Aerobic In aerobic cells with sufficient oxygen, as in most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen. Gluconeogenesis In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate. The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.

45

Proteins
Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant molecules called substrates; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme.

A schematic of hemoglobin. The red and blue ribbons represent the protein globin; the green structures are the heme groups.

The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell

Biochemistry as a whole. In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, —NH2, and one is a carboxylic acid group, —COOH (although these exist as —NH3+ and —COO− under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter. Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined carboxylic acid group. The resulting together as a dipeptide. molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues. The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-…". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet; some α-helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit. Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can synthesize only half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids. If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein. A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Likewise, bony fish can

46

Biochemistry release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.

47

Lipids
The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids, and terpenoids (e.g., retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid. Most lipids have some polar character in addition to being largely nonpolar. In general, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below. Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.

Nucleic acids
A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate, the primary energy-carrier molecule found in all living organisms. Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g., DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

Biochemistry

48

Relationship to other "molecular-scale" biological sciences
Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas developed in the fields of genetics, molecular biology and biophysics. There has never been a hard-line between these disciplines in terms of content and technique. Today, the terms molecular biology and biochemistry are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields: • Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.

Schematic relationship between biochemistry, genetics, and molecular biology

• Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g., one gene). The study of "mutants" – organisms with a changed gene that leads to the organism being different with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" or "knock-in" studies. • Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA. • Chemical Biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).

Notes
a.   It should be noted that fructose is not the only sugar found in fruits. Glucose and sucrose are also found in varying quantities in various fruits, and indeed sometimes exceed the fructose present. For example, 32 % of the edible portion of date is glucose, compared with 23.70 % fructose and 8.20 % sucrose. However, peaches contain more sucrose (6.66 %) than they do fructose (0.93 %) or glucose (1.47 %).[6]

References
[1] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6. . [2] Wöhler, F. (1828). "Ueber künstliche Bildung des Harnstoffs". Ann. Phys. Chem. 12: 253–256. [3] Kauffman, G. B. and Chooljian, S.H. (2001). "Friedrich Wöhler (1800–1882), on the Bicentennial of His Birth". The Chemical Educator 6 (2): 121–133. doi:10.1007/s00897010444a. [4] Ultratrace minerals. Authors: Nielsen, Forrest H. USDA, ARS Source: Modern nutrition in health and disease / editors, Maurice E. Shils ... et al.. Baltimore : Williams & Wilkins, c1999., p. 283-303. Issue Date: 1999 URI: (http:/ / hdl. handle. net/ 10113/ 46493)

Biochemistry
[5] Whiting, G.C (1970). "Sugars". In A.C. Hulme. The Biochemistry of Fruits and their Products. Volume 1. London & New York: Academic Press. pp. 1=31 [6] Whiting, G.C. (1970), p.5

49

Further reading
• Hunter, Graeme K. (2000). Vital Forces: The Discovery of the Molecular Basis of Life. San Diego: Academic Press. ISBN 0-12-361810-X. OCLC 162129355 191848148 44187710.

External links
• The Virtual Library of Biochemistry and Cell Biology (http://www.biochemweb.org/) • Biochemistry, 5th ed. (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=stryer. TOC&depth=2) Full text of Berg, Tymoczko, and Stryer, courtesy of NCBI. • Biochemistry, 2nd ed. (http://www.web.virginia.edu/Heidi/home.htm) Full text of Garrett and Grisham. • Biochemistry Animation (http://www.1lec.com/Biochemistry/) (Narrated Flash animations.) • SystemsX.ch - The Swiss Initiative in Systems Biology (http://www.systemsX.ch/) • Biochemistry Online Resources (http://www.icademic.org/97445/Biochemistry/) – Lists of Biochemistry departments, websites, journals, books and reviews, employment opportunities and events.
biochemical families: proteins (amino acids/intermediates) · nucleic acids (constituents/intermediates) · carbohydrates (glycoproteins, alcohols, glycosides) lipids (fatty acids/intermediates, phospholipids, steroids, sphingolipids, eicosanoids) · tetrapyrroles/intermediates

Biological membrane
A biological membrane or biomembrane is an enclosing or separating membrane that acts as a selective barrier, within or around a cell. It consists of a lipid bilayer with embedded proteins that may constitute close to 50% of membrane content.[1] The cellular membranes should not be confused with isolating tissues formed by layers of cells, such as mucous and basement membranes.

Function
Membranes in cells typically define enclosed spaces or compartments in which cells may maintain a chemical or biochemical environment that differs from the outside. For example, the membrane around peroxisomes shields the rest of the cell from peroxides, and the cell membrane separates a cell from its surrounding medium. Most organelles are defined by such membranes, and are called "membrane-bound" organelles.

Cross section view of the structures that can be formed by phospholipids in aqueous solutions

Probably the most important feature of a biomembrane is that it is a selectively permeable structure. This means that the size, charge, and other chemical properties of the atoms and molecules attempting to cross it will determine whether they succeed in doing so. Selective permeability is essential for effective separation of a cell or organelle from its surroundings. Biological membranes also have certain mechanical or elastic properties.

Biological membrane Particles that are required for cellular function but are unable to diffuse freely across a membrane enter through a membrane transport protein or are taken in by means of endocytosis.

50

Diversity of biological membranes
Many types of specialized plasma membranes can separate cell from external environment: apical, basolateral, presynaptic and postsynaptic ones, membranes of flagella, cilia, microvillus, filopodia and lamellipodia, the sarcolemma of muscle cells, as well as specialized myelin and dendritic spine membranes of neurons. Plasma membranes can also form different types of "supramembrane" structures such as caveola, postsynaptic density, podosome, invadopodium, desmosome, hemidesmosome, focal adhesion, and cell junctions. These types of membranes differ in lipid and protein composition. Distinct types of membranes also create intracellular organelles: endosome; smooth and rough endoplasmic reticulum; sarcoplasmic reticulum; Golgi apparatus; lysosome; mitochondrion (inner and outer membranes); nucleus (inner and outer membranes); peroxisome; vacuole; cytoplasmic granules; cell vesicles (phagosome, autophagosome, clathrin-coated vesicles, COPI-coated and COPII-coated vesicles) and secretory vesicles (including synaptosome, acrosomes, melanosomes, and chromaffin granules). Different types of biological membranes have diverse lipid and protein compositions. The content of membranes defines their physical and biological properties. Some components of membranes play a key role in medicine, such as the efflux pumps that pump drugs out of a cell.

References
[1] Mark L. Latash (2007). Neurophysiological basis of movement. Human Kinetics Publishers. ISBN 978-0-7360-6367-8.

• von Heijne G, Rees D (August 2008). "Membranes: reading between the lines" (http://linkinghub.elsevier.com/ retrieve/pii/S0959-440X(08)00091-2). Curr. Opin. Struct. Biol. 18 (4): 403–5. doi:10.1016/j.sbi.2008.06.003. PMID 18634876.

External links
• Membranes (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Membranes) at the US National Library of Medicine Medical Subject Headings (MeSH)

Blood

51

Blood
Blood is a specialized bodily fluid in animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away from those same cells. In vertebrates, it is composed of blood cells suspended in a liquid called blood plasma. Plasma, which constitutes 55% of blood fluid, is mostly water (92% by volume),[1] and contains dissipated proteins, glucose, mineral ions, hormones, carbon dioxide (plasma being the main medium for excretory product transportation), and blood cells themselves. Albumin is the main protein in plasma, and it functions to regulate the colloidal osmotic pressure of blood. The blood cells are mainly red blood cells (also called RBCs or erythrocytes) and white blood cells, including leukocytes and platelets. The most abundant cells in vertebrate blood are red blood cells. These contain hemoglobin, an iron-containing protein, which facilitates transportation of oxygen by reversibly binding to this respiratory gas and greatly increasing its solubility in blood. In contrast, carbon dioxide is almost entirely transported extracellularly dissolved in plasma as bicarbonate ion.

Human blood smear: a – erythrocytes; b – neutrophil; c – eosinophil; d – lymphocyte.

A scanning electron microscope (SEM) image of a normal red blood cell, a platelet, and a white blood cell.

Vertebrate blood is bright red when its hemoglobin is oxygenated. Some animals, such as crustaceans and mollusks, use hemocyanin to carry oxygen, instead of hemoglobin. Insects and some mollusks use a fluid called hemolymph instead of blood, the difference being that hemolymph is not contained in a closed circulatory system. In most insects, this "blood" does not contain oxygen-carrying molecules such as hemoglobin because their bodies are small enough for their tracheal system to suffice for supplying oxygen.

Blood

52

Jawed vertebrates have an adaptive immune system, based largely on white blood cells. White blood cells help to resist infections and parasites. Platelets are important in the clotting of blood.[2] Arthropods, using hemolymph, have hemocytes as part of their immune system. Blood is circulated around the body through blood vessels by the pumping action of the heart. In animals with lungs, arterial blood carries oxygen from inhaled air to the tissues of the body, and venous blood carries carbon dioxide, a waste product of metabolism produced by cells, from the tissues to the lungs to be exhaled. Medical terms related to blood often begin with hemo- or hemato(also spelled haemo- and haemato-) from the Ancient Greek word αἷμα (haima) for "blood". In terms of anatomy and histology, blood is considered a specialized form of connective tissue, given its origin in the bones and the presence of potential molecular fibers in the form of fibrinogen.

Blood circulation: Red = oxygenated Blue = deoxygenated

Human blood magnified 600 times

Frog blood magnified 600 times

Blood

53

Fish blood magnified 600 times

Functions
Blood performs many important functions within the body including: • Supply of oxygen to tissues (bound to hemoglobin, which is carried in red cells) • Supply of nutrients such as glucose, amino acids, and fatty acids (dissolved in the blood or bound to plasma proteins (e.g., blood lipids)) • Removal of waste such as carbon dioxide, urea, and lactic acid • Immunological functions, including circulation of white blood cells, and detection of foreign material by antibodies • Coagulation, which is one part of the body's self-repair mechanism (blood clotting after an open wound in order to stop bleeding) • Messenger functions, including the transport of hormones and the signaling of tissue damage • Regulation of body pH • Regulation of core body temperature • Hydraulic functions
Hemoglobin green = heme groups red & blue = protein subunits

Heme

Blood

54

Constituents of human blood
Blood accounts for 8% of the human body weight,[3] with an average density of approximately 1060 kg/m3, very close to pure water's density of 1000 kg/m3.[4] The average adult has a blood volume of roughly 5 liters (1.3 gal), composed of plasma and several kinds of cells (occasionally called corpuscles); these formed elements of the blood are erythrocytes (red blood cells, RBCs), leukocytes (white blood cells), and thrombocytes (platelets). By volume, the red blood cells constitute about 45% of whole blood, the plasma about 54.3%, and white cells about 0.7%. Whole blood (plasma and cells) exhibits non-Newtonian fluid dynamics; its flow properties are adapted to flow effectively through tiny capillary blood vessels with less resistance than plasma by itself. In addition, if all human hemoglobin were free in the plasma rather than being contained in RBCs, the circulatory fluid would be too viscous for the cardiovascular system to function effectively.

Cells
Further information: Complete blood count One microliter of blood contains:

Two tubes of EDTA-anticoagulated blood. Left tube: after standing, the RBCs have settled at the bottom of the tube. Right tube: contains freshly drawn blood.

• 4.7 to 6.1 million (male), 4.2 to 5.4 million (female) Erythrocytes:[5] Red blood cells contain the blood's hemoglobin and distribute oxygen. Mature red blood cells lack a nucleus and organelles in mammals. The red blood cells (together with endothelial vessel cells and other cells) are also marked by glycoproteins that define the different blood types. The proportion of blood occupied by red blood cells is referred to as the hematocrit, and is normally about 45%. The combined surface area of all red blood cells of the human body would be roughly 2,000 times as great as the body's exterior surface.[6] • 4,000–11,000 Leukocytes:[7] White blood cells are part of the body's immune system; they destroy and remove old or aberrant cells and cellular debris, as well as attack infectious agents (pathogens) and foreign substances. The cancer of leukocytes is called leukemia. • 200,000–500,000 Thrombocytes:[7]: Also called platelets, thrombocytes are responsible for blood clotting (coagulation). They change fibrinogen into fibrin. This fibrin creates a mesh onto which red blood cells collect and clot, which then stops more blood from leaving the body and also helps to prevent bacteria from entering the body.

Constitution of normal blood
Parameter Hematocrit Value 45 ± 7 (38–52%) for males 42 ± 5 (37–47%) for females 7.35–7.45 −3 to +3 10–13 kPa (80–100 mm Hg) 4.8–5.8 kPa (35–45 mm Hg) 21–27 mM

pH base excess PO2 PCO2 HCO3−

Oxygen saturation Oxygenated: 98–99% Deoxygenated: 75%

Blood

55

Plasma
About 55% of blood is blood plasma, a fluid that is the blood's liquid medium, which by itself is straw-yellow in color. The blood plasma volume totals of 2.7–3.0 liters (2.8–3.2 quarts) in an average human. It is essentially an aqueous solution containing 92% water, 8% blood plasma proteins, and trace amounts of other materials. Plasma circulates dissolved nutrients, such as glucose, amino acids, and fatty acids (dissolved in the blood or bound to plasma proteins), and removes waste products, such as carbon dioxide, urea, and lactic acid. Other important components include: • • • • • • Serum albumin Blood-clotting factors (to facilitate coagulation) Immunoglobulins (antibodies) lipoprotein particles Various other proteins Various electrolytes (mainly sodium and chloride)

The term serum refers to plasma from which the clotting proteins have been removed. Most of the proteins remaining are albumin and immunoglobulins.

Narrow range of pH values
Blood pH is regulated to stay within the narrow range of 7.35 to 7.45, making it slightly alkaline.[8][9] Blood that has a pH below 7.35 is too acidic, whereas blood pH above 7.45 is too alkaline. Blood pH, partial pressure of oxygen (pO2), partial pressure of carbon dioxide (pCO2), and HCO3− are carefully regulated by a number of homeostatic mechanisms, which exert their influence principally through the respiratory system and the urinary system in order to control the acid-base balance and respiration. An arterial blood gas will measure these. Plasma also circulates hormones transmitting their messages to various tissues. The list of normal reference ranges for various blood electrolytes is extensive. Bones are especially affected by blood pH as they tend to be used as a mineral source for pH buffering. Consuming a high ratio of animal protein to vegetable protein is implicated in bone loss in women.[10]

Blood in non-human vertebrates
Human blood is typical of that of mammals, although the precise details concerning cell numbers, size, protein structure, and so on, vary somewhat between species. In non-mammalian vertebrates, however, there are some key differences:[11] • Red blood cells of non-mammalian vertebrates are flattened and ovoid in form, and retain their cell nuclei • There is considerable variation in the types and proportions of white blood cells; for example, acidophils are generally more common than in humans • Platelets are unique to mammals; in other vertebrates, small nucleated, spindle cells are responsible for blood clotting instead

Blood

56

Physiology
Cardiovascular system
Blood is circulated around the body through blood vessels by the pumping action of the heart. In humans, blood is pumped from the strong left ventricle of the heart through arteries to peripheral tissues and returns to the right atrium of the heart through veins. It then enters the right ventricle and is pumped through the pulmonary artery to the lungs and returns to the left atrium through the pulmonary veins. Blood then enters the left ventricle to be circulated again. Arterial blood carries oxygen from inhaled air to all of the cells of the body, and venous blood carries carbon dioxide, a waste product of metabolism by cells, to the lungs to be exhaled. However, one exception includes pulmonary arteries, which contain the most deoxygenated blood in the body (which is a blue purple color), while the pulmonary veins contain oxygenated blood.

The circulation of blood through the human heart

Additional return flow may be generated by the movement of skeletal muscles, which can compress veins and push blood through the valves in veins toward the right atrium. The blood circulation was famously described by William Harvey in 1628.[12]

Production and degradation of blood cells
In vertebrates, the various cells of blood are made in the bone marrow in a process called hematopoiesis, which includes erythropoiesis, the production of red blood cells; and myelopoiesis, the production of white blood cells and platelets. During childhood, almost every human bone produces red blood cells; as adults, red blood cell production is limited to the larger bones: the bodies of the vertebrae, the breastbone (sternum), the ribcage, the pelvic bones, and the bones of the upper arms and legs. In addition, during childhood, the thymus gland, found in the mediastinum, is an important source of lymphocytes.[13] The proteinaceous component of blood (including clotting proteins) is produced predominantly by the liver, while hormones are produced by the endocrine glands and the watery fraction is regulated by the hypothalamus and maintained by the kidney. Healthy erythrocytes have a plasma life of about 120 days before they are degraded by the spleen, and the Kupffer cells in the liver. The liver also clears some proteins, lipids, and amino acids. The kidney actively secretes waste products into the urine.

Blood

57

Oxygen transport
About 98.5% of the oxygen in a sample of arterial blood in a healthy human breathing air at sea-level pressure is chemically combined with the Hgb. About 1.5% is physically dissolved in the other blood liquids and not connected to Hgb. The hemoglobin molecule is the primary transporter of oxygen in mammals and many other species (for exceptions, see below). Hemoglobin has an oxygen binding capacity of between 1.36 and 1.37 ml O2 per gram Hemoglobin,[14] which increases the total blood oxygen capacity seventyfold,[15] compared to if oxygen solely was carried by its solubility of 0.03 mL O2 per liter blood per mmHg partial pressure of oxygen (approximately 100 mmHg in arteries).[15] With the exception of pulmonary and umbilical arteries and their corresponding veins, arteries carry oxygenated blood away from the heart and deliver it to the body via arterioles and capillaries, where the oxygen is consumed; afterwards, venules, and veins carry deoxygenated blood back to the heart.
Basic hemoglobin saturation curve. It is moved to the right in higher acidity (more dissolved carbon dioxide) and to the left in lower acidity (less dissolved carbon dioxide)

Under normal conditions in adult humans at rest; hemoglobin in blood leaving the lungs is about 98–99% saturated with oxygen, achieving an oxygen delivery of between 950 - 1150 mL/min[16] to the body. In a healthy adult at rest, oxygen consumption is approximately 200 - 250 mL/min,[16] and deoxygenated blood returning to the lungs is still approximately 75%[17][18] (70 to 78%)[16] saturated. Increased oxygen consumption during sustained exercise reduces the oxygen saturation of venous blood, which can reach less than 15% in a trained athlete; although breathing rate and blood flow increase to compensate, oxygen saturation in arterial blood can drop to 95% or less under these conditions.[19] Oxygen saturation this low is considered dangerous in an individual at rest (for instance, during surgery under anesthesia. Sustained hypoxia (oxygenation of less than 90%), is dangerous to health, and severe hypoxia (saturations of less than 30%) may be rapidly fatal.[20] A fetus, receiving oxygen via the placenta, is exposed to much lower oxygen pressures (about 21% of the level found in an adult's lungs), and, so, fetuses produce another form of hemoglobin with a much higher affinity for oxygen (hemoglobin F) in order to function under these conditions.[21]

Carbon dioxide transport
CO2 is carried in blood in three different ways. (The exact percentages vary depending whether it is arterial or venous blood). Most of it (about 70% to 80%) is converted to bicarbonate ions HCO by the enzyme carbonic anhydrase in the red blood cells,[22] by the reaction CO2 + H2O → H2CO3 → H+ + HCO 5% – 10% is dissolved in the plasma,[22] and 5% – 10% is bound to hemoglobin as carbamino compounds[22] Hemoglobin, the main oxygen-carrying molecule in red blood cells, carries both oxygen and carbon dioxide. However, the CO2 bound to hemoglobin does not bind to the same site as oxygen. Instead, it combines with the N-terminal groups on the four globin chains. However, because of allosteric effects on the hemoglobin molecule, the binding of CO2 decreases the amount of oxygen that is bound for a given partial pressure of oxygen. The decreased binding to carbon dioxide in the blood due to increased oxygen levels is known as the Haldane effect, and is important in the transport of carbon dioxide from the tissues to the lungs. A rise in the partial pressure of CO2 or a lower pH will cause offloading of oxygen from hemoglobin, which is known as the Bohr effect.

Blood

58

Transport of hydrogen ions
Some oxyhemoglobin loses oxygen and becomes deoxyhemoglobin. Deoxyhemoglobin binds most of the hydrogen ions as it has a much greater affinity for more hydrogen than does oxyhemoglobin.

Lymphatic system
In mammals, blood is in equilibrium with lymph, which is continuously formed in tissues from blood by capillary ultrafiltration. Lymph is collected by a system of small lymphatic vessels and directed to the thoracic duct, which drains into the left subclavian vein where lymph rejoins the systemic blood circulation.

Thermoregulation
Blood circulation transports heat throughout the body, and adjustments to this flow are an important part of thermoregulation. Increasing blood flow to the surface (e.g., during warm weather or strenuous exercise) causes warmer skin, resulting in faster heat loss. In contrast, when the external temperature is low, blood flow to the extremities and surface of the skin is reduced and to prevent heat loss and is circulated to the important organs of the body, preferentially.

Hydraulic functions
The restriction of blood flow can also be used in specialized tissues to cause engorgement, resulting in an erection of that tissue; examples are the erectile tissue in the penis and clitoris. Another example of a hydraulic function is the jumping spider, in which blood forced into the legs under pressure causes them to straighten for a powerful jump, without the need for bulky muscular legs.[23]

Invertebrates
In insects, the blood (more properly called hemolymph) is not involved in the transport of oxygen. (Openings called tracheae allow oxygen from the air to diffuse directly to the tissues). Insect blood moves nutrients to the tissues and removes waste products in an open system. Other invertebrates use respiratory proteins to increase the oxygen-carrying capacity. Hemoglobin is the most common respiratory protein found in nature. Hemocyanin (blue) contains copper and is found in crustaceans and mollusks. It is thought that tunicates (sea squirts) might use vanabins (proteins containing vanadium) for respiratory pigment (bright-green, blue, or orange). In many invertebrates, these oxygen-carrying proteins are freely soluble in the blood; in vertebrates they are contained in specialized red blood cells, allowing for a higher concentration of respiratory pigments without increasing viscosity or damaging blood filtering organs like the kidneys. Giant tube worms have unusual hemoglobins that allow them to live in extraordinary environments. These hemoglobins also carry sulfides normally fatal in other animals.

Blood

59

Color
Hemoglobin
Hemoglobin is the principal determinant of the color of blood in vertebrates. Each molecule has four heme groups, and their interaction with various molecules alters the exact color. In vertebrates and other hemoglobin-using creatures, arterial blood and capillary blood are bright red, as oxygen imparts a strong red color to the heme group. Deoxygenated blood is a darker shade of red; this is present in veins, and can be seen during blood donation and when venous blood samples are taken. Blood in carbon monoxide poisoning is bright red, because carbon monoxide causes the formation of carboxyhemoglobin. In cyanide poisoning, the body cannot utilize oxygen, so the venous blood remains oxygenated, increasing the redness. While hemoglobin-containing blood is never blue, there are several conditions and diseases wherein the color of the heme groups make the skin appear blue. If the heme is oxidized, methaemoglobin, which is more brownish and cannot transport oxygen, is formed. In the rare condition sulfhemoglobinemia, arterial hemoglobin is partially oxygenated, and appears dark red with a bluish hue (cyanosis). Veins in the skin appear blue for a variety of reasons only weakly dependent on the color of the blood. Light scattering in the skin, and the visual processing of color play roles as well.[24]

Capillary blood from a bleeding finger

Venous blood collected during blood donation

Skinks in the genus Prasinohaema have green blood due to a buildup of the waste product biliverdin.[25]

Hemocyanin
The blood of most mollusks – including cephalopods and gastropods – as well as some arthropods, such as horseshoe crabs, is blue, as it contains the copper-containing protein hemocyanin at concentrations of about 50 grams per liter.[26] Hemocyanin is colorless when deoxygenated and dark blue when oxygenated. The blood in the circulation of these creatures, which generally live in cold environments with low oxygen tensions, is grey-white to pale yellow,[26] and it turns dark blue when exposed to the oxygen in the air, as seen when they bleed.[26] This is due to change in color of hemocyanin when it is oxidized.[26] Hemocyanin carries oxygen in extracellular fluid, which is in contrast to the intracellular oxygen transport in mammals by hemoglobin in RBCs.[26]

Blood

60

Hemovanadin
The blood of some species of ascidians and tunicates, also known as sea squirts and sea cucumbers, contains proteins called vanabins. These proteins are based on vanadium, and give the creatures a concentration of vanadium in their bodies 100 times higher than the surrounding sea water. It is not clear whether these vanabins actually carry oxygen. When exposed to oxygen, however, vanabins turn a mustard yellow.

Pathology
General medical disorders
• Disorders of volume • Injury can cause blood loss through bleeding.[27] A healthy adult can lose almost 20% of blood volume (1 L) before the first symptom, restlessness, begins, and 40% of volume (2 L) before shock sets in. Thrombocytes are important for blood coagulation and the formation of blood clots, which can stop bleeding. Trauma to the internal organs or bones can cause internal bleeding, which can sometimes be severe. • Dehydration can reduce the blood volume by reducing the water content of the blood. This would rarely result in shock (apart from the very severe cases) but may result in orthostatic hypotension and fainting. • Disorders of circulation • Shock is the ineffective perfusion of tissues, and can be caused by a variety of conditions including blood loss, infection, poor cardiac output. • Atherosclerosis reduces the flow of blood through arteries, because atheroma lines arteries and narrows them. Atheroma tends to increase with age, and its progression can be compounded by many causes including smoking, high blood pressure, excess circulating lipids (hyperlipidemia), and diabetes mellitus. • Coagulation can form a thrombosis, which can obstruct vessels. • Problems with blood composition, the pumping action of the heart, or narrowing of blood vessels can have many consequences including hypoxia (lack of oxygen) of the tissues supplied. The term ischemia refers to tissue that is inadequately perfused with blood, and infarction refers to tissue death (necrosis), which can occur when the blood supply has been blocked (or is very inadequate)

Hematological disorders
• Anemia • Insufficient red cell mass (anemia) can be the result of bleeding, blood disorders like thalassemia, or nutritional deficiencies; and may require blood transfusion. Several countries have blood banks to fill the demand for transfusable blood. A person receiving a blood transfusion must have a blood type compatible with that of the donor. • Sickle-cell anemia • Disorders of cell proliferation • Leukemia is a group of cancers of the blood-forming tissues. • Non-cancerous overproduction of red cells (polycythemia vera) or platelets (essential thrombocytosis) may be premalignant. • Myelodysplastic syndromes involve ineffective production of one or more cell lines. • Disorders of coagulation • Hemophilia is a genetic illness that causes dysfunction in one of the blood's clotting mechanisms. This can allow otherwise inconsequential wounds to be life-threatening, but more commonly results in hemarthrosis, or bleeding into joint spaces, which can be crippling. • Ineffective or insufficient platelets can also result in coagulopathy (bleeding disorders).

Blood • Hypercoagulable state (thrombophilia) results from defects in regulation of platelet or clotting factor function, and can cause thrombosis. • Infectious disorders of blood • Blood is an important vector of infection. HIV, the virus that causes AIDS, is transmitted through contact with blood, semen or other body secretions of an infected person. Hepatitis B and C are transmitted primarily through blood contact. Owing to blood-borne infections, bloodstained objects are treated as a biohazard. • Bacterial infection of the blood is bacteremia or sepsis. Viral Infection is viremia. Malaria and trypanosomiasis are blood-borne parasitic infections.

61

Carbon monoxide poisoning
Substances other than oxygen can bind to hemoglobin; in some cases this can cause irreversible damage to the body. Carbon monoxide, for example, is extremely dangerous when carried to the blood via the lungs by inhalation, because carbon monoxide irreversibly binds to hemoglobin to form carboxyhemoglobin, so that less hemoglobin is free to bind oxygen, and fewer oxygen molecules can be transported throughout the blood. This can cause suffocation insidiously. A fire burning in an enclosed room with poor ventilation presents a very dangerous hazard, since it can create a build-up of carbon monoxide in the air. Some carbon monoxide binds to hemoglobin when smoking tobacco.

Medical treatments
Blood products
Further information: Blood transfusion Blood for transfusion is obtained from human donors by blood donation and stored in a blood bank. There are many different blood types in humans, the ABO blood group system, and the Rhesus blood group system being the most important. Transfusion of blood of an incompatible blood group may cause severe, often fatal, complications, so crossmatching is done to ensure that a compatible blood product is transfused. Other blood products administered intravenously are platelets, blood plasma, cryoprecipitate, and specific coagulation factor concentrates.

Intravenous administration
Many forms of medication (from antibiotics to chemotherapy) are administered intravenously, as they are not readily or adequately absorbed by the digestive tract. After severe acute blood loss, liquid preparations, generically known as plasma expanders, can be given intravenously, either solutions of salts (NaCl, KCl, CaCl2 etc.) at physiological concentrations, or colloidal solutions, such as dextrans, human serum albumin, or fresh frozen plasma. In these emergency situations, a plasma expander is a more effective life-saving procedure than a blood transfusion, because the metabolism of transfused red blood cells does not restart immediately after a transfusion.

Blood

62

Bloodletting
In modern evidence-based medicine, bloodletting is used in management of a few rare diseases, including hemochromatosis and polycythemia. However, bloodletting and leeching were common unvalidated interventions used until the 19th century, as many diseases were incorrectly thought to be due to an excess of blood, according to Hippocratic medicine.

History
According to the Oxford English Dictionary, the word "blood" dates to the oldest English, circa 1000 AD. The word is derived from Middle English, which is derived from the Old English word blôd, which is akin to the Old High German word bluot, meaning blood. The modern German word is (das) Blut.

Classical Greek medicine
In classical Greek medicine, blood was associated with air, with Springtime, and with a merry and gluttonous (sanguine) personality. It was also believed to be produced exclusively by the liver.

Hippocratic medicine
In Hippocratic medicine, blood was considered to be one of the four humors, the others being phlegm, yellow bile, and black bile.

Cultural and religious beliefs
Due to its importance to life, blood is associated with a large number of beliefs. One of the most basic is the use of blood as a symbol for family relationships through birth/parentage; to be "related by blood" is to be related by ancestry or descendance, rather than marriage. This bears closely to bloodlines, and sayings such as "blood is thicker than water" and "bad blood", as well as "Blood brother". Blood is given particular emphasis in the Jewish and Christian religions because Leviticus 17:11 says "the life of a creature is in the blood." This phrase is part of the Levitical law forbidding the drinking of blood or eating meat with the blood still intact instead of being poured off. Mythic references to blood can sometimes be connected to the life-giving nature of blood, seen in such events as childbirth, as contrasted with the blood of injury or death.

Indigenous Australians
In many indigenous Australian Aboriginal peoples' traditions, ochre (particularly red) and blood, both high in iron content and considered Maban, are applied to the bodies of dancers for ritual. As Lawlor states: In many Aboriginal rituals and ceremonies, red ochre is rubbed all over the naked bodies of the dancers. In secret, sacred male ceremonies, blood extracted from the veins of the participant's arms is exchanged and rubbed on their bodies. Red ochre is used in similar ways in less-secret ceremonies. Blood is also used to fasten the feathers of birds onto people's bodies. Bird feathers contain a protein that is highly magnetically sensitive.[28] Lawlor comments that blood employed in this fashion is held by these peoples to attune the dancers to the invisible energetic realm of the Dreamtime. Lawlor then connects these invisible energetic realms and magnetic fields, because iron is magnetic.

Blood

63

European paganism
Among the Germanic tribes (such as the Anglo-Saxons and the Norsemen), blood was used during their sacrifices; the Blóts. The blood was considered to have the power of its originator, and, after the butchering, the blood was sprinkled on the walls, on the statues of the gods, and on the participants themselves. This act of sprinkling blood was called blóedsian in Old English, and the terminology was borrowed by the Roman Catholic Church becoming to bless and blessing. The Hittite word for blood, ishar was a cognate to words for "oath" and "bond", see Ishara. The Ancient Greeks believed that the blood of the gods, ichor, was a substance that was poisonous to mortals. As a relic of Germanic Law the cruentation, an ordeal where the corpse of the victim was supposed to start bleeding in the presence of the murderer was used until the early 17th. century.

Judaism
In Judaism, animal blood cannot be consumed even in the smallest quantity (Leviticus 3:17 and elsewhere); this is reflected in Jewish dietary laws (Kashrut). Blood is purged from meat by salting and soaking in water. Blood from fish however, need not be removed. Another ritual involving blood involves the covering of the blood of fowl and game after slaughtering (Leviticus 17:13); the reason given by the Torah is: "Because the life of the animal is [in] its blood" (ibid 17:14). Also if a person of the orthodox Jewish faith suffers a violent death, religious laws order the collection of their blood for burial with them.

Christianity
Some Christian churches, including Roman Catholicism, Eastern Orthodoxy, Oriental Orthodoxy, and the Assyrian Church of the East teach that, when consecrated, the Eucharistic wine actually becomes the blood of Jesus for worshippers to drink. Thus in the consecrated wine, Jesus becomes spiritually and physically present. This teaching is rooted in the Last Supper, as written in the four gospels of the Bible, in which Jesus stated to his disciples that the bread that they ate was his body, and the wine was his blood. "This cup is the new testament in my blood, which is shed for you." (Luke 22:20). Most forms of Protestantism, especially those of a Wesleyan or Presbyterian lineage, teach that the wine is no more than a symbol of the blood of Christ, who is spiritually but not physically present. Lutheran theology teaches that the body and blood is present together "in, with, and under" the bread and wine of the Eucharistic feast. Christ's blood is the means for the atonement of sins. Also, ″… the blood of Jesus Christ his [God] Son cleanseth us from all sin.” (1 John 1:7), “… Unto him [God] that loved us, and washed us from our sins in his own blood.” (Revelation 1:5), and “And they overcame him (Satan) by the blood of the Lamb [Jesus the Christ], and by the word of their testimony …” (Revelation 12:11). At the Council of Jerusalem, the apostles prohibited Christians from consuming blood (except Jesus'), probably because this was a command given to Noah (Genesis 9:4, see Noahide Law). This command continued to be observed by the Eastern Orthodox. It is also found in the Bible that when the Angel of Death came around to the Hebrew house that the first born child would not die if the angel saw lambs blood wiped across the doorway.

Blood

64

Islam
Consumption of food containing blood is forbidden by Islamic dietary laws. This is derived from the statement in the Qur'an, sura Al-Ma'ida (5:3): "Forbidden to you (for food) are: dead meat, blood, the flesh of swine, and that on which has been invoked the name of other than Allah." Blood is considered as unclean and in Islam cleanliness is part of the faith, hence there are specific methods to obtain physical and ritual status of cleanliness once bleeding has occurred. Specific rules and prohibitions apply to menstruation, postnatal bleeding and irregular vaginal bleeding.

Jehovah's Witnesses
Based on their interpretation of scriptures such as Acts 15:28, 29 ("Keep abstaining...from blood."), Jehovah's Witnesses neither consume blood nor accept transfusions of whole blood or its major components: red blood cells, white blood cells, platelets (thrombocytes), and plasma. Members may personally decide whether they will accept medical procedures that involve their own blood or substances that are further fractionated from the four major components.[29]

East Asian culture
In Chinese popular culture, it is often said that if a man's nose produces a small flow of blood, he is experiencing sexual desire. This often appears in Chinese-language and Hong Kong films as well as in Japanese and Korean culture parodied in anime, manga, and drama. Characters, mostly males, will often be shown with a nosebleed if they have just seen someone nude or in little clothing, or if they have had an erotic thought or fantasy; this is based on the idea that a male's blood pressure will spike dramatically when aroused.[30]

Blood libel
Various religious and other groups have been falsely accused of using human blood in rituals; such accusations are known as blood libel. The most common form of this is blood libel against Jews. Although there is no ritual involving human blood in Jewish law or custom, fabrications of this nature (often involving the murder of children) were widely used during the Middle Ages to justify Antisemitic persecution.

Vampire legends
Vampires are mythical creatures that drink blood directly for sustenance, usually with a preference for human blood. Cultures all over the world have myths of this kind; for example the 'Nosferatu' legend, a human who achieves damnation and immortality by drinking the blood of others, originates from Eastern European folklore. Ticks, leeches, female mosquitoes, vampire bats, and an assortment of other natural creatures do consume the blood of other animals, but only bats are associated with vampires. This has no relation to vampire bats, which are new world creatures discovered well after the origins of the European myths.

Blood

65

Applications
In the applied sciences
Blood residue can help forensic investigators identify weapons, reconstruct a criminal action, and link suspects to the crime. Through bloodstain pattern analysis, forensic information can also be gained from the spatial distribution of bloodstains. Blood residue analysis is also a technique used in archeology.

In art
Blood is one of the body fluids that has been used in art.[31] In particular, the performances of Viennese Actionist Hermann Nitsch, Franko B, Lennie Lee, Ron Athey, Yang Zhichao, and Kira O' Reilly, along with the photography of Andres Serrano, have incorporated blood as a prominent visual element. Marc Quinn has made sculptures using frozen blood, including a cast of his own head made using his own blood.

In genealogy and family history
The term, blood, is used in genealogical circles to refer to one's ancestry, origins, and ethnic background, as in the word, bloodline. Other terms where blood is used in a family history sense are blue-blood, royal blood, mixed-blood and blood relative.

References
[1] The Franklin Institute Inc.. "Blood – The Human Heart" (http:/ / www. fi. edu/ learn/ heart/ blood/ blood. html). . Retrieved 19 March 2009. [2] Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN 0-13-981176-1. [3] Alberts, Bruce (2005). "Leukocyte functions and percentage breakdown" (http:/ / www. ncbi. nlm. nih. gov/ sites/ entrez?cmd=Search& db=books& doptcmdl=GenBookHL& rid=mboc4. table. 4143). Molecular Biology of the Cell. NCBI Bookshelf. . Retrieved 2007-04-14. [4] Shmukler, Michael (2004). "Density of Blood" (http:/ / hypertextbook. com/ facts/ 2004/ MichaelShmukler. shtml). The Physics Factbook. . Retrieved 2006-10-04. [5] "Medical Encyclopedia: RBC count" (http:/ / www. nlm. nih. gov/ medlineplus/ ency/ article/ 003644. htm#Normal Values). Medline Plus. . Retrieved 18 November 2007. [6] Robert B. Tallitsch; Martini, Frederic; Timmons, Michael J. (2006). Human anatomy (5th ed.). San Francisco: Pearson/Benjamin Cummings. p. 529. ISBN 0-8053-7211-3. [7] Ganong, William F. (2003). Review of medical physiology (21 ed.). New York: Lange Medical Books/McGraw-Hill. p. 518. ISBN 0-07-121765-7. [8] Waugh, Anne; Grant, Allison (2007). "2". Anatomy ans Physiology in Health and Illness (Tenth ed.). Churchill Livingstone Elsevier. pp. 22. ISBN 978-0-443-10102-1. [9] Acid-Base Regulation and Disorders (http:/ / www. merck. com/ mmpe/ sec12/ ch157/ ch157a. html) at Merck Manual of Diagnosis and Therapy Professional Edition [10] Sellmeyer DE, Stone KL, Sebastian A, Cummings SR (January 2001). "A high ratio of dietary animal to vegetable protein increases the rate of bone loss and the risk of fracture in postmenopausal women. Study of Osteoporotic Fractures Research Group" (http:/ / www. ajcn. org/ cgi/ content/ full/ 73/ 1/ 118). Am. J. Clin. Nutr. 73 (1): 118–22. PMID 11124760. . [11] Romer, Alfred Sherwood; Parsons, Thomas S. (1977). The Vertebrate Body. Philadelphia, PA: Holt-Saunders International. pp. 404–406. ISBN 0-03-910284-X. [12] Harvey, William (1628). "[[Exercitatio Anatomica de Motu Cordis et Sanguinis in Animalibus (http:/ / www. rarebookroom. org/ Control/ hvyexc/ index. html)]"] (in Latin). . [13] Williams, Peter W.; Gray, Henry David (1989). Gray's anatomy (37th ed.). New York: C. Livingstone. ISBN 0-443-02588-6. [14] Dominguez de Villota ED, Ruiz Carmona MT, Rubio JJ, de Andrés S (December 1981). "Equality of the in vivo and in vitro oxygen-binding capacity of haemoglobin in patients with severe respiratory disease". Br J Anaesth 53 (12): 1325–8. doi:10.1093/bja/53.12.1325. PMID 7317251. [15] Costanzo, Linda S. (2007). Physiology. Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN 0-7817-7311-3. [16] Edwards Lifesciences LLC > Normal Hemodynamic Parameters – Adult (http:/ / www. edwards. com/ SiteCollectionImages/ edwards/ products/ presep/ ar04313hemodynpocketcard. pdf) 2009 [17] Ventilation and Endurance Performance (http:/ / home. hia. no/ ~stephens/ ventphys. htm)

Blood
[18] Transplant Support- Lung, Heart/Lung, Heart (http:/ / groups. msn. com/ TransplantSupportLungHeartLungHeart/ oxygen2. msnw) MSN groups [19] Mortensen SP, Dawson EA, Yoshiga CC, et al. (July 2005). "Limitations to systemic and locomotor limb muscle oxygen delivery and uptake during maximal exercise in humans". J. Physiol. (Lond.) 566 (Pt 1): 273–85. doi:10.1113/jphysiol.2005.086025. PMC 1464731. PMID 15860533. [20] The 'St George' Guide To Pulmonary Artery Catheterisation (http:/ / www. manbit. com/ PAC/ chapters/ P30. cfm) [21] Oxygen Carriage in Blood - High Altitude (http:/ / members. aol. com/ Bio50/ LecNotes/ lecnot20. html) [22] "Carbon dioxide" (http:/ / www. solarnavigator. net/ solar_cola/ carbon_dioxide. htm). solarnavigator.net. . Retrieved 2007-10-12. [23] "Spiders: circulatory system" (http:/ / www. britannica. com/ eb/ topic-559817/ spider). Encyclopædia Britannica online. . Retrieved 2007-11-25. [24] Kienle, Alwin; Lothar Lilge, I. Alex Vitkin, Michael S. Patterson, Brian C. Wilson, Raimund Hibst, and Rudolf Steiner (March 1, 1996). "Why do veins appear blue? A new look at an old question" (http:/ / www. imt. liu. se/ edu/ courses/ TBMT36/ pdf/ blue. pdf) (PDF). Applied Optics 35 (7): 1151–60. doi:10.1364/AO.35.001151. PMID 21085227. . [25] Austin CC, Perkins SL (2006). "Parasites in a biodiversity hotspot: a survey of hematozoa and a molecular phylogenetic analysis of Plasmodium in New Guinea skinks". J. Parasitol. 92 (4): 770–7. doi:10.1645/GE-693R.1. PMID 16995395. [26] Shuster, Carl N (2004). "Chapter 11: A blue blood: the circulatory system" (http:/ / books. google. com/ ?id=0OSAKny-6M4C& printsec=frontcover#PRA1-PA276,M1). In Shuster, Carl N, Jr; Barlow, Robert B; Brockmann, H. Jane. The American Horseshoe Crab. Harvard University Press. pp. 276–7. ISBN 0-674-01159-7. . [27] "Blood - The Human heart" (http:/ / www. fi. edu/ learn/ heart/ blood/ blood. html). The Franklin Institute. . Retrieved 19 March 2009. [28] Lawlor, Robert (1991). Voices of the first day: awakening in the Aboriginal dreamtime. Rochester, Vt: Inner Traditions International. pp. 102–3. ISBN 0-89281-355-5. [29] The Watchtower 15 June 2004, page 22, "Be Guided by the Living God" [30] Law of Anime #40 aka Law of Nasal Sanguination at ABCB.com (http:/ / www. abcb. com/ laws/ index. htm), The Anime Cafe. [31] "Nostalgia" (http:/ / artscad. com/ A. nsf/ Opra/ SRVV-6MDNX5) Artwork in blood

66

External links
• Blood Groups and Red Cell Antigens. (http://www.ncbi.nlm.nih.gov/books/NBK2261) Free online book at NCBI Bookshelf ID: NBK2261 • Blood (http://www.bbc.co.uk/programmes/p00548ym) on In Our Time at the BBC. ( listen now (http:// www.bbc.co.uk/iplayer/console/p00548ym/In_Our_Time_Blood))

Blood cell

67

Blood cell
A blood cell, also called a haematocyte, is a cell produced by haematopoiesis and normally found in blood. In mammals, these fall into three general categories: • Red blood cells — Erythrocytes • White blood cells — Leukocytes • Platelets — Thrombocytes. Together, these three kinds of blood cells add up to a total 45% of the blood tissue by volume, with the remaining 55% of the volume composed of plasma, the liquid component of blood.[1] This volume percentage (e.g., 45%) of cells to total volume is called hematocrit, determined by centrifuge or flow cytometry. Hemoglobin (the main component of red blood cells) is an iron-containing protein that facilitates transportation of oxygen and other respiratory gases to tissues.

Red and white human blood cells as seen under a microscope using a blue slide stain

Red blood cells (Erythrocytes)
Red blood cells primarily carry oxygen and some carbon dioxide through the use of hemoglobin, and have a lifetime of about 120 days. In the process of being formed they go through being a monopotent stem cell.

White blood cells (Leukocytes)
White blood cells, or leukocytes (also spelled "leucocytes", leuco- Ancient Greek "white"), are cells of the immune system involved in defending the body against both infectious disease and foreign materials. Five[1] different and diverse types of leukocytes exist, but they are all produced and derived from a multipotent cell in the bone marrow known as a hematopoietic stem cell. They live for about 3 to 4 days in the average human body. Leukocytes are found throughout the body, including the blood and lymphatic system.

Platelets (Thrombocytes)
Platelets, or thrombocytes (from Greek θρόμβος, "clot" and κύτος, "cell"), are small, irregularly shaped clear cell fragments (i.e. cells that do not have a nucleus containing DNA), 2–3 µm in diameter, which derive from fragmentation of precursor megakaryocytes. The average lifespan of a platelet is normally just 5 to 9 days. Platelets are a natural source of growth factors. They circulate in the blood of mammals and are involved in hemostasis, leading to the formation of blood clots. Platelets release thread-like fibers to form these clots. If the number of platelets is too low, excessive bleeding can occur. However, if the number of platelets is too high, blood clots can form (thrombosis), which may obstruct blood vessels and result in such events as a stroke, myocardial infarction, pulmonary embolism—or blockage of blood vessels to other parts of the body, such as the extremities of the arms or legs. An abnormality or disease of the platelets is called a thrombocytopathy, which can be either a low number of platelets (thrombocytopenia), a decrease in function of platelets (thrombasthenia), or an increase in the number of platelets (thrombocytosis). There are disorders that reduce the number of platelets, such as heparin-induced thrombocytopenia (HIT) or thrombotic thrombocytopenic purpura (TTP) that typically cause thromboses, or clots, instead of bleeding. Platelets release a multitude of growth factors including Platelet-derived growth factor (PDGF), a potent chemotactic agent, and TGF beta, which stimulates the deposition of extracellular matrix. Both of these growth factors have been

Blood cell shown to play a significant role in the repair and regeneration of connective tissues. Other healing-associated growth factors produced by platelets include basic fibroblast growth factor, insulin-like growth factor 1, platelet-derived epidermal growth factor, and vascular endothelial growth factor. Local application of these factors in increased concentrations through Platelet-rich plasma (PRP) has been used as an adjunct to wound healing for several decades

68

References
[1] Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN 0-13-981176-1.

External links
• What is Blood? (http://gslc.genetics.utah.edu/units/basics/blood/blood.cfm) from the Genetic Science Learning Center at the University of Utah. • Cells of the blood (http://www.microbiologybytes.com/iandi/bloodmap/Blood.html)

Bone
Bones are rigid organs that constitute part of the endoskeleton of vertebrates. They support and protect the various organs of the body, produce red and white blood cells and store minerals. Bone tissue is a type of dense connective tissue. Bones come in a variety of shapes and have a complex internal and external structure, are lightweight yet strong and hard, and serve multiple functions. One of the types of tissue that makes up bone is the mineralized osseous tissue, also called bone tissue, that gives it rigidity and a coral-like three-dimensional internal structure. Other types of tissue found in bones include marrow, endosteum, periosteum, nerves, blood vessels and cartilage. At birth, there are over 270 bones in an infant human's body,[1] but many of these fuse together as the child grows, leaving a total of 206 separate bones in an adult. The largest bone in the human body is the femur and the smallest bones are auditory ossicles.[2]

Functions
Bones have eleven main functions:
Drawing of a human femur

Mechanical
• Protection — bones can serve to protect internal organs, such as the skull protecting the brain or the ribs protecting the heart and lungs. • Structure — bones provide a frame to keep the body supported. • Movement — bones, skeletal muscles, tendons, ligaments and joints function together to generate and transfer forces so that individual body parts or the whole body can be manipulated in three-dimensional space. The interaction between bone and muscle is studied in biomechanics. • Sound transduction — bones are important in the mechanical aspect of overshadowed hearing.

Bone

69

Synthetic
• Blood production — the marrow, located within the medullary cavity of long bones and interstices of cancellous bone, produces blood cells in a process called hematopoiesis.

Metabolic
• Mineral storage — bones act as reserves of minerals important for the body, most notably calcium and phosphorus. • Growth factor storage — mineralized bone matrix stores important growth factors such as insulin-like growth factors, transforming growth factor, bone morphogenetic proteins and others. • Fat storage — the yellow bone marrow acts as a storage reserve of fatty acids. • Acid-base balance — bone buffers the blood against excessive pH changes by absorbing or releasing alkaline salts. • Detoxification — bone tissues can also store heavy metals and other foreign elements, removing them from the blood and reducing their effects on other tissues. These can later be gradually released for excretion. • Endocrine organ — bone controls phosphate metabolism by releasing fibroblast growth factor – 23 (FGF-23), which acts on kidneys to reduce phosphate reabsorption. Bone cells also release a hormone called osteocalcin, which contributes to the regulation of blood sugar (glucose) and fat deposition. Osteocalcin increases both the insulin secretion and sensitivity, in addition to boosting the number of insulin-producing cells and reducing stores of fat.[3]

Mechanical properties
The primary tissue of bone, osseous tissue, is a relatively hard and lightweight composite material, formed mostly of calcium phosphate in the chemical arrangement termed calcium hydroxylapatite (this is the osseous tissue that gives bones their rigidity). It has relatively high compressive strength, of about 170 MPa (1800 kgf/cm²)[4] but poor tensile strength of 104–121 MPa and very low shear stress strength (51.6 MPa),[5] meaning it resists pushing forces well, but not pulling or torsional forces. While bone is essentially brittle, it does have a significant degree of elasticity, contributed chiefly by collagen. All bones consist of living and dead cells embedded in the mineralized organic matrix that makes up the osseous tissue.

Structure
Bone structure

An illustration

Bone

70

A femur head with a cortex of compact bone and medulla of trabecular bone

Bone is not a uniformly solid material, but rather has some spaces between its hard elements. Compact (cortical) bone The hard outer layer of bones is composed of compact bone tissue, so-called due to its minimal gaps and spaces. Its porosity is 5–30%.[6] This tissue gives bones their smooth, white, and solid appearance, and accounts for 80% of the total bone mass of an adult skeleton. Compact bone may also be referred to as dense bone. Trabecular (cancellous) bone Filling the interior of the bone is the trabecular bone tissue (an open cell porous network also called cancellous or spongy bone), which is composed of a network of rod- and plate-like elements that make the overall organ lighter and allow room for blood vessels and marrow. Trabecular bone accounts for the remaining 20% of total bone mass but has nearly ten times the surface area of compact bone. Its porosity is 30–90%.[6] If, for any reason, there is an alteration in the strain the cancellous is subjected to, there is a rearrangement of the trabeculae. The microscopic difference between compact and cancellous bone is that compact bone consists of haversian sites and osteons, while cancellous bones do not. Also, bone surrounds blood in the compact bone, while blood surrounds bone in the cancellous bone.

Cellular structure
There are several types of cells constituting the bone; • Osteoblasts are mononucleate bone-forming cells that descend from osteoprogenitor cells. They are located on the surface of osteoid seams and make a protein mixture known as osteoid, which mineralizes to become bone. The osteiod seam is a narrow region of newly formed organic matrix, not yet mineralized, located on the surface of a bone. Osteoid is primarily composed of Type I collagen. Osteoblasts also manufacture hormones, such as prostaglandins, to act on the bone itself. They robustly produce alkaline phosphatase, an enzyme that has a role in the mineralisation of bone, as well as many matrix proteins. Osteoblasts are the immature bone cells, and eventually become entrapped in the bone matrix to become osteocytes- the mature bone cell. • Bone lining cells are essentially inactive osteoblasts. They cover all of the available bone surface and function as a barrier for certain ions. • Osteocytes originate from osteoblasts that have migrated into and become trapped and surrounded by bone matrix that they themselves produce. The spaces they occupy are known as lacunae. Osteocytes have many processes that reach out to meet osteoblasts and other osteocytes probably for the purposes of communication. Their functions include, to varying degrees: formation of bone; matrix maintenance; and calcium homeostasis. They have also been shown to act as mechano-sensory receptors — regulating the bone's response to stress and mechanical load. They are mature bone cells. • Osteoclasts are the cells responsible for bone resorption, thus they break down bone. New bone is then formed by the osteoblasts (remodeling of bone to reduce its volume). Osteoclasts are large, multinucleated cells located on

Bone bone surfaces in what are called Howship's lacunae or resorption pits. These lacunae, or resorption pits, are left behind after the breakdown of the bone surface. Because the osteoclasts are derived from a monocyte stem-cell lineage, they are equipped with phagocytic-like mechanisms similar to circulating macrophages. Osteoclasts mature and/or migrate to discrete bone surfaces. Upon arrival, active enzymes, such as tartrate resistant acid phosphatase, are secreted against the mineral substrate.

71

Molecular structure
Matrix
The majority of bone is made of the bone matrix. It has inorganic and organic parts. Bone is formed by the hardening of this matrix entrapping the cells. When these cells become entrapped from osteoblasts they become osteocytes. Inorganic The inorganic composition of bone (bone mineral) is formed from carbonated hydroxyapatite [7][8] (Ca10(PO4)6(OH)2) with lower crystallinity.[7][9] The matrix is initially laid down as unmineralised osteoid (manufactured by osteoblasts). Mineralisation involves osteoblasts secreting vesicles containing alkaline phosphatase. This cleaves the phosphate groups and acts as the foci for calcium and phosphate deposition. The vesicles then rupture and act as a centre for crystals to grow on. More particularly, bone mineral is formed from globular and plate structures,[9][10] distributed among the collagen fibrils of bone and forming yet larger structure.

Electronic micrography 10000 magnification of Bone mineral

Organic The organic part of matrix is mainly composed of Type I collagen. This is synthesised intracellularly as tropocollagen and then exported, forming fibrils. The organic part is also composed of various growth factors, the functions of which are not fully known. Factors present include glycosaminoglycans, osteocalcin, osteonectin, bone sialo protein, osteopontin and Cell Attachment Factor. One of the main things that distinguishes the matrix of a bone from that of another cell is that the matrix in bone is hard.

Woven or lamellar
Two types of bone can be identified microscopically according to the pattern of collagen forming the osteoid (collagenous support tissue of type I collagen embedded in glycosaminoglycan gel): • Woven bone, which is characterized by haphazard organization of collagen fibers and is mechanically weak • Lamellar bone, which has a regular parallel alignment of collagen into sheets (lamellae) and is mechanically strong
Collagen fibers of woven bone

Woven bone is produced when osteoblasts produce osteoid rapidly, which occurs initially in all fetal bones (but is later replaced by more resilient lamellar bone). In adults woven bone is created after fractures

Bone or in Paget's disease. Woven bone is weaker, with a smaller number of randomly oriented collagen fibers, but forms quickly; it is for this appearance of the fibrous matrix that the bone is termed woven. It is soon replaced by lamellar bone, which is highly organized in concentric sheets with a much lower proportion of osteocytes to surrounding tissue. Lamellar bone, which makes its first appearance in the fetus during the third trimester,[11] is stronger and filled with many collagen fibers parallel to other fibers in the same layer (these parallel columns are called osteons). In cross-section, the fibers run in opposite directions in alternating layers, much like in plywood, assisting in the bone's ability to resist torsion forces. After a fracture, woven bone forms initially and is gradually replaced by lamellar bone during a process known as "bony substitution." Compared to woven bone, lamellar bone formation takes place more slowly. The orderly deposition of collagen fibers restricts the formation of osteoid to about 1 to 2 µm per day. Lamellar bone also requires a relatively flat surface to lay the collagen fibers in parallel or concentric layers. These terms are histologic, in that a microscope is necessary to differentiate between the two.

72

Types
There are five types of bones in the human body: long, short, flat, irregular, and sesamoid. • Long bones are characterized by a shaft, the diaphysis, that is much longer than it is wide. They are made up mostly of compact bone, with lesser amounts of marrow, located within the medullary cavity, and spongy bone. Most bones of the limbs, including those of the fingers and toes, are long bones. The exceptions are those of the wrist, ankle and kneecap. • Short bones are roughly cube-shaped, and have only a thin layer of compact bone surrounding a spongy interior. The bones of the wrist and ankle are short bones, as are the sesamoid bones. • Flat bones are thin and generally curved, with two parallel layers of compact bones sandwiching a layer of spongy bone. Most of the bones of the skull are flat bones, as is the sternum. • Sesamoid bones are bones embedded in tendons. Since they act to hold the tendon further away from the joint, the angle of the tendon is increased and thus the leverage of the muscle is increased. Examples of sesamoid bones are the patella and the pisiform. • Irregular bones do not fit into the above categories. They consist of thin layers of compact bone surrounding a spongy interior. As implied by the name, their shapes are irregular and complicated. The bones of the spine and hips are irregular bones.

Bone

73

Formation
The formation of bone during the fetal stage of development occurs by two processes: Intramembranous ossification and endochondral ossification.

Intramembranous ossification
Intramembranous ossification mainly occurs during formation of the flat bones of the skull but also the mandible, maxilla, and clavicles; the bone is formed from connective tissue such as mesenchyme tissue rather than from cartilage. The steps in intramembranous ossification are: 1. 2. 3. 4. Development of ossification center Calcification Formation of trabeculae Development of periosteum

Endochondral ossification
Endochondral ossification, on the other hand, occurs in long bones and most of the rest of the bones in the body; it involves an initial hyaline cartilage that continues to grow. The steps in endochondral ossification are: 1. Development of cartilage model 2. Growth of cartilage model 3. Development of the primary ossification center 4. Development of the secondary ossification center 5. Formation of articular cartilage and epiphyseal plate

Endochondral ossification

Endochondral ossification begins with points in the cartilage called "primary ossification centers." They mostly appear during fetal development, though a few short bones begin their primary ossification after birth. They are responsible for the formation of the diaphyses of long bones, short bones and certain parts of irregular bones. Secondary ossification occurs after birth, and forms the epiphyses of long bones and the extremities of irregular and flat bones. The diaphysis and both epiphyses of a long bone are separated by a growing zone of cartilage (the epiphyseal plate). When the child reaches skeletal maturity (18 to 25 years of age), all of the cartilage is replaced by bone, fusing the diaphysis and both epiphyses together (epiphyseal closure).

Bone

74

Bone marrow
Bone marrow can be found in almost any bone that holds cancellous tissue. In newborns, all such bones are filled exclusively with red marrow, but as the child ages it is mostly replaced by yellow, or fatty marrow. In adults, red marrow is mostly found in the marrow bones of the femur, the ribs, the vertebrae and pelvic bones.

Remodeling
Remodeling or bone turnover is the process of resorption followed by replacement of bone with little change in shape and occurs throughout a person's life. Osteoblasts and osteoclasts, coupled together via paracrine cell signalling, are referred to as bone remodeling units.

Purpose
The purpose of remodeling is to regulate calcium homeostasis, repair micro-damaged bones (from everyday stress) but also to shape and sculpture the skeleton during growth. Calcium balance The process of bone resorption by the osteoclasts releases stored calcium into the systemic circulation and is an important process in regulating calcium balance. As bone formation actively fixes circulating calcium in its mineral form, removing it from the bloodstream, resorption actively unfixes it thereby increasing circulating calcium levels. These processes occur in tandem at site-specific locations.

Bone volume
Bone volume is determined by the rates of bone formation and bone resorption. Recent research has suggested that certain growth factors may work to locally alter bone formation by increasing osteoblast activity. Numerous bone-derived growth factors have been isolated and classified via bone cultures. These factors include insulin-like growth factors I and II, transforming growth factor-beta, fibroblast growth factor, platelet-derived growth factor, and bone morphogenetic proteins.[12] Evidence suggests that bone cells produce growth factors for extracellular storage in the bone matrix. The release of these growth factors from the bone matrix could cause the proliferation of osteoblast precursors. Essentially, bone growth factors may act as potential determinants of local bone formation.[12] Research has suggested that trabecular bone volume in postemenopausal osteoporosis may be determined by the relationship between the total bone forming surface and the percent of surface resorption.[13] Repair Repeated stress, such as weight-bearing exercise or bone healing, results in the bone thickening at the points of maximum stress (Wolff's law). It has been hypothesized that this is a result of bone's piezoelectric properties, which cause bone to generate small electrical potentials under stress.[14]

Paracrine cell signalling
The action of osteoblasts and osteoclasts are controlled by a number of chemical factors that either promote or inhibit the activity of the bone remodeling cells, controlling the rate at which bone is made, destroyed, or changed in shape. The cells also use paracrine signalling to control the activity of each other.

Bone

75

Osteoblast stimulation
Osteoblasts can be stimulated to increase bone mass through increased secretion of osteoid and by inhibiting the ability of osteoclasts to break down osseous tissue. Bone building through increased secretion of osteoid is stimulated by the secretion of growth hormone by the pituitary, thyroid hormone and the sex hormones (estrogens and androgens). These hormones also promote increased secretion of osteoprotegerin.[15] Osteoblasts can also be induced to secrete a number of cytokines that promote reabsorbtion of bone by stimulating osteoclast activity and differentiation from progenitor cells. Vitamin D, parathyroid hormone and stimulation from osteocytes induce osteoblasts to increase secretion of RANK-ligand and interleukin 6, which cytokines then stimulate increased reabsorbtion of bone by osteoclasts. These same compounds also increase secretion of macrophage colony-stimulating factor by osteoblasts, which promotes the differentiation of progenitor cells into osteoclasts, and decrease secretion of osteoprotegerin.

Osteoclast inhibition
The rate at which osteoclasts resorb bone is inhibited by calcitonin and osteoprotegerin. Calcitonin is produced by parafollicular cells in the thyroid gland, and can bind to receptors on osteoclasts to directly inhibit osteoclast activity. Osteoprotegerin is secreted by osteoblasts and is able to bind RANK-L, inhibiting osteoclast stimulation.[15]

Disorders
There are many disorders of the skeleton. One of the more prominent is osteoporosis.

Osteoporosis
Osteoporosis is a disease of bone, leading to an increased risk of fracture. In osteoporosis, the bone mineral density (BMD) is reduced, bone microarchitecture is disrupted, and the amount and variety of non-collagenous proteins in bone is altered. Osteoporosis is defined by the World Health Organization (WHO) in women as a bone mineral density 2.5 standard deviations below peak bone mass (20-year-old sex-matched healthy person average) as measured by DEXA; the term "established osteoporosis" includes the presence of a fragility fracture.[16] Osteoporosis is most common in women after the menopause, when it is called postmenopausal osteoporosis, but may develop in men and premenopausal women in the presence of particular hormonal disorders and other chronic diseases or as a result of smoking and medications, specifically glucocorticoids, when the disease is called steroidor glucocorticoid-induced osteoporosis (SIOP or GIOP). Osteoporosis can be prevented with lifestyle advice and medication, and preventing falls in people with known or suspected osteoporosis is an established way to prevent fractures. Osteoporosis can be treated with bisphosphonates and various other medical treatments.

Other
Other disorders of bone include: • • • • • • • Bone fractures Bone mineral Osteomyelitis Osteosarcoma Osteogenesis imperfecta Osteochondritis dissecans Bone metastases

• Neurofibromatosis type I

Bone

76

Osteology
The study of bones and teeth is referred to as osteology. It is frequently used in anthropology, archeology and forensic science for a variety of tasks. This can include determining the nutritional, health, age or injury status of the individual the bones were taken from. Preparing fleshed bones for these types of studies can involve maceration – boiling fleshed bones to remove large particles, then hand-cleaning. Typically anthropologists and archeologists study bone tools made by Homo sapiens and Homo neanderthalensis. Bones can serve a number of uses such as projectile points or artistic pigments, and can be made from endoskeletal or external bones such as antler or tusk.

Alternatives to bony endoskeletons
There are several evolutionary alternatives to mammillary bone; though they have some similar functions, they are not completely functionally analogous to bone. • Exoskeletons offer support, protection and levers for movement similar to endoskeletal bone. Different types of exoskeletons include shells, carapaces (consisting of calcium compounds or silica) and chitinous exoskeletons. • A true endoskeleton (that is, protective tissue derived from mesoderm) is also present in Echinoderms. Porifera (sponges) possess simple endoskeletons that consist of calcareous or siliceous spicules and a spongin fiber network.

Exposed bone
Bone penetrating the skin and being exposed to the outside can be both a natural process in some animals, and due to injury: • • • • A deer's antlers are composed of bone.[17] Instead of teeth, the extinct predatory fish Dunkleosteus had sharp edges of hard exposed bone along its jaws. A compound fracture occurs when the edges of a broken bone puncture the skin. Though not strictly speaking exposed, a bird's beak is primarily bone covered in a layer of keratin over a vascular layer containing blood vessels and nerve endings.

Uses
Bones from slaughtered animals have a number of uses. It has been used as crafting material for buttons, handles, ornaments etc. A special genre is scrimshaw. Ground bones are used an organic phosphorus-nitrogen fertilizer and as additive in animal feed. Bones, in particular after calcination to bone ash is used as source of calcium phosphate for the production of bone china and previously also phosphorus chemicals.

Terminology
Several terms are used to refer to features and components of bones throughout the body:

Bone

77

Bone feature

Definition

articular process A projection that contacts an adjacent bone. articulation canal condyle crest eminence epicondyle facet foramen fossa fovea labyrinth line malleolus meatus process ramus sinus spine suture trochanter tubercle tuberosity The region where adjacent bones contact each other — a joint. A long, tunnel-like foramen, usually a passage for notable nerves or blood vessels. A large, rounded articular process. A prominent ridge. A relatively small projection or bump. A projection near to a condyle but not part of the joint. A small, flattened articular surface. An opening through a bone. A broad, shallow depressed area. A small pit on the head of a bone. A cavity within a bone. A long, thin projection, often with a rough surface. Also known as a ridge. One of two specific protuberances of bones in the ankle. A short canal that finishes as a dead end, so it has only the entrance. A relatively large projection or prominent bump.(gen.) An arm-like branch off the body of a bone. A cavity within a cranial bone. A relatively long, thin projection or bump. Articulation between cranial bones. One of two specific tuberosities located on the femur. A projection or bump with a roughened surface, generally smaller than a tuberosity. A projection or bump with a roughened surface.

Several terms are used to refer to specific features of long bones:
Bone feature diaphysis epiphysis epiphyseal plate head metaphysis neck Definition The long, relatively straight main body of a long bone; region of primary ossification. Also known as the shaft. The end regions of a long bone; regions of secondary ossification. Also known as the growth plate or physis. In a long bone it is a thin disc of hyaline cartilage that is positioned transversely between the epiphysis and metaphysis. In the long bones of humans, the epiphyseal plate disappears by twenty years of age. The proximal articular end of the bone. The region of a long bone lying between the epiphysis and diaphysis. The region of bone between the head and the shaft.

Bone

78

Footnotes
[1] Steele, D. Gentry; Claud A. Bramblett (1988). The Anatomy and Biology of the Human Skeleton. Texas A&M University Press. p. 4. ISBN 0-89096-300-2. [2] Schmiedeler, Edgar; Mary Rosa McDonough (1934). Parent and Child: An Introductory Study of Parent Education. D. Appleton-Century. p. 31. [3] Lee, Na Kyung; et al. (10 August 2007). "Endocrine Regulation of Energy Metabolism by the Skeleton" (http:/ / download. cell. com/ pdfs/ 0092-8674/ PIIS0092867407007015. pdf). Cell 130 (3): 456–469. doi:10.1016/j.cell.2007.05.047. PMC 2013746. PMID 17693256. . Retrieved 2008-03-15. [4] Schmidt-Nielsen, Knut (1984). Scaling: Why is animal size so important?. Cambridge: Cambridge University Press. p. 6. ISBN 05213198700 . [5] Turner, C.H.; Wang, T.; Burr, D.B. (2001). "Shear Strength and Fatigue Properties of Human Cortical Bone Determined from Pure Shear Tests". Calcified Tissue International 69 (6): 373–378. doi:10.1007/s00223-001-1006-1. PMID 11800235. [6] Hall, Susan. (2007) Basic Biomechanics. Fifth Edition. p. 88 ISBN 0-07-126041-2 [7] Legros, R; Balmain, N; Bonel, G (1987). "Age-related changes in mineral of rat and bovine cortical bone". Calcified tissue international 41 (3): 137–44. PMID 3117340. [8] Field, RA; Riley, ML; Mello, FC; Corbridge, MH; Kotula, AW (1974). "Bone composition in cattle, pigs, sheep and poultry". Journal of animal science 39 (3): 493–9. PMID 4412232. [9] Bertazzo, S. & Bertran, C. A. (2006). "Morphological and dimensional characteristics of bone mineral crystals". Bioceramics 309–311 (Pt. 1, 2): 3–10. doi:10.4028/www.scientific.net/KEM.309-311.3. [10] Bertazzo, S.; Bertran, C.A.; Camilli, J.A. (2006). "Morphological Characterization of Femur and Parietal Bone Mineral of Rats at Different Ages". Key Engineering Materials 309–311: 11–14. doi:10.4028/www.scientific.net/KEM.309-311.11. [11] Salentijn, L. Biology of Mineralized Tissues: Cartilage and Bone, Columbia University College of Dental Medicine post-graduate dental lecture series, 2007 [12] Mohan, S.; Baylink, D. J. (1991). "Bone growth factors". Clinical orthopaedics and related research (263): 30–48. PMID 1993386. [13] http:/ / www. sciencedirect. com/ science/ article/ pii/ S0140673681905262 [14] Netter, Frank H. (1987). Musculoskeletal system: anatomy, physiology, and metabolic disorders. New Jersey, Summit: Ciba-Geigy Corporation. ISBN 0-914168-88-6 pp. 187–189. [15] Boulpaep, Emile L.; Boron, Walter F. (2005). Medical physiology: a cellular and molecular approach. Philadelphia: Saunders. pp. 1089–1091. ISBN 1-4160-2328-3. [16] WHO (1994). "Assessment of fracture risk and its application to screening for postmenopausal osteoporosis. Report of a WHO Study Group". World Health Organization technical report series 843: 1–129. PMID 7941614. [17] Hans J. Rolf; Alfred Enderle (1999). "Hard fallow deer antler: a living bone till antler casting?". The Anatomical Record 255 (1): 69–77. doi:10.1002/(SICI)1097-0185(19990501)255:1<69::AID-AR8>3.0.CO;2-R. PMID 10321994.

References
• Katja Hoehn; Marieb, Elaine Nicpon (2007). Human Anatomy & Physiology (7th Edition). San Francisco: Benjamin Cummings. ISBN 0-8053-5909-5. • Bryan H. Derrickson; Tortora, Gerard J. (2005). Principles of anatomy and physiology. New York: Wiley. ISBN 0-471-68934-3.

External links
• Educational resource materials (including animations) by the American Society for Bone and Mineral Research (http://depts.washington.edu/bonebio/ASBMRed/ASBMRed.html) • Review (including references) of piezoelectricity and bone remodelling (http://silver.neep.wisc.edu/~lakes/ BoneElectr.html) • A good basic overview of bone biology from the Science Creative Quarterly (http://www.scq.ubc.ca/?p=400)

Bone marrow

79

Bone marrow
Bone marrow

A simplified illustration of cells in bone marrow Latin MeSH Code Medulla ossium Bone+Marrow
[1] [2]

TA A13.1.01.001

Bone marrow (Latin: medulla ossium) is the flexible tissue found in the interior of bones. In humans, red blood cells are produced in the heads of long bones, in a process known as hematopoesis. On average, bone marrow constitutes 4% of the total body mass of humans; in an adult weighing 65 kilograms (unknown operator: u'strong' lb), bone marrow accounts for approximately 2.6 kilograms (unknown operator: u'strong' lb). The hematopoietic compartment of bone marrow produces approximately 500 billion blood cells per day, which use the bone marrow vasculature as a conduit to the body's systemic circulation.[3] Bone marrow is also a key component of the lymphatic system, producing the lymphocytes that support the body's immune system.[4]

Marrow types
The two types of bone marrow are medulla ossium rubra (red marrow), which consists mainly of hematopoietic tissue, and medulla ossium flava (yellow marrow), which is mainly made up of fat cells. Red blood cells, platelets and most white blood cells arise in red marrow. Both types of bone marrow contain numerous blood vessels and capillaries. At birth, all bone marrow is red. With age, more and more of it is converted to the yellow type; only around half of adult bone marrow is red. Red marrow is found mainly in the flat bones, such as the pelvis, sternum, cranium, ribs, vertebrae and scapulae, and in the cancellous ("spongy") material at the epiphyseal ends of long bones such as the femur and humerus. Yellow marrow is found in the medullary cavity, the hollow interior of the middle portion of long bones. In cases of severe blood loss, the body can convert yellow marrow back to red marrow to increase blood cell production.

A femoral head with a cortex of cortical bone and medulla of trabecular bone. Both red bone marrow and a focus of yellow bone marrow are visible.

Stroma
The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. Yellow bone marrow makes up the majority of bone marrow stroma, in addition to smaller concentrations of stromal cells located in the red bone marrow. Though not as active as parenchymal red marrow, stroma is indirectly involved in

Bone marrow hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, which have a significant effect on hematopoiesis. Cells that constitute the bone marrow stroma are: • • • • • • fibroblasts (reticular connective tissue) macrophages adipocytes osteoblasts osteoclasts endothelial cells, which form the sinusoids. These derive from endothelial stem cells, which are also present in the bone marrow.[5]

80

Macrophages contribute especially to red blood cell production, as they deliver iron for hemoglobin production.

Bone marrow barrier
The blood vessels of the bone marrow constitute a barrier, inhibiting immature blood cells from leaving the marrow. Only mature blood cells contain the membrane proteins required to attach to and pass the blood vessel endothelium. Hematopoietic stem cells may also cross the bone marrow barrier, and may thus be harvested from blood.

Mesenchymal stem cells
The bone marrow stroma contain mesenchymal stem cells (MSCs),[5] also known as marrow stromal cells. These are multipotent stem cells that can differentiate into a variety of cell types. MSCs have been shown to differentiate, in vitro or in vivo, into osteoblasts, chondrocytes, myocytes, adipocytes and beta-pancreatic islets cells. MSCs can also transdifferentiate into neuronal cells.

Red marrow parenchyma
Types of cells

Hematopoietic precursor cells: promyelocyte in the center, two metamyelocytes next to it and band cells from a bone marrow aspirate.

Bone marrow

81

Cellular constitution of the red bone marrow parenchyma[6]
Group Cell type Average Reference fraction range 0.9% 3.3% 12.7% 0.8% 15.9% 1.2% 12.4% 0.9% 7.4% 0.5% 0.2-1.5 2.1-4.1 8.2-15.7 0.2-1.3 9.6-24.6 0.4-2.2 9.5-15.3 0.2-2.4 6.0-12.0 0.0-1.3 0.0-0.2 0.2-1.3 0.5-2.4 17.9-29.2 0.4-4.6 0.0-0.4 0.4-3.9 0.0-0.9 11.1-23.2 0.0-0.8

Cells of myelopoiesis

Myeloblasts Promyelocytes Neutrophilic myelocytes Eosinophilic myelocytes Neutrophilic metamyelocytes Eosinophilic metamyelocytes Neutrophilic band cells Eosinophilic band cells Segmented neutrophils Segmented eosinophils

Segmented basophils and mast cells 0.1% Cells of erythropoiesis Pronormoblasts Basophilic normoblasts Polychromatic normoblasts Orthochromatic normoblast Other cell types Megakaryocytes Plasma cells Reticular cells Lymphocytes Monocytes 0.6% 1.4% 21.6% 2.0% < 0.1% 1.3% 0.3% 16.2% 0.3%

In addition, the bone marrow contains hematopoietic stem cells, which give rise to the three classes of blood cells that are found in the circulation: white blood cells (leukocytes), red blood cells (erythrocytes), and platelets (thrombocytes).[5]

Compartmentalization
Biological compartmentalization is evident within the bone marrow, in that certain cell types tend to aggregate in specific areas. For instance, erythrocytes, macrophages, and their precursors tend to gather around blood vessels, while granulocytes gather at the borders of the bone marrow.

Lymphatic role
The red bone marrow is a key element of the lymphatic system, being one of the primary lymphoid organs that generate lymphocytes from immature hematopoietic progenitor cells.[4] The bone marrow and thymus constitute the primary lymphoid tissues involved in the production and early selection of lymphocytes. Furthermore, bone marrow performs a valve-like function to prevent the backflow of lymphatic fluid in the lymphatic system.

Bone marrow

82

Diseases involving the bone marrow
The normal bone marrow architecture can be displaced by malignancies, aplastic anemia, or infections such as tuberculosis, leading to a decrease in the production of blood cells and blood platelets. In addition, cancers of the hematologic progenitor cells in the bone marrow can arise; these are the leukemias. Exposure to radiation or chemotherapy will kill many of the rapidly dividing cells of the bone marrow, and will therefore result in a depressed immune system. Many of the symptoms of radiation sickness are due to damage to the bone marrow cells. To diagnose diseases involving the bone marrow, a bone marrow aspiration is sometimes performed. This typically involves using a hollow needle to acquire a sample of red bone marrow from the crest of the ilium under general or local anesthesia.

Examination
Bone marrow examination is the pathologic analysis of samples of bone marrow obtained via biopsy and bone marrow aspiration. Bone marrow examination is used in the diagnosis of a number of conditions, including leukemia, multiple myeloma, anemia, and pancytopenia. The bone marrow produces the cellular elements of the blood, including platelets, red blood cells and white blood cells. While much information can be gleaned by testing the blood itself (drawn from a vein by phlebotomy), it is sometimes necessary to examine the source of the blood cells in the bone marrow to obtain more information on hematopoiesis; this is the role of bone marrow aspiration and biopsy. The ratio between myeloid series and erythroid cells is relevant to bone marrow function, and also to diseases of the bone marrow and peripheral blood, such as leukemia and anemias. The normal myeloid-to-erythroid ratio is around 3:1; this ratio may increase in myelogenous leukemias, decrease in polycythemias, and reverse in cases of thalassemia.
A Wright's-stained bone marrow aspirate smear from a patient with leukemia.

Donation and transplantation
In a bone marrow transplant, hematopoietic stem cells are removed from a person and infused into another person (allogenic) or into the same person at a later time (autologous). If the donor and recipient are compatible, these infused cells will then travel to the bone marrow and initiate blood cell production. Transplantation from one person to another is performed in severe cases of bone marrow disease. The patient's own marrow is first killed off with drugs or radiation, and then the new stem cells are introduced. Before radiation therapy or chemotherapy in cases of cancer, some of the patient's hematopoietic stem cells are sometimes harvested and later infused back when the therapy is finished to restore the immune system.

A bone marrow harvest in progress.

Bone marrow

83

Harvesting
The stem cells are typically harvested directly from the red marrow in the iliac crest, often under general anesthesia. The procedure is minimally invasive and does not require stitches afterwards. Depending on the donor's health and reaction to the procedure, the actual harvesting can be an outpatient procedure, or can require 1–2 days of recovery in the hospital.[7] Another option is to administer certain drugs that stimulate the release of stem cells from the bone marrow into circulating blood.[8] An IV is inserted into the donor's arm, and the stem cells are filtered out of the blood. This procedure is similar to donating blood or platelets. Bone marrow may also be taken from the sternum. The tibia may seem a good source, since it is very superficial, but adult tibia bone marrow does not contain any substantial amount of red marrow.[9] In newborns, stem cells may be retrieved from the umbilical cord.[10]

Food
Many cultures have used bone marrow as food throughout history. Anthropologists believe that early humans were scavengers rather than hunters in some regions of the world. Marrow would have been a useful food source (largely due to its fat content) for tool-using hominids, who were able to crack open the bones of carcasses left by apex predators such as lions.[11] European diners in the 18th century often used a marrow scoop (or marrow spoon), often of silver and with a long, thin bowl, as a table implement for removing marrow from a bone. Bone marrow was also used in various preparations, such as pemmican. Bone marrow's popularity as a food is now relatively limited in the western world, but it remains in use in some gourmet restaurants, and is popular among food enthusiasts.[12]

In some parts of Germany, beef soup is served with Markklößchen (bone marrow balls).

In Vietnam, beef bone marrow is used as the soup base for the national staple dish, phở, while in the Philippines, the soup bulalo is made primarily of beef stock and marrow bones, seasoned with vegetables and boiled meat; a similar soup in the Philippines is called kansi.[13] In Indonesia, bone marrow is called sumsum and can be found especially in Minangkabau cuisine. Sumsum is often cooked as soup or as gulai (a curry-like dish). In India and Pakistan, slow-cooked marrow is the core ingredient of the dish nalli nihari. In Hungary, tibia is a main ingredient of beef soup; the bone is chopped into short (10–15 cm) pieces and the ends are covered with salt to prevent the marrow from leaking from the bone while cooking. Upon serving the soup, the marrow is usually spread on toast. Beef bone marrow is also the main ingredient in Italian dish ossobuco (braised veal shanks), and beef marrow bones are often included in the French pot-au-feu broth, the cooked marrow being traditionally eaten on toasted bread with sprinkled coarse sea salt. In Iranian cuisine, lamb shanks are usually broken before cooking to allow diners to suck out and eat the marrow when the dish is served. Similar practices are also common in Pakistani cuisine. Some Native Alaskans eat the bone marrow of caribou and moose.

Bone marrow

84

References
[1] http:/ / www. nlm. nih. gov/ cgi/ mesh/ 2011/ MB_cgi?mode=& term=Bone+ Marrow [2] http:/ / www. unifr. ch/ ifaa/ Public/ EntryPage/ ViewTA/ TAa13. html [3] "Challenges in Cardiac Tissue Engineering"; Gordana Vunjak-Novakovic, Ph.D.,Nina Tandon, Ph.D., Amandine Godier, B.S.,1 Robert Maidhof, M.S.,Anna Marsano, Ph.D., Timothy P. Martens, M.D., Ph.D., and Milica Radisic, Ph.D.; TISSUE ENGINEERING: Part B; Volume 16, Number 2, 2010 [4] The Lymphatic System (http:/ / allonhealth. com/ health-news/ par-lymphatic-system. htm). Allonhealth.com. Retrieved 2011-12-05. [5] Raphael Rubin and David S. Strayer (2007). Rubin's Pathology: Clinicopathologic Foundations of Medicine. Lippincott Williams & Wilkins. p. 90. ISBN 0-7817-9516-8. [6] Appendix A:IV (http:/ / www. msd. com. mx/ secure/ ebooks/ WintrobesClinicalHematology/ sid4266054. html) in: Wintrobe's clinical hematology, 9th ed. Philadelphia: Lea & Febiger, 1993. [7] National Marrow Donor Program Donor Guide (http:/ / www. marrow. org/ DONOR/ When_You_re_Asked_to_Donate_fo/ index. html) [8] Mayo Clinic: Bone marrow donation: What to expect when you donate (http:/ / www. mayoclinic. com/ health/ bone-marrow/ CA00047) [9] Semester 4 medical lectures at Uppsala University 2008 by Leif Jansson [10] Production of stem cells with embryonic characteristics from human umbilical cord blood (http:/ / www3. interscience. wiley. com/ journal/ 118705649/ abstract). Wiley Online Library, 11 August 2005. Retrieved 2012-01-29. [11] Bruce Bower. Hunting ancient scavengers – some anthropologists say early humans were scavengers, not hunters (http:/ / findarticles. com/ p/ articles/ mi_m1200/ is_v127/ ai_3677563). Science News. March 9, 1985 [12] La Petite Bouche (Food Blog): Roasted Bone Marrow (http:/ / lapetitebouche. blogspot. com/ 2010/ 08/ roasted-bone-marrow. html). 30 August 2010. Retrieved 2011-12-05. [13] "Kansi" (http:/ / www. flickr. com/ photos/ kamums/ 4378949248/ ) Flickr

Further reading
• Cooper, B (2011). "The origins of bone marrow as the seedbed of our blood: from antiquity to the time of Osler" (http://baylorhealth.edu/proceedings/24_2/24_2_Cooper.pdf). Baylor University Medical Center Proceedings 24 (2): 115–8. PMC 3069519. PMID 21566758.

Carbohydrate
A carbohydrate is an organic compound that consists only of carbon, hydrogen, and oxygen, usually with a hydrogen:oxygen atom ratio of 2:1 (as in water); in other words, with the empirical formula Cm(H2O)n. (Some exceptions exist; for example, deoxyribose, a component of DNA, has the empirical formula C5H10O4.) Carbohydrates are not technically hydrates of carbon. Structurally it is more accurate to view them as polyhydroxy aldehydes and ketones.

Lactose is a disaccharide found in milk. It consists of a molecule of D-galactose and a molecule of D-glucose bonded by beta-1-4 glycosidic linkage. It has a formula of C12H22O11.

The term is most common in biochemistry, where it is a synonym of saccharide. The carbohydrates (saccharides) are divided into four chemical groupings: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to as sugars.[1] The word saccharide comes from the Greek word σάκχαρον (sákkharon), meaning "sugar". While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides

Carbohydrate and disaccharides very often end in the suffix -ose. For example, blood sugar is the monosaccharide glucose, table sugar is the disaccharide sucrose, and milk sugar is the disaccharide lactose (see illustration). Carbohydrates perform numerous roles in living organisms. Polysaccharides serve for the storage of energy (e.g., starch and glycogen), and as structural components (e.g., cellulose in plants and chitin in arthropods). The 5-carbon monosaccharide ribose is an important component of coenzymes (e.g., ATP, FAD, and NAD) and the backbone of the genetic molecule known as RNA. The related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development.[2] In food science and in many informal contexts, the term carbohydrate often means any food that is particularly rich in the complex carbohydrate starch (such as cereals, bread, and pasta) or simple carbohydrates, such as sugar (found in candy, jams, and desserts).

85

Structure
Formerly the name "carbohydrate" was used in chemistry for any compound with the formula Cm (H2O) n. Following this definition, some chemists considered formaldehyde (CH2O) to be the simplest carbohydrate,[3] while others claimed that title for glycolaldehyde.[4] Today the term is generally understood in the biochemistry sense, which excludes compounds with only one or two carbons. Natural saccharides are generally built of simple carbohydrates called monosaccharides with general formula (CH2O)n where n is three or more. A typical monosaccharide has the structure H-(CHOH)x(C=O)-(CHOH)y-H, that is, an aldehyde or ketone with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. Examples of monosaccharides are glucose, fructose, and glyceraldehydes. However, some biological substances commonly called "monosaccharides" do not conform to this formula (e.g., uronic acids and deoxy-sugars such as fucose), and there are many chemicals that do conform to this formula but are not considered to be monosaccharides (e.g., formaldehyde CH2O and inositol (CH2O)6).[5] The open-chain form of a monosaccharide often coexists with a closed ring form where the aldehyde/ketone carbonyl group carbon (C=O) and hydroxyl group (-OH) react forming a hemiacetal with a new C-O-C bridge. Monosaccharides can be linked together into what are called polysaccharides (or oligosaccharides) in a large variety of ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetyl glucosamine, a nitrogen-containing form of glucose.

Carbohydrate

86

Monosaccharides
Monosaccharides are the simplest carbohydrates in that they cannot be hydrolyzed to smaller carbohydrates. They are aldehydes or ketones with two or more hydroxyl groups. The general chemical formula of an unmodified monosaccharide is (C•H2O) n, literally a "carbon hydrate." Monosaccharides are important fuel molecules as well as building blocks for nucleic acids. The smallest monosaccharides, for which n = 3, are dihydroxyacetone and D- and L-glyceraldehydes.

Classification of monosaccharides

The α and β anomers of glucose. Note the position of the hydroxyl group (red or green) on the anomeric carbon relative to the CH2OH group bound to carbon 5: they are either on the opposite sides (α), or the same side (β).

Monosaccharides are classified according to three different characteristics: the placement of its carbonyl group, the number of carbon atoms it contains, and its chiral handedness. If the carbonyl group is an aldehyde, the monosaccharide is an aldose; if the carbonyl group is a ketone, the monosaccharide is a ketose. Monosaccharides with three carbon atoms are called trioses, those with four are called tetroses, five are called pentoses, six are hexoses, and so on.[6] These two systems of classification are often combined. For example, glucose is an aldohexose (a six-carbon aldehyde), ribose is an aldopentose (a five-carbon aldehyde), and fructose is a ketohexose (a six-carbon ketone). Each carbon atom bearing a hydroxyl group (-OH), with the exception of the first and last carbons, are asymmetric, making them stereo centers with two possible configurations each (R or S). Because of this asymmetry, a number of isomers may exist for any given monosaccharide formula. The aldohexose D-glucose, for example, has the formula (C·H2O) 6, of which all but two of its six carbons atoms are stereogenic, making D-glucose one of 24 = 16 possible stereoisomers. In the case of glyceraldehydes, an aldotriose, there is one pair of possible stereoisomers, which are enantiomers and epimers. 1, 3-dihydroxyacetone, the ketose corresponding to the aldose glyceraldehydes, is a symmetric molecule with no stereo centers). The assignment of D or L is made according to the orientation of the asymmetric carbon furthest from the carbonyl group: in a standard Fischer projection if the hydroxyl group is on the right the molecule is a D sugar, otherwise it is an L sugar. The "D-" and "L-" prefixes should not be confused with "d-" or "l-", which indicate the direction that the sugar rotates plane polarized light. This usage of "d-" and "l-" is no longer followed in carbohydrate chemistry.[7]

D-glucose is an aldohexose with the formula (C·H2O)6. The red atoms highlight the aldehyde group, and the blue atoms highlight the asymmetric center furthest from the aldehyde; because this -OH is on the right of the Fischer projection, this is a D sugar.

Carbohydrate

87

Ring-straight chain isomerism
The aldehyde or ketone group of a straight-chain monosaccharide will react reversibly with a hydroxyl group on a different carbon atom to form a hemiacetal or hemiketal, forming a heterocyclic ring with an oxygen bridge between two carbon atoms. Rings with five and six atoms are called furanose and pyranose forms, respectively, and exist in equilibrium with the straight-chain form.[8] During the conversion from straight-chain form to the cyclic form, the carbon atom containing the carbonyl oxygen, called the anomeric carbon, becomes a stereogenic center with two possible Glucose can exist in both a straight-chain and ring configurations: The oxygen atom may take a position either above form. or below the plane of the ring. The resulting possible pair of stereoisomers is called anomers. In the α anomer, the -OH substituent on the anomeric carbon rests on the opposite side (trans) of the ring from the CH2OH side branch. The alternative form, in which the CH2OH substituent and the anomeric hydroxyl are on the same side (cis) of the plane of the ring, is called the β anomer.

Use in living organisms
Monosaccharides are the major source of fuel for metabolism, being used both as an energy source (glucose being the most important in nature) and in biosynthesis. When monosaccharides are not immediately needed by many cells they are often converted to more space-efficient forms, often polysaccharides. In many animals, including humans, this storage form is glycogen, especially in liver and muscle cells. In plants, starch is used for the same purpose.

Disaccharides
Two joined monosaccharides are called a disaccharide and these are the simplest polysaccharides. Examples include sucrose and lactose. They are composed of two monosaccharide units bound together by a covalent bond known as a glycosidic linkage formed via a dehydration reaction, resulting in the loss of a hydrogen atom from one monosaccharide and a hydroxyl group from the other. The formula of unmodified disaccharides is C12H22O11. Although there are numerous kinds of disaccharides, a handful of disaccharides are particularly notable.

Sucrose, also known as table sugar, is a common disaccharide. It is composed of two monosaccharides: D-glucose (left) and D-fructose (right).

Sucrose, pictured to the right, is the most abundant disaccharide, and the main form in which carbohydrates are transported in plants. It is composed of one D-glucose molecule and one D-fructose molecule. The systematic name for sucrose, O-α-D-glucopyranosyl-(1→2)-D-fructofuranoside, indicates four things: • Its monosaccharides: glucose and fructose • Their ring types: glucose is a pyranose, and fructose is a furanose • How they are linked together: the oxygen on carbon number 1 (C1) of α-D-glucose is linked to the C2 of D-fructose. • The -oside suffix indicates that the anomeric carbon of both monosaccharides participates in the glycosidic bond.

Carbohydrate Lactose, a disaccharide composed of one D-galactose molecule and one D-glucose molecule, occurs naturally in mammalian milk. The systematic name for lactose is O-β-D-galactopyranosyl-(1→4)-D-glucopyranose. Other notable disaccharides include maltose (two D-glucoses linked α-1,4) and cellulobiose (two D-glucoses linked β-1,4). disaccharides can be classified into two types.They are reducing and non-reducing disaccahrides if the functional group is present in bonding with another sugar unit it is called a reducing disaccharide or biose.

88

Nutrition
Foods high in carbohydrate include fruits, sweets, soft drinks, breads, pastas, beans, potatoes, bran, rice, and cereals. Carbohydrates are a common source of energy in living organisms; however, no carbohydrate is an essential nutrient in humans.[9] Carbohydrates are not necessary building blocks of other molecules, and the body can obtain all its energy from protein and fats.[10][11] The brain and neurons generally cannot burn fat for energy, but use glucose or ketones. Humans can synthesize some glucose (in a set of processes known as gluconeogenesis) from specific amino acids, from the glycerol backbone in triglycerides and in some cases from fatty acids. Carbohydrate and protein contain 4 kilocalories per gram, while fats contain 9 kilocalories per gram. In the case of protein, this is somewhat misleading as only some amino acids are usable for fuel. Organisms typically cannot metabolize all types of carbohydrate to yield energy. Glucose is a nearly universal and accessible source of Grain products: rich sources of carbohydrates calories. Many organisms also have the ability to metabolize other monosaccharides and Disaccharides, though glucose is preferred. In Escherichia coli, for example, the lac operon will express enzymes for the digestion of lactose when it is present, but if both lactose and glucose are present the lac operon is repressed, resulting in the glucose being used first (see: Diauxie). Polysaccharides are also common sources of energy. Many organisms can easily break down starches into glucose, however, most organisms cannot metabolize cellulose or other polysaccharides like chitin and arabinoxylans. These carbohydrates types can be metabolized by some bacteria and protists. Ruminants and termites, for example, use microorganisms to process cellulose. Even though these complex carbohydrates are not very digestible, they may comprise important dietary elements for humans. Called dietary fiber, these carbohydrates enhance digestion among other benefits.[12] Based on the effects on risk of heart disease and obesity,[13] the Institute of Medicine recommends that American and Canadian adults get between 45–65% of dietary energy from carbohydrates.[14] The Food and Agriculture Organization and World Health Organization jointly recommend that national dietary guidelines set a goal of 55–75% of total energy from carbohydrates, but only 10% directly from sugars (their term for simple carbohydrates).[15]

Classification
Historically nutritionists have classified carbohydrates as either simple or complex. However, the exact delineation of these categories is ambiguous. Today, simple carbohydrate typically refers to monosaccharides and disaccharides and complex carbohydrate means polysaccharides (and oligosaccharides). However, the term complex carbohydrate was first used in slightly different context in the U.S. Senate Select Committee on Nutrition and Human Needs publication Dietary Goals for the United States (1977). In this work, complex carbohydrate were defined as "fruit, vegetables and whole-grains".[16] Some nutritionists use complex carbohydrate to refer to any sort of digestible

Carbohydrate saccharide present in a whole food, where fiber, vitamins and minerals are also found (as opposed to processed carbohydrates, which provide calories but few other nutrients). Some simple carbohydrates (e.g. fructose) are digested very slowly, while some complex carbohydrates (starches), especially if processed, raise blood sugar rapidly. The speed of digestion is determined by a variety of factors including which other nutrients are consumed with the carbohydrate, how the food is prepared, individual differences in metabolism, and the chemistry of the carbohydrate. The USDA's Dietary Guidelines for Americans 2010 call for moderate- to high-carbohydrate consumption from a balanced diet that includes six one-ounce servings of grain foods each day, at least half from whole grain sources and the rest from enriched.[17] The glycemic index (GI) and glycemic load concepts have been developed to characterize food behavior during human digestion. They rank carbohydrate-rich foods based on the rapidity and magnitude of their effect on blood glucose levels. Glycemic index is a measure of how quickly food glucose is absorbed, while glycemic load is a measure of the total absorbable glucose in foods. The insulin index is a similar, more recent classification method that ranks foods based on their effects on blood insulin levels, which are caused by glucose (or starch) and some amino acids in food.

89

Metabolism
Catabolism
Catabolism is the metabolic reaction in which cells undergo to extract energy. There are two major metabolic pathways of monosaccharide catabolism: glycolysis and the citric acid cycle. In glycolysis, oligo/polysaccharides are cleaved first to smaller monosaccharides by enzymes called glycoside hydrolases. The monosaccharide units can then enter into monosaccharide catabolism. In some cases, as with humans, not all carbohydrate types are usable as the digestive and metabolic enzymes necessary are not present.

Carbohydrate chemistry
Carbohydrate chemistry is a large and economically important branch of organic chemistry. Some of the main organic reactions that involve carbohydrates are: • • • • • • • Carbohydrate acetalisation Cyanohydrin reaction Lobry-de Bruyn-van Ekenstein transformation Amadori rearrangement Nef reaction Wohl degradation Koenigs–Knorr reaction

Carbohydrate

90

References
[1] Flitsch, SL & Ulijn, RV (2003). "Sugars tied to the spot." Nature 421: 219–220 (http:/ / www. nature. com/ nature/ journal/ v421/ n6920/ pdf/ 421219a. pdf). [2] Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. pp. 52–59. ISBN 0-13-981176-1. [3] John Merle Coulter, Charler Reid Barnes, Henry Chandler Cowles (1930), A Textbook of Botany for Colleges and Universities (http:/ / books. google. com. br/ books?id=WyZnVpCiTHIC& pg=PA375& dq=simplest+ carbohydrate)" [4] Carl A. Burtis, Edward R. Ashwood, Norbert W. Tietz (2000), Tietz fundamentals of clinical chemistry (http:/ / books. google. com/ books?id=l5hqAAAAMAAJ& q=simplest+ carbohydrate) [5] Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin Cummings. ISBN 0-8053-3066-6 [6] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6. . [7] Pigman, Ward; Horton, D. (1972). "Chapter 1: Stereochemistry of the Monosaccharides". In Pigman and Horton. The Carbohydrates: Chemistry and Biochemistry Vol 1A (2nd ed.). San Diego: Academic Press. pp. 1–67. [8] Pigman, Ward; Anet, E.F.L.J. (1972). "Chapter 4: Mutarotations and Actions of Acids and Bases". In Pigman and Horton. The Carbohydrates: Chemistry and Biochemistry Vol 1A (2nd ed.). San Diego: Academic Press. pp. 165–194. [9] http:/ / www. ajcn. org/ content/ 75/ 5/ 951. 2. full [10] Is dietary carbohydrate essential for human nutrition? - Westman 75 (5): 951 - American Journal of Clinical Nutrition (http:/ / www. ajcn. org/ cgi/ content/ full/ 75/ 5/ 951-a) [11] A High-Protein, High-Fat, Carbohydrate-Free Diet Reduces Energy Intake, Hepatic Lipogenesis, and Adiposity in Rats - Pichon et al. 136 (5): 1256 - Journal of Nutrition (http:/ / jn. nutrition. org/ cgi/ reprint/ 136/ 5/ 1256?ijkey=ebf0450b5cf21e8d83dd43f62b5559254694f65f) [12] Dietary Fiber Intake and Mortality in the NIH-AARP Diet and Health Study - Part, et al. 171 (12): 1061 - Archives of Internal Medicine (http:/ / archinte. ama-assn. org/ cgi/ content/ short/ archinternmed. 2011. 18) [13] Effect of increased consumption of whole-grain foods on blood pressure and other cardiovascular risk markers in healthy middle-aged persons: a randomized, controlled trial - Tighe, et al. 92 (4): 733 - American Journal of Clinical Nutrition (http:/ / www. ajcn. org/ content/ 92/ 4/ 733. abstract?sid=f97a2937-5a29-4143-8f1a-676f100177ab) [14] Food and Nutrition Board (2002/2005). Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids (http:/ / newton. nap. edu/ books/ 0309085373/ html). Washington, D.C.: The National Academies Press. Page 769 (http:/ / newton. nap. edu/ books/ 0309085373/ html/ 769. html). ISBN 0-309-08537-3. [15] Joint WHO/FAO expert consultation (2003). Diet, Nutrition and the Prevention of Chronic Diseases (http:/ / www. who. int/ hpr/ NPH/ docs/ who_fao_expert_report. pdf) (PDF). Geneva: World Health Organization. Pages 55–56. ISBN 92-4-120916-X. [16] Joint WHO/FAO expert consultation (1998), Carbohydrates in human nutrition, chapter 1 (http:/ / www. fao. org/ docrep/ W8079E/ w8079e07. htm). ISBN 92-5-104114-8. [17] DHHS and USDA, Dietary Guidelines for Americans 2010, (http:/ / www. cnpp. usda. gov/ DietaryGuidelines. htm)

External links
• Carbohydrates, including interactive models and animations (http://www2.ufp.pt/~pedros/bq/carb_en.htm) (Requires MDL Chime (http://www.mdl.com/products/framework/chime/)) • IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN): Carbohydrate Nomenclature (http:// www.chem.qmw.ac.uk/iupac/2carb/) • Carbohydrates detailed (http://www.cem.msu.edu/~reusch/VirtualText/carbhyd.htm) • Complex And Simple Carbohydrates (http://evilcyber.com/nutrition/complex-and-simple-carbohydrates/) Explanation of the differences • Carbohydrates and Glycosylation - The Virtual Library of Biochemistry and Cell Biology (http://www. biochemweb.org/carbohydrates.shtml) • Functional Glycomics Gateway (http://www.functionalglycomics.org/), a collaboration between the Consortium for Functional Glycomics and Nature Publishing Group • Wine Carbohydrates (http://www.wineclubwizard.com/wine-carbohydrates.html)

Cell (biology)

91

Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life.[1] Organisms can be classified as unicellular (consisting of a single cell; including most bacteria) or multicellular (including plants and animals). Humans contain about 10 trillion (1013) cells. Most plant and animal cells are between 1 and 100 µm and therefore are visible only under the microscope.[2]
Allium cells in different phases of the cell cycle The cell was discovered by Robert Hooke in 1665. In 1835, before the final cell theory was developed, Jan Evangelista Purkyně observed small "granules" while looking at the plant tissue through a microscope. The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that The cells of eukaryotes (left) and prokaryotes (right) vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.[3]

The word cell comes from the Latin cella, meaning "small room". The descriptive term for the smallest living biological structure was coined by Robert Hooke in a book he published in 1665 when he compared the cork cells he saw through his microscope to the small rooms monks lived in.[4]

Anatomy
There are two types of cells: eukaryotic and prokaryotic. Prokaryotic cells are usually independent, while eukaryotic cells are often found in multicellular organisms.

Cell (biology)

92

Table 1: Comparison of features of prokaryotic and eukaryotic cells
Prokaryotes Typical organisms Typical size Type of nucleus DNA bacteria, archaea ~ 1–10 µm protists, fungi, plants, animals ~ 10–100 µm (sperm cells, apart from the tail, are smaller) Eukaryotes

nucleoid region; no real nucleus real nucleus with double membrane circular (usually) linear molecules (chromosomes) with histone proteins RNA-synthesis inside the nucleus protein synthesis in cytoplasm 60S+40S highly structured by endomembranes and a cytoskeleton flagella and cilia containing microtubules; lamellipodia and filopodia containing actin one to several thousand (though some lack mitochondria) in algae and plants single cells, colonies, higher multicellular organisms with specialized cells

RNA-/protein-synthesis coupled in cytoplasm

Ribosomes

50S+30S

Cytoplasmatic structure very few structures Cell movement Mitochondria Chloroplasts Organization Cell division flagella made of flagellin none none usually single cells

Binary fission (simple division) Mitosis (fission or budding) Meiosis

Prokaryotic cells
The prokaryote cell is simpler, and therefore smaller, than a eukaryote cell, lacking a nucleus and most of the other organelles of eukaryotes. There are two kinds of prokaryotes: bacteria and archaea; these share a similar structure. Nuclear material of prokaryotic cell consist of a single chromosome that is in direct contact with cytoplasm. Here, the undefined nuclear region in the cytoplasm is called nucleoid. A prokaryotic cell architectural regions: has three

• On the outside, flagella and pili project from the cell's surface. These are structures (not present in all prokaryotes) made of proteins that facilitate movement and communication between cells;

Diagram of a typical prokaryotic cell

• Enclosing the cell is the cell envelope – generally consisting of a cell wall covering a plasma membrane though some bacteria also have a further covering layer called a capsule. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, serving as a protective filter. Though most prokaryotes have a cell wall, there are exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea). The cell wall

Cell (biology) consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and finally bursting (cytolysis) from osmotic pressure against a hypotonic environment. Some eukaryote cells (plant cells and fungi cells) also have a cell wall; • Inside the cell is the cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions. A prokaryotic chromosome is usually a circular molecule (an exception is that of the bacterium Borrelia burgdorferi, which causes Lyme disease). Though not forming a nucleus, the DNA is condensed in a nucleoid. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular. Plasmids enable additional functions, such as antibiotic resistance.

93

Eukaryotic cells
Plants, animals, fungi, slime moulds, protozoa, and algae are all eukaryotic. These cells are about 15 times wider than a typical prokaryote and can be as much as 1000 times greater in volume. The major difference between prokaryotes and eukaryotes is that eukaryotic cells contain membrane-bound compartments in which specific metabolic activities take place. Most important among these is a cell nucleus, a membrane-delineated compartment that houses the eukaryotic cell's DNA. This nucleus gives the eukaryote its name, which means "true nucleus." Other differences include: • The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present. • The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria also contain some DNA. • Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, mechanosensation, and thermosensation. Cilia may thus be "viewed as sensory cellular antennae that coordinate a large number of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation."[5] • Eukaryotes can move using motile cilia or flagella. The flagella are more complex than those of prokaryotes.

Structure of a typical animal cell

Structure of a typical plant cell

Cell (biology)

94

Table 2: Comparison of structures between animal and plant cells
Typical animal cell Organelles • • • • • • • • • • • Nucleus • Nucleolus (within nucleus) Rough endoplasmic reticulum (ER) Smooth ER Ribosomes Cytoskeleton Golgi apparatus Cytoplasm Mitochondria Vesicles Lysosomes Centrosome • Centrioles • • • • • • • • • • • Typical plant cell Nucleus • Nucleolus (within nucleus) Rough ER Smooth ER Ribosomes Cytoskeleton Golgi apparatus (dictiosomes) Cytoplasm Mitochondria Plastids and its derivatives Vacuole(s) Cell wall

Subcellular components
All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, separates its interior from its environment, regulates what moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells. This article lists these primary components of the cell, then briefly describe their function.

Membrane
The cytoplasm of a cell is surrounded by a cell membrane or plasma membrane. The plasma membrane in plants and prokaryotes is usually covered by a cell wall. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of lipids (hydrophobic fat-like molecules) and hydrophilic phosphorus molecules. Hence, the layer is called a phospholipid bilayer. It may also be called a fluid mosaic membrane. Embedded within this membrane is a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell. The membrane is said to be 'semi-permeable', in that it can either let a substance (molecule or ion) pass through freely, pass through to a limited extent or not pass through at all. Cell surface membranes also contain receptor proteins that allow cells to detect external signaling molecules such as hormones.

Cell (biology)

95

Cytoskeleton
The cytoskeleton acts to organize and maintain the cell's shape; anchors organelles in place; helps during endocytosis, the uptake of external materials by a cell, and cytokinesis, the separation of daughter cells after cell division; and moves parts of the cell in processes of growth and mobility. The eukaryotic cytoskeleton is composed of microfilaments, intermediate filaments and microtubules. There is a great number of proteins associated with them, each controlling a cell's structure by directing, bundling, and aligning filaments. The prokaryotic cytoskeleton is less well-studied but is involved in the maintenance of cell shape, polarity and cytokinesis.[6]

Genetic material

Bovine Pulmonary Artery Endothelial cell: nuclei stained blue, mitochondria stained red, and F-actin, an important component in microfilaments, stained green. Cell imaged on a fluorescent microscope.

Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Most organisms use DNA for their long-term information storage, but some viruses (e.g., retroviruses) have RNA as their genetic material. The biological information contained in an organism is encoded in its DNA or RNA sequence. RNA is also used for information transport (e.g., mRNA) and enzymatic functions (e.g., ribosomal RNA) in organisms that use DNA for the genetic code itself. Transfer RNA (tRNA) molecules are used to add amino acids during protein translation. Prokaryotic genetic material is organized in a simple circular DNA molecule (the bacterial chromosome) in the nucleoid region of the cytoplasm. Eukaryotic genetic material is divided into different, linear molecules called chromosomes inside a discrete nucleus, usually with additional genetic material in some organelles like mitochondria and chloroplasts (see endosymbiotic theory). A human cell has genetic material contained in the cell nucleus (the nuclear genome) and in the mitochondria (the mitochondrial genome). In humans the nuclear genome is divided into 23 pairs of linear DNA molecules called chromosomes. The mitochondrial genome is a circular DNA molecule distinct from the nuclear DNA. Although the mitochondrial DNA is very small compared to nuclear chromosomes, it codes for 13 proteins involved in mitochondrial energy production and specific tRNAs. Foreign genetic material (most commonly DNA) can also be artificially introduced into the cell by a process called transfection. This can be transient, if the DNA is not inserted into the cell's genome, or stable, if it is. Certain viruses also insert their genetic material into the genome.

Organelles
The human body contains many different organs, such as the heart, lung, and kidney, with each organ performing a different function. Cells also have a set of "little organs," called organelles, that are adapted and/or specialized for carrying out one or more vital functions. Both eukaryotic and prokaryotic cells have organelles but organelles in eukaryotes are generally more complex and may be membrane bound. There are several types of organelles in a cell. Some (such as the nucleus and golgi apparatus) are typically solitary, while others (such as mitochondria, peroxisomes and lysosomes) can be numerous (hundreds to thousands). The cytosol is the gelatinous fluid that fills the cell and surrounds the organelles.

Cell (biology)

96

• Cell nucleus – eukaryotes only - A cell's information center, the cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell's chromosomes, and is the place where almost all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and separated from the cytoplasm by a double membrane called the nuclear envelope. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called messenger RNA (mRNA). This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. The nucleolus is a specialized region within the nucleus where ribosome subunits are assembled. In prokaryotes, DNA processing takes place in the cytoplasm.

Diagram of a cell nucleus

• Mitochondria and Chloroplasts – eukaryotes only - the power generators: Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. Mitochondria play a critical role in generating energy in the eukaryotic cell. Mitochondria generate the cell's energy by oxidative phosphorylation, using oxygen to release energy stored in cellular nutrients (typically pertaining to glucose) to generate ATP. Mitochondria multiply by splitting in two. Respiration occurs in the cell mitochondria. • Endoplasmic reticulum – eukaryotes only: The endoplasmic reticulum (ER) is the transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface and secretes proteins into the cytoplasm, and the smooth ER, which lacks them. Smooth ER plays a role in calcium sequestration and release. • Golgi apparatus – eukaryotes only : The primary function of the Golgi apparatus is to process and package the macromolecules such as proteins and lipids that are synthesized by the cell. • Ribosomes: The ribosome is a large complex of RNA and protein molecules. They each consist of two subunits, and act as an Diagram of an endomembrane system assembly line where RNA from the nucleus is used to synthesise proteins from amino acids. Ribosomes can be found either floating freely or bound to a membrane (the rough endoplasmatic reticulum in eukaryotes, or the cell membrane in prokaryotes).[7] • Lysosomes and Peroxisomes – eukaryotes only: Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. Peroxisomes have enzymes that rid the cell of toxic peroxides. The cell could not house these destructive enzymes if they were not contained in a membrane-bound system. • Centrosome – the cytoskeleton organiser: The centrosome produces the microtubules of a cell – a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells. • Vacuoles: Vacuoles store food and waste. Some vacuoles store extra water. They are often described as liquid filled space and are surrounded by a membrane. Some cells, most notably Amoeba, have contractile vacuoles,

Cell (biology) which can pump water out of the cell if there is too much water. The vacuoles of eukaryotic cells are usually larger in those of plants than animals.

97

Structures outside the cell membrane
Many cells also have structures which exist wholly or partially outside the cell membrane. These structures are notable because they are not protected from the external environment by the impermeable cell membrane. In order to assemble these structures export processes to carry macromolecules across the cell membrane must be used.

Cell wall
Many types of prokaryotic and eukaryotic cell have a cell wall. The cell wall acts to protect the cell mechanically and chemically from its environment, and is an additional layer of protection to the cell membrane. Different types of cell have cell walls made up of different materials; plant cell walls are primarily made up of pectin, fungi cell walls are made up of chitin and bacteria cell walls are made up of peptidoglycan.

Prokaryotic
Capsule A gelatinous capsule is present in some bacteria outside the cell membrane and cell wall. The capsule may be polysaccharide as in pneumococci, meningococci or polypeptide as Bacillus anthracis or hyaluronic acid as in streptococci. Capsules are not marked by normal staining protocols and can be detected by special stain. Flagella Flagella are organelles for cellular mobility. The bacterial flagellum stretches from cytoplasm through the cell membrane(s) and extrudes through the cell wall. They are long and thick thread-like appendages, protein in nature. Are most commonly found in bacteria cells but are found in animal cells as well. Fimbriae (pili) They are short and thin hair like filaments, formed of protein called pilin (antigenic). Fimbriae are responsible for attachment of bacteria to specific receptors of human cell (adherence). There are special types of pili called (sex pili) involved in conjunction.

Functions
Growth and metabolism
Between successive cell divisions, cells grow through the functioning of cellular metabolism. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules and perform other biological functions. Complex sugars consumed by the organism can be broken down into a less chemically complex sugar molecule called glucose. Once inside the cell, glucose is broken down to make adenosine triphosphate (ATP), a form of energy, through two different pathways. The first pathway, glycolysis, requires no oxygen and is referred to as anaerobic metabolism. Each reaction is designed to produce some hydrogen ions that can then be used to make energy packets (ATP). In prokaryotes, glycolysis is the only method used for converting energy. The second pathway, called the Krebs cycle, or citric acid cycle, occurs inside the mitochondria and can generate enough ATP to run all the cell functions.

Cell (biology)

98

Creation
Cell division involves a single cell (called a mother cell) dividing into two daughter cells. This leads to growth in multicellular organisms (the growth of tissue) and to procreation (vegetative reproduction) in unicellular organisms. Prokaryotic cells divide by binary fission. Eukaryotic cells usually undergo a process of nuclear division, called mitosis, followed by division of the cell, called cytokinesis. A diploid cell may also undergo meiosis to produce haploid cells, usually four. Haploid cells serve as gametes in multicellular organisms, fusing to form new diploid cells. DNA replication, or the process of duplicating a cell's genome, is required every time a cell divides. Replication, like all cellular activities, requires specialized proteins for carrying out the job.

Protein synthesis
Cells are capable of synthesizing new proteins, which are essential for the modulation and maintenance of cellular activities. This process involves the formation of new protein molecules from amino acid building blocks based on information encoded in DNA/RNA. Protein synthesis generally consists of two major steps: transcription and translation. Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol, where they are translated into polypeptide sequences. The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to the polypeptide sequence by binding to transfer RNA (tRNA) adapter molecules in binding pockets within the ribosome. The new polypeptide then folds into a functional three-dimensional protein molecule.

Movement or motility

Cells can move during many processes: such as wound healing, the immune response and cancer metastasis. For wound healing to occur, white blood cells and cells that ingest bacteria move to the wound site to kill the microorganisms that cause infection. At the same time fibroblasts (connective tissue cells) move there to remodel damaged structures. In the case of tumor development, cells from a primary tumor move away and spread to other parts of the body. Cell motility involves many receptors, crosslinking, bundling, binding, adhesion, motor and other proteins.[8] The process is divided into three steps – protrusion of the leading edge of the cell, adhesion of the leading edge and de-adhesion at the cell body and rear, and cytoskeletal contraction to pull the cell forward. Each step is driven by physical forces generated by unique segments of the cytoskeleton.[9][10]

An overview of protein synthesis.Within the nucleus of the cell (light blue), genes (DNA, dark blue) are transcribed into RNA. This RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA (red) that is then transported out of the nucleus and into the cytoplasm (peach), where it undergoes translation into a protein. mRNA is translated by ribosomes (purple) that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. Newly synthesized proteins (black) are often further modified, such as by binding to an effector molecule (orange), to become fully active.

Cell (biology)

99

Origins
The origin of cells has to do with the origin of life, which began the history of life on Earth.

Origin of the first cell
There are several theories about the origin of small molecules that could lead to life in an early Earth. One is that they came from meteorites (see Murchison meteorite). Another is that they were created at deep-sea vents. A third is that they were synthesized by lightning in a reducing atmosphere (see Miller–Urey experiment); although it is not clear if Earth had such an atmosphere. There are essentially no experimental data defining what the first self-replicating forms were. RNA is generally assumed the earliest self-replicating molecule, as it is capable of both storing genetic information and catalyzing chemical reactions (see RNA world hypothesis). But some other entity with the potential to self-replicate could have preceded RNA, like clay or peptide nucleic acid.[11] Cells emerged at least 4.0–4.3 billion years ago. The current belief is that these cells were heterotrophs. An important characteristic of cells is the cell membrane, composed of a bilayer of lipids. The early cell membranes were probably more simple and permeable than modern ones, with only a single fatty acid chain per lipid. Lipids are known to spontaneously form bilayered vesicles in water, and could have preceded RNA, but the first cell membranes could also have been produced by catalytic RNA, or even have required structural proteins before they could form.[12]

Origin of eukaryotic cells
The eukaryotic cell seems to have evolved from a symbiotic community of prokaryotic cells. DNA-bearing organelles like the mitochondria and the chloroplasts are almost certainly what remains of ancient symbiotic oxygen-breathing proteobacteria and cyanobacteria, respectively, where the rest of the cell appears derived from an ancestral archaean prokaryote cell—an idea called the endosymbiotic theory. There is still considerable debate about whether organelles like the hydrogenosome predated the origin of mitochondria, or viceversa: see the hydrogen hypothesis for the origin of eukaryotic cells. Sex, as the stereotyped choreography of meiosis and syngamy that persists in nearly all extant eukaryotes, may have played a role in the transition from prokaryotes to eukaryotes. An 'origin of sex as vaccination' theory suggests that the eukaryote genome accreted from prokaryan parasite genomes in numerous rounds of lateral gene transfer. Sex-as-syngamy (fusion sex) arose when infected hosts began swapping nuclearized genomes containing co-evolved, vertically transmitted symbionts that conveyed protection against horizontal infection by more virulent symbionts.[13]

History of research
• 1632–1723: Antonie van Leeuwenhoek teaches himself to grind lenses, builds a microscope and draws protozoa, such as Vorticella from rain water, and bacteria from his own mouth. • 1665: Robert Hooke discovers cells in cork, then in living plant tissue using an early microscope.[4] • 1839: Theodor Schwann and Matthias Jakob Schleiden elucidate the principle that plants and animals are made of cells, concluding that cells are a common unit of structure and development, and thus founding the cell theory. • The belief that life forms can occur spontaneously (generatio spontanea) is contradicted by Louis Pasteur (1822–1895) (although Francesco Redi had performed an experiment in 1668 that suggested the same conclusion). • 1855: Rudolf Virchow states that cells always emerge from cell divisions (omnis cellula ex cellula). • 1931: Ernst Ruska builds first transmission electron microscope (TEM) at the University of Berlin. By 1935, he has built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles. • 1953: Watson and Crick made their first announcement on the double-helix structure for DNA on February 28.

Cell (biology) • 1981: Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic theory.

100

References
[1] Cell Movements and the Shaping of the Vertebrate Body (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term=Cell+ Movements+ and+ the+ Shaping+ of+ the+ Vertebrate+ Body+ AND+ mboc4[book]+ AND+ 374635[uid]& rid=mboc4. section. 3919) in Chapter 21 of Molecular Biology of the Cell (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term=cell+ biology+ AND+ mboc4[book]+ AND+ 373693[uid]& rid=mboc4) fourth edition, edited by Bruce Alberts (2002) published by Garland Science. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos. It is also common to describe small molecules such as amino acids as " molecular building blocks (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term="all+ cells"+ AND+ mboc4[book]+ AND+ 372023[uid]& rid=mboc4. section. 4#23)". [2] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6. . [3] Maton, Anthea; Hopkins, Jean Johnson, Susan LaHart, David Quon Warner, Maryanna Wright, Jill D (1997). Cells Building Blocks of Life. New Jersey: Prentice Hall. ISBN 0-13-423476-6. [4] "... I could exceedingly plainly perceive it to be all perforated and porous, much like a Honey-comb, but that the pores of it were not regular [..] these pores, or cells, [..] were indeed the first microscopical pores I ever saw, and perhaps, that were ever seen, for I had not met with any Writer or Person, that had made any mention of them before this. . ." – Hooke describing his observations on a thin slice of cork. Robert Hooke (http:/ / www. ucmp. berkeley. edu/ history/ hooke. html) [5] Satir, P; Christensen, ST; Søren T. Christensen (2008-03-26). "Structure and function of mammalian cilia" (http:/ / www. springerlink. com/ content/ x5051hq648t3152q/ ). Histochemistry and Cell Biology (Springer Berlin / Heidelberg) 129 (6): 687–693. doi:10.1007/s00418-008-0416-9. PMC 2386530. PMID 18365235. 1432-119X. . Retrieved 2009-09-12. [6] Michie K, Löwe J (2006). "Dynamic filaments of the bacterial cytoskeleton". Annu Rev Biochem 75: 467–92. doi:10.1146/annurev.biochem.75.103004.142452. PMID 16756499. [7] Ménétret JF, Schaletzky J, Clemons WM, et al., CW; Akey (December 2007). "Ribosome binding of a single copy of the SecY complex: implications for protein translocation". Mol. Cell 28 (6): 1083–92. doi:10.1016/j.molcel.2007.10.034. PMID 18158904. [8] Revathi Ananthakrishnan1 *, Allen Ehrlicher2 ✉. "The Forces Behind Cell Movement" (http:/ / www. biolsci. org/ v03p0303. htm). Biolsci.org. . Retrieved 2009-04-17. [9] Alberts B, Johnson A, Lewis J. et al. Molecular Biology of the Cell, 4e. Garland Science. 2002 [10] Ananthakrishnan R, Ehrlicher A. The Forces Behind Cell Movement. Int J Biol Sci 2007; 3:303–317. http:/ / www. biolsci. org/ v03p0303. htm [11] Orgel LE (1998). "The origin of life--a review of facts and speculations". Trends Biochem Sci 23 (12): 491–5. doi:10.1016/S0968-0004(98)01300-0. PMID 9868373. [12] Griffiths G (December 2007). "Cell evolution and the problem of membrane topology". Nature reviews. Molecular cell biology 8 (12): 1018–24. doi:10.1038/nrm2287. PMID 17971839. [13] Sterrer W (2002). "On the origin of sex as vaccination". Journal of Theoretical Biology 216: 387–396. doi:10.1006/jtbi.2002.3008. PMID 12151256.

 This article incorporates public domain material from the NCBI document "Science Primer" (http://www. ncbi.nlm.nih.gov/About/primer/index.html).

External links
• Inside the Cell (http://publications.nigms.nih.gov/insidethecell/) • Virtual Cell's Educational Animations (http://vcell.ndsu.nodak.edu/animations/) • The Inner Life of A Cell (http://www.studiodaily.com/main/searchlist/6850.html), a flash video showing what happens inside of a cell. Daniel Reda of Singularity University narrates (beginning at 22:24) (http://www. youtube.com/watch?v=It83JKAxejM) • The Virtual Cell (http://www.ibiblio.org/virtualcell/tour/cell/cell.htm) • Cells Alive! (http://www.cellsalive.com/) • Journal of Cell Biology (http://www.jcb.org/) • The Biology Project > Cell Biology (http://www.biology.arizona.edu/cell_bio/cell_bio.html) • Centre of the Cell online (http://www.centreofthecell.org/) • The Image & Video Library of The American Society for Cell Biology (http://cellimages.ascb.org/), a collection of peer-reviewed still images, video clips and digital books that illustrate the structure, function and

Cell (biology) biology of the cell. • HighMag Blog (http://highmagblog.blogspot.com/), still images of cells from recent research articles. • New Microscope Produces Dazzling 3D Movies of Live Cells (http://www.hhmi.org/news/betzig20110304. html), March 4, 2011 - Howard Hughes Medical Institute. • WormWeb.org: Interactive Visualization of the C. elegans Cell lineage (http://wormweb.org/celllineage) Visualize the entire cell lineage tree of the nematode C. elegans

101

Textbooks
• Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (http://www. ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2) (4th ed.). Garland. ISBN 0-8153-3218-1. • Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.TOC) (5th ed.). WH Freeman: New York, NY. ISBN 978-0-7167-4366-8. • Cooper GM (2000). The cell: a molecular approach (http://www.ncbi.nlm.nih.gov/books/bv. fcgi?rid=cooper.TOC&depth=2) (2nd ed.). Washington, D.C: ASM Press. ISBN 0-87893-102-3.

Cell biology
Cell biology (formerly cytology, from the Greek kytos, "contain") is a scientific discipline that studies cells – their physiological properties, their structure, the organelles they contain, interactions with their environment, their life cycle, division and death. This is done both on a microscopic and molecular level. Cell biology research encompasses both the great diversity of single-celled organisms like bacteria and protozoa, as well as the many specialized cells in multicellular organisms such as humans. Knowing the components of cells and how cells work is fundamental to all biological sciences. Appreciating the similarities and differences between cell types is particularly important to the fields of cell and molecular biology as well as to biomedical fields such as cancer research and developmental biology. These fundamental similarities and differences provide a unifying theme, sometimes allowing the principles learned from studying one cell type to be extrapolated and generalized to other cell types. Therefore, research in cell biology is closely related to genetics, biochemistry, molecular biology, immunology, and developmental biology.

Cell biology

102

Processes

Understanding cells in terms of their molecular components.

Movement of proteins
Each type of protein is usually sent to a particular part of the cell. An important part of cell biology is the investigation of molecular mechanisms by which proteins are moved to different places inside cells or secreted from cells. Most proteins are synthesized by ribosomes in the rough endoplasmic reticulum.Ribosomes contain the nucleic acid RNA, which assembles and joins amino acids to make proteins. They can be found alone or in groups within the cytoplasm as well as on the RER. This process is known as protein biosynthesis. Biosynthesis (also called biogenesis) is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products (also simply known as protein translation). Some proteins, such as those to be incorporated Endothelial cells under the microscope. Nuclei are stained blue with DAPI, microtubles are in membranes (known as membrane proteins), are transported into the marked green by an antibody and actin filaments "rough" endoplasmic reticulum (ER) during synthesis. This process are labelled red with phalloidin. can be followed by transportation and processing in the Golgi apparatus. The Golgi apparatus is a large organelle that processes proteins and prepares them for use both inside and outside the cell. The Golgi apparatus is somewhat like a post office. It receives items (proteins from the ER), packages and labels them, and then sends them on to their destinations (to different parts of the cell or to the cell membrane for transport out of the cell).[1] From the Golgi, membrane proteins can move to the plasma membrane, to other sub-cellular compartments, or they can be secreted from the cell. The ER and Golgi can be thought of as the "membrane protein synthesis compartment" and the "membrane protein processing compartment", respectively. There is a semi-constant flux of proteins through these compartments. ER and Golgi-resident proteins associate with other proteins but remain in their respective compartments. Other proteins "flow" through the ER and Golgi to the plasma membrane. Motor proteins transport membrane protein-containing vesicles along cytoskeletal tracks to distant parts of cells such as axon terminals.

Cell biology Some proteins that are made in the cytoplasm contain structural features that target them for transport into mitochondria or the nucleus. Some mitochondrial proteins are made inside mitochondria and are coded for by mitochondrial DNA. In plants, chloroplasts also make some cell proteins. Extracellular and cell surface proteins destined to be degraded can move back into intracellular compartments upon being incorporated into endocytosed vesicles some of which fuse with lysosomes where the proteins are broken down to their individual amino acids. The degradation of some membrane proteins begins while still at the cell surface when they are separated by secretases. Proteins that function in the cytoplasm are often degraded by proteasomes.

103

Other cellular processes
• • • • Active transport and Passive transport - Movement of molecules into and out of cells. Autophagy - The process whereby cells "eat" their own internal components or microbial invaders. Adhesion - Holding together cells and tissues. Reproduction - Made possible by the combination of sperm made in the testiculi (contained in some male cells' nuclei) and the egg made in the ovary (contained in the nucleus of a female cell). When the sperm breaks through the hard outer shell of the egg a new cell embryo is formed, which, in humans, grows to full size in 9 months. • Cell movement: Chemotaxis, Contraction, cilia and flagella. • • • • Cell signaling - Regulation of cell behavior by signals from outside. DNA repair and Cell death Metabolism: Glycolysis, respiration, Photosynthesis Transcription and mRNA splicing - gene expression.

Internal cellular structures
• Chloroplast - key organelle for photosynthesis (only found in plant cells) • Cilium - motile microtubule-containing structure of eukaryotes • Cytoplasm - contents of the main fluid-filled space inside cells • Cytoskeleton - protein filaments inside cells • Endoplasmic reticulum - major site of membrane protein synthesis • Flagellum - motile structure of bacteria, archaea and eukaryotes • Golgi apparatus - site of protein glycosylation in the endomembrane system • Lipid bilayer - fundamental organizational structure of cell membranes • Lysosome - break down cellular waste products and debris into simple compounds (only found in animal cells) • Membrane lipid and protein barrier • Mitochondrion - major energy-producing organelle by releasing it in the form of ATP • • • • Nucleus - holds most of the DNA of eukaryotic cells and controls all cellular activities Organelle - term used for major subcellular structures Ribosome - RNA and protein complex required for protein synthesis in cells Vesicle - small membrane-bounded spheres inside cells
Electron micrograph.

Cell biology

104

Techniques used to study cells
Cells may be observed under the microscope. This includes the Optical Microscope, Transmission Electron Microscope, Scanning Electron Microscope, Fluorescence Microscope, and by Confocal Microscopy. Several different techniques exist to study cells are • Cell culture is the basic technique of growing cells in a laboratory independent of an organism. • Immunostaining, also known as immunohistochemistry, is a specialized histological method used to localize proteins in cells or tissue slices. Unlike regular histology, which uses stains to identify cells, cellular components or protein classes, immunostaining requires the reaction of an antibody directed against the protein of interest within the tissue or cell. Through the use of proper controls and published protocols (need to add reference links here), specificity of the antibody-antigen reaction can be achieved. Once this complex is formed, it is identified via either a "tag" attached directly to the antibody, or added in an additional technical step. Commonly used "tags" include fluorophores or enzymes. In the case of the former, detection of the location of the "immuno-stained" protein occurs via fluorescence microscopy. With an enzymatic tag, such as horse radish peroxidase, a chemical reaction is carried out that results in a dark color in the location of the protein of interest. This darkened pattern is then detected using light microscopy. • • • • • • Computational genomics is used to find patterns in genomic information [2] DNA microarrays identify changes in transcript levels between different experimental conditions. Gene knockdown mutates a selected gene. In situ hybridization shows which cells are expressing a particular RNA transcript. PCR can be used to determine how many copies of a gene are present in a cell. Transfection introduces a new gene into a cell, usually an expression construct

Purification of cells and their parts Purification may be performed using the following methods: • Cell fractionation • Release of cellular organelles by disruption of cells. • Separation of different organelles by centrifugation. • Flow cytometry • Immunoprecipitation • Proteins extracted from cell membranes by detergents and salts or other kinds of chemicals.

Cell biology

105

References
• Cell and Molecular Biology by Karp 5th Ed., ISBN 0-471-46580-1 •  This article incorporates public domain material from the NCBI document "Science Primer" [3].
[1] Open Content Flexbook- Cellular Structure & functions(for ribosomes and Golgi body info) (http:/ / www. ck12. org/ flexbook/ chapter/ 8485) [2] Cristianini, N. and Hahn, M. Introduction to Computational Genomics (http:/ / www. computational-genomics. net/ ), Cambridge University Press, 2006. (ISBN 9780521671910 | ISBN 0-521-67191-4) [3] http:/ / www. ncbi. nlm. nih. gov/ About/ primer/ index. html

• Aging Cell (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1474-9726)

External links
• Cell Centered Database (http://ccdb.ucsd.edu/sand/main?event=showMPByType&typeid=0&start=1&pl=y) • Cell Biology (http://www.dmoz.org/Science/Biology/Cell_Biology/) at the Open Directory Project

Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment.[1] The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells.[2] It basically protects the cell from outside forces. It consists of the lipid bilayer with embedded proteins. Cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity and cell signaling and serve as the attachment surface for several extracellular structures, including the cell wall, glycocalyx, and intracellular cytoskeleton. Cell membranes can be artificially reassembled.[3][4][5]

Function
The cell membrane surrounds the Illustration of a Eukaryotic cell membrane cytoplasm of a cell and, in animal cells, physically separates the intracellular components from the extracellular environment. Fungi, bacteria and plants also have the cell wall which provides a mechanical support for the cell and precludes the passage of larger molecules. The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell, and in attaching to the extracellular matrix and other cells to help group cells together to form tissues.

Cell membrane The membrane is selectively permeable and able to regulate what enters and exits the cell, thus facilitating the transport of materials needed for survival. The movement of substances across the membrane can be either "passive", occurring without the input of cellular energy, or active, requiring the cell to expend energy in transporting it. The membrane also maintains the cell potential. The cell membrane thus works as a selective filter that allows only certain things to come inside or go outside the cell. Cell employs a number of transport mechanisms that involve biological membranes: 1. Passive diffusion and osmosis: Some substances (small molecules, ions) such as carbon dioxide (CO2), oxygen (O2), and water, can move across the plasma membrane by diffusion, which is a passive transport process. Because the membrane acts as a barrier for certain molecules and ions, they can occur in different concentrations on the two sides of the membrane. Such a concentration gradient across a semipermeable membrane sets up an osmotic flow for the water. 2. Transmembrane protein channels and transporters: Nutrients, such as sugars or amino acids, must enter the cell, and certain products of metabolism must leave the cell. Such molecules are pumped across the membrane by transmembrane transporters or diffuse through protein channels. These proteins, also called permeases, are usually quite specific, recognizing and transporting only a limited group of chemical substances, often even only a single substance. 3. Endocytosis: Endocytosis is the process in which cells absorb molecules by engulfing them. The plasma membrane creates a small deformation inward, called an invagination, in which the substance to be transported is captured. The deformation then pinches off from the membrane on the inside of the cell, creating a vesicle containing the captured substance. Endocytosis is a pathway for internalizing solid particles (cell eating or phagocytosis), small molecules and ions (cell drinking or pinocytosis), and macromolecules. Endocytosis requires energy and is thus a form of active transport. 4. Exocytosis: Just as material can be brought into the cell by invagination and formation of a vesicle, the membrane of a vesicle can be fused with the plasma membrane, extruding its contents to the surrounding medium. This is the process of exocytosis. Exocytosis occurs in various cells to remove undigested residues of substances brought in by endocytosis, to secrete substances such as hormones and enzymes, and to transport a substance completely across a cellular barrier. In the process of exocytosis, the undigested waste-containing food vacuole or the secretory vesicle budded from Golgi apparatus, is first moved by cytoskeleton from the interior of the cell to the surface. The vesicle membrane comes in contact with the plasma membrane. The lipid molecules of the two bilayers rearrange themselves and the two membranes are, thus, fused. A passage is formed in the fused membrane and the vesicles discharges its contents outside the cell.

106

Prokaryotes
Gram-negative bacteria have a plasma membrane and an outer membrane separated by a periplasmic space. Other prokaryotic species have only a plasma membrane. Prokaryotic cells are also surrounded by a cell wall composed of peptidoglycan (amino acid and sugar). Some eukaryotic cells also have cells walls, but none that are made of peptidoglycan.

Structure
Fluid mosaic model
According to the fluid mosaic model of S.J. Singer and G.L. Nicolson (1972), which replaced the earlier model of Davson and Danielli, biological membranes can be considered as a two-dimensional liquid in which lipid and protein molecules diffuse more or less easily.[6] Although the lipid bilayers that form the basis of the membranes do indeed form two-dimensional liquids by themselves, the plasma membrane also contains a large quantity of proteins, which provide more structure. Examples of such structures are protein-protein complexes, pickets and fences formed by the

Cell membrane actin-based cytoskeleton, and potentially lipid rafts.

107

Lipid bilayer
Lipid bilayers form through the process of self-assembly. The cell membrane consists primarily of a thin layer of amphipathic phospholipids which spontaneously arrange so that the hydrophobic "tail" regions are isolated from the surrounding polar fluid, causing the more hydrophilic "head" regions to associate with the intracellular (cytosolic) and extracellular faces of the resulting bilayer. This forms a continuous, spherical lipid bilayer. Forces such as van der Waals, electrostatic, hydrogen bonds, and noncovalent interactions, are all forces that contribute to the formation of the lipid bilayer. Overall, hydrophobic interactions are the major driving force in the formation of lipid bilayers.

Diagram of the arrangement of amphipathic lipid molecules to form a lipid bilayer. The yellow polar head groups separate the grey hydrophobic tails from the aqueous cytosolic and extracellular environments.

Lipid bilayers are generally impermeable to ions and polar molecules. The arrangement of hydrophilic heads and hydrophobic tails of the lipid bilayer prevent polar solutes (e.g. amino acids, nucleic acids, carbohydrates, proteins, and ions) from diffusing across the membrane, but generally allows for the passive diffusion of hydrophobic molecules. This affords the cell the ability to control the movement of these substances via transmembrane protein complexes such as pores, channels and gates. Flippases and scramblases concentrate phosphatidyl serine, which carries a negative charge, on the inner membrane. Along with NANA, this creates an extra barrier to charged moieties moving through the membrane. Membranes serve diverse functions in eukaryotic and prokaryotic cells. One important role is to regulate the movement of materials into and out of cells. The phospholipid bilayer structure (fluid mosaic model) with specific membrane proteins accounts for the selective permeability of the membrane and passive and active transport mechanisms. In addition, membranes in prokaryotes and in the mitochondria and chloroplasts of eukaryotes facilitate the synthesis of ATP through chemiosmosis.

Membrane polarity
The apical membrane of a polarized cell is the surface of the plasma membrane that faces the lumen. This is particularly evident in epithelial and endothelial cells, but also describes other polarized cells, such as neurons. The basolateral membrane of a polarized cell is the surface of the plasma membrane that forms its basal and lateral surfaces. It faces outwards, towards the interstitium, and away from the lumen. Basolateral membrane is a compound phrase referring to the terms "basal (base) membrane" and "lateral (side) membrane", which, especially in epithelial cells, are identical in composition and activity.

Alpha intercalated cell

Cell membrane Proteins (such as ion channels and pumps) are free to move from the basal to the lateral surface of the cell or vice versa in accordance with the fluid mosaic model. Tight junctions join epithelial cells near their apical surface to prevent the migration of proteins from the basolateral membrane to the apical membrane. The basal and lateral surfaces thus remain roughly equivalent to one another, yet distinct from the apical surface.

108

Membrane structures
Cell membrane can form different types of "supramembrane" structures such as caveola, postsynaptic density, podosome, invadopodium, focal adhesion, and different types of cell junctions. These structures are usually responsible for cell adhesion, communication, endocytosis and exocytosis. They can be visualized by electron microscopy or fluorescence microscopy. They are composed of specific proteins, such as integrins and cadherins.

Cytoskeleton
The cytoskeleton is found underlying the cell membrane in the cytoplasm and provides a scaffolding for membrane proteins to anchor to, as well as forming organelles that extend from the cell. Indeed, cytoskeletal elements interact extensively and intimately with the cell membrane.[7] Anchoring proteins restricts them to a particular cell surface — for example, the apical surface of epithelial cells that line the vertebrate gut — and limits how far they may diffuse within the bilayer. The cytoskeleton is able to form appendage-like organelles, such as cilia, which are microtubule-based extensions covered by the cell membrane, and filopodia, which are actin-based extensions. These extensions are ensheathed in membrane and project from the surface of the cell in order to sense the external environment and/or make contact with the substrate or other cells. The apical surfaces of epithelial cells are dense with actin-based finger-like projections known as microvilli, which increase cell surface area and thereby increase the absorption rate of nutrients. Localized decoupling of the cytoskeleton and cell membrane results in formation of a bleb.

Composition
Cell membranes contain a variety of biological molecules, notably lipids and proteins. Material is incorporated into the membrane, or deleted from it, by a variety of mechanisms: • Fusion of intracellular vesicles with the membrane (exocytosis) not only excretes the contents of the vesicle but also incorporates the vesicle membrane's components into the cell membrane. The membrane may form blebs around extracellular material that pinch off to become vesicles (endocytosis). • If a membrane is continuous with a tubular structure made of membrane material, then material from the tube can be drawn into the membrane continuously. • Although the concentration of membrane components in the aqueous phase is low (stable membrane components have low solubility in water), there is an exchange of molecules between the lipid and aqueous phases.

Cell membrane

109

Lipids
The cell membrane consists of three classes of amphipathic lipids: phospholipids, glycolipids, and cholesterols. The amount of each depends upon the type of cell, but in the majority of cases phospholipids are the most abundant.[8] In RBC studies, 30% of the plasma membrane is lipid. The fatty chains in phospholipids and glycolipids usually contain an even number of carbon atoms, typically between 16 and 20. The 16- and 18-carbon fatty acids are the most common. Fatty acids may be saturated or unsaturated, with the configuration of the double bonds nearly always "cis". The length and the degree of unsaturation of fatty acid chains have a profound effect on membrane fluidity[9] as unsaturated lipids create a kink, preventing the fatty Examples of the major membrane phospholipids and glycolipids: phosphatidylcholine acids from packing together as tightly, (PtdCho), phosphatidylethanolamine (PtdEtn), phosphatidylinositol (PtdIns), thus decreasing the melting temperature phosphatidylserine (PtdSer). (increasing the fluidity) of the membrane. The ability of some organisms to regulate the fluidity of their cell membranes by altering lipid composition is called homeoviscous adaptation. The entire membrane is held together via non-covalent interaction of hydrophobic tails, however the structure is quite fluid and not fixed rigidly in place. Under physiological conditions phospholipid molecules in the cell membrane are in the liquid crystalline state. It means the lipid molecules are free to diffuse and exhibit rapid lateral diffusion along the layer in which they are present. However, the exchange of phospholipid molecules between intracellular and extracellular leaflets of the bilayer is a very slow process. Lipid rafts and caveolae are examples of cholesterol-enriched microdomains in the cell membrane. In animal cells cholesterol is normally found dispersed in varying degrees throughout cell membranes, in the irregular spaces between the hydrophobic tails of the membrane lipids, where it confers a stiffening and strengthening effect on the membrane.[2]

Phospholipids forming lipid vesicles
Lipid vesicles or liposomes are circular pockets that are enclosed by a lipid bilayer. These structures are used in laboratories to study the effects of chemicals in cells by delivering these chemicals directly to the cell, as well as getting more insight into cell membrane permeability. Lipid vesicles and liposomes are formed by first suspending a lipid in an aqueous solution then agitating the mixture through sonication, resulting in a vesicle. By measuring the rate of efflux from that of the inside of the vesicle to the ambient solution, allows researcher to better understand membrane permeability. Vesicles can be formed with molecules and ions inside the vesicle by forming the vesicle with the desired molecule or ion present in the solution. Proteins can also be embedded into the membrane through solubilizing the desired proteins in the presence of detergents and attaching them to the phospholipids in which the

Cell membrane liposome is formed. These provide researchers with a tool to examine various membrane protein functions.

110

Carbohydrates
Plasma membranes also contain carbohydrates, predominantly glycoproteins, but with some glycolipids (cerebrosides and gangliosides). For the most part, no glycosylation occurs on membranes within the cell; rather generally glycosylation occurs on the extracellular surface of the plasma membrane. The glycocalyx is an important feature in all cells, especially epithelia with microvilli. Recent data suggest the glycocalyx participates in cell adhesion, lymphocyte homing, and many others. The penultimate sugar is galactose and the terminal sugar is sialic acid, as the sugar backbone is modified in the golgi apparatus. Sialic acid carries a negative charge, providing an external barrier to charged particles.

Proteins
Type Integral proteins or transmembrane proteins Description Span the membrane and have a hydrophilic cytosolic domain, which interacts with internal molecules, a hydrophobic membrane-spanning domain that anchors it within the cell membrane, and a hydrophilic extracellular domain that interacts with external molecules. The hydrophobic domain consists of one, multiple, or a combination of α-helices and β sheet protein motifs. Covalently bound to single or multiple lipid molecules; hydrophobically insert into the cell membrane and anchor the protein. The protein itself is not in contact with the membrane. Attached to integral membrane proteins, or associated with peripheral regions of the lipid bilayer. These proteins tend to have only temporary interactions with biological membranes, and, once reacted the molecule, dissociates to carry on its work in the cytoplasm. Examples Ion channels, proton pumps, G protein-coupled receptor

Lipid anchored proteins Peripheral proteins

G proteins

Some enzymes, some hormones

The cell membrane has large content of proteins, typically around 50% of membrane volume[9] These proteins are important for cell because they are responsible for various biological activities. Approximately a third of the genes in yeast code specifically for them, and this number is even higher in multicellular organisms.[8] The cell membrane, being exposed to the outside environment, is an important site of cell-cell communication. As such, a large variety of protein receptors and identification proteins, such as antigens, are present on the surface of the membrane. Functions of membrane proteins can also include cell-cell contact, surface recognition, cytoskeleton contact, signaling, enzymatic activity, or transporting substances across the membrane. Most membrane proteins must be inserted in some way into the membrane. For this to occur, an N-terminus "signal sequence" of amino acids directs proteins to the endoplasmic reticulum, which inserts the proteins into a lipid bilayer. Once inserted, the proteins are then transported to their final destination in vesicles, where the vesicle fuses with the target membrane.

Variation
The cell membrane has different lipid and protein compositions in distinct types of cells and may have therefore specific names for certain cell types: • • • • Sarcolemma in myocytes Oolemma in oocytes Axolemma in neuronal processes - axons Historically, the plasma membrane was also referred to as the plasmalemma

Cell membrane

111

Permeability
The permeability of a membrane is the rate of passive diffusion of molecules through the membrane. These molecules are known as permeant molecules. Permeability depends mainly on the electric charge and polarity of the molecule and to a lesser extent the molar mass of the molecule. Due to the cell membrane's hydrophobic nature, small electrically neutral molecules pass through the membrane easier than charged, large ones. The inability of charged molecules to pass through the cell membrane results in pH partition of substances throughout the fluid compartments of the body.

References
[1] Kimball's Biology Pages (http:/ / users. rcn. com/ jkimball. ma. ultranet/ BiologyPages/ C/ CellMembranes. html), Cell Membranes [2] Alberts B, Johnson A, Lewis J, et al. (2002). Molecular Biology of the Cell (http:/ / www. ncbi. nlm. nih. gov/ books/ bv. fcgi?rid=mboc4. section. 1864) (4th ed.). New York: Garland Science. ISBN 0-8153-3218-1. . [3] Budin, Itay; Devaraj, Neal K. (December 29, 2011). "Membrane Assembly Driven by a Biomimetic Coupling Reaction" (http:/ / pubs. acs. org/ doi/ abs/ 10. 1021/ ja2076873). Journal of the American Chemical Society 134 (2): 751–753. doi:10.1021/ja2076873. . Retrieved February 18, 2012. [4] Staff (January 25, 2012). "Chemists Synthesize Artificial Cell Membrane" (http:/ / www. sciencedaily. com/ releases/ 2012/ 01/ 120125132822. htm). ScienceDaily. . Retrieved February 18, 2012. [5] Staff (January 26, 2012). "Chemists create artificial cell membrane" (http:/ / www. kurzweilai. net/ chemists-create-artificial-cell-membrane). kurzweilai.net. . Retrieved February 18, 2012. [6] Singer SJ, Nicolson GL (Feb 1972). "The fluid mosaic model of the structure of cell membranes" (http:/ / www. sciencemag. org/ cgi/ content/ abstract/ 175/ 4023/ 720). Science 175 (4023): 720–31. doi:10.1126/science.175.4023.720. PMID 4333397. . [7] Doherty GJ and McMahon HT (2008). "Mediation, Modulation and Consequences of Membrane-Cytoskeleton Interactions" (http:/ / arjournals. annualreviews. org/ doi/ abs/ 10. 1146/ annurev. biophys. 37. 032807. 125912). Annual Review of Biophysics 37: 65–95. doi:10.1146/annurev.biophys.37.032807.125912. PMID 18573073. . [8] Lodish H, Berk A, Zipursky LS, et al. (2004). Molecular Cell Biology (4th ed.). New York: Scientific American Books. ISBN 0-7167-3136-3. [9] Jesse Gray, Shana Groeschler, Tony Le, Zara Gonzalez (2002). "Membrane Structure" (http:/ / www. bio. davidson. edu/ people/ macampbell/ 111/ memb-swf/ membranes. swf) (SWF). Davidson College. . Retrieved 2007-01-11.

External links
• Lipids, Membranes and Vesicle Trafficking - The Virtual Library of Biochemistry and Cell Biology (http:// www.biochemweb.org/lipids_membranes.shtml) • Cell membrane protein extraction protocol (http://www.westernblotting.org/protocol membrane extraction. htm) • Membrane homeostasis, tension regulation, mechanosensitive membrane exchange and membrane traffic (http:// www.phys.unsw.edu.au/~jw/tension.html) • 3D structures of proteins associated with plasma membrane of eukaryotic cells (http://opm.phar.umich.edu/ localization.php?localization=Eukaryotic plasma membrane) • Lipid composition and proteins of some eukariotic membranes (http://opm.phar.umich.edu/atlas. php?membrane=Eukaryotic plasma membrane) • (http://www.etap.org/demo/biology1/instruction3tutor.html)

Cell nucleus

112

Cell nucleus
In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel) is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's nuclear genome. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression — the nucleus is, therefore, the control center HeLa cells stained for the cell nucleus DNA with the Blue Hoechst dye. The central and of the cell. The main structures making rightmost cell are in interphase, thus their entire nuclei are labeled. On the left, a cell is going through mitosis and its DNA has condensed ready for division. up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and unifies its contents from the cellular cytoplasm, and the nucleoskeleton (which includes nuclear lamina), a meshwork within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole. Because the nuclear membrane is impermeable to large molecules, nuclear pores are required to allow movement of molecules across the envelope. These pores cross both of the membranes, providing a Schematic of typical animal cell, showing subcellular components. Organelles: (1) channel that allows free movement of Nucleolus (2) Nucleus (3) Ribosomes (little dots) (4) Vesicle (5) Rough endoplasmic small molecules and ions. The reticulum (ER) (6) Golgi apparatus (7) Cytoskeleton (8) Smooth ER (9) Mitochondria movement of larger molecules such as (10) Vacuole (11) Cytosol (12) Lysosome (13) Centrioles within Centrosome proteins is carefully controlled, and requires active transport regulated by carrier proteins. Nuclear transport is crucial to cell function, as movement through the pores is required for both gene expression and chromosomal maintenance. The interior of the nucleus does not contain any membrane-bound subcompartments, its contents are not uniform, and a number of subnuclear bodies exist, made up of unique proteins, RNA molecules, and particular parts of the chromosomes. The best-known of these is the nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.

Cell nucleus

113

History
The nucleus was the first organelle to be discovered. What is most likely the oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek (1632 – 1723). He observed a "Lumen", the nucleus, in the red blood cells of salmon.[1] Unlike mammalian red blood cells, those of other vertebrates still Oldest known depiction of cells and their nuclei by Antonie van Leeuwenhoek, 1719. possess nuclei. The nucleus was also described by Franz Bauer in 1804[2] and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids under microscope when he observed an opaque area, which he called the areola or nucleus, in the cells of the flower's outer layer.[3] He did not suggest a potential function. In 1838, Matthias Schleiden proposed that the nucleus plays a role in generating cells, thus he introduced the name "Cytoblast" (cell builder). He believed that he had observed new cells assembling around "cytoblasts". Franz Meyen was a strong opponent of this view, having already described cells Drawing of a Chironomus salivary gland cell multiplying by division and believing that many published by Walther Flemming in 1882. The cells would have no nuclei. The idea that cells can nucleus contains Polytene chromosomes. be generated de novo, by the "cytoblast" or otherwise, contradicted work by Robert Remak (1852) and Rudolf Virchow (1855) who decisively propagated the new paradigm that cells are generated solely by cells ("Omnis cellula e cellula"). The function of the nucleus remained unclear.[4] Between 1877 and 1878, Oscar Hertwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus. This was the first time it was suggested that an individual develops from a (single) nucleated cell. This was in contradiction to Ernst Haeckel's theory that the complete phylogeny of a species would be repeated during embryonic development, including generation of the first nucleated cell from a "Monerula", a structureless mass of primordial mucus ("Urschleim"). Therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other animal groups, e.g., amphibians and molluscs. Eduard Strasburger produced the same results for plants (1884). This paved the way to assign the nucleus an important role in heredity. In 1873, August Weismann postulated the equivalence of the maternal and paternal germ cells for heredity. The function of the nucleus as carrier of genetic information became clear only later, after mitosis was discovered and the Mendelian rules were rediscovered at the beginning of the 20th century; the chromosome theory of heredity was developed.[4]

Cell nucleus

114

Structures
The nucleus is the largest cellular organelle in animals.[5] In mammalian cells, the average diameter of the nucleus is approximately 6 micrometers (μm), which occupies about 10% of the total cell volume.[6] The viscous liquid within it is called nucleoplasm, and is similar in composition to the cytosol found outside the nucleus.[7] It appears as a dense, roughly spherical organelle.

Nuclear envelope and pores

The eukaryotic cell nucleus. Visible in this diagram are the ribosome-studded double membranes of the nuclear envelope, the DNA (complexed as chromatin), and the nucleolus. Within the cell nucleus is a viscous liquid called nucleoplasm, similar to the cytoplasm found outside the nucleus.

A cross section of a nuclear pore on the surface of the nuclear envelope (1). Other diagram labels show (2) the outer ring, (3) spokes, (4) basket, and (5) filaments.

The outer envelope, otherwise known as nuclear membrane, consists of two cellular membranes, an inner and an outer membrane, arranged parallel to one another and separated by 10 to 50 nanometers (nm). The nuclear envelope completely encloses the nucleus and separates the cell's genetic material from the surrounding cytoplasm, serving as a barrier to prevent macromolecules from diffusing freely between the nucleoplasm and the cytoplasm.[8] The outer nuclear membrane is continuous with the membrane of the rough endoplasmic reticulum (RER), and is similarly studded with ribosomes.[8] The space between the membranes is called the perinuclear space and is continuous with the RER lumen. Nuclear pores, which provide aqueous channels through the envelope, are composed of multiple proteins, collectively referred to as nucleoporins. The pores are about 125 million daltons in molecular weight and consist of around 50 (in yeast) to 100 proteins (in vertebrates).[5] The pores are 100 nm in total diameter; however, the gap through which molecules freely diffuse is only about 9 nm wide, due to the presence of regulatory systems within the center of the pore. This size allows the not-free passage of small water-soluble molecules while preventing larger molecules, such as nucleic acids and larger proteins, from inappropriately entering or exiting the nucleus. These large molecules must be actively transported into the nucleus instead. The nucleus of a typical mammalian cell will have about 3000 to 4000 pores throughout its envelope,[9] each of which contains a donut-shaped, eightfold-symmetric ring-shaped structure at a position where the inner and outer membranes fuse.[10] Attached to the ring is a structure called the nuclear basket that extends into the nucleoplasm, and a series of filamentous extensions that reach into the cytoplasm. Both structures serve to mediate binding to nuclear transport proteins.[5] Most proteins, ribosomal subunits, and some DNAs are transported through the pore complexes in a process mediated by a family of transport factors known as karyopherins. Those karyopherins that mediate movement into

Cell nucleus the nucleus are also called importins, whereas those that mediate movement out of the nucleus are called exportins. Most karyopherins interact directly with their cargo, although some use adaptor proteins.[11] Steroid hormones such as cortisol and aldosterone, as well as other small lipid-soluble molecules involved in intercellular signaling, can diffuse through the cell membrane and into the cytoplasm, where they bind nuclear receptor proteins that are trafficked into the nucleus. There they serve as transcription factors when bound to their ligand; in the absence of ligand, many such receptors function as histone deacetylases that repress gene expression.[5]

115

Nuclear lamina
In animal cells, two networks of intermediate filaments provide the nucleus with mechanical support: The nuclear lamina forms an organized meshwork on the internal face of the envelope, while less organized support is provided on the cytosolic face of the envelope. Both systems provide structural support for the nuclear envelope and anchoring sites for chromosomes and nuclear pores.[6] The nuclear lamina is composed mostly of lamin proteins. Like all proteins, lamins are synthesized in the cytoplasm and later transported into the nucleus interior, where they are assembled before being incorporated into the existing network of nuclear lamina.[12][13] Lamins found on the cytosolic face of the membrane, such as emerin and nesprin, bind to the cytoskeleton to provide structural support. Lamins are also found inside the nucleoplasm where they form another regular structure, known as the nucleoplasmic veil,[14] that is visible using fluorescence microscopy. The actual function of the veil is not clear, although it is excluded from the nucleolus and is present during interphase.[15] Lamin structures that make up the veil, such as LEM3, bind chromatin and disrupting their structure inhibits transcription of protein-coding genes.[16] Like the components of other intermediate filaments, the lamin monomer contains an alpha-helical domain used by two monomers to coil around each other, forming a dimer structure called a coiled coil. Two of these dimer structures then join side by side, in an antiparallel arrangement, to form a tetramer called a protofilament. Eight of these protofilaments form a lateral arrangement that is twisted to form a ropelike filament. These filaments can be assembled or disassembled in a dynamic manner, meaning that changes in the length of the filament depend on the competing rates of filament addition and removal.[6] Mutations in lamin genes leading to defects in filament assembly are known as laminopathies. The most notable laminopathy is the family of diseases known as progeria, which causes the appearance of premature aging in its sufferers. The exact mechanism by which the associated biochemical changes give rise to the aged phenotype is not well understood.[17]

Cell nucleus

116

Chromosomes
The cell nucleus contains the majority of the cell's genetic material in the form of multiple linear DNA molecules organized into structures called chromosomes. Each human cell contains 2m of DNA. During most of the cell cycle these are organized in a DNA-protein complex known as chromatin, and during cell division the chromatin can be seen to form the well-defined chromosomes familiar from a karyotype. A small fraction of the cell's genes are located instead in the mitochondria. There are two types of chromatin. Euchromatin is the less compact DNA form, and contains genes that are frequently expressed by the cell.[18] The other type, heterochromatin, is the more compact form, and contains DNA that are infrequently transcribed. This structure is further categorized into facultative heterochromatin, A mouse fibroblast nucleus in which DNA is stained blue. The distinct chromosome territories of consisting of genes that are organized as heterochromatin only in chromosome 2 (red) and chromosome 9 (green) are certain cell types or at certain stages of development, and stained with fluorescent in situ hybridization. constitutive heterochromatin that consists of chromosome structural components such as telomeres and centromeres.[19] During interphase the chromatin organizes itself into discrete individual patches,[20] called chromosome territories.[21] Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.[22] Antibodies to certain types of chromatin organization, in particular, nucleosomes, have been associated with a number of autoimmune diseases, such as systemic lupus erythematosus.[23] These are known as anti-nuclear antibodies (ANA) and have also been observed in concert with multiple sclerosis as part of general immune system dysfunction.[24] As in the case of progeria, the role played by the antibodies in inducing the symptoms of autoimmune diseases is not obvious.

Nucleolus
The nucleolus is a discrete densely stained structure found in the nucleus. It is not surrounded by a membrane, and is sometimes called a suborganelle. It forms around tandem repeats of rDNA, DNA coding for ribosomal RNA (rRNA). These regions are called nucleolar organizer regions (NOR). The main roles of the nucleolus are to synthesize rRNA and assemble ribosomes. The structural cohesion of the nucleolus depends on its activity, as ribosomal assembly in the nucleolus results in the transient association of nucleolar components, facilitating further ribosomal assembly, and hence further association. This model is supported by observations that inactivation of rDNA results in intermingling of nucleolar structures.[25]
An electron micrograph of a cell nucleus, showing the darkly stained nucleolus.

In the first step of ribosome assembly, a protein called RNA polymerase I transcribes rDNA, which forms a large pre-rRNA precursor. This is cleaved into the subunits 5.8S, 18S, and 28S

Cell nucleus rRNA.[26] The transcription, post-transcriptional processing, and assembly of rRNA occurs in the nucleolus, aided by small nucleolar RNA (snoRNA) molecules, some of which are derived from spliced introns from messenger RNAs encoding genes related to ribosomal function. The assembled ribosomal subunits are the largest structures passed through the nuclear pores.[5] When observed under the electron microscope, the nucleolus can be seen to consist of three distinguishable regions: the innermost fibrillar centers (FCs), surrounded by the dense fibrillar component (DFC), which in turn is bordered by the granular component (GC). Transcription of the rDNA occurs either in the FC or at the FC-DFC boundary, and, therefore, when rDNA transcription in the cell is increased, more FCs are detected. Most of the cleavage and modification of rRNAs occurs in the DFC, while the latter steps involving protein assembly onto the ribosomal subunits occur in the GC.[21]

117

Other subnuclear bodies
Structure name Structure diameter Cajal bodies PIKA PML bodies Paraspeckles Speckles 0.2–2.0 µm 5 µm 0.2–1.0 µm 0.2–1.0 µm 20–25 nm
[27] [28] [29] [30] [28]

|+ Subnuclear structure sizes Besides the nucleolus, the nucleus contains a number of other non-membrane-delineated bodies. These include Cajal bodies, Gemini of coiled bodies, polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, paraspeckles, and splicing speckles. Although little is known about a number of these domains, they are significant in that they show that the nucleoplasm is not uniform mixture, but rather contains organized functional subdomains.[29] Other subnuclear structures appear as part of abnormal disease processes. For example, the presence of small intranuclear rods has been reported in some cases of nemaline myopathy. This condition typically results from mutations in actin, and the rods themselves consist of mutant actin as well as other cytoskeletal proteins.[31] Cajal bodies and gems A nucleus typically contains between 1 and 10 compact structures called Cajal bodies or coiled bodies (CB), whose diameter measures between 0.2 µm and 2.0 µm depending on the cell type and species.[27] When seen under an electron microscope, they resemble balls of tangled thread[28] and are dense foci of distribution for the protein coilin.[32] CBs are involved in a number of different roles relating to RNA processing, specifically small nucleolar RNA (snoRNA) and small nuclear RNA (snRNA) maturation, and histone mRNA modification.[27] Similar to Cajal bodies are Gemini of coiled bodies, or gems, whose name is derived from the Gemini constellation in reference to their close "twin" relationship with CBs. Gems are similar in size and shape to CBs, and in fact are virtually indistinguishable under the microscope.[32] Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs), but do contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis,[33] though it has also been suggested from microscopy evidence that CBs and gems are different manifestations of the same structure.[32]

Cell nucleus RAFA and PTF domains RAFA domains, or polymorphic interphase karyosomal associations, were first described in microscopy studies in 1991. Their function was and remains unclear, though they were not thought to be associated with active DNA replication, transcription, or RNA processing.[34] They have been found to often associate with discrete domains defined by dense localization of the transcription factor PTF, which promotes transcription of snRNA.[35] PML bodies Promyelocytic leukaemia bodies (PML bodies) are spherical bodies found scattered throughout the nucleoplasm, measuring around 0.2–1.0 µm. They are known by a number of other names, including nuclear domain 10 (ND10), Kremer bodies, and PML oncogenic domains. They are often seen in the nucleus in association with Cajal bodies and cleavage bodies. It has been suggested that they play a role in regulating transcription.[29] Paraspeckles Discovered by Fox et al. in 2002, paraspeckles are irregularly shaped compartments in the nucleus' interchromatin space.[36] First documented in HeLa cells, where there are generally 10–30 per nucleus,[37] paraspeckles are now known to also exist in all human primary cells, transformed cell lines, and tissue sections.[38] Their name is derived from their distribution in the nucleus; the "para" is short for parallel and the "speckles" refers to the splicing speckles to which they are always in close proximity.[37] Paraspeckles are dynamic structures that are altered in response to changes in cellular metabolic activity. They are transcription dependent[36] and in the absence of RNA Pol II transcription, the paraspeckle disappears and all of its associated protein components (PSP1, p54nrb, PSP2, CFI(m)68, and PSF) form a crescent shaped perinucleolar cap in the nucleolus. This phenomenon is demonstrated during the cell cycle. In the cell cycle, paraspeckles are present during interphase and during all of mitosis except for telophase. During telophase, when the two daughter nuclei are formed, there is no RNA Pol II transcription so the protein components instead form a perinucleolar cap.[38] Splicing speckles Speckles are subnuclear structures that are enriched in pre-messenger RNA splicing factors and are located in the interchromatin regions of the nucleoplasm of mammalian cells. At the fluorescence-microscope level they appear as irregular, punctate structures, which vary in size and shape, and when examined by electron microscopy they are seen as clusters of interchromatin granules. Speckles are dynamic structures, and both their protein and RNA-protein components can cycle continuously between speckles and other nuclear locations, including active transcription sites. Studies on the composition, structure and behaviour of speckles have provided a model for understanding the functional compartmentalization of the nucleus and the organization of the gene-expression machinery.[39] Sometimes referred to as interchromatin granule clusters or as splicing-factor compartments, speckles are rich in splicing snRNPs[40][41] and other splicing proteins necessary for pre-mRNA processing.[42] Because of a cell's changing requirements, the composition and location of these bodies changes according to mRNA transcription and regulation via phosphorylation of specific proteins.[43]

118

Cell nucleus

119

Function
The main function of the cell nucleus is to control gene expression and mediate the replication of DNA during the cell cycle. The nucleus provides a site for genetic transcription that is segregated from the location of translation in the cytoplasm, allowing levels of gene regulation that are not available to prokaryotes.

Cell compartmentalization
The nuclear envelope allows the nucleus to control its contents, and separate them from the rest of the cytoplasm where necessary. This is important for controlling processes on either side of the nuclear membrane. In most cases where a cytoplasmic process needs to be restricted, a key participant is removed to the nucleus, where it interacts with transcription factors to downregulate the production of certain enzymes in the pathway. This regulatory mechanism occurs in the case of glycolysis, a cellular pathway for breaking down glucose to produce energy. Hexokinase is an enzyme responsible for the first the step of glycolysis, forming glucose-6-phosphate from glucose. At high concentrations of fructose-6-phosphate, a molecule made later from glucose-6-phosphate, a regulator protein removes hexokinase to the nucleus,[44] where it forms a transcriptional repressor complex with nuclear proteins to reduce the expression of genes involved in glycolysis.[45] In order to control which genes are being transcribed, the cell separates some transcription factor proteins responsible for regulating gene expression from physical access to the DNA until they are activated by other signaling pathways. This prevents even low levels of inappropriate gene expression. For example, in the case of NF-κB-controlled genes, which are involved in most inflammatory responses, transcription is induced in response to a signal pathway such as that initiated by the signaling molecule TNF-α, binds to a cell membrane receptor, resulting in the recruitment of signalling proteins, and eventually activating the transcription factor NF-κB. A nuclear localisation signal on the NF-κB protein allows it to be transported through the nuclear pore and into the nucleus, where it stimulates the transcription of the target genes.[6] The compartmentalization allows the cell to prevent translation of unspliced mRNA.[46] Eukaryotic mRNA contains introns that must be removed before being translated to produce functional proteins. The splicing is done inside the nucleus before the mRNA can be accessed by ribosomes for translation. Without the nucleus, ribosomes would translate newly transcribed (unprocessed) mRNA, resulting in misformed and nonfunctional proteins.

Cell nucleus

120

Gene expression
Gene expression first involves transcription, in which DNA is used as a template to produce RNA. In the case of genes encoding proteins, that RNA produced from this process is messenger RNA (mRNA), which then needs to be translated by ribosomes to form a protein. As ribosomes are located outside the nucleus, mRNA produced needs to be exported.[47] Since the nucleus is the site of transcription, it also contains a variety of proteins that either directly mediate transcription or are involved in regulating the process. These proteins include helicases, which unwind the double-stranded DNA molecule to facilitate access to it, RNA polymerases, which synthesize the growing RNA molecule, topoisomerases, which change the amount of supercoiling in DNA, helping it wind and unwind, as well as a large variety of transcription factors that regulate expression.[48]
A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. "Begin" indicates the 5' end of the DNA, where new RNA synthesis begins; "end" indicates the 3' end, where the primary transcripts are almost complete.

Processing of pre-mRNA

Newly synthesized mRNA molecules are known as primary transcripts or pre-mRNA. They must undergo post-transcriptional modification in the nucleus before being exported to the cytoplasm; mRNA that appears in the cytoplasm without these modifications is degraded rather than used for protein translation. The three main modifications are 5' capping, 3' polyadenylation, and RNA splicing. While in the nucleus, pre-mRNA is associated with a variety of proteins in complexes known as heterogeneous ribonucleoprotein particles (hnRNPs). Addition of the 5' cap occurs co-transcriptionally and is the first step in post-transcriptional modification. The 3' poly-adenine tail is only added after transcription is complete. RNA splicing, carried out by a complex called the spliceosome, is the process by which introns, or regions of DNA that do not code for protein, are removed from the pre-mRNA and the remaining exons connected to re-form a single continuous molecule. This process normally occurs after 5' capping and 3' polyadenylation but can begin before synthesis is complete in transcripts with many exons.[5] Many pre-mRNAs, including those encoding antibodies, can be spliced in multiple ways to produce different mature mRNAs that encode different protein sequences. This process is known as alternative splicing, and allows production of a large variety of proteins from a limited amount of DNA.

Cell nucleus

121

Dynamics and regulation
Nuclear transport
The entry and exit of large molecules from the nucleus is tightly controlled by the nuclear pore complexes. Although small molecules can enter the nucleus without regulation,[49] macromolecules such as RNA and proteins require association karyopherins called importins to enter the nucleus and exportins to exit. "Cargo" proteins that must be translocated from the cytoplasm to the nucleus contain short amino acid sequences known as nuclear localization signals, which are bound Macromolecules, such as RNA and proteins, are actively transported across the nuclear by importins, while those transported membrane in a process called the Ran-GTP nuclear transport cycle. from the nucleus to the cytoplasm carry nuclear export signals bound by exportins. The ability of importins and exportins to transport their cargo is regulated by GTPases, enzymes that hydrolyze the molecule guanosine triphosphate to release energy. The key GTPase in nuclear transport is Ran, which can bind either GTP or GDP (guanosine diphosphate), depending on whether it is located in the nucleus or the cytoplasm. Whereas importins depend on RanGTP to dissociate from their cargo, exportins require RanGTP in order to bind to their cargo.[11] Nuclear import depends on the importin binding its cargo in the cytoplasm and carrying it through the nuclear pore into the nucleus. Inside the nucleus, RanGTP acts to separate the cargo from the importin, allowing the importin to exit the nucleus and be reused. Nuclear export is similar, as the exportin binds the cargo inside the nucleus in a process facilitated by RanGTP, exits through the nuclear pore, and separates from its cargo in the cytoplasm. Specialized export proteins exist for translocation of mature mRNA and tRNA to the cytoplasm after post-transcriptional modification is complete. This quality-control mechanism is important due to these molecules' central role in protein translation; mis-expression of a protein due to incomplete excision of exons or mis-incorporation of amino acids could have negative consequences for the cell; thus, incompletely modified RNA that reaches the cytoplasm is degraded rather than used in translation.[5]

Cell nucleus

122

Assembly and disassembly
During its lifetime, a nucleus may be broken down, either in the process of cell division or as a consequence of apoptosis, a regulated form of cell death. During these events, the structural components of the nucleus — the envelope and lamina — can be systematically degraded. In most cells, the disassembly of the nuclear envelope marks the end of the prophase of mitosis. However, this disassembly of the nucleus is not a universal feature of mitosis and does not occur in all cells. Some unicellular eukaryotes (e.g., yeasts) undergo so-called closed mitosis, in which the nuclear envelope remains intact. In closed mitosis, the daughter chromosomes migrate to opposite poles of the nucleus, which then divides in two. The cells of higher eukaryotes, however, usually undergo open mitosis, which is characterized by breakdown of the nuclear envelope. The daughter chromosomes then migrate to opposite poles of the mitotic spindle, and new nuclei reassemble around them

An image of a newt lung cell stained with fluorescent dyes during metaphase. The mitotic spindle can be seen, stained green, attached to the two sets of chromosomes, stained light blue. All chromosomes but one are already at the metaphase plate.

At a certain point during the cell cycle in open mitosis, the cell divides to form two cells. In order for this process to be possible, each of the new daughter cells must have a full set of genes, a process requiring replication of the chromosomes as well as segregation of the separate sets. This occurs by the replicated chromosomes, the sister chromatids, attaching to microtubules, which in turn are attached to different centrosomes. The sister chromatids can then be pulled to separate locations in the cell. In many cells, the centrosome is located in the cytoplasm, outside the nucleus; the microtubules would be unable to attach to the chromatids in the presence of the nuclear envelope.[50] Therefore the early stages in the cell cycle, beginning in prophase and until around prometaphase, the nuclear membrane is dismantled.[14] Likewise, during the same period, the nuclear lamina is also disassembled, a process regulated by phosphorylation of the lamins by protein kinases such as the CDC2 protein kinase.[51] Towards the end of the cell cycle, the nuclear membrane is reformed, and around the same time, the nuclear lamina are reassembled by dephosphorylating the lamins.[51] However, in dinoflagellates, the nuclear envelope remains intact, the centrosomes are located in the cytoplasm, and the microtubules come in contact with chromosomes, whose centromeric regions are incorporated into the nuclear envelope (the so-called closed mitosis with extranuclear spindle). In many other protists (e.g., ciliates, sporozoans) and fungi, the centrosomes are intranuclear, and their nuclear envelope also does not disassemle during cell division. Apoptosis is a controlled process in which the cell's structural components are destroyed, resulting in death of the cell. Changes associated with apoptosis directly affect the nucleus and its contents, for example, in the condensation of chromatin and the disintegration of the nuclear envelope and lamina. The destruction of the lamin networks is controlled by specialized apoptotic proteases called caspases, which cleave the lamin proteins and, thus, degrade the nucleus' structural integrity. Lamin cleavage is sometimes used as a laboratory indicator of caspase activity in assays for early apoptotic activity.[14] Cells that express mutant caspase-resistant lamins are deficient in nuclear changes related to apoptosis, suggesting that lamins play a role in initiating the events that lead to apoptotic degradation of the nucleus.[14] Inhibition of lamin assembly itself is an inducer of apoptosis.[52] The nuclear envelope acts as a barrier that prevents both DNA and RNA viruses from entering the nucleus. Some viruses require access to proteins inside the nucleus in order to replicate and/or assemble. DNA viruses, such as herpesvirus replicate and assemble in the cell nucleus, and exit by budding through the inner nuclear membrane. This

Cell nucleus process is accompanied by disassembly of the lamina on the nuclear face of the inner membrane.[14]

123

Anucleated and multinucleated cells
Although most cells have a single nucleus, some eukaryotic cell types have no nucleus, and others have many nuclei. This can be a normal process, as in the maturation of mammalian red blood cells, or a result of faulty cell division. Anucleated cells contain no nucleus and are, therefore, incapable of dividing to produce daughter cells. The best-known anucleated cell is the mammalian red blood cell, or erythrocyte, which also lacks other organelles such as mitochondria, and serves primarily as a transport vessel to ferry oxygen from the lungs to the body's tissues. Erythrocytes mature through erythropoiesis in the bone marrow, where they lose their nuclei, organelles, and ribosomes. The nucleus is expelled during the process of differentiation from an erythroblast to a reticulocyte, which is the immediate precursor of the mature erythrocyte.[53] The presence of mutagens may induce the release of some immature "micronucleated" erythrocytes into the bloodstream.[54][55] Anucleated cells can also arise from flawed cell division in which one daughter lacks a nucleus and the other has two nuclei.

Human red blood cells, like those of other mammals, lack nuclei. This occurs as a normal part of the cells' development.

Multinucleated cells contain multiple nuclei. Most acantharean species of protozoa[56] and some fungi in mycorrhizae[57] have naturally multinucleated cells. Other examples include the intestinal parasites in the genus Giardia, which have two nuclei per cell.[58] In humans, skeletal muscle cells, called myocytes and syncytium, become multinucleated during development; the resulting arrangement of nuclei near the periphery of the cells allows maximal intracellular space for myofibrils.[5] Multinucleated and binucleated cells can also be abnormal in humans; for example, cells arising from the fusion of monocytes and macrophages, known as giant multinucleated cells, sometimes accompany inflammation[59] and are also implicated in tumor formation.[60]

Evolution
As the major defining characteristic of the eukaryotic cell, the nucleus' evolutionary origin has been the subject of much speculation. Four major theories have been proposed to explain the existence of the nucleus, although none have yet earned widespread support.[61] The theory known as the "syntrophic model" proposes that a symbiotic relationship between the archaea and bacteria created the nucleus-containing eukaryotic cell. (Organisms of the Archaea and Bacteria domain have no cell nucleus.[62]) It is hypothesized that the symbiosis originated when ancient archaea, similar to modern methanogenic archaea, invaded and lived within bacteria similar to modern myxobacteria, eventually forming the early nucleus. This theory is analogous to the accepted theory for the origin of eukaryotic mitochondria and chloroplasts, which are thought to have developed from a similar endosymbiotic relationship between proto-eukaryotes and aerobic bacteria.[63] The archaeal origin of the nucleus is supported by observations that archaea and eukarya have similar genes for certain proteins, including histones. Observations that myxobacteria are motile, can form multicellular complexes, and possess kinases and G proteins similar to eukarya, support a bacterial origin for the eukaryotic cell.[64] A second model proposes that proto-eukaryotic cells evolved from bacteria without an endosymbiotic stage. This model is based on the existence of modern planctomycetes bacteria that possess a nuclear structure with primitive pores and other compartmentalized membrane structures.[65] A similar proposal states that a eukaryote-like cell, the chronocyte, evolved first and phagocytosed archaea and bacteria to generate the nucleus and the eukaryotic cell.[66]

Cell nucleus The most controversial model, known as viral eukaryogenesis, posits that the membrane-bound nucleus, along with other eukaryotic features, originated from the infection of a prokaryote by a virus. The suggestion is based on similarities between eukaryotes and viruses such as linear DNA strands, mRNA capping, and tight binding to proteins (analogizing histones to viral envelopes). One version of the proposal suggests that the nucleus evolved in concert with phagocytosis to form an early cellular "predator".[67] Another variant proposes that eukaryotes originated from early archaea infected by poxviruses, on the basis of observed similarity between the DNA polymerases in modern poxviruses and eukaryotes.[68][69] It has been suggested that the unresolved question of the evolution of sex could be related to the viral eukaryogenesis hypothesis.[70] A very recent proposal suggests that traditional variants of the endosymbiont theory are insufficiently powerful to explain the origin of the eukaryotic nucleus. This model, termed the exomembrane hypothesis, suggests that the nucleus instead originated from a single ancestral cell that evolved a second exterior cell membrane; the interior membrane enclosing the original cell then became the nuclear membrane and evolved increasingly elaborate pore structures for passage of internally synthesized cellular components such as ribosomal subunits.[71]

124

References
[1] Leeuwenhoek, A. van: Opera Omnia, seu Arcana Naturae ope exactissimorum Microscopiorum detecta, experimentis variis comprobata, Epistolis ad varios illustres viros. J. Arnold et Delphis, A. Beman, Lugdinum Batavorum 1719–1730. Cited after: Dieter Gerlach, Geschichte der Mikroskopie. Verlag Harry Deutsch, Frankfurt am Main, Germany, 2009. ISBN 978-3-8171-1781-9. [2] Harris, H (1999). The Birth of the Cell. New Haven: Yale University Press. ISBN 0-300-07384-4. [3] Brown, Robert (1866). "On the Organs and Mode of Fecundation of Orchidex and Asclepiadea". Miscellaneous Botanical Works I: 511–514. [4] Cremer, Thomas (1985). Von der Zellenlehre zur Chromosomentheorie. Berlin, Heidelberg, New York, Tokyo: Springer Verlag. ISBN 3-540-13987-7. Online Version here (http:/ / www. t-cremer. de/ main_de/ cremer/ personen/ info_T_Cremer. htm#book) [5] Lodish, H; Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Cell Biology (5th ed.). New York: WH Freeman. ISBN 0-7167-2672-6. [6] Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, ed. (2002). Molecular Biology of the Cell, Chapter 4, pages 191–234 (4th ed.). Garland Science. [7] Clegg JS (February 1984). "Properties and metabolism of the aqueous cytoplasm and its boundaries" (http:/ / ajpregu. physiology. org/ cgi/ pmidlookup?view=reprint& pmid=6364846). Am. J. Physiol. 246 (2 Pt 2): R133–51. PMID 6364846. . [8] Paine P, Moore L, Horowitz S (1975). "Nuclear envelope permeability". Nature 254 (5496): 109–114. doi:10.1038/254109a0. PMID 1117994. [9] Rodney Rhoades, Richard Pflanzer, ed. (1996). "Ch3". Human Physiology (3rd ed.). Saunders College Publishing. [10] Shulga N, Mosammaparast N, Wozniak R, Goldfarb D (2000). "Yeast nucleoporins involved in passive nuclear envelope permeability". J Cell Biol 149 (5): 1027–1038. doi:10.1083/jcb.149.5.1027. PMID 10831607. [11] Pemberton L, Paschal B (2005). "Mechanisms of receptor-mediated nuclear import and nuclear export". Traffic 6 (3): 187–198. doi:10.1111/j.1600-0854.2005.00270.x. PMID 15702987. [12] Stuurman N, Heins S, Aebi U (1998). "Nuclear lamins: their structure, assembly, and interactions". J Struct Biol 122 (1–2): 42–66. doi:10.1006/jsbi.1998.3987. PMID 9724605. [13] Goldman A, Moir R, Montag-Lowy M, Stewart M, Goldman R (1992). "Pathway of incorporation of microinjected lamin A into the nuclear envelope". J Cell Biol 119 (4): 725–735. doi:10.1083/jcb.119.4.725. PMID 1429833. [14] Goldman R, Gruenbaum Y, Moir R, Shumaker D, Spann T (2002). "Nuclear lamins: building blocks of nuclear architecture" (http:/ / www. genesdev. org/ cgi/ content/ full/ 16/ 5/ 533). Genes Dev 16 (5): 533–547. doi:10.1101/gad.960502. PMID 11877373. . [15] Moir RD, Yoona M, Khuona S, Goldman RD. (2000). "Nuclear Lamins A and B1: Different Pathways of Assembly during Nuclear Envelope Formation in Living Cells". Journal of Cell Biology 151 (6): 1155–1168. doi:10.1083/jcb.151.6.1155. PMID 11121432. [16] Spann TP, Goldman AE, Wang C, Huang S, Goldman RD. (2002). "Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription". Journal of Cell Biology 156 (4): 603–608. doi:10.1083/jcb.200112047. PMID 11854306. [17] Mounkes LC, Stewart CL (2004). "Aging and nuclear organization: lamins and progeria". Current Opinion in Cell Biology 16 (3): 322–327. doi:10.1016/j.ceb.2004.03.009. PMID 15145358. [18] Ehrenhofer-Murray A (2004). "Chromatin dynamics at DNA replication, transcription and repair". Eur J Biochem 271 (12): 2335–2349. doi:10.1111/j.1432-1033.2004.04162.x. PMID 15182349. [19] Grigoryev S, Bulynko Y, Popova E (2006). "The end adjusts the means: heterochromatin remodelling during terminal cell differentiation". Chromosome Res 14 (1): 53–69. doi:10.1007/s10577-005-1021-6. PMID 16506096. [20] Schardin, Margit; Cremer, T; Hager, HD; Lang, M (December 1985). "Specific staining of human chromosomes in Chinese hamster x man hybrid cell lines demonstrates interphase chromosome territories" (http:/ / www. springerlink. com/ content/ lv101t8w17306071/ ). Human Genetics (Springer Berlin / Heidelberg) 71 (4): 281–287. doi:10.1007/BF00388452. PMID 2416668. .

Cell nucleus
[21] Lamond, Angus I.; William C. Earnshaw (1998-04-24). "Structure and Function in the Nucleus". Science 280 (5363): 547–553. doi:10.1126/science.280.5363.547. PMID 9554838. [22] Kurz, A; Lampel, S; Nickolenko, JE; Bradl, J; Benner, A; Zirbel, RM; Cremer, T; Lichter, P (1996). "Active and inactive genes localize preferentially in the periphery of chromosome territories" (http:/ / intl. jcb. org/ cgi/ content/ abstract/ 135/ 5/ 1195). The Journal of Cell Biology (The Rockefeller University Press) 135 (5): 1195–1205. doi:10.1083/jcb.135.5.1195. PMC 2121085. PMID 8947544. . [23] NF Rothfield, BD Stollar (1967). "The Relation of Immunoglobulin Class, Pattern of Antinuclear Antibody, and Complement-Fixing Antibodies to DNA in Sera from Patients with Systemic Lupus Erythematosus". J Clin Invest 46 (11): 1785–1794. doi:10.1172/JCI105669. PMC 292929. PMID 4168731. [24] S Barned, AD Goodman, DH Mattson (1995). "Frequency of anti-nuclear antibodies in multiple sclerosis". Neurology 45 (2): 384–385. PMID 7854544. [25] Hernandez-Verdun, Daniele (2006). "Nucleolus: from structure to dynamics". Histochem. Cell. Biol 125 (1-2): 127–137. doi:10.1007/s00418-005-0046-4. PMID 16328431. [26] Lamond, Angus I.; Judith E. Sleeman. "Nuclear substructure and dynamics". current biology 13 (21): R825–828. doi:10.1016/j.cub.2003.10.012. PMID 14588256. [27] Cioce M, Lamond A (2005). "Cajal bodies: a long history of discovery". Annu Rev Cell Dev Biol 21: 105–131. doi:10.1146/annurev.cellbio.20.010403.103738. PMID 16212489. [28] Pollard, Thomas D.; William C. Earnshaw (2004). Cell Biology. Philadelphia: Saunders. ISBN 0-7216-3360-9. [29] Dundr, Miroslav; Tom Misteli (2001). "Functional architecture in the cell nucleus". Biochem. J. (356): 297–310. PMID 11368755. [30] Fox, Archa (2007-03-07). Paraspeckle Size. Interview with R. Sundby. E-mail Correspondence. [31] Goebel, H.H.; I Warlow (January 1997). "Nemaline myopathy with intranuclear rods—intranuclear rod myopathy". Neuromuscular Disorders 7 (1): 13–19. doi:10.1016/S0960-8966(96)00404-X. PMID 9132135. [32] Matera AG, Frey MA. (1998). "Coiled Bodies and Gems: Janus or Gemini?". American Journal of Human Genetics 63 (2): 317–321. doi:10.1086/301992. PMID 9683623. [33] Matera, A. Gregory (1998). "Of Coiled Bodies, Gems, and Salmon". Journal of Cellular Biochemistry (70): 181–192. PMID 9671224. [34] Saunders WS, Cooke CA, Earnshaw WC (1991). "Compartmentalization within the nucleus: discovery of a novel subnuclear region.". Journal of Cellular Biology 115 (4): 919–931. doi:10.1083/jcb.115.4.919. PMID 1955462 [35] Pombo A, Cuello P, Schul W, Yoon J, Roeder R, Cook P, Murphy S (1998). "Regional and temporal specialization in the nucleus: a transcriptionally active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle". EMBO J 17 (6): 1768–1778. doi:10.1093/emboj/17.6.1768. PMID 9501098. [36] Fox, Archa; Lam, YW; Leung, AK; Lyon, CE; Andersen, J; Mann, M; Lamond, AI (2002). "Paraspeckles:A Novel Nuclear Domain" (http:/ / www. current-biology. com/ content/ article/ abstract?uid=PIIS0960982201006327). Current Biology 12 (1): 13–25. doi:10.1016/S0960-9822(01)00632-7. PMID 11790299. . [37] Fox, Archa; Wendy Bickmore (2004). "Nuclear Compartments: Paraspeckles" (http:/ / web. archive. org/ web/ 20060502134554/ http:/ / npd. hgu. mrc. ac. uk/ compartments/ paraspeckles. html). Nuclear Protein Database. Archived from the original (http:/ / npd. hgu. mrc. ac. uk/ compartments/ paraspeckles. html) on May 2, 2006. . Retrieved 2007-03-06. [38] Fox, A. et al. (2005). "P54nrb Forms a Heterodimer with PSP1 That Localizes to Paraspeckles in an RNA-dependent Manner" (http:/ / www. molbiolcell. org/ cgi/ reprint/ 16/ 11/ 5304). Molecular Biology of the Cell 16 (11): 5304–5315. doi:10.1091/mbc.E05-06-0587. PMC 1266428. PMID 16148043. . [39] Lamond AI, Spector DL (August 2003). "Nuclear speckles: a model for nuclear organelles". Nat. Rev. Mol. Cell Biol. 4 (8): 605–12. doi:10.1038/nrm1172. PMID 12923522. [40] Tripathi K, Parnaik VK (September 2008). "Differential dynamics of splicing factor SC35 during the cell cycle" (http:/ / www. ias. ac. in/ jbiosci/ sep2008/ 345. pdf) (PDF). J. Biosci. 33 (3): 345–54. doi:10.1007/s12038-008-0054-3. PMID 19005234. . [41] Tripathi, K.; Parnaik, V. K. (2008). "Differential dynamics of splicing factor SC35 during the cell cycle". Journal of biosciences 33 (3): 345–354. doi:10.1007/s12038-008-0054-3. PMID 19005234. [42] Lamond AI, Spector DL (August 2003). "Nuclear speckles: a model for nuclear organelles". Nat. Rev. Mol. Cell Biol. 4 (8): 605–12. doi:10.1038/nrm1172. PMID 12923522. [43] Handwerger, Korie E.; Joseph G. Gall (January 2006). "Subnuclear organelles: new insights into form and function". TRENDS in Cell Biology 16 (1): 19–26. doi:10.1016/j.tcb.2005.11.005. PMID 16325406. [44] Lehninger, Albert L.; David L. Nelson, Michael M. Cox. (2000). Lehninger principles of biochemistry (3rd ed.). New York: Worth Publishers. ISBN 1-57259-931-6. [45] Moreno F, Ahuatzi D, Riera A, Palomino CA, Herrero P. (2005). "Glucose sensing through the Hxk2-dependent signalling pathway.". Biochem Soc Trans 33 (1): 265–268. doi:10.1042/BST0330265. PMID 15667322. PMID 15667322 [46] Görlich, Dirk; Ulrike Kutay (1999). "Transport between the cell nucleus and the cytoplasm". Ann. Rev. Cell Dev. Biol. 15 (1): 607–660. doi:10.1146/annurev.cellbio.15.1.607. PMID 10611974. [47] Nierhaus, Knud H.; Daniel N. Wilson (2004). Protein Synthesis and Ribosome Structure: Translating the Genome. Wiley-VCH. ISBN 3-527-30638-2. [48] Nicolini, Claudio A. (1997). Genome Structure and Function: From Chromosomes Characterization to Genes Technology. Springer. ISBN 0-7923-4565-7.

125

Cell nucleus
[49] Watson, JD; Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). "Ch9–10". Molecular Biology of the Gene (5th ed.). Peason Benjamin Cummings; CSHL Press.. ISBN 0-8053-9603-9. [50] Lippincott-Schwartz, Jennifer (2002-03-07). "Cell biology: Ripping up the nuclear envelope". Nature 416 (6876): 31–32. doi:10.1038/416031a. PMID 11882878. [51] Boulikas T (1995). "Phosphorylation of transcription factors and control of the cell cycle". Crit Rev Eukaryot Gene Expr 5 (1): 1–77. PMID 7549180. [52] Steen R, Collas P (2001). "Mistargeting of B-type lamins at the end of mitosis: implications on cell survival and regulation of lamins A/C expression". J Cell Biol 153 (3): 621–626. doi:10.1083/jcb.153.3.621. PMID 11331311. [53] Skutelsky, E.; Danon D. (June 1970). "Comparative study of nuclear expulsion from the late erythroblast and cytokinesis". J Cell Biol (60(3)): 625–635. doi:10.1016/0014-4827(70)90536-7. PMID 5422968. [54] Torous, DK; Dertinger SD, Hall NE, Tometsko CR. (2000). "Enumeration of micronucleated reticulocytes in rat peripheral blood: a flow cytometric study". Mutat Res (465(1–2)): 91–99. doi:10.1016/S1383-5718(99)00216-8. PMID 10708974. [55] Hutter, KJ; Stohr M. (1982). "Rapid detection of mutagen induced micronucleated erythrocytes by flow cytometry". Histochemistry 75 (3): 353–362. PMID 7141888. [56] Zettler, LA; Sogin ML, Caron DA (1997). "Phylogenetic relationships between the Acantharea and the Polycystinea: A molecular perspective on Haeckel's Radiolaria". Proc Natl Acad Sci USA 94 (21): 11411–11416. doi:10.1073/pnas.94.21.11411. PMC 23483. PMID 9326623. [57] Horton, TR (2006). "The number of nuclei in basidiospores of 63 species of ectomycorrhizal Homobasidiomycetes". Mycologia 98 (2): 233–238. doi:10.3852/mycologia.98.2.233. PMID 16894968. [58] Adam RD (December 1991). "The biology of Giardia spp" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=1779932). Microbiol. Rev. 55 (4): 706–32. PMC 372844. PMID 1779932. . [59] McInnes, A; Rennick DM (1988). "Interleukin 4 induces cultured monocytes/macrophages to form giant multinucleated cells". J Exp Med (167): 598–611. doi:10.1084/jem.167.2.598. PMID 3258008. [60] Goldring, SR; Roelke MS, Petrison KK, Bhan AK (1987). "Human giant cell tumors of bone identification and characterization of cell types". J Clin Invest 79 (2): 483–491. doi:10.1172/JCI112838. PMC 424109. PMID 3027126. [61] Pennisi E. (2004). "Evolutionary biology. The birth of the nucleus". Science 305 (5685): 766–768. doi:10.1126/science.305.5685.766. PMID 15297641. [62] C.Michael Hogan. 2010. Archaea. eds. E.Monosson & C.Cleveland, Encyclopedia of Earth. National Council for Science and the Environment, Washington DC. (http:/ / www. eoearth. org/ article/ Archaea?topic=49496) [63] Margulis, Lynn (1981). Symbiosis in Cell Evolution. San Francisco: W. H. Freeman and Company. pp. 206–227. ISBN 0-7167-1256-3. [64] Lopez-Garcia P, Moreira D. (2006). "Selective forces for the origin of the eukaryotic nucleus". Bioessays 28 (5): 525–533. doi:10.1002/bies.20413. PMID 16615090. [65] Fuerst JA. (2005). "Intracellular compartmentation in planctomycetes". Annu Rev Microbiol. 59: 299–328. doi:10.1146/annurev.micro.59.030804.121258. PMID 15910279. [66] Hartman H, Fedorov A. (2002). "The origin of the eukaryotic cell: a genomic investigation". Proc Natl Acad Sci U S A. 99 (3): 1420–1425. doi:10.1073/pnas.032658599. PMC 122206. PMID 11805300. [67] Bell PJ (September 2001). "Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus?". J. Mol. Evol. 53 (3): 251–6. doi:10.1007/s002390010215. PMID 11523012. [68] Takemura M (2001). "Poxviruses and the origin of the eukaryotic nucleus". J Mol Evol 52 (5): 419–425. doi:10.1007/s002390010171. PMID 11443345. [69] Villarreal L, DeFilippis V (2000). "A hypothesis for DNA viruses as the origin of eukaryotic replication proteins". J Virol 74 (15): 7079–7084. doi:10.1128/JVI.74.15.7079-7084.2000. PMC 112226. PMID 10888648. [70] Bell PJ (November 2006). "Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus". J. Theor. Biol. 243 (1): 54–63. doi:10.1016/j.jtbi.2006.05.015. PMID 16846615. [71] de Roos AD (2006). "The origin of the eukaryotic cell based on conservation of existing interfaces". Artif Life 12 (4): 513–523.. doi:10.1162/artl.2006.12.4.513. PMID 16953783.

126

Further reading
• Goldman, Robert D.; Gruenbaum, Y; Moir, RD; Shumaker, DK; Spann, TP (2002). "Nuclear lamins: building blocks of nuclear architecture". Genes & Dev. 16 (5): 533–547. doi:10.1101/gad.960502. PMID 11877373. A review article about nuclear lamins, explaining their structure and various roles • Görlich, Dirk; Kutay, U (1999). "Transport between the cell nucleus and the cytoplasm". Ann. Rev. Cell Dev. Biol. 15: 607–660. doi:10.1146/annurev.cellbio.15.1.607. PMID 10611974. A review article about nuclear transport, explains the principles of the mechanism, and the various transport pathways

Cell nucleus • Lamond, Angus I.; Earnshaw, WC (1998-04-24). "Structure and Function in the Nucleus". Science 280 (5363): 547–553. doi:10.1126/science.280.5363.547. PMID 9554838. A review article about the nucleus, explaining the structure of chromosomes within the organelle, and describing the nucleolus and other subnuclear bodies • Pennisi E. (2004). "Evolutionary biology. The birth of the nucleus". Science 305 (5685): 766–768. doi:10.1126/science.305.5685.766. PMID 15297641. A review article about the evolution of the nucleus, explaining a number of different theories • Pollard, Thomas D.; William C. Earnshaw (2004). Cell Biology. Philadelphia: Saunders. ISBN 0-7216-3360-9. A university level textbook focusing on cell biology. Contains information on nucleus structure and function, including nuclear transport, and subnuclear domains

127

External links
• cellnucleus.com (http://www.cellnucleus.com/education_main.htm) Website covering structure and function of the nucleus from the Department of Oncology at the University of Alberta. • http://npd.hgu.mrc.ac.uk/user/?page=compartment The Nuclear Protein Database] Information on nuclear components. • The Nucleus Collection (http://cellimages.ascb.org/cdm4/browse.php?CISOROOT=/p4041coll6) in the Image & Video Library (http://cellimages.ascb.org/) of The American Society for Cell Biology (http://www. ascb.org/) contains peer-reviewed still images and video clips that illustrate the nucleus. • Nuclear Envelope and Nuclear Import Section (http://cellimages.ascb.org/u?/p4041coll11,62) from Landmark Papers in Cell Biology (http://cellimages.ascb.org/cdm4/browse.php?CISOROOT=/p4041coll11), Joseph G. Gall, J. Richard McIntosh, eds., contains digitized commentaries and links to seminal research papers on the nucleus. Published online in the Image & Video Library (http://cellimages.ascb.org/) of The American Society for Cell Biology (http://www.ascb.org/) • Cytoplasmic patterns generated by human antibodies (http://www.antibodypatterns.com/cytoplasmic.php)

Gallery

Comparison of human and chimpanzee chromosomes.

Mouse chromosome territories in different cell types.

24 chromosome territories in human cells.

Cell wall

128

Cell wall
The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, in addition to acting as a filtering mechanism. A major function of the cell wall is to act as a pressure vessel, preventing over-expansion when water enters the cell. Cell walls are found in plants, bacteria, fungi, algae, and some archaea. Animals and protozoa do not have cell walls. The material in the cell wall varies between species, and can also differ depending on cell type and developmental stage. In bacteria, peptidoglycan forms the cell wall. Archaean cell walls have various compositions, and may be formed of glycoprotein S-layers, pseudopeptidoglycan, or polysaccharides. Fungi possess cell walls made of the glucosamine polymer chitin, and algae typically possess walls made of glycoproteins and polysaccharides. Unusually, diatoms have a cell wall composed of biogenic silica. Often, other accessory molecules are found anchored to the cell wall.

Properties
The cell wall serves a similar purpose in those organisms that possess them. The wall gives cells rigidity and strength, offering protection against mechanical stress. In multicellular organisms, it permits the organism to build and hold its shape (morphogenesis). The cell wall also limits the entry of large molecules that may be toxic to the cell. It further permits the creation of a stable osmotic environment by preventing osmotic lysis and helping to retain water. The composition, properties, and form of the cell wall may change during the cell cycle and depend on growth conditions.
Diagram of the plant cell, with the cell wall in green.

Rigidity of cell walls
The rigidity of the cell walls is often over-estimated. In most cells, the cell wall is flexible, meaning that it will bend rather than holding a fixed shape, but has considerable tensile strength. The apparent rigidity of primary plant tissues is enabled by cell walls, but not due to the walls' stiffness. Hydraulic turgor pressure creates this rigidity, along with the wall structure. The flexibility of the cell walls is seen when plants wilt, so that the stems and leaves begin to droop, or in seaweeds that bend in water currents. As John Howland states it: Think of the cell wall as a wicker basket in which a balloon has been inflated so that it exerts pressure from the inside. Such a basket is very rigid and resistant to mechanical damage. Thus does the prokaryote cell (and eukaryotic cell that possesses a cell wall) gain strength from a flexible plasma membrane pressing against a rigid cell wall.[1] The rigidity of the cell wall thus results in part from inflation of the cell contained. This inflation is a result of the passive uptake of water. In plants, a secondary cell wall is a thicker additional layer of cellulose which increases wall rigidity. Additional layers may be formed containing lignin in xylem cell walls, or containing suberin in cork cell walls. These compounds are rigid and waterproof, making the secondary wall stiff. Both wood and bark cells of trees have secondary walls. Other parts of plants such as the leaf stalk may acquire similar reinforcement to resist the strain of

Cell wall physical forces. Certain single-cell protists and algae also produce a rigid wall. Diatoms build a frustule from silica extracted from the surrounding water; radiolarians also produce a test from minerals. Many green algae, such as the Dasycladales encase their cells in a secreted skeleton of calcium carbonate. In each case, the wall is rigid and essentially inorganic.

129

Permeability
The primary cell wall of most plant cells is semi-permeable and permits the passage of small molecules and small proteins, with size exclusion estimated to be 30-60 kDa. Key nutrients, especially water and carbon dioxide, are distributed throughout the plant from cell wall to cell wall in apoplastic flow. The pH is an important factor governing the transport of molecules through cell walls.[2]

Plant cell walls
Many plant cells have walls that are strong enough to withstand the osmotic pressure from the difference in solute concentration between the cell interior and distilled water.[3] Plant cell walls vary from 1/10 to several µm thick.[4]

Layers
Up to three strata or layers may be found in plant cell walls:[5] • The middle lamella, a layer rich in pectins. This outermost layer forms the interface between adjacent plant cells and glues them together. • The primary cell wall, generally a thin, flexible and extensible layer formed while the cell is growing. • The secondary cell wall, a thick layer formed inside the primary cell wall after the cell is fully grown. It is not found in all cell types. Some cells, such as the conducting cells in xylem, possess a secondary wall containing lignin, which strengthens and waterproofs the wall.

Molecular structure of the primary cell wall in plants.

Composition
In the primary (growing) plant cell wall, the major carbohydrates are cellulose, hemicellulose and pectin. The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan. In grass cell walls, xyloglucan and pectin are reduced in abundance and partially replaced by glucuronarabinoxylan, a hemicellulose. Primary cell walls characteristically extend (grow) by a mechanism called acid growth, which involves turgor-driven movement of the strong cellulose microfibrils within the weaker hemicellulose/pectin matrix, catalyzed by expansin proteins. The outer part of the primary cell wall of the plant epidermis is usually impregnated with cutin and wax, forming a permeability barrier known as the plant cuticle. Secondary cell walls contain a wide range of additional compounds that modify their mechanical properties and permeability. The major polymers that make up wood (largely secondary cell walls) include: • cellulose, 35-50% • xylan, 20-35%, a type of hemicellulose • lignin, 10-25%, a complex phenolic polymer that penetrates the spaces in the cell wall between cellulose, hemicellulose and pectin components, driving out water and strengthening the wall.

Cell wall Additionally, structural proteins (1-5%) are found in most plant cell walls; they are classified as hydroxyproline-rich glycoproteins (HRGP), arabinogalactan proteins (AGP), glycine-rich proteins (GRPs), and proline-rich proteins (PRPs). Each class of glycoprotein is defined by a characteristic, highly repetitive protein sequence. Most are glycosylated, contain hydroxyproline (Hyp) and become cross-linked in the cell wall. These proteins are often concentrated in specialized cells and in cell corners. Cell walls of the epidermis and endodermis may also contain suberin or cutin, two polyester-like polymers that protect the cell from herbivores.[6] The relative composition of carbohydrates, secondary compounds and protein varies between plants and between the cell type and age. Plant cells walls also contain numerous enzymes, such as hydrolases, esterases, peroxidases, and transglycosylases, that cut, trim and cross-link wall polymers. The walls of cork cells in the bark of trees are impregnated with suberin, and suberin also forms the permeability barrier in primary roots known as the Casparian strip. Secondary walls - especially in grasses - may also contain microscopic silica crystals, which may strengthen the wall and protect it from herbivores. Cell walls in some plant tissues also function as storage depots for carbohydrates that can be broken down and resorbed to supply the metabolic and growth needs of the plant. For example, endosperm cell walls in the seeds of cereal grasses, nasturtium, and other species, are rich in glucans and other polysaccharides that are readily digested by enzymes during seed germination to form simple sugars that nourish the growing embryo. Cellulose microfibrils are not readily digested by plants, however.

130

Formation
The middle lamella is laid down first, formed from the cell plate during cytokinesis, and the primary cell wall is then deposited inside the middle lamella. The actual structure of the cell wall is not clearly defined and several models exist - the covalently linked cross model, the tether model, the diffuse layer model and the stratified layer model. However, the primary cell wall, can be defined as composed of cellulose microfibrils aligned at all angles. Microfibrils are held together by hydrogen bonds to provide a high tensile strength. The cells are held together and share the gelatinous membrane called the middle lamella, which contains magnesium and calcium pectates (salts of pectic acid). Cells interact though plasmodesma(ta), which are inter-connecting channels of cytoplasm that connect to the protoplasts of adjacent cells across the cell wall. In some plants and cell types, after a maximum size or point in development has been reached, a secondary wall is constructed between the plasma membrane and primary wall.[7] Unlike the primary wall, the microfibrils are aligned mostly in the same direction, and with each additional layer the orientation changes slightly. Cells with secondary cell walls are rigid. Cell to cell communication is possible through pits in the secondary cell wall that allow plasmodesma to connect cells through the secondary cell walls.

Cell wall

131

Algal cell walls
Like plants, algae have cell walls.[8] Algal cell walls contain either polysaccharides (such as cellulose (a glucan)) or a variety of glycoproteins (Volvocales) or both. The inclusion of additional polysaccharides in algal cells walls is used as a feature for algal taxonomy. • Mannans: They form microfibrils in the cell walls of a number of marine green algae including those from the genera, Codium, Dasycladus, and Acetabularia as well as in the walls of some red algae, like Porphyra and Bangia. • Xylans: • Alginic acid: It is a common polysaccharide in the cell walls of brown algae.

• Sulfonated polysaccharides: They occur in the cell walls of most algae; those common in red algae include agarose, carrageenan, porphyran, furcelleran and funoran.

Scanning electron micrographs of diatoms showing the external appearance of the cell wall

Other compounds that may accumulate in algal cell walls include sporopollenin and calcium ions. The group of algae known as the diatoms synthesize their cell walls (also known as frustules or valves) from silicic acid (specifically orthosilicic acid, H4SiO4). The acid is polymerised intra-cellularly, then the wall is extruded to protect the cell. Significantly, relative to the organic cell walls produced by other groups, silica frustules require less energy to synthesize (approximately 8%), potentially a major saving on the overall cell energy budget[9] and possibly an explanation for higher growth rates in diatoms.[10]

Fungal cell walls
There are several groups of organisms that may be called "fungi". Some of these groups have been transferred out of the Kingdom Fungi, in part because of fundamental biochemical differences in the composition of the cell wall. Most true fungi have a cell wall consisting largely of chitin and other polysaccharides.[11] True fungi do not have cellulose in their cell walls, but some fungus-like organisms do.

True fungi

Chemical structure of a unit from a chitin polymer chain.

Not all species of fungi have cell walls but in those that do, the plasma membrane is followed by three layers of cell wall material. From inside out these are: • a chitin layer (polymer consisting mainly of unbranched chains of N-acetyl-D-glucosamine) • a layer of β-1,3-glucan (zymosan) • a layer of mannoproteins (mannose-containing glycoproteins) which are heavily glycosylated at the outside of the cell.

Cell wall

132

Fungus-like protists
The group Oomycetes, also known as water molds, are saprotrophic plant pathogens like fungi. Until recently they were widely believed to be fungi, but structural and molecular evidence[12] has led to their reclassification as heterokonts, related to autotrophic brown algae and diatoms. Unlike fungi, oomycetes typically possess cell walls of cellulose and glucans rather than chitin, although some genera (such as Achlya and Saprolegnia) do have chitin in their walls.[13] The fraction of cellulose in the walls is no more than 4 to 20%, far less than the fraction comprised by glucans.[13] Oomycete cell walls also contain the amino acid hydroxyproline, which is not found in fungal cell walls. The dictyostelids are another group formerly classified among the fungi. They are slime molds that feed as unicellular amoebae, but aggregate into a reproductive stalk and sporangium under certain conditions. Cells of the reproductive stalk, as well as the spores formed at the apex, possess a cellulose wall.[14] The spore wall has been shown to possess three layers, the middle of which is composed primarily of cellulose, and the innermost is sensitive to cellulase and pronase.[14]

Prokaryotic cell walls
Bacterial cell walls
Around the outside of the cell membrane is the bacterial cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids.[15] Bacterial cell walls are different from the cell walls of plants and fungi which are made of cellulose and chitin, respectively.[16] The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, although L-form bacteria can be produced in the laboratory that lack a cell wall.[17] The antibiotic penicillin is able to kill bacteria by Diagram of a typical gram-negative bacterium, with the thin cell wall sandwiched between the red outer membrane and the thin green plasma membrane preventing the cross-linking of peptidoglycan and this causes the cell wall to weaken and lyse.[16] The lysozyme enzyme can also damage bacterial cell walls. There are broadly speaking two different types of cell wall in bacteria, called Gram-positive and Gram-negative. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.[18]

Cell wall

133

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.[19] These differences in structure can produce differences in antibiotic susceptibility, for instance vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.[20]

Schematic of typical gram-positive cell wall showing arrangement of N-Acetylglucosamine and N-Acetlymuramic acid

Archaeal cell walls
Although not truly unique, the cell walls of Archaea are unusual. Whereas peptidoglycan is a standard component of all bacterial cell walls, all archaeal cell walls lack peptidoglycan,[21] with the exception of one group of methanogens.[1] In that group, the peptidoglycan is a modified form very different from the kind found in bacteria.[21] There are four types of cell wall currently known among the Archaea. One type of archaeal cell wall is that composed of pseudopeptidoglycan (also called pseudomurein). This type of wall is found in some methanogens, such as Methanobacterium and Methanothermus.[22] While the overall structure of archaeal pseudopeptidoglycan superficially resembles that of bacterial peptidoglycan, there are a number of significant chemical differences. Like the peptidoglycan found in bacterial cell walls, pseudopeptidoglycan consists of polymer chains of glycan cross-linked by short peptide connections. However, unlike peptidoglycan, the sugar N-acetylmuramic acid is replaced by N-acetyltalosaminuronic acid,[21] and the two sugars are bonded with a β,1-3 glycosidic linkage instead of β,1-4. Additionally, the cross-linking peptides are L-amino acids rather than D-amino acids as they are in bacteria.[22] A second type of archaeal cell wall is found in Methanosarcina and Halococcus. This type of cell wall is composed entirely of a thick layer of polysaccharides, which may be sulfated in the case of Halococcus.[22] Structure in this type of wall is complex and as yet is not fully investigated. A third type of wall among the Archaea consists of glycoprotein, and occurs in the hyperthermophiles, Halobacterium, and some methanogens. In Halobacterium, the proteins in the wall have a high content of acidic amino acids, giving the wall an overall negative charge. The result is an unstable structure that is stabilized by the presence of large quantities of positive sodium ions that neutralize the charge.[22] Consequently, Halobacterium thrives only under conditions with high salinity. In other Archaea, such as Methanomicrobium and Desulfurococcus, the wall may be composed only of surface-layer proteins,[1] known as an S-layer. S-layers are common in bacteria, where they serve as either the sole cell-wall component or an outer layer in conjunction with polysaccharides. Most Archaea are Gram-negative, though at least one Gram-positive member is known.[1]

Cell wall

134

References
[1] Howland, John L. (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. pp. 69–71. ISBN 0-19-511183-4. [2] C.Michael Hogan. 2010. Abiotic factor. Encyclopedia of Earth. eds Emily Monosson and C. Cleveland. National Council for Science and the Environment (http:/ / www. eoearth. org/ article/ Abiotic_factor?topic=49461). Washington DC [3] http:/ / www. madsci. org/ posts/ archives/ 2006-11/ 1164842041. Cb. r. html [4] Campbell, Neil A.; Reece, Jane B.; Urry, Lisa A.; Cain, Michael L.; Wasserman, Steven A.; Minorsky, Peter V.; Jackson, Robert B. (2008). Biology (8th ed.). p. 118. ISBN 978-0-8053-6844-4. [5] Buchanan; Gruissem, Jones (2000). Biochemistry & molecular biology of plants (1st ed.). American society of plant physiology. ISBN 0-943088-39-9. [6] Laurence Moire, Alain Schmutz, Antony Buchala, Bin Yan, Ruth E. Stark, and Ulrich Ryser (1999). "Glycerol Is a Suberin Monomer. New Experimental Evidence for an Old Hypothesis" (http:/ / www. plantphysiol. org/ cgi/ content/ full/ 119/ 3/ 1137). Plant Physiol 119 (3): 1137–1146. doi:10.1104/pp.119.3.1137. PMC 32096. PMID 10069853. . [7] Campbell, Neil A.; Reece, Jane B.; Urry, Lisa A.; Cain, Michael L.; Wasserman, Steven A.; Minorsky, Peter V.; Jackson, Robert B. (2008). Biology (8th ed.). p. 119. ISBN 978-0-8053-6844-4. [8] Sendbusch, Peter V. (2003-07-31). " Cell Walls of Algae (http:/ / www. biologie. uni-hamburg. de/ b-online/ e26/ 26d. htm)". Botany Online. Retrieved on 2007-10-29. [9] Raven, J. A. (1983). "The transport and function of silicon in plants". Biol. Rev. 58 (2): 179–207. doi:10.1111/j.1469-185X.1983.tb00385.x. [10] Furnas, M. J. (1990). "In situ growth rates of marine phytoplankton : Approaches to measurement, community and species growth rates". J. Plankton Res. 12 (6): 1117–1151. doi:10.1093/plankt/12.6.1117. [11] Hudler, George W. (1998). Magical Mushrooms, Mischievous Molds. Princeton, NJ: Princeton University Press, 7. ISBN 0-691-02873-7. [12] Sengbusch, Peter V. (2003-07-31). " Interactions between Plants and Fungi: the Evolution of their Parasitic and Symbiotic Relations (http:/ / www. biologie. uni-hamburg. de/ b-online/ e33/ 33. htm)". biologie.uni-hamburg.de. Retrieved on 2007-10-29. [13] Alexopoulos, C. J., C. W. Mims, & M. Blackwell (1996). Introductory Mycology 4. New York: John Wiley & Sons, 687-688. ISBN 0-471-52229-5. [14] Raper, Kenneth B. (1984). The Dictyostelids. Princeton, NJ: Princeton University Press, 99-100. ISBN 0-691-08345-2. [15] van Heijenoort J (2001). "Formation of the glycan chains in the synthesis of bacterial peptidoglycan" (http:/ / glycob. oxfordjournals. org/ cgi/ content/ full/ 11/ 3/ 25R). Glycobiology 11 (3): 25R – 36R. doi:10.1093/glycob/11.3.25R. PMID 11320055. . [16] Koch A (2003). "Bacterial wall as target for attack: past, present, and future research" (http:/ / cmr. asm. org/ cgi/ content/ full/ 16/ 4/ 673?view=long& pmid=14557293). Clin Microbiol Rev 16 (4): 673–87. doi:10.1128/CMR.16.4.673-687.2003. PMC 207114. PMID 14557293. . [17] Joseleau-Petit D, Liébart JC, Ayala JA, D'Ari R (September 2007). "Unstable Escherichia coli L forms revisited: growth requires peptidoglycan synthesis" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=17586646). J. Bacteriol. 189 (18): 6512–20. doi:10.1128/JB.00273-07. PMC 2045188. PMID 17586646. . [18] Gram, HC (1884). "Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten". Fortschr. Med. 2: 185–189. [19] Hugenholtz P; Rogozin, Igor B; Grishin, Nick V; Tatusov, Roman L; Koonin, Eugene V (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biol 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374. [20] Walsh F, Amyes S (2004). "Microbiology and drug resistance mechanisms of fully resistant pathogens.". Curr Opin Microbiol 7 (5): 439–44. doi:10.1016/j.mib.2004.08.007. PMID 15451497. [21] White, David. (1995) The Physiology and Biochemistry of Prokaryotes, pages 6, 12-21. (Oxford: Oxford University Press). ISBN 0-19-508439-X. [22] Brock, Thomas D., Michael T. Madigan, John M. Martinko, & Jack Parker. (1994) Biology of Microorganisms, 7th ed., pages 818-819, 824 (Englewood Cliffs, NJ: Prentice Hall). ISBN 0-13-042169-3.

External links
• Cell wall ultrastructure (http://micro.magnet.fsu.edu/cells/plants/cellwall.html) • The Cell Wall (http://www.palaeos.com/Fungi/FPieces/CellWall.html)

Cellular microbiology

135

Cellular microbiology
Cellular microbiology is a discipline that bridges microbiology and cell biology. The term "cellular microbiology" was coined in 1996 [1] in a Science article. Cooperation and mutual dependency between microbiology and cell biology had been increasing in the years before that, and the emergence of a new discipline had been suggested and discussed in several scientific conferences. Cellular microbiology attempts to use pathogenic microbes as tools for cell-biology research, and to employ cell-biology methods to understand the pathogenicity of microbes. Toxins and Salmonella bacteria (red) invade cultured human cells virulence factors from microbes have been used for decades to influence processes in eukaryotic cells and to study them. It has increasingly appeared that applying a purified toxin on a cell does not always provide the complete picture, and that understanding the role of the toxin in pathogenicity, the way the toxin promotes the microbe, the way the toxin is produced and the co-evolution of the toxin and its host-cell counterparts, is crucial. Numerous eukaryotic cellular processes have been clarified using microbial "tools". A major subject in this category is the cytoskeleton. Many microbes modify and influence the synthesis or degradation of the host-cell cytoskeleton, in particular the actin network[2]. Intracellular microbes, such as the bacteria Salmonella and Shigella, elicit actin polymerization in host cells that otherwise do not internalize microbes (non-phagocytes). This causes the formation of projections that eventually engulf the bacteria. Bacteria such as Yersinia inhibit actin polymerization in phagocytes, thereby preventing their uptake. Cellular microbiology tries to understand these processes and how they promote infection. Other eukaryotic processes that microbes influence and that are researched using microbes are signal transduction, metabolism, vesicle trafficking, cell cycle and transcriptional regulation, to name but a few. Recently, the field of Cellular Microbiology has been expanded to incorporate investigation of the cell biology of microbes themselves [3][4]. "The field of cellular microbiology is a coalescence of two fields: molecular microbiology and cell biology," said Professor Jacek Hawiger, Chair of Microbiology and Immunology at Vanderbuilt University [4]. Particularly in the case of bacterial cells, new technology is starting to be used to reveal a high level of organization within the bacterial cells themselves. For example, high-resolution fluorescence microscopy [5] and atomic force microscopy [6] are both being used to show just how sophisticated bacterial cells are.

Cellular microbiology

136

References
[1] Cossart P, Boquet P, Normark S, Rappuoli R (1996). "Cellular microbiology emerging". Science 271 (5247): 315–317. doi:10.1126/science.271.5247.315. [2] Dramsi S and Cossart P (1998). "Intracellular pathogens and the actin cytoskeleton". Annu Rev Cell Dev Biol 14 (1): 137–166. doi:10.1146/annurev.cellbio.14.1.137. PMID 9891781. [3] NHMRC Program in Cellular Microbiology (http:/ / med. monash. edu/ biochem/ nhmrc/ ) [4] NIH Cellular and Molecular Microbiology (CMM) training program (http:/ / www. mc. vanderbilt. edu/ reporter/ index. html?ID=988) [5] Ebersbach G, Jacobs-Wagner C. “Exploration into the spatial and temporal mechanisms of bacterial polarity.”Trends Microbiol. 2007 Mar;15(3):101-8 [6] Dufrêne YF. “Towards nanomicrobiology using atomic force microscopy.” Nat Rev Microbiol. 2008 Sep;6(9):674-80

Collagen
Collagen (  /ˈkɒlədʒɪn/) is a group of naturally occurring proteins found in animals, especially in the flesh and connective tissues of mammals.[1] It is the main component of connective tissue, and is the most abundant protein in mammals,[2] making up about 25% to 35% of the whole-body protein content. Collagen, in the form of elongated fibrils, is mostly found in fibrous tissues such as tendon, ligament and skin, and is also abundant in cornea, cartilage, bone, blood vessels, the gut, and intervertebral disc. The fibroblast is the most common cell which creates collagen. In muscle tissue, it serves as a major component of the endomysium. Collagen constitutes one to two percent of muscle tissue, and accounts for 6% of the weight of strong, tendinous muscles.[3] Gelatin, which is used in food and industry, is collagen that has been irreversibly hydrolyzed.

History and background
The molecular and packing structures of collagen have eluded scientists over decades of research. The first evidence that it possesses a regular structure at the molecular level was presented in the mid-1930s.[4][5] Since that time, many prominent scholars, including Nobel laureates Crick, Pauling, Rich and Yonath, and others, including Brodsky, Berman, and Ramachandran, concentrated on the conformation of the collagen monomer. Several competing models, although correctly dealing with the conformation of each individual peptide chain, gave way to the triple-helical "Madras" model, which provided an essentially correct model of the molecule's quaternary structure[6][7][8] although this model still required some refinement.[9][10][11][12] The packing structure of collagen has not been defined to the same Tropocollagen triple degree outside of the fibrillar collagen types, although it has been long known to be hexagonal helix [13][14][15] or quasi-hexagonal. As with its monomeric structure, several conflicting models alleged that either the packing arrangement of collagen molecules is 'sheet-like' or microfibrillar.[16][17] The microfibrillar structure of collagen fibrils in tendon, cornea and cartilage has been directly imaged by electron microscopy.[18][19][20] In 2006, the microfibrillar structure of adult tendon, as described by Fraser, Miller, and Wess (amongst others), was confirmed as being closest to the observed structure, although it oversimplified the topological progression of neighboring collagen molecules, and hence did not predict the correct conformation of the discontinuous D-periodic pentameric arrangement termed simply: the microfibril.[21] Various cross linking agents like dopaquinone, embelin, potassium embelate and 5-O-methyl embelin could be developed as potential cross-linking/stabilization agent of collagen preparation and its application as wound dressing sheet in clinical applications is enhanced.[22]

Collagen

137

Chemistry of Collagen
Collagen is a composed of a triple helix, which generally consists of two identical chains (α1) and an additional chain that differs slightly in its chemical composition (α2).[23] The amino acid composition of collagen is atypical for proteins, particularly with respect to its high hydroxyproline content. The most common motifs in the amino acid sequence of collagen are Glycine-Proline-X and Glycine-X-Hydroxyproline, where X is any amino acid other than glycine, proline or hydroxyproline. The average amino acid composition for fish and mammal skin is given.[23]
Amino Acid Abundance in Mammal Skin (Residues/1000) Abundance in Fish Skin (Residues/1000) Asp Hyp Thr Ser Glu Pro Gly Ala Val Met Ile Leu Tyr Phe Hyl Lys His Arg 47 95 19 36 74 126 329 109 22 6 11 24 3 13 6 29 5 49 47 67 26 46 76 108 339 114 21 13 11 23 3 14 8 26 7 52

Synthesis
First, a three dimensional stranded structure is assembled, with the amino acids glycine and proline as its principal components. This is not yet collagen but its precursor, procollagen. A recent study shows that vitamin C must have an important role in its synthesis. Prolonged exposure of cultures of human connective-tissue cells to ascorbate induced an eight-fold increase in the synthesis of collagen with no increase in the rate of synthesis of other proteins (Murad et al., 1981). Since the production of procollagen must precede the production of collagen, vitamin C must have a role in this step. The conversion involves a reaction that substitutes a hydroxyl group, OH, for a hydrogen atom, H, in the proline residues at certain points in the polypeptide chains, converting those residues to hydroxyproline. This hydroxylation reaction secures the chains in the triple helix of collagen. The hydroxylation, next, of the residues of the amino acid lysine, transforming them to hydroxylysine, is then needed to permit the cross-linking of the triple helices into the fibers and networks of the tissues. These hydroxylation reactions are catalyzed by two different enzymes: prolyl-4-hydroxylase and lysyl-hydroxylase. Vitamin C also serves with them in inducing these reactions. It has recently been shown by Myllyla and his colleagues that, in this service, one molecule of vitamin C is destroyed for each H replaced by OH. [24] The synthesis of collagen occurs inside and outside of the cell. The formation of collagen which results in fibrillary collagen (most

Collagen common form) is discussed here. Meshwork collagen, which is often involved in the formation of filtration systems is the other form of collagen. It should be noted that all types of collagens are triple helixes, and the differences lie in the make-up of the alpha peptides created in step 2. 1. Transcription of mRNA: There are approximately 34 genes associated with collagen formation, each coding for a specific mRNA sequence, and typically have the "COL" prefix. The beginning of collagen synthesis begins with turning on genes which are associated with the formation of a particular alpha peptide (typically alpha 1, 2 or 3). 2. Pre-pro-peptide Formation: Once the final mRNA exits from the cell nucleus and enters into the cytoplasm it links with the ribosomal subunits and the process of translation occurs. The early/first part of the new peptide is known as the signal sequence. The signal sequence on the N-terminal of the peptide is recognized by a signal recognition particle on the endoplasmic reticulum, which will be responsible for directing the pre-pro-peptide into the endoplasmic reticulum. Therefore, once the synthesis of new peptide is finished, it goes directly into the endoplasmic reticulum for post-translational processing. Note that it is now known as pre-pro-collagen. 3. Alpha Peptide to Procollagen: Three modifications of the pre-pro-peptide occurs leading to the formation of the alpha peptide. Secondly, the triple helix known as procollagen is formed before being transported in a transport vesicle to the golgi apparatus. 1) The signal peptide on the N-terminal is dissolved, and the molecule is now known as propeptide (not procollagen). 2) Hydroxylation of lysines and prolines on propeptide by the enzymes prolyl hydroxylase and lysyl hydroxylase (to produce hydroxyproline and hydroxylysine) occurs to aid crosslinking of the alpha peptides. It is this enzymatic step that requires vitamin C as a cofactor. In scurvy, the lack of hydroxylation of prolines and lysines causes a looser triple helix (which is formed by 3 alpha peptides). 3) Glycosylation occurs by adding either glucose or galactose monomers onto the hydroxy groups that were placed onto lysines, but not on prolines. From here the hydroxylated and glycosylated propeptide twists towards the left very tightly and then three propeptides will form a triple helix. It is important to remember that this molecule, now known as procollagen (not propeptide) is composed of a twisted portion (center) and two loose ends on either end. At this point the procollagen is packaged into a transfer vesicle destined for the golgi apparatus. 4. Golgi Apparatus Modification: In the golgi apparatus, the procollagen goes through one last post-translational modification before being secreted out of the cell. In this step oligosaccharides (not monosaccharides like in step 3) are added, and then the procollagen is packaged into a secretory vesicle destined for the extracellular space. 5. Formation of Tropocollagen: Once outside the cell, membrane bound enzymes known as collagen peptidases, remove the "loose ends" of the procollagen molecule. What is left is known as tropocollagen. Defect in this step produces one of the many collagenopathies known as Ehlers-Danlos syndrome. This step is absent when synthesizing type III, a type of fibrilar collagen. 6. Formation of the Collagen Fibril: Lysyl oxidase and extracellular enzyme produces the final step in the collagen synthesis pathway. This enzyme acts on lysines and hydroxylysines producing aldehyde groups, which will eventually undergo covalent bonding between tropocollagen molecules. This polymer of tropocollogen is known as a collagen fibril.

138

Molecular structure
The tropocollagen or collagen molecule is a subunit of larger collagen aggregates such as fibrils. At approximately 300 nm long and 1.5 nm in diameter, it is made up of three polypeptide strands (called alpha peptides, see step 2), each possessing the conformation of a left-handed helix (its name is not to be confused with the commonly occurring alpha helix, a right-handed structure). These three left-handed helices are twisted together into a right-handed coiled coil, a triple helix or "super helix", a cooperative quaternary structure stabilized by numerous hydrogen bonds. With type I collagen and possibly all fibrillar collagens if not all collagens, each triple-helix associates into a right-handed super-super-coil referred to as the collagen microfibril. Each microfibril is interdigitated with its neighboring microfibrils to a degree that might suggest they are individually unstable, although within collagen fibrils, they are so well ordered as to be crystalline.

Collagen A distinctive feature of collagen is the regular arrangement of amino acids in each of the three chains of these collagen subunits. The sequence often follows the pattern Gly-Pro-X or Gly-X-Hyp, where X may be any of various other amino acid residues.[23] Proline or hydroxyproline constitute about 1/6 of the total sequence. With glycine accounting for the 1/3 of the sequence, this means approximately half of the collagen sequence is not glycine, proline or hydroxyproline, a fact often missed due to the distraction of the unusual GX1X2 character of collagen alpha-peptides. The high glycine content of collagen is important with respect to stabilization of the collagen helix as this allows the very close association of the collagen fibers within the molecule, facilitating hydrogen bonding and the formation of intermolecular cross-links.[23] This kind of regular repetition and high glycine content is found in only a few other fibrous proteins, such as silk fibroin. About 75-80% of silk is (approximately) -Gly-Ala-Gly-Alawith 10% serine, and elastin is rich in glycine, proline, and alanine (Ala), whose side group is a small, inert methyl group. Such high glycine and regular repetitions are never found in globular proteins save for very short sections of their sequence. Chemically-reactive side groups are not needed in structural proteins, as they are in enzymes and transport proteins; however, collagen is not quite just a structural protein. Due to its key role in the determination of cell phenotype, cell adhesion, tissue regulation and infrastructure, many sections of its nonproline-rich regions have cell or matrix association / regulation roles. The relatively high content of proline and hydroxyproline rings, with their geometrically constrained carboxyl and (secondary) amino groups, along with the rich abundance of glycine, accounts for the tendency of the individual polypeptide strands to form left-handed helices spontaneously, without any intrachain hydrogen bonding. Because glycine is the smallest amino acid with no side chain, it plays a unique role in fibrous structural proteins. In collagen, Gly is required at every third position because the assembly of the triple helix puts this residue at the interior (axis) of the helix, where there is no space for a larger side group than glycine’s single hydrogen atom. For the same reason, the rings of the Pro and Hyp must point outward. These two amino acids help stabilize the triple helix—Hyp even more so than Pro; a lower concentration of them is required in animals such as fish, whose body temperatures are lower than most warm-blooded animals. Lower proline and hydroxyproline contents are characteristic of cold-water, but not warm-water fish; the latter tend to have similar proline and hydroxyproline contents to mammals.[23] The lower proline and hydroxproline contents of cold-water fish and other poikilotherm animals leads to their collagen having a lower thermal stability than mammalian collagen.[23] This lower thermal stability means that gelatin derived from fish collagen is not suitable for many Gelatin. The tropocollagen subunits spontaneously self-assemble, with regularly staggered ends, into even larger arrays in the extracellular spaces of tissues.[25][26] In the fibrillar collagens, the molecules are staggered from each other by about 67 nm (a unit that is referred to as ‘D’ and changes depending upon the hydration state of the aggregate). Each D-period contains four plus a fraction collagen molecules, because 300 nm divided by 67 nm does not give an integer (the length of the collagen molecule divided by the stagger distance D). Therefore, in each D-period repeat of the microfibril, there is a part containing five molecules in cross-section, called the “overlap”, and a part containing only four molecules, called the "gap".[21] The triple-helices are also arranged in a hexagonal or quasihexagonal array in cross-section, in both the gap and overlap regions.[13][21] There is some covalent crosslinking within the triple helices, and a variable amount of covalent crosslinking between tropocollagen helices forming well organized aggregates (such as fibrils).[27] Larger fibrillar bundles are formed with the aid of several different classes of proteins (including different collagen types), glycoproteins and proteoglycans to form the different types of mature tissues from alternate combinations of the same key players.[26] Collagen's insolubility was a barrier to the study of monomeric collagen until it was found that tropocollagen from young animals can be extracted because it is not yet fully crosslinked. However, advances in microscopy techniques electron microscopy (EM) and atomic force microscopy (AFM)) and X-ray diffraction have enabled researchers to obtain increasingly detailed images of collagen structure in situ. These later advances are particularly important to better understanding the way in which collagen structure affects cell-cell and cell-matrix communication, and how tissues are constructed in growth and repair, and changed in development and disease.[28][29] For example using AFM –based nanoindentation it has been shown that a single collagen fibril is a heterogeneous material along its

139

Collagen axial direction with significantly different mechanical properties in its gap and overlap regions, correlating with its different molecular organizations in these two regions.[30] Collagen fibrils are semicrystalline aggregates of collagen molecules. Collagen fibers are bundles of fibrils. Collagen fibrils/aggregates are arranged in different combinations and concentrations in various tissues to provide varying tissue properties. In bone, entire collagen triple helices lie in a parallel, staggered array. 40 nm gaps between the ends of the tropocollagen subunits (approximately equal to the gap region) probably serve as nucleation sites for the deposition of long, hard, fine crystals of the mineral component, which is (approximately) C6H12O6 with some phosphate. It is in this way that certain kinds of cartilage turn into bone. Type I collagen gives bone its tensile strength.

140

Types and associated disorders
Collagen occurs in many places throughout the body. Over 90% of the collagen in the body, however, is of type one.[31] So far, 28 types of collagen have been identified and described. The five most common types are: • Collagen I: skin, tendon, vascular ligature, organs, bone (main component of the organic part of bone) • Collagen II: cartilage (main component of cartilage) • Collagen III: reticulate (main component of reticular fibers), commonly found alongside type I. • Collagen IV: forms bases of cell basement membrane • Collagen V: cell surfaces, hair and placenta Collagen-related diseases most commonly arise from genetic defects or nutritional deficiencies that affect the biosynthesis, assembly, postranslational modification, secretion, or other processes involved in normal collagen production.
Type I Notes This is the most abundant collagen of the human body. It is present in scar tissue, the end product when tissue heals by repair. It is found in tendons, skin, artery walls, cornea, the endomysium of myofibrils, fibrocartilage, and the organic part of bones and teeth. Hyaline cartilage, makes up 50% of all cartilage protein. Vitreous humour of the eye. Gene(s) COL1A1, COL1A2 Disorders Osteogenesis imperfecta, Ehlers–Danlos syndrome, Infantile cortical hyperostosis aka Caffey's disease Collagenopathy, types II and XI

II

COL2A1

III

This is the collagen of granulation tissue, and is produced quickly by young COL3A1 fibroblasts before the tougher type I collagen is synthesized. Reticular fiber. Also found in artery walls, skin, intestines and the uterus Basal lamina; eye lens. Also serves as part of the filtration system in capillaries and the glomeruli of nephron in the kidney. COL4A1, COL4A2, COL4A3, COL4A4, COL4A5, COL4A6 COL5A1, COL5A2, COL5A3 COL6A1, COL6A2, COL6A3, COL6A5 COL7A1 COL8A1, COL8A2

Ehlers–Danlos syndrome, Dupuytren's contracture

IV

Alport syndrome, Goodpasture's syndrome

V

Most interstitial tissue, assoc. with type I, associated with placenta

Ehlers–Danlos syndrome (Classical) Ulrich myopathy, Bethlem [32] myopathy, Atopic dermatitis Epidermolysis bullosa dystrophica Posterior polymorphous corneal dystrophy 2 EDM2 and EDM3

VI

Most interstitial tissue, assoc. with type I

VII VIII

Forms anchoring fibrils in dermoepidermal junctions Some endothelial cells

IX

FACIT collagen, cartilage, assoc. with type II and XI fibrils

COL9A1, COL9A2, COL9A3 COL10A1

X

Hypertrophic and mineralizing cartilage

Schmid metaphyseal dysplasia

Collagen

141
Cartilage FACIT collagen, interacts with type I containing fibrils, decorin and glycosaminoglycans Transmembrane collagen, interacts with integrin a1b1, fibronectin and components of basement membranes like nidogen and perlecan. FACIT collagen – – Transmembrane collagen, also known as BP180, a 180 kDa protein COL11A1, COL11A2 Collagenopathy, types II and XI COL12A1 –

XI XII

XIII

COL13A1

XIV XV XVI XVII

COL14A1 COL15A1 COL16A1 COL17A1

– – – Bullous pemphigoid and certain forms of junctional epidermolysis bullosa – – – – – – – – – – –

XVIII XIX XX XXI XXII XXIII XXIV XXV XXVI XXVII

Source of endostatin FACIT collagen – FACIT collagen – MACIT collagen – – – –

COL18A1 COL19A1 COL20A1 COL21A1 COL22A1 COL23A1 COL24A1 COL25A1 EMID2 COL27A1 COL28A1

XXVIII –

In addition to the above mentioned disorders, excessive deposition of collagen occurs in scleroderma.

Collagen

142

Staining
In histology, collagen is brightly eosinophilic (pink) in standard H&E slides. The dye methyl violet may be used to stain the collagen in tissue samples. The dye methyl blue can also be used to stain collagen and immunohistochemical stains are available if required. The best stain for use in differentiating collagen from other fibers is Masson's trichrome stain.

Synthesis
Amino acids
Collagen has an unusual amino acid composition and sequence: • Glycine (Gly) is found at almost every third residue • Proline (Pro) makes up about 17% of collagen • Collagen contains two uncommon derivative amino acids not directly inserted during translation. These amino acids are found at specific locations relative to glycine and are modified post-translationally by different enzymes, both of which require vitamin C as a cofactor. • Hydroxyproline (Hyp), derived from proline. • Hydroxylysine (Hyl), derived from lysine (Lys). Depending on the type of collagen, varying numbers of hydroxylysines are glycosylated (mostly having disaccharides attached). Cortisol stimulates degradation of (skin) collagen into amino acids.[33]

Collagen I formation
Most collagen forms in a similar manner, but the following process is typical for type I: 1. Inside the cell
Action of lysyl oxidase

1. Two types of peptide chains are formed during translation on ribosomes along the rough endoplasmic reticulum (RER): alpha-1 and alpha-2 chains. These peptide chains (known as preprocollagen) have registration peptides on each end and a signal peptide. 2. Polypeptide chains are released into the lumen of the RER. 3. Signal peptides are cleaved inside the RER and the chains are now known as pro-alpha chains. 4. Hydroxylation of lysine and proline amino acids occurs inside the lumen. This process is dependent on ascorbic acid (Vitamin C) as a cofactor. 5. Glycosylation of specific hydroxylysine residues occurs. 6. Triple helical structure is formed inside the endoplasmic reticulum from each two alpha-1 chains and one alpha-2 chain. 7. Procollagen is shipped to the Golgi apparatus, where it is packaged and secreted by exocytosis. 2. Outside the cell 1. Registration peptides are cleaved and tropocollagen is formed by procollagen peptidase. 2. Multiple tropocollagen molecules form collagen fibrils, via covalent cross-linking (aldol reaction) by lysyl oxidase which links hydroxylysine and lysine residues. Multiple collagen fibrils form into collagen fibers. 3. Collagen may be attached to cell membranes via several types of protein, including fibronectin and integrin.

Collagen

143

Synthetic pathogenesis
Vitamin C deficiency causes scurvy, a serious and painful disease in which defective collagen prevents the formation of strong connective tissue. Gums deteriorate and bleed, with loss of teeth; skin discolors, and wounds do not heal. Prior to the eighteenth century, this condition was notorious among long duration military, particularly naval, expeditions during which participants were deprived of foods containing Vitamin C. An autoimmune disease such as lupus erythematosus or rheumatoid arthritis[34] may attack healthy collagen fibers. Many bacteria and viruses have virulence factors which destroy collagen or interfere with its production.

Characteristics
Collagen is one of the long, fibrous structural proteins whose functions are quite different from those of globular proteins such as enzymes. Tough bundles of collagen called collagen fibers are a major component of the extracellular matrix that supports most tissues and gives cells structure from the outside, but collagen is also found inside certain cells. Collagen has great tensile strength, and is the main component of fascia, cartilage, ligaments, tendons, bone and skin.[35][36] Along with soft keratin, it is responsible for skin strength and elasticity, and its degradation leads to wrinkles that accompany aging.[37][38] It strengthens blood vessels and plays a role in tissue development. It is present in the cornea and lens of the eye in crystalline form.

Uses
Collagen has a wide variety of applications, from food to medical. For instance, it is used in cosmetic surgery and burns surgery. It is widely used in the form of collagen casings for sausages. If collagen is sufficiently denatured, e.g. by heating, the three tropocollagen strands separate partially or completely into globular domains, containing a different secondary structure to the normal collagen polyproline II (PPII), e.g. random coils. This process describes the formation of gelatin, which is used in many foods, including flavored gelatin desserts. Besides food, gelatin has been used in pharmaceutical, cosmetic, and photography industries.[39] From a nutritional point of view, collagen and gelatin are a poor-quality sole source of protein since they do not contain all the essential amino acids in the proportions that the human body requires—they are not 'complete proteins' (as defined by food science, not that they are partially structured). Manufacturers of collagen-based dietary supplements claim that their products can improve skin and fingernail quality as well as joint health. However, mainstream scientific research has not shown strong evidence to support these claims. Individuals with problems in these areas are more likely to be suffering from some other underlying condition (such as normal aging, dry skin, arthritis etc.) rather than just a protein deficiency. From the Greek for glue, kolla, the word collagen means "glue producer" and refers to the early process of boiling the skin and sinews of horses and other animals to obtain glue. Collagen adhesive was used by Egyptians about 4,000 years ago, and Native Americans used it in bows about 1,500 years ago. The oldest glue in the world, carbon-dated as more than 8,000 years old, was found to be collagen—used as a protective lining on rope baskets and embroidered fabrics, and to hold utensils together; also in crisscross decorations on human skulls.[40] Collagen normally converts to gelatin, but survived due to the dry conditions. Animal glues are thermoplastic, softening again upon reheating, and so they are still used in making musical instruments such as fine violins and guitars, which may have to be reopened for repairs—an application incompatible with tough, synthetic plastic adhesives, which are permanent. Animal sinews and skins, including leather, have been used to make useful articles for millennia. Gelatin-resorcinol-formaldehyde glue (and with formaldehyde replaced by less-toxic pentanedial and ethanedial) has been used to repair experimental incisions in rabbit lungs.[41]

Collagen

144

Medical uses
Cardiac applications
The four dense collagen valve rings, the central body of the heart and the cardiac skeleton of the heart are histologically bound to the myocardium. Collagen contribution to heart performance summarily represents an essential, unique and moving solid anchor opposed to the fluid mechanics of blood within the heart. This structure is an impermeable firewall that excludes both blood and electrical influence (except through anatomical channels) from the upper to the lower chambers of the heart. As proof, one could posit that atrial fibrillation almost never deteriorates to ventricular fibrillation. Individual valvular leaflets are held in sail shape by collagen under variable pressure. Calcium deposition within collagen occurs as a natural consequence of aging. Calcium rich fixed points in an otherwise moving display of blood and muscle enable current cardiac imaging technology to arrive at ratios essentially stating blood in cardiac input and blood out cardiac output. Specified imaging such as calcium scoring illustrates the utility of this methodology, especially in an aging patient subject to pathology of the collagen underpinning.

Type II Collagen and Rheumatoid Arthritis
According to a study[42] published in the journal Science, oral administration of type II collagen improves symptoms of rheumatoid arthritis. The authors conducted a randomized, double-blind trial involving 60 patients with severe, active rheumatoid arthritis. A decrease in the number of swollen joints and tender joints occurred in subjects fed with chicken type II collagen for 3 months, but not in those that received a placebo. Four patients in the collagen group had complete remission of the disease. No side effects were evident.

Cosmetic surgery
Collagen has been widely used in cosmetic surgery, as a healing aid for burn patients for reconstruction of bone and a wide variety of dental, orthopedic and surgical purposes. Both human and bovine collagen is widely used as dermal fillers for treatment of wrinkles and skin aging.[38] Some points of interest are: 1. when used cosmetically, there is a chance of allergic reactions causing prolonged redness; however, this can be virtually eliminated by simple and inconspicuous patch testing prior to cosmetic use, and 2. most medical collagen is derived from young beef cattle (bovine) from certified BSE (bovine spongiform encephalopathy) free animals. Most manufacturers use donor animals from either "closed herds", or from countries which have never had a reported case of BSE such as Australia, Brazil and New Zealand. 3. porcine (pig) tissue is also widely used for producing collagen sheet for a variety of surgical purposes. 4. alternatives using the patient's own fat, hyaluronic acid or polyacrylamide gels which are readily available.

Reconstructive surgical uses
Collagens are widely employed in the construction of artificial skin substitutes used in the management of severe burns. These collagens may be derived from bovine, equine or porcine, and even human sources and are sometimes used in combination with silicones, glycosaminoglycans, fibroblasts, growth factors and other substances. Collagen is also sold as a pill commercially as a joint mobility supplement with poor references.[43] Because proteins are broken down into amino acids before absorption, there is no reason for orally ingested collagen to affect connective tissue in the body, except through the effect of individual amino acid supplementation. Although it cannot be absorbed through the skin, collagen is now being used as a main ingredient for some cosmetic makeup.[44] Collagen is also frequently used in scientific research applications for cell culture, studying cell behavior and cellular interactions with the extracellular environment.[45] Suppliers such as Trevigen [46] manufacture rat and bovine

Collagen Collagen I and mouse Collagen IV.

145

Wound care management uses
Collagen is one of the body’s key natural resources and a component of skin tissue that can benefit all stages of the wound healing process. When collagen is made available to the wound bed, closure can occur. Wound deterioration, followed sometimes by procedures such as amputation, can thus be avoided. Throughout the 4 phases of wound healing, collagen performs the following functions in wound healing: • Guiding Function: Collagen fibers serve to guide fibroblasts. Fibroblasts migrate along a connective tissue matrix. • Chemotactic Properties: The large surface area available on collagen fibers can attract fibrogenic cells which help in healing. • Nucleation: Collagen, in the presence of certain neutral salt molecules can act as a nucleating agent causing formation of fibrillar structures. A collagen wound dressing might serve as a guide for orienting new collagen deposition and capillary growth. • Hemostatic properties: Blood platelets interact with the collagen to make a hemostatic plug. Suppliers such as Human BioSciences [47] manufacture bovine type 1 collagen into wound care bandages.

Paleontology and Archaeology
Because the synthesis of collagen requires a high level of atmospheric oxygen, complex animals may not have been able to evolve until the atmosphere was oxygenic enough for collagen synthesis.[48] The origin of collagen may have allowed cuticle, shell and muscle formation. However, the preservation of collagen in the fossil record is very scarce.[49] There is mounting evidence—which remains controversial—that collagen has been preserved in dinosaur specimens dated as long ago as 80 [50] million years ago.[51] Also worth noting are the actinofibrils, collagen fibers present on the wings of pterosaurs. Collagen is regularly extracted from the bones of prehistoric animals for use in radiocarbon dating and stable isotope analysis. The integrity of the molecule can be assessed with a number of measurements (collagen yield, C:N ratio, %C and %N).[23] With respect to radiometric dating, extracted collagen produces a 'more pure' form of carbon that can be dated than does bulk bone, which contains a high amount of carbonated apatite, which is prone to exchange with environmental sources of carbon, causing contamination. Stable isotope analysis of carbon and nitrogen are commonly used to study diet in past populations of humans, as well as to reconstruct ecological conditions.

Art
Using the atomic coordinates deposited in the Protein Data Bank, German-American artist Julian Voss-Andreae has created sculptures based on the structure of collagen and other proteins.[52] In Unraveling Collagen the triangular cut-outs reveal the dominant force lines, reminiscent of contemporary steel construction.[53][54]

References
[1] Müller, Werner E. G. (2003). "The Origin of Metazoan Complexity: Porifera as Integrated Animals". Integrated Computational Biology 43 (1): 3–10. doi:10.1093/icb/43.1.3. [2] Di Lullo, Gloria A.; Sweeney, Shawn M.; Körkkö, Jarmo; Ala-Kokko, Leena & San Antonio, James D. (2002). "Mapping the Ligand-binding Sites and Disease-associated Mutations on the Most Abundant Protein in the Human, Type I Collagen". J. Biol. Chem. 277 (6): 4223–4231. doi:10.1074/jbc.M110709200. PMID 11704682. Julian Voss-Andreae's sculpture Unraveling Collagen (2005), stainless steel, height 11 ft 3 in (3.40 m).

[3] Sikorski, Zdzisław E. (2001). Chemical and Functional Properties of Food Proteins. Boca Raton: CRC Press. p. 242. ISBN 1-56676-960-4.

Collagen
[4] Wyckoff, R.; Corey, R. & Biscoe, J. (1935). "X-ray reflections of long spacing from tendon". Science 82 (2121): 175–176. doi:10.1126/science.82.2121.175. PMID 17810172. [5] Clark, G.; Parker, E.; Schaad, J. & Warren, W. J. (1935). "New measurements of previously unknown large interplanar spacings in natural materials". J. Amer. Chem. Soc 57 (8): 1509. doi:10.1021/ja01311a504. [6] "GNR — A Tribute - Resonance - October 2001" (http:/ / www. ias. ac. in/ resonance/ Oct2001/ Oct2001p2-5. html). . [7] Leonidas, Demetres D.; et al., GB; Jardine, AM; Li, S; Shapiro, R; Acharya, KR (2001). "Binding of Phosphate and pyrophosphate ions at the active site of human angiogenin as revealed by X-ray crystallography". Protein Science 10 (8): 1669–1676. doi:10.1110/ps.13601. PMC 2374093. PMID 11468363. [8] Subramanian, Easwara (2001). "Obituary: G.N. Ramachandran". Nature Structural & Molecular Biology 8 (6): 489–491. doi:10.1038/88544. PMID 11373614. [9] Fraser, R. D.; MacRae, T. P. & Suzuki, E. (1979). "Chain conformation in the collagen molecule". J Mol Biol 129 (3): 463–481. doi:10.1016/0022-2836(79)90507-2. PMID 458854. [10] Okuyama, K.; et al., K; Arnott, S; Takayanagi, M; Kakudo, M (1981). "Crystal and molecular structure of a collagen-like polypeptide (Pro-Pro-Gly)10". J Mol Biol 152 (2): 427–443. doi:10.1016/0022-2836(81)90252-7. PMID 7328660. [11] Traub, W.; Yonath, A. & Segal, D. M. (1969). "On the molecular structure of collagen". Nature 221 (5184): 914–917. doi:10.1038/221914a0. [12] Bella, J.; Eaton, M.; Brodsky, B.; Berman, H. M. (1994). "Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution". Science 266 (5182): 75–81. doi:10.1126/science.7695699. PMID 7695699. [13] Hulmes, D. J. & Miller, A. (1979). "Quasi-hexagonal molecular packing in collagen fibrils". Nature 282 (5741): 878–880. doi:10.1038/282878a0. PMID 514368. [14] Jesior, J. C.; Miller, A. & Berthet-Colominas, C. (1980). "Crystalline three-dimensional packing is general characteristic of type I collagen fibrils". FEBS Lett 113 (2): 238–240. doi:10.1016/0014-5793(80)80600-4. PMID 7389896. [15] Fraser, R. D. B. & MacRae, T. P. (1981). "Unit cell and molecular connectivity in tendon collagen". Int. J. Biol. Macromol. 3 (3): 193–200. doi:10.1016/0141-8130(81)90063-5. [16] Fraser, R. D.; MacRae, T. P.; Miller, A. (1987). "Molecular packing in type I collagen fibrils". J Mol Biol 193 (1): 115–125. doi:10.1016/0022-2836(87)90631-0. PMID 3586015. [17] Wess, T. J.; et al., AP; Wess, L; Miller, A (1998). "Molecular packing of type I collagen in tendon". J Mol Biol 275 (2): 255–267. doi:10.1006/jmbi.1997.1449. PMID 9466908. [18] Raspanti, M.; Ottani, V.; Ruggeri, A. (1990). "Subfibrillar architecture and functional properties of collagen: a comparative study in rat tendons". J Anat. 172: 157–164. PMC 1257211. PMID 2272900. [19] Holmes, D. F.; Gilpin, C. J.; Baldock, C.; Ziese, U.; Koster, A. J.; Kadler, K. E. (2001). "Corneal collagen fibril structure in three dimensions: Structural insights into fibril assembly, mechanical properties, and tissue organization". PNAS 98 (13): 7307–7312. doi:10.1073/pnas.111150598. PMC 34664. PMID 11390960. [20] Holmes, D. F.; Kadler, KE (2006). "The 10+4 microfibril structure of thin cartilage fibrils". PNAS 103 (46): 17249–17254. doi:10.1073/pnas.0608417103. PMC 1859918. PMID 17088555. [21] Orgel, J. P.; et al., TC; Miller, A; Wess, TJ (2006). "Microfibrillar structure of type I collagen in situ". PNAS 103 (24): 9001–9005. doi:10.1073/pnas.0502718103. PMC 1473175. PMID 16751282. [22] >narayanaswamy, Radhakrishnan; Shanmugasamy, Sangeetha; Shanmugasamy, Sangeetha; Gopal, Ramesh; Mandal, Asit (2011). "Bioinformatics in crosslinking chemistry of collagen with selective crosslinkers". BMC 4: 399. doi:10.1186/1756-0500-4-399. [23] Szpak, Paul (2011). "Fish bone chemistry and ultrastructure: implications for taphonomy and stable isotope analysis" (http:/ / uwo. academia. edu/ PaulSzpak/ Papers/ 827788/ Fish_Bone_Chemistry_and_Ultrastructure_Implications_for_Taphonomy_and_Stable_Isotope_Analysis). Journal of Archaeological Science 38 (12): 3358–3372. doi:10.1016/j.jas.2011.07.022. . [24] [Myllyla et al., "Ascorbate is Consumed Stoichiometrically in the Uncoupled Reactions Catalyzed by Prolyl-4-Hydroxylase and Lysyl Hydroxylase. Journal of Biological Chemistry 259:5403-5405. 1984] [25] Hulmes, D. J. (2002). "Building collagen molecules, fibrils, and suprafibrillar structures". J Struct Biol 137 (1–2): 2–10. doi:10.1006/jsbi.2002.4450. PMID 12064927. [26] Hulmes, D. J. (1992). "The collagen superfamily—diverse structures and assemblies". Essays Biochem 27: 49–67. PMID 1425603. [27] Perumal, S.; Antipova, O. & Orgel, J. P. (2008). "Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis". PNAS 105 (8): 2824–2829. doi:10.1073/pnas.0710588105. PMC 2268544. PMID 18287018. [28] Sweeney, S. M.; et al., JP; Fertala, A; McAuliffe, JD; Turner, KR; Di Lullo, GA; Chen, S; Antipova, O et al. (2008). "Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates". J Biol Chem 283 (30): 21187–21197. doi:10.1074/jbc.M709319200. PMC 2475701. PMID 18487200. [29] Twardowski, T.; et al., A.; Orgel, J. P.R.O.; San Antonio, J. D. (2007). "Type I collagen and collagen mimetics as angiogenesis promoting superpolymers" (http:/ / www. ingentaconnect. com/ content/ ben/ cpd/ 2007/ 00000013/ 00000035/ art00009). Curr Pharm Des 13 (35): 3608–3621. doi:10.2174/138161207782794176. . [30] M. Minary-Jolandan and M.-F. Yu, "Nanomechanical Heterogeneity in the Gap and Overlap Regions of Type I Collagen Fibrils with Implications for Bone Heterogeneity", Biomacromolecules 10, 2565 (2009) [31] Sabiston textbook of surgery board review, 7th edition. Chapter 5 wound healing, question 14

146

Collagen
[32] Söderhäll, C.; Marenholz, I.; Kerscher, T.; Rüschendorf, F; Rüschendorf, F.; Esparza-Gordillo, J.; et al., C; Mayr, G et al. (2007). "Variants in a Novel Epidermal Collagen Gene (COL29A1) Are Associated with Atopic Dermatitis". PLoS Biology 5 (9): e242. doi:10.1371/journal.pbio.0050242. PMC 1971127. PMID 17850181. [33] Houck, J. C.; Sharma, V. K.; Patel, Y. M.; Gladner, J. A. (1968). "Induction of Collagenolytic and Proteolytic Activities by AntiInflammatory Drugs in the Skin and Fibroblasts". Biochemical Pharmacology 17 (10): 2081–2090. doi:10.1016/0006-2952(68)90182-2. PMID 4301453. [34] Al-Hadithy, H.; et al., DA; Addison, IE; Goldstone, AH; Snaith, ML (1982). "Neutrophil function in systemic lupus erythematosus and other collagen diseases". Ann Rheum Dis 41 (1): 33–38. doi:10.1136/ard.41.1.33. PMC 1000860. PMID 7065727. [35] Fratzl, P. (2008). Collagen: Structure and Mechanics. New York: Springer. ISBN 0-387-73905-X. [36] Buehler, M. J. (2006). "Nature designs tough collagen: Explaining the nanostructure of collagen fibrils". PNAS 103 (33): 12285–12290. doi:10.1073/pnas.0603216103. PMC 1567872. PMID 16895989. [37] Structure of Skin | The Aging Skin (http:/ / pharmaxchange. info/ press/ 2011/ 03/ the-aging-skin-part-1-structure-of-skin-and-introduction/ ) [38] Dermal Fillers | The Ageing Skin (http:/ / pharmaxchange. info/ press/ 2011/ 03/ the-ageing-skin-part-4e-dermal-fillers/ ) [39] "Gelatin's Advantages: Health, Nutrition and Safety" (http:/ / www. gmap-gelatin. com/ gelatin_adv. html). . [40] Walker, Amélie A. (May 21, 1998). "Oldest Glue Discovered" (http:/ / www. archaeology. org/ online/ news/ glue. html). Archaeology. . [41] Ennker, I. C.; et al., JüRgen; Schoon, Doris; Schoon, Heinz Adolf; Rimpler, Manfred; Hetzer, Roland (1994). "Formaldehyde-free collagen glue in experimental lung gluing" (http:/ / ats. ctsnetjournals. org/ cgi/ content/ abstract/ 57/ 6/ 1622). Ann Thorac Surg. 57 (6): 1622–1627. doi:10.1016/0003-4975(94)90136-8. PMID 8010812. . [42] Trentham, D.; Dynesius-Trentham, R.; Orav, J.; Combitchi, D.; Lorenzo, C.; Sewell, K.; Hafler, D. & Weiner, H. (1993). "Effects of Oral Administration of Type II Collagen on Rheumatoid Arthritis". Science 261 (5119): 1727–1730. doi:10.1126/science.8378772. [43] "Hydrolyzed Collagen pills usages" (http:/ / www. articlecat. com/ Article/ Hydrolyzed-Collagen--Protein-Hydrate/ 21273). . [44] "www.articlesbase.com" (http:/ / www. articlesbase. com/ skin-care-articles/ can-collagen-be-absorbed-into-the-skin-or-is-it-all-just-one-big-hoax-674325. html). . [45] Blow, Nathan (2009). "Cell culture: building a better matrix". Nature Methods 6 (8): 619–622. doi:10.1038/nmeth0809-619. [46] http:/ / www. trevigen. com/ angiocell/ cultrex. php [47] http:/ / www. humanbiosciences. com [48] http:/ / facstaff. gpc. edu/ ~pgore/ geology/ geo102/ cambrian. htm [49] We, K. M. T. O. (1996). "Fossil preservation in the Burgess Shale". Lethaia 29 (1): 107–108. doi:10.1111/j.1502-3931.1996.tb01844.x. [50] http:/ / toolserver. org/ ~verisimilus/ Timeline/ Timeline. php?Ma=80 [51] Schweitzer, H. .; Zheng, W. .; Organ, L. .; Avci, R. .; Suo, Z. .; Freimark, M. .; Lebleu, S. .; Duncan, B. . et al.; Wenxia Zheng,1 Chris L. Organ,3 Recep Avci,4 Zhiyong Suo,4 Lisa M. Freimark,5 Valerie S. Lebleu,6,7 Michael B. Duncan,6,7 Matthew G. Vander Heiden,8 John M. Neveu,9 William S. Lane,9 John S. Cottrell,10 John R. Horner,11 Lewis C. Cantley,5,12 Raghu Kalluri,6,7,13 John M. Asara5,14,* (May 2009). "Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. Canadensis". Science 324 (5927): 626–631. Bibcode 2009Sci...324..626S. doi:10.1126/science.1165069. ISSN 0036-8075. PMID 19407199. [52] "PDB Community Focus: Julian Voss-Andreae, Protein Sculptor" (ftp:/ / ftp. wwpdb. org/ pub/ pdb/ doc/ newsletters/ rcsb_pdb/ news32_jan07. pdf). Protein Data Bank Newsletter (32). Winter 2007. . [53] Ward, Barbara (April 2006). "'Unraveling Collagen' structure to be installed in Orange Memorial Park Sculpture Garden" (http:/ / www. future-drugs. com/ doi/ pdf/ 10. 1586/ 14789450. 3. 2. 169). Expert Rev. Proteomics 3 (2) (2): 174. doi:10.1586/14789450.3.2.169. . [54] Interview with J. Voss-Andreae "Seeing Below the Surface" in Seed Magazine (http:/ / seedmagazine. com/ news/ 2006/ 05/ seeing_below_the_surface. php)

147

External links
• • • • • • • • The Collagen Protein (http://macromoleculeinsights.com/collagen.php) Variant Collagen Products Range (http://sstwo-mall.com) collagen 6000mg (http://www.collypink.net/ข้à¸à¸¡à¸¹à¸¥-collypink.html) 12 types of collagen (http://themedicalbiochemistrypage.org/extracellularmatrix.html) Database of type I and type III collagen mutations (http://www.le.ac.uk/genetics/collagen/) Science.dirbix Collagen (http://science.dirbix.com/biology/collagen) Collagen Stability Calculator (http://compbio.cs.princeton.edu/csc/) Computer-generated animations of the assembly of Type I and Type IV Collagens (http://www.mc.vanderbilt. edu/cmb/collagen/)

• Integrin-Collagen interface, PMAP (http://www.youtube.com/watch?v=_a8q2OWrdvM) (The Proteolysis Map)—animation • Integrin-Collagen binding model, PMAP (http://www.youtube.com/watch?v=8BMFqRmbbes) (The Proteolysis Map)—animation

Collagen • Collagen-Integrin atomic detail, PMAP (http://www.youtube.com/watch?v=8L3a7oqQPRY) (The Proteolysis Map)—animation

148

Connective tissue
"Connective tissue" is a fibrous and most diverse tissue.[1] It is one of the four traditional classes of tissues (the others being epithelial, muscle and nervous tissue). Connective Tissue (CT) is found throughout the body. In fact the whole framework of the skeleton and the different specialized connective tissues from the crown of the head to the toes determine the form of the body and act as an entity. CT has 3 main components: cells, fibers, and extracellular matrix, all embedded in the body fluids. Fibroblasts are the cells responsible for the production of connective tissue. The interaction of the fibers, the extracellular matrix and the water, together, form the pliable connective tissue as a whole. Connective tissue makes up a variety of physical structures including tendons and the connective framework of fibers in muscles, capsules and ligaments around joints, cartilage, bone, adipose tissue, blood and lymphatic tissue. CT is classified into three subtypes; Embryonic CT, Proper CT, and Special CT. The Proper CT subtype includes dense regular CT, dense irregular CT, and loose CT. The Special CT subtype includes cartilage, bone, adipose tissue, blood, hematopoietic tissue (tissue that makes blood cells) and lymphatic tissue. as well as the most abundant protein in mammals, Type-I collagen, making up about 25% of the total protein content.[2]

Functions of connective tissue
• • • • Storage of energy Protection of organs Providing structural framework for the body Connection of body tissues

Fiber types and characteristics of the connective tissue
Not to be confused with muscle fibers. Characteristics of connective tissue: • Cells are spread through an extracellular fluid. • Ground Substance - A clear, colorless, and viscous fluid containing glycosaminoglycans and proteoglycans to fix the bodywater and the collagen fibers in the intercellular spaces. Ground substance slows the spread of pathogens. • Fibers. Not all types of connective tissues are fibrous though. Examples are adipose tissue and blood. Adipose tissue gives "mechanical cushioning" to our body. Although there is no dense collagen network in adipose tissue, groups of adipose cells are kept together by collagen fibers and collagen sheets in order to keep fat tissue under compression in place (for example the sole of the foot). The matrix of blood is plasma. • Both the ground substance and proteins(fibers) create the matrix for connective tissue.

Connective tissue

149

Tissue Collagenous fibers Elastic fibers

Purpose -

Components Alpha polypeptide chains

Location tendon, ligament, skin, cornea, cartilage, bone, blood vessels, gut, and intervertebral disc. extracellular matrix

-

elastic microfibrill & elastin -

Reticular fibers

-

liver, bone marrow, lymphatic organs

Disorders of connective tissue
Various connective tissue conditions have been identified; these can be both inherited and environmental. • Marfan syndrome - a genetic disease causing abnormal fibrillin. • Scurvy - caused by a dietary deficiency in vitamin C, leading to abnormal collagen. • Ehlers-Danlos syndrome - deficient type III collagen- a genetic disease causing progressive deterioration of collagens, with different EDS types affecting different sites in the body, such as joints, heart valves, organ walls, arterial walls, etc. • Loeys-Dietz syndrome - a genetic disease related to Marfan syndrome, with an emphasis on vascular deterioration. • Pseudoxanthoma elasticum - an autosomal recessive hereditary disease, caused by calcification and fragmentation of elastic fibres, affecting the skin, the eyes and the cardiovascular system. • Systemic lupus erythematosus - a chronic, multisystem, inflammatory disorder of probable autoimmune etiology, occurring predominantly in young women. • Osteogenesis imperfecta (brittle bone disease) - caused by insufficient production of good quality collagen to produce healthy, strong bones. • Fibrodysplasia ossificans progressiva - disease of the connective tissue, caused by a defective gene which turns connective tissue into bone. • Spontaneous pneumothorax - collapsed lung, believed to be related to subtle abnormalities in connective tissue. • Sarcoma - a neoplastic process originating within connective tissue. • Hemangiopericytoma - a neoplastic process

Staining of connective tissue
For microscopic viewing the majority of the connective tissue staining techniques color tissue fibers in contrasting shades. Collagen may be differentially stained by any of the following techniques: • • • • • • Van Gieson's stain Masson's Trichrome stain Mallory's Aniline Blue stain Azocarmine stain Krajian's Aniline Blue stain Eosin

Connective tissue

150

References
[1] " connective tissue (http:/ / web. archive. org/ web/ 20090616022448/ http:/ / www. mercksource. com/ pp/ us/ cns/ cns_hl_dorlands_split. jsp?pg=/ ppdocs/ us/ common/ dorlands/ dorland/ eight/ 000109061. htm)" at Dorland's Medical Dictionary [2] Di Lullo, G. A. (2002). "Mapping the Ligand-binding Sites and Disease-associated Mutations on the Most Abundant Protein in the Human, Type I Collagen" (http:/ / www. jbc. org/ cgi/ content/ abstract/ 277/ 6/ 4223). Journal of Biological Chemistry 277 (6): 4223–31. doi:10.1074/jbc.M110709200. PMID 11704682. .

External links
• connective+tissue (http://www.emedicinehealth.com/script/main/srchcont_dict.asp?src=connective+tissue) at eMedicine Dictionary • Encyclopaedia Britannica, Connective Tissue (http://www.britannica.com/eb/article-9110162/ connective-tissue) • Overview at kumc.edu (http://www.kumc.edu/instruction/medicine/anatomy/histoweb/ct/ct.htm) • UIUC Histology Subject 230 (https://histo.life.illinois.edu/histo/atlas/oimages.php?oid=230) • Connective tissue atlas at uiowa.edu (http://www.medicine.uiowa.edu/anatomy/dental/genhisto/GHWIN/ unit3/index.html)

Copolymer
A heteropolymer or copolymer is a polymer derived from two (or more) monomeric species, as opposed to a homopolymer where only one monomer is used.[1] Copolymerization refers to methods used to chemically synthesize a copolymer. Commercially relevant copolymers include ABS plastic, SBR, Nitrile rubber, styrene-acrylonitrile, styrene-isoprene-styrene (SIS) and ethylene-vinyl acetate.

Vinyl Copolymer Milk

Copolymer

151

Types of copolymers
Since a copolymer consists of at least two types of constituent units (also structural units), copolymers can be classified based on how these units are arranged along the chain.[2] These include: • Alternating copolymers with regular alternating A and B units (2) • Periodic copolymers with A and B units arranged in a repeating sequence (e.g. (A-B-A-B-B-A-A-A-A-B-B-B)n)

Different types of copolymers

• Statistical copolymers are copolymers in which the sequence of monomer residues follows a statistical rule. If the probability of finding a given type monomer residue at a particular point in the chain is equal to the mole fraction of that monomer residue in the chain, then the polymer may be referred to as a truly random copolymer[3] (3). • Block copolymers comprise two or more homopolymer subunits linked by covalent bonds (4). The union of the homopolymer subunits may require an intermediate non-repeating subunit, known as a junction block. Block copolymers with two or three distinct blocks are called diblock copolymers and triblock copolymers, respectively. Copolymers may also be described in terms of the existence of or arrangement of branches in the polymer structure. Linear copolymers consist of a single main chain whereas branched copolymers consist of a single main chain with one or more polymeric side chains. Other special types of branched copolymers include star copolymers, brush copolymers, and comb copolymers. In gradient copolymers the monomer composition changes gradually along the chain. A terpolymer is a copolymer consisting of three distinct monomers. The term is derived from ter (Latin), meaning thrice, and polymer. • Stereoblock copolymers A special structure can be formed from one monomer where now the distinguishing feature is the tacticity of each block.

Graft copolymers
Graft copolymers are a special type of branched copolymer in which the side chains are structurally distinct from the main chain. The illustration (5) depicts a special case where the main chain and side chains are composed of distinct homopolymers. However, the individual chains of a graft copolymer may be homopolymers or copolymers. Note that different copolymer sequencing is sufficient to define a structural difference, thus an A-B diblock copolymer with A-B alternating copolymer side chains is properly called a graft copolymer. For example, suppose we perform a free-radical polymerization of styrene in the presence of polybutadiene, a synthetic rubber, which retains one reactive C=C double bond per residue. We get polystyrene chains growing out in either direction from some of the places where there were double bonds, with a one-carbon rearrangement. Or to look at it the other way around, the result is a polystyrene backbone with polybutadiene chains growing out of it in

Copolymer both directions. This is an interesting copolymer variant in that one of the ingredients was a polymer to begin with. As with block copolymers, the quasi-composite product has properties of both "components". In the example cited, the rubbery chains absorb energy when the substance is hit, so it is much less brittle than ordinary polystyrene. The product is called high-impact polystyrene, or HIPS.

152

Block copolymers
A special kind of copolymer is called a "block copolymer". Block copolymers are made up of blocks of different polymerized monomers.[4] For example, PS-b-PMMA is short for polystyrene-b-poly(methyl methacrylate) and is usually made by first polymerizing styrene, and then subsequently polymerizing MMA from the reactive end of the polystyrene chains. This polymer is a "diblock copolymer" because it contains two different chemical blocks. Triblocks, tetrablocks, multiblocks, etc. can also be made. Diblock copolymers are made using living polymerization techniques, such as atom transfer free radical polymerization (ATRP), reversible addition fragmentation chain transfer (RAFT), ring-opening metathesis polymerization (ROMP), and living cationic or living anionic polymerizations.[5] An emerging technique is chain shuttling polymerization. The most powerful strategy to prepare block copolymers is the chemoselective stepwise coupling between polymeric precursors and heterofunctional linking agents.[6] This method enables access to peculiarly exotic structures such as tetrablock quarterpolymers ABCD.[7] Recent research in block copolymers suggests that they may be useful in creating self-constructing fabrics with potential utility in semiconductor arrays (for example, computer memory devices) by assembling fine details atop a structured base created using conventional microlithography methods.[8] Phase separation Block copolymers are interesting because they can "microphase separate" to form periodic nanostructures, as in the styrene-butadiene-styrene block copolymer shown at right. The polymer is known as Kraton and is used for shoe soles and adhesives. Owing to the microfine structure, the transmission electron microscope or TEM was needed to examine the structure. The butadiene matrix was stained with osmium tetroxide to provide contrast in the image. The material was made by living polymerization so that the blocks are almost monodisperse, so helping to create a very regular SBS block copolymer in TEM microstructure. The molecular weight of the polystyrene blocks in the main picture is 102,000; the inset picture has a molecular weight of 91,000, producing slightly smaller domains. Microphase separation is a situation similar to that of oil and water. Oil and water are immiscible - they phase separate. Due to incompatibility between the blocks, block copolymers undergo a similar phase separation. Because the blocks are covalently bonded to each other, they cannot demix macroscopically as water and oil. In "microphase separation" the blocks form nanometer-sized structures. Depending on the relative lengths of each block, several morphologies can be obtained. In diblock copolymers, sufficiently different block lengths lead to nanometer-sized spheres of one block in a matrix of the second (for example PMMA in polystyrene). Using less different block lengths, a "hexagonally packed cylinder" geometry can be obtained.

SBS block copolymer schematic microstructure

Copolymer Blocks of similar length form layers (often called lamellae in the technical literature). Between the cylindrical and lamellar phase is the gyroid phase. The nanoscale structures created from block copolymers could potentially be used for creating devices for use in computer memory, nanoscale-templating and nanoscale separations. Polymer scientists use thermodynamics to describe how the different blocks interact. The product of the degree of polymerization, n, and the Flory-Huggins interaction parameter, , gives an indication of how incompatible the two blocks are and whether or not they will microphase separate. For example, a diblock copolymer of symmetric composition will microphase separate if the product is greater than 10.5. If is less than 10.5, the blocks will mix and microphase separation is not observed.

153

Copolymer equation
An alternating copolymer has the formula: -A-B-A-B-A-B-A-B-A-B-, or -(-A-B-)n-. The molar ratios of the monomer in the polymer is close to one, which happens when the reactivity ratios r1 & r2 are close to zero, as given by the Mayo-Lewis equation also called the copolymerization equation:[9]

where r1 = k11/k12 & r2 = k22/k21

Copolymer engineering
Copolymerization is used to modify the properties of manufactured plastics to meet specific needs, for example to reduce crystallinity, modify glass transition temperature or to improve solubility. It is a way of improving mechanical properties, in a technique known as rubber toughening. Elastomeric phases within a rigid matrix act as crack arrestors, and so increase the energy absorption when the material is impacted for example. Acrylonitrile butadiene styrene is a common example.

References
[1] Odian, G. (2004). "6" (http:/ / books. google. com/ ?id=6cjgZbFHI4kC& pg=PA464). Principles of Polymerization. Wiley-Interscience. p. 464. ISBN 0-471-27400-3. . [2] Jenkins, A. D.; Kratochvíl, P.; Stepto, R. F. T.; Suter, U. W. (1996). "Glossary of Basic Terms in Polymer Science". Pure Appl. Chem. 68 (12): 2287–2311. doi:10.1351/pac199668122287. [3] Painter P. C. and Coleman M. M., Fundamentals of Polymer Science, CRC Press, 1997, p 14. [4] Polymer Research Laboratory (http:/ / www. princeton. edu/ ~polymer/ block. html) (Princeton.edu accessed Aug 15, 2008) [5] Hadjichristidis N., Pispas S., Floudas G. Block copolymers: synthetic strategies, physical properties, and applications – Wiley, 2003. [6] Bellas, Vasilios; Rehahn, Matthias (2007). "Universal Methodology for Block Copolymer Synthesis" (http:/ / www3. interscience. wiley. com/ cgi-bin/ fulltext/ 114280481/ PDFSTART). Macromolecular Rapid Communications 28 (13): 1415. doi:10.1002/marc.200700127. . [7] Bellas, Vasilios; Rehahn, Matthias (2009). "Block Copolymer Synthesis via Chemoselective Stepwise Coupling Reactions". Macromolecular Chemistry and Physics 210 (5): 320. doi:10.1002/macp.200800463. [8] Self-growing material promises chip, storage advances (http:/ / www. networkworld. com/ community/ node/ 31115) (NetworkWorld accessed Aug 15, 2008) [9] Copolymerization. I. A Basis for Comparing the Behavior of Monomers in Copolymerization; The Copolymerization of Styrene and Methyl MethacrylateFrank R. Mayo and Frederick M. Lewis J. Am. Chem. Soc.; 1944; 66(9) pp 1594 - 1601; doi:10.1021/ja01237a052

External links
• Introduction to Polymer Chemistry (http://www.chem.rochester.edu/~chem421/copoly.htm)

Cytoplasm

154

Cytoplasm
The cytoplasm is the gel-like substance residing between the cell membrane holding all the cell's internal sub-structures (called organelles), except for the nucleus. All the contents of the cells of prokaryote organisms (which lack a cell nucleus) are contained within the cytoplasm. Within the cells of eukaryote organisms the contents of the cell nucleus are separated from the cytoplasm, and are then called the nucleoplasm. The cytoplasm is about 70% to 90% water and usually transparent.

Schematic of typical animal cell, showing subcellular components. Organelles: (1) Nucleolus (2) Nucleus (3) Ribosomes (little dots) (4) Vesicle (5) Rough endoplasmic reticulum (ER) (6) Golgi apparatus (7) Cytoskeleton (8) Smooth ER (9) Mitochondria (10) Vacuole (11) Cytosol (12) Lysosome (13) Centrioles within Centrosome

It is within the cytoplasm that most cellular activities occur, such as many metabolic pathways including glycolysis, and processes such as cell division. The inner, granular mass is called the endoplasm and the outer, clear and glassy layer is called the cell cortex or the ectoplasm. The part of the cytoplasm that is not held within organelles is called the cytosol. The cytosol is a complex mixture of cytoskeleton filaments, dissolved molecules, and water that fills much of the volume of a cell. The cytosol is a gel, with a network of fibers dispersed in water. Due to this network of fibres and high concentrations of dissolved macromolecules, such as proteins, an effect called macromolecular crowding occurs and the cytosol does not act as an ideal solution. This crowding effect alters how the components of the cytosol interact with each other. Movement of calcium ions in and out of the cytoplasm is thought to be a signaling activity for metabolic processes.[1] In plants, movements of the cytoplasm around vacuoles are known as cyclosis.

Constituents
The cytoplasm has three major elements; the cytosol, organelles and inclusions.

Cytosol
The cytosol is the portion of the cytoplasm not contained within membrane-bound organelles. Cytosol makes up about 70% of the cell volume and is composed of water, salts and organic molecules.[2] The cytosol also contains the protein filaments that make up the cytoskeleton, as well as soluble proteins and small structures such as ribosomes, proteasomes, and the mysterious vault complexes.[3] The inner, granular and more fluid portion of the cytoplasm is referred to as endoplasm.

Cytoplasm

155

Organelles
Organelles, literally little organs, are membrane-bound structures inside the cell that have specific functions. Some major organelles that are suspended in the cytosol are the mitochondria, the endoplasmic reticulum, the Golgi apparatus, vacuoles, lysosomes, and in plant cells chloroplasts.

Cytoplasmic inclusions
The inclusions are small particles of insoluble substances suspended in the cytosol. A huge range of inclusions exist in different cell types, and range from crystals of calcium oxalate or silicon dioxide in plants,[4][5] to granules of energy-storage materials such as starch,[6] glycogen,[7] or polyhydroxybutyrate.[8] A particularly widespread example are lipid droplets, which are spherical droplets composed of lipids and proteins that are used in both prokaryotes and eukaryotes as a way of storing lipids such as fatty acids and sterols.[9] Lipid droplets make up much of the volume of adipocytes, which are specialized lipid-storage cells, but they are also found in a range of other cell types.

Proteins in different cellular compartments and structures tagged with green fluorescent protein

Notes
[1] C. Michael Hogan. 2010. Calcium. eds. A.Jorgensen, C. Cleveland. Encyclopedia of Earth (http:/ / www. eoearth. org/ article/ Calcium?topic=49557). National Council for Science and the Environment. [2] Cytoplasm Composition (http:/ / sun. menloschool. org/ ~birchler/ cells/ animals/ cytoplasm/ ) [3] van Zon A, Mossink MH, Scheper RJ, Sonneveld P, Wiemer EA (September 2003). "The vault complex". Cell. Mol. Life Sci. 60 (9): 1828–37. doi:10.1007/s00018-003-3030-y. PMID 14523546. [4] Prychid, Christina J.; Rudall, Paula J. (1999). "Calcium Oxalate Crystals in Monocotyledons: A Review of their Structure and Systematics" (http:/ / aob. oxfordjournals. org/ cgi/ content/ abstract/ 84/ 6/ 725). Annals of Botany 84 (6): 725. doi:10.1006/anbo.1999.0975. . [5] Prychid, C. J.; Rudall, P. J.; Gregory, M. (2003). "Systematics and Biology of Silica Bodies in Monocotyledons" (http:/ / www. bioone. org/ perlserv/ ?request=get-abstract). The Botanical Review 69 (4): 377–440. doi:10.1663/0006-8101(2004)069[0377:SABOSB]2.0.CO;2. . [6] Ball SG, Morell MK (2003). "From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule". Annu Rev Plant Biol 54: 207–33. doi:10.1146/annurev.arplant.54.031902.134927. PMID 14502990. [7] Shearer J, Graham TE (April 2002). "New perspectives on the storage and organization of muscle glycogen". Can J Appl Physiol 27 (2): 179–203. doi:10.1139/h02-012. PMID 12179957. [8] Anderson AJ, Dawes EA (1 December 1990). "Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=2087222). Microbiol. Rev. 54 (4): 450–72. PMC 372789. PMID 2087222. . [9] Murphy DJ (September 2001). "The biogenesis and functions of lipid bodies in animals, growth and microorganisms". Prog. Lipid Res. 40 (5): 325–438. doi:10.1016/S0163-7827(01)00013-3. PMID 11470496.

Cytoplasm

156

External links
• Luby-Phelps K (2000). "Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area" (http://www.rpgroup.caltech.edu/courses/aph161/Handouts/Luby-Phelps2000. pdf) (PDF). Int Rev Cytol 192: 189–221.

DNA
Deoxyribonucleic acid ( i /diˌɒksiˌraɪbɵ.njuːˌkleɪ.ɪkˈæsɪd/; DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms (with the exception of RNA viruses). The DNA segments carrying this genetic information are called genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester The structure of the DNA double helix. The atoms in the structure are colour coded by bonds. These two strands run in element and the detailed structure of two base pairs is shown in the bottom right. opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription.

DNA

157

Within cells DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts.[1] In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

The structure of part of a DNA double helix

DNA

158

Properties
DNA is a long polymer made from repeating units called nucleotides.[2][3][4] As first discovered by James D. Watson and Francis Crick, the structure of DNA of all species comprises two helical chains each coiled round the same axis, and each with a pitch of 34 Ångströms (3.4 nanometres) and a radius of 10 Ångströms (1.0 nanometres).[5] According to another study, when measured in a particular solution, the DNA chain measured 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit measured 3.3 Å (0.33 nm) long.[6] Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.[7] In living organisms DNA does not usually Chemical structure of DNA. Hydrogen bonds shown as dotted lines. exist as a single molecule, but instead as a pair of molecules that are held tightly together.[5][8] These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a nucleobase, which interacts with the other DNA strand in the helix. A nucleobase linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. Polymers comprising multiple linked nucleotides (as in DNA) are called a polynucleotide.[9] The backbone of the DNA strand is made from alternating phosphate and sugar residues.[10] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel. The asymmetric ends of DNA strands are called the 5′ (five prime) and 3′ (three prime) ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.[8]

DNA

159

The DNA double helix is stabilized primarily by two forces: hydrogen bonds between nucleotides and base-stacking interactions among the aromatic nucleobases.[12] In the aqueous environment of the cell, the conjugated π bonds of nucleotide bases align perpendicular to the axis of the DNA molecule, minimizing their interaction with the solvation shell and therefore, the Gibbs free energy. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate. The nucleobases are classified into two types: the purines, A and G, being fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T.[8] A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. In addition to RNA and DNA a large number of artificial nucleic acid analogues have also been created to study the proprieties of nucleic acids, or for use in biotechnology.[13]

A section of DNA. The bases lie horizontally between the two [11] spiraling strands. Animated version at File:DNA orbit animated.gif.

Grooves
Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.[14] The narrowness of the minor groove means that the edges of the bases are more accessible in the Major and minor grooves of DNA. Minor groove major groove. As a result, proteins like transcription factors that can is a binding site for the dye Hoechst 33258. bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.[15] This situation varies in unusual conformations of DNA within the cell (see below), but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.

Base pairing
In a DNA double helix, each type of nucleobase on one strand normally interacts with just one type of nucleobase on the other strand. This is called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.[16] As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.[3]

DNA

160

Top, a GC base pair with three hydrogen bonds. Bottom, an AT base pair with two hydrogen bonds. Non-covalent hydrogen bonds between the pairs are shown as dashed lines. The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, right). DNA with high GC-content is more stable than DNA with low GC-content. As noted above, most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double stranded structure (dsDNA) is maintained largely by the intrastrand base stacking interactions, which are strongest for G,C stacks. The two strands can come apart – a process known as melting – to form two ss DNA molecules. Melting occurs when conditions favor ssDNA; such conditions are high temperature, low salt and high pH (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used). The stability of the dsDNA form depends not only on the GC-content (% G,C basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the "melting temperature", which is the temperature at which 50% of the ds molecules are converted to ss molecules; melting temperature is dependent on ionic strength and the concentration of DNA. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC-content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands.[17] In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.[18] In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules (ssDNA) have no single common shape, but some conformations are more stable than others.[19]

Sense and antisense
A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein.[20] The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear.[21] One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.[22] A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction between sense and antisense strands by having overlapping genes.[23] In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction along the other strand. In bacteria, this overlap may be involved in the regulation of gene transcription,[24] while in viruses,

DNA overlapping genes increase the amount of information that can be encoded within the small viral genome.[25]

161

Supercoiling
DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.[26] If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases.[27] These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.[28]

Alternate DNA structures
DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although, only B-DNA and Z-DNA have been directly observed in functional organisms.[10] The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases, the type and concentration of metal ions, as well as the presence of polyamines in solution.[29]

The first published reports of A-DNA X-ray diffraction patterns— and also B-DNA used analyses based on Patterson transforms that provided only a limited amount of structural information for oriented fibers of DNA.[30][31] An alternate analysis was then proposed by Wilkins et al., in 1953, for the in vivo B-DNA X-ray diffraction/scattering patterns of highly hydrated DNA fibers in terms of squares of Bessel functions.[32] In the same journal, James D. Watson and Francis Crick presented their molecular modeling analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double-helix.[5] Although the `B-DNA form' is most common under the conditions found in cells,[33] it is not a well-defined conformation but a family of related DNA conformations[34] that occur at the high hydration levels present in living cells. Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder.[35][36] Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in partially dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.[37][38] Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.[39] These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.[40]

From left to right, the structures of A, B and Z DNA

DNA

162

Alternate DNA chemistry
For a number of years exobiologists have proposed the existence of a shadow biosphere, a postulated microbial biosphere of Earth that uses radically different biochemical and molecular processes than currently known life. One of the proposals was the existence of lifeforms that use arsenic instead of phosphorus in DNA. A December 2010 NASA press conference stated that the bacterium GFAJ-1, which has evolved in an arsenic-rich environment, is the first terrestrial lifeform found which may have this ability. The bacterium was found in Mono Lake, east of Yosemite National Park. GFAJ-1 is a rod-shaped extremophile bacterium in the family Halomonadaceae that, when starved of phosphorus, may be capable of incorporating the usually poisonous element arsenic in its DNA.[41] This discovery may lend weight to the long-standing idea that extraterrestrial life could have a different chemical makeup from life on Earth.[41][42] The research was carried out by a team led by Felisa Wolfe-Simon, a geomicrobiologist and geobiochemist, a Postdoctoral Fellow of the NASA Astrobiology Institute with Arizona State University. This finding has, however, faced strong criticism from the scientific community; scientists have argued that there is no evidence that arsenic is actually incorporated into biomolecules.[42][43] Independent confirmation of this finding has also not yet been possible.

Quadruplex structures
At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes.[44] These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected.[45] In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.[46] These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.[48] These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit.[49] Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins.[50] At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.[48]

DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone [47] is very different from the typical DNA helix.

Single branch Multiple branches

DNA
Branched DNA can form networks containing multiple branches.

163

Branched DNA
In DNA fraying occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand. Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible.[51] Branched DNA can be used in nanotechnology to construct geometric shapes, see the section on uses in technology below.

Vibration
DNA may carry out low-frequency collective motion as observed by the Raman spectroscopy[52][53] and analyzed with a quasi-continuum model.[54][55]

Chemical modifications

cytosine

5-methylcytosine

thymine

Structure of cytosine with and without the 5-methyl group. Deamination converts 5-methylcytosine into thymine.

Base modifications
The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called chromatin. Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of methylation of cytosine bases. For example, cytosine methylation, produces 5-methylcytosine, which is important for X-chromosome inactivation.[56] The average level of methylation varies between organisms – the worm Caenorhabditis elegans lacks cytosine methylation, while vertebrates have higher levels, with up to 1% of their DNA containing 5-methylcytosine.[57] Despite the importance of 5-methylcytosine, it can deaminate to leave a thymine base, so methylated cytosines are particularly prone to mutations.[58] Other base modifications include adenine methylation in bacteria, the presence of 5-hydroxymethylcytosine in the brain,[59] and the glycosylation of uracil to produce the "J-base" in kinetoplastids.[60][61]

DNA

164

Damage
DNA can be damaged by many sorts of mutagens, which change the DNA sequence. Mutagens include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. The type of DNA damage produced depends on the type of mutagen. For example, UV light can damage DNA by producing thymine dimers, which are cross-links between pyrimidine bases.[63] On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, and double-strand breaks.[64] A typical human cell contains about 150,000 bases that have suffered oxidative damage.[65] Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations.[66] These mutations can cause cancer. Because of inherent limitations in the DNA repair mechanisms, if humans lived long enough, they would all eventually develop cancer.[67][68]

Many mutagens fit into the space between two adjacent base pairs, this is called intercalation. Most intercalators are aromatic and planar molecules; examples include ethidium bromide, acridines, daunomycin, and doxorubicin. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. This inhibits both transcription and DNA replication, causing toxicity and mutations.[69] As a result, DNA intercalators may be carcinogens, and in the case of thalidomide, a teratogen.[70] Others such as benzo[a]pyrene diol epoxide and aflatoxin form DNA adducts which induce errors in replication.[71] Nevertheless, due to their ability to inhibit DNA transcription and replication, other similar toxins are also used in chemotherapy to inhibit rapidly growing cancer cells.[72]

A covalent adduct between a metabolically activated form of benzo[a]pyrene, the major [62] mutagen in tobacco smoke, and DNA

Biological functions
DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes.[73] The information carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation, which depends on the same interaction between RNA nucleotides. In alternative fashion, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here we focus on the interactions between DNA and other molecules that mediate the function of the genome.

DNA

165

Genes and genomes
Genomic DNA is tightly and orderly packed in the process called DNA condensation to fit the small available volumes of the cell. In eukaryotes, DNA is located in the cell nucleus, as well as small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.[74] The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame. In many species, only a small fraction of the total sequence of the genome encodes protein. For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences.[75] The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, or C-value, among species represent a long-standing puzzle known as the "C-value enigma".[76] However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression.[77] Some noncoding DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes.[45][79] An abundant form of noncoding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation.[80] These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence.[81]
T7 RNA polymerase (blue) producing a mRNA [78] (green) from a DNA template (orange).

Transcription and translation

A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT). In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons ( combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.

DNA

166

Replication
Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are DNA replication. The double helix is unwound by a helicase and topoisomerase. Next, separated and then each strand's one DNA polymerase produces the leading strand copy. Another DNA polymerase binds complementary DNA sequence is to the lagging strand. This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together. recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix.[82] In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

Interactions with proteins
All the functions of DNA depend on interactions with proteins. These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence. Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.

DNA-binding proteins

Interaction of DNA (shown in orange) with histones (shown in blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA. Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved.[83][84] The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.[85] Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation.[86] These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.[87] Other non-specific

DNA DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted DNA.[88] These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes.[89] A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair.[90] These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases. In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.[92] Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.[93] As these DNA targets can occur throughout an organism's genome, changes in The lambda repressor the activity of one type of transcription factor can affect thousands of genes.[94] helix-turn-helix transcription factor Consequently, these proteins are often the targets of the signal transduction [91] bound to its DNA target processes that control responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible.[15]

167

DNA-modifying enzymes
Nucleases and ligases Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands. The most frequently used nucleases in molecular biology are the restriction endonucleases, which The restriction enzyme EcoRV (green) in a [95] cut DNA at specific sequences. For instance, the EcoRV enzyme complex with its substrate DNA shown to the left recognizes the 6-base sequence 5′-GATATC-3′ and makes a cut at the vertical line. In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system.[96] In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting. Enzymes called DNA ligases can rejoin cut or broken DNA strands.[97] Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template. They are also used in DNA repair and genetic recombination.[97]

DNA Topoisomerases and helicases Topoisomerases are enzymes with both nuclease and ligase activity. These proteins change the amount of supercoiling in DNA. Some of these enzymes work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break.[27] Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix.[98] Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.[28] Helicases are proteins that are a type of molecular motor. They use the chemical energy in nucleoside triphosphates, predominantly ATP, to break hydrogen bonds between bases and unwind the DNA double helix into single strands.[99] These enzymes are essential for most processes where enzymes need to access the DNA bases. Polymerases Polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates. The sequence of their products are copies of existing polynucleotide chains – which are called templates. These enzymes function by adding nucleotides onto the 3′ hydroxyl group of the previous nucleotide in a DNA strand. As a consequence, all polymerases work in a 5′ to 3′ direction.[100] In the active site of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template. Polymerases are classified according to the type of template that they use. In DNA replication, a DNA-dependent DNA polymerase makes a copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a proofreading activity. Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3′ to 5′ exonuclease activity is activated and the incorrect base removed.[101] In most organisms, DNA polymerases function in a large complex called the replisome that contains multiple accessory subunits, such as the DNA clamp or helicases.[102] RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an RNA strand into DNA. They include reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses, and telomerase, which is required for the replication of telomeres.[44][103] Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.[45] Transcription is carried out by a DNA-dependent RNA polymerase that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a promoter and separates the DNA strands. It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.[104]

168

DNA

169

Genetic recombination

Structure of the Holliday junction intermediate in genetic recombination. The four separate DNA strands are coloured red, blue, green and yellow.[105] A DNA helix usually does not interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories".[106] This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is during chromosomal crossover when they recombine. Chromosomal crossover is when two DNA helices break, swap a section and then rejoin. Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of [107] new proteins. Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.[108] The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as recombinases, such as RAD51.[109] The first step in recombination is a double-stranded break either caused by an endonuclease or damage to the DNA.[110] A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one Holliday junction, in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. The Holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA.[111]
Recombination involves the breakage and rejoining of two chromosomes (M and F) to produce two re-arranged chromosomes (C1 and C2).

DNA

170

Evolution
DNA contains the genetic information that allows all modern living things to function, grow and reproduce. However, it is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material.[100][112] RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes.[113] This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. This would occur, since the number of different bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes.[114] However, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible. This is because DNA will survive in the environment for less than one million years and slowly degrades into short fragments in solution.[115] Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old,[116] but these claims are controversial.[117][118] On August 8, 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA (adenine, guanine and related organic molecules) may have been formed extraterrestrially in outer space.[119][120][121]

Uses in technology
Genetic engineering
Methods have been developed to purify DNA from organisms, such as phenol-chloroform extraction, and to manipulate it in the laboratory, such as restriction digests and the polymerase chain reaction. Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology. Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector.[122] The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research,[123] or be grown in agriculture.[124][125]

Forensics
Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a crime scene to identify a matching DNA of an individual, such as a perpetrator. This process is formally termed DNA profiling, but may also be called "genetic fingerprinting". In DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA.[126] However, identification can be complicated if the scene is contaminated with DNA from several people.[127] DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys,[128] and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murders case.[129] The development of forensic science, and the ability to now obtain genetic matching on minute samples of blood, skin, saliva or hair has led to a re-examination of a number of cases. Evidence can now be uncovered that was not scientifically possible at the time of the original examination. Combined with the removal of the double jeopardy law in some places, this can allow cases to be reopened where previous trials have failed to produce sufficient evidence to convince a jury. People charged with serious crimes may be required to provide a sample of DNA for matching purposes. The most obvious defence to DNA matches obtained forensically is to claim that cross-contamination of evidence has taken place. This has resulted in meticulous strict handling procedures with new cases of serious crime. DNA profiling is also be used to identify victims of mass casualty incidents.[130] As well as positively identifying bodies or body parts in serious accidents, DNA profiling is being successfully used to identify individual victims in mass war graves – matching to family members.

DNA

171

Bioinformatics
Bioinformatics involves the manipulation, searching, and data mining of biological data, and this includes DNA sequence data. The development of techniques to store and search DNA sequences have led to widely applied advances in computer science, especially string searching algorithms, machine learning and database theory.[131] String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides.[132] The DNA sequence may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations that make them distinct. These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function.[133] Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without the annotations that identify the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by gene finding algorithms, which allow researchers to predict the presence of particular gene products and their possible functions in an organism even before they have been isolated experimentally.[134] Entire genomes may also be compared which can shed light on the evolutionary history of particular organism and permit the examination of complex evolutionary events.

DNA nanotechnology
DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties.[135] DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional periodic lattices (both tile-based as well as using the "DNA origami" method) as well as three-dimensional The DNA structure at left (schematic shown) will self-assemble into the structure structures in the shapes of visualized by atomic force microscopy at right. DNA nanotechnology is the field that seeks to design nanoscale structures using the molecular recognition properties of DNA polyhedra.[136] Nanomechanical molecules. Image from Strong, 2004 (doi:10.1371/journal.pbio.0020073). devices and algorithmic self-assembly have also been demonstrated,[137] and these DNA structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins.[138]

History and anthropology
Because DNA collects mutations over time, which are then inherited, it contains historical information, and, by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their phylogeny.[139] This field of phylogenetics is a powerful tool in evolutionary biology. If DNA sequences within a species are compared, population geneticists can learn the history of particular populations. This can be used in studies ranging from ecological genetics to anthropology; For example, DNA evidence is being used to try to identify the Ten Lost Tribes of Israel.[140][141] DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of Sally Hemings and Thomas Jefferson. This usage is closely related to the use of DNA in criminal

DNA investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual.[142]

172

History of DNA research
DNA was first isolated by the Swiss physician Friedrich Miescher who, in 1869, discovered a microscopic substance in the pus of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein".[143] In 1878, Albrecht Kossel isolated the non-protein component of "nuclein", nucleic acid, and later isolated its five primary nucleobases.[144] In 1919, Phoebus Levene identified the base, sugar and phosphate nucleotide unit.[145] Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups. However, Levene thought the chain was short and the bases repeated in a fixed order. In 1937 William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure.[146]

James D. Watson and Francis Crick (right), co-originators of the double-helix model, with Maclyn McCarty (left).

In 1927 Nikolai Koltsov proposed that inherited traits would be inherited via a "giant hereditary molecule" which would be made up of "two mirror strands that would replicate in a semi-conservative fashion using each strand as a template".[147] In 1928, Frederick Griffith discovered that traits of the "smooth" form of the Pneumococcus could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form.[148] This system provided the first clear suggestion that DNA carries genetic information—the Avery–MacLeod–McCarty experiment—when Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943.[149] DNA's role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the Hershey–Chase experiment showed that DNA is the genetic material of the T2 phage.[150] In 1953, James D. Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal Nature.[5] Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as "Photo 51")[151] taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases are paired — also obtained through private communications from Erwin Chargaff in the previous years. Chargaff's rules played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA. Experimental evidence supporting the Watson and Crick model were published in a series of five articles in the same issue of Nature.[152] Of these, Franklin and Gosling's paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the Watson and Crick model;[31][153] this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and in vivo B-DNA X-ray patterns also supported the presence in vivo of the double-helical DNA configurations as proposed by Crick and Watson for their double-helix molecular model of DNA in the previous two pages of Nature.[32] In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine.[154] However, Nobel rules of the time allowed only living recipients, but a vigorous debate continues on who should receive credit for the discovery.[155] In an influential presentation in 1957, Crick laid out the central dogma of molecular biology, which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis".[156] Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the Meselson–Stahl experiment.[157] Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W. Holley and Marshall

DNA Warren Nirenberg to decipher the genetic code.[158] These findings represent the birth of molecular biology. In 2010, NASA research confirms discovery of Bactrial DNA with arsenic instead of phosphorus at Mono Lake, California.[159]

173

References
[1] Russell, Peter (2001). iGenetics. New York: Benjamin Cummings. ISBN 0-8053-4553-1. [2] Saenger, Wolfram (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag. ISBN 0-387-90762-9. [3] Alberts, Bruce; Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walters (2002). Molecular Biology of the Cell; Fourth Edition (http:/ / www. ncbi. nlm. nih. gov/ books/ bv. fcgi?call=bv. View. . ShowTOC& rid=mboc4. TOC& depth=2). New York and London: Garland Science. ISBN 0-8153-3218-1. OCLC 145080076 48122761 57023651 69932405. . [4] Butler, John M. (2001). Forensic DNA Typing. Elsevier. ISBN 978-0-12-147951-0. OCLC 223032110 45406517. pp. 14–15. [5] Watson J.D. and Crick F.H.C. (1953). "A Structure for Deoxyribose Nucleic Acid" (http:/ / www. nature. com/ nature/ dna50/ watsoncrick. pdf) (PDF). Nature 171 (4356): 737–738. Bibcode 1953Natur.171..737W. doi:10.1038/171737a0. PMID 13054692. . [6] Mandelkern M, Elias J, Eden D, Crothers D (1981). "The dimensions of DNA in solution". J Mol Biol 152 (1): 153–61. doi:10.1016/0022-2836(81)90099-1. PMID 7338906. [7] Gregory S; Barlow, KF; McLay, KE; Kaul, R; Swarbreck, D; Dunham, A; Scott, CE; Howe, KL et al. (2006). "The DNA sequence and biological annotation of human chromosome 1". Nature 441 (7091): 315–21. Bibcode 2006Natur.441..315G. doi:10.1038/nature04727. PMID 16710414. [8] Berg J., Tymoczko J. and Stryer L. (2002) Biochemistry. W. H. Freeman and Company ISBN 0-7167-4955-6 [9] Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents (http:/ / www. chem. qmul. ac. uk/ iupac/ misc/ naabb. html) IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Retrieved 03 January 2006. [10] Ghosh A, Bansal M (2003). "A glossary of DNA structures from A to Z". Acta Crystallogr D 59 (4): 620–6. doi:10.1107/S0907444903003251. PMID 12657780. [11] Created from PDB 1D65 (http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1D65) [12] Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006). "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix". Nucleic Acids Res. 34 (2): 564–74. doi:10.1093/nar/gkj454. PMC 1360284. PMID 16449200. [13] Verma S, Eckstein F (1998). "Modified oligonucleotides: synthesis and strategy for users". Annu. Rev. Biochem. 67: 99–134. doi:10.1146/annurev.biochem.67.1.99. PMID 9759484. [14] Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson R (1980). "Crystal structure analysis of a complete turn of B-DNA". Nature 287 (5784): 755–8. Bibcode 1980Natur.287..755W. doi:10.1038/287755a0. PMID 7432492. [15] Pabo C, Sauer R (1984). "Protein-DNA recognition". Annu Rev Biochem 53: 293–321. doi:10.1146/annurev.bi.53.070184.001453. PMID 6236744. [16] Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub H (2000). "Mechanical stability of single DNA molecules". Biophys J 78 (4): 1997–2007. Bibcode 2000BpJ....78.1997C. doi:10.1016/S0006-3495(00)76747-6. PMC 1300792. PMID 10733978. [17] Chalikian T, Völker J, Plum G, Breslauer K (1999). "A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques". Proc Natl Acad Sci USA 96 (14): 7853–8. Bibcode 1999PNAS...96.7853C. doi:10.1073/pnas.96.14.7853. PMC 22151. PMID 10393911. [18] deHaseth P, Helmann J (1995). "Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA". Mol Microbiol 16 (5): 817–24. doi:10.1111/j.1365-2958.1995.tb02309.x. PMID 7476180. [19] Isaksson J, Acharya S, Barman J, Cheruku P, Chattopadhyaya J (2004). "Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern". Biochemistry 43 (51): 15996–6010. doi:10.1021/bi048221v. PMID 15609994. [20] Designation of the two strands of DNA (http:/ / www. chem. qmul. ac. uk/ iubmb/ newsletter/ misc/ DNA. html) JCBN/NC-IUB Newsletter 1989, Accessed 07 May 2008 [21] Hüttenhofer A, Schattner P, Polacek N (2005). "Non-coding RNAs: hope or hype?". Trends Genet 21 (5): 289–97. doi:10.1016/j.tig.2005.03.007. PMID 15851066. [22] Munroe S (2004). "Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns". J Cell Biochem 93 (4): 664–71. doi:10.1002/jcb.20252. PMID 15389973. [23] Makalowska I, Lin C, Makalowski W (2005). "Overlapping genes in vertebrate genomes". Comput Biol Chem 29 (1): 1–12. doi:10.1016/j.compbiolchem.2004.12.006. PMID 15680581. [24] Johnson Z, Chisholm S (2004). "Properties of overlapping genes are conserved across microbial genomes". Genome Res 14 (11): 2268–72. doi:10.1101/gr.2433104. PMC 525685. PMID 15520290. [25] Lamb R, Horvath C (1991). "Diversity of coding strategies in influenza viruses". Trends Genet 7 (8): 261–6. doi:10.1016/0168-9525(91)90326-L. PMID 1771674. [26] Benham C, Mielke S (2005). "DNA mechanics". Annu Rev Biomed Eng 7: 21–53. doi:10.1146/annurev.bioeng.6.062403.132016. PMID 16004565.

DNA
[27] Champoux J (2001). "DNA topoisomerases: structure, function, and mechanism". Annu Rev Biochem 70: 369–413. doi:10.1146/annurev.biochem.70.1.369. PMID 11395412. [28] Wang J (2002). "Cellular roles of DNA topoisomerases: a molecular perspective". Nat Rev Mol Cell Biol 3 (6): 430–40. doi:10.1038/nrm831. PMID 12042765. [29] Basu H, Feuerstein B, Zarling D, Shafer R, Marton L (1988). "Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies". J Biomol Struct Dyn 6 (2): 299–309. PMID 2482766. [30] Franklin RE, Gosling RG (6 March 1953). "The Structure of Sodium Thymonucleate Fibres I. The Influence of Water Content" (http:/ / hekto. med. unc. edu:8080/ CARTER/ carter_WWW/ Bioch_134/ PDF_files/ Franklin_Gossling. pdf). Acta Crystallogr 6 (8–9): 673–7. doi:10.1107/S0365110X53001939. . Franklin RE, Gosling RG (1953). "The structure of sodium thymonucleate fibres. II. The cylindrically symmetrical Patterson function". Acta Crystallogr 6 (8–9): 678–85. doi:10.1107/S0365110X53001940. [31] Franklin, Rosalind and Gosling, Raymond (1953). "Molecular Configuration in Sodium Thymonucleate. Franklin R. and Gosling R.G" (http:/ / www. nature. com/ nature/ dna50/ franklingosling. pdf) (PDF). Nature 171 (4356): 740–1. Bibcode 1953Natur.171..740F. doi:10.1038/171740a0. PMID 13054694. . [32] Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. (1953). "Molecular Structure of Deoxypentose Nucleic Acids" (http:/ / www. nature. com/ nature/ dna50/ wilkins. pdf) (PDF). Nature 171 (4356): 738–740. Bibcode 1953Natur.171..738W. doi:10.1038/171738a0. PMID 13054693. . [33] Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL (1980). "Polymorphism of DNA double helices". J. Mol. Biol. 143 (1): 49–72. doi:10.1016/0022-2836(80)90124-2. PMID 7441761. [34] Baianu, I.C. (1980). "Structural Order and Partial Disorder in Biological systems". Bull. Math. Biol. 42 (4): 137–141. http:/ / cogprints. org/ 3822/ [35] Hosemann R., Bagchi R.N., Direct analysis of diffraction by matter, North-Holland Publs., Amsterdam – New York, 1962. [36] Baianu, I.C. (1978). "X-ray scattering by partially disordered membrane systems". Acta Crystallogr A 34 (5): 751–753. Bibcode 1978AcCrA..34..751B. doi:10.1107/S0567739478001540. [37] Wahl M, Sundaralingam M (1997). "Crystal structures of A-DNA duplexes". Biopolymers 44 (1): 45–63. doi:10.1002/(SICI)1097-0282(1997)44:1<45::AID-BIP4>3.0.CO;2-#. PMID 9097733. [38] Lu XJ, Shakked Z, Olson WK (2000). "A-form conformational motifs in ligand-bound DNA structures". J. Mol. Biol. 300 (4): 819–40. doi:10.1006/jmbi.2000.3690. PMID 10891271. [39] Rothenburg S, Koch-Nolte F, Haag F (2001). "DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles". Immunol Rev 184: 286–98. doi:10.1034/j.1600-065x.2001.1840125.x. PMID 12086319. [40] Oh D, Kim Y, Rich A (2002). "Z-DNA-binding proteins can act as potent effectors of gene expression in vivo". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16666–71. Bibcode 2002PNAS...9916666O. doi:10.1073/pnas.262672699. PMC 139201. PMID 12486233. [41] "Arsenic-loving bacteria may help in hunt for alien life" (http:/ / www. bbc. co. uk/ news/ science-environment-11886943). BBC News. December 2, 2010. . Retrieved 2010-12-02. [42] Bortman, Henry (2010-12-02). "Arsenic-Eating Bacteria Opens New Possibilities for Alien Life" (http:/ / www. space. com/ scienceastronomy/ arsenic-bacteria-alien-life-101202. html). Space.Com web site (http:/ / www. space. com/ ) (Space.com). . Retrieved 2010-12-02. [43] Katsnelson, Alla (2 December 2010). "Arsenic-eating microbe may redefine chemistry of life" (http:/ / www. nature. com/ news/ 2010/ 101202/ full/ news. 2010. 645. html). Nature News. doi:10.1038/news.2010.645. . [44] Greider C, Blackburn E (1985). "Identification of a specific telomere terminal transferase activity in Tetrahymena extracts". Cell 43 (2 Pt 1): 405–13. doi:10.1016/0092-8674(85)90170-9. PMID 3907856. [45] Nugent C, Lundblad V (1998). "The telomerase reverse transcriptase: components and regulation". Genes Dev 12 (8): 1073–85. doi:10.1101/gad.12.8.1073. PMID 9553037. [46] Wright W, Tesmer V, Huffman K, Levene S, Shay J (1997). "Normal human chromosomes have long G-rich telomeric overhangs at one end". Genes Dev 11 (21): 2801–9. doi:10.1101/gad.11.21.2801. PMC 316649. PMID 9353250. [47] Created from NDB UD0017 (http:/ / ndbserver. rutgers. edu/ atlas/ xray/ structures/ U/ ud0017/ ud0017. html) [48] Burge S, Parkinson G, Hazel P, Todd A, Neidle S (2006). "Quadruplex DNA: sequence, topology and structure". Nucleic Acids Res 34 (19): 5402–15. doi:10.1093/nar/gkl655. PMC 1636468. PMID 17012276. [49] Parkinson G, Lee M, Neidle S (2002). "Crystal structure of parallel quadruplexes from human telomeric DNA". Nature 417 (6891): 876–80. doi:10.1038/nature755. PMID 12050675. [50] Griffith J, Comeau L, Rosenfield S, Stansel R, Bianchi A, Moss H, de Lange T (1999). "Mammalian telomeres end in a large duplex loop". Cell 97 (4): 503–14. doi:10.1016/S0092-8674(00)80760-6. PMID 10338214. [51] Seeman NC (2005). "DNA enables nanoscale control of the structure of matter". Q. Rev. Biophys. 38 (4): 363–71. doi:10.1017/S0033583505004087. PMID 16515737. [52] Painter PC, Mosher LE, Rhoads C (1982). "Low-frequency modes in the Raman spectra of proteins". Biopolymers 21 (7): 1469–72. doi:10.1002/bip.360210715. PMID 7115900. [53] Urabe H, Tominaga Y, Kubota K (1983). "Experimental evidence of collective vibrations in DNA double helix (Raman spectroscopy)". Journal of Chemical Physics 78 (10): 5937–5939. Bibcode 1983JChPh..78.5937U. doi:10.1063/1.444600. [54] Chou KC (1984). "Low-frequency vibrations of DNA molecules". Biochem. J. 221 (1): 27–31. PMC 1143999. PMID 6466317.

174

DNA
[55] Chou KC, Maggiora GM, Mao B (1989). "Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA". Biophys. J. 56 (2): 295–305. Bibcode 1989BpJ....56..295C. doi:10.1016/S0006-3495(89)82676-1. PMC 1280479. PMID 2775828. [56] Klose R, Bird A (2006). "Genomic DNA methylation: the mark and its mediators". Trends Biochem Sci 31 (2): 89–97. doi:10.1016/j.tibs.2005.12.008. PMID 16403636. [57] Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev 16 (1): 6–21. doi:10.1101/gad.947102. PMID 11782440. [58] Walsh C, Xu G (2006). "Cytosine methylation and DNA repair". Curr Top Microbiol Immunol. Current Topics in Microbiology and Immunology 301: 283–315. doi:10.1007/3-540-31390-7_11. ISBN 3-540-29114-8. PMID 16570853. [59] Kriaucionis S, Heintz N (2009). "The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain". Science 324 (5929): 929–30. Bibcode 2009Sci...324..929K. doi:10.1126/science.1169786. PMC 3263819. PMID 19372393. [60] Ratel D, Ravanat J, Berger F, Wion D (2006). "N6-methyladenine: the other methylated base of DNA". BioEssays 28 (3): 309–15. doi:10.1002/bies.20342. PMC 2754416. PMID 16479578. [61] Gommers-Ampt J, Van Leeuwen F, de Beer A, Vliegenthart J, Dizdaroglu M, Kowalak J, Crain P, Borst P (1993). "beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei". Cell 75 (6): 1129–36. doi:10.1016/0092-8674(93)90322-H. PMID 8261512. [62] Created from PDB 1JDG (http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1JDG) [63] Douki T, Reynaud-Angelin A, Cadet J, Sage E (2003). "Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar UVA radiation". Biochemistry 42 (30): 9221–6. doi:10.1021/bi034593c. PMID 12885257. [64] Cadet J, Delatour T, Douki T, Gasparutto D, Pouget J, Ravanat J, Sauvaigo S (1999). "Hydroxyl radicals and DNA base damage". Mutat Res 424 (1–2): 9–21. doi:10.1016/S0027-5107(99)00004-4. PMID 10064846. [65] Beckman KB, Ames BN (1997). "Oxidative decay of DNA". J. Biol. Chem. 272 (32): 19633–6. doi:10.1074/jbc.272.32.19633. PMID 9289489. [66] Valerie K, Povirk L (2003). "Regulation and mechanisms of mammalian double-strand break repair". Oncogene 22 (37): 5792–812. doi:10.1038/sj.onc.1206679. PMID 12947387. [67] Johnson, George (28 December 2010). "Unearthing Prehistoric Tumors, and Debate" (http:/ / www. nytimes. com/ 2010/ 12/ 28/ health/ 28cancer. html). The New York Times. . ""If we lived long enough, sooner or later we all would get cancer."" [68] Alberts, B, Johnson A, Lewis J, et al. (2002). "The Preventable Causes of Cancer" (http:/ / www. ncbi. nlm. nih. gov/ books/ NBK26897/ ). Molecular biology of the cell (4th ed.). New York: Garland Science. ISBN 0-8153-4072-9. . "A certain irreducible background incidence of cancer is to be expected regardless of circumstances: mutations can never be absolutely avoided, because they are an inescapable consequence of fundamental limitations on the accuracy of DNA replication, as discussed in Chapter 5. If a human could live long enough, it is inevitable that at least one of his or her cells would eventually accumulate a set of mutations sufficient for cancer to develop." [69] Ferguson L, Denny W (1991). "The genetic toxicology of acridines". Mutat Res 258 (2): 123–60. PMID 1881402. [70] Stephens T, Bunde C, Fillmore B (2000). "Mechanism of action in thalidomide teratogenesis". Biochem Pharmacol 59 (12): 1489–99. doi:10.1016/S0006-2952(99)00388-3. PMID 10799645. [71] Jeffrey A (1985). "DNA modification by chemical carcinogens". Pharmacol Ther 28 (2): 237–72. doi:10.1016/0163-7258(85)90013-0. PMID 3936066. [72] Braña M, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A (2001). "Intercalators as anticancer drugs". Curr Pharm Des 7 (17): 1745–80. doi:10.2174/1381612013397113. PMID 11562309. [73] Venter J; Adams, MD; Myers, EW; Li, PW; Mural, RJ; Sutton, GG; Smith, HO; Yandell, M et al. (2001). "The sequence of the human genome". Science 291 (5507): 1304–51. Bibcode 2001Sci...291.1304V. doi:10.1126/science.1058040. PMID 11181995. [74] Thanbichler M, Wang S, Shapiro L (2005). "The bacterial nucleoid: a highly organized and dynamic structure". J Cell Biochem 96 (3): 506–21. doi:10.1002/jcb.20519. PMID 15988757. [75] Wolfsberg T, McEntyre J, Schuler G (2001). "Guide to the draft human genome". Nature 409 (6822): 824–6. doi:10.1038/35057000. PMID 11236998. [76] Gregory T (2005). "The C-value enigma in plants and animals: a review of parallels and an appeal for partnership". Ann Bot (Lond) 95 (1): 133–46. doi:10.1093/aob/mci009. PMID 15596463. [77] The ENCODE Project Consortium (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. Bibcode 2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346. [78] Created from PDB 1MSW (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1MSW) [79] Pidoux A, Allshire R (2005). "The role of heterochromatin in centromere function". Philos Trans R Soc Lond B Biol Sci 360 (1455): 569–79. doi:10.1098/rstb.2004.1611. PMC 1569473. PMID 15905142. [80] Harrison P, Hegyi H, Balasubramanian S, Luscombe N, Bertone P, Echols N, Johnson T, Gerstein M (2002). "Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22". Genome Res 12 (2): 272–80. doi:10.1101/gr.207102. PMC 155275. PMID 11827946. [81] Harrison P, Gerstein M (2002). "Studying genomes through the aeons: protein families, pseudogenes and proteome evolution". J Mol Biol 318 (5): 1155–74. doi:10.1016/S0022-2836(02)00109-2. PMID 12083509. [82] Albà M (2001). "Replicative DNA polymerases". Genome Biol 2 (1): REVIEWS3002. doi:10.1186/gb-2001-2-1-reviews3002. PMC 150442. PMID 11178285. [83] Sandman K, Pereira S, Reeve J (1998). "Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome". Cell Mol Life Sci 54 (12): 1350–64. doi:10.1007/s000180050259. PMID 9893710.

175

DNA
[84] Dame RT (2005). "The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin". Mol. Microbiol. 56 (4): 858–70. doi:10.1111/j.1365-2958.2005.04598.x. PMID 15853876. [85] Luger K, Mäder A, Richmond R, Sargent D, Richmond T (1997). "Crystal structure of the nucleosome core particle at 2.8 A resolution". Nature 389 (6648): 251–60. Bibcode 1997Natur.389..251L. doi:10.1038/38444. PMID 9305837. [86] Jenuwein T, Allis C (2001). "Translating the histone code". Science 293 (5532): 1074–80. doi:10.1126/science.1063127. PMID 11498575. [87] Ito T (2003). "Nucleosome assembly and remodelling". Curr Top Microbiol Immunol. Current Topics in Microbiology and Immunology 274: 1–22. doi:10.1007/978-3-642-55747-7_1. ISBN 978-3-540-44208-0. PMID 12596902. [88] Thomas J (2001). "HMG1 and 2: architectural DNA-binding proteins". Biochem Soc Trans 29 (Pt 4): 395–401. doi:10.1042/BST0290395. PMID 11497996. [89] Grosschedl R, Giese K, Pagel J (1994). "HMG domain proteins: architectural elements in the assembly of nucleoprotein structures". Trends Genet 10 (3): 94–100. doi:10.1016/0168-9525(94)90232-1. PMID 8178371. [90] Iftode C, Daniely Y, Borowiec J (1999). "Replication protein A (RPA): the eukaryotic SSB". Crit Rev Biochem Mol Biol 34 (3): 141–80. doi:10.1080/10409239991209255. PMID 10473346. [91] Created from PDB 1LMB (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1LMB) [92] Myers L, Kornberg R (2000). "Mediator of transcriptional regulation". Annu Rev Biochem 69: 729–49. doi:10.1146/annurev.biochem.69.1.729. PMID 10966474. [93] Spiegelman B, Heinrich R (2004). "Biological control through regulated transcriptional coactivators". Cell 119 (2): 157–67. doi:10.1016/j.cell.2004.09.037. PMID 15479634. [94] Li Z, Van Calcar S, Qu C, Cavenee W, Zhang M, Ren B (2003). "A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells". Proc Natl Acad Sci USA 100 (14): 8164–9. Bibcode 2003PNAS..100.8164L. doi:10.1073/pnas.1332764100. PMC 166200. PMID 12808131. [95] Created from PDB 1RVA (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1RVA) [96] Bickle T, Krüger D (1993). "Biology of DNA restriction". Microbiol Rev 57 (2): 434–50. PMC 372918. PMID 8336674. [97] Doherty A, Suh S (2000). "Structural and mechanistic conservation in DNA ligases". Nucleic Acids Res 28 (21): 4051–8. doi:10.1093/nar/28.21.4051. PMC 113121. PMID 11058099. [98] Schoeffler A, Berger J (2005). "Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism". Biochem Soc Trans 33 (Pt 6): 1465–70. doi:10.1042/BST20051465. PMID 16246147. [99] Tuteja N, Tuteja R (2004). "Unraveling DNA helicases. Motif, structure, mechanism and function". Eur J Biochem 271 (10): 1849–63. doi:10.1111/j.1432-1033.2004.04094.x. PMID 15128295. [100] Joyce C, Steitz T (1995). "Polymerase structures and function: variations on a theme?". J Bacteriol 177 (22): 6321–9. PMC 177480. PMID 7592405. [101] Hubscher U, Maga G, Spadari S (2002). "Eukaryotic DNA polymerases". Annu Rev Biochem 71: 133–63. doi:10.1146/annurev.biochem.71.090501.150041. PMID 12045093. [102] Johnson A, O'Donnell M (2005). "Cellular DNA replicases: components and dynamics at the replication fork". Annu Rev Biochem 74: 283–315. doi:10.1146/annurev.biochem.73.011303.073859. PMID 15952889. [103] Tarrago-Litvak L, Andréola M, Nevinsky G, Sarih-Cottin L, Litvak S (1 May 1994). "The reverse transcriptase of HIV-1: from enzymology to therapeutic intervention". FASEB J 8 (8): 497–503. PMID 7514143. [104] Martinez E (2002). "Multi-protein complexes in eukaryotic gene transcription". Plant Mol Biol 50 (6): 925–47. doi:10.1023/A:1021258713850. PMID 12516863. [105] Created from PDB 1M6G (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1M6G) [106] Cremer T, Cremer C (2001). "Chromosome territories, nuclear architecture and gene regulation in mammalian cells". Nat Rev Genet 2 (4): 292–301. doi:10.1038/35066075. PMID 11283701. [107] Pál C, Papp B, Lercher M (2006). "An integrated view of protein evolution". Nat Rev Genet 7 (5): 337–48. doi:10.1038/nrg1838. PMID 16619049. [108] O'Driscoll M, Jeggo P (2006). "The role of double-strand break repair – insights from human genetics". Nat Rev Genet 7 (1): 45–54. doi:10.1038/nrg1746. PMID 16369571. [109] Vispé S, Defais M (1997). "Mammalian Rad51 protein: a RecA homologue with pleiotropic functions". Biochimie 79 (9–10): 587–92. doi:10.1016/S0300-9084(97)82007-X. PMID 9466696. [110] Neale MJ, Keeney S (2006). "Clarifying the mechanics of DNA strand exchange in meiotic recombination". Nature 442 (7099): 153–8. Bibcode 2006Natur.442..153N. doi:10.1038/nature04885. PMID 16838012. [111] Dickman M, Ingleston S, Sedelnikova S, Rafferty J, Lloyd R, Grasby J, Hornby D (2002). "The RuvABC resolvasome". Eur J Biochem 269 (22): 5492–501. doi:10.1046/j.1432-1033.2002.03250.x. PMID 12423347. [112] Orgel L (2004). "Prebiotic chemistry and the origin of the RNA world". Crit Rev Biochem Mol Biol 39 (2): 99–123. doi:10.1080/10409230490460765. PMID 15217990. [113] Davenport R (2001). "Ribozymes. Making copies in the RNA world". Science 292 (5520): 1278. doi:10.1126/science.292.5520.1278a. PMID 11360970. [114] Szathmáry E (1992). "What is the optimum size for the genetic alphabet?". Proc Natl Acad Sci USA 89 (7): 2614–8. Bibcode 1992PNAS...89.2614S. doi:10.1073/pnas.89.7.2614. PMC 48712. PMID 1372984.

176

DNA
[115] Lindahl T (1993). "Instability and decay of the primary structure of DNA". Nature 362 (6422): 709–15. Bibcode 1993Natur.362..709L. doi:10.1038/362709a0. PMID 8469282. [116] Vreeland R, Rosenzweig W, Powers D (2000). "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal". Nature 407 (6806): 897–900. doi:10.1038/35038060. PMID 11057666. [117] Hebsgaard M, Phillips M, Willerslev E (2005). "Geologically ancient DNA: fact or artefact?". Trends Microbiol 13 (5): 212–20. doi:10.1016/j.tim.2005.03.010. PMID 15866038. [118] Nickle D, Learn G, Rain M, Mullins J, Mittler J (2002). "Curiously modern DNA for a "250 million-year-old" bacterium". J Mol Evol 54 (1): 134–7. doi:10.1007/s00239-001-0025-x. PMID 11734907. [119] Callahan, M.P.; Smith, K.E.; Cleaves, H.J.; Ruzica, J.; Stern, J.C.; Glavin, D.P.; House, C.H.; Dworkin, J.P. (11 August 2011). "Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases" (http:/ / www. pnas. org/ content/ early/ 2011/ 08/ 10/ 1106493108). PNAS. doi:10.1073/pnas.1106493108. . Retrieved 2011-08-15. [120] Steigerwald, John (8 August 2011). "NASA Researchers: DNA Building Blocks Can Be Made in Space" (http:/ / www. nasa. gov/ topics/ solarsystem/ features/ dna-meteorites. html). NASA. . Retrieved 2011-08-10. [121] ScienceDaily Staff (9 August 2011). "DNA Building Blocks Can Be Made in Space, NASA Evidence Suggests" (http:/ / www. sciencedaily. com/ releases/ 2011/ 08/ 110808220659. htm). ScienceDaily. . Retrieved 2011-08-09. [122] Goff SP, Berg P (1976). "Construction of hybrid viruses containing SV40 and lambda phage DNA segments and their propagation in cultured monkey cells". Cell 9 (4 PT 2): 695–705. doi:10.1016/0092-8674(76)90133-1. PMID 189942. [123] Houdebine L (2007). "Transgenic animal models in biomedical research". Methods Mol Biol 360: 163–202. doi:10.1385/1-59745-165-7:163. ISBN 1-59745-165-7. PMID 17172731. [124] Daniell H, Dhingra A (2002). "Multigene engineering: dawn of an exciting new era in biotechnology". Curr Opin Biotechnol 13 (2): 136–41. doi:10.1016/S0958-1669(02)00297-5. PMID 11950565. [125] Job D (2002). "Plant biotechnology in agriculture". Biochimie 84 (11): 1105–10. doi:10.1016/S0300-9084(02)00013-5. PMID 12595138. [126] Collins A, Morton N (1994). "Likelihood ratios for DNA identification". Proc Natl Acad Sci USA 91 (13): 6007–11. Bibcode 1994PNAS...91.6007C. doi:10.1073/pnas.91.13.6007. PMC 44126. PMID 8016106. [127] Weir B, Triggs C, Starling L, Stowell L, Walsh K, Buckleton J (1997). "Interpreting DNA mixtures". J Forensic Sci 42 (2): 213–22. PMID 9068179. [128] Jeffreys A, Wilson V, Thein S (1985). "Individual-specific 'fingerprints' of human DNA". Nature 316 (6023): 76–9. Bibcode 1985Natur.316...76J. doi:10.1038/316076a0. PMID 2989708. [129] Colin Pitchfork — first murder conviction on DNA evidence also clears the prime suspect (http:/ / web. archive. org/ web/ 20061214004903/ http:/ / www. forensic. gov. uk/ forensic_t/ inside/ news/ list_casefiles. php?case=1) Forensic Science Service Accessed 23 December 2006 [130] "DNA Identification in Mass Fatality Incidents" (http:/ / massfatality. dna. gov/ Introduction/ ). National Institute of Justice. September 2006. . [131] Baldi, Pierre; Brunak, Soren (2001). Bioinformatics: The Machine Learning Approach. MIT Press. ISBN 978-0-262-02506-5. OCLC 45951728. [132] Gusfield, Dan. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, 15 January 1997. ISBN 978-0-521-58519-4. [133] Sjölander K (2004). "Phylogenomic inference of protein molecular function: advances and challenges". Bioinformatics 20 (2): 170–9. doi:10.1093/bioinformatics/bth021. PMID 14734307. [134] Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2 ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 0-87969-712-1. OCLC 55106399. [135] Rothemund PW (2006). "Folding DNA to create nanoscale shapes and patterns". Nature 440 (7082): 297–302. Bibcode 2006Natur.440..297R. doi:10.1038/nature04586. PMID 16541064. [136] Andersen ES, Dong M, Nielsen MM (2009). "Self-assembly of a nanoscale DNA box with a controllable lid". Nature 459 (7243): 73–6. Bibcode 2009Natur.459...73A. doi:10.1038/nature07971. PMID 19424153. [137] Ishitsuka Y, Ha T (2009). "DNA nanotechnology: a nanomachine goes live". Nat Nanotechnol 4 (5): 281–2. Bibcode 2009NatNa...4..281I. doi:10.1038/nnano.2009.101. PMID 19421208. [138] Aldaye FA, Palmer AL, Sleiman HF (2008). "Assembling materials with DNA as the guide". Science 321 (5897): 1795–9. Bibcode 2008Sci...321.1795A. doi:10.1126/science.1154533. PMID 18818351. [139] Wray G; Martindale, Mark Q. (2002). "Dating branches on the Tree of Life using DNA". Genome Biol 3 (1): REVIEWS0001. doi:10.1046/j.1525-142X.1999.99010.x. PMC 150454. PMID 11806830. [140] Lost Tribes of Israel, NOVA, PBS airdate: 22 February 2000. Transcript available from PBS.org (http:/ / www. pbs. org/ wgbh/ nova/ transcripts/ 2706israel. html). Retrieved 4 March 2006. [141] Kleiman, Yaakov. "The Cohanim/DNA Connection: The fascinating story of how DNA studies confirm an ancient biblical tradition". (http:/ / www. aish. com/ societywork/ sciencenature/ the_cohanim_-_dna_connection. asp) aish.com (January 13, 2000). Retrieved 4 March 2006. [142] Bhattacharya, Shaoni. "Killer convicted thanks to relative's DNA". (http:/ / www. newscientist. com/ article. ns?id=dn4908) newscientist.com (20 April 2004). Retrieved 22 December 06.

177

DNA
[143] Dahm R (2008). "Discovering DNA: Friedrich Miescher and the early years of nucleic acid research". Hum. Genet. 122 (6): 565–81. doi:10.1007/s00439-007-0433-0. PMID 17901982. [144] Jones, Mary Ellen (September 1953). "Albrecht Kossel, A Biographical Sketch". Yale Journal of Biology and Medicine (National Center for Biotechnology Information) 26 (1): 80–97. PMC 2599350. PMID 13103145. [145] Levene P, (1 December 1919). "The structure of yeast nucleic acid". J Biol Chem 40 (2): 415–24. [146] Astbury W, (1947). "Nucleic acid". Symp. SOC. Exp. Biol. 1 (66). [147] Valery N. Soyfer (2001). "The consequences of political dictatorship for Russian science". Nature Reviews Genetics 2 (9): 723–729. doi:10.1038/35088598. PMID 11533721. [148] Lorenz MG, Wackernagel W (1994). "Bacterial gene transfer by natural genetic transformation in the environment". Microbiol. Rev. 58 (3): 563–602. PMC 372978. PMID 7968924. [149] Avery O, MacLeod C, McCarty M (1944). "STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES : INDUCTION OF TRANSFORMATION BY A DESOXYRIBONUCLEIC ACID FRACTION ISOLATED FROM PNEUMOCOCCUS TYPE III". J Exp Med 79 (2): 137–158. doi:10.1084/jem.79.2.137. PMC 2135445. PMID 19871359. [150] Hershey A, Chase M (1952). "INDEPENDENT FUNCTIONS OF VIRAL PROTEIN AND NUCLEIC ACID IN GROWTH OF BACTERIOPHAGE". J Gen Physiol 36 (1): 39–56. doi:10.1085/jgp.36.1.39. PMC 2147348. PMID 12981234. [151] The B-DNA X-ray pattern on the right of this linked image (http:/ / osulibrary. oregonstate. edu/ specialcollections/ coll/ pauling/ dna/ pictures/ sci9. 001. 5. html) was obtained by Rosalind Franklin and Raymond Gosling in May 1952 at high hydration levels of DNA and it has been labeled as "Photo 51" [152] Nature Archives Double Helix of DNA: 50 Years (http:/ / www. nature. com/ nature/ dna50/ archive. html) [153] "Original X-ray diffraction image" (http:/ / osulibrary. oregonstate. edu/ specialcollections/ coll/ pauling/ dna/ pictures/ franklin-typeBphoto. html). Osulibrary.oregonstate.edu. . Retrieved 2011-02-06. [154] The Nobel Prize in Physiology or Medicine 1962 (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1962/ ) Nobelprize .org Accessed 22 December 06 [155] Brenda Maddox (23 January 2003). "The double helix and the 'wronged heroine'" (http:/ / www. biomath. nyu. edu/ index/ course/ hw_articles/ nature4. pdf) (PDF). Nature 421 (6921): 407–408. doi:10.1038/nature01399. PMID 12540909. . [156] Crick, F.H.C. On degenerate templates and the adaptor hypothesis (PDF). (http:/ / genome. wellcome. ac. uk/ assets/ wtx030893. pdf) genome.wellcome.ac.uk (Lecture, 1955). Retrieved 22 December 2006. [157] Meselson M, Stahl F (1958). "THE REPLICATION OF DNA IN ESCHERICHIA COLI". Proc Natl Acad Sci USA 44 (7): 671–82. Bibcode 1958PNAS...44..671M. doi:10.1073/pnas.44.7.671. PMC 528642. PMID 16590258. [158] The Nobel Prize in Physiology or Medicine 1968 (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1968/ ) Nobelprize.org Accessed 22 December 06 [159] NASA Discovers Life Built With Toxic Chemical (http:/ / www. nasa. gov/ topics/ universe/ features/ astrobiology_toxic_chemical. html)(Arsenic in DNA)

178

Further reading
• Berry, Andrew; Watson, James D. (2003). DNA: the secret of life. New York: Alfred A. Knopf. ISBN 0-375-41546-7. • Calladine, Chris R.; Drew, Horace R.; Luisi, Ben F. and Travers, Andrew A. (2003). Understanding DNA: the molecule & how it works. Amsterdam: Elsevier Academic Press. ISBN 0-12-155089-3. • Dennis, Carina; Julie Clayton (2003). 50 years of DNA. Basingstoke: Palgrave Macmillan. ISBN 1-4039-1479-6. • Judson, Horace F. 1979. The Eighth Day of Creation: Makers of the Revolution in Biology. Touchstone Books, ISBN 0-671-22540-5. 2nd edition: Cold Spring Harbor Laboratory Press, 1996 paperback: ISBN 0-87969-478-5. • Olby, Robert C. (1994). The path to the double helix: the discovery of DNA. New York: Dover Publications. ISBN 0-486-68117-3., first published in October 1974 by MacMillan, with foreword by Francis Crick;the definitive DNA textbook,revised in 1994 with a 9 page postscript • Micklas, David. 2003. DNA Science: A First Course. Cold Spring Harbor Press: ISBN 978-0-87969-636-8 • Ridley, Matt (2006). Francis Crick: discoverer of the genetic code. Ashland, OH: Eminent Lives, Atlas Books. ISBN 0-06-082333-X. • Olby, Robert C. (2009). Francis Crick: A Biography. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 0-87969-798-9. • Rosenfeld, Israel. 2010. DNA: A Graphic Guide to the Molecule that Shook the World. Columbia University Press: ISBN 978-0-231-14271-7

DNA • Schultz, Mark and Zander Cannon. 2009. The Stuff of Life: A Graphic Guide to Genetics and DNA. Hill and Wang: ISBN 0-8090-8947-5 • Stent, Gunther Siegmund; Watson, James D. (1980). The double helix: a personal account of the discovery of the structure of DNA. New York: Norton. ISBN 0-393-95075-1. • Watson, James D. 2004. DNA: The Secret of Life. Random House: ISBN 978-0-09-945184-6 • Wilkins, Maurice (2003). The third man of the double helix the autobiography of Maurice Wilkins. Cambridge, Eng: University Press. ISBN 0-19-860665-6.

179

External links
• DNA (http://www.dmoz.org/Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/ Nucleic_Acids/DNA//) at the Open Directory Project • DNA binding site prediction on protein (http://pipe.scs.fsu.edu/displar.html) • DNA the Double Helix Game (http://nobelprize.org/educational_games/medicine/dna_double_helix/) From the official Nobel Prize web site • DNA under electron microscope (http://www.fidelitysystems.com/Unlinked_DNA.html) • Dolan DNA Learning Center (http://www.dnalc.org/) • Double Helix: 50 years of DNA (http://www.nature.com/nature/dna50/archive.html), Nature • Proteopedia DNA (http://www.proteopedia.org/wiki/index.php/DNA) • Double Helix 1953–2003 (http://www.ncbe.reading.ac.uk/DNA50/) National Centre for Biotechnology Education • Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974 (http://www.bbc.co.uk/bbcfour/ audiointerviews/profilepages/crickwatson1.shtml) • Genetic Education Modules for Teachers (http://www.genome.gov/10506718)—DNA from the Beginning Study Guide • Olby R (2003). "Quiet debut for the double helix". Nature 421 (6921): 402–5. doi:10.1038/nature01397. PMID 12540907. • DNA from the Beginning (http://www.dnaftb.org/dnaftb/) Another DNA Learning Center site on DNA, genes, and heredity from Mendel to the human genome project. • PDB Molecule of the Month pdb23_1 (http://www.rcsb.org/pdb/static.do?p=education_discussion/ molecule_of_the_month/pdb23_1.html) • Rosalind Franklin's contributions to the study of DNA (http://mason.gmu.edu/~emoody/rfranklin.html) • The Register of Francis Crick Personal Papers 1938 – 2007 (http://orpheus.ucsd.edu/speccoll/testing/html/ mss0660a.html#abstract) at Mandeville Special Collections Library, University of California, San Diego • U.S. National DNA Day (http://www.genome.gov/10506367)—watch videos and participate in real-time chat with top scientists • Clue to chemistry of heredity found (http://www.nytimes.com/packages/pdf/science/dna-article.pdf) The New York Times June 1953. First American newspaper coverage of the discovery of the DNA structure

Fecal fat test

180

Fecal fat test
In medicine, the fecal fat test is a diagnostic test for fat malabsorption conditions, which lead to excess fat in the feces (steatorrhea).

Background
In the small intestine, dietary fat (primarily triglycerides) is digested by enzymes such as pancreatic lipase into smaller molecules which can be absorbed through the wall of the small intestine and enter the circulation for metabolism and storage. As fat is a valuable nutrient, human feces normally contain very little undigested fat. However, a number of diseases of the pancreas and gastrointestinal tract are characterized by fat malabsorption. Examples of such diseases are: • disorders of exocrine pancreatic function, such as chronic pancreatitis, cystic fibrosis and Shwachman–Diamond syndrome (these are characterized by deficiency of pancreatic digestive enzymes) • celiac disease (in which the fat malabsorption in severe cases is due to inflammatory damage to the integrity of the intestinal lining) • short bowel syndrome (in which much of the small intestine has had to be surgically removed and the remaining portion cannot completely absorb all of the fat). • small bowel bacterial overgrowth syndrome

Microscopy
In the simplest form of the fecal fat test, a random fecal specimen is submitted to the hospital laboratory and examined under a microscope after staining with a Sudan III or Sudan IV dye ("Sudan staining"). Visible amounts of fat indicate some degree of fat malabsorption.

Quantitative fecal fat test
Quantitative fecal fat tests measure and report an amount of fat. This usually done over a period of three days, the patient collecting all of their feces into a container. The container is thoroughly mixed to homogenize the feces, this can be done with a paint mixer. A small sample from the feces is collected. The fat content is extracted with solvents and measured by saponification (turning the fat into soap). Normally up to 7 grams of fat can be malabsorbed in people consuming 100 grams of fat per day. In patients with diarrhea, up to 12 grams of fat may be malabsorbed since the presence of diarrhea interferes with fat absorption, even when the diarrhea is not due to fat malabsorption.

Flow cytometry

181

Flow cytometry
Flow cytometry is a laser based, biophysical technology employed in Cell counting, sorting, biomarker detection and protein engineering, by suspending them in a stream of fluid and passing them by an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of up to thousands of particles per second. Flow cytometry is routinely used in the diagnosis of health disorders, especially blood cancers, but has many other applications in basic research, clinical practice and clinical trials. A common variation is to physically sort particles based on their properties, so as to purify populations of interest.

Analysis of a marine sample of photosynthetic picoplankton by flow cytometry showing three different populations (Prochlorococcus, Synechococcus, and picoeukaryotes)

History
The first impedance-based flow cytometry device, using the Coulter principle, was disclosed in U.S. Patent 2,656,508, issued in 1953, to Wallace H. Coulter. Mack Fulwyler was the inventor of the forerunner to today's flow cytometers - particularly the cell sorter.[1] Fulwyler developed this in 1965 with his publication in Science.[2] The first fluorescence-based flow cytometry device (ICP 11) was developed in 1968 by Wolfgang Göhde from the University of Münster, filed for patent on 18th December 1968[3] and first commercialized in 1968/69 by German developer and manufacturer Partec through Phywe AG in Göttingen. At that time, absorption methods were still widely favored by other scientists over fluorescence methods.[4] Soon after, flow cytometry instruments were developed, including the Cytofluorograph (1971) from Bio/Physics Systems Inc. (later: Ortho Diagnostics), the PAS 8000 (1973) from Partec, the first FACS instrument from Becton Dickinson (1974), the ICP 22 (1975) from Partec/Phywe and the Epics from Coulter (1977/78).

Name of the technology
The original name of the flow cytometry technology was "pulse cytophotometry" (German: Impulszytophotometrie), based on the first patent application on fluorescence-based flow cytometry. At the 5th American Engineering Foundation Conference on Automated Cytology in Pensacola (Florida) in 1976 - eight years after the introduction of the first fluorescence-based flow cytometer (1968) - it was agreed to commonly use the name "flow cytometry", a term that quickly became popular[5].

Flow cytometry

182

Principle
A beam of light (usually laser light) of a single wavelength is directed onto a hydrodynamically-focused stream of liquid. A number of detectors are aimed at the point where the stream passes through the light beam: one in line with the light beam (Forward Scatter or FSC) and several perpendicular to it (Side Scatter or SSC) and one or more fluorescence detectors. Each suspended particle from 0.2 to 150 micrometers passing through the beam scatters the ray, and fluorescent chemicals found in the particle or attached to the particle may be excited into emitting light at a longer wavelength than the light source. This combination of scattered and fluorescent light is picked up by the detectors, and, by analysing fluctuations in brightness at each detector (one for each fluorescent emission peak), it is then possible to derive various types of information about the physical and chemical structure of each individual particle. FSC correlates with the cell volume and SSC depends on the inner complexity of the particle (i.e., shape of the nucleus, the amount and type of cytoplasmic granules or the membrane roughness). This is because the light is scattered off of the internal components of the cell. Some flow cytometers on the market have eliminated the need for fluorescence and use only light scatter for measurement. Other flow cytometers form images of each cell's fluorescence, scattered light, and transmitted light.

Flow cytometers
Modern flow cytometers are able to analyze several thousand particles every second, in "real time," and can actively separate and isolate particles having specified properties. A flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers "high-throughput" (for a large number of cells) automated quantification of set parameters. To analyze solid tissues, a single-cell suspension must first be prepared. A flow cytometer has five main components: • a flow cell - liquid stream (sheath fluid), which carries and aligns the cells so that they pass single file through the light beam for sensing
Front of desktop flow cytometer - the Becton-Dickinson Fluorescence activated cell sorter (FACSCalibur)

• a measuring system - commonly used are measurement of impedance (or conductivity) and optical systems lamps (mercury, xenon); high-power water-cooled lasers (argon, krypton, dye laser); low-power air-cooled lasers (argon (488 nm), red-HeNe (633 nm), green-HeNe, HeCd (UV)); diode lasers (blue, green, red, violet) resulting in light signals • a detector and Analogue-to-Digital Conversion (ADC) system - which generates FSC and SSC as well as fluorescence signals from light into electrical signals that can be processed by a computer • an amplification system - linear or logarithmic • a computer for analysis of the signals. The process of collecting data from samples using the flow cytometer is termed 'acquisition'. Acquisition is mediated by a computer physically connected to the flow cytometer, and the software which handles the digital interface with the cytometer. The software is capable of adjusting parameters (i.e. voltage, compensation, etc.) for the sample being tested, and also assists in displaying initial sample information while acquiring sample data to insure that parameters are set correctly. Early flow cytometers were, in general, experimental devices, but technological advances have enabled widespread applications for use in a variety of both clinical and research purposes. Due to these developments, a considerable market for instrumentation, analysis software, as well as the reagents used in acquisition such as fluorescently-labeled antibodies has developed. Modern instruments usually have multiple lasers and fluorescence detectors. The current record for a commercial instrument is four lasers and 18 fluorescence detectors. Increasing the number of lasers and detectors allows for

Flow cytometry multiple antibody labeling, and can more precisely identify a target population by their phenotypic markers. Certain instruments can even take digital images of individual cells, allowing for the analysis of fluorescent signal location within or on the surface of cells.

183

Data analysis
Gating
The data generated by flow-cytometers can be plotted in a single dimension, to produce a histogram, or in two-dimensional dot plots or even in three dimensions. The regions on these plots can be sequentially separated, based on fluorescence intensity, by creating a series of subset extractions, termed "gates." Specific gating protocols exist for diagnostic and clinical purposes especially in relation to hematology. The plots are often made on logarithmic scales. Because different fluorescent dyes' emission spectra overlap,[6] signals at the detectors have to be compensated electronically as well as computationally. Data accumulated using the flow cytometer can be analyzed using software, e.g., WinMDI[7] (only one which is freeware), Flowjo, FCS Express, VenturiOne, CellQuest Pro, or Cytospec.[8] Once the data are collected, there is no need to stay connected to the flow cytometer. For this reason, analysis is most often performed on a separate computer. This is especially necessary in core facilities where usage of these machines is in high demand.

Computational analysis
Recent progress on automated population identification using computational methods has offered an alternative to traditional gating strategies. Automated identification systems could potentially help findings of rare and hidden populations. Representative automated methods include FLOCK [9] in Immunology Database and Analysis Portal (ImmPort),[10] FLAME [11] in GenePattern and flowClust,[12][13][14] in Bioconductor. Collaborative efforts have resulted in an open project called FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods,[15]) to provide an objective way to compare and evaluate the flow cytometry data clustering methods, and also to establish guidance about appropriate use and application of these methods.

Fluorescence-activated cell sorting

Flow cytometry

184

Fluorescence-activated cell sorting (FACS) is a specialized type of flow cytometry. It provides a method for sorting a heterogeneous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell. It is a useful scientific instrument, as it provides fast, objective and quantitative recording of fluorescent signals from individual cells as well as physical separation of cells of particular interest. The acronym FACS is trademarked and owned by Becton, Dickinson and Company.[16] Among the large majority of researchers who use this technology for sorting or analysis, this term has become generic in common usage, much like xerox or kleenex. The first cell sorter was invented by Mack Fulwyler in 1965, using the Coulter principle, a relatively difficult technique and one no longer used in modern instruments. The technique was expanded by Len Herzenberg, who was responsible for coining the term FACS[17]. Herzenberg won the Kyoto Prize in 2006 for his seminal work in flow cytometry. The cell suspension is entrained in the center of a narrow, rapidly flowing stream of liquid. The flow is arranged so that there is a large separation between cells relative to their diameter. A vibrating mechanism causes the stream of cells to break into individual droplets. The system is adjusted so that there is a low probability of more than one cell per droplet. Just before the stream breaks into droplets, the flow passes through a fluorescence measuring station where the fluorescent character of interest of each cell is measured. An electrical charging ring is placed just at the point where the stream breaks into droplets. A charge is placed on the ring based on the immediately prior fluorescence intensity measurement, and the opposite charge is trapped on the droplet as it breaks from the stream. The charged droplets then fall through an electrostatic deflection system that diverts droplets into containers based upon their charge. In some systems, the charge is applied directly to the stream, and the droplet breaking off retains charge of the same sign as the stream. The stream is then returned to neutral after the droplet breaks off.

Labels
Fluorescent labels
A wide range of fluorophores can be used as labels in flow cytometry. Fluorophores, or simply "fluors", are typically attached to an antibody that recognises a target feature on or in the cell; they may also be attached to a chemical entity with affinity for the cell membrane or another cellular structure. Each fluorophore has a characteristic peak excitation and emission wavelength, and the emission spectra often overlap. Consequently, the combination of labels

Flow cytometry which can be used depends on the wavelength of the lamp(s) or laser(s) used to excite the fluorochromes and on the detectors available.[18] The maximum number of distinguishable fluorescent labels is thought to be 17 or 18, and this level of complexity necessitates laborious optimization to limit artifacts, as well as complex deconvolution algorithms to separate overlapping spectra.[19]

185

Quantum dots
Quantum dots are sometimes used in place of traditional fluorophores because of their narrower emission peaks.

Isotope labeling
In one approach to overcoming the fluorescent labeling limit, lanthanide isotopes are attached to antibodies. This method could theoretically allow the use of 40 to 60 distinguishable labels and has been demonstrated for Use of flow cytometry to measure copy number variation of a specific DNA sequence 30 labels.[19] Cells are introduced into (Flow-FISH) a plasma, ionizing them and allowing time-of-flight mass spectrometry to identify the associated isotopes. Although this method permits the use of a large number of labels, it currently has lower throughput capacity than traditional flow cytometry. It also destroys the analysed cells, precluding their recovery by sorting.[19]

Measurable parameters
This list is very long and constantly expanding. • • • • • • • • • • • • • • • • volume and morphological complexity of cells cell pigments such as chlorophyll or phycoerythrin total DNA content (cell cycle analysis, cell kinetics, proliferation, ploidy, aneuploidy, endoreduplication, etc.) total RNA content DNA copy number variation (by Flow-FISH or BACs-on-Beads technology) chromosome analysis and sorting (library construction, chromosome paint) protein expression and localization Protein modifications, phospho-proteins transgenic products in vivo, particularly the Green fluorescent protein or related Fluorescent Proteins cell surface antigens (Cluster of differentiation (CD) markers) intracellular antigens (various cytokines, secondary mediators, etc.) nuclear antigens enzymatic activity pH, intracellular ionized calcium, magnesium, membrane potential membrane fluidity apoptosis (quantification, measurement of DNA degradation, mitochondrial membrane potential, permeability changes, caspase activity)

• cell viability • monitoring electropermeabilization of cells

Flow cytometry • • • • • oxidative burst characterising multidrug resistance (MDR) in cancer cells glutathione various combinations (DNA/surface antigens, etc.) cell adherence (for instance pathogen-host cell adherence)

186

Applications
The technology has applications in a number of fields, including molecular biology, pathology, immunology, plant biology and marine biology. It has broad application in medicine (especially in transplantation, hematology, tumor immunology and chemotherapy, prenatal diagnosis, genetics and sperm sorting for sex preselection). In marine biology, the autofluorescent properties of photosynthetic plankton can be exploited by flow cytometry in order to characterise abundance and community structure. In protein engineering, flow cytometry is used in conjunction with yeast display and bacterial display to identify cell surface-displayed protein variants with desired properties.

Bibliography
• Flow Cytometry First Principles by Alice Longobardi Givan. ISBN 0-471-38224-8 • • • • • Practical Flow Cytometry by Howard M. Shapiro. ISBN 0-471-41125-6 Flow Cytometry for Biotechnology by Larry A. Sklar. ISBN 0-19-515234-4 Handbook of Flow Cytometry Methods by J. Paul Robinson, et al. ISBN 0-471-59634-5 Current Protocols in Cytometry, Wiley-Liss Pub. ISSN 1934-9297 Flow Cytometry in Clinical Diagnosis, v4, (Carey, McCoy, and Keren, eds), ASCP Press, 2007. ISBN 0-89189-548-5 • Ormerod, M.G. (ed.) (2000) Flow Cytometry — A practical approach. 3rd edition. Oxford University Press, Oxford, UK. ISBN 0-19-963824-1 • Ormerod, M.G. (1999) Flow Cytometry. 2nd edition. BIOS Scientific Publishers, Oxford. ISBN 1-85996-107-X • Flow Cytometry — A basic introduction. Michael G. Ormerod, 2008. ISBN 978-0-9559812-0-3

References
[1] US 3380584 (http:/ / worldwide. espacenet. com/ textdoc?DB=EPODOC& IDX=US3380584), Mack Fulwyler, "Particle Separator", issued 1965-06-01 [2] Fulwyler, M. J. (1965). "Electronic separation of biological cells by volume". Science 150 (698): 910–911. doi:10.1126/science.150.3698.910. PMID 5891056. [3] DE 1815352 (http:/ / worldwide. espacenet. com/ textdoc?DB=EPODOC& IDX=DE1815352), Wolfgang Dittrich & Wolfgang Göhde, "Flow-through Chamber for Photometers to Measure and Count Particles in a Dispersion Medium" [4] Kamentsky in Proceedings of the 1968 Conference „Cytology Automation" (1970), edited by D. M. D. Evans. [5] Sack et al., Ulrich. Zelluläre Diagnostik. Karger Publishers (2006). [6] http:/ / pingu. salk. edu/ flow/ fluo. html [7] "TSRI Cytometry Software Page" (http:/ / facs. scripps. edu/ software. html). . Retrieved 2009-09-03. [8] "PUCL Cytometry Software Page" (http:/ / www. cyto. purdue. edu/ Purdue_software). . Retrieved 2011-07-07. [9] Qian, Yu; Wei, Chungwen; Eun-Hyung Lee, F.; Campbell, John; Halliley, Jessica; Lee, Jamie A.; Cai, Jennifer; Kong, Y. Megan et al. (2010). "Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data". Cytometry Part B: Clinical Cytometry 78B: S69. doi:10.1002/cyto.b.20554. [10] "Immunology Database and Analysis Portal" (https:/ / www. immport. org/ immportWeb/ home/ home. do?loginType=full). . Retrieved 2009-09-03. [11] "FLow analysis with Automated Multivariate Estimation (FLAME)" (http:/ / www. broadinstitute. org/ cancer/ software/ genepattern/ modules/ FLAME/ ). . Retrieved 2009-09-03. [12] "flowClust" (http:/ / www. bioconductor. org/ packages/ 2. 5/ bioc/ html/ flowClust. html). . Retrieved 2009-09-03. [13] http:/ / www3. interscience. wiley. com/ journal/ 117925662/ abstract?CRETRY=1& SRETRY=0 [14] http:/ / www. biomedcentral. com/ 1471-2105/ 10/ 145

Flow cytometry
[15] "FlowCAP - Flow Cytometry: Critical Assessment of Population Identification Methods" (http:/ / flowcap. flowsite. org/ ). . Retrieved 2009-09-03. [16] "FACS MultiSET System" (http:/ / www. bdbiosciences. com/ pdfs/ brochures/ 23-3428-02. pdf) (PDF). Becton Dickinson. . Retrieved 2007-02-09. [17] Herzenberg, LA; Julius MH, Masuda T (1972). "Demonstration that antigen-binding cells are precursors of antibody-producing cells after purification with a fluorescence-activated cell sorter.". PNAS 69 (7): 1934–8. PMC 426835. PMID 4114858. [18] Loken MR (1990). Immunofluorescence Techniques in Flow Cytometry and Sorting (2nd ed.). Wiley. pp. 341–53. [19] Ornatsky, O.; Bandura, D.; Baranov, V.; Nitz, M.; Winnik, M. A.; Tanner, S. (2010). "Highly multiparametric analysis by mass cytometry". Journal of Immunological Methods 361 (1–2): 1–20. doi:10.1016/j.jim.2010.07.002. PMID 20655312.

187

External links
• Flow cytometry - How does it work? (http://www.unsolvedmysteries.oregonstate.edu/flow_06) (Oregon State University) • How a flow cytometer operates (http://sciencepark.mdanderson.org/fcores/flow/files/Operation.html) (MD Anderson Cancer Center) • Learn About Flow Cytometry (http://www.millipore.com/flowcytometry/fc4/learn) (Millipore) • Powerpoint lectures on flow cytometry (http://www.cyto.purdue.edu/flowcyt/educate/pptslide.htm) (Purdue University) • Tutorials on fluorescence and flow cytometry (http://probes.invitrogen.com/resources/education/) (Invitrogen) • Searchable database of fluorescent dyes (http://www.fluorophores.tugraz.at/) (Graz University of Technology) • Table of fluorochromes (http://pingu.salk.edu/flow/fluo.html) (Salk Institute) • Java Fluorescence Spectrum Viewer (http://www.bdbiosciences.com/spectra/) (Becton, Dickinson and Company) • Flow+cytometry (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Flow+cytometry) at the US National Library of Medicine Medical Subject Headings (MeSH) • FICCS (http://www.ficcs.org/) - the Flow Informatics and Computation Cytometry Society • History of Flow Cytometry by Bob Auer (http://www.coulterflow.com/bciflow/history.php) (hosted by Beckman Coulter) • Flow Cytometry - A Basic Introduction (http://flowbook.denovosoftware.com/) (hosted by De Novo Software) • Clinical Flow Wiki (http://wiki.clinicalflow.com/) • The History of the Cell Sorter Interviews (http://siarchives.si.edu/collections/siris_arc_217722) from the Smithsonian Institution Archives

Glucose

188

Glucose
D-glucose

Identifiers Abbreviations CAS number PubChem ChemSpider UNII EC number KEGG MeSH ChEBI ChEMBL RTECS number ATC code Beilstein Reference Gmelin Reference 3DMet Jmol-3D images Glc 50-99-7 5793 5589
[2] [3]   [4]   [1]  

5SL0G7R0OK 200-075-1 C00031 Glucose
[5]  

[6]

[7] [8]   [9]  

CHEBI:4167

CHEMBL1222250 LZ6600000 B05 CX01 1281604 83256 B04623
[13] [14] [10]

,V04 CA02

[11]

, V06 DC01

[12]

Image 1 [15] Image 2 Properties

Molecular formula Molar mass Density Melting point Solubility in water

CH O

6 12 6

180.16 g/mol 1.54 g/cm3 α-D-glucose: 146 °C β-D-glucose: 150 °C 91 g/100 mL

Glucose

189
Thermochemistry Std enthalpy of formation ΔfHo298 Std enthalpy of combustion ΔcHo298 Standard molar entropy So298 −1271 kJ/mol

−2805 kJ/mol

209.2 J K−1 mol−1 Hazards

MSDS EU Index
  (verify) [17]

ICSC 0865 not listed

[16]

 (what is:  / ?) Except where noted otherwise, data are given for materials in their standard state (at 25 °C, 100 kPa)

Infobox references

Glucose (/ˈɡluːkoʊs/ or /ʔkoʊz/; C6H12O6, also known as D-glucose, dextrose, or grape sugar) is a simple sugar (monosaccharide) and an important carbohydrate in biology. Cells use it as the primary source of energy[18] and a metabolic intermediate. Glucose is one of the main products of photosynthesis and fuels for cellular respiration. Glucose exists in several different molecular structures, but all of these structures can be divided into two families of mirror-images (stereoisomers). Only one set of these isomers exists in nature, those derived from the "right-handed form" of glucose, denoted D-glucose. D-glucose is sometimes referred to as dextrose, although the use of this name is strongly discouraged. The term dextrose is derived from dextrorotatory glucose.[19] This name is therefore confusing when applied to the enantiomer, which rotates light the opposite direction. Starch and cellulose are polymers derived from the dehydration of D-glucose. The other stereoisomer, called L-glucose, is hardly ever found in nature. The name "glucose" comes from the Greek word glukus (γλυκύς), meaning "sweet", and is the preferred name. The suffix "-ose" denotes a sugar.

Glucose

190

Function
Scientists can speculate on the reasons that glucose, and not another monosaccharide such as fructose, is so widely used in organisms. One reason might be that glucose has a lower tendency, relative to other hexose sugars, to react non-specifically with the amino groups of proteins. This reaction (glycation) reduces or destroys the function of many enzymes. The low rate of glycation is due to glucose's preference for the less reactive cyclic isomer. Nevertheless, many of the long-term complications of diabetes (e.g., blindness, renal failure, and peripheral neuropathy) are probably due to the glycation of proteins or lipids.[20] In contrast, enzyme-regulated addition of glucose to proteins by glycosylation is often essential to their function.

Analyte in medical blood test
Glucose is a common medical analyte measured in blood samples. Eating or fasting prior to taking a blood sample has an effect on the result. Higher than usual glucose levels may be a sign of prediabetes or diabetes mellitus.

Glucose metabolism and various forms of it in the process. -Glucose-containing compounds and isomeric forms are digested and taken up by the body in the intestines, including starch, glycogen, disaccharides and monosaccharides. -Glucose is stored in mainly the liver and muscles as glycogen. -It is distributed and utilized in tissues as free glucose.

As an energy source
Glucose is a ubiquitous fuel in biology. It is used as an energy source in most organisms, from bacteria to humans. Use of glucose may be by either aerobic respiration, anaerobic respiration, or fermentation. Glucose is the human body's key source of energy, through aerobic respiration, providing approximately 3.75 kilocalories (16 kilojoules) of food energy per gram.[21] Breakdown of carbohydrates (e.g. starch) yields mono- and disaccharides, most of which is glucose. Through glycolysis and later in the reactions of the citric acid cycle (TCAC), glucose is oxidized to eventually form CO2 and water, yielding energy sources, mostly in the form of ATP. The insulin reaction, and other mechanisms, regulate the concentration of glucose in the blood. A high fasting blood sugar level is an indication of prediabetic and diabetic conditions. Glucose is a primary source of energy for the brain, and hence its availability influences psychological processes. When glucose is low, psychological processes requiring mental effort (e.g., self-control, effortful decision-making) are impaired.[22][23][24][25]

Glucose in glycolysis
α-D-Glucose Hexokinase α-D-Glucose-6-phosphate

ATP

ADP

[26] [27] [28] Compound C00031 at KEGG Pathway Database. Enzyme 2.7.1.1 at KEGG Pathway Database. Compound C00668 at KEGG [29] Pathway Database. Reaction R01786 at KEGG Pathway Database.

Glucose

191

Use of glucose as an energy source in cells is via aerobic or anaerobic respiration. Both of these start with the early steps of the glycolysis metabolic pathway. The first step of this is the phosphorylation of glucose by hexokinase to prepare it for later breakdown to provide energy. The major reason for the immediate phosphorylation of glucose by a hexokinase is to prevent diffusion out of the cell. The phosphorylation adds a charged phosphate group so the glucose 6-phosphate cannot easily cross the cell membrane. Irreversible first steps of a metabolic pathway are common for regulatory purposes. In anaerobic respiration one glucose molecule produces a net gain of two ATP molecules (four ATP molecules are produced during glycolysis but two are required by enzymes used during the process).[30] In aerobic respiration a molecule of glucose is much more profitable in that a net worth of 34 ATP molecules are generated (32 gross with two being required in the process).[31]

As a precursor
Organisms use glucose as a precursor for the synthesis of several important substances. Starch, cellulose, and glycogen ("animal starch") are common glucose polymers (polysaccharides). Some of these polymers like starch or glycogen serve as energy stores while others like cellulose and chitin (which is made from a derivative of glucose) have structural roles. Oligosaccharides of glucose combined with other sugars serve as important energy stores. These include lactose, the predominant sugar in milk which a glucose-galactose disaccharide and sucrose, another disaccharide of glucose and fructose. Glucose is also added onto certain proteins and lipids in a process called glycosylation. This is often critical for their functioning. The enzymes that join glucose to other molecules usually use phosphorylated glucose to power the formation of the new bond by breaking the glucose-phosphate bond. Other than its direct use as a monomer, glucose can be broken down to synthesize a wide variety of other biomolecules. This is important as glucose serves both as a primary store of energy but also as a source of organic carbon. Glucose can be broken down and converted into lipids and amino acids. It is also a precursor for the synthesis of other important molecules like vitamin C (ascorbic acid). Though plants and some microbes can create all the compounds they need from glucose given the necessary minerals, all animals and many microbes cannot synthesize some or the other essential nutrient. For example, humans cannot synthesize Vitamin C and certain essential amino acids and need them in their diet.

Glucose Industrial use In industry, glucose is used as a precursor to make vitamin C (L-ascorbic acid) in the Reichstein process, to make citric acid, gluconic acid, bio-ethanol, polylactic acid, sorbitol.

192

Structure and nomenclature
Glucose is a monosaccharide with formula C6H12O6 or H-(C=O)-(CHOH)5-H, whose five hydroxyl (OH) groups are arranged in a specific way along its six-carbon backbone.

Open-chain form
In its fleeting open-chain form, the glucose molecule has an open (as opposed to cyclic) and unbranched backbone of six carbon atoms, C-1 through C-6; where C-1 is part of an aldehyde group H(C=O)-, and each of the other five carbons bears one hydroxyl group -OH. The remaining bonds of the backbone carbons are satisfied by hydrogen atoms -H. Therefore glucose is an hexose and an aldose, or an aldohexose. Each of the four carbons C-2 through C-5 is a stereocenter, meaning that its four bonds connect to four different substituents. (Carbon C-2, for example, connects to -(C=O)H, -OH, -H, and -(CHOH)4H.) In D-glucose, these four parts must be in a specific three-dimensional arrangement. Namely, when the molecule is drawn in the Fischer projection, the hydroxyls on C-2, C-4, and C-5 must be on the right side, while that on C-3 must be on the left side.

The positions of those four hydroxyls are exactly reversed in the Fischer diagram of L-glucose. D- and L-glucose are two of the 16 possible aldohexoses; the other 14 are allose, altrose, mannose, gulose, idose, galactose, and talose, each with two isomers, "D-" and "L-".

D-glucose in Fischer projection

Cyclic forms
In solutions, the open-chain form of glucose (either "D-" or "L-") exists in equilibrium with several cyclic isomers, each containing a ring of carbons closed by one oxygen atom. In aqueous solution, however, glucose exists as pyranose for more than 99%. The open-chain form is limited to about 0.25% and furanose exists in negligible amounts. The terms "glucose" and "D-glucose" are generally used for these cyclic forms as well. The ring arises from the open-chain form by a nucleophilic addition reaction between the aldehyde group -(C=O)H at C-1 and the hydroxyl group -OH at C-4 or C-5, yielding a hemiacetal group -C(OH)H-O-. The reaction between C-1 and C-5 creates a molecule with a six-membered ring, called pyranose, after the cyclic ether pyran, the simplest molecule with the same carbon-oxygen ring. The (much rarer) reaction between C-1 and C-4 creates a molecule with a five-membered ring, called furanose, after the cyclic ether furan. In either case, each carbon in the ring has one hydrogen and one hydroxyl attached, except for the last carbon (C-4 or C-5) where the hydroxyl is replaced by the remainder of the open molecule (which is -(CHOH)2-H or -(CHOH)-H, respectively). The ring-closing reaction makes carbon C-1 chiral, too, since its four bonds lead to -H, to -OH, to carbon C-2, and to the ring oxygen. These four parts of the molecule may be arranged around C-1 (the anomeric carbon) in two distinct ways, designated by the prefixes "α-" and "β-". When a glucopyranose molecule is drawn in the Haworth projection, the designation "α-" means that the hydroxyl group attached to C-1 and the -CH2OH group at C-5 lies on opposite sides of the ring's plane (a trans arrangement), while "β-" means that they are on the same side of the plane (a cis arrangement). Therefore, the open isomer D-glucose gives rise to four distinct cyclic isomers: α-D-glucopyranose, β-D-glucopyranose, α-D-glucofuranose, and β-D-glucofuranose; which are all chiral.

Glucose

193

α-Dβ-Dα-Dβ-DGlucopyranose Glucopyranose Glucofuranose Glucofuranose

α-D-Glucopyranose

β-D-Glucopyranose

The other open-chain isomer L-glucose similarly gives rise to four distinct cyclic forms of L-glucose, each the mirror image of the corresponding D-glucose. The rings are not planar but twisted in three dimensions. The glucopyranose ring (α or β) can assume several non-planar shapes, analogous to the "chair" and "boat" conformations of cyclohexane. Similarly, the glucofuranose ring may assume several shapes, analogous to the "envelope" conformations of cyclopentane. The glucopyranose forms of glucose predominate in solution, and are the only forms observed in the solid state. They are crystalline colorless solids, highly soluble in water and acetic acid, poorly soluble in methanol and ethanol. They melt at 146 °C (unknown operator: u'strong' °F) (α) and 150 °C (unknown operator: u'strong' °F) (β), and decompose at higher temperatures into carbon and water.

Rotational isomers
Each glucose isomer is subject to rotational isomerism. Within the cyclic form of glucose, rotation may occur around the O6-C6-C5-O5 torsion angle, termed the ω-angle, to form three staggered rotamer conformations called gauche-gauche (gg), gauche-trans (gt) and trans-gauche (tg). For methyl α-D-glucopyranose at equilibrium the ratio of molecules in each rotamer conformation is reported as 57:38:5 gg:gt:tg.[32] This tendency for the ω-angle to prefer to adopt a gauche conformation is attributed to the gauche effect.

Glucose

194

Physical properties
Solutions
All forms of glucose are colorless and easily soluble in water, acetic acid, and several other solvents. They are only sparingly soluble in methanol and ethanol. The open-chain form is thermodynamically unstable, and it spontaneously tautomerizes to the cyclic forms. (Although the ring closure reaction could in theory create four- or three-atom rings, these would be highly strained and are not observed.) In solutions at room temperature, the four cyclic isomers interconvert over a timescale of hours, in a process called mutarotation.[33] Starting from any proportions, the mixture converges stable ratio of α:β 36:64. The ratio would be α:β 11:89 if it were not for the influence of the anomeric effect.[34] Mutarotation is considerably slower at temperatures close to 0 °C. Mutarotation consists of a temporary reversal of the ring-forming reaction, resulting in the open-chain form, followed by a re-forming of the ring. The ring closure step may use a different -OH group than the one recreated by the opening step (thus switching between pyranose and furanose forms), and/or the new hemiacetal group created on C-1 may have the same or opposite handedness as the original one (thus switching between the α and β forms). Thus, even though the open-chain form is barely detectable in solution, it is an essential component of the equilibrium.

Solid state
Depending on conditions, three major solid forms of glucose can be crystallised from water solutions: α-glucopyranose, β-glucopyranose, and β-glucopyranose hydrate.[35]

Optical activity
Whether in water or in the solid form, D-glucose is dextrorotatory, meaning that it will rotate the direction of polarized light clockwise. The effect is due to the chirality of the molecules, and indeed the mirror-image isomer, L-glucose, is levorotatory (rotates polarized light counterclockwise) by the same amount. The strength of the effect is different for each of the five tautomers. Note that the D- prefix does not refer directly to the optical properties of the compound. It indicates that the C-2 chiral center has the same handedness as that of D-glyceraldehyde (which was so labeled because it is dextrorotatory). The fact that D-glucose is dextrorotatory is a combined effect of its four chiral centers, not just of C-2; and indeed some of the other D-aldohexoses are levorotatory.

Production
Biosynthesis
In plants and some prokaryotes, glucose is a product of photosynthesis. In animals and fungi, glucose results from the breakdown of glycogen, a process known as glycogenolysis. In plants the breakdown substrate is starch. In animals, glucose is synthesized in the liver and kidneys from non-carbohydrate intermediates, such as pyruvate and glycerol, by a process known as gluconeogenesis. In some deep-sea bacteria glucose is produced by chemosynthesis.
Glucose tablets

Glucose

195

Commercial
Glucose is produced commercially via the enzymatic hydrolysis of starch. Many crops can be used as the source of starch. Maize, rice, wheat, cassava, corn husk and sago are all used in various parts of the world. In the United States, cornstarch (from maize) is used almost exclusively. Most commercial glucose occurs as a component of invert sugar, an approximately 1:1 mixture of glucose and fructose. In principle, cellulose could be hydrolysed to glucose, but this process is not yet commercially practical.[35]

Sources and absorption
Most dietary carbohydrates contain glucose, either as their only building block, as in starch and glycogen, or together with another monosaccharide, as in sucrose and lactose. In the lumen of the duodenum and small intestine, the glucose oligo- and polysaccharides are broken down to monosaccharides by the pancreatic and intestinal glycosidases. Other polysaccharides cannot be processed by the human intestine and require assistance by intestinal flora if they are to be broken down; the most notable exceptions are sucrose (fructose-glucose) and lactose (galactose-glucose). Glucose is then transported across the apical membrane of the enterocytes by SLC5A1, and later across their basal membrane by SLC2A2.[36] Some of the glucose is converted to lactic acid by astrocytes, which is then utilized as an energy source by brain cells, some of the glucose is used by intestinal cells and red blood cells, while the rest reaches the liver, adipose tissue and muscle cells, where it is absorbed and stored as glycogen (under the influence of insulin). Liver cell glycogen can be converted to glucose and returned to the blood when insulin is low or absent; muscle cell glycogen is not returned to the blood because of a lack of enzymes. In fat cells, glucose is used to power reactions that synthesize some fat types and have other purposes. Glycogen is the body's "glucose energy storage" mechanism, because it is much more "space efficient" and less reactive than glucose itself.

History
Because glucose is a basic necessity of many organisms, a correct understanding of its chemical makeup and structure contributed greatly to a general advancement in organic chemistry. This understanding occurred largely as a result of the investigations of Emil Fischer, a German chemist who received the 1902 Nobel Prize in Chemistry as a result of his findings.[37] The synthesis of glucose established the structure of organic material and consequently formed the first definitive validation of Jacobus Henricus van't Hoff's theories of chemical kinetics and the arrangements of chemical bonds in carbon-bearing molecules.[38] Between 1891 and 1894, Fischer established the stereochemical configuration of all the known sugars and correctly predicted the possible isomers, applying van't Hoff's theory of asymmetrical carbon atoms.

References
[1] http:/ / www. commonchemistry. org/ ChemicalDetail. aspx?ref=50-99-7 [2] http:/ / pubchem. ncbi. nlm. nih. gov/ summary/ summary. cgi?cid=5793 [3] http:/ / www. chemspider. com/ 5589 [4] http:/ / fdasis. nlm. nih. gov/ srs/ srsdirect. jsp?regno=5SL0G7R0OK [5] http:/ / esis. jrc. ec. europa. eu/ lib/ einecs_IS_reponse. php?genre=ECNO& entree=200-075-1 [6] http:/ / www. kegg. jp/ entry/ C00031 [7] http:/ / www. nlm. nih. gov/ cgi/ mesh/ 2007/ MB_cgi?mode=& term=Glucose [8] https:/ / www. ebi. ac. uk/ chebi/ searchId. do?chebiId=4167 [9] https:/ / www. ebi. ac. uk/ chembldb/ index. php/ compound/ inspect/ CHEMBL1222250 [10] http:/ / www. whocc. no/ atc_ddd_index/ ?code=B05CX01 [11] http:/ / www. whocc. no/ atc_ddd_index/ ?code=V04CA02 [12] http:/ / www. whocc. no/ atc_ddd_index/ ?code=V06DC01 [13] http:/ / www. 3dmet. dna. affrc. go. jp/ html/ B04623. html

Glucose

196

[14] http:/ / chemapps. stolaf. edu/ jmol/ jmol. php?model=OC%5BC%40H%5D1OC%28O%29%5BC%40H%5D%28O%29%5BC%40%40H%5D%28O%29%5BC%40%40H%5D1O [15] http:/ / chemapps. stolaf. edu/ jmol/ jmol. php?model=C%28%5BC%40%40H%5D1%5BC%40H%5D%28%5BC%40%40H%5D%28%5BC%40H%5D%28%5BC%40H%5D%28O1%29O%29O%29O% [16] http:/ / www. inchem. org/ documents/ icsc/ icsc/ eics0865. htm [17] http:/ / en. wikipedia. org/ wiki/ Special%3Acomparepages?rev1=480476804& page2=%3AGlucose [18] Clark, D.; Sokoloff, L. (1999), Basic Neurochemistry: Molecular, Cellular and Medical Aspects, Lippincott, pp. 637–670 [19] "dextrose" (http:/ / www. m-w. com/ dictionary/ dextrose), Merriam-Webster Online Dictionary, , retrieved 2009-09-02. [20] High Blood Glucose and Diabetes Complications: The buildup of molecules known as AGEs may be the key link (http:/ / forecast. diabetes. org/ magazine/ features/ high-blood-glucose-and-diabetes-complications), American Diabetes Association, 2010, ISSN 0095-8301, [21] "Chapter 3: Calculation of the Energy Content of Foods – Energy Conversion Factors" (http:/ / www. fao. org/ docrep/ 006/ Y5022E/ y5022e04. htm), Food energy — methods of analysis and conversion factors, FAO Food and Nutrition Paper 77, Rome: Food and Agriculture Organization, 2003, ISBN 92-5-105014-7, . [22] Fairclough, Stephen H.; Houston, Kim (2004), "A metabolic measure of mental effort", Biol. Psychol. 66 (2): 177–90, doi:10.1016/j.biopsycho.2003.10.001, PMID 15041139. [23] Gailliot, Matthew T.; Baumeister, Roy F.; DeWall, C. Nathan; Plant, E. Ashby; Brewer, Lauren E.; Schmeichel, Brandon J.; Tice, Dianne M.; Maner, Jon K. (2007), "Self-Control Relies on Glucose as a Limited Energy Source: Willpower is More than a Metaphor", J. Personal. Soc. Psychol. 92 (2): 325–36, doi:10.1037/0022-3514.92.2.325, PMID 17279852. [24] Gailliot, Matthew T.; Baumeister, Roy F. (2007), "The Physiology of Willpower: Linking Blood Glucose to Self-Control", Personal. Soc. Psychol. Rev. 11 (4): 303–27, doi:10.1177/1088868307303030, PMID 18453466. [25] Masicampo, E. J.; Baumeister, Roy F. (2008), "Toward a Physiology of Dual-Process Reasoning and Judgment: Lemonade, Willpower, and Expensive Rule-Based Analysis", Psychol. Sci. 19 (3): 255–60, doi:10.1111/j.1467-9280.2008.02077.x, PMID 18315798. [26] http:/ / www. genome. jp/ dbget-bin/ www_bget?compound+ C00031 [27] http:/ / www. genome. jp/ dbget-bin/ www_bget?enzyme+ 2. 7. 1. 1 [28] http:/ / www. genome. jp/ dbget-bin/ www_bget?compound+ C00668 [29] http:/ / www. genome. jp/ dbget-bin/ www_bget?rn+ R01786 [30] Medical Biochemistry at a Glance @Google books (http:/ / books. google. co. uk/ books?id=9BtxCWxrWRoC& pg=PA52), Blackwell Publishing, 2006, ISBN 978-1-4051-1322-9, [31] Medical Biochemistry at a Glance @Google books (http:/ / books. google. co. uk/ books?id=9BtxCWxrWRoC& pg=PA50), Blackwell Publishing, 2006, ISBN 978-1-4051-1322-9, [32] Kirschner, Karl N.; Woods, Robert J. (2001), "Solvent interactions determine carbohydrate conformation", Proc. Natl. Acad. Sci. USA 98 (19): 10541–45, doi:10.1073/pnas.191362798, PMC 58501, PMID 11526221 [33] McMurry, John E. (1988), Organic Chemistry (2nd ed.), Brooks/Cole, p. 866, ISBN 0534079687. [34] Juaristi, Eusebio; Cuevas, Gabriel (1995), The Anomeric Effect, CRC Press, pp. 9–10, ISBN 0-8493-8941-0. [35] Fred W. Schenck “Glucose and Glucose-Containing Syrups” in Ullmann's Encyclopedia of Industrial Chemistry 2006, Wiley-VCH, Weinheim. doi: 10.1002/14356007.a12_457.pub2 [36] Ferraris, Ronaldo P. (2001), "Dietary and developmental regulation of intestinal sugar transport" (http:/ / www. biochemj. org/ bj/ 360/ 0265/ bj3600265. htm), Biochem. J. 360 (Pt 2): 265–76, doi:10.1042/0264-6021:3600265, PMC 1222226, PMID 11716754, . [37] Emil Fischer (http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1902/ fischer-bio. html), Nobel Foundation, , retrieved 2009-09-02. [38] Fraser-Reid, Bert, "van't Hoff's Glucose", Chem. Eng. News 77 (39): 8.

External links
• International Chemical Safety Card 0865 (http://www.inchem.org/documents/icsc/icsc/eics0865.htm)

Glycogen

197

Glycogen
Glycogen is a multibranched polysaccharide that serves as a form of energy storage in animals[2] and fungi. In humans, glycogen is made and stored primarily in the cells of the liver and the muscles, and functions as the secondary long-term energy storage (with the primary energy stores being fats held in adipose tissue). Glycogen can also be made via glycogenesis within the brain and stomach.[3] Glycogen is the analogue of starch, a glucose polymer in plants, and is sometimes referred to as animal starch, having a similar structure to amylopectin but more extensively branched and compact than starch. Glycogen is found in the form of granules in the cytosol/cytoplasm in many cell types, and plays an important role in the glucose cycle. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, but one that is less compact than the energy reserves of triglycerides (lipids). In the liver hepatocytes, glycogen can compose up to eight percent of the fresh weight (100–120 g in an adult) soon after a meal.[4] Only the glycogen stored in the liver can be made accessible to other organs. In the muscles, glycogen is found in a low concentration (one to two percent of the muscle mass). The amount of glycogen stored in the body—especially within the muscles, liver, and red blood [5][6][7] cells —mostly depends on physical training, basal metabolic rate, and eating habits such as intermittent fasting. Small amounts of glycogen are found in the kidneys, and even smaller amounts in certain glial cells in the brain and white blood cells. The uterus also stores glycogen during pregnancy to nourish the embryo.[8]

Schematic 2-D cross-sectional view of glycogen. A core protein of glycogenin is surrounded by branches of glucose units. The entire globular granule may contain [1] approximately 30,000 glucose units.

A view of the atomic structure of a single branched strand of glucose units in a glycogen molecule.

Glycogen

198

Structure
Glycogen is a branched biopolymer consisting of linear chains of glucose residues with further chains branching off every ten glucoses or so. Glucoses are linked together linearly by α(1→4) glycosidic bonds from one glucose to the next. Branches are linked to the chains they are branching off from by α(1→6) glycosidic bonds between the first glucose of the new branch and a glucose on the stem chain. [9]

Schematic of glycogen structure

Due to the way that glycogen is synthesised, every glycogen granule has at its core a glycogenin protein.[10]

Function
Liver
As a meal containing carbohydrates is eaten and digested, blood glucose levels rise, and the pancreas secretes insulin. Glucose from the portal vein enters liver cells (hepatocytes). Insulin acts on the hepatocytes to stimulate the action of several enzymes, including glycogen synthase. Glucose molecules are added to the chains of glycogen as long as both insulin and glucose remain plentiful. In this postprandial or "fed" state, the liver takes in more glucose from the blood than it releases. After a meal has been digested and glucose levels begin to fall, insulin secretion is reduced, and glycogen synthesis stops. When it is needed for energy, glycogen is broken down and converted again to glucose. Glycogen phosphorylase is the primary enzyme of glycogen breakdown. For the next 8–12 hours, glucose derived from liver glycogen will be the primary source of blood glucose to be used by the rest of the body for fuel. Glucagon is another hormone produced by the pancreas, which in many respects serves as a counter-signal to insulin. In response to insulin level below normal (when blood levels of glucose begin to fall below the normal range), glucagon is secreted in increasing amounts to stimulate glycogenolysis and gluconeogenesis pathways.

Muscle
Muscle cell glycogen appears to function as an immediate reserve source of available glucose for muscle cells. Other cells that contain small amounts use it locally as well. Muscle cells lack the enzyme glucose-6-phosphatase, which is required to pass glucose into the blood, so the glycogen they store is destined for internal use and is not shared with other cells. (This is in contrast to liver cells, which, on demand, readily do break down their stored glycogen into glucose and send it through the blood stream as fuel for the brain or muscles). Glycogen is also a suitable storage substance due to its insolubility in water, which means it does not affect the osmotistic levels and pressure of a cell.

Glycogen

199

Metabolism
Synthesis
Glycogen synthesis is, unlike its breakdown, endergonic. This means that glycogen synthesis requires the input of energy. Energy for glycogen synthesis comes from UTP, which reacts with glucose-1-phosphate, forming UDP-glucose, in a reaction catalysed by UDP-glucose pyrophosphorylase. Glycogen is synthesized from monomers of UDP-glucose by the enzyme glycogen synthase, which progressively lengthens the glycogen chain with (α1→4) bonded glucose. As glycogen synthase can lengthen only an existing chain, the protein glycogenin is needed to initiate the synthesis of glycogen. The glycogen-branching enzyme, amylo (α1→4) to (α1→6) transglycosylase, catalyzes the transfer of a terminal fragment of 6-7 glucose residues from a nonreducing end to the C-6 hydroxyl group of a glucose residue deeper into the interior of the glycogen molecule. The branching enzyme can act upon only a branch having at least 11 residues, and the enzyme may transfer to the same glucose chain or adjacent glucose chains.

Breakdown
Glycogen is cleaved from the nonreducing ends of the chain by the enzyme glycogen phosphorylase to produce monomers of glucose-1-phosphate, which is then converted to glucose 6-phosphate Action of Glycogen Phosphorylase on Glycogen by phosphoglucomutase. A special debranching enzyme is needed to remove the alpha(1-6) branches in branched glycogen and reshape the chain into linear polymer. The G6P monomers produced have three possible fates: • G6P can continue on the glycolysis pathway and be used as fuel. • G6P can enter the pentose phosphate pathway via the enzyme Glucose-6-phosphate dehydrogenase to produce NADPH and 5-carbon sugars. • In the liver and kidney, G6P can be dephosphorylated back to Glucose by the enzyme Glucose 6-phosphatase. This is the final step in the gluconeogenesis pathway.

Clinical relevance
Disorders of glycogen metabolism
The most common disease in which glycogen metabolism becomes abnormal is diabetes, in which, because of abnormal amounts of insulin, liver glycogen can be abnormally accumulated or depleted. Restoration of normal glucose metabolism usually normalizes glycogen metabolism as well. In hypoglycemia caused by excessive insulin, liver glycogen levels are high, but the high insulin level prevents the glycogenolysis necessary to maintain normal blood sugar levels. Glucagon is a common treatment for this type of hypoglycemia. Various inborn errors of metabolism are caused by deficiencies of enzymes necessary for glycogen synthesis or breakdown. These are collectively referred to as glycogen storage diseases.

Glycogen

200

Glycogen depletion and endurance exercise
Long-distance athletes such as marathon runners, cross-country skiers, and cyclists often experience glycogen depletion, where almost all of the athlete's glycogen stores are depleted after long periods of exertion without enough energy consumption. This phenomenon is referred to as "hitting the wall". In marathon runners, it normally happens around the 20-mile (32 km) point of a marathon, depending on the size of the runner and the race course. Glycogen depletion can be forestalled in four possible ways. First, during exercise carbohydrates with the highest possible rate of conversion to blood glucose per time (high glycemic Index) are ingested continuously. The best possible outcome of this strategy replaces about 35% of glucose consumed at heart rates above about 80% of maximum. Second, through training, the body can be conditioned to burn fat earlier, faster, and more efficiently, sparing carbohydrate use from all sources. Third, by consuming foods low on the glycemic Index for 12–18 hours before the event, the liver and muscles will store the resulting slow but steady stream of glucose as glycogen, instead of fat. This process is known as carbohydrate loading. When experiencing glycogen debt, athletes often experience extreme fatigue to the point that it is difficult to move. As a reference, the very best professional cyclists in the world will usually finish a 4-5hr stage race right at the limit of glycogen depletion using the first 3 strategies. A study published in the Journal of Applied Physiology (online May 8, 2008) suggests that, when athletes ingest both carbohydrate and caffeine following exhaustive exercise, their glycogen is replenished more rapidly.[11][12]

References
[1] Page 12 in: (http:/ / books. google. dk/ books?id=SRptlOx7yj4C& printsec=frontcover& hl=en) Exercise physiology: energy, nutrition, and human performance By William D. McArdle, Frank I. Katch, Victor L. Katch Edition: 6, illustrated Published by Lippincott Williams & Wilkins, 2006 ISBN 0-7817-4990-5, ISBN 978-0-7817-4990-9, 1068 pages [2] Sadava et al (2011). Life (9th, International ed.). W. H. Freeman. ISBN 9781429254311. [3] Anatomy and Physiology. Saladin, Kenneth S. McGraw-Hill, 2007. [4] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6. . [5] Moses SW, Bashan N, Gutman A (December 1972). "Glycogen metabolism in the normal red blood cell" (http:/ / www. bloodjournal. org/ cgi/ pmidlookup?view=long& pmid=5083874). Blood 40 (6): 836–43. PMID 5083874. . [6] http:/ / jeb. biologists. org/ cgi/ reprint/ 129/ 1/ 141. pdf [7] Miwa I, Suzuki S (November 2002). "An improved quantitative assay of glycogen in erythrocytes". Annals of Clinical Biochemistry 39 (Pt 6): 612–3. doi:10.1258/000456302760413432. PMID 12564847. [8] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6. . [9] Berg, Tymoczko & Stryer (2012). Biochemistry (7th, International ed.). W. H. Freeman. p. 338. ISBN 1429203145. [10] Berg et al (2012). Biochemistry (7th, International ed.). W. H. Freeman. p. 650. [11] Pedersen DJ, Lessard SJ, Coffey VG, et al. (July 2008). "High rates of muscle glycogen resynthesis after exhaustive exercise when carbohydrate is coingested with caffeine". Journal of Applied Physiology 105 (1): 7–13. doi:10.1152/japplphysiol.01121.2007. PMID 18467543. [12] Post-exercise Caffeine Helps Muscles Refuel (http:/ / newswise. com/ articles/ view/ 542216/ ) Newswise, Retrieved on July 6, 2008.

External links
• Glycogen detection using Periodic Acid Schiff Staining (http://www.histochem.net/protocol periodic acid schiff.htm) • Glycogen storage disease - McArdle's Disease Website (http://mcardlesdisease.org) • Glycogen (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Glycogen) at the US National Library of Medicine Medical Subject Headings (MeSH)

Glycoprotein

201

Glycoprotein
Glycoproteins are proteins that contain oligosaccharide chains (glycans) covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending extracellularly, the extracellular segments are often glycosylated. Glycoproteins are often important integral membrane proteins, where they play a role in cell–cell interactions. Glycoproteins are also formed in the cytosol, but their functions and the pathways producing these modifications in this compartment are less well understood.[2]

N-glycosylation and O-glycosylation
There are two types of glycoproteins:

N-linked protein glycosylation (N-glycosylation of N-glycans) at Asn residues (Asn-x-Ser/Thr [1] motifs) in glycoproteins.

• In N-glycosylation (see on the right), the addition of sugar chains can happen at the amide nitrogen on the side-chain of the asparagine. • In O-glycosylation, the addition of sugar chains can happen on the hydroxyl oxygen on the side-chain of hydroxylysine, hydroxyproline, serine, or threonine.

Monosaccharides
Monosaccharides commonly found in eukaryotic glycoproteins include:[3]:526

Eight sugars commonly found in glycoproteins.

Glycoprotein

202

The principal sugars found in human glycoproteins[4]
Sugar β-D-Glucose β-D-Galactose β-D-Mannose α-L-Fucose N-Acetylgalactosamine N-Acetylglucosamine Hexose Hexose Hexose Deoxyhexose Aminohexose Aminohexose Type Abbreviation Glc Gal Man Fuc GalNAc GlcNAc NeuNAc

N-Acetylneuraminic acid Aminononulosonic acid (Sialic acid) Xylose Pentose

Xyl

The sugar group(s) can assist in protein folding or improve proteins' stability.

Examples
One example of glycoproteins found in the body is mucins, which are secreted in the mucus of the respiratory and digestive tracts. The sugars attached to mucins give them considerable water-holding capacity and also make them resistant to proteolysis by digestive enzymes. Glycoproteins are important for white blood cell recognition, especially in mammals. Examples of glycoproteins in the immune system are: • molecules such as antibodies (immunoglobulins), which interact directly with antigens. • molecules of the major histocompatibility complex (or MHC), which are expressed on the surface of cells and interact with T cells as part of the adaptive immune response. Other examples of glycoproteins include: • glycoprotein IIb/IIIa, an integrin found on platelets that is required for normal platelet aggregation and adherence to the endothelium. • components of the zona pellucida, which surrounds the oocyte, and is important for sperm-egg interaction. • structural glycoproteins, which occur in connective tissue. These help bind together the fibers, cells, and ground substance of connective tissue. They may also help components of the tissue bind to inorganic substances, such as calcium in bone. • Glycoprotein-41 (gp41) and glycoprotein-120 (gp120) are HIV viral coat proteins. Soluble glycoproteins often show a high viscosity, for example, in egg white and blood plasma. • Miraculin, which alters human tongue receptors to recognize sour foods as sweet.

Glycoprotein

203

Hormones
Hormones that are glycoproteins include: • • • • • • Follicle-stimulating hormone Luteinizing hormone Thyroid-stimulating hormone Human chorionic gonadotropin Alpha-fetoprotein Erythropoietin (EPO)

Functions
Some functions served by glycoproteins[3]:524
Function Structural molecule Lubricant and protective agent Transport molecule Immunologic molecule Hormone Enzyme Cell attachment-recognition site Collagens Mucins Transferrin, ceruloplasmin Immunoglobins, histocompatibility antigens Human chorionic gonadotropin (HCG), thyroid-stimulating hormone (TSH) Various, e.g., alkaline phosphatase Various proteins involved in cell–cell (e.g., sperm–oocyte), virus–cell, bacterium–cell, and hormone–cell interactions Certain plasma proteins of coldwater fish Lectins, selectins (cell adhesion lectins), antibodies Glycoproteins

Antifreeze protein Interact with specific carbohydrates Receptor Affect folding of certain proteins Regulation of development Hemostasis (and thrombosis)

Various proteins involved in hormone and drug action Calnexin, calreticulin Notch and its analogs, key proteins in development Specific glycoproteins on the surface membranes of platelets

Analysis
A variety of methods used in detection, purification, and structural analysis of glycoproteins are[3]:525[5]

Glycoprotein

204

Some important methods used to study glycoproteins
Method Periodic acid-Schiff stain Use Detects glycoproteins as pink bands after electrophoretic separation.

Incubation of cultured cells with glycoproteins Leads to detection of a radioactive sugar after electrophoretic separation. as radioactive decay bands Treatment with appropriate endo- or exoglycosidase or phospholipases Resultant shifts in electrophoretic migration help distinguish among proteins with N-glycan, O-glycan, or GPI linkages and also between high mannose and complex N-glycans.

Agarose-lectin column chromatography, lectin To purify glycoproteins or glycopeptides that bind the particular lectin used. affinity chromatography Lectin affinity electrophoresis Resultant shifts in electrophoretic migration help distinguish and characterize glycoforms, i.e. variants of a glycoprotein differing in carbohydrate. Identifies sugars that the glycoprotein contains and their stoichiometry.

Compositional analysis following acid hydrolysis Mass spectrometry

Provides information on molecular mass, composition, sequence, and sometimes branching of a glycan chain. To identify specific sugars, their sequence, linkages, and the anomeric nature of glycosidic chain. Measures the mechanisms underlying the biomolecular interactions, including reaction rates, affinities and associated conformational changes. To determine linkage between sugars. Determination of amino acid sequence.

NMR spectroscopy Dual Polarisation Interferometry

Methylation (linkage) analysis Amino acid or cDNA sequencing

References
[1] Ruddock & Molinari (2006) Journal of Cell Science 119, 4373–4380 [2] Funakoshi Y, Suzuki T (January 2009). "Glycobiology in the cytosol: The bitter side of a sweet world". Biochim. Biophys. Acta 1790 (2): 81–94. doi:10.1016/j.bbagen.2008.09.009. PMID 18952151. [3] Robert K. Murray, Daryl K. Granner & Victor W. Rodwell: "Harper's Illustrated Biochemistry 27th Ed.", McGraw-Hill, 2006 [4] https:/ / www. sigmaaldrich. com/ img/ assets/ 15880/ glycan_classification. pdf [5] Anne Dell, Howard R Morris: "Glycoprotein structure determination by mass spectrometry", Science 291(5512), 2351–2356 (2001), Review

External links
• Structure of Glycoprotein and Carbohydrate Chain (http://www.ecosci.jp/chem10/weekmol101j_e.html) – Home Page for Learning Environmental Chemistry • Biochemistry 5thE 11.3. Carbohydrates Can Be Attached to Proteins to Form Glycoproteins (http://www.ncbi. nlm.nih.gov/books/bv.fcgi?indexed=google&rid=stryer.section.1531) • Carbohydrate Chemistry and Glycobiology: A Web Tour (http://www.sciencemag.org/feature/data/ carbohydrates.dtl#glycoproteins) SPECIAL WeB SUPPLEMENT Science 23 March 2001 Vol 291, Issue 5512, Pages 2263–2502 • Glycoproteins (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Glycoproteins) at the US National Library of Medicine Medical Subject Headings (MeSH)

Histology

205

Histology
Histology (compound of the Greek words: ἱστός "tissue", and -λογία -logia) is the study of the microscopic anatomy of cells and tissues of plants and animals. It is commonly performed by examining cells and tissues by sectioning and staining, followed by examination under a light microscope or electron microscope. Histological studies may be conducted via tissue culture, where live cells can be isolated and maintained in a proper environment outside the body for various research projects. The ability to visualize or differentially identify microscopic structures is frequently enhanced through the use of histological stains. Histology is an essential tool of biology and medicine. Histopathology, the microscopic study of diseased tissue, is an important tool in anatomical pathology, since accurate diagnosis of cancer and other diseases usually requires histopathological examination of samples. Trained medical doctors, frequently board-certified as pathologists, are the personnel who perform histopathological examination and provide diagnostic information based on their observations. The trained scientists who perform the preparation of histological sections are histotechnicians, histology technicians Microscopic view of a histologic specimen of human lung tissue stained with hematoxylin and eosin. (HT), histology technologists (HTL), medical scientists, medical laboratory technicians, or biomedical scientists. Their field of study is called histotechnology.

A stained histologic specimen, sandwiched between a glass microscope slide and coverslip, mounted on the stage of a light microscope.

Histology
Fixing
Chemical fixation with formaldehyde or other chemicals Chemical fixatives are used to preserve tissue from degradation, and to maintain the structure of the cell and of sub-cellular components such as cell organelles (e.g., nucleus, endoplasmic reticulum, mitochondria). The most common fixative for light microscopy is 10% neutral buffered formalin (4% formaldehyde in phosphate buffered

Histology saline). For electron microscopy, the most commonly used fixative is glutaraldehyde, usually as a 2.5% solution in phosphate buffered saline. These fixatives preserve tissues or cells mainly by irreversibly cross-linking proteins. The main action of these aldehyde fixatives is to cross-link amino groups in proteins through the formation of CH2 (methylene) linkage, in the case of formaldehyde, or by a C5H10 cross-links in the case of glutaraldehyde. This process, while preserving the structural integrity of the cells and tissue can damage the biological functionality of proteins, particularly enzymes, and can also denature them to a certain extent. This can be detrimental to certain histological techniques. Further fixatives are often used for electron microscopy such as osmium tetroxide or uranyl acetate Formalin fixation leads to degradation of mRNA, miRNA and DNA in tissues. However, extraction, amplification and analysis of these nucleic acids from formalin-fixed, paraffin-embedded tissues is possible using appropriate protocols.[1] Frozen section fixation Frozen section is a rapid way to fix and mount histology sections. It is used in surgical removal of tumors, and allow rapid determination of margin (that the tumor has been completely removed). It is done using a refrigeration device called a cryostat. The frozen tissue is sliced using a microtome, and the frozen slices are mounted on a glass slide and stained the same way as other methods. It is a necessary way to fix tissue for certain stain such as antibody linked immunofluorescence staining. It can also be used to determine if a tumour is malignant when it is found incidentally during surgery on a patient.

206

Processing - dehydration, clearing, and infiltration
The aim of Tissue Processing is to remove water from tissues and replace with a medium that solidifies to allow thin sections to be cut. Biological tissue must be supported in a hard matrix to allow sufficiently thin sections to be cut, typically 5 μm (micrometres; 1000 micrometres = 1 mm) thick for light microscopy and 80-100 nm (nanometre; 1,000,000 nanometres = 1 mm) thick for electron microscopy. For light microscopy, paraffin wax is most frequently used. Since it is immiscible with water, the main constituent of biological tissue, water must first be removed in the process of dehydration. Samples are transferred through baths of progressively more concentrated ethanol to remove the water. This is followed by a hydrophobic clearing agent (such as xylene) to remove the alcohol, and finally molten paraffin wax, the infiltration agent, which replaces the xylene. Paraffin wax does not provide a sufficiently hard matrix for cutting very thin sections for electron microscopy. Instead, resins are used. Epoxy resins are the most commonly employed embedding media, but acrylic resins are also used, particularly where immunohistochemistry is required. Thicker sections (0.35μm to 5μm) of resin-embedded tissue can also be cut for light microscopy. Again, the immiscibility of most epoxy and acrylic resins with water necessitates the use of dehydration, usually with ethanol.

Embedding
After the tissues have been dehydrated, cleared, and infiltrated with the embedding material, they are ready for external embedding. During this process the tissue samples are placed into molds along with liquid embedding material (such as agar, gelatine, or wax) which is then hardened. This is achieved by cooling in the case of paraffin wax and heating (curing) in the case of the epoxy resins. The acrylic resins are polymerised by heat, ultraviolet light, or chemical catalysts. The hardened blocks containing the tissue samples are then ready to be sectioned. Because Formalin-fixed, paraffin-embedded (FFPE) tissues may be stored indefinitely at room temperature, and nucleic acids (both DNA and RNA) may be recovered from them decades after fixation, FFPE tissues are an important resource for historical studies in medicine. Embedding can also be accomplished using frozen, non-fixed tissue in a water-based medium. Pre-frozen tissues are placed into molds with the liquid embedding material, usually a water-based glycol, OCT, TBS, Cryogel, or resin, which is then frozen to form hardened blocks.

Histology

207

Sectioning
Sectioning can be done in limited ways. Vertical sectioning perpendicular to the surface of the tissue is the usual method. Horizontal sectioning is often done in the evaluation of the hair follicles and pilosebaceous units. Tangential to horizontal sectioning is done in Mohs surgery and in methods of CCPDMA. For light microscopy, a steel knife mounted in a microtome is used to cut 10-micrometer-thick tissue sections which are mounted on a glass microscope slide. For transmission electron microscopy, a diamond knife mounted in an ultramicrotome is used to cut 50-nanometer-thick tissue sections which are mounted on a 3-millimeter-diameter copper grid. Then the mounted sections are treated with the appropriate stain. Frozen tissue embedded in a freezing medium is cut on a microtome in a cooled machine called a cryostat.

Staining
Biological tissue has little inherent contrast in either the light or electron microscope. Staining is employed to give both contrast to the tissue as well as highlighting particular features of interest. Where the underlying mechanistic chemistry of staining is understood, the term histochemistry is used. Hematoxylin and eosin (H&E stain) is the most commonly used light microscopical stain in histology and histopathology. Hematoxylin, a basic dye, stains nuclei blue due to an affinity to nucleic acids in the cell nucleus; eosin, an acidic dye, stains the cytoplasm pink. Uranyl acetate and lead citrate are commonly used to impart contrast to tissue in the electron microscope. Special staining: There are hundreds of various other techniques that have been used to selectively stain cells and cellular components. Other compounds used to color tissue sections include safranin, oil red o, Congo red, fast green FCF, silver salts, and numerous natural and artificial dyes that were usually originated from the development dyes for the textile industry. Histochemistry refers to the science of using chemical reactions between laboratory chemicals and components within tissue. A commonly performed histochemical technique is the Perls Prussian blue reaction, used to demonstrate iron deposits in diseases like hemochromatosis. Histology samples have often been examined by radioactive techniques. In historadiography, a slide (sometimes stained histochemically) is X-rayed. More commonly, autoradiography is used to visualize the locations to which a radioactive substance has been transported within the body, such as cells in S phase (undergoing DNA replication) which incorporate tritiated thymidine, or sites to which radiolabeled nucleic acid probes bind in in situ hybridization. For autoradiography on a microscopic level, the slide is typically dipped into liquid nuclear tract emulsion, which dries to form the exposure film. Individual silver grains in the film are visualized with dark field microscopy. Recently, antibodies have been used to specifically visualize proteins, carbohydrates, and lipids. This process is called immunohistochemistry, or when the stain is a fluorescent molecule, immunofluorescence. This technique has greatly increased the ability to identify categories of cells under a microscope. Other advanced techniques, such as nonradioactive in situ hybridization, can be combined with immunochemistry to identify specific DNA or RNA molecules with fluorescent probes or tags that can be used for immunofluorescence and enzyme-linked fluorescence amplification (especially alkaline phosphatase and tyramide signal amplification). Fluorescence microscopy and confocal microscopy are used to detect fluorescent signals with good intracellular detail. Digital cameras are increasingly used to capture histological and histopathological image

Histology

208

Common laboratory stains
Stain Common use Nucleus Cytoplasm Red blood cell (RBC) N/A N/A Collagen fibers N/A Specifically stains

Haematoxylin

General staining when paired with eosin (i.e. H&E)

Blue

Nucleic acids—blue ER (endoplasmic reticulum)—blue Elastic fibers—pink Collagen fibers—pink Reticular fibers—pink Mast cells granules—purple Cartilage—blue/green Muscle fibers—red Keratin—orange Cartilage—blue Bone matrix—deep blue Muscle fibers—red Elastic fibers—blue/black

Eosin

General staining when paired N/A with haematoxylin (i.e. H&E)

Pink

Orange/red

Pink

Toluidine blue Masson's trichrome stain Mallory's trichrome stain

General staining Connective tissue

Blue Black

Blue Red/pink

Blue Red

Blue Blue/green

Connective tissue

Red

Pale red

Orange

Deep blue

Weigert's elastic stain Heidenhain's AZAN trichrome stain

Elastic fibers

Blue/black

N/A

N/A

N/A

Distinguishing cells from extracellular components

Red/purple

Pink

Red

Blue

Muscle fibers—red Cartilage—blue Bone matrix—blue Reticular fibers—brown/black Nerve fibers—brown/black Fungi—black Neutrophil granules—purple/pink Eosinophil granules—bright red/orange Basophil granules—deep purple/violet Platelet granules—red/purple Elastic fibres—dark brown Mast cells granules—purple Smooth muscle—light blue Glycogen and other carbohydrates—magenta

Silver stain

Reticular fibers, nerve fibers, fungi

N/A

N/A

N/A

N/A

Wright's stain

Blood cells

Bluish/purple Bluish/gray Red/pink

N/A

Orcein stain

Elastic fibres

Deep blue

N/A

Bright red

Pink

Periodic acid-Schiff stain (PAS)

Basement membrane, localizing carbohydrates

Blue

N/A

N/A

Pink

Table sourced from Michael H. Ross, Wojciech Pawlina, (2006). Histology: A Text and Atlas. Hagerstown, MD: Lippincott Williams & Wilkins. ISBN 0-7817-5056-3. The Nissl method and Golgi's method are useful in identifying neurons.

Alternative techniques
Alternative techniques include cryosection. The tissue is frozen using a cryostat, and cut. Tissue staining methods are similar to those of wax sections. Plastic embedding is commonly used in the preparation of material for electron microscopy. Tissues are embedded in epoxy resin. Very thin sections (less than 0.1 micrometer) are cut using diamond or glass knives. The sections are stained with electron dense stains (uranium and lead) so that they can possibly be seen with the electron microscope.

Histology

209

History
In the 19th century, histology was an academic discipline in its own right. The 1906 Nobel Prize in Physiology or Medicine was awarded to histologists Camillo Golgi and Santiago Ramon y Cajal. They had dueling interpretations of the neural structure of the brain based in differing interpretations of the same images. Cajal won the prize for his correct theory and Golgi for the staining technique he invented to make it possible.

Histological classification of animal tissues
There are four basic types of tissues: muscle tissue, nervous tissue, connective tissue, and epithelial tissue. All tissue types are subtypes of these four basic tissue types (for example, blood cells are classified as connective tissue, since they generally originate inside bone marrow). • • • • • • • •
Santiago Ramón y Cajal in his laboratory

Epithelium: the lining of glands, bowel, skin, and some organs like the liver, lung, and kidney Endothelium: the lining of blood and lymphatic vessels Mesothelium: the lining of pleural and pericardial spaces Mesenchyme: the cells filling the spaces between the organs, including fat, muscle, bone, cartilage, and tendon cells Blood cells: the red and white blood cells, including those found in lymph nodes and spleen Neurons: any of the conducting cells of the nervous system Germ cells: reproductive cells (spermatozoa in men, oocytes in women) Placenta: an organ characteristic of true mammals during pregnancy, joining mother and offspring, providing endocrine secretion and selective exchange of soluble, but not particulate, blood-borne substances through an apposition of uterine and trophoblastic vascularised parts Stem cells: cells with the ability to develop into different cell types

Note that tissues from plants, fungi, and microorganisms can also be examined histologically. Their structure is very different from animal tissues.

Related sciences
• Cell biology is the study of living cells, their DNA and RNA and the proteins they express. • Anatomy is the study of organs visible by the naked eye. • Morphology studies entire organisms.

Artifacts
Artifacts are structures or features in tissue that interfere with normal histological examination. These are not always present in normal tissue and can come from outside sources. Artifacts interfere with histology by changing the tissues appearance and hiding structures. These can be divided into two categories:

Histology

210

Pre-histology
These are features and structures that have been introduced prior to the collection of the tissues. A common example of these include: ink from tattoos and freckles (melanin) in skin samples.

Post-histology
Artifacts can result from tissue processing. Processing commonly leads to changes like shrinkage, washing out of particular cellular components, color changes in different tissues types and alterations of the structures in the tissue. Because these are caused in a laboratory the majority of post histology artifacts can be avoided or removed after being discovered. A common example is mercury pigment left behind after using Zenker's fixative to fix a section.

Notes
[1] Weiss AT, Delcour NM, Meyer A, Klopfleisch R. (2010). "Efficient and Cost-Effective Extraction of Genomic DNA From Formalin-Fixed and Paraffin-Embedded Tissues". Veterinary Pathology 227 (4): 834–8. doi:10.1177/0300985810380399. PMID 20817894.

References
1. Merck Source (2002). Dorland's Medical Dictionary. Retrieved 2005-01-26. 2. Stedman's Medical Dictionaries (2005). Stedman's Online Medical Dictionary (http://stedmans.com/). Retrieved 2005-01-26. 3. 4,000‫ﻱ‬online histology images (2007). (http://histology-online.com)

External links
• • • • • • • • • • • • • • Meyer's Histology - a complete online histology course (http://meyershistology.moodle.com.au/) Histology-online (http://histology-online.com/) Histology Protocols (http://www.ihcworld.com/protocol_database.htm) Histology atlas and more (http://sites.google.com/site/estudehistologia/) Histoweb (http://www.kumc.edu/instruction/medicine/anatomy/histoweb) SIU SOM Histology (http://www.siumed.edu/~dking2/index.htm) Visual Histology Atlas (http://www.visualhistology.com/Visual_Histology_Atlas/) Histology Glossary (http://www.histology-world.com/glossary/glossary1.htm) Histology Group of Victoria Incorporated (http://www.hgv.org.au) Histology Photomicrographs (http://www.histology-world.com/photoalbum/) Virtual Slidebox (http://www.path.uiowa.edu/virtualslidebox) Blue Histology (http://www.lab.anhb.uwa.edu.au/mb140/) BiMed - 20.000 histology images of fundamental tissues (http://www.informed.unal.edu.co/) The Histology Image Dataset (histologyDS) (http://www.informed.unal.edu.co/histologyDS/)

Immunohistochemistry

211

Immunohistochemistry
Immunohistochemistry or IHC refers to the process of detecting antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues.[1] IHC takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). Immunohistochemical staining is widely used in the diagnosis of abnormal cells such as those found in cancerous tumors. Specific molecular markers are characteristic of particular cellular events such as proliferation or cell death (apoptosis). IHC is also widely used in basic research to understand the distribution and localization of biomarkers and differentially expressed proteins in different parts of a biological tissue.

Immunohistochemistry labels individual proteins, such as TH (green) in the axons of sympathetic autonomic neurons.

Visualising an antibody-antigen interaction can be accomplished in a number of ways. In the most common instance, an antibody is conjugated to an enzyme, such as peroxidase, that can catalyse a colour-producing reaction (see immunoperoxidase staining). Alternatively, the antibody can also be tagged to a fluorophore, such as fluorescein or rhodamine (see immunofluorescence).

Sample preparation
While using the right antibodies to target the correct antigens and amplify the signal is important for visualization, complete preparation of the sample is critical to maintain cell morphology, tissue architecture and the antigenicity of target epitopes. This requires proper tissue collection, fixation and sectioning. Paraformaldehyde is usually used with fixation. Depending on the purpose and the thickness of the experimental sample, either thin (about 4-40 μm) sections are sliced from the tissue of interest, or if the tissue is not very thick and is penetrable it is used whole. The slicing is usually accomplished through the use of a microtome, and slices are mounted on slides. "Free-floating IHC" uses slices that are not mounted; these slices are normally produced using a vibrating microtome. Because of the method of fixation and tissue preservation, the sample may require additional steps to make the epitopes available for antibody binding, including deparaffinization and antigen retrieval (microwave method, enzyme method, hot incubation method); these steps often make the difference between staining and no staining. Additionally, depending on the tissue type and the method of antigen detection, endogenous biotin or enzymes may need to be blocked or quenched, respectively, prior to antibody staining. Unlike immunocytochemistry, the tissue does not need to be permeabilized because this has already been accomplished by the microtome blade during sample preparation. Detergents like Triton X-100 are generally used in immunohistochemistry to reduce surface tension, allowing less reagent to be used to achieve better and more even coverage of the sample. Although antibodies show preferential avidity for specific epitopes, they may partially or weakly bind to sites on nonspecific proteins (also called reactive sites) that are similar to the cognate binding sites on the target antigen. In the context of antibody-mediated antigen detection, nonspecific binding causes high background staining that can mask the detection of the target antigen. To reduce background staining in IHC, ICC and any other immunostaining application, the samples are incubated with a buffer that blocks the reactive sites to which the primary or secondary antibodies may otherwise bind. Common blocking buffers include normal serum, non-fat dry milk, BSA, or gelatin. Commercial blocking buffers with proprietary formulations are available for greater efficiency.

Immunohistochemistry

212

Sample Labeling
Antibody types
The antibodies used for specific detection can be polyclonal or monoclonal. Polyclonal antibodies are made by injecting animals with peptide Ag and, after a secondary immune response is stimulated, isolating antibodies from whole serum. Thus, polyclonal antibodies are a heterogeneous mix of antibodies that recognize several epitopes. Monoclonal antibodies show specificity for a single epitope and are therefore considered more specific to the target antigen than polyclonal antibodies. For IHC detection strategies, antibodies are classified as primary or secondary reagents. Primary antibodies are raised against an antigen of interest and are typically unconjugated (unlabelled), while secondary antibodies are raised against immunoglobulins of the primary antibody species. The secondary antibody is usually conjugated to a linker molecule, such as biotin, that then recruits reporter molecules, or the secondary antibody is directly bound to the reporter molecule itself.

IHC reporters
Reporter molecules vary based on the nature of the detection method, and the most popular methods of detection are with enzyme- and fluorophore-mediated chromogenic and fluorescence detection, respectively. With chromogenic reporters, an enzyme label is reacted with a substrate to yield an intensely colored product that can be analyzed with an ordinary light microscope. While the list of enzyme substrates is extensive, Alkaline phosphatase (AP) and horseradish peroxidase (HRP) are the two enzymes used most extensively as labels for protein detection. An array of chromogenic, fluorogenic and chemiluminescent substrates is available for use with either enzyme, including DAB or BCIP/NBT, which produce a brown or purple staining, respectively, wherever the enzymes are bound. Reaction with DAB can be enhanced using nickel, producing a deep purple/black staining. Fluorescent reporters are small, organic molecules used for IHC detection and traditionally include FITC, TRITC and AMCA, while commercial derivatives, including the Alexa Fluors and Dylight Fluors, show similar enhanced performance but vary in price. For chromogenic and fluorescent detection methods, densitometric analysis of the signal can provide semiand fully quantitative data, respectively, to correlate the level of reporter signal to the level of protein expression or localization.

Target antigen detection methods
The direct method is a one-step staining method and involves a labeled antibody (e.g. FITC-conjugated antiserum) reacting directly with the antigen in tissue sections. While this technique utilizes only one antibody and therefore is simple and rapid, the sensitivity is lower due to little signal amplification, such as with indirect methods, and is less commonly used than indirect methods.

The direct method of immunohistochemical staining uses one labelled antibody, which binds directly to the antigen being stained for.

The indirect method involves an unlabeled primary antibody (first layer) that binds to the target antigen in the tissue and a labeled

Immunohistochemistry

213

secondary antibody (second layer) that reacts with the primary antibody. As mentioned above, the secondary antibody must be raised against the IgG of the animal species in which the primary antibody has been raised. This method is more sensitive than direct detection strategies because of signal amplification due to the binding of several secondary antibodies to each primary antibody if the secondary antibody is conjugated to the fluorescent or enzyme reporter.

The indirect method of immunohistochemical staining uses one antibody against the antigen being probed for, and a second, labelled, antibody against the first.

Further amplification can be achieved if the secondary antibody is conjugated to several biotin molecules, which can recruit complexes of avidin-, streptavidin or NeutrAvidin proteinbound-enzyme. The difference between these three biotin-binding proteins is their individual binding affinity to endogenous tissue targets leading to nonspecific binding and high background; the ranking of these proteins based on their nonspecific binding affinities, from highest to lowest, is: 1) avidin, 2) streptavidin and 3) Neutravidin protein. The indirect method, aside from its greater sensitivity, also has the advantage that only a relatively small number of standard conjugated (labeled) secondary antibodies needs to be generated. For example, a labeled secondary antibody raised against rabbit IgG, which can be purchased "off the shelf," is useful with any primary antibody raised in rabbit. With the direct method, it would be necessary to label each primary antibody for every antigen of interest.

Counterstains
After immunohistochemical staining of the target antigen, a second stain is often applied to provide contrast that helps the primary stain stand out. Many of these stains show specificity for discrete cellular compartments or antigens, while others will stain the whole cell. Both chromogenic and fluorescent dyes are available for IHC to provide a vast array of reagents to fit every experimental design, and include: hematoxylin, Hoechst stain and DAPI are commonly used.

IHC Troubleshooting
In immunohistochemical techniques, there are several steps prior to the final staining of the tissue antigen, and many potential problems affect the outcome of the procedure. The major problem areas in IHC staining include strong background staining, weak target antigen staining and autofluorescence. Endogenous biotin or reporter enzymes or primary/secondary antibody cross-reactivity are common causes of strong background staining, while weak staining may be caused by poor enzyme activity or primary antibody potency. Furthermore, autofluorescence may be due to the nature of the tissue or the fixation method. These aspects of IHC tissue prep and antibody staining must be systematically addressed to identify and overcome staining issues.

Immunohistochemistry

214

Diagnostic IHC markers
IHC is an excellent detection technique and has the tremendous advantage of being able to show exactly where a given protein is located within the tissue examined. It is also an effective way to examine the tissues .This has made it a widely used technique in the neurosciences, enabling researchers to examine protein expression within specific brain structures. Its major disadvantage is that, unlike immunoblotting techniques where staining is checked against a molecular weight ladder, it is impossible to show in IHC that the staining corresponds with the protein of interest. For this reason, primary antibodies must be well-validated in a Western Blot or similar Immunohistochemical staining of normal kidney procedure. The technique is even more widely used in diagnostic with CD10. surgical pathology for typing tumors (e.g. immunostaining for e-cadherin to differentiate between DCIS (ductal carcinoma in situ: stains positive) and LCIS (lobular carcinoma in situ: does not stain positive)[2]). • • • • • • • • • • Carcinoembryonic antigen (CEA): used for identification of adenocarcinomas. Not specific for site. Cytokeratins: used for identification of carcinomas but may also be expressed in some sarcomas.[3] CD15 and CD30 : used for Hodgkin's disease Alpha fetoprotein: for yolk sac tumors and hepatocellular carcinoma CD117 (KIT): for gastrointestinal stromal tumors (GIST) CD10 (CALLA): for renal cell carcinoma and acute lymphoblastic leukemia Prostate specific antigen (PSA): for prostate cancer estrogens and progesterone staining for tumour identification Identification of B-cell lymphomas using CD20 Identification of T-cell lymphomas using CD3

Directing therapy
A variety of molecular pathways are altered in cancer and some of the alterations can be targeted in cancer therapy. Immunohistochemistry can be used to assess which tumors are likely to respond to therapy, by detecting the presence or elevated levels of the molecular target.

Chemical inhibitors
Tumor biology allows for a number of potential intracellular targets. Many tumors are hormone dependent. The presence of hormone receptors can be used to determine if a tumor is potentially responsive to antihormonal therapy. One of the first therapies was the antiestrogen, tamoxifen, used to treat breast cancer. Such hormone receptors can be detected by immunohistochemistry.[4] Imatinib, an intracellualar tyrosine kinase inhibitor, was developed to treat chronic myelogenous leukemia, a disease characterized by the formation of a specific abnormal tyrosine kinase. Imitanib has proven effective in tumors, that express other tyrosine kinases, most notably KIT. Most gastrointestinal stromal tumors express KIT, which can be detected by immunohistochemistry.[5]

Immunohistochemistry

215

Monoclonal antibodies
Many proteins shown to be highly upregulated in pathological states by immunohistochemistry are potential targets for therapies utilising monoclonal antibodies. Monoclonal antibodies, due to their size, are utilized against cell surface targets. Among the overexpressed targets, the members of the epidermal growth factor receptor (EGFR) family, transmembrane proteins with an extracellular receptor domain regulating an intracellular tyrosine kinase,[6] Of these, HER2/neu (also known as Erb-B2) was the first to be developed. The molecule is highly expressed in a variety of cancer cell types, most notably breast cancer. As such, antibodies against HER2/neu have been FDA approved for clinical treatment of cancer under the drug name Herceptin. There are commercially available immunohistochemical tests, Dako HercepTest [7] and Ventana Pathway.[8] Similarly, EGFR (HER-1) is overexpressed in a variety of cancers including head and neck and colon. Immunohistochemistry is used to determine patients who may benefit from therapeutic antibodies such as Erbitux (cetuximab).[9] Commercial systems to detect EGFR by immunohistochemistry include the Dako pharmDx [10].

References
[1] Ramos-Vara, JA (2005). "Technical Aspects of Immunohistochemistry" (http:/ / www. vetpathology. org/ cgi/ content/ short/ 42/ 4/ 405). Vet Pathol 42 (4): 405–426. doi:10.1354/vp.42-4-405. PMID 16006601. . [2] O'Malley F and Pinder S, Breast Pathology, 1st. Ed. Elsevier 2006. ISBN 978-0-443-06680-1 [3] Leader M, Patel J, Makin C, Henry K (December 1986). "An analysis of the sensitivity and specificity of the cytokeratin marker CAM 5.2 for epithelial tumours. Results of a study of 203 sarcomas, 50 carcinomas and 28 malignant melanomas". Histopathology 10 (12): 1315–24. doi:10.1111/j.1365-2559.1986.tb02574.x. PMID 2434403. [4] Jørgensen, Jan Trøst; Kirsten Vang Nielsen, Bent Ejlertsen (April 2007). "Pharmacodiagnostics and targeted therapies - a rational approach for individualizing medical anticancer therapy in breast cancer" (http:/ / theoncologist. alphamedpress. org/ cgi/ content/ full/ 12/ 4/ 397). The Oncologist (United States: AlphaMed Press) 12 (4): 397–405. doi:10.1634/theoncologist.12-4-397. ISSN 1083-7159. PMID 17470682. . Retrieved 2008-03-14. [5] Gold JS, Dematteo RP (August 2006). "Combined Surgical and Molecular Therapy: The Gastrointestinal Stromal Tumor Model". Ann. Surg. 244 (2): 176–84. doi:10.1097/01.sla.0000218080.94145.cf. PMC 1602162. PMID 16858179. [6] Harari, P M (December 2004). "Epidermal growth factor receptor inhibition strategies in oncology" (http:/ / erc. endocrinology-journals. org/ cgi/ content/ full/ 11/ 4/ 689?ijkey=9caa7985e4396550fdc851b303ea7958513e070e). Endocrine-Related Cancer (England: Society for Endocrinology) 11 (4): 689–708. doi:10.1677/erc.1.00600. ISSN 1351-0088. PMID 15613446. . Retrieved 2008-03-14. [7] http:/ / www. dakousa. com/ index/ prod_search/ prod_baseproducts. htm?productareaid=1& productgroupid=3& productsubgroupid=1003000 [8] Press, Michael F.; Guido Sauter, Leslie Bernstein, Ivonne E.Villalobos, MartinaMirlacher, Jian-Yuan Zhou, RoobaWardeh, Yong-Tian Li, Roberta Guzman, Yanling Ma, Jane Sullivan-Halley, Angela Santiago, Jinha M. Park, Alessandro Riva, Dennis J.Slamon (September 15, 2005). "Diagnostic evaluation of HER-2 as a molecular target: an assessment of accuracy and reproducibility of laboratory testing in large, prospective, randomized clinical trials" (http:/ / clincancerres. aacrjournals. org/ cgi/ content/ full/ 11/ 18/ 6598). Clinical Cancer Research (United States: American Association for Cancer Research.) 2005 15;11(18): (18): 6598–6607. doi:10.1158/1078-0432.CCR-05-0636. ISSN 1078-0432. PMID 16166438. . Retrieved 2008-03-14. [9] Bibeau F, Boissière-Michot F, Sabourin JC, et al. (September 2006). "Assessment of epidermal growth factor receptor (EGFR) expression in primary colorectal carcinomas and their related metastases on tissue sections and tissue microarray". Virchows Arch. 449 (3): 281–7. doi:10.1007/s00428-006-0247-9. PMC 1888717. PMID 16865406. [10] http:/ / www. dakousa. com/ index/ prod_search/ prod_groups. htm?productareaid=1

Immunohistochemistry

216

External links
• Overview of Immunohistochemistry--describes all aspects of IHC including sample prep, staining and troubleshooting (http://www.piercenet.com/browse. cfm?fldID=F95B91A9-3DC1-4B56-8E8D-59CA044A8BA7) • Yale Core Tissue Microarray Facility (http://tissuearray.org/yale/) • Histochemical Staining Methods (http://www.urmc.rochester.edu/path/zqu/Histostain/index.html) University of Rochester Department of Pathology • Immunohistochemistry Staining Protocol (http://www.prosci-inc.com/Immunohistochemistry-Protocol.html) • HistoWiki entry for Immunohistochemistry (http://www.ihcworld.com/histowiki/doku. php?id=immunohistochemistry#immunohistochemistry) • Burnett R, Guichard Y, Barale E (1997). "Immunohistochemistry for light microscopy in safety evaluation of therapeutic agents: an overview". Toxicology 119 (1): 83–93. doi:10.1016/S0300-483X(96)03600-1. PMID 9129199. • Immunohistochemistry (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=& term=Immunohistochemistry) at the US National Library of Medicine Medical Subject Headings (MeSH) • Joyner, A.; Wall, N. (2008). "Immunohistochemistry of Whole-Mount Mouse Embryos". Cold Spring Harbor Protocols 2008 (2): pdb.prot4820. doi:10.1101/pdb.prot4820.

Immunology
Immunology is a branch of biomedical science that covers the study of all aspects of the immune system in all organisms.[1] It deals with the physiological functioning of the immune system in states of both health and diseases; malfunctions of the immune system in immunological disorders (autoimmune diseases, hypersensitivities, immune deficiency, transplant rejection); the physical, chemical and physiological characteristics of the components of the immune system in vitro, in situ, and in vivo. Immunology has applications in several disciplines of science, and as such is further divided. Even before the concept of immunity (from immunis, Latin for "exempt") was developed, numerous early physicians characterized organs that would later prove to be part of the immune system. The key primary lymphoid organs of the immune system are the thymus and bone marrow, and secondary lymphatic tissues such as spleen, tonsils, lymph vessels, lymph nodes, adenoids, and skin and liver. When health conditions warrant, immune system organs including the thymus, spleen, portions of bone marrow, lymph nodes and secondary lymphatic tissues can be surgically excised for examination while patients are still alive. Many components of the immune system are actually cellular in nature and not associated with any specific organ but rather are embedded or circulating in various tissues located throughout the body.

Classical immunology
Classical immunology ties in with the fields of epidemiology and medicine. It studies the relationship between the body systems, pathogens, and immunity. The earliest written mention of immunity can be traced back to the plague of Athens in 430 BCE. Thucydides noted that people who had recovered from a previous bout of the disease could nurse the sick without contracting the illness a second time. Many other ancient societies have references to this phenomenon, but it was not until the 19th and 20th centuries before the concept developed into scientific theory. The study of the molecular and cellular components that comprise the immune system, including their function and interaction, is the central science of immunology. The immune system has been divided into a more primitive innate immune system, and acquired or adaptive immune system of vertebrates, the latter of which is further divided into humoral and cellular components.

Immunology The humoral (antibody) response is defined as the interaction between antibodies and antigens. Antibodies are specific proteins released from a certain class of immune cells (B lymphocytes). Antigens are defined as anything that elicits generation of antibodies, hence they are Antibody Generators. Immunology itself rests on an understanding of the properties of these two biological entities. However, equally important is the cellular response, which can not only kill infected cells in its own right, but is also crucial in controlling the antibody response. Put simply, both systems are highly interdependent. In the 21st century, immunology has broadened its horizons with much research being performed in the more specialized niches of immunology. This includes the immunological function of cells, organs and systems not normally associated with the immune system, as well as the function of the immune system outside classical models of immunity (Yemeserach 2010).

217

Clinical immunology
Clinical immunology is the study of diseases caused by disorders of the immune system (failure, aberrant action, and malignant growth of the cellular elements of the system). It also involves diseases of other systems, where immune reactions play a part in the pathology and clinical features. The diseases caused by disorders of the immune system fall into two broad categories: immunodeficiency, in which parts of the immune system fail to provide an adequate response (examples include chronic granulomatous disease), and autoimmunity, in which the immune system attacks its own host's body (examples include systemic lupus erythematosus, rheumatoid arthritis, Hashimoto's disease and myasthenia gravis). Other immune system disorders include different hypersensitivities, in which the system responds inappropriately to harmless compounds (asthma and other allergies) or responds too intensely. The most well-known disease that affects the immune system itself is AIDS, caused by HIV. AIDS is an immunodeficiency characterized by the lack of CD4+ ("helper") T cells, dendritic cells and macrophages, which are destroyed by HIV. Clinical immunologists also study ways to prevent transplant rejection, in which the immune system attempts to destroy allografts.

Developmental immunology
The body’s capability to react to antigen depends on a person's age, antigen type, maternal factors and the area where the antigen is presented.[2] Neonates are said to be in a state of physiological immunodeficiency, because both their innate and adaptive immunological responses are greatly suppressed. Once born, a child’s immune system responds favorably to protein antigens while not as well to glycoproteins and polysaccharides. In fact, many of the infections acquired by neonates are caused by low virulence organisms like Staphylococcus and Pseudomonas. In neonates, opsonic activity and the ability to activate the complement cascade is very limited. For example, the mean level of C3 in a newborn is approximately 65% of that found in the adult. Phagocytic activity is also greatly impaired in newborns. This is due to lower opsonic activity, as well as diminished up-regulation of integrin and selectin receptors, which limit the ability of neutrophils to interact with adhesion molecules in the endothelium. Their monocytes are slow and have a reduced ATP production, which also limits the newborns phagocytic activity. Although, the number of total lymphocytes is significantly higher than in adults, the cellular and humoral immunity is also impaired. Antigen presenting cells in newborns have a reduced capability to activate T cells. Also, T cells of a newborn proliferate poorly and produce very small amounts of cytokines like IL-2, IL-4, IL-5, IL-12, and IFN-g which limits their capacity to activate the humoral response as well as the phagocitic activity of macrophage. B cells develop early in gestation but are not fully active.[3]

Immunology

218

Maternal factors also play a role in the body’s immune response. At birth most of the immunoglobulin is present is maternal IgG. Because IgM, IgD, IgE and IgA don’t cross the placenta, they are almost undetectable at birth. Although some IgA is provided in breast milk. These passively acquired antibodies can protect the newborn up to 18 months, but their response is usually short-lived and of low affinity.[3] Monocytes: An Artist's Impression These antibodies can also produce a negative response. If a child is exposed to the antibody for a particular antigen before being exposed to the antigen itself then the child will produce a dampened response. Passively acquired maternal antibodies can suppress the antibody response to active immunization. Similarly the response of T-cells to vaccination differs in children compared to adults, and vaccines that induce Th1 responses in adults do not readily elicit these same responses in neonates.[3] By 6-9 months after birth, a child’s immune system begins to respond more strongly to glycoproteins. Not until 12-24 months of age is there a marked improvement in the body’s response to polysaccharides. This can be the reason for the specific time frames found in vaccination schedules.[4][5] During adolescence the human body undergoes several physical, physiological and immunological changes. These changes are started and mediated by different hormones. Depending on the sex either testosterone or 17-β-oestradiol, act on male and female bodies accordingly, start acting at ages of 12 and 10 years.[6] There is evidence that these steroids act directly not only on the primary and secondary sexual characteristics, but also have an effect on the development and regulation of the immune system.[7] There is an increased risk in developing autoimmunity for pubescent and post pubescent females and males.[8] There is also some evidence that cell surface receptors on B cells and macrophages may detect sex hormones in the system.[9] The female sex hormone 17-β-oestradiol has been shown to regulate the level of immunological response.[10] Similarly, some male androgens, like testosterone, seem to suppress the stress response to infection; but other androgens like DHEA have the opposite effect, as it increases the immune response instead of down playing it.[11] As in females, the male sex hormones seem to have more control of the immune system during puberty and the time right after than in fully developed adults. Other than hormonal changes physical changes like the involution of the Thymus during puberty will also affect the immunological response of the subject or patient.[12]

Immunotherapy
The use of immune system components to treat a disease or disorder is known as immunotherapy. Immunotherapy is most commonly used in the context of the treatment of cancers together with chemotherapy (drugs) and radiotherapy (radiation). However, immunotherapy is also often used in the immunosuppressed (such as HIV patients) and people suffering from other immune deficiencies or autoimmune diseases.

Diagnostic immunology
The specificity of the bond between antibody and antigen has made it an excellent tool in the detection of substances in a variety of diagnostic techniques. Antibodies specific for a desired antigen can be conjugated with a radiolabel, fluorescent label, or color-forming enzyme and are used as a "probe" to detect it. However, the similarity between some antigens can lead to false positives and other errors in such tests by antibodies cross-reacting with antigens that aren't exact matches.[13]

Immunology

219

Evolutionary immunology
Study of the immune system in extant species is capable of giving us a key understanding of the evolution of species and the immune system. A development of complexity of the immune system can be seen from simple phagocytotic protection of single celled organisms, to circulating antimicrobial peptides in insects to lymphoid organs in vertebrates. However, it is important to recognize that every organism living today has an immune system that has evolved to be absolutely capable of protecting it from most forms of harm; those organisms that did not adapt their immune systems to external threats are no longer around to be observed. Insects and other arthropods, while not possessing true adaptive immunity, show highly evolved systems of innate immunity, and are additionally protected from external injury (and exposure to pathogens) by their chitinous shells.

Reproductive immunology
This area of the immunology is devoted to the study of immunological aspects of the reproductive process including fetus acceptance. The term has also been used by fertility clinics to address fertility problems, recurrent miscarriages, premature deliveries, and dangerous complications such as pre-eclampsia.

Immunologist
Immunologist
Occupation Activity sectors Science, Laboratory, Medicine Description Education required Doctor of Philosophy, Doctor of Medicine, Doctor of Osteopathic Medicine

According to the American Academy of Allergy, Asthma, and Immunology (AAAAI), "an immunologist is a research scientist who investigates the immune system of vertebrates (including the human immune system). Immunologists include research scientists (Ph.D.) who work in laboratories. Immunologists also include physicians who, for example, treat patients with immune system disorders. Some immunologists are physician-scientists who combine laboratory research with patient care."[14]

References
[1] Janeway's Immunobiology textbook (http:/ / www. ncbi. nlm. nih. gov/ books/ bv. fcgi?rid=imm. TOC& depth=2) Searchable free online version at the National Center for Biotechnology Information [2] Goldsby RA, Kindt TK, Osborne BA and Kuby J (2003). Immunology (5th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-4947-5. [3] Jaspan HB, Lawn SD, Safrit JT, Bekker LG (February 2006). "The maturing immune system: implications for development and testing HIV-1 vaccines for children and adolescents". AIDS 20 (4): 483–94. doi:10.1097/01.aids.0000210602.40267.60. PMID 16470112. [4] Glezen WP (December 2001). "Maternal vaccines". Prim. Care 28 (4): 791–806, vi–vii. doi:10.1016/S0095-4543(05)70041-5. PMID 11739030. [5] Holt PG, Macaubas C, Cooper D, Nelson DJ, McWilliam AS (1997). "Th-1/Th-2 switch regulation in immune responses to inhaled antigens. Role of dendritic cells in the aetiology of allergic respiratory disease". Adv. Exp. Med. Biol. 417: 301–6. PMID 9286377. [6] Sizonenko PC, Paunier L (November 1975). "Hormonal changes in puberty III: Correlation of plasma dehydroepiandrosterone, testosterone, FSH, and LH with stages of puberty and bone age in normal boys and girls and in patients with Addison's disease or hypogonadism or with premature or late adrenarche". J. Clin. Endocrinol. Metab. 41 (5): 894–904. doi:10.1210/jcem-41-5-894. PMID 127002. [7] Verthelyi D (June 2001). "Sex hormones as immunomodulators in health and disease". Int. Immunopharmacol. 1 (6): 983–93. doi:10.1016/S1567-5769(01)00044-3. PMID 11407317. [8] Stimson WH (September 1988). "Oestrogen and human T lymphocytes: presence of specific receptors in the T-suppressor/cytotoxic subset". Scand. J. Immunol. 28 (3): 345–50. doi:10.1111/j.1365-3083.1988.tb01459.x. PMID 2973658.

Immunology
[9] Benten WP, Stephan C, Wunderlich F (June 2002). "B cells express intracellular but not surface receptors for testosterone and estradiol". Steroids 67 (7): 647–54. doi:10.1016/S0039-128X(02)00013-2. PMID 11996938. [10] Beagley KW, Gockel CM (August 2003). "Regulation of innate and adaptive immunity by the female sex hormones oestradiol and progesterone". FEMS Immunol. Med. Microbiol. 38 (1): 13–22. doi:10.1016/S0928-8244(03)00202-5. PMID 12900050. [11] Kanda N, Tamaki K (February 1999). "Estrogen enhances immunoglobulin production by human PBMCs". J. Allergy Clin. Immunol. 103 (2 Pt 1): 282–8. doi:10.1016/S0091-6749(99)70503-8. PMID 9949320. [12] McFarland RD, Douek DC, Koup RA, Picker LJ (April 2000). "Identification of a human recent thymic emigrant phenotype". Proc. Natl. Acad. Sci. U.S.A. 97 (8): 4215–20. doi:10.1073/pnas.070061597. PMC 18202. PMID 10737767. [13] Miller JJ, Valdes R (February 1991). "Approaches to minimizing interference by cross-reacting molecules in immunoassays". Clin. Chem. 37 (2): 144–53. PMID 1993317. [14] "Office of Science Education - LifeWorks - Immunologist" (http:/ / science. education. nih. gov/ LifeWorks. nsf/ Alphabetical+ List/ Immunologist). . Retrieved 2009-09-10.

220

External links
• • • • The Immunology Link, a rich resource for Immunology information (http://www.immunologylink.com/) American Academy of Allergy, Asthma & Immunology (http://www.aaaai.org/) British Society for Immunology (http://bsi.immunology.org/) Annual Review of Immunology (journal) (http://arjournals.annualreviews.org/loi/immunol)

• BMC: Immunology (http://www.biomedcentral.com/bmcimmunol/)- BioMed Central:Immunology is an open access journal publishing original peer-reviewed research articles. • journal home Nature Reviews Immunology (http://www.nature.com/nri/index.html) • The Immunology Database and Analysis Portal (http://www.immport.org) - an NIAID-funded database resource of reference and experiment data covering the entire immunology domain • Current discussions on Immunology in a scientific community (https://www.researchgate.net/group/ Immunology)

Lipid

221

Lipid
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules.[4][5] Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesicles, liposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits [1] [2] Structures of some common lipids. At the top are cholesterol and oleic acid. The or "building-blocks": ketoacyl and middle structure is a triglyceride composed of oleoyl, stearoyl, and palmitoyl chains attached to a glycerol backbone. At the bottom is the common phospholipid, isoprene groups.[4] Using this [3] phosphatidylcholine. approach, lipids may be divided into eight categories: fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).[4] Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-, di-, monoglycerides, and phospholipids), as well as other sterol-containing metabolites such as cholesterol.[6] Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet.

Categories of lipids
Fatty acids
Fatty acids, or fatty acid residues when they form part of a lipid, are a diverse group of molecules synthesized by chain-elongation of an acetyl-CoA primer with malonyl-CoA or methylmalonyl-CoA groups in a process called fatty acid synthesis.[7][8] They are made of a hydrocarbon chain that terminates with a carboxylic acid group; this arrangement confers the molecule with a polar, hydrophilic end, and a nonpolar, hydrophobic end that is insoluble in water. The fatty acid structure is one of the most fundamental categories of biological lipids, and is commonly used as a building-block of more structurally complex lipids.[9] The carbon chain, typically between four and 24 carbons long,[10] may be saturated or unsaturated, and may be attached to functional groups containing oxygen, halogens,

Lipid nitrogen, and sulfur. Where a double bond exists, there is the possibility of either a cis or a trans geometric isomerism, which significantly affects the molecule's molecular configuration. Cis-double bonds cause the fatty acid chain to bend, an effect that is more pronounced the more double bonds there are in a chain. This in turn plays an important role in the structure and function of cell membranes.[11] Most naturally occurring fatty acids are of the cis configuration, although the trans form does exist in some natural and partially hydrogenated fats and oils.[12] Examples of biologically important fatty acids are the eicosanoids, derived primarily from arachidonic acid and eicosapentaenoic acid, that include prostaglandins, leukotrienes, and thromboxanes. Docosahexaenoic acid is also important in biological systems, particularly with respect to sight.[13][14] Other major lipid classes in the fatty acid category are the fatty esters and fatty amides. Fatty esters include important biochemical intermediates such as wax esters, fatty acid thioester coenzyme A derivatives, fatty acid thioester ACP derivatives and fatty acid carnitines. The fatty amides include N-acyl ethanolamines, such as the cannabinoid neurotransmitter anandamide.[15]

222

Glycerolipids
Glycerolipids are composed mainly of mono-, di-, and tri-substituted glycerols,[16] the most well-known being the fatty acid triesters of glycerol, called triglycerides. The word triacylglycerol is sometimes used synonymously with triglyceride, however this is misleading with respect to these compounds as they contain no hydroxyl group. In these compounds, the three hydroxyl groups of glycerol are each esterified, typically by different fatty acids. Because they function as an energy store, these lipids comprise the bulk of storage fat in animal tissues. The hydrolysis of the ester bonds of triglycerides and the release of glycerol and fatty acids from adipose tissue are the initial steps in metabolising fat.[17] Additional subclasses of glycerolipids are represented by glycosylglycerols, which are characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage. Examples of structures in this category are the digalactosyldiacylglycerols found in plant membranes[18] and seminolipid from mammalian sperm cells.[19]

Glycerophospholipids
Glycerophospholipids, usually referred to as phospholipids, are ubiquitous in nature and are key components of the lipid bilayer of cells,[20] as well as being involved in metabolism and cell signaling .[21] Neural tissue (including the brain) contains relatively high amounts of glycerophospholipids, and alterations in their composition has been implicated in various neurological disorders.[22] Glycerophospholipids may be subdivided into distinct classes, based on the nature of the polar headgroup at the sn-3 position of the glycerol backbone in eukaryotes and eubacteria, or the sn-1 position in the case of archaebacteria.[23] Examples of glycerophospholipids found in biological membranes are phosphatidylcholine (also known as PC, GPCho or lecithin), phosphatidylethanolamine (PE or GPEtn) and phosphatidylserine (PS or GPSer). In addition to serving as a primary component of cellular membranes and binding sites for intra- and intercellular proteins, some glycerophospholipids in eukaryotic cells, such as phosphatidylinositols Phosphatidylethanolamine and phosphatidic acids are either precursors of or, themselves, [24] membrane-derived second messengers. Typically, one or both of these hydroxyl groups are acylated with long-chain fatty acids, but there are also alkyl-linked and 1Z-alkenyl-linked (plasmalogen) glycerophospholipids, as well as dialkylether variants in archaebacteria.[25]

Lipid

223

Sphingolipids
Sphingolipids are a complicated family of compounds[26] that share a common structural feature, a sphingoid base backbone that is synthesized de novo from the amino acid serine and a long-chain fatty acyl CoA, then converted into ceramides, phosphosphingolipids, glycosphingolipids and other compounds. The major sphingoid base of mammals is commonly referred to as sphingosine. Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or mono-unsaturated with chain lengths from 16 to 26 carbon atoms.[27] The major phosphosphingolipids of mammals are sphingomyelins (ceramide phosphocholines),[28] whereas insects contain mainly ceramide phosphoethanolamines[29] and fungi have phytoceramide phosphoinositols and mannose-containing headgroups.[30] The Sphingomyelin glycosphingolipids are a diverse family of molecules composed of one or more sugar residues linked via a glycosidic bond to the sphingoid base. Examples of these are the simple and complex glycosphingolipids such as cerebrosides and gangliosides.

Sterol lipids
Sterol lipids, such as cholesterol and its derivatives, are an important component of membrane lipids,[31] along with the glycerophospholipids and sphingomyelins. The steroids, all derived from the same fused four-ring core structure, have different biological roles as hormones and signaling molecules. The eighteen-carbon (C18) steroids include the estrogen family whereas the C19 steroids comprise the androgens such as testosterone and androsterone. The C21 subclass includes the progestogens as well as the glucocorticoids and mineralocorticoids.[32] The secosteroids, comprising various forms of vitamin D, are characterized by cleavage of the B ring of the core structure.[33] Other examples of sterols are the bile acids and their conjugates,[34] which in mammals are oxidized derivatives of cholesterol and are synthesized in the liver. The plant equivalents are the phytosterols, such as β-sitosterol, stigmasterol, and brassicasterol; the latter compound is also used as a biomarker for algal growth.[35] The predominant sterol in fungal cell membranes is ergosterol.[36]

Prenol lipids
Prenol lipids are synthesized from the five-carbon-unit precursors isopentenyl diphosphate and dimethylallyl diphosphate that are produced mainly via the mevalonic acid (MVA) pathway.[37] The simple isoprenoids (linear alcohols, diphosphates, etc.) are formed by the successive addition of C5 units, and are classified according to number of these terpene units. Structures containing greater than 40 carbons are known as polyterpenes. Carotenoids are important simple isoprenoids that function as antioxidants and as precursors of vitamin A.[38] Another biologically important class of molecules is exemplified by the quinones and hydroquinones, which contain an isoprenoid tail attached to a quinonoid core of non-isoprenoid origin.[39] Vitamin E and vitamin K, as well as the ubiquinones, are examples of this class. Prokaryotes synthesize polyprenols (called bactoprenols) in which the terminal isoprenoid unit attached to oxygen remains unsaturated, whereas in animal polyprenols (dolichols) the terminal isoprenoid is reduced.[40]

Lipid

224

Saccharolipids
Saccharolipids describe compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a monosaccharide substitutes for the glycerol backbone present in glycerolipids and glycerophospholipids. The most familiar saccharolipids are the acylated glucosamine precursors of the Lipid A component of the lipopolysaccharides in Gram-negative bacteria. Typical lipid A molecules are disaccharides of glucosamine, which are derivatized with as many as seven fatty-acyl chains. The minimal lipopolysaccharide required for growth in E. coli is Kdo2-Lipid A, a hexa-acylated disaccharide of glucosamine that is glycosylated with two 3-deoxy-D-manno-octulosonic acid (Kdo) residues.[41]

[41] Structure of the saccharolipid Kdo2-Lipid A. Glucosamine residues in blue, Kdo residues in red, acyl chains in black and phosphate groups in green.

Polyketides
Polyketides are synthesized by polymerization of acetyl and propionyl subunits by classic enzymes as well as iterative and multimodular enzymes that share mechanistic features with the fatty acid synthases. They comprise a large number of secondary metabolites and natural products from animal, plant, bacterial, fungal and marine sources, and have great structural diversity.[42][43] Many polyketides are cyclic molecules whose backbones are often further modified by glycosylation, methylation, hydroxylation, oxidation, and/or other processes. Many commonly used anti-microbial, anti-parasitic, and anti-cancer agents are polyketides or polyketide derivatives, such as erythromycins, tetracyclines, avermectins, and antitumor epothilones.[44]

Biological functions
Membranes
Eukaryotic cells are compartmentalized into membrane-bound organelles that carry out different biological functions. The glycerophospholipids are the main structural component of biological membranes, such as the cellular plasma membrane and the intracellular membranes of organelles; in animal cells the plasma membrane physically separates the intracellular components from the extracellular environment. The glycerophospholipids are amphipathic molecules (containing both hydrophobic and hydrophilic regions) that contain a glycerol core linked to two fatty acid-derived "tails" by ester linkages and to one "head" group by a phosphate ester linkage. While glycerophospholipids are the major component of biological membranes, other non-glyceride lipid components such as sphingomyelin and sterols (mainly cholesterol in animal cell membranes) are also found in biological membranes.[45] In plants and algae, the galactosyldiacylglycerols,[46] and sulfoquinovosyldiacylglycerol,[18] which lack a phosphate group, are important components of membranes of chloroplasts and related organelles and are the most abundant lipids in photosynthetic tissues, including those of higher plants, algae and certain bacteria.

Lipid Bilayers have been found to exhibit high levels of birefringence, which can be used to probe the degree of order (or disruption) within the bilayer using techniques such as dual polarization interferometry and Circular dichroism. A biological membrane is a form of lipid bilayer. The formation of lipid bilayers is an energetically preferred process when the glycerophospholipids described above are in an aqueous environment.[47] This is known as the hydrophobic effect. In an aqueous system, the polar heads of lipids align towards the polar, aqueous environment, while the hydrophobic tails minimize their contact with water and tend to cluster together, forming a vesicle; depending on the concentration of the lipid, this biophysical interaction may result in the formation of micelles, liposomes, or lipid bilayers. Other aggregations are also observed and form part of the polymorphism of amphiphile (lipid) behavior. Phase behavior is an area of study within biophysics and is the subject of current academic research.[48][49] Micelles and bilayers form in the polar medium by a process known as the hydrophobic effect.[50] When dissolving a lipophilic or amphiphilic substance in a polar environment, the polar molecules (i.e., water in Self-organization of phospholipids: a spherical liposome, a micelle, an aqueous solution) become more ordered around the and a lipid bilayer. dissolved lipophilic substance, since the polar molecules cannot form hydrogen bonds to the lipophilic areas of the amphiphile. So in an aqueous environment, the water molecules form an ordered "clathrate" cage around the dissolved lipophilic molecule.[51]

225

Energy storage
Triglycerides, stored in adipose tissue, are a major form of energy storage both in animals and plants. The adipocyte, or fat cell, is designed for continuous synthesis and breakdown of triglycerides in animals, with breakdown controlled mainly by the activation of hormone-sensitive enzyme lipase.[52] The complete oxidation of fatty acids provides high caloric content, about 9 kcal/g, compared with 4 kcal/g for the breakdown of carbohydrates and proteins. Migratory birds that must fly long distances without eating use stored energy of triglycerides to fuel their flights.[53]

Signaling
In recent years, evidence has emerged showing that lipid signaling is a vital part of the cell signaling.[54][55] Lipid signaling may occur via activation of G protein-coupled or nuclear receptors, and members of several different lipid categories have been identified as signaling molecules and cellular messengers.[56] These include sphingosine-1-phosphate, a sphingolipid derived from ceramide that is a potent messenger molecule involved in regulating calcium mobilization,[57] cell growth, and apoptosis;[58] diacylglycerol (DAG) and the phosphatidylinositol phosphates (PIPs), involved in calcium-mediated activation of protein kinase C;[59] the prostaglandins, which are one type of fatty-acid derived eicosanoid involved in inflammation and immunity;[60] the steroid hormones such as estrogen, testosterone and cortisol, which modulate a host of functions such as reproduction, metabolism and blood pressure; and the oxysterols such as 25-hydroxy-cholesterol that are liver X receptor agonists.[61]

Lipid

226

Other functions
The "fat-soluble" vitamins (A, D, E and K) – which are isoprene-based lipids – are essential nutrients stored in the liver and fatty tissues, with a diverse range of functions. Acyl-carnitines are involved in the transport and metabolism of fatty acids in and out of mitochondria, where they undergo beta oxidation.[62] Polyprenols and their phosphorylated derivatives also play important transport roles, in this case the transport of oligosaccharides across membranes. Polyprenol phosphate sugars and polyprenol diphosphate sugars function in extra-cytoplasmic glycosylation reactions, in extracellular polysaccharide biosynthesis (for instance, peptidoglycan polymerization in bacteria), and in eukaryotic protein N-glycosylation.[63][64] Cardiolipins are a subclass of glycerophospholipids containing four acyl chains and three glycerol groups that are particularly abundant in the inner mitochondrial membrane.[65][66][67] They are believed to activate enzymes involved with oxidative phosphorylation.[68] Lipids also form the basis of steroid hormones.[69]

Metabolism
The major dietary lipids for humans and other animals are animal and plant triglycerides, sterols, and membrane phospholipids. The process of lipid metabolism synthesizes and degrades the lipid stores and produces the structural and functional lipids characteristic of individual tissues.

Biosynthesis
In animals, when there is an oversupply of dietary carbohydrate, the excess carbohydrate is converted to triglycerides. This involves the synthesis of fatty acids from acetyl-CoA and the esterification of fatty acids in the production of triglycerides, a process called lipogenesis.[70] Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acetyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups, in animals and fungi all these fatty acid synthase reactions are carried out by a single multifunctional protein,[71] while in plant plastids and bacteria separate enzymes perform each step in the pathway.[72][73] The fatty acids may be subsequently converted to triglycerides that are packaged in lipoproteins and secreted from the liver. The synthesis of unsaturated fatty acids involves a desaturation reaction, whereby a double bond is introduced into the fatty acyl chain. For example, in humans, the desaturation of stearic acid by stearoyl-CoA desaturase-1 produces oleic acid. The doubly unsaturated fatty acid linoleic acid as well as the triply unsaturated α-linolenic acid cannot be synthesized in mammalian tissues, and are therefore essential fatty acids and must be obtained from the diet.[74] Triglyceride synthesis takes place in the endoplasmic reticulum by metabolic pathways in which acyl groups in fatty acyl-CoAs are transferred to the hydroxyl groups of glycerol-3-phosphate and diacylglycerol.[75] Terpenes and isoprenoids, including the carotenoids, are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate.[76] These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA,[77] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[76][78] One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol.[79] Lanosterol can then be converted into other steroids such as cholesterol and ergosterol.[79][80]

Lipid

227

Degradation
Beta oxidation is the metabolic process by which fatty acids are broken down in the mitochondria and/or in peroxisomes to generate acetyl-CoA. For the most part, fatty acids are oxidized by a mechanism that is similar to, but not identical with, a reversal of the process of fatty acid synthesis. That is, two-carbon fragments are removed sequentially from the carboxyl end of the acid after steps of dehydrogenation, hydration, and oxidation to form a beta-keto acid, which is split by thiolysis. The acetyl-CoA is then ultimately converted into ATP, CO2, and H2O using the citric acid cycle and the electron transport chain. Hence the Krebs Cycle can start at acetyl-CoA when fat is being broken down for energy if there is little or no glucose available. The energy yield of the complete oxidation of the fatty acid palmitate is 106 ATP.[81] Unsaturated and odd-chain fatty acids require additional enzymatic steps for degradation.

Nutrition and health
Most of the fat found in food is in the form of triglycerides, cholesterol, and phospholipids. Some dietary fat is necessary to facilitate absorption of fat-soluble vitamins (A, D, E, and K) and carotenoids.[82] Humans and other mammals have a dietary requirement for certain essential fatty acids, such as linoleic acid (an omega-6 fatty acid) and alpha-linolenic acid (an omega-3 fatty acid) because they cannot be synthesized from simple precursors in the diet.[74] Both of these fatty acids are 18-carbon polyunsaturated fatty acids differing in the number and position of the double bonds. Most vegetable oils are rich in linoleic acid (safflower, sunflower, and corn oils). Alpha-linolenic acid is found in the green leaves of plants, and in selected seeds, nuts, and legumes (in particular flax, rapeseed, walnut, and soy).[83] Fish oils are particularly rich in the longer-chain omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).[84] A large number of studies have shown positive health benefits associated with consumption of omega-3 fatty acids on infant development, cancer, cardiovascular diseases, and various mental illnesses, such as depression, attention-deficit hyperactivity disorder, and dementia.[85][86] In contrast, it is now well-established that consumption of trans fats, such as those present in partially hydrogenated vegetable oils, are a risk factor for cardiovascular disease.[87][88][89] A few studies have suggested that total dietary fat intake is linked to an increased risk of obesity[90][91] and diabetes.[92][93] However, a number of very large studies, including the Women's Health Initiative Dietary Modification Trial, an eight year study of 49,000 women, the Nurses' Health Study and the Health Professionals Follow-up Study, revealed no such links.[94][95][96] None of these studies suggested any connection between percentage of calories from fat and risk of cancer, heart disease, or weight gain. The Nutrition Source, a website maintained by the Department of Nutrition at the Harvard School of Public Health, summarizes the current evidence on the impact of dietary fat: "Detailed research—much of it done at Harvard—shows that the total amount of fat in the diet isn't really linked with weight or disease."[97]

Lipid

228

References
[1] [2] [3] [4] Maitland, Jr Jones (1998). Organic Chemistry. W W Norton & Co Inc (Np). p. 139. ISBN 0-393-97378-6. Stryer et al., p. 328. Stryer et al., p. 330. Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T, Spener F, Van Meer G, Wakelam M and Dennis E.A (2009). "Update of the LIPID MAPS comprehensive classification system for lipids". Journal of Lipid Research 50 (Supplement): S9–S14. doi:10.1194/jlr.R800095-JLR200. PMC 2674711. PMID 19098281. [5] Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR and Maurya MR (2011). "Bioinformatics and Systems Biology of the Lipidome" (http:/ / pubs. acs. org/ doi/ abs/ 10. 1021/ cr200295k). Chemical Reviews 111 (10): 6452–6490. doi:10.1021/cr200295k. PMID 21939287. . [6] Michelle A, Hopkins J, McLaughlin CW, Johnson S, Warner MQ, LaHart D, Wright JD (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN 0-13-981176-1. OCLC 32308337. [7] Vance JE, Vance DE (2002). Biochemistry of Lipids, Lipoproteins and Membranes. Amsterdam: Elsevier. ISBN 0-444-51139-3. OCLC 51001207. [8] Brown HA, ed. (2007). Lipodomics and Bioactive Lipids: Mass Spectrometry Based Lipid Analysis, Volume 432 (Methods in Enzymology). Boston: Academic Press. ISBN 0-12-373895-4. OCLC 166624879. [9] "Types of Lipids" (http:/ / www. news-medical. net/ health/ Types-of-Lipids. aspx). . [10] Hunt SM, Groff JL, Gropper SAS (1995). Advanced Nutrition and Human Metabolism. Belmont, CA: West Pub. Co. p. 98. ISBN 0-314-04467-1. [11] Devlin, pp. 193–95. [12] Hunter JE (November 2006). "Dietary trans fatty acids: review of recent human studies and food industry responses". Lipids 41 (11): 967–92. doi:10.1007/s11745-006-5049-y. PMID 17263298. [13] "A Long Lipid, a Long Name: Docosahexaenoic Acid" (http:/ / www. samuelfurse. com/ 2011/ 12/ a-long-name-a-long-lipid-docosahexaenoic-acid/ ). The Lipid Chronicles. . Retrieved 2011-12-31. [14] "DHA FOR OPTIMAL BRAIN AND VISUAL FUNCTIONING" (http:/ / www. dhaomega3. org/ Overview/ DHA-for-Optimal-Brain-and-Visual-Functioning). DHA/EPA Omega-3 Institute. . [15] Fezza F, De Simone C, Amadio D, Maccarrone M (2008). "Fatty acid amide hydrolase: a gate-keeper of the endocannabinoid system". Subcellular Biochemistry. Subcellular Biochemistry 49: 101–32. doi:10.1007/978-1-4020-8831-5_4. ISBN 978-1-4020-8830-8. PMID 18751909. [16] Coleman RA, Lee DP (2004). "Enzymes of triglyceride synthesis and their regulation". Progress in Lipid Research 43 (2): 134–76. doi:10.1016/S0163-7827(03)00051-1. PMID 14654091. [17] van Holde and Mathews, p. 630–31. [18] Hölzl G, Dörmann P (2007). "Structure and function of glycoglycerolipids in plants and bacteria" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0163-7827(07)00015-X). Progress in Lipid Research 46 (5): 225–43. doi:10.1016/j.plipres.2007.05.001. PMID 17599463. . [19] Honke K, Zhang Y, Cheng X, Kotani N, Taniguchi N (2004). "Biological roles of sulfoglycolipids and pathophysiology of their deficiency" (http:/ / www. kluweronline. com/ art. pdf?issn=0282-0080& volume=21& page=59). Glycoconjugates Journal 21 (1–2): 59–62. doi:10.1023/B:GLYC.0000043749.06556.3d. PMID 15467400. . [20] "The Structure of a Membrane" (http:/ / www. samuelfurse. com/ 2011/ 11/ the-structure-of-a-membrane/ ). The Lipid Chronicles. . Retrieved 2011-12-31. [21] Berridge MJ, Irvine RF (1989). "Inositol phosphates and cell signalling" (http:/ / www. nature. com/ nature/ journal/ v341/ n6239/ pdf/ 341197a0. pdf). Nature Journal 341 (1): 197–205. doi:10.1038/341197a0. . [22] Farooqui AA, Horrocks LA, Farooqui T (2000). "Glycerophospholipids in brain: their metabolism, incorporation into membranes, functions, and involvement in neurological disorders" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0009-3084(00)00128-6). Chemistry and Physics of Lipids 106 (1): 1–29. doi:10.1016/S0009-3084(00)00128-6. PMID 10878232. . Retrieved 2009-04-12. [23] Ivanova PT, Milne SB, Byrne MO, Xiang Y, Brown HA (2007). "Glycerophospholipid identification and quantitation by electrospray ionization mass spectrometry". Methods in Enzymology. Methods in Enzymology 432: 21–57. doi:10.1016/S0076-6879(07)32002-8. ISBN 9780123738950. PMID 17954212. [24] van Holde and Mathews, p. 844. [25] Paltauf F (1994). "Ether lipids in biomembranes". Chemistry and Physics of Lipids 74 (2): 101–39. doi:10.1016/0009-3084(94)90054-X. PMID 7859340. [26] Merrill AH, Sandhoff K. (2002). "Sphingolipids: metabolism and cell signaling",in New Comprehensive Biochemistry: Biochemistry of Lipids, Lipoproteins,and Membranes, Vance, D.E. and Vance, J.E., eds. Elsevier Science, NY. Ch. 14. [27] Devlin, pp. 421–22. [28] Hori T, Sugita M (1993). "Sphingolipids in lower animals". Prog. Lipid Res 32 (1): 25–45. doi:10.1016/0163-7827(93)90003-F. PMID 8415797. [29] Wiegandt H (1992). "Insect glycolipids". Biochimica et Biophysica Acta 1123 (2): 117–26. doi:10.1016/0005-2760(92)90101-Z. PMID 1739742.

Lipid
[30] Guan X, Wenk MR (2008). "Biochemistry of inositol lipids". Frontiers in Bioscience 13 (13): 3239–51. doi:10.2741/2923. PMID 18508430. [31] Bach D, Wachtel E (2003). "Phospholipid/cholesterol model membranes: formation of cholesterol crystallites". Biochim Biophys Acta 1610 (2): 187–97. doi:10.1016/S0005-2736(03)00017-8. PMID 12648773. [32] Stryer et al., p. 749. [33] Bouillon R, Verstuyf A, Mathieu C, Van Cromphaut S, Masuyama R, Dehaes P, Carmeliet G (2006). "Vitamin D resistance" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S1521-690X(06)00079-0). Best Practice & Research. Clinical Endocrinology & Metabolism 20 (4): 627–45. doi:10.1016/j.beem.2006.09.008. PMID 17161336. . [34] Russell DW (2003). "The enzymes, regulation, and genetics of bile acid synthesis". Annual Review of Biochemistry 72: 137–74. doi:10.1146/annurev.biochem.72.121801.161712. PMID 12543708. [35] Villinski JC, Hayes JM, Brassell SC, Riggert VL, Dunbar RB (2008). "Sedimentary sterols as biogeochemical indicators in the Southern Ocean". Organic Geochemistry 39 (5): 567–88. doi:10.1016/j.orggeochem.2008.01.009. [36] Deacon J (2005). Fungal Biology. Cambridge, MA: Blackwell Publishers. p. 342. ISBN 1-4051-3066-0. [37] Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the isoprene units". Natural Product Reports 20 (2): 171–83. doi:10.1039/b109860h. PMID 12735695. [38] Rao AV, Rao LG (2007). "Carotenoids and human health" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S1043-6618(07)00035-7). Pharmacological Research : the Official Journal of the Italian Pharmacological Society 55 (3): 207–16. doi:10.1016/j.phrs.2007.01.012. PMID 17349800. . [39] Brunmark A, Cadenas E (1989). "Redox and addition chemistry of quinoid compounds and its biological implications". Free Radical Biology & Medicine 7 (4): 435–77. doi:10.1016/0891-5849(89)90126-3. PMID 2691341. [40] Swiezewska E, Danikiewicz W (2005). "Polyisoprenoids: structure, biosynthesis and function" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0163-7827(05)00022-6). Progress in Lipid Research 44 (4): 235–58. doi:10.1016/j.plipres.2005.05.002. PMID 16019076. . [41] Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC Jr, Ribeiro AA, Murphy RC,Ulevitch RJ, Fearns C, Reichart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA (2006). "Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4". Journal of Lipid Research 47 (5): 1097–111. doi:10.1194/jlr.M600027-JLR200. PMID 16479018. [42] Walsh CT (2004). "Polyketide and nonribosomal peptide antibiotics: modularity and versatility". Science 303 (5665): 1805–10. doi:10.1126/science.1094318. PMID 15031493. [43] Caffrey P, Aparicio JF, Malpartida F, Zotchev SB (2008). "Biosynthetic engineering of polyene macrolides towards generation of improved antifungal and antiparasitic agents" (http:/ / www. bentham-direct. org/ pages/ content. php?CTMC/ 2008/ 00000008/ 00000008/ 0003R. SGM). Current Topics in Medicinal Chemistry 8 (8): 639–53. doi:10.2174/156802608784221479. PMID 18473889. . Retrieved 2009-04-12. [44] Minto RE, Blacklock BJ (2008). "Biosynthesis and function of polyacetylenes and allied natural products" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0163-7827(08)00015-5). Progress in Lipid Research 47 (4): 233–306. doi:10.1016/j.plipres.2008.02.002. PMC 2515280. PMID 18387369. . Retrieved 2009-04-12. [45] Stryer et al., pp. 329–331 [46] Heinz E.(1996). Plant glycolipids: structure, isolation and analysis. in Advances in Lipid Methodology - 3, pp. 211–332 (ed. W.W. Christie, Oily Press, Dundee) [47] Stryer et al., pp. 333–34. [48] van Meer G, Voelker DR, Feigenson GW (2008). "Membrane lipids: where they are and how they behave". Nature Reviews Molecular Cell Biology 9 (2): 112–24. doi:10.1038/nrm2330. PMC 2642958. PMID 18216768. [49] Feigenson GW (2006). "Phase behavior of lipid mixtures". Nature Chemical Biology 2 (11): 560–63. doi:10.1038/nchembio1106-560. PMC 2685072. PMID 17051225. [50] Wiggins PM (1990). "Role of water in some biological processes". Microbiological Reviews 54 (4): 432–49. PMC 372788. PMID 2087221. [51] Raschke TM, Levitt M (2005). "Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them". Proceedings of the National Academy of Sciences U.S.A 102 (19): 6777–82. doi:10.1073/pnas.0500225102. PMC 1100774. PMID 15867152. [52] Brasaemle DL (December 2007). "Thematic review series: adipocyte biology. The perilipin family of structural lipid droplet proteins: stabilization of lipid droplets and control of lipolysis" (http:/ / www. jlr. org/ cgi/ content/ full/ 48/ 12/ 2547). J. Lipid Res 48 (12): 2547–59. doi:10.1194/jlr.R700014-JLR200. PMID 17878492. . [53] Stryer et al., p. 619. [54] Wang X (2004). "Lipid signaling". Current Opinions in Plant Biology 7 (3): 329–36. doi:10.1016/j.pbi.2004.03.012. PMID 15134755. [55] Dinasarapu AR,Saunders B,Ozerlat I,Azam K, and Subramaniam S (2011). "Signaling gateway molecule pages—a data model perspective". Bioinformatics 27 (12): 1736–1738. doi:10.1093/bioinformatics/btr190. PMC 3106186. PMID 21505029. [56] Eyster KM (2007). "The membrane and lipids as integral participants in signal transduction". Advances in Physiology Education 31 (1): 5–16. doi:10.1152/advan.00088.2006. PMID 17327576. [57] Hinkovska-Galcheva V, VanWay SM, Shanley TP, Kunkel RG (2008). "The role of sphingosine-1-phosphate and ceramide-1-phosphate in calcium homeostasis". Current Opinion in Investigational Drugs 9 (11): 1192–205. PMID 18951299. [58] Saddoughi SA, Song P, Ogretmen B (2008). "Roles of bioactive sphingolipids in cancer biology and therapeutics". Subcellular Biochemistry. Subcellular Biochemistry 49: 413–40. doi:10.1007/978-1-4020-8831-5_16. ISBN 978-1-4020-8830-8. PMC 2636716.

229

Lipid
PMID 18751921. [59] Klein C, Malviya AN (2008). "Mechanism of nuclear calcium signaling by inositol 1,4,5-trisphosphate produced in the nucleus, nuclear located protein kinase C and cyclic AMP-dependent protein kinase" (http:/ / www. bioscience. org/ 2008/ v13/ af/ 2756/ fulltext. htm). Frontiers in Bioscience 13 (13): 1206–26. doi:10.2741/2756. PMID 17981624. . [60] Boyce JA (2008). "Eicosanoids in asthma, allergic inflammation, and host defense" (http:/ / www. bentham-direct. org/ pages/ content. php?CMM/ 2008/ 00000008/ 00000005/ 0003M. SGM). Current Molecular Medicine 8 (5): 335–49. doi:10.2174/156652408785160989. PMID 18691060. . [61] Bełtowski J (2008). "Liver X receptors (LXR) as therapeutic targets in dyslipidemia". Cardiovascular Therapy 26 (4): 297–316. doi:10.1111/j.1755-5922.2008.00062.x. PMID 19035881. [62] Indiveri C, Tonazzi A, Palmieri F (October 1991). "Characterization of the unidirectional transport of carnitine catalyzed by the reconstituted carnitine carrier from rat liver mitochondria". Biochim. Biophys. Acta 1069 (1): 110–6. doi:10.1016/0005-2736(91)90110-T. PMID 1932043. [63] Parodi AJ, Leloir LF (April 1979). "The role of lipid intermediates in the glycosylation of proteins in the eucaryotic cell". Biochim. Biophys. Acta 559 (1): 1–37. doi:10.1016/0304-4157(79)90006-6. PMID 375981. [64] Helenius A, Aebi M (2001). "Intracellular functions of N-linked glycans". Science 291 (5512): 2364–69. doi:10.1126/science.291.5512.2364. PMID 11269317. [65] M. Nowicki and M. Frentzen (2005). "Cardiolipin synthase of Arabidopsis thaliana". FEBS Letters 579 (10): 2161–2165. doi:10.1016/j.febslet.2005.03.007. PMID 15811335. [66] M. Nowicki (2006). "Characterization of the Cardiolipin Synthase from Arabidopsis thaliana" (http:/ / darwin. bth. rwth-aachen. de/ opus/ volltexte/ 2006/ 1629/ ). Ph.D. thesis, RWTH-Aachen University. . [67] Gohil VM, Greenberg ML (2009). "Mitochondrial membrane biogenesis: phospholipids and proteins go hand in hand" (http:/ / jcb. rupress. org/ cgi/ content/ full/ 184/ 4/ 469). Journal of Cell Biology 184 (4): 469–72. doi:10.1083/jcb.200901127. PMC 2654137. PMID 19237595. . [68] Hoch FL (1992). "Cardiolipins and biomembrane function". Biochimica et Biophysica Acta 1113 (1): 71–133. PMID 10206472. [69] http:/ / www. elmhurst. edu/ ~chm/ vchembook/ 556steroids. html [70] Stryer et al., p. 634. [71] Chirala S, Wakil S (2004). "Structure and function of animal fatty acid synthase". Lipids 39 (11): 1045–53. doi:10.1007/s11745-004-1329-9. PMID 15726818. [72] White S, Zheng J, Zhang Y (2005). "The structural biology of type II fatty acid biosynthesis". Annual Review of Biochemistry 74: 791–831. doi:10.1146/annurev.biochem.74.082803.133524. PMID 15952903. [73] Ohlrogge J, Jaworski J (1997). "Regulation of fatty acid synthesis". Annual Review of Plant Physiology and Plant Molecular Biology 48: 109–136. doi:10.1146/annurev.arplant.48.1.109. PMID 15012259. [74] Stryer et al., p. 643. [75] Stryer et al., pp. 733–39. [76] Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the isoprene units". Natural Product Reports 20 (2): 171–83. doi:10.1039/b109860h. PMID 12735695. [77] Grochowski L, Xu H, White R (2006). "Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate". Journal of Bacteriology 188 (9): 3192–98. doi:10.1128/JB.188.9.3192-3198.2006. PMC 1447442. PMID 16621811. [78] Lichtenthaler H (1999). "The 1-Dideoxy-D-xylulose-5-phosphate pathway of isoprenoid biosynthesis in plants". Annual Review of Plant Physiology and Plant Molecular Biology 50: 47–65. doi:10.1146/annurev.arplant.50.1.47. PMID 15012203. [79] Schroepfer G (1981). "Sterol biosynthesis". Annual Review of Biochemistry 50: 585–621. doi:10.1146/annurev.bi.50.070181.003101. PMID 7023367. [80] Lees N, Skaggs B, Kirsch D, Bard M (1995). "Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae—a review". Lipids 30 (3): 221–26. doi:10.1007/BF02537824. PMID 7791529. [81] Stryer et al., pp. 625–26. [82] Bhagavan, p. 903. [83] Russo GL (2009). "Dietary n-6 and n-3 polyunsaturated fatty acids: from biochemistry to clinical implications in cardiovascular prevention" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0006-2952(08)00777-6). Biochemical Pharmacology 77 (6): 937–46. doi:10.1016/j.bcp.2008.10.020. PMID 19022225. . [84] Bhagavan, p. 388. [85] Riediger ND, Othman RA, Suh M, Moghadasian MH (2009). "A systemic review of the roles of n-3 fatty acids in health and disease". Journal of the American Dietetic Association 109 (4): 668–79. doi:10.1016/j.jada.2008.12.022. PMID 19328262. [86] Galli C, Risé P (2009). "Fish consumption, omega 3 fatty acids and cardiovascular disease. The science and the clinical trials". Nutrition and Health (Berkhamsted, Hertfordshire) 20 (1): 11–20. doi:10.1177/026010600902000102. PMID 19326716. [87] Micha R, Mozaffarian D (2008). "Trans fatty acids: effects on cardiometabolic health and implications for policy". Prostaglandins, Leukotrienes, and Essential Fatty Acids 79 (3–5): 147–52. doi:10.1016/j.plefa.2008.09.008. PMC 2639783. PMID 18996687. [88] Dalainas I, Ioannou HP (2008). "The role of trans fatty acids in atherosclerosis, cardiovascular disease and infant development". International Angiology: a Journal of the International Union of Angiology 27 (2): 146–56. PMID 18427401.

230

Lipid
[89] Mozaffarian D, Willett WC (2007). "Trans fatty acids and cardiovascular risk: a unique cardiometabolic imprint?". Current Atherosclerosis Reports 9 (6): 486–93. doi:10.1007/s11883-007-0065-9. PMID 18377789. [90] Astrup A, Dyerberg J, Selleck M, Stender S (2008). "Nutrition transition and its relationship to the development of obesity and related chronic diseases". Obesity Review 9 Suppl 1: 48–52. doi:10.1111/j.1467-789X.2007.00438.x. PMID 18307699. [91] Astrup A (2005). "The role of dietary fat in obesity". Seminars in Vascular Medicine 5 (1): 40–47. doi:10.1055/s-2005-871740. PMID 15968579. [92] Ma Y. et al (2006). "Low-carbohydrate and high-fat intake among adult patients with poorly controlled type 2 diabetes mellitus". Nutrition 22 (11–12): 1129–1136. doi:10.1016/j.nut.2006.08.006. PMC 2039705. PMID 17027229. [93] Astrup A (2008). "Dietary management of obesity". JPEN Journal of Parenteral and Enteral Nutrition 32 (5): 575–77. doi:10.1177/0148607108321707. PMID 18753397. [94] Beresford SA, Johnson KC, Ritenbaugh C, et al. (2006). "Low-fat dietary pattern and risk of colorectal cancer: the Women's Health Initiative Randomized Controlled Dietary Modification Trial". JAMA: the Journal of the American Medical Association 295 (6): 643–54. doi:10.1001/jama.295.6.643. PMID 16467233. [95] Howard BV, Manson JE, Stefanick ML, et al. (2006). "Low-fat dietary pattern and weight change over 7 years: the Women's Health Initiative Dietary Modification Trial" (http:/ / jama. ama-assn. org/ cgi/ pmidlookup?view=long& pmid=16391215). JAMA: the Journal of the American Medical Association 295 (1): 39–49. doi:10.1001/jama.295.1.39. PMID 16391215. . [96] Howard BV, Van Horn L, Hsia J, et al. (2006). "Low-fat dietary pattern and risk of cardiovascular disease: the Women's Health Initiative Randomized Controlled Dietary Modification Trial". JAMA : the Journal of the American Medical Association 295 (6): 655–66. doi:10.1001/jama.295.6.655. PMID 16467234. [97] "Fats and Cholesterol: Out with the Bad, In with the Good — What Should You Eat? - The Nutrition Source — Harvard School of Public Health" (http:/ / www. hsph. harvard. edu/ nutritionsource/ what-should-you-eat/ fats-full-story/ index. html). . Retrieved 2009-05-12.

231

Bibliography
• Bhagavan NV (2002). Medical Biochemistry (http://books.google.com/?id=vT9YttFTPi0C& printsec=frontcover). San Diego: Harcourt/Academic Press. ISBN 0-12-095440-0. • Devlin TM (1997). Textbook of Biochemistry: With Clinical Correlations (4th ed.). Chichester: John Wiley & Sons. ISBN 0-471-17053-4. • Stryer L, Berg JM, Tymoczko JL (2007). Biochemistry (6th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-8724-5. • Van Holde KE, Mathews CK (1996). Biochemistry (2nd ed.). Menlo Park, Calif: Benjamin/Cummings Pub. Co. ISBN 0-8053-3931-0.

External links
Introductory • • • • • List of lipid-related web sites (http://www.cyberlipid.org/cyberlip/link0041.htm) Nature Lipidomics Gateway (http://www.lipidmaps.org/) - Round-up and summaries of recent lipid research Lipid Library (http://www.lipidlibrary.co.uk/) - General reference on lipid chemistry and biochemistry Cyberlipid.org (http://www.cyberlipid.org/) - Resources and history for lipids. Molecular Computer Simulations (http://www.fos.su.se/~sasha/Lipid_membranes.html) - Modeling of Lipid Membranes • Lipids, Membranes and Vesicle Trafficking (http://www.biochemweb.org/lipids_membranes.shtml) - The Virtual Library of Biochemistry and Cell Biology Nomenclature • IUPAC nomenclature of lipids (http://www.chem.qmul.ac.uk/iupac/lipid/) • IUPAC glossary entry for the lipid class of molecules (http://www.chem.qmul.ac.uk/iupac/class/lipid.html) Databases • LIPID MAPS (http://www.lipidmaps.org/data/databases.html) - Comprehensive lipid and lipid-associated gene/protein databases. • LipidBank (http://lipidbank.jp/) - Japanese database of lipids and related properties, spectral data and references.

Lipid • LIPIDAT (http://www.lipidat.tcd.ie/) - Database composed mainly of phospholipids and associated thermodynamic data. General • ApolloLipids (http://www.apollolipids.org/) - Provides dyslipidemia and cardiovascular disease prevention and treatment information as well as continuing medical education programs • National Lipid Association (http://www.lipid.org/) - Professional medical education organization for health care professionals who seek to prevent morbidity and mortality stemming from dyslipidemias and other cholesterol-related disorders.

232

Lipopolysaccharide
Lipopolysaccharides (LPS), also known as lipoglycans, are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins and elicit strong immune responses in animals.

Functions
LPS is the major component of the outer membrane of Gram-negative bacteria, contributing greatly to the structural integrity of the bacteria, and protecting the membrane from certain kinds of chemical attack. LPS also increases the negative charge of the cell membrane and helps stabilize the overall membrane structure. It is of crucial importance to gram-negative bacteria, whose death results if it is mutated or removed. LPS is an endotoxin, and induces a strong response from normal animal immune systems. It has also been implicated in non-pathogenic aspects of bacterial ecology, including surface adhesion, bacteriophage sensitivity, and interactions with predators such as amoebae. LPS is required for the proper conformation of Omptin activity; however, smooth LPS will sterically hinder omptins. LPS acts as the prototypical endotoxin because it binds the CD14/TLR4/MD2 receptor complex, which promotes the secretion of pro-inflammatory cytokines in many cell types, but especially in macrophages and B cells. In Immunology, the term "LPS challenge" refers to the process of exposing a subject to an LPS that may act as a toxin. LPS is also an exogenous pyrogen (external fever-inducing substance). Being of crucial importance to gram-negative bacteria, these molecules make candidate targets for new antimicrobial agents. Some researchers doubt reports of generalized toxic effects attributed to all lipopolysaccharides, in particular, for cyanobacteria.[1]

Structure of a lipopolysaccharide

Lipopolysaccharide

233

Composition
It comprises three parts: 1. O antigen (or O polysaccharide) 2. Core oligosaccharide 3. Lipid A

O-antigen
A repetitive glycan polymer contained within an LPS is referred to as the O antigen, O polysaccharide, or O side-chain of the bacteria. The O antigen is attached to the core oligosaccharide, and comprises the outermost domain of the LPS molecule. The composition of the O chain varies from strain to strain. For example, there are over 160 different O antigen structures produced by different E. coli strains.[2] The presence The saccharolipid Kdo2-Lipid A. Glucosamine residues in blue, Kdo residues in or absence of O chains determines whether red, acyl chains in black and phosphate groups in green. the LPS is considered rough or smooth. Full-length O-chains would render the LPS smooth, whereas the absence or reduction of O-chains would make the LPS rough.[3] Bacteria with rough LPS usually have more penetrable cell membranes to hydrophobic antibiotics, since a rough LPS is more hydrophobic.[4] O antigen is exposed on the very outer surface of the bacterial cell, and, as a consequence, is a target for recognition by host antibodies.

Core
The Core domain always contains an oligosaccharide component that attaches directly to lipid A and commonly contains sugars such as heptose and 3-deoxy-D-mannooctulosonic Acid (also known as KDO, keto-deoxyoctulosonate).[5] The LPS Cores of many bacteria also contain non-carbohydrate components, such as phosphate, amino acids, and ethanolamine substitutents.

Lipid A
Lipid A is, in normal circumstances, a phosphorylated glucosamine disaccharide decorated with multiple fatty acids. These hydrophobic fatty acid chains anchor the LPS into the bacterial membrane, and the rest of the LPS projects from the cell surface. The lipid A domain is responsible for much of the toxicity of Gram-negative bacteria. When bacterial cells are lysed by the immune system, fragments of membrane containing lipid A are released into the circulation, causing fever, diarrhea, and possible fatal endotoxic shock (also called septic shock).

Lipopolysaccharide

234

Biosynthesis and Transport LPS modifications
The making of LPS can be modified in order to present a specific sugar structure. Those can be recognised by either other LPS (which enables to inhibit LPS toxins) or glycosyltransferases that use those sugar structure to add more specific sugars. It has recently been shown that a specific enzyme in the intestine (alkaline phosphatase) can detoxify LPS by removing the two phosphate groups found on LPS carbohydrates.[8] This may function as an adaptive mechanism to help the host manage potentially toxic effects of gram-negative bacteria normally found in the small intestine.

LPS Final Assembly: O-antigen subunits are translocated across the inner membrane (by Wzx) where they are polymerized (by Wzy, chain length determined by Wzz) and ligated (by WaaL) on to complete Core-Lipid A molecules (which were translocated by [6] MsbA).

LPS Transport: Completed LPS molecules are transported across the periplasm and [7] outer membrane by the proteins LptA, B, C, D, E, F, and G

Lipopolysaccharide

235

Variability and effect upon specificity
O-antigens (the outer carbohydrates) are the most variable portion of the LPS molecule, imparting the antigenic specificity. In contrast, lipid A is the most conserved part. However, lipid A composition also may vary (e.g., in number and nature of acyl chains even within or between genera). Some of these variations may impart antagonistic properties to these LPS. For example Rhodobacter sphaeroides diphosphoryl lipid A (RsDPLA) is a potent antagonist of LPS in human cells, but is an agonist in hamster and equine cells. It has been speculated that conical Lipid A Toll-like receptors of the innate immune system recognize LPS and trigger an (e.g., from E. coli) are more agonistic, less immune response. conical lipid A like those of Porphyromonas gingivalis may activate a different signal (TLR2 instead of TLR4), and completely cylindrical lipid A like that of Rhodobacter sphaeroides is antagonistic to TLRs.[9][10] Lipopolysaccharide gene clusters are highly variable between different strains, subspecies, species of bacterial pathogens of plants and animals.[11][12]

Immune response
LPS function has been under experimental research for several years due to its role in activating many transcription factors. LPS challenge also produces many types of mediators involved in septic shock. Humans are much more sensitive to LPS than other animals (e.g., mice). A dose of 1 µg/kg induces shock in humans, but mice will tolerate a dose up to a thousand times higher.[13] This may relate to differences in the level of circulating natural antibodies between the two species.[14][15] Said et al. showed that LPS causes an IL-10-dependent inhibition of CD4 T-cell expansion and function by up-regulating PD-1 levels on monocytes which leads to IL-10 production by monocytes after binding of PD-1 by PD-L.[16] Bruce Beutler was awarded a portion of the 2011 Nobel Prize in Physiology or Medicine for his work demonstrating that TLR4 is the LPS receptor.[17][18]

References
[1] Stewart I, Schluter PJ, Shaw GR (2006). "Cyanobacterial lipopolysaccharides and human health – a review". Environ Health 5: 7. doi:10.1186/1476-069X-5-7. PMC 1489932. PMID 16563160. [2] Christian Raetz and Chris Whitfield (2002) Lipopolysaccharide Endotoxins Annu. Rev. Biochem. 71:635-700 [3] Rittig MG et al. (2004). "Smooth and rough lipopolysaccharide phenotypes of Brucella induce different intracellular trafficking and cytokine/chemokine release in human monocytes". Journal of Leukocyte Biology 5 (4): 196–200. doi:10.1189/jlb.0103015. PMID 12960272. [4] Tsujimoto H et al. (2003). "Diffusion of macrolide antibiotics through the outer membrane of Moraxella catarrhalis". Journal of Infection and Chemotherapy 74 (4): 1045–1055. doi:10.1007/s101569900025. PMID 11810516. [5] Hershberger C and Binkley SB (1968). "Chemistry and Metabolism of 3-Deoxy-d-mannooctulosonic Acid. I. STEREOCHEMICAL DETERMINATION" (http:/ / www. jbc. org/ cgi/ reprint/ 243/ 7/ 1578?maxtoshow=& HITS=10& hits=10& RESULTFORMAT=& fulltext=3-Deoxy-D-mannooctulosonic+ Acid+ & searchid=1& FIRSTINDEX=0& volume=243& issue=7& resourcetype=HWCIT). Journal of Biological Chemistry 243 (7): 1578–1584. PMID 4296687. . [6] Wang, Xiaoyuan and Quinn, Peter J. (2010). "Lipopolysaccharide:Biosynthetic pathway and structure modification". Progress in Lipid Research 49 (2): 97–107. doi:10.1016/j.plipres.2009.06.002. PMID 19815028.

Lipopolysaccharide
[7] Ruiz, Natividad; Kahne, Daniel; Silhavy, Thomas J (2009). "Transport of lipopolysaccharide across the cell envelope: the long road of discovery". Nature Reviews Microbiology 7 (9): 677–683. doi:10.1038/nrmicro2184. PMC 2790178. PMID 19633680. [8] Bates J.M. et al. (2007). "Intestinal Alkaline Phosphatase Detoxifies Lipopolysaccharide and Prevents Inflammation in Response to the Gut Microbiota". Cell Host and Microbe 2 (6): 371–382. doi:10.1016/j.chom.2007.10.010. PMC 2730374. PMID 18078689. [9] Netea M et al. (2002). "Does the shape of lipid A determine the interaction of LPS with Toll-like receptors?". Trends Immunol 23 (3): 135–9. doi:10.1016/S1471-4906(01)02169-X. PMID 11864841. [10] Seydel U, Oikawa M, Fukase K, Kusumoto S, Brandenburg K (2000). "Intrinsic conformation of lipid A is responsible for agonistic and antagonistic activity". Eur J Biochem 267 (10): 3032–9. doi:10.1046/j.1432-1033.2000.01326.x. PMID 10806403. [11] Reeves P, Wang L (2002). "Genomic organization of LPS-specific loci". Curr Top Microbiol Immunol. Current Topics in Microbiology and Immunology 264 (1): 109–35. doi:10.1007/978-3-642-56031-6_7. ISBN 978-3-540-42682-0. PMID 12014174. [12] Patil P, Sonti R (2004). "Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice". BMC Microbiol 4: 40. doi:10.1186/1471-2180-4-40. PMC 524487. PMID 15473911. [13] Warren, HS; Fitting, C; Hoff, E; Adib-Conquy, M; Beasley-Topliffe, L; Tesini, B; Liang, X; Valentine, C et al. (2010). "Resilience to bacterial infection: difference between species could be due to proteins in serum". J Infect Dis 201 (2): 223–232. doi:10.1086/649557. PMC 2798011. PMID 20001600. [14] Reid RR, Prodeus AP, Khan W, Hsu T, Rosen FS, Carroll MC (1997). "Endotoxin shock in antibody-deficient mice: unraveling the role of natural antibody and complement in the clearance of lipopolysaccharide". J. Immunol. 159 (2): 970–5. PMID 9218618. [15] Boes M, Prodeus AP, Schmidt T, Carroll MC, Chen J (1998). "A Critical Role of Natural Immunoglobulin M in Immediate Defense Against Systemic Bacterial Infection". J. Exp. Med. 188 (12): 2381–6. doi:10.1084/jem.188.12.2381. PMC 2212438. PMID 9858525. [16] Said EA et al. (2010). "Programmed death-1-induced interleukin-10 production by monocytes impairs CD4+ T cell activation during HIV infection". Nature Medicine 16 (4): 452–9. doi:10.1038/nm.2106. PMID 20208540. [17] Poltorak A et al. (1998). "Defective LPS Signaling in C3H/HeJ and C57BL/10ScCr Mice: Mutations in Tlr4 Gene". Science 282 (5396): 2085–2088. doi:10.1126/science.282.5396.2085. PMID 9851930. [18] http:/ / www. nobelprize. org/ nobel_prizes/ medicine/ laureates/ 2011/ press. html

236

External links
• Lipopolysaccharides (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Lipopolysaccharides) at the US National Library of Medicine Medical Subject Headings (MeSH)

Metabolism

237

Metabolism
Metabolism (from Greek: μεταβολή "metabolē", "change" or Greek: μεταβολισμός metabolismos, "outthrow") is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Structure of adenosine triphosphate (ATP), a central intermediate in energy metabolism

Metabolism is usually divided into two categories. Catabolism breaks down organic matter, for example to harvest energy in cellular respiration. Anabolism uses energy to construct components of cells such as proteins and nucleic acids. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy and will not occur by themselves, by coupling them to spontaneous reactions that release energy. As enzymes act as catalysts they allow these reactions to proceed quickly and efficiently. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells. The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food. A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species.[2] For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants.[3] These striking similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and being retained because of their efficacy.[4][5]

Metabolism

238

Key biochemicals
Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and lipids (often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or breaking them down and using them as a source of energy, in the digestion and use of food. Many important biochemicals can be joined together to make polymers such as DNA and proteins. These macromolecules are essential.

Structure of a triacylglycerol lipid

Type of molecule Name of monomer forms Amino acids Carbohydrates Nucleic acids Amino acids Monosaccharides Nucleotides

Name of polymer forms

Examples of polymer forms

Proteins (also called polypeptides) Fibrous proteins and globular proteins Polysaccharides Polynucleotides Starch, glycogen and cellulose DNA and RNA

Amino acids and proteins
Proteins are made of amino acids arranged in a linear chain and joined together by peptide bonds. Many proteins are the enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as the proteins that form the cytoskeleton, a system of scaffolding that maintains the cell shape.[6] Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle.[7]

Lipids
Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes such as the cell membrane, or as a source of energy.[7] Lipids are usually defined as hydrophobic or amphipathic biological molecules that will dissolve in organic solvents such as benzene or chloroform.[8] The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acid esters is a triacylglyceride.[9] Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, and hydrophilic groups such as phosphate in phospholipids. Steroids such as cholesterol are another major class of lipids that are made in cells.[10]

Metabolism

239

Carbohydrates
Carbohydrates are aldehydes or ketones with many hydroxyl groups that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals).[7] The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.[11]

Nucleotides

Glucose can exist in both a straight-chain and ring form.

The two nucleic acids, DNA and RNA are polymers of nucleotides, each nucleotide comprising a phosphate group, a ribose sugar group, and a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, through the processes of transcription and protein biosynthesis.[7] This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome, for example HIV, which uses reverse transcription to create a DNA template from its viral RNA genome.[12] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic group transfer reactions.[13]

Coenzymes
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups.[14] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different [13] reactions. These group-transfer Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the extreme left. intermediates are called coenzymes. Each class of group-transfer reaction is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously being made, consumed and then recycled.[15] One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day.[15] ATP acts as a bridge between catabolism and anabolism, with catabolic reactions generating ATP and anabolic reactions consuming it. It also serves as a carrier of phosphate groups in phosphorylation reactions. A vitamin is an organic compound needed in small quantities that cannot be made in the cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated

Metabolism or are coupled to nucleotides when they are used in cells.[16] Nicotinamide adenine dinucleotide (NADH), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates.[17] Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.

240

Minerals and cofactors
Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and potassium) while others function at minute concentrations. About 99% of a mammal's mass is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur.[19] Organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water.[19] The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate and the organic ion bicarbonate. The maintenance of Structure of hemoglobin. The protein subunits are in red and blue, and the [18] precise gradients across cell membranes iron-containing heme groups in green. From PDB 1GZX . maintains osmotic pressure and pH.[20] Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cytosol.[21] Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules.[22] Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant.[23][24] These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin.[25] Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as ferritin or metallothionein when not being used.[26][27]

Catabolism
Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on

Metabolism redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate.[28] In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.[7]

241

Classification of organisms based on their metabolism
Energy source sunlight photo-troph

Preformed molecules chemoElectron donor organic compound inorganic compound Carbon source organic compound inorganic compound organolithoheteroauto-

The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

Digestion
Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into monosaccharides. Microbes simply secrete digestive enzymes into their surroundings,[29][30] while animals only secrete these enzymes from specialized cells in their guts.[31] The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transport proteins.[32][33]

Metabolism

242

Energy from organic compounds
Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides.[34] Once inside, the major route of breakdown is glycolysis, where sugars such as glucose and fructose are converted into pyruvate and some ATP is generated.[35] Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a A simplified outline of the catabolism of proteins, carbohydrates and fats waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids. Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy.[36] The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate.[37] The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).[38]

Energy transformations
Oxidative phosphorylation
In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell's inner membrane.[39] These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane.[40]

Metabolism

243

Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient.[41] This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate – turning it into ATP.[15]

Energy from inorganic compounds
Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of Mechanism of ATP synthase. ATP is shown in red, ADP and [42] phosphate in pink and the rotating stalk subunit in black. inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate),[1] ferrous iron (FeII)[43] or ammonia[44] as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite.[45] These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility.[46][47]

Energy from light
The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.[48][49] In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves energy being stored as a proton concentration gradient and this proton motive force then driving ATP synthesis.[15] The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres or rhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.[50] In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast.[7] These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.[51]

Anabolism
Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. Firstly, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

Metabolism Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.

244

Carbon fixation
Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide (CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin – Benson cycle.[52] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions.[53]

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a reversed citric acid cycle,[54] or the carboxylation of acetyl-CoA.[55][56] Prokaryotic chemoautotrophs also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.[57]

Carbohydrates and glycans
In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol, glycerate 3-phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis.[35] However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle.[58][59] Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery.[60] As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids.[61] In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose.[60][62] Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures.[63] The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called

Metabolism oligosaccharyltransferases.[64][65]

245

Fatty acids, isoprenoids and steroids
Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups, in animals and fungi all these fatty acid synthase reactions are carried out by a single multifunctional type I protein,[66] while in plant plastids and bacteria separate type II enzymes perform each step in the pathway.[67][68] Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products.[69] These compounds are made by the assembly and modification of isoprene units Simplified version of the steroid synthesis pathway with the intermediates isopentenyl donated from the reactive precursors pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate isopentenyl pyrophosphate and (GPP) and squalene shown. Some intermediates are omitted for clarity. dimethylallyl pyrophosphate.[70] These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA,[71] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[70][72] One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol.[73] Lanosterol can then be converted into other steroids such as cholesterol and ergosterol.[73][74]

Proteins
Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food.[7] Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts.[75] All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.[76] Amino acids are made into proteins by being joined together in a chain by peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be

Metabolism combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[77] This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.[78]

246

Nucleotide synthesis and salvage
Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy.[79] Consequently, most organisms have efficient systems to salvage preformed nucleotides.[79][80] Purines are synthesized as nucleosides (bases attached to ribose). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate.[81]

Xenobiotics and redox metabolism
All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics.[82] Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases,[83] UDP-glucuronosyltransferases,[84] and glutathione S-transferases.[85] This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills.[86] Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds.[87] A related problem for aerobic organisms is oxidative stress.[88] Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide.[89] These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases.[90][91]

Thermodynamics of living organisms
Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any closed system, the amount of entropy (disorder) will tend to increase. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments.[92] The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder.[93]

Metabolism

247

Regulation and control
As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis.[94][95] Metabolic regulation also allows organisms to respond to signals and interact actively with their environments.[96] Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway).[97] For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.[98] There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the flux through the pathway to compensate.[97] This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway.[99] Extrinsic control involves a cell in a multicellular Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor organism changing its metabolism in (1), which in turn starts many protein activation cascades (2). These include: response to signals from other cells. These translocation of Glut-4 transporter to the plasma membrane and influx of glucose (3), glycogen synthesis (4), glycolysis (5) and fatty acid synthesis (6). signals are usually in the form of soluble messengers such as hormones and growth factors and are detected by specific receptors on the cell surface.[100] These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins.[101] A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin.[102] Insulin is produced in response to rises in blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and glycogen.[103] The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating protein phosphatases and producing a decrease in the phosphorylation of these enzymes.[104]

Metabolism

248

Evolution
The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal ancestor.[3][105] This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid [106][107] metabolism. The retention of these ancient pathways during later evolution may be the result of these reactions being an optimal solution to their particular metabolic problems, Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of with pathways such as glycolysis and some of the phyla included are shown around the tree. the citric acid cycle producing their end products highly efficiently and in a [4][5] minimal number of steps. Mutation changes that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for whom the mutation occurs.[108] The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, with previous metabolic pathways being part of the ancient RNA world.[109] Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway.[110] The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions being created from pre-existing steps in the pathway.[111] An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database)[112] These recruitment processes result in an evolutionary enzymatic mosaic.[113] A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules.[114] As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host.[115] Similar reduced metabolic capabilities are seen in endosymbiotic organisms.[116]

Metabolism

249

Investigation and manipulation
Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products.[117] The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.[118]

An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes.[119] However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior.[120] These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies.[121] Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research.[122] These models are now being used in network analysis, to classify human diseases into groups that share common proteins or metabolites.[123][124] Bacterial metabolic networks are a striking example of bow-tie[125][126][127] organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies. A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid.[128] These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.[129]

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines.

Metabolism

250

History
The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow".[130] The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina.[131] He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration". In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue.[132] In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances Santorio Santorio in his steelyard within the yeast cells he called "ferments". He wrote that "alcoholic balance, from Ars de statica medicina, fermentation is an act correlated with the life and organization of the yeast first published 1614 cells, not with the death or putrefaction of the cells."[133] This discovery, along with the publication by Friedrich Wöhler in 1828 of the chemical synthesis of urea,[134] notable for being the first organic compound prepared from wholly inorganic precursors, proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry.[135] The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism.[136] He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.[137][62] Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

References
[1] Friedrich C (1998). "Physiology and genetics of sulfur-oxidizing bacteria". Adv Microb Physiol 39: 235–89. doi:10.1016/S0065-2911(08)60018-1. PMID 9328649. [2] Pace NR (January 2001). "The universal nature of biochemistry". Proc. Natl. Acad. Sci. U.S.A. 98 (3): 805–8. Bibcode 2001PNAS...98..805P. doi:10.1073/pnas.98.3.805. PMC 33372. PMID 11158550. [3] Smith E, Morowitz H (2004). "Universality in intermediary metabolism" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=15340153). Proc Natl Acad Sci USA 101 (36): 13168–73. Bibcode 2004PNAS..10113168S. doi:10.1073/pnas.0404922101. PMC 516543. PMID 15340153. . [4] Ebenhöh O, Heinrich R (2001). "Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems". Bull Math Biol 63 (1): 21–55. doi:10.1006/bulm.2000.0197. PMID 11146883. [5] Meléndez-Hevia E, Waddell T, Cascante M (1996). "The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution". J Mol Evol 43 (3): 293–303. doi:10.1007/BF02338838. PMID 8703096. [6] Michie K, Löwe J (2006). "Dynamic filaments of the bacterial cytoskeleton". Annu Rev Biochem 75: 467–92. doi:10.1146/annurev.biochem.75.103004.142452. PMID 16756499.

Metabolism
[7] Nelson, David L.; Michael M. Cox (2005). Lehninger Principles of Biochemistry. New York: W. H. Freeman and company. pp. 841. ISBN 0-7167-4339-6. [8] Fahy E, Subramaniam S, Brown H, Glass C, Merrill A, Murphy R, Raetz C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze M, White S, Witztum J, Dennis E (2005). "A comprehensive classification system for lipids" (http:/ / www. jlr. org/ cgi/ content/ full/ 46/ 5/ 839). J Lipid Res 46 (5): 839–61. doi:10.1194/jlr.E400004-JLR200. PMID 15722563. . [9] "Nomenclature of Lipids" (http:/ / www. chem. qmul. ac. uk/ iupac/ lipid/ ). IUPAC-IUB Commission on Biochemical Nomenclature (CBN). . Retrieved 2007-03-08. [10] Hegardt F (1999). "Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase: a control enzyme in ketogenesis". Biochem J 338 (Pt 3): 569–82. doi:10.1042/0264-6021:3380569. PMC 1220089. PMID 10051425. [11] Raman R, Raguram S, Venkataraman G, Paulson J, Sasisekharan R (2005). "Glycomics: an integrated systems approach to structure-function relationships of glycans". Nat Methods 2 (11): 817–24. doi:10.1038/nmeth807. PMID 16278650. [12] Sierra S, Kupfer B, Kaiser R (2005). "Basics of the virology of HIV-1 and its replication". J Clin Virol 34 (4): 233–44. doi:10.1016/j.jcv.2005.09.004. PMID 16198625. [13] Wimmer M, Rose I (1978). "Mechanisms of enzyme-catalyzed group transfer reactions". Annu Rev Biochem 47: 1031–78. doi:10.1146/annurev.bi.47.070178.005123. PMID 354490. [14] Mitchell P (1979). "The Ninth Sir Hans Krebs Lecture. Compartmentation and communication in living systems. Ligand conduction: a general catalytic principle in chemical, osmotic and chemiosmotic reaction systems". Eur J Biochem 95 (1): 1–20. doi:10.1111/j.1432-1033.1979.tb12934.x. PMID 378655. [15] Dimroth P, von Ballmoos C, Meier T (March 2006). "Catalytic and mechanical cycles in F-ATP synthases: Fourth in the Cycles Review Series". EMBO Rep 7 (3): 276–82. doi:10.1038/sj.embor.7400646. PMC 1456893. PMID 16607397. [16] Coulston, Ann; Kerner, John; Hattner, JoAnn; Srivastava, Ashini (2006). "Nutrition Principles and Clinical Nutrition". Stanford School of Medicine Nutrition Courses. SUMMIT. [17] Pollak N, Dölle C, Ziegler M (2007). "The power to reduce: pyridine nucleotides – small molecules with a multitude of functions". Biochem J 402 (2): 205–18. doi:10.1042/BJ20061638. PMC 1798440. PMID 17295611. [18] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1GZX [19] Heymsfield S, Waki M, Kehayias J, Lichtman S, Dilmanian F, Kamen Y, Wang J, Pierson R (1991). "Chemical and elemental analysis of humans in vivo using improved body composition models". Am J Physiol 261 (2 Pt 1): E190–8. PMID 1872381. [20] Sychrová H (2004). "Yeast as a model organism to study transport and homeostasis of alkali metal cations" (http:/ / www. biomed. cas. cz/ physiolres/ pdf/ 53 Suppl 1/ 53_S91. pdf) (PDF). Physiol Res 53 Suppl 1: S91–8. PMID 15119939. . [21] Levitan I (1988). "Modulation of ion channels in neurons and other cells". Annu Rev Neurosci 11: 119–36. doi:10.1146/annurev.ne.11.030188.001003. PMID 2452594. [22] Dulhunty A (2006). "Excitation-contraction coupling from the 1950s into the new millennium". Clin Exp Pharmacol Physiol 33 (9): 763–72. doi:10.1111/j.1440-1681.2006.04441.x. PMID 16922804. [23] Mahan D, Shields R (1998). "Macro- and micromineral composition of pigs from birth to 145 kilograms of body weight" (http:/ / jas. fass. org/ cgi/ reprint/ 76/ 2/ 506). J Anim Sci 76 (2): 506–12. PMID 9498359. . [24] Husted S, Mikkelsen B, Jensen J, Nielsen N (2004). "Elemental fingerprint analysis of barley (Hordeum vulgare) using inductively coupled plasma mass spectrometry, isotope-ratio mass spectrometry, and multivariate statistics". Anal Bioanal Chem 378 (1): 171–82. doi:10.1007/s00216-003-2219-0. PMID 14551660. [25] Finney L, O'Halloran T (2003). "Transition metal speciation in the cell: insights from the chemistry of metal ion receptors". Science 300 (5621): 931–6. Bibcode 2003Sci...300..931F. doi:10.1126/science.1085049. PMID 12738850. [26] Cousins R, Liuzzi J, Lichten L (2006). "Mammalian zinc transport, trafficking, and signals" (http:/ / www. jbc. org/ cgi/ content/ full/ 281/ 34/ 24085). J Biol Chem 281 (34): 24085–9. doi:10.1074/jbc.R600011200. PMID 16793761. . [27] Dunn L, Rahmanto Y, Richardson D (2007). "Iron uptake and metabolism in the new millennium". Trends Cell Biol 17 (2): 93–100. doi:10.1016/j.tcb.2006.12.003. PMID 17194590. [28] Nealson K, Conrad P (1999). "Life: past, present and future" (http:/ / rstb. royalsocietypublishing. org/ cgi/ pmidlookup?view=long& pmid=10670014). Philos Trans R Soc Lond B Biol Sci 354 (1392): 1923–39. doi:10.1098/rstb.1999.0532. PMC 1692713. PMID 10670014. . [29] Häse C, Finkelstein R (December 1993). "Bacterial extracellular zinc-containing metalloproteases" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=8302217). Microbiol Rev 57 (4): 823–37. PMC 372940. PMID 8302217. . [30] Gupta R, Gupta N, Rathi P (2004). "Bacterial lipases: an overview of production, purification and biochemical properties". Appl Microbiol Biotechnol 64 (6): 763–81. doi:10.1007/s00253-004-1568-8. PMID 14966663. [31] Hoyle T (1997). "The digestive system: linking theory and practice". Br J Nurs 6 (22): 1285–91. PMID 9470654. [32] Souba W, Pacitti A (1992). "How amino acids get into cells: mechanisms, models, menus, and mediators". JPEN J Parenter Enteral Nutr 16 (6): 569–78. doi:10.1177/0148607192016006569. PMID 1494216. [33] Barrett M, Walmsley A, Gould G (1999). "Structure and function of facilitative sugar transporters". Curr Opin Cell Biol 11 (4): 496–502. doi:10.1016/S0955-0674(99)80072-6. PMID 10449337. [34] Bell G, Burant C, Takeda J, Gould G (1993). "Structure and function of mammalian facilitative sugar transporters". J Biol Chem 268 (26): 19161–4. PMID 8366068. [35] Bouché C, Serdy S, Kahn C, Goldfine A (2004). "The cellular fate of glucose and its relevance in type 2 diabetes" (http:/ / edrv. endojournals. org/ cgi/ content/ full/ 25/ 5/ 807). Endocr Rev 25 (5): 807–30. doi:10.1210/er.2003-0026. PMID 15466941. .

251

Metabolism
[36] Sakami W, Harrington H (1963). "Amino acid metabolism". Annu Rev Biochem 32: 355–98. doi:10.1146/annurev.bi.32.070163.002035. PMID 14144484. [37] Brosnan J (2000). "Glutamate, at the interface between amino acid and carbohydrate metabolism" (http:/ / jn. nutrition. org/ cgi/ content/ full/ 130/ 4/ 988S). J Nutr 130 (4S Suppl): 988S–90S. PMID 10736367. . [38] Young V, Ajami A (2001). "Glutamine: the emperor or his clothes?" (http:/ / jn. nutrition. org/ cgi/ content/ full/ 131/ 9/ 2449S). J Nutr 131 (9 Suppl): 2449S–59S; discussion 2486S–7S. PMID 11533293. . [39] Hosler J, Ferguson-Miller S, Mills D (2006). "Energy Transduction: Proton Transfer Through the Respiratory Complexes". Annu Rev Biochem 75: 165–87. doi:10.1146/annurev.biochem.75.062003.101730. PMC 2659341. PMID 16756489. [40] Schultz B, Chan S (2001). "Structures and proton-pumping strategies of mitochondrial respiratory enzymes". Annu Rev Biophys Biomol Struct 30: 23–65. doi:10.1146/annurev.biophys.30.1.23. PMID 11340051. [41] Capaldi R, Aggeler R (2002). "Mechanism of the F(1)F(0)-type ATP synthase, a biological rotary motor". Trends Biochem Sci 27 (3): 154–60. doi:10.1016/S0968-0004(01)02051-5. PMID 11893513. [42] Friedrich B, Schwartz E (1993). "Molecular biology of hydrogen utilization in aerobic chemolithotrophs". Annu Rev Microbiol 47: 351–83. doi:10.1146/annurev.mi.47.100193.002031. PMID 8257102. [43] Weber K, Achenbach L, Coates J (2006). "Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction". Nat Rev Microbiol 4 (10): 752–64. doi:10.1038/nrmicro1490. PMID 16980937. [44] Jetten M, Strous M, van de Pas-Schoonen K, Schalk J, van Dongen U, van de Graaf A, Logemann S, Muyzer G, van Loosdrecht M, Kuenen J (1998). "The anaerobic oxidation of ammonium". FEMS Microbiol Rev 22 (5): 421–37. doi:10.1111/j.1574-6976.1998.tb00379.x. PMID 9990725. [45] Simon J (2002). "Enzymology and bioenergetics of respiratory nitrite ammonification". FEMS Microbiol Rev 26 (3): 285–309. doi:10.1111/j.1574-6976.2002.tb00616.x. PMID 12165429. [46] Conrad R (1996). "Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO)" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=8987358). Microbiol Rev 60 (4): 609–40. PMC 239458. PMID 8987358. . [47] Barea J, Pozo M, Azcón R, Azcón-Aguilar C (2005). "Microbial co-operation in the rhizosphere" (http:/ / jxb. oxfordjournals. org/ cgi/ content/ full/ 56/ 417/ 1761). J Exp Bot 56 (417): 1761–78. doi:10.1093/jxb/eri197. PMID 15911555. . [48] van der Meer M, Schouten S, Bateson M, Nübel U, Wieland A, Kühl M, de Leeuw J, Sinninghe Damsté J, Ward D (July 2005). "Diel Variations in Carbon Metabolism by Green Nonsulfur-Like Bacteria in Alkaline Siliceous Hot Spring Microbial Mats from Yellowstone National Park" (http:/ / aem. asm. org/ cgi/ pmidlookup?view=long& pmid=16000812). Appl Environ Microbiol 71 (7): 3978–86. doi:10.1128/AEM.71.7.3978-3986.2005. PMC 1168979. PMID 16000812. . [49] Tichi M, Tabita F (2001). "Interactive Control of Rhodobacter capsulatus Redox-Balancing Systems during Phototrophic Metabolism" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=11591679). J Bacteriol 183 (21): 6344–54. doi:10.1128/JB.183.21.6344-6354.2001. PMC 100130. PMID 11591679. . [50] Allen J, Williams J (1998). "Photosynthetic reaction centers". FEBS Lett 438 (1–2): 5–9. doi:10.1016/S0014-5793(98)01245-9. PMID 9821949. [51] Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, Tasaka M, Shikanai T (2004). "Cyclic electron flow around photosystem I is essential for photosynthesis". Nature 429 (6991): 579–82. Bibcode 2004Natur.429..579M. doi:10.1038/nature02598. PMID 15175756. [52] Miziorko H, Lorimer G (1983). "Ribulose-1,5-bisphosphate carboxylase-oxygenase". Annu Rev Biochem 52: 507–35. doi:10.1146/annurev.bi.52.070183.002451. PMID 6351728. [53] Dodd A, Borland A, Haslam R, Griffiths H, Maxwell K (2002). "Crassulacean acid metabolism: plastic, fantastic" (http:/ / jxb. oxfordjournals. org/ cgi/ content/ full/ 53/ 369/ 569). J Exp Bot 53 (369): 569–80. doi:10.1093/jexbot/53.369.569. PMID 11886877. . [54] Hügler M, Wirsen C, Fuchs G, Taylor C, Sievert S (May 2005). "Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic Acid Cycle by Members of the ɛ Subdivision of Proteobacteria" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=15838028). J Bacteriol 187 (9): 3020–7. doi:10.1128/JB.187.9.3020-3027.2005. PMC 1082812. PMID 15838028. . [55] Strauss G, Fuchs G (1993). "Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle". Eur J Biochem 215 (3): 633–43. doi:10.1111/j.1432-1033.1993.tb18074.x. PMID 8354269. [56] Wood H (1991). "Life with CO or CO2 and H2 as a source of carbon and energy" (http:/ / www. fasebj. org/ cgi/ reprint/ 5/ 2/ 156). FASEB J 5 (2): 156–63. PMID 1900793. . [57] Shively J, van Keulen G, Meijer W (1998). "Something from almost nothing: carbon dioxide fixation in chemoautotrophs". Annu Rev Microbiol 52: 191–230. doi:10.1146/annurev.micro.52.1.191. PMID 9891798. [58] Boiteux A, Hess B (1981). "Design of glycolysis". Philos Trans R Soc Lond B Biol Sci 293 (1063): 5–22. Bibcode 1981RSPTB.293....5B. doi:10.1098/rstb.1981.0056. PMID 6115423. [59] Pilkis S, el-Maghrabi M, Claus T (1990). "Fructose-2,6-bisphosphate in control of hepatic gluconeogenesis. From metabolites to molecular genetics". Diabetes Care 13 (6): 582–99. doi:10.2337/diacare.13.6.582. PMID 2162755. [60] Ensign S (2006). "Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation". Mol Microbiol 61 (2): 274–6. doi:10.1111/j.1365-2958.2006.05247.x. PMID 16856935. [61] Finn P, Dice J (2006). "Proteolytic and lipolytic responses to starvation". Nutrition 22 (7–8): 830–44. doi:10.1016/j.nut.2006.04.008. PMID 16815497. [62] Kornberg H, Krebs H (1957). "Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle". Nature 179 (4568): 988–91. Bibcode 1957Natur.179..988K. doi:10.1038/179988a0. PMID 13430766.

252

Metabolism
[63] Rademacher T, Parekh R, Dwek R (1988). "Glycobiology". Annu Rev Biochem 57: 785–838. doi:10.1146/annurev.bi.57.070188.004033. PMID 3052290. [64] Opdenakker G, Rudd P, Ponting C, Dwek R (1993). "Concepts and principles of glycobiology" (http:/ / www. fasebj. org/ cgi/ reprint/ 7/ 14/ 1330). FASEB J 7 (14): 1330–7. PMID 8224606. . [65] McConville M, Menon A (2000). "Recent developments in the cell biology and biochemistry of glycosylphosphatidylinositol lipids (review)". Mol Membr Biol 17 (1): 1–16. doi:10.1080/096876800294443. PMID 10824734. [66] Chirala S, Wakil S (2004). "Structure and function of animal fatty acid synthase". Lipids 39 (11): 1045–53. doi:10.1007/s11745-004-1329-9. PMID 15726818. [67] White S, Zheng J, Zhang Y (2005). "The structural biology of type II fatty acid biosynthesis". Annu Rev Biochem 74: 791–831. doi:10.1146/annurev.biochem.74.082803.133524. PMID 15952903. [68] Ohlrogge J, Jaworski J (1997). "Regulation of fatty acid synthesis". Annu Rev Plant Physiol Plant Mol Biol 48: 109–136. doi:10.1146/annurev.arplant.48.1.109. PMID 15012259. [69] Dubey V, Bhalla R, Luthra R (2003). "An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants" (http:/ / www. ias. ac. in/ jbiosci/ sep2003/ 637. pdf) (PDF). J Biosci 28 (5): 637–46. doi:10.1007/BF02703339. PMID 14517367. . [70] Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the isoprene units". Nat Prod Rep 20 (2): 171–83. doi:10.1039/b109860h. PMID 12735695. [71] Grochowski L, Xu H, White R (May 2006). "Methanocaldococcus jannaschii Uses a Modified Mevalonate Pathway for Biosynthesis of Isopentenyl Diphosphate" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=16621811). J Bacteriol 188 (9): 3192–8. doi:10.1128/JB.188.9.3192-3198.2006. PMC 1447442. PMID 16621811. . [72] Lichtenthaler H (1999). "The 1-Ddeoxy-D-xylulose-5-phosphate pathway of isoprenoid biosynthesis in plants". Annu Rev Plant Physiol Plant Mol Biol 50: 47–65. doi:10.1146/annurev.arplant.50.1.47. PMID 15012203. [73] Schroepfer G (1981). "Sterol biosynthesis". Annu Rev Biochem 50: 585–621. doi:10.1146/annurev.bi.50.070181.003101. PMID 7023367. [74] Lees N, Skaggs B, Kirsch D, Bard M (1995). "Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae—a review". Lipids 30 (3): 221–6. doi:10.1007/BF02537824. PMID 7791529. [75] Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R (November 1996). "Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae" (http:/ / www. ncbi. nlm. nih. gov/ pmc/ articles/ PMC146264/ ?tool=pubmed). Nucleic Acids Res. 24 (22): 4420–49. PMC 146264. PMID 8948633. . [76] Guyton, Arthur C.; John E. Hall (2006). Textbook of Medical Physiology. Philadelphia: Elsevier. pp. 855–6. ISBN 0-7216-0240-1. [77] Ibba M, Söll D (2001). "The renaissance of aminoacyl-tRNA synthesis" (http:/ / www. molcells. org/ home/ journal/ include/ downloadPdf. asp?articleuid={A158E3B4-2423-4806-9A30-4B93CDA76DA0}). EMBO Rep 2 (5): 382–7. doi:10.1093/embo-reports/kve095. PMC 1083889. PMID 11375928. . [78] Lengyel P, Söll D (1969). "Mechanism of protein biosynthesis". Bacteriol Rev 33 (2): 264–301. PMC 378322. PMID 4896351. [79] Rudolph F (1994). "The biochemistry and physiology of nucleotides". J Nutr 124 (1 Suppl): 124S–127S. PMID 8283301. Zrenner R, Stitt M, Sonnewald U, Boldt R (2006). "Pyrimidine and purine biosynthesis and degradation in plants". Annu Rev Plant Biol 57: 805–36. doi:10.1146/annurev.arplant.57.032905.105421. PMID 16669783. [80] Stasolla C, Katahira R, Thorpe T, Ashihara H (2003). "Purine and pyrimidine nucleotide metabolism in higher plants". J Plant Physiol 160 (11): 1271–95. doi:10.1078/0176-1617-01169. PMID 14658380. [81] Smith J (1995). "Enzymes of nucleotide synthesis". Curr Opin Struct Biol 5 (6): 752–7. doi:10.1016/0959-440X(95)80007-7. PMID 8749362. [82] Testa B, Krämer S (2006). "The biochemistry of drug metabolism—an introduction: part 1. Principles and overview". Chem Biodivers 3 (10): 1053–101. doi:10.1002/cbdv.200690111. PMID 17193224. [83] Danielson P (2002). "The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans". Curr Drug Metab 3 (6): 561–97. doi:10.2174/1389200023337054. PMID 12369887. [84] King C, Rios G, Green M, Tephly T (2000). "UDP-glucuronosyltransferases". Curr Drug Metab 1 (2): 143–61. doi:10.2174/1389200003339171. PMID 11465080. [85] Sheehan D, Meade G, Foley V, Dowd C (November 2001). "Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily" (http:/ / www. biochemj. org/ bj/ 360/ 0001/ bj3600001. htm). Biochem J 360 (Pt 1): 1–16. doi:10.1042/0264-6021:3600001. PMC 1222196. PMID 11695986. . [86] Galvão T, Mohn W, de Lorenzo V (2005). "Exploring the microbial biodegradation and biotransformation gene pool". Trends Biotechnol 23 (10): 497–506. doi:10.1016/j.tibtech.2005.08.002. PMID 16125262. [87] Janssen D, Dinkla I, Poelarends G, Terpstra P (2005). "Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities". Environ Microbiol 7 (12): 1868–82. doi:10.1111/j.1462-2920.2005.00966.x. PMID 16309386. [88] Davies K (1995). "Oxidative stress: the paradox of aerobic life". Biochem Soc Symp 61: 1–31. PMID 8660387. [89] Tu B, Weissman J (2004). "Oxidative protein folding in eukaryotes: mechanisms and consequences" (http:/ / www. jcb. org/ cgi/ content/ full/ 164/ 3/ 341). J Cell Biol 164 (3): 341–6. doi:10.1083/jcb.200311055. PMC 2172237. PMID 14757749. . [90] Sies H (1997). "Oxidative stress: oxidants and antioxidants" (http:/ / ep. physoc. org/ cgi/ reprint/ 82/ 2/ 291. pdf) (PDF). Exp Physiol 82 (2): 291–5. PMID 9129943. . [91] Vertuani S, Angusti A, Manfredini S (2004). "The antioxidants and pro-antioxidants network: an overview". Curr Pharm Des 10 (14): 1677–94. doi:10.2174/1381612043384655. PMID 15134565.

253

Metabolism
[92] von Stockar U, Liu J (1999). "Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth". Biochim Biophys Acta 1412 (3): 191–211. doi:10.1016/S0005-2728(99)00065-1. PMID 10482783. [93] Demirel Y, Sandler S (2002). "Thermodynamics and bioenergetics". Biophys Chem 97 (2–3): 87–111. doi:10.1016/S0301-4622(02)00069-8. PMID 12050002. [94] Albert R (2005). "Scale-free networks in cell biology" (http:/ / jcs. biologists. org/ cgi/ content/ full/ 118/ 21/ 4947). J Cell Sci 118 (Pt 21): 4947–57. doi:10.1242/jcs.02714. PMID 16254242. . [95] Brand M (1997). "Regulation analysis of energy metabolism" (http:/ / jeb. biologists. org/ cgi/ reprint/ 200/ 2/ 193). J Exp Biol 200 (Pt 2): 193–202. PMID 9050227. . [96] Soyer O, Salathé M, Bonhoeffer S (2006). "Signal transduction networks: topology, response and biochemical processes". J Theor Biol 238 (2): 416–25. doi:10.1016/j.jtbi.2005.05.030. PMID 16045939. [97] Salter M, Knowles R, Pogson C (1994). "Metabolic control". Essays Biochem 28: 1–12. PMID 7925313. [98] Westerhoff H, Groen A, Wanders R (1984). "Modern theories of metabolic control and their applications (review)". Biosci Rep 4 (1): 1–22. doi:10.1007/BF01120819. PMID 6365197. [99] Fell D, Thomas S (1995). "Physiological control of metabolic flux: the requirement for multisite modulation". Biochem J 311 (Pt 1): 35–9. PMC 1136115. PMID 7575476. [100] Hendrickson W (2005). "Transduction of biochemical signals across cell membranes". Q Rev Biophys 38 (4): 321–30. doi:10.1017/S0033583506004136. PMID 16600054. [101] Cohen P (2000). "The regulation of protein function by multisite phosphorylation—a 25 year update". Trends Biochem Sci 25 (12): 596–601. doi:10.1016/S0968-0004(00)01712-6. PMID 11116185. [102] Lienhard G, Slot J, James D, Mueckler M (1992). "How cells absorb glucose". Sci Am 266 (1): 86–91. doi:10.1038/scientificamerican0192-86. PMID 1734513. [103] Roach P (2002). "Glycogen and its metabolism". Curr Mol Med 2 (2): 101–20. doi:10.2174/1566524024605761. PMID 11949930. [104] Newgard C, Brady M, O'Doherty R, Saltiel A (2000). "Organizing glucose disposal: emerging roles of the glycogen targeting subunits of protein phosphatase-1" (http:/ / diabetes. diabetesjournals. org/ cgi/ reprint/ 49/ 12/ 1967. pdf) (PDF). Diabetes 49 (12): 1967–77. doi:10.2337/diabetes.49.12.1967. PMID 11117996. . [105] Romano A, Conway T (1996). "Evolution of carbohydrate metabolic pathways". Res Microbiol 147 (6–7): 448–55. doi:10.1016/0923-2508(96)83998-2. PMID 9084754. [106] Koch A (1998). "How did bacteria come to be?". Adv Microb Physiol. Advances in Microbial Physiology 40: 353–99. doi:10.1016/S0065-2911(08)60135-6. ISBN 978-0-12-027740-7. PMID 9889982. [107] Ouzounis C, Kyrpides N (1996). "The emergence of major cellular processes in evolution". FEBS Lett 390 (2): 119–23. doi:10.1016/0014-5793(96)00631-X. PMID 8706840. [108] C.Michael Hogan. 2010. Mutation. ed. E.Monosson and C.J.Cleveland. Encyclopedia of Earth. National Council for Science and the Environment. Washington DC (http:/ / www. eoearth. org/ article/ Mutation?topic=49496) [109] Caetano-Anolles G, Kim HS, Mittenthal JE (2007). "The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture". Proc Natl Acad Sci USA 104 (22): 9358–63. Bibcode 2007PNAS..104.9358C. doi:10.1073/pnas.0701214104. PMC 1890499. PMID 17517598. [110] Schmidt S, Sunyaev S, Bork P, Dandekar T (2003). "Metabolites: a helping hand for pathway evolution?". Trends Biochem Sci 28 (6): 336–41. doi:10.1016/S0968-0004(03)00114-2. PMID 12826406. [111] Light S, Kraulis P (2004). "Network analysis of metabolic enzyme evolution in Escherichia coli". BMC Bioinformatics 5: 15. doi:10.1186/1471-2105-5-15. PMC 394313. PMID 15113413. Alves R, Chaleil R, Sternberg M (2002). "Evolution of enzymes in metabolism: a network perspective". J Mol Biol 320 (4): 751–70. doi:10.1016/S0022-2836(02)00546-6. PMID 12095253. [112] Kim HS, Mittenthal JE, Caetano-Anolles G (2006). "MANET: tracing evolution of protein architecture in metabolic networks". BMC Bioinformatics 7: 351. doi:10.1186/1471-2105-7-351. PMC 1559654. PMID 16854231. [113] Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C (2001). "Small-molecule metabolsim: an enzyme mosaic". Trends Biotechnol 19 (12): 482–6. doi:10.1016/S0167-7799(01)01813-3. PMID 11711174. [114] Spirin V, Gelfand M, Mironov A, Mirny L (June 2006). "A metabolic network in the evolutionary context: Multiscale structure and modularity" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=16731630). Proc Natl Acad Sci USA 103 (23): 8774–9. Bibcode 2006PNAS..103.8774S. doi:10.1073/pnas.0510258103. PMC 1482654. PMID 16731630. . [115] Lawrence J (2005). "Common themes in the genome strategies of pathogens". Curr Opin Genet Dev 15 (6): 584–8. doi:10.1016/j.gde.2005.09.007. PMID 16188434. Wernegreen J (2005). "For better or worse: genomic consequences of intracellular mutualism and parasitism". Curr Opin Genet Dev 15 (6): 572–83. doi:10.1016/j.gde.2005.09.013. PMID 16230003. [116] Pál C, Papp B, Lercher M, Csermely P, Oliver S, Hurst L (2006). "Chance and necessity in the evolution of minimal metabolic networks". Nature 440 (7084): 667–70. Bibcode 2006Natur.440..667P. doi:10.1038/nature04568. PMID 16572170. [117] Rennie M (1999). "An introduction to the use of tracers in nutrition and metabolism". Proc Nutr Soc 58 (4): 935–44. doi:10.1017/S002966519900124X. PMID 10817161. [118] Phair R (1997). "Development of kinetic models in the nonlinear world of molecular cell biology". Metabolism 46 (12): 1489–95. doi:10.1016/S0026-0495(97)90154-2. PMID 9439549. [119] Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de Peer Y (2007). "How many genes are there in plants (... and why are they there)?". Curr Opin Plant Biol 10 (2): 199–203. doi:10.1016/j.pbi.2007.01.004. PMID 17289424.

254

Metabolism
[120] Borodina I, Nielsen J (2005). "From genomes to in silico cells via metabolic networks". Curr Opin Biotechnol 16 (3): 350–5. doi:10.1016/j.copbio.2005.04.008. PMID 15961036. [121] Gianchandani E, Brautigan D, Papin J (2006). "Systems analyses characterize integrated functions of biochemical networks". Trends Biochem Sci 31 (5): 284–91. doi:10.1016/j.tibs.2006.03.007. PMID 16616498. [122] Duarte NC, Becker SA, Jamshidi N, et al. (February 2007). "Global reconstruction of the human metabolic network based on genomic and bibliomic data" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=17267599). Proc. Natl. Acad. Sci. U.S.A. 104 (6): 1777–82. Bibcode 2007PNAS..104.1777D. doi:10.1073/pnas.0610772104. PMC 1794290. PMID 17267599. . [123] Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL (May 2007). "The human disease network". Proc. Natl. Acad. Sci. U.S.A. 104 (21): 8685–90. Bibcode 2007PNAS..104.8685G. doi:10.1073/pnas.0701361104. PMC 1885563. PMID 17502601. [124] Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabási AL (July 2008). "The implications of human metabolic network topology for disease comorbidity" (http:/ / www. pnas. org/ lookup/ pmid?view=long& pmid=18599447). Proc. Natl. Acad. Sci. U.S.A. 105 (29): 9880–9885. Bibcode 2008PNAS..105.9880L. doi:10.1073/pnas.0802208105. PMC 2481357. PMID 18599447. . [125] Csete M, Doyle J (2004). "Bow ties, metabolism and disease". Trends Biotechnol. 22 (9): 446–50. doi:10.1016/j.tibtech.2004.07.007. PMID 15331224. [126] Ma HW, Zeng AP (2003). "The connectivity structure, giant strong component and centrality of metabolic networks". Bioinformatics 19 (11): 1423–30. doi:10.1093/bioinformatics/btg177. PMID 12874056. [127] Zhao J, Yu H, Luo JH, Cao ZW, Li YX (2006). "Hierarchical modularity of nested bow-ties in metabolic networks". BMC Bioinformatics 7: 386. doi:10.1186/1471-2105-7-386. PMC 1560398. PMID 16916470. [128] Thykaer J, Nielsen J (2003). "Metabolic engineering of beta-lactam production". Metab Eng 5 (1): 56–69. doi:10.1016/S1096-7176(03)00003-X. PMID 12749845. González-Pajuelo M, Meynial-Salles I, Mendes F, Andrade J, Vasconcelos I, Soucaille P (2005). "Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol". Metab Eng 7 (5–6): 329–36. doi:10.1016/j.ymben.2005.06.001. PMID 16095939. Krämer M, Bongaerts J, Bovenberg R, Kremer S, Müller U, Orf S, Wubbolts M, Raeven L (2003). "Metabolic engineering for microbial production of shikimic acid". Metab Eng 5 (4): 277–83. doi:10.1016/j.ymben.2003.09.001. PMID 14642355. [129] Koffas M, Roberge C, Lee K, Stephanopoulos G (1999). "Metabolic engineering". Annu Rev Biomed Eng 1: 535–57. doi:10.1146/annurev.bioeng.1.1.535. PMID 11701499. [130] "Metabolism" (http:/ / www. etymonline. com/ index. php?term=metabolism). The Online Etymology Dictionary. . Retrieved 2007-02-20. [131] Eknoyan G (1999). "Santorio Sanctorius (1561–1636) – founding father of metabolic balance studies". Am J Nephrol 19 (2): 226–33. doi:10.1159/000013455. PMID 10213823. [132] Williams, H. S. (1904) A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences (http:/ / etext. lib. virginia. edu/ toc/ modeng/ public/ Wil4Sci. html) Harper and Brothers (New York) Retrieved on 2007-03-26 [133] Dubos J. (1951). "Louis Pasteur: Free Lance of Science, Gollancz. Quoted in Manchester K. L. (1995) Louis Pasteur (1822–1895)—chance and the prepared mind". Trends Biotechnol 13 (12): 511–515. doi:10.1016/S0167-7799(00)89014-9. PMID 8595136. [134] Kinne-Saffran E, Kinne R (1999). "Vitalism and synthesis of urea. From Friedrich Wöhler to Hans A. Krebs". Am J Nephrol 19 (2): 290–4. doi:10.1159/000013463. PMID 10213830. [135] Eduard Buchner's 1907 Nobel lecture (http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1907/ buchner-lecture. html) at http:/ / nobelprize. org Accessed 2007-03-20 [136] Kornberg H (2000). "Krebs and his trinity of cycles". Nat Rev Mol Cell Biol 1 (3): 225–8. doi:10.1038/35043073. PMID 11252898. [137] Krebs HA, Henseleit K (1932). "Untersuchungen über die Harnstoffbildung im tierkorper". Z. Physiol. Chem. 210: 33–66. doi:10.1515/bchm2.1932.210.1-2.33. Krebs H, Johnson W (April 1937). "Metabolism of ketonic acids in animal tissues". Biochem J 31 (4): 645–60. PMC 1266984. PMID 16746382.

255

Further reading
Introductory • Rose, S. and Mileusnic, R., The Chemistry of Life. (Penguin Press Science, 1999), ISBN 0-14-027273-9 • Schneider, E. D. and Sagan, D., Into the Cool: Energy Flow, Thermodynamics, and Life. (University Of Chicago Press, 2005), ISBN 0-226-73936-8 • Lane, N., Oxygen: The Molecule that Made the World. (Oxford University Press, USA, 2004), ISBN 0-19-860783-0 Advanced • Price, N. and Stevens, L., Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. (Oxford University Press, 1999), ISBN 0-19-850229-X • Berg, J. Tymoczko, J. and Stryer, L., Biochemistry. (W. H. Freeman and Company, 2002), ISBN 0-7167-4955-6

Metabolism • Cox, M. and Nelson, D. L., Lehninger Principles of Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-7167-4339-6 • Brock, T. D. Madigan, M. T. Martinko, J. and Parker J., Brock's Biology of Microorganisms. (Benjamin Cummings, 2002), ISBN 0-13-066271-2 • Da Silva, J.J.R.F. and Williams, R. J. P., The Biological Chemistry of the Elements: The Inorganic Chemistry of Life. (Clarendon Press, 1991), ISBN 0-19-855598-9 • Nicholls, D. G. and Ferguson, S. J., Bioenergetics. (Academic Press Inc., 2002), ISBN 0-12-518121-3

256

External links
biochemical families: proteins (amino acids/intermediates) · nucleic acids (constituents/intermediates) · carbohydrates (glycoproteins, alcohols, glycosides) lipids (fatty acids/intermediates, phospholipids, steroids, sphingolipids, eicosanoids) · tetrapyrroles/intermediates

Microbial ecology
Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses.[1] Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine.[2][3] As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5 × 10 30 cells, eight orders of magnitude greater than the number of stars in the observable universe [4][5] ) microbes, by virtue of their biomass alone, constitute the single largest carbon sink.[6] Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling.[7] The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life these processes would likely continue unchanged.[8]

Symbiosis
Microbes, especially bacteria, often engage in symbiotic relationships (either positive or negative) with other organisms, and these relationships affect the ecosystem. One example of these fundamental symbioses are chloroplasts, which allow eukaryotes to conduct photosynthesis. Chloroplasts are considered to be endosymbiotic cyanobacteria, a group of bacteria that are thought to be the origins of aerobic photosynthesis. Some theories state that this invention coincides with a major shift in the early earth's atmosphere, from a reducing atmosphere to an oxygen-rich atmosphere. Some theories go as far as saying that this shift in the balance of gases might have triggered a global ice-age known as the Snowball Earth.

Microbial ecology

257

Roles
They are the backbone of all ecosystems, but even more so in the zones where light cannot approach and thus photosynthesis cannot be the basic means to collect energy. In such zones, chemosynthetic microbes provide energy and carbon to the other organisms. Other microbes are decomposers, with the ability to recycle nutrients from other organisms' waste poducts. These microbes play a vital role in biogeochemical cycles.[6] The nitrogen cycle, the phosphorus cycle and the carbon cycle all depend on microorganisms in one way or another. For example, nitrogen which makes up 78% of the planet's atmosphere is "indigestible" for most organisms, and the flow of nitrogen into the biosphere depends on a microbial process called fixation. Due to the high level of horizontal gene transfer among microbial communities,[9] microbial ecology is also of importance to studies of evolution.[10]

Microbial resource management
Biotechnology may be used alongside microbial ecology to address a number of environmental and economic challenges. For example, molecular techniques such as community fingerprinting can be used to track changes in microbial communities over time or assess their biodiversity. Managing the carbon cycle to sequester carbon dioxide and prevent excess methanogenesis is important in mitigating global warming, and the prospects of bioenergy are being expanded by the development of microbial fuel cells. Microbial resource management advocates a more progressive attitude towards disease, whereby biological control agents are favoured over attempts at eradication. Fluxes in microbial communities has to be better characterized for this field's potential to be realised.[11] In addition, there are also clinical implications, as marine microbial symbioses are a valuable source of existing and novel antimicrobial agents, and thus offer another line of inquiry in the evolutionary arms race of antibiotic resistance, a pressing concern for researchers.[12]

References
[1] Ogilvie, LA; Hirsch, PR (editor) (2012). Microbial Ecological Theory: Current Perspectives. Caister Academic Press. ISBN 978-1-908230-09-6. [2] Bowler, C.; D. M Karl, R. R Colwell (2009). "Microbial oceanography in a sea of opportunity". Nature 458 (7244): 180–184.(subscription

required)
[3] Konopka, Allan (2009-11). "What is microbial community ecology?" (http:/ / www. ncbi. nlm. nih. gov/ pubmed/ 19657372). The ISME Journal 3 (11): 1223–1230. doi:10.1038/ismej.2009.88. ISSN 1751-7370. PMID 19657372. . Retrieved 2011-02-27. [4] Whitman, W B; D C Coleman, W J Wiebe (1998-06-09). "Prokaryotes: the unseen majority". Proceedings of the National Academy of Sciences of the United States of America 95 (12): 6578–6583. doi:10.1073/pnas.95.12.6578. ISSN 0027-8424. PMC 33863. PMID 9618454. [5] "number of stars in the observable universe - Wolfram" (http:/ / www. wolframalpha. com/ input/ ?i=number+ of+ stars+ in+ the+ observable+ universe). . Retrieved 2011-11-22. [6] Fenchel, Tom (1998). Bacterial biogeochemistry : the ecophysiology of mineral cycling (2nd ed. ed.). San Diego: Academic Press. [7] DeLong, Edward F. (2009-05). "The microbial ocean from genomes to biomes". Nature 459 (7244): 200–206. doi:10.1038/nature08059. ISSN 0028-0836. PMID 19444206.(subscription required) [8] Lupp, Claudia (2009-05). "Microbial oceanography". Nature 459 (7244): 179. doi:10.1038/459179a.(subscription required) [9] McDaniel, Lauren D.; Elizabeth Young, Jennifer Delaney, Fabian Ruhnau, Kim B. Ritchie, John H. Paul (2010-10-01). "High Frequency of Horizontal Gene Transfer in the Oceans". Science 330 (6000): 50. doi:10.1126/science.1192243.(subscription required) [10] Smets, B. F; T. Barkay (2005). "Horizontal gene transfer: perspectives at a crossroads of scientific disciplines". Nature Reviews Microbiology 3 (9): 675–678.(subscription required) [11] W. Verstraete (May 2007). "Microbial ecology and environmental biotechnology". The ISME Journal 1 (1): 4–8. doi:10.1038/ismej.2007.7. PMID 18043608.(subscription required) [12] Ott, J. (2005). "Marine Microbial Thiotrophic Ectosymbioses". Oceanography and marine biology. 42: 95–118.

Microbial ecology

258

External links
• International Society for Microbial Biology (http://www.microbes.org/) • DeLong, Edward F. (2007-05-28). "Microbial Communities in Nature and Laboratory - Interview". Journal of Visualized Experiments : JoVE (4). doi:10.3791/202. ISSN 1940-087X.

Microbial genetics
Microbial genetics is a subject area within microbiology and genetic engineering. It studies the genetics of very small (micro) organisms. This involves the study of the genotype of microbial species and also the expression system in the form of phenotypes.It also involves the study of genetic processes taking place in these micro organisms i.e., recombination etc.

Microbiology
Microbiology (from Greek μῑκρος, mīkros, "small"; βίος, bios, "life"; and -λογία, -logia) is the study of microscopic organisms, which are defined as any living organism that is either a single cell (unicellular), a cell cluster, or has no cells at all (acellular).[1] This includes eukaryotes, such as fungi and protists, and prokaryotes. Viruses[2] and prions, though not strictly classed as living organisms, are also studied. Microbiology typically includes the study of the immune system, or immunology. Generally, immune systems interact with pathogenic microbes; these two disciplines often intersect which is why many colleges offer a paired degree such as "Microbiology and Immunology".

An agar plate streaked with microorganisms

Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology, immunology and other branches. A microbiologist is a specialist in microbiology and these related topics. Microbiological procedures usually must be aseptic, and use a variety of tools such as light microscopes with a combination of stains and dyes.The most commonly used stains are called basic dyes, and are composed of positively charged molecules. Two types of basic dyes are simple stains and differential stains. Simple stains consist of one dye and identify the shape and multicell arrangement of bacteria. Methylene blue, carbolfuchsin, safranin, and crystal violet are some of the most commonly used stains. Differential stains on the other hand, use two or more dyes and help us to distinguish between two or more organisms or two or different parts of the organism. Types of differential stains are gram, Ziehl-Neelsen acid fast, negative, flagella, and endospore. Specific constraints apply to particular fields of microbiology, such as parasitology, which heavily utilizes the light microscopy, whereas microscopy's utility in bacteriology is limited due to the similarity is many cells physiology. Indeed, most means of differentiating bacteria is based on growth or biochemical reactions. Virology has very little need for light microscopes, relying on almost entirely molecular means. Mycology relies on all technologies the most evenly, from macroscopy to molecular techniques. Microbiology is actively researched, and the field is advancing continuously. It is estimated that only about one percent of the microorganisms present in a given environmental sample are culturable[3] and the number of bacterial cells and species on Earth is still not possible to be determined, recent estimates indicate that it can be extremely high (5 Exp 30 cells on Earth, unknown number of species). Although microbes were directly observed over three hundred years ago, the precise determination, quantitation and description of its functions is far to be complete,

Microbiology given the overwhelming diversity detected by genetic and culture-independent means.

259

History
Ancient
The existence of microorganisms was hypothesized for many centuries before their actual discovery. The existence of unseen microbiological life was postulated by Jainism which is based on Mahavira’s teachings as early as 6th century BCE.[4] Paul Dundas notes that Mahavira asserted existence of unseen microbiological creatures living in earth, water, air and fire.[5] Jain scriptures also describe nigodas which are sub-microscopic creatures living in large clusters and having a very short life and are said to pervade each and every part of the universe, even in tissues of plants and flesh of animals.[6] The Roman Marcus Terentius Varro made references to microbes when he warned against locating a homestead in the vicinity of swamps "because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there by cause serious diseases."[7] In 1546 Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission.[8] However, early claims about the existence of microorganisms were speculative, and not based on microscopic observation. Actual observation and discovery of microbes had to await the invention of the microscope in the 17th century.

Modern
In 1676, Anton van Leeuwenhoek observed bacteria and other microorganisms, using a single-lens microscope of his own design.[1] While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the fruiting bodies of molds, in 1665.[9] The first observation of microbes using a microscope is generally credited to the Dutch draper and haberdasher, Antonie van Leeuwenhoek, who lived for most of his life in Delft, Holland. It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe micro-organisms.[10] He was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses.[10] One of his books contains a chapter in Latin, which reads in translation – ‘Concerning the wonderful structure of things in nature, Anton van Leeuwenhoek, is considered to be the investigated by Microscope. Here, he wrote ‘who would believe that first to observe microorganisms using a vinegar and milk abound with an innumerable multitude of worms.’ He microscope. also noted that putrid material is full of innumerable creeping animalcule. These observations antedate Robert Hooke’s Micrographia by nearly 20 years and were published some 29 years before van Leeuwenhoek saw protozoa and 37 years before he described having seen bacteria.[10]

Microbiology

260

The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria and discover spores.[11] Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are often considered to be the father of microbiology[10] and medical microbiology, respectively.[12] Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology’s identity as a biological science.[13] Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies.[1] Koch is best known for his contributions to the germ theory of disease, Innovative laboratory glassware and experimental proving that specific diseases were caused by specific pathogenic methods developed by Louis Pasteur and other biologists contributed to the young field of micro-organisms. He developed a series of criteria that have become bacteriology in the late 19th century. known as the Koch's postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis.[1] While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on micro-organisms having direct medical relevance. It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky, the founders of general microbiology (an older term encompassing aspects of microbial physiology, diversity and ecology), that the true breadth of microbiology was revealed.[1] Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques.[14] While his work on the Tobacco Mosaic Virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by micro-organisms in geochemical processes.[15] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.[1]

Branches
The branches of microbiology can be classified into pure and applied sciences.[16] Microbiology can be also classified based on taxonomy, in the cases of bacteriology, mycology, protozoology, and phycology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines.

Pure microbiology
Taxonomic arrangement • • • • Bacteriology: The study of bacteria. Mycology: The study of fungi. Protozoology: The study of protozoa. Phycology (or algology): The study of algae.

• Parasitology: The study of parasites. • Immunology: The study of the immune system. • Virology: The study of the viruses.

Microbiology • Nematology:The study of the nematodes Integrative arrangement • Microbial cytology: The study of microscopic and submicroscopic details of microorganisms. • Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure. • Microbial ecology: The relationship between microorganisms and their environment. • Microbial genetics: The study of how genes are organized and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology. • Cellular microbiology: A discipline bridging microbiology and cell biology. • Evolutionary microbiology: The study of the evolution of microbes. This field can be subdivided into: • Microbial taxonomy: The naming and classification of microorganisms. • Microbial systematics: The study of the diversity and genetic relationship of microorganisms. • Generation microbiology: The study of those microorganisms that have the same characters as their parents. • Systems microbiology: A discipline bridging systems biology and microbiology. • Molecular microbiology: The study of the molecular principles of the physiological processes in microorganisms. Other • Nano microbiology: The study of those microorganisms on nano level. • Exo microbiology (or Astro microbiology): The study of microorganisms in outer space. • Weapon microbiology: The study of those microorganisms which are using in weapon industries.

261

Applied microbiology
• Medical microbiology: The study of the pathogenic microbes and the role of microbes in human illness. Includes the study of microbial pathogenesis and epidemiology and is related to the study of disease pathology and immunology. • Pharmaceutical microbiology: The study of microorganisms that are related to the production of antibiotics, enzymes, vitamins,vaccines, and other pharmaceutical products and that cause pharmaceutical contamination and spoil. • Industrial microbiology: The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and wastewater treatment. Closely linked to the biotechnology industry. This field also includes brewing, an important application of microbiology. • Microbial biotechnology: The manipulation of microorganisms at the genetic and molecular level to generate useful products. • Food microbiology and Dairy microbiology: The study of microorganisms causing food spoilage and foodborne illness. Using microorganisms to produce foods, for example by fermentation. • Agricultural microbiology: The study of agriculturally relevant microorganisms. This field can be further classified into the following: • Plant microbiology and Plant pathology: The study of the interactions between microorganisms and plants and plant pathogens. • Soil microbiology: The study of those microorganisms that are found in soil. • Veterinary microbiology: The study of the role in microbes in veterinary medicine or animal taxonomy. • Environmental microbiology: The study of the function and diversity of microbes in their natural environments. This involves the characterization of key bacterial habitats such as the rhizosphere and phyllosphere, soil and groundwater ecosystems, open oceans or extreme environments (extremophiles). This field includes other branches of microbiology such as:

Microbiology • Microbial ecology • Microbially-mediated nutrient cycling • Geomicrobiology • Microbial diversity • Bioremediation • Water microbiology (or Aquatic microbiology): The study of those microorganisms that are found in water. • Aeromicrobiology (or Air microbiology): The study of airborne microorganisms. • Epidemiology: The study of the incidence, spread, and control of disease.

262

Benefits
Whilst there are undoubtedly some who fear all microbes due to the association of some microbes with various human illnesses, many microbes are also responsible for numerous beneficial processes such as industrial fermentation (e.g. the production of alcohol, vinegar and dairy products), antibiotic production and as vehicles for cloning in more complex organisms such as plants. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system.

Fermenting tanks with yeast being used to brew beer

Bacteria can be used for the industrial production of amino acids. Corynebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.[17] A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. Microorganisms are used for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery. Microorganisms are used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides and polysaccharide, and polyhydroxyalkanoates.[18] Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species and strains, each specific to the biodegradation of one or more types of contaminants.[19] There are also various claims concerning the contributions to human and animal health by consuming probiotics (bacteria potentially beneficial to the digestive system) and/or prebiotics (substances consumed to promote the growth of probiotic microorganisms).[20] Recent research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors. Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins has been demonstrated in a variety of preclinical models.[21]

Microbiology

263

References
[1] Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (13th ed.). Pearson Education. p. 1096. ISBN 0-321-73551-X. [2] Rice G (2007-03-27). "Are Viruses Alive?" (http:/ / serc. carleton. edu/ microbelife/ yellowstone/ viruslive. html). . Retrieved 2007-07-23. [3] Nitesh RAI, Ludwig W, Schleifer KH (2011). "Phylogenetic identification and in situ detection of individual microbial cells without cultivation". Microbiology Rev. 59 (1): 143–169. PMC 239358. PMID 7535888. [4] Mahavira is dated 599 BC - 527 BC. See. Dundas, Paul; John Hinnels ed. (2002). The Jain. London: Routledge. ISBN 0-415-26606-8. p. 24 [5] Dundas, Paul (2002) p. 88 [6] *Jaini, Padmanabh (1998). The Jaina Path of Purification. New Delhi: Motilal Banarsidass. ISBN 81-208-1578-5. p. 109 [7] Varro on Agriculture 1, xii Loeb. [8] Fracastoro, Girolamo (1546), De Contagione et Contagiosis Morbis transl. Wilmer Cave Wright (1930). New York: G.P. Putnam's [9] Gest H (2005). "The remarkable vision of Robert Hooke (1635-1703): first observer of the microbial world". Perspect. Biol. Med. 48 (2): 266–72. doi:10.1353/pbm.2005.0053. PMID 15834198. [10] Wainwright, Milton (2003). An Alternative View of the Early History of Microbiology. "Advances in Applied Microbiology Volume 52". Advances in applied microbiology. Advances in Applied Microbiology 52: 333–55. doi:10.1016/S0065-2164(03)01013-X. ISBN 978-0-12-002654-8. PMID 12964250. [11] Drews G (1999). "Ferdinand Cohn, among the Founder of Microbiology". ASM News 65 (8): 547. [12] Ryan KJ, Ray CG (editors) (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. ISBN 0-8385-8529-9. [13] Bordenave G (2003). "Louis Pasteur (1822-1895)". Microbes Infect. 5 (6): 553–60. doi:10.1016/S1286-4579(03)00075-3. PMID 12758285. [14] Johnson J (2001) [1998]. "Martinus Willem Beijerinck" (http:/ / www. apsnet. org/ Education/ feature/ TMV/ intro. html). APSnet. American Phytopathological Society. . Retrieved May 2, 2010. [15] Paustian T, Roberts G (2009). "Beijerinck and Winogradsky Initiate the Field of Environmental Microbiology" (http:/ / www. microbiologytext. com/ index. php?module=Book& func=displayarticle& art_id=32). Through the Microscope: A Look at All Things Small (3rd ed.). Textbook Consortia. § 1–14. . Retrieved May 2, 2010. [16] Pharmaceutical Microbiology Principles and Applications (http:/ / books. google. com/ books?id=VN9Oj2MKTkQC& pg=SA1-PA1). Nirali Prakashan. pp. 1.1–1.2. ISBN 978-81-85790-61-9. . Retrieved 18 June 2011. [17] Burkovski A (editor). (2008). Corynebacteria: Genomics and Molecular Biology (http:/ / www. horizonpress. com/ cory). Caister Academic Press. . . [18] Rehm BHA (editor). (2008). Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives (http:/ / www. horizonpress. com/ biopolymers). Caister Academic Press. . . [19] Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (http:/ / www. horizonpress. com/ biod) (1st ed.). Caister Academic Press. . . [20] Tannock GW (editor). (2005). Probiotics and Prebiotics: Scientific Aspects (http:/ / www. horizonpress. com/ pro3). Caister Academic Press. . . [21] Mengesha et al. (2009). "Clostridia in Anti-tumor Therapy". Clostridia: Molecular Biology in the Post-genomic Era. Caister Academic Press. ISBN 978-1-904455-38-7.

External links
• Microbiology (http://www.bbc.co.uk/programmes/b007753d) on In Our Time at the BBC. ( listen now (http:/ /www.bbc.co.uk/iplayer/console/b007753d/In_Our_Time_Microbiology)) • Bacteriology Made Easy | Medchrome (http://medchrome.com/basic-science/microbiology/bacteriology-easy/ ) • Online lectures in microbiology (http://media.med.sc.edu/microbiology2007/) University of South Carolina • Microbiology Online (http://www.ocean.edu/academics/programs_of_study/science/MicrobiologyOnline. htm) • Online Microbiology textbook (http://www.microbiologytext.com/index.php?module=Book&func=toc& book_id=4) • Online Medical Microbiology textbook (http://www.microbiologybook.org/) • Institute of Microbiology of the Swiss Federal Institute of Technology (http://www.micro.biol.ethz.ch/) • Annual Review of Microbiology (http://arjournals.annualreviews.org/loi/micro/)

Mitochondrion

264

Mitochondrion
In cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle found in most eukaryotic cells.[1] These organelles range from 0.5 to 1.0 micrometer (μm) in diameter. Mitochondria are sometimes described as "cellular power plants" because they generate most of the cell's supply of adenosine triphosphate (ATP), used as a source of chemical energy.[2] In addition to supplying cellular energy, mitochondria are involved in a range of other processes, such as signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth.[3] Mitochondria have been implicated in several human diseases, including mitochondrial disorders[4] and cardiac dysfunction,[5] and may play a role in the aging process. The word mitochondrion comes from the Greek μίτος mitos, thread, + χονδρίον chondrion, granule.

Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy

Several characteristics make mitochondria unique. The number of mitochondria in a cell varies widely by Schematic of typical animal cell, showing subcellular components. Organelles: (1) organism and tissue type. Many cells Nucleolus (2) Nucleus (3) Ribosomes (little dots) (4) Vesicle (5) Rough endoplasmic have only a single mitochondrion, reticulum (ER) (6) Golgi apparatus (7) Cytoskeleton (8) Smooth ER (9) Mitochondria (10) Vacuole (11) Cytosol (12) Lysosome (13) Centrioles within Centrosome whereas others can contain several [6][7] thousand mitochondria. The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix. Mitochondrial proteins vary depending on the tissue and the species. In humans, 615 distinct types of proteins have been identified from cardiac mitochondria,[8] whereas in Murinae (rats), 940 proteins encoded by distinct genes have been reported.[9] The mitochondrial proteome is thought to be dynamically regulated.[10] Although most of a cell's DNA is contained in the cell nucleus, the mitochondrion has its own independent genome. Further, its DNA shows substantial similarity to bacterial genomes.[11]

History
The first observations of intracellular structures that probably represent mitochondria were published in the 1840s.[12] Richard Altmann, in 1894, established them as cell organelles and called them 'bioblasts'.[12] The term 'mitochondria' itself was coined by Carl Benda in 1898.[12] Friedrich Meves, in 1904, made the first recorded

Mitochondrion observation of mitochondria in plants (Nymphea).[12] B. F. Kingsbury, in 1912, first related them with cell respiration, but almost exclusively based on morphological observations.[12] Philip Siekevitz, in 1957, dubbed them 'the powerhouse of the cell'.[13]

265

Structure
A mitochondrion contains outer and inner membranes composed of phospholipid bilayers and proteins.[6] The two membranes, however, have different properties. Because of this double-membraned organization, there are five distinct compartments within the mitochondrion. They are: 1. the outer mitochondrial membrane, 2. the intermembrane space (the space between the outer and inner membranes), 3. the inner mitochondrial membrane, 4. the cristae space (formed by infoldings of the inner membrane), and 5. the matrix (space within the inner membrane).

Outer membrane
The outer mitochondrial membrane, which encloses the entire organelle, has a protein-to-phospholipid ratio similar to that of the eukaryotic plasma membrane (about 1:1 by weight). It contains large numbers of integral proteins called porins. These porins form channels that allow molecules 5000 Daltons or less in molecular weight to freely diffuse from one side of the membrane to the other.[6] Larger proteins can enter the mitochondrion if a signaling sequence at their N-terminus binds to a large multisubunit protein called translocase of the outer membrane, which then actively moves them across the membrane.[14] Disruption of the outer membrane permits proteins in the intermembrane space to leak into the cytosol, leading to certain cell death.[15] The mitochondrial outer membrane can associate with the endoplasmic reticulum (ER) membrane, in a structure called MAM (mitochondria-associated ER-membrane). This is important in the ER-mitochondria calcium signaling and involved in the transfer of lipids between the ER and mitochondria.[16]

Intermembrane space
The intermembrane space is the space between the outer membrane and the inner membrane. Because the outer membrane is freely permeable to small molecules, the concentrations of small molecules such as ions and sugars in the intermembrane space is the same as the cytosol.[6] However, large proteins must have a specific signaling sequence to be transported across the outer membrane, so the protein composition of this space is different from the protein composition of the cytosol. One protein that is localized to the intermembrane space in this way is cytochrome c.[15]

Mitochondrion

266

Inner membrane
The inner mitochondrial membrane contains proteins with five types of functions:[6] 1. 2. 3. 4. 5. Those that perform the redox reactions of oxidative phosphorylation ATP synthase, which generates ATP in the matrix Specific transport proteins that regulate metabolite passage into and out of the matrix Protein import machinery. Mitochondria fusion and fission protein

It contains more than 151 different polypeptides, and has a very high protein-to-phospholipid ratio (more than 3:1 by weight, which is about 1 protein for 15 phospholipids). The inner membrane is home to around 1/5 of the total protein in a mitochondrion.[6] In addition, the inner membrane is rich in an unusual phospholipid, cardiolipin. This phospholipid was originally discovered in cow hearts in 1942, and is usually characteristic of mitochondrial and bacterial plasma membranes.[17] Cardiolipin contains four fatty acids rather than two, and may help to make the inner membrane impermeable.[6] Unlike the outer membrane, the inner membrane doesn't contain porins, and is highly impermeable to all molecules. Almost all ions and molecules require special membrane transporters to enter or exit the matrix. Proteins are ferried into the matrix via the translocase of the inner membrane (TIM) complex or via Oxa1.[14] In addition, there is a membrane potential across the inner membrane, formed by the action of the enzymes of the electron transport chain. Cristae The inner mitochondrial membrane is compartmentalized into numerous cristae, which expand the surface area of the inner mitochondrial membrane, enhancing its ability to produce ATP. For typical liver mitochondria, the area of the inner membrane is about five times as great as the outer membrane. This ratio is variable and mitochondria from cells that have a greater demand for ATP, such as muscle cells, contain even more cristae. These folds are studded with small round bodies known as F1 particles or oxysomes. These are not simple random folds but rather invaginations of the inner membrane, which can affect overall chemiosmotic function.[18]

Cross-sectional image of cristae in rat liver mitochondrion to demonstrate the likely 3D structure and relationship to the inner membrane.

One recent mathematical modeling study has suggested that the optical properties of the cristae in filamentous mitochondria may affect the generation and propagation of light within the tissue.[19]

Matrix
The matrix is the space enclosed by the inner membrane. It contains about 2/3 of the total protein in a mitochondrion.[6] The matrix is important in the production of ATP with the aid of the ATP synthase contained in the inner membrane. The matrix contains a highly-concentrated mixture of hundreds of enzymes, special mitochondrial ribosomes, tRNA, and several copies of the mitochondrial DNA genome. Of the enzymes, the major functions include oxidation of pyruvate and fatty acids, and the citric acid cycle.[6] Mitochondria have their own genetic material, and the machinery to manufacture their own RNAs and proteins (see: protein biosynthesis). A published human mitochondrial DNA sequence revealed 16,569 base pairs encoding 37 total genes: 22 tRNA, 2 rRNA, and 13 peptide genes.[20] The 13 mitochondrial peptides in humans are integrated into the

Mitochondrion inner mitochondrial membrane, along with proteins encoded by genes that reside in the host cell's nucleus.

267

Mitochondria-associated ER membrane (MAM)
The mitochondria-associated ER membrane (MAM) is another structural element that is increasingly recognized for its critical role in cellular physiology and homeostasis. Once considered a technical snag in cell fractionation techniques, the alleged ER vesicle contaminants that invariably appeared in the mitochondrial fraction have been re-identified as membranous structures derived from the MAM—the interface between mitochondria and the ER.[21] Physical coupling between these two organelles had previously been observed in electron micrographs and has more recently been probed with fluorescence microscopy.[21] Such studies estimate that at the MAM, which may comprise up to 20% of the mitochondrial outer membrane, the ER and mitochondria are separated by a mere 10-25 nm and held together by protein tethering complexes.[21][22][23] Purified MAM from subcellular fractionation has shown to be enriched in enzymes involved in phospholipid exchange, in addition to channels associated with Ca2+ signaling.[21][23] These hints of a prominent role for the MAM in the regulation of cellular lipid stores and signal transduction have been borne out, with significant implications for mitochondrial-associated cellular phenomena, as discussed below. Not only has the MAM provided insight into the mechanistic basis underlying such physiological processes as intrinsic apoptosis and the propagation of calcium signaling, but it also favors a more refined view of the mitochondria. Though often seen as static, isolated ‘powerhouses’ hijacked for cellular metabolism through an ancient endosymbiotic event, the evolution of the MAM underscores the extent to which mitochondria have been integrated into overall cellular physiology, with intimate physical and functional coupling to the endomembrane system. Phospholipid transfer The MAM is enriched in enzymes involved in lipid biosynthesis, such as phosphatidylserine synthase on the ER face and phosphatidylserine decarboxylase on the mitochondrial face.[24][25] Because mitochondria are dynamic organelles constantly undergoing fission and fusion events, they require a constant and well-regulated supply of phospholipids for membrane integrity.[26][27] But mitochondria are not only a destination for the phospholipids they finish synthesis of; rather, this organelle also plays a role in inter-organelle trafficking of the intermediates and products of phospholipid biosynthetic pathways, ceramide and cholesterol metabolism, and glycosphingolipid anabolism.[25][27] Such trafficking capacity depends on the MAM, which has been shown to facilitate transfer of lipid intermediates between organelles.[24] In contrast to the standard vesicular mechanism of lipid transfer, evidence indicates that the physical proximity of the ER and mitochondrial membranes at the MAM allows for lipid flipping between opposed bilayers.[27] Despite this unusual and seemingly energetically unfavorable mechanism, such transport does not require ATP.[27] Instead, it has been shown to be dependent on a multiprotein tethering structure termed the ER-mitochondria encounter structure, or ERMES, although it remains unclear whether this structure directly mediates lipid transfer or is required to keep the membranes in sufficiently close proximity to lower the energy barrier for lipid flipping.[27][28] The MAM may also be part of the secretory pathway, in addition to its role in intracellular lipid trafficking. In particular, the MAM appears to be an intermediate destination between the rough ER and the Golgi in the pathway that leads to very-low-density lipoprotein, or VLDL, assembly and secretion.[25][29] The MAM thus serves as a critical metabolic and trafficking hub in lipid metabolism.

Mitochondrion Calcium signaling A critical role for the ER in calcium signaling was acknowledged before such a role for the mitochondria was widely accepted, in part because the low affinity of Ca2+ channels localized to the outer mitochondrial membrane seemed to fly in the face of this organelle’s purported responsiveness to changes in intracellular Ca2+ flux.[21] But the presence of the MAM resolves this apparent contradiction: the close physical association between the two organelles results in Ca2+ microdomains at contact points that facilitate efficient Ca2+ transmission from the ER to the mitochondria.[21] Transmission occurs in response to so-called “Ca2+ puffs” generated by spontaneous clustering and activation of IP3R, a canonical ER membrane Ca2+ channel.[21][22] The fate of these puffs—in particular, whether they remain restricted to isolated locales or integrated into Ca2+ waves for propagation throughout the cell—is determined in large part by MAM dynamics. Although reuptake of Ca2+ by the ER (concomitant with its release) modulates the intensity of the puffs, thus insulating mitochondria to a certain degree from high Ca2+ exposure, the MAM often serves as a firewall that essentially buffers Ca2+ puffs by acting as a sink into which free ions released into the cytosol can be funneled.[21][30][31] This Ca2+ tunneling occurs through the low-affinity Ca2+ receptor VDAC1, which recently has been shown to be physically tethered to the IP3R clusters on the ER membrane and enriched at the MAM.[21][22][32] The ability of mitochondria to serve as a Ca2+ sink is a result of the electrochemical gradient generated during oxidative phosphorylation, which makes tunneling of the cation an exergonic process.[32] But transmission of Ca2+ is not unidirectional; rather, it is a two-way street. The properties of the Ca2+ pump SERCA and the channel IP3R present on the ER membrane facilitate feedback regulation coordinated by MAM function. In particular, clearance of Ca2+ by the MAM allows for spatio-temporal patterning of Ca2+ signaling because Ca2+ alters IP3R activity in a biphasic manner.[21] SERCA is likewise affected by mitochondrial feedback: uptake of Ca2+ by the MAM stimulates ATP production, thus providing energy that enables SERCA to reload the ER with Ca2+ for continued Ca2+ efflux at the MAM.[30][32] Thus, the MAM is not a passive buffer for Ca2+ puffs; rather it helps modulate further Ca2+ signaling through feedback loops that affect ER dynamics. Regulating ER release of Ca2+ at the MAM is especially critical because only a certain window of Ca2+ uptake sustains the mitochondria, and consequently the cell, at homeostasis. Sufficient intraorganelle Ca2+ signaling is required to stimulate metabolism by activating dehydrogenase enzymes critical to flux through the citric acid cycle.[33] However, once Ca2+ signaling in the mitochondria passes a certain threshold, it stimulates the intrinsic pathway of apoptosis in part by collapsing the mitochondrial membrane potential required for metabolism.[21] Studies examining the role of pro- and anti-apoptotic factors support this model; for example, the anti-apoptotic factor Bcl-2 has been shown to interact with IP3Rs to reduce Ca2+ filling of the ER, leading to reduced efflux at the MAM and preventing collapse of the mitochondrial membrane potential post-apoptotic stimuli.[21] Given the need for such fine regulation of Ca2+ signaling, it is perhaps unsurprising that dysregulated mitochondrial Ca2+ has been implicated in several neurodegenerative diseases, while the catalogue of tumor suppressors includes a few that are enriched at the MAM.[32] Molecular basis for tethering Recently advances in the identification of the tethers between the mitochondrial and ER membranes suggest that the scaffolding function of the molecular elements involved is secondary to other, non-structural functions. ERMES, a multiprotein complex of interacting ER- and mitochondrial-resident membrane proteins, is required for lipid transfer at the MAM and exemplifies this principle. One of its components, for example, is also a constituent of the protein complex required for insertion of transmembrane beta-barrel proteins into the lipid bilayer.[27] Other proteins implicated in scaffolding likewise have functions independent of structural tethering at the MAM; for example, ER-resident and mitochondrial-resident mitofusins form heterocomplexes that regulate the number of inter-organelle contact sites, although mitofusins were first identified for their role in fission and fusion events between individual mitochondria.[21] Glucose-related protein 75 (grp75) is another dual-function protein. In addition to the matrix pool

268

Mitochondrion of grp75, a portion serves as a chaperone that physically links the mitochondrial and ER Ca2+ channels VDAC and IP3R for efficient Ca2+ transmission at the MAM.[21][22] Another prominent tether is Sigma-1R, another chaperone whose stabilization of ER-resident IP3R has been proposed to preserve communication at the MAM during the metabolic stress response.[21][32] Perspective The MAM is a critical signaling, metabolic, and trafficking hub in the cell that allows for the integration of ER and mitochondrial physiology. Coupling between these organelles is not simply structural but functional as well and critical for overall cellular physiology and homeostasis. The MAM thus offers a perspective on mitochondria that diverges from the traditional view of this organelle as a static, isolated unit appropriated for its metabolic capacity by the cell. Instead, this mitochondrial-ER interface emphasizes the integration of the mitochondria, the product of an endosymbiotic event, into diverse cellular processes.
Model of the multimeric tethering complex, ERMES.

269

Organization and distribution
Mitochondria are found in nearly all eukaryotes. They vary in number and location according to cell type. A single mitochondrion is often found in unicellular organisms. Conversely, numerous mitochondria are found in human liver cells, with about 1000–2000 mitochondria per cell, making up 1/5 of the cell volume.[6] The mitochondrial content of otherwise similar cells can vary substantially in size and membrane potential,[34] with differences arising from sources including uneven partitioning at cell divisions, leading to extrinsic differences in ATP levels and downstream cellular processes.[35] The mitochondria can be found nestled between myofibrils of muscle or wrapped around the sperm flagellum.[6] Often they form a complex 3D branching network inside the cell with the cytoskeleton. The association with the cytoskeleton determines mitochondrial shape, which can affect the function as well.[36] Recent evidence suggests that vimentin, one of the components of the cytoskeleton, is critical to the association with the cytoskeleton.[37]

Function
The most prominent roles of mitochondria are to produce the energy currency of the cell, ATP (i.e., phosphorylation of ADP), through respiration, and to regulate cellular metabolism.[7] The central set of reactions involved in ATP production are collectively known as the citric acid cycle, or the Krebs Cycle. However, the mitochondrion has many other functions in addition to the production of ATP.

Energy conversion
A dominant role for the mitochondria is the production of ATP, as reflected by the large number of proteins in the inner membrane for this task. This is done by oxidizing the major products of glucose, pyruvate, and NADH, which are produced in the cytosol.[7] This process of cellular respiration, also known as aerobic respiration, is dependent on the presence of oxygen. When oxygen is limited, the glycolytic products will be metabolized by anaerobic fermentation, a process that is independent of the mitochondria.[7] The production of ATP from glucose has an approximately 13-times higher yield during aerobic respiration compared to fermentation.[38] Recently it has been

Mitochondrion shown that plant mitochondria can produce a limited amount of ATP without oxygen by using the alternate substrate nitrite.[39] Pyruvate and the citric acid cycle Each pyruvate molecule produced by glycolysis is actively transported across the inner mitochondrial membrane, and into the matrix where it is oxidized and combined with coenzyme A to form CO2, acetyl-CoA, and NADH.[7] The acetyl-CoA is the primary substrate to enter the citric acid cycle, also known as the tricarboxylic acid (TCA) cycle or Krebs cycle. The enzymes of the citric acid cycle are located in the mitochondrial matrix, with the exception of succinate dehydrogenase, which is bound to the inner mitochondrial membrane as part of Complex II.[40] The citric acid cycle oxidizes the acetyl-CoA to carbon dioxide, and, in the process, produces reduced cofactors (three molecules of NADH and one molecule of FADH2) that are a source of electrons for the electron transport chain, and a molecule of GTP (that is readily converted to an ATP).[7] NADH and FADH2: the electron transport chain The redox energy from NADH and FADH2 is transferred to oxygen (O2) in several steps via the electron transport chain. These energy-rich molecules are produced within the matrix via the citric acid cycle but are also produced in the cytoplasm by glycolysis. Reducing equivalents from the cytoplasm can be imported via the malate-aspartate shuttle system of antiporter proteins or feed into the electron transport chain using a glycerol phosphate shuttle.[7] Diagram of the electron transport chain in the mitonchondrial intermembrane space Protein complexes in the inner membrane (NADH dehydrogenase, cytochrome c reductase, and cytochrome c oxidase) perform the transfer and the incremental release of energy is used to pump protons (H+) into the intermembrane space. This process is efficient, but a small percentage of electrons may prematurely reduce oxygen, forming reactive oxygen species such as superoxide.[7] This can cause oxidative stress in the mitochondria and may contribute to the decline in mitochondrial function associated with the aging process.[41] As the proton concentration increases in the intermembrane space, a strong electrochemical gradient is established across the inner membrane. The protons can return to the matrix through the ATP synthase complex, and their potential energy is used to synthesize ATP from ADP and inorganic phosphate (Pi).[7] This process is called chemiosmosis, and was first described by Peter Mitchell[42][43] who was awarded the 1978 Nobel Prize in Chemistry for his work. Later, part of the 1997 Nobel Prize in Chemistry was awarded to Paul D. Boyer and John E. Walker for their clarification of the working mechanism of ATP synthase.[44] Heat production Under certain conditions, protons can re-enter the mitochondrial matrix without contributing to ATP synthesis. This process is known as proton leak or mitochondrial uncoupling and is due to the facilitated diffusion of protons into the matrix. The process results in the unharnessed potential energy of the proton electrochemical gradient being released as heat.[7] The process is mediated by a proton channel called thermogenin, or UCP1.[45] Thermogenin is a 33kDa protein first discovered in 1973.[46] Thermogenin is primarily found in brown adipose tissue, or brown fat, and is responsible for non-shivering thermogenesis. Brown adipose tissue is found in mammals, and is at its highest levels in early life and in hibernating animals. In humans, brown adipose tissue is present at birth and decreases with

270

Mitochondrion age.[45]

271

Storage of calcium ions
The concentrations of free calcium in the cell can regulate an array of reactions and is important for signal transduction in the cell. Mitochondria can transiently store calcium, a contributing process for the cell's homeostasis of calcium.[47] In fact, their ability to rapidly take in calcium for later release makes them very good "cytosolic buffers" for calcium.[48][49][50] The endoplasmic reticulum (ER) is the most Mitochondria (M) within a chondrocyte stained for calcium as shown by electron significant storage site of calcium, and there microscopy. is a significant interplay between the mitochondrion and ER with regard to calcium.[51] The calcium is taken up into the matrix by a calcium uniporter on the inner mitochondrial membrane.[52] It is primarily driven by the mitochondrial membrane potential.[47] Release of this calcium back into the cell's interior can occur via a sodium-calcium exchange protein or via "calcium-induced-calcium-release" pathways.[52] This can initiate calcium spikes or calcium waves with large changes in the membrane potential. These can activate a series of second messenger system proteins that can coordinate processes such as neurotransmitter release in nerve cells and release of hormones in endocrine cells. Ca2+ influx to the mitochondrial matrix has recently been implicated as a mechanism to regulate respiratory bioenergetics by allowing the electrochemical potential across the membrane to transiently "pulse" from ΔΨ-dominated to pH-dominated, facilitating a reduction of oxidative stress.[53]

Additional functions
Mitochondria play a central role in many other metabolic tasks, such as: • Regulation of the membrane potential[7] • Apoptosis-programmed cell death[54] • Calcium signaling (including calcium-evoked apoptosis)[55] • Regulation of cellular metabolism[56] • Certain heme synthesis reactions[57] (see also: porphyrin) • Steroid synthesis.[48] Some mitochondrial functions are performed only in specific types of cells. For example, mitochondria in liver cells contain enzymes that allow them to detoxify ammonia, a waste product of protein metabolism. A mutation in the genes regulating any of these functions can result in mitochondrial diseases.

Cellular proliferation regulation
The relationship between cellular proliferation and mitochondria has been investigated using cervical cancer Hela cells. Tumor cells require an ample amount of ATP (Adenosine triphosphate) in order to synthesize bioactive compounds such as lipids, proteins, and nucleotides for rapid cell proliferation.[58] The majority of ATP in tumor cells is generated via the Oxidative Phosphorylation pathway (OxPhos).[59] Interference with OxPhos have shown to cause cell cycle arrest suggesting that mitochondria plays a role in cell proliferation.[59] Mitochondrial ATP production is also vital for cell division in addition to other basic functions in the cell including the regulation of cell

Mitochondrion volume, solute concentration, and cellular architecture.[60][61][62] ATP levels differ at various stages of the cell cycle suggesting that there is a relationship between the abundance of ATP and the cell's ability to enter a new cell cyle.[63] ATP’s role in the basic functions of the cell make the cell cycle sensitive to changes in the availability of mitochondrial derived ATP.[63] The variation in ATP levels at different stages of the cell cycle support the hypothesis that mitochondria plays an important role in cell cycle regulation.[63] Although the specific mechanisms between mitochondria and the cell cycle regulation is not well understood, studies have shown that low energy cell cycle checkpoints monitor the energy capability before committing to another round of cell division.[64]

272

Origin
Mitochondria have many features in common with prokaryotes. As a result, they are thought to be originally derived from endosymbiotic prokaryotes. A mitochondrion contains DNA, which is organized as several copies of a single, circular chromosome. This mitochondrial chromosome contains genes for redox proteins such as those of the respiratory chain. The CoRR hypothesis proposes that this co-location is required for redox regulation. The mitochondrial genome codes for some RNAs of ribosomes, and the twenty-two tRNAs necessary for the translation of messenger RNAs into protein. The circular structure is also found in prokaryotes, and the similarity is extended by the fact that mitochondrial DNA is organized with a variant genetic code similar to that of Proteobacteria.[65] This suggests that their ancestor, the so-called proto-mitochondrion, was a member of the Proteobacteria.[65] In particular, the proto-mitochondrion was probably closely related to the rickettsia.[66] However, the exact relationship of the ancestor of mitochondria to the alpha-proteobacteria and whether the mitochondrion was formed at the same time or after the nucleus, remains controversial.[67] A recent study[68] by researchers of the University of Hawaiʻi at Mānoa and the Oregon State University indicates that the SAR11 clade of bacteria shares a relatively recent common ancestor with the mitochondria existing in most eukaryotic cells.
Phylogeny of Rickettsiales

Other alphaproteobacteria Rhodospirillales, Sphingomonadales, Rhodobacteraceae, Rhizobiales, etc.

SAR11 clade Pelagibacter ubique

Mitochondria

Ehrlichia Rickettsiales Anaplasmataceae Anaplasma

Wolbachia

Neorickettsia

Rickettsiaceae

Rickettsia

Mitochondrion

273
[69]

Robust phylogeny of Rickettsiales from Williams et al. (2007)

The ribosomes coded for by the mitochondrial DNA are similar to those from bacteria in size and structure.[70] They closely resemble the bacterial 70S ribosome and not the 80S cytoplasmic ribosomes, which are coded for by nuclear DNA. The endosymbiotic relationship of mitochondria with their host cells was popularized by Lynn Margulis.[71] The endosymbiotic hypothesis suggests that mitochondria descended from bacteria that somehow survived endocytosis by another cell, and became incorporated into the cytoplasm. The ability of these bacteria to conduct respiration in host cells that had relied on glycolysis and fermentation would have provided a considerable evolutionary advantage. In a similar manner, host cells with symbiotic bacteria capable of photosynthesis would have had an advantage. The incorporation of symbiotes would have increased the number of environments in which the cells could survive. This symbiotic relationship probably developed 1.7[72] to 2[73] billion years ago. A few groups of unicellular eukaryotes lack mitochondria: the microsporidians, metamonads, and archamoebae.[74] These groups appear as the most primitive eukaryotes on phylogenetic trees constructed using rRNA information, which once suggested that they appeared before the origin of mitochondria. However, this is now known to be an artifact of long-branch attraction—they are derived groups and retain genes or organelles derived from mitochondria (e.g., mitosomes and hydrogenosomes).[1]

Genome
The human mitochondrial genome is a circular DNA molecule of about 16 kilobases.[75] It encodes 37 genes: 13 for subunits of respiratory complexes I, III, IV and V, 22 for mitochondrial tRNA (for the 20 standard amino acids, plus an extra gene for leucine and serine), and 2 for rRNA.[75] One mitochondrion can contain two to ten copies of its DNA.[76] As in prokaryotes, there is a very high proportion of coding DNA and an absence of repeats. Mitochondrial genes are transcribed as multigenic transcripts, which are cleaved and polyadenylated to yield Mitochondrial DNA. mature mRNAs. Not all proteins necessary for mitochondrial function are encoded by the mitochondrial genome; most are coded by genes in the cell nucleus and the corresponding proteins are imported into the mitochondrion.[20] The exact number of genes encoded by the nucleus and the mitochondrial genome differs between species. In general, mitochondrial genomes are circular, although exceptions have been reported.[77] In general, mitochondrial DNA lacks introns, as is the case in the human mitochondrial genome;[20] however, introns have been observed in some eukaryotic mitochondrial DNA,[78] such as that of yeast[79] and protists,[80] including Dictyostelium discoideum.[81] In animals the mitochondrial genome is typically a single circular chromosome that is approximately 16-kb long and has 37 genes. The genes, while highly conserved, may vary in location. Curiously, this pattern is not found in the human body louse (Pediculus humanus). Instead this mitochondrial genome is arranged in 18 minicircular chromosomes, each of which is 3–4 kb long and has one to three genes.[82] This pattern is also found in other sucking lice, but not in chewing lice. Recombination has been shown to occur between the minichromosomes. The reason for this difference is not known. While slight variations on the standard code had been predicted earlier,[83] none was discovered until 1979, when researchers studying human mitochondrial genes determined that they used an alternative code.[84] Many slight variants have been discovered since,[85] including various alternative mitochondrial codes.[86] Further, the AUA, AUC, and AUU codons are all allowable start codons.

Mitochondrion

274

Exceptions to the universal genetic code (UGC) in mitochondria[6]
Organism Mammals Invertebrates Fungi Codon Standard Mitochondria Stop codon Serine Threonine Methionine

AGA, AGG Arginine AGA, AGG Arginine CUA Leucine Isoleucine

All of the above AUA UGA

Stop codon Tryptophan

Some of these differences should be regarded as pseudo-changes in the genetic code due to the phenomenon of RNA editing, which is common in mitochondria. In higher plants, it was thought that CGG encoded for tryptophan and not arginine; however, the codon in the processed RNA was discovered to be the UGG codon, consistent with the universal genetic code for tryptophan.[87] Of note, the arthropod mitochondrial genetic code has undergone parallel evolution within a phylum, with some organisms uniquely translating AGG to lysine.[88] Mitochondrial genomes have far fewer genes than the bacteria from which they are thought to be descended. Although some have been lost altogether, many have been transferred to the nucleus, such as the respiratory complex II protein subunits.[75] This is thought to be relatively common over evolutionary time. A few organisms, such as the Cryptosporidium, actually have mitochondria that lack any DNA, presumably because all their genes have been lost or transferred.[89] In Cryptosporidium, the mitochondria have an altered ATP generation system that renders the parasite resistant to many classical mitochondrial inhibitors such as cyanide, azide, and atovaquone.[89]

Replication and inheritance
Mitochondria divide by binary fission similar to bacterial cell division; unlike bacteria, however, mitochondria can also fuse with other mitochondria.[75][90] The regulation of this division differs between eukaryotes. In many single-celled eukaryotes, their growth and division is linked to the cell cycle. For example, a single mitochondrion may divide synchronously with the nucleus. This division and segregation process must be tightly controlled so that each daughter cell receives at least one mitochondrion. In other eukaryotes (in mammals for example), mitochondria may replicate their DNA and divide mainly in response to the energy needs of the cell, rather than in phase with the cell cycle. When the energy needs of a cell are high, mitochondria grow and divide. When the energy use is low, mitochondria are destroyed or become inactive. In such examples, and in contrast to the situation in many single celled eukaryotes, mitochondria are apparently randomly distributed to the daughter cells during the division of the cytoplasm. Understanding of mitochondrial dynamics, which is described as the balance between mitochondrial fusion and fission, has revealed that functional and structural alterations in mitochondrial morphology are important factors in pathologies associated with several disease conditions.[91] An individual's mitochondrial genes are not inherited by the same mechanism as nuclear genes. At fertilization of an egg cell by a sperm, the egg nucleus and sperm nucleus each contribute equally to the genetic makeup of the zygote nucleus. In contrast, the mitochondria, and therefore the mitochondrial DNA, usually comes from the egg only. The sperm's mitochondria enter the egg but do not contribute genetic information to the embryo.[92] Instead, paternal mitochondria are marked with ubiquitin to select them for later destruction inside the embryo.[93] The egg cell contains relatively few mitochondria, but it is these mitochondria that survive and divide to populate the cells of the adult organism. Mitochondria are, therefore, in most cases inherited down the female line, known as maternal inheritance. This mode is seen in most organisms including all animals. However, mitochondria in some species can sometimes be inherited paternally. This is the norm among certain coniferous plants, although not in pine trees and yew trees.[94] It has been suggested that it occurs at a very low level in humans.[95] Uniparental inheritance leads to little opportunity for genetic recombination between different lineages of mitochondria, although a single mitochondrion can contain 2–10 copies of its DNA.[76] For this reason,

Mitochondrion mitochondrial DNA usually is thought to reproduce by binary fission. What recombination does take place maintains genetic integrity rather than maintaining diversity. However, there are studies showing evidence of recombination in mitochondrial DNA. It is clear that the enzymes necessary for recombination are present in mammalian cells.[96] Further, evidence suggests that animal mitochondria can undergo recombination.[97] The data are a bit more controversial in humans, although indirect evidence of recombination exists.[98][99] If recombination does not occur, the whole mitochondrial DNA sequence represents a single haplotype, which makes it useful for studying the evolutionary history of populations.

275

Population genetic studies
The near-absence of genetic recombination in mitochondrial DNA makes it a useful source of information for scientists involved in population genetics and evolutionary biology.[100] Because all the mitochondrial DNA is inherited as a single unit, or haplotype, the relationships between mitochondrial DNA from different individuals can be represented as a gene tree. Patterns in these gene trees can be used to infer the evolutionary history of populations. The classic example of this is in human evolutionary genetics, where the molecular clock can be used to provide a recent date for mitochondrial Eve.[101][102] This is often interpreted as strong support for a recent modern human expansion out of Africa.[103] Another human example is the sequencing of mitochondrial DNA from Neanderthal bones. The relatively large evolutionary distance between the mitochondrial DNA sequences of Neanderthals and living humans has been interpreted as evidence for lack of interbreeding between Neanderthals and anatomically-modern humans.[104] However, mitochondrial DNA reflects the history of only females in a population and so may not represent the history of the population as a whole. This can be partially overcome by the use of paternal genetic sequences, such as the non-recombining region of the Y-chromosome.[103] In a broader sense, only studies that also include nuclear DNA can provide a comprehensive evolutionary history of a population.[105]

Dysfunction and disease
Mitochondrial diseases
With their central place in cell metabolism, damage — and subsequent dysfunction — in mitochondria is an important factor in a wide range of human diseases. Mitochondrial disorders often present themselves as neurological disorders, but can manifest as myopathy, diabetes, multiple endocrinopathy, or a variety of other systemic manifestations.[106] Diseases caused by mutation in the mtDNA include Kearns-Sayre syndrome, MELAS syndrome and Leber's hereditary optic neuropathy.[107] In the vast majority of cases, these diseases are transmitted by a female to her children, as the zygote derives its mitochondria and hence its mtDNA from the ovum. Diseases such as Kearns-Sayre syndrome, Pearson's syndrome, and progressive external ophthalmoplegia are thought to be due to large-scale mtDNA rearrangements, whereas other diseases such as MELAS syndrome, Leber's hereditary optic neuropathy, myoclonic epilepsy with ragged red fibers (MERRF), and others are due to point mutations in mtDNA.[106] In other diseases, defects in nuclear genes lead to dysfunction of mitochondrial proteins. This is the case in Friedreich's ataxia, hereditary spastic paraplegia, and Wilson's disease.[108] These diseases are inherited in a dominance relationship, as applies to most other genetic diseases. A variety of disorders can be caused by nuclear mutations of oxidative phosphorylation enzymes, such as coenzyme Q10 deficiency and Barth syndrome.[106] Environmental influences may interact with hereditary predispositions and cause mitochondrial disease. For example, there may be a link between pesticide exposure and the later onset of Parkinson's disease.[109][110] Other pathologies with etiology involving mitochondrial dysfunction include schizophrenia, bipolar disorder, dementia, Alzheimer's disease,[111] Parkinson's disease, epilepsy, stroke, cardiovascular disease, retinitis pigmentosa, and diabetes mellitus.[112][113] A common thread thought to link these seemingly-unrelated conditions is cellular

Mitochondrion damage causing oxidative stress. How exactly mitochondrial dysfunction fits into the etiology of these pathologies is yet to be elucidated. Mitochondria-mediated oxidative stress plays a role in cardiomyopathy in Type 2 diabetics. Increased fatty acid delivery to the heart increases fatty acid uptake by cardiomyocytes, resulting in increased fatty acid oxidation in these cells. This process increases the reducing equivalents available to the electron transport chain of the mitochondria, ultimately increasing reactive oxygen species (ROS) production. ROS increases uncoupling proteins (UCPs) and potentiate proton leakage through the adenine nucleotide translocator (ANT), the combination of which uncouples the mitochondria. Uncoupling then increases oxygen consumption by the mitochondria, compounding the increase in fatty acid oxiation. This creates a vicious cycle of uncoupling; furthermore, even though oxygen consumption increases, ATP synthesis does not increase proportionally because the mitochondria is uncoupled. Less ATP availability ultimately results in an energy deficit presenting as reduced cardiac efficiency and contractile dysfunction. To compound the problem, impaired sarcoplasmic reticulum calcium release and reduced mitochondrial reuptake limits peak cytosolic levels of the important signaling ion during muscle contraction. The decreased intra-mitochondrial calcium concentration increases dehydrogenase activation and ATP synthesis. So in addition to lower ATP synthesis due to fatty acid oxidation, ATP synthesis is impaired by poor calcium signaling as well, causing cardiac problems for diabetics.[114]

276

Possible relationships to aging
Given the role of mitochondria as the cell's powerhouse, there may be some leakage of the high-energy electrons in the respiratory chain to form reactive oxygen species. This was thought to result in significant oxidative stress in the mitochondria with high mutation rates of mitochondrial DNA (mtDNA).[115] Hypothesized links between aging and oxidative stress are not new and were proposed over 50 years ago.[116] A vicious cycle was thought to occur, as oxidative stress leads to mitochondrial DNA mutations, which can lead to enzymatic abnormalities and further oxidative stress. However, recent measurements of the rate of accumulation of mutation observed in mitochondrial DNA[117] were estimated to be 1 mutation every 7884 years (10^-7 to 10^-9 per base per year, dating back to the most recent common ancestor of humans and apes), consistent with other estimates of mutation rates of autosomal dna ( 10^-8 per base per generation[118]) A number of changes can occur to mitochondria during the aging process.[119] Tissues from elderly patients show a decrease in enzymatic activity of the proteins of the respiratory chain.[120] However, mutated mtDNA can only be found in about 0.2% of very old cells.[121] Large deletions in the mitochondrial genome have been hypothesized to lead to high levels of oxidative stress and neuronal death in Parkinson's disease.[122] However, there is much debate over whether mitochondrial changes are causes of aging or merely characteristics of aging. One notable study in mice demonstrated shortened lifespan but no increase in reactive oxygen species despite increasing mitochondrial DNA mutations.[123] However, it has to be noted that aging non-mutant mice do not seem to accumulate a great number of mutations in mitochondrial DNA imposing a cloud of doubt on the involvement of mitochondrial DNA mutations in "natural" aging. As a result, the exact relationships between mitochondria, oxidative stress, and aging have not yet been settled.

Mitochondrion

277

In popular culture
In Madeleine L'Engle's A Wind in the Door, the Farandolae are fictional creatures that live inside mitochondria, and do circular "dances" around their "trees of origin".

References
[1] Henze K, Martin W; Martin, William (2003). "Evolutionary biology: essence of mitochondria". Nature 426 (6963): 127–8. doi:10.1038/426127a. PMID 14614484. [2] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6. . [3] McBride HM, Neuspiel M, Wasiak S (2006). "Mitochondria: more than just a powerhouse". Curr. Biol. 16 (14): R551–60. doi:10.1016/j.cub.2006.06.054. PMID 16860735. [4] Gardner A, Boles RG (2005). "Is a "Mitochondrial Psychiatry" in the Future? A Review". Curr. Psychiatry Review 1 (3): 255–271. doi:10.2174/157340005774575064. [5] Lesnefsky EJ, et al. (2001). "Mitochondrial dysfuntion in cardiac disease ischemia-reperfusion, aging and heart failure". J. Mol. Cell. Cardiol. 33 (6): 1065–1089. doi:10.1006/jmcc.2001.1378. PMID 11444914. [6] Alberts, Bruce; Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter (1994). Molecular Biology of the Cell. New York: Garland Publishing Inc.. ISBN 0-8153-3218-1. [7] Voet, Donald; Judith G. Voet, Charlotte W. Pratt (2006). Fundamentals of Biochemistry, 2nd Edition. John Wiley and Sons, Inc.. pp. 547. ISBN 0-471-21495-7. [8] Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, Ghosh SS (2003 March). "Characterization of the human heart mitochondrial proteome". Nat Biotechnol. 21 (3): 281–6. doi:10.1038/nbt793. PMID 12592411. [9] Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang J, Korge P, Honda H, Weiss JN, Apweiler R, Ping P (2008). "Systematic Characterization of the Murine Mitochondrial Proteome Using Functionally Validated Cardiac Mitochondria". Proteomics 8 (8): 1564–1575. doi:10.1002/pmic.200700851. PMC 2799225. PMID 18348319. [10] Zhang J, Liem DA, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Yang J, Korge P, Drews O, Maclellan WR, Honda H, Weiss JN, Apweiler R, Ping P (2008). "Altered Proteome Biology of Cardiac Mitochondria Under Stress Conditions". J. Proteome Res 7 (6): 2204–14. doi:10.1021/pr070371f. PMID 18484766. [11] Andersson SG, Karlberg O, Canbäck B, Kurland CG (January 2003). "On the origin of mitochondria: a genomics perspective". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 358 (1429): 165–77; discussion 177–9. doi:10.1098/rstb.2002.1193. PMC 1693097. PMID 12594925. [12] Ernster L, Schatz G (1981). "Mitochondria: a historical review". The Journal of Cell Biology. 91 (3 Pt 2): 227s–255s. doi:10.1083/jcb.91.3.227s. PMC 2112799. PMID 7033239. [13] Siekevitz P (1957). "Powerhouse of the cell". Scientific American. 1: 131–140. [14] Herrmann JM, Neupert W (2000 April). "Protein transport into mitochondria". Curr Opin Microbiol 3 (2): 210–214. doi:10.1016/S1369-5274(00)00077-1. PMID 10744987. [15] Chipuk JE, Bouchier-Hayes L, Green DR (2006). "Mitochondrial outer membrane permeabilization during apoptosis: the innocent bystander scenario". Cell Death and Differentiation. 13 (8): 1396–1402. doi:10.1038/sj.cdd.4401963. PMID 16710362. [16] Hayashi T, Rizzuto R, Hajnoczky G, Su TP (February 2009). "MAM: more than just a housekeeper". Trends Cell Biol. 19 (2): 81–8. doi:10.1016/j.tcb.2008.12.002. PMC 2750097. PMID 19144519. [17] McMillin JB, Dowhan W (2002 December). "Cardiolipin and apoptosis". Biochim. Et Biophys. Acta. 1585 (2–3): 97–107. doi:10.1016/S1388-1981(02)00329-3. PMID 12531542. [18] Mannella CA (2006). "Structure and dynamics of the mitochondrial inner membrane cristae ". Biochimica et Biophysica Acta 1763 (5–6): 542–548.
doi:10.1016/j.bbamcr.2006.04.006. PMID 16730811.

[19] Thar, R.; Kühl, Michael (2004). "Propagation of electromagetic radiation in mitochondria?" (http:/ / www. mbl. ku. dk/ MKuhl/ pages/ PDF/ Thar& Kuhl2004. pdf) (PDF). J. Theoretical Biology 230 (2): 261–270. doi:10.1016/j.jtbi.2004.05.021. . [20] Anderson S, Bankier AT, Barrell BG, de-Bruijn MHL, Coulson AR, et al. (1981). "Sequence and organization of the human mitochondrial genome". Nature 290 (5806): 427–465. doi:10.1038/290457a0. PMID 7219534. [21] Rizzuto, R et al. (2009). "Ca2+ transfer from the ER to mitochondria: when, how and why". Biochim Biophys Acta. 1787 (11): 1342–51. doi:10.1016/j.bbabio.2009.03.015. PMC 2730423. PMID 19341702. [22] Hayashi, T. et al. (2009). "MAM: more than just a housekeeper". Trends Cell Biol. 19 (2): 81–88. doi:10.1016/j.tcb.2008.12.002. PMC 2750097. PMID 19144519. [23] de Brito, OM et al. (2010). "An intimate liaison: spatial organization of the endoplasmic reticulum–mitochondria relationship". EMBO J. 29 (16): 2715–2723. doi:10.1038/emboj.2010.177. PMC 2924651. PMID 20717141. [24] Vance, JE. et al. (1996). "Intracellular trafficking of phospholipids: import of phosphatidylserine into mitochondria". Anticancer Research 16 (3B): 1333–9. PMID 8694499. [25] Lebiedzinska, M et al. (2009). "Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles". Int J Biochem Cell Biol 41 (10): 1805–16. doi:10.1016/j.biocel.2009.02.017. PMID 19703651.

Mitochondrion
[26] Twig, G et al. (2008). "Fission and selective fusion govern mitochondrial segregation and elimination by autophagy". EMBO J 27 (2): 433–446. doi:10.1038/sj.emboj.7601963. PMC 2234339. PMID 18200046. [27] Osman, C et al. (2011). "Making heads or tails of phospholipids in mitochondria". J Cell Biol 192 (1): 7–16. doi:10.1083/jcb.201006159. PMC 3019561. PMID 21220505. [28] Kornmann, B. et al. (2009). "An ER-Mitochondria Tethering Complex Revealed by a Synthetic Biology Screen". Science 325 (24): 477–481. doi:10.1126/science.1175088. PMC 2933203. PMID 19556461. [29] Rusinol, AE et al. (1994). "A Unique Mitochondria-associated Membrane Fraction from Rat Liver Has a High Capacity for Lipid Synthesis and Contains Pre-Golgi Secretory Proteins Including Nascent Lipoprotein". J Biol Chem 269 (44): 27494–27502. PMID 7961664. [30] Kopach, O et al. (2008). "Functional coupling between ryanodine receptors, mitochondria and Ca2+ ATPases in rat submandibular acinar cells". Cell Calcium 43 (5): 469–481. doi:10.1016/j.ceca.2007.08.001. PMID 17889347. [31] Csordas, G et al. (2001). "Sorting of calcium signals at the junctions of endoplasmic reticulum and mitochondria". Cell Calcium. 29 (4): 249–262. doi:10.1054/ceca.2000.0191. PMID 11243933. [32] Decuypere, JP et al. (2011). "The IP3 receptor–mitochondria connection in apoptosis and autophagy". Biochim Biophys Acta 1813 (5): 1003–13. doi:10.1016/j.bbamcr.2010.11.023. PMID 21146562. [33] Hajnoczky, G. et al. (2011). "Old players in a new role: mitochondria-associated membranes, VDAC, and ryanodine receptors as contributors to calcium signal propagation from endoplasmic reticulum to the mitochondria". Cell Calcium 32 (5–6): 363–377. doi:10.1016/S0143416002001872. PMID 12543096. [34] das Neves RP, Jones NS, Andreu L, Gupta R, Enver T, Iborra FJ (2010). "Connecting Variability in Global Transcription Rate to Mitochondrial Variability". PLoS Biol. 8 (12): e1000560. doi:10.1371/journal.pbio.1000560. [35] Johnston IG, Gaal B, das Neves RP, Enver T, Iborra FJ, Jones NS (2012). "Mitochondrial Variability as a Source of Extrinsic Cellular Noise". PLoS Comput. Biol. 8 (3): e1002416. doi:10.1371/journal.pcbi.1002416. [36] Rappaport L, Oliviero P, Samuel JL (1998). "Cytoskeleton and mitochondrial morphology and function". Mol and Cell Biochem. 184: 101–105. doi:10.1023/A:1006843113166. [37] Tang HL, Lung HL, Wu KC, Le AP, Tang HM, Fung MC (2007). "Vimentin supports mitochondrial morphology and organization". Biochemical J 410 (1): 141–6. doi:10.1042/BJ20071072. PMID 17983357. [38] Rich PR (2003). "The molecular machinery of Keilin's respiratory chain" (http:/ / www. biochemsoctrans. org/ bst/ 031/ 1095/ bst0311095. htm). Biochem. Soc. Trans. 31 (Pt 6): 1095–105. doi:10.1042/BST0311095. PMID 14641005. . [39] Stoimenova M, Igamberdiev AU, Gupta KJ, Hill RD (July 2007). "Nitrite-driven anaerobic ATP synthesis in barley and rice root mitochondria". Planta 226 (2): 465–74. doi:10.1007/s00425-007-0496-0. PMID 17333252. [40] King A, Selak MA, Gottlieb E (2006). "Succinate dehydrogenase and fumarate hydratase: linking mitochondrial dysfunction and cancer". Oncogene. 25 (34): 4675–4682. doi:10.1038/sj.onc.1209594. PMID 16892081. [41] Huang, K.; K. G. Manton (2004). "The role of oxidative damage in mitochondria during aging: A review". Frontiers in Bioscience 9: 1100–1117. doi:10.2741/1298. PMID 14977532. [42] Mitchell P, Moyle J (1967-01-14). "Chemiosmotic hypothesis of oxidative phosphorylation". Nature. 213 (5072): 137–9. doi:10.1038/213137a0. PMID 4291593. [43] Mitchell P (1967-06-24). "Proton current flow in mitochondrial systems". Nature. 25 (5095): 1327–8. doi:10.1038/2141327a0. PMID 6056845. [44] Nobel Foundation. "Chemistry 1997" (http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1997/ ). . Retrieved 2007-12-16. [45] Mozo J, Emre Y, Bouillaud F, Ricquier D, Criscuolo F (2005 November). "Thermoregulation: What Role for UCPs in Mammals and Birds?". Bioscience Reports. 25 (3–4): 227–249. doi:10.1007/s10540-005-2887-4. PMID 16283555. [46] Nicholls DG, Lindberg O (1973). "Brown-adipose-tissue mitochondria. The influence of albumin and nucleotides on passive ion permeabilities". Eur. J. Biochem. 37 (3): 523–30. doi:10.1111/j.1432-1033.1973.tb03014.x. PMID 4777251. [47] Editor-in-chief, George J. Siegel; editors, Bernard W. Agranoff... [et al.]; illustrations by Lorie M. Gavulic (1999). Siegel GJ, Agranoff BW, Fisher SK, Albers RW, Uhler MD. ed. Basic Neurochemistry (6 ed.). Lippincott Williams & Wilkins. ISBN 0-397-51820-X. [48] Rossier MF (2006). "T channels and steroid biosynthesis: in search of a link with mitochondria". Cell Calcium. 40 (2): 155–64. doi:10.1016/j.ceca.2006.04.020. PMID 16759697. [49] Brighton Carl T., Hunt Robert M. (1974). "Mitochondrial calcium and its role in calcification". Clinical Orthopaedics and Related Research 100 (100): 406–416. doi:10.1097/00003086-197405000-00057. PMID 4134194. [50] Brighton, Carl T. and Robert M. Hunt (1978): "The role of mitochondria in growth plate calcification as demonstrated in a rachitic model", Journal of Bone and Joint Surgery, 60-A: 630-639. [51] Pizzo P, Pozzan T (2007 October). "Mitochondria–endoplasmic reticulum choreography: structure and signaling dynamics". Trends Cell Bio. 17 (10): 511–517. doi:10.1016/j.tcb.2007.07.011. PMID 17851078. [52] Miller RJ (1998). "Mitochondria – the kraken wakes!". Trends in Neurosci. 21 (3): 95–97. doi:10.1016/S0166-2236(97)01206-X. [53] Schwarzlander M, Logan DC, Johnston IG, Jones NS, Meyer AJ, Fricker MD, Sweetlove LJ (2012). "Pulsing of Membrane Potential in Individual Mitochondria: A Stress-Induced Mechanism to Regulate Respiratory Bioenergetics in Arabidopsis". Plant Cell. doi:10.1105/tpc.112.096438. [54] Green DR (1998 September). "Apoptotic pathways: the roads to ruin". Cell. 94 (6): 695–8. doi:10.1016/S0092-8674(00)81728-6. PMID 9753316.

278

Mitochondrion
[55] Hajnóczky G, Csordás G, Das S, Garcia-Perez C, Saotome M, Sinha Roy S, Yi M (2006). "Mitochondrial calcium signalling and cell death: approaches for assessing the role of mitochondrial Ca2+ uptake in apoptosis". Cell Calcium 40 (5–6): 553–60. doi:10.1016/j.ceca.2006.08.016. PMC 2692319. PMID 17074387. [56] McBride HM, Neuspiel M, Wasiak S (2006 July). "Mitochondria: more than just a powerhouse". Curr Biol. 16 (14): R551–60. doi:10.1016/j.cub.2006.06.054. PMID 16860735. [57] Oh-hama T (1997 August). "Evolutionary consideration on 5-aminolevulinate synthase in nature". Orig Life Evol Biosph. 27 (4): 405–12. doi:10.1023/A:1006583601341. PMID 9249985. [58] Weinberg, Frank; Chandel, Navdeep S. (2009). "Mitochondrial Metabolism and Cancer". Annals of the New York Academy of Sciences 1177 (1): 66–73. doi:10.1111/j.1749-6632.2009.05039.x. ISSN 00778923. [59] Moreno-Sánchez, Rafael; Rodríguez-Enríquez, Sara; Marín-Hernández, Alvaro; Saavedra, Emma (2007). "Energy metabolism in tumor cells". FEBS Journal 274 (6): 1393–1418. doi:10.1111/j.1742-4658.2007.05686.x. ISSN 1742464X. PMID 17302740. [60] Pedersen, Peter L. (1994). "ATP Synthase: The machine that makes ATP". Current Biology 4 (12): 1138–1141. doi:10.1016/S0960-9822(00)00257-8. ISSN 09609822. [61] Pattappa, Girish; Heywood, Hannah K.; de Bruijn, Joost D.; Lee, David A. (2011). "The metabolism of human mesenchymal stem cells during proliferation and differentiation". Journal of Cellular Physiology 226 (10): 2562–2570. doi:10.1002/jcp.22605. ISSN 00219541. [62] Agarwal, Bhawana (2011). "A role for anions in ATP synthesis and its molecular mechanistic interpretation". Journal of Bioenergetics and Biomembranes 43 (3): 299–310. doi:10.1007/s10863-011-9358-3. ISSN 0145-479X. [63] Sweet, S.; Singh, G. (1999). "Changes in mitochondrial mass, membrane potential, and cellular adenosine triphosphate content during the cell cycle of human leukemic (HL-60) cells". Journal of Cellular Physiology 180 (1): 91–96. doi:10.1002/(SICI)1097-4652(199907)180:1<91::AID-JCP10>3.0.CO;2-6. ISSN 0021-9541. [64] McBride, Heidi M.; Neuspiel, Margaret; Wasiak, Sylwia (2006). "Mitochondria: More Than Just a Powerhouse". Current Biology 16 (14): R551–R560. doi:10.1016/j.cub.2006.06.054. ISSN 09609822. PMID 16860735. [65] Futuyma DJ (2005). "On Darwin's Shoulders". Natural History 114 (9): 64–68. [66] Emelyanov VV (2003). "Mitochondrial connection to the origin of the eukaryotic cell". Eu J Biochem. 270 (8): 1599–1618. doi:10.1046/j.1432-1033.2003.03499.x. PMID 12694174. [67] Gray MW, Burger G, Lang BF (March 1999). "Mitochondrial evolution". Science 283 (5407): 1476–81. doi:10.1126/science.283.5407.1476. PMID 10066161. [68] J. Cameron Thrash, Alex Boyd, Megan J. Huggett, Jana Grote, Paul Carini, Ryan J. Yoder, Barbara Robbertse, Joseph W. Spatafora, Michael S. Rappé, Stephen J. Giovannoni (June 2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade" (http:/ / www. nature. com/ srep/ 2011/ 110614/ srep00013/ pdf/ srep00013. pdf). Scientific Reports 1. doi:10.1038/srep00013. . [69] Williams, K. P.; Sobral, B. W.; Dickerman, A. W. (2007). "A Robust Species Tree for the Alphaproteobacteria". Journal of Bacteriology 189 (13): 4578–4586. doi:10.1128/JB.00269-07. PMC 1913456. PMID 17483224. [70] O'Brien TW (2003 September). "Properties of human mitochondrial ribosomes". IUBMB Life. 55 (9): 505–13. doi:10.1080/15216540310001626610. PMID 14658756. [71] Lynn Sagan (1967). "On the origin of mitosing cells". J Theor Bio. 14 (3): 255–274. doi:10.1016/0022-5193(67)90079-3. PMID 11541392. [72] Emelyanov VV (2001). "Rickettsiaceae, rickettsia-like endosymbionts, and the origin of mitochondria". Biosci. Rep. 21 (1): 1–17. doi:10.1023/A:1010409415723. PMID 11508688. [73] Feng D-F, Cho G, Doolittle RF (1997). "Determining divergence times with a protein clock: Update and reevaluation". Proc. Natl. Acad. Sci. 94 (24): 13028–13033. doi:10.1073/pnas.94.24.13028. PMC 24257. PMID 9371794. [74] Cavalier-Smith T (1991). "Archamoebae: the ancestral eukaryotes?". Biosystems. 25 (1–2): 25–38. doi:10.1016/0303-2647(91)90010-I. PMID 1854912. [75] Chan DC (2006-06-30). "Mitochondria: Dynamic Organelles in Disease, Aging, and Development". Cell 125 (7): 1241–1252. doi:10.1016/j.cell.2006.06.010. PMID 16814712. [76] Wiesner RJ, Ruegg JC, Morano I (1992). "Counting target molecules by exponential polymerase chain reaction, copy number of mitochondrial DNA in rat tissues". Biochim Biophys Acta 183 (2): 553–559. doi:10.1016/0006-291X(92)90517-O. PMID 1550563. [77] Fukuhara H, Sor F, Drissi R, Dinouël N, Miyakawa I, Rousset, and Viola AM (1993). "Linear mitochondrial DNAs of yeasts: frequency of occurrence and general features". Mol Cell Biol. 13 (4): 2309–2314. PMC 359551. PMID 8455612. [78] Bernardi G (1978). "Intervening sequences in the mitochondrial genome". Nature. 276 (5688): 558–559. doi:10.1038/276558a0. PMID 214710. [79] Hebbar SK, Belcher SM, Perlman PS (1992 April). "A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro". Nucleic Acids Res. 20 (7): 1747–54. doi:10.1093/nar/20.7.1747. PMC 312266. PMID 1579468. [80] Gray MW, Lang BF, Cedergren R, Golding GB, Lemieux C, Sankoff D, et al. (1998). "Genome structure and gene content in protist mitochondrial DNAs". Nucl Acids Res. 26 (4): 865–878. doi:10.1093/nar/26.4.865. PMC 147373. PMID 9461442. [81] Gray MW, Lang BF, Burger G (2004). "Mitochondria of protists". Ann Rev of Genetics. 38: 477–524. doi:10.1146/annurev.genet.37.110801.142526. PMID 15568984. [82] Shao R, Kirkness EF, Barker SC (March 2009). "The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus". Genome Res. 19 (5): 904–12. doi:10.1101/gr.083188.108. PMC 2675979. PMID 19336451.

279

Mitochondrion
[83] Crick, F. H. C. and Orgel, L. E. (1973) "Directed panspermia." Icarus 19:341-346. p. 344: "It is a little surprising that organisms with somewhat different codes do not coexist." (Further discussion at (http:/ / www. talkorigins. org/ faqs/ comdesc/ section1. html)) [84] Barrell BG, Bankier AT, Drouin J (1979). "A different genetic code in human mitochondria". Nature. 282 (5735): 189–194. doi:10.1038/282189a0. PMID 226894. [85] NCBI: "The Genetic Codes", Compiled by Andrzej (Anjay) Elzanowski and Jim Ostell (http:/ / 130. 14. 29. 110/ Taxonomy/ Utils/ wprintgc. cgi?mode=c) [86] Jukes TH, Osawa S (1990-12-01). "The genetic code in mitochondria and chloroplasts". Experientia. 46 (11–12): 1117–26. doi:10.1007/BF01936921. PMID 2253709. [87] Hiesel R, Wissinger B, Schuster W, Brennicke A (2006). "RNA editing in plant mitochondria". Science. 246 (4937): 1632–4. doi:10.1126/science.2480644. PMID 2480644. [88] Abascal F, Posada D, Knight RD, Zardoya R (2006). "Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes". PLoS Biology. 4 (5): 0711–0718. doi:10.1371/journal.pbio.0040127. PMC 1440934. PMID 16620150. [89] Henriquez FL, Richards TA, Roberts F, McLeod R, Roberts CW (2005 February). "The unusual mitochondrial compartment of Cryptosporidium parvum". Trends Parasitol. 21 (2): 68–74. doi:10.1016/j.pt.2004.11.010. PMID 15664529. [90] Hermann GJ, Thatcher JW, Mills JP, Hales KG, Fuller MT, Nunnari J, Shaw JM (1998 October). "Mitochondrial Fusion in Yeast Requires the Transmembrane GTPase Fzo1p". J. Cell. Bio. 143 (2): 359–373. doi:10.1083/jcb.143.2.359. PMC 2132826. PMID 9786948. [91] Seo AY, Joseph AM, Dutta D, Hwang JC, Aris JP, Leeuwenburgh C (2010 August). "New insights into the role of mitochondria in aging: mitochondrial dynamics and more". J. Cell. Sci. 123 (15): 2533–42. doi:10.1242/jcs.070490. PMC 2912461. PMID 20940129. [92] Kimball, J.W. (2006) "Sexual Reproduction in Humans: Copulation and Fertilization," (http:/ / home. comcast. net/ ~john. kimball1/ BiologyPages/ S/ Sexual_Reproduction. html#Copulation_and_Fertilization) Kimball's Biology Pages (based on Biology, 6th ed., 1996)] [93] Sutovsky, P., et al. (1999). "Ubiquitin tag for sperm mitochondria". Nature 402 (6760): 371–372. doi:10.1038/46466. PMID 10586873. Discussed in Science News (http:/ / www. sciencenews. org/ 20000101/ fob3. asp). [94] Mogensen HL (1996). "The Hows and Whys of Cytoplasmic Inheritance in Seed Plants". American Journal of Botany 83 (3): 383–404. doi:10.2307/2446172. JSTOR 2446172. [95] Johns, D. R. (2003). "Paternal transmission of mitochondrial DNA is (fortunately) rare". Annals of Neurology 54 (4): 422–4. doi:10.1002/ana.10771. PMID 14520651. [96] Thyagarajan B, Padua RA, Campbell C (1996). "Mammalian mitochondria possess homologous DNA recombination activity". J. Biol. Chem. 271 (44): 27536–27543. doi:10.1074/jbc.271.44.27536. PMID 8910339. [97] Lunt DB, Hyman BC (15 May 1997). "Animal mitochondrial DNA recombination". Nature 387 (6630): 247. doi:10.1038/387247a0. PMID 9153388. [98] Eyre-Walker A, Smith NH, Maynard Smith J (1999-03-07). "How clonal are human mitochondria?". Proc. Royal Soc. Biol. Sci. (Series B) 266 (1418): 477–483. doi:10.1098/rspb.1999.0662. PMC 1689787. PMID 10189711. [99] Awadalla P, Eyre-Walker A, Maynard Smith J (24 December 1999). "Linkage Disequilibrium and Recombination in Hominid Mitochondrial DNA". Science. 286 (5449): 2524–2525. doi:10.1126/science.286.5449.2524. PMID 10617471. [100] Castro JA, Picornell A, Ramon M (1998). "Mitochondrial DNA: a tool for populational genetics studies". Int Microbiol. 1 (4): 327–32. PMID 10943382. [101] Cann RL, Stoneking M, Wilson AC (1987 January). "Mitochondrial DNA and human evolution". Nature. 325 (6099): 31–36. doi:10.1038/325031a0. PMID 3025745. [102] Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ (2006). "Harvesting the fruit of the human mtDNA tree". Trends Genet. 22 (6): 339–45. doi:10.1016/j.tig.2006.04.001. PMID 16678300. [103] Garrigan D, Hammer MF (2006). "Reconstructing human origins in the genomic era". Nat. Rev. Genet. 7 (9): 669–80. doi:10.1038/nrg1941. PMID 16921345. [104] Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997). "Neandertal DNA sequences and the origin of modern humans". Cell 90 (1): 19–30. doi:10.1016/S0092-8674(00)80310-4. PMID 9230299. [105] Harding RM, Fullerton SM, Griffiths RC, Bond J, Cox MJ, Schneider JA, Moulin DS, Clegg JB (1997 April). "Archaic African and Asian lineages in the genetic ancestry of modern humans". Am J Hum Genet. 60 (4): 772–89. PMC 1712470. PMID 9106523. [106] Zeviani M, Di Donato S (2004). "Mitochondrial disorders". Brain. 127 (Pt 10): 2153–2172. doi:10.1093/brain/awh259. PMID 15358637. [107] Taylor RW, Turnbull DM (2005). "MITOCHONDRIAL DNA MUTATIONS IN HUMAN DISEASE". Nat. Rev. Genet. 6 (5): 389–402. doi:10.1038/nrg1606. PMC 1762815. PMID 15861210. [108] Chinnery PF, Schon EA (2003). "Mitochondria". J. Neurol. Neurosurg. Psychiatr. 74 (9): 1188–99. doi:10.1136/jnnp.74.9.1188. PMC 1738655. PMID 12933917. [109] Sherer TB, Betarbet R, Greenamyre JT (2002). "Environment, mitochondria, and Parkinson's disease". The Neuroscientist. 8 (3): 192–7. doi:10.1177/1073858402008003004. PMID 12061498. [110] Gomez C, Bandez MJ, Navarro A (2007). "Pesticides and impairment of mitochondrial function in relation with the parkinsonian syndrome". Front. Biosci. 12: 1079–93. doi:10.2741/2128. PMID 17127363. [111] Lim YA et al. (2010). "Abeta and human amylin share a common toxicity pathway via mitochondrial dysfunction". Proteomics 10 (8): 1621–33. doi:10.1002/pmic.200900651. PMID 20186753. [112] Schapira AH (2006). "Mitochondrial disease". Lancet 368 (9529): 70–82. doi:10.1016/S0140-6736(06)68970-8. PMID 16815381.

280

Mitochondrion
[113] Pieczenik SR, Neustadt J (2007). "Mitochondrial dysfunction and molecular pathways of disease". Exp. Mol. Pathol. 83 (1): 84–92. doi:10.1016/j.yexmp.2006.09.008. PMID 17239370. [114] Bugger H, Abel ED (2010). "Mitochondria in the diabetic heart". Cardiovascular Research 88 (2): 229–240. doi:10.1093/cvr/cvq239. [115] Richter C, Park J, Ames BN (1988 September). "Normal oxidative damage to mitochondrial and nuclear DNA is extensive". PNAS 85 (17): 6465–6467. doi:10.1073/pnas.85.17.6465. PMC 281993. PMID 3413108. [116] Harman D (1956). "Aging: a theory based on free radical and radiation chemistry". J. Gerontol. 11 (3): 298–300. PMID 13332224. [117] Soares et al, Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock (http:/ / www. ncbi. nlm. nih. gov/ pmc/ articles/ PMC2694979/ ?tool=pubmed) Am J Hum Genet. 2009 June 12; 84(6): 740–759. [118] Michael W. Nachman and Susan L. Crowell Estimate of the Mutation Rate per Nucleotide in Humans (http:/ / www. genetics. org/ content/ 156/ 1/ 297. full) Genetics, Vol. 156, 297-304, September 2000 [119] "Mitochondria and Aging." (http:/ / www. circuitblue. com/ biogerontology/ mito. shtml). . [120] Boffoli D, Scacco SC, Vergari R, Solarino G, Santacroce G, Papa S (1994). "Decline with age of the respiratory chain activity in human skeletal muscle". Biochim. Biophys. Acta. 1226 (1): 73–82. doi:10.1016/0925-4439(94)90061-2. PMID 8155742. [121] de Grey, Aubrey (Fall 2004). " Mitochondrial Mutations in Mammalian Aging: An Over-Hasty About-Turn? (http:/ / www. mprize. com/ files/ sens/ polg-PP. pdf)" Rejuvenation Res. 7 (3): 171–4. doi:10.1089/rej.2004.7.171. PMID 15588517. [122] Bender A, Krishnan KJ, Morris CM, Taylor GA, Reeve AK, Perry RH, Jaros E, Hersheson JS, Betts J, Klopstock T, Taylor RW, Turnbull DM (2006). "High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease". Nat Gen. 38 (5): 515–517. doi:10.1038/ng1769. PMID 16604074. [123] Trifunovic A, Hansson A, Wredenberg A, Rovio AT, Dufour E, Khvorostov I, Spelbrink JN, Wibom R, Jacobs HT, Larsson NG (2005). "Somatic mtDNA mutations cause aging phenotypes without affecting reactive oxygen species production". PNAS 102 (50): 17993–8. doi:10.1073/pnas.0508886102. PMC 1312403. PMID 16332961.

281

External links
• Mitochondria Atlas (http://www.uni-mainz.de/FB/Medizin/Anatomie/workshop/EM/EMMitoE.html) at University of Mainz • Mitochondria Research Portal (http://www.mitochondrial.net) at mitochondrial.net • Mitochondria: Architecture dictates function (http://www.cytochemistry.net/Cell-biology/mitoch1.htm) at cytochemistry.net • Mitochondria links (http://bama.ua.edu/~hsmithso/class/bsc_495/mito-plastids/mito_web.html) at University of Alabama • MIP (http://www.mitophysiology.org/) Mitochondrial Physiology Society • 3D structures of proteins from inner mitochondrial membrane (http://opm.phar.umich.edu/localization. php?localization=Mitochondrial inner membrane) at University of Michigan • 3D structures of proteins associated with outer mitochondrial membrane (http://opm.phar.umich.edu/ localization.php?localization=Mitochondrial outer membrane) at University of Michigan • Mitochondrial Protein Partnership (http://www.mitoproteins.org) at University of Wisconsin • Mitochondrion - Cell Centered Database (http://ccdb.ucsd.edu/sand/main?stype=lite& keyword=mitochondrion&Submit=Go&event=display&start=1) • Mitochondrion Reconstructed by Electron Tomography (http://www.sci.sdsu.edu/TFrey/MitoMovie.htm) at San Diego State University • Video Clip of Rat-liver Mitochondrion from Cryo-electron Tomography (http://www.wadsworth.org/databank/ electron/cryomito_dis2.html)  This article incorporates public domain material from the NCBI document "Science Primer" (http:/ / www. ncbi. nlm.nih.gov/About/primer/index.html).

Molecular microbiology

282

Molecular microbiology
Molecular microbiology is the branch of microbiology devoted to the study of the molecular principles of the physiological processes involved in the life cycle of prokaryotic and eukaryotic microorganisms such as bacteria, viruses, unicellular algae, fungi, and protozoa. This includes gene expression and regulation, genetic transfer, the synthesis of macromolecules, sub-cellular organization, cell to cell communication, and molecular aspects of pathogenicity and virulence. Molecular microbiology is primarily involved in the interactions between the various cell systems of microorganisms including the interrelationship of DNA, RNA and protein biosynthesis and the manner in which these interactions are regulated.

Bacteria
Mainly because of their relative simplicity, ease of manipulation and growth in vitro, and importance in medicine, bacteria were instrumental in the development of molecular biology. The complete genome sequence for a large number of bacterial species is now available. A list of sequenced prokaryotic genomes is available. Molecular microbiology techniques are currently being used in the development of new genetically engineered vaccines, in bioremediation,[1] biotechnology, food microbiology,[2] probiotic research,[3] antibacterial development[4] and environmental microbiology.[5] Many bacteria have become model organisms for molecular studies. Molecular techniques have had a direct influence on the clinical practice of medical microbiology. In many cases where traditional phenotypic methods of microbial identification and typing are insufficient or time-consuming, molecular techniques can provide rapid and accurate data, potentially improving clinical outcomes. Specific examples include: • 16s rRNA sequencing to provide bacterial identifications • Pulsed Field Gel Electrophoresis for strain typing of epidemiologically related organisms. • Direct detection of genes related to resistance mechanisms, such as mecA gene in Staphylococcus aureus

Gene expression and regulation
Bacteria have evolved abilities to regulate gene expression in response to signals in the intracellular and extracellular environment. Key to this are the diverse macromolecules (proteins or RNA) that sense change through direct interactions with chemical or physical stimuli.[6]

Bacterial pathogenesis
New infectious diseases are emerging and bacteria-induced illnesses, such as tuberculosis, whooping cough and typhoid fever, are still a major cause of global mortality. In recent decades the development of molecular biology and genetic tools has led to extensive studies on the molecular and cellular aspects of the virulence properties of pathogenic bacteria.[7]

Molecular microbiology

283

Bacterial glycomics
Glycans play diverse roles in bacterial physiology. Progress in the study of bacterial glycomics is advancing rapidly due to improvements in analytical methodologies and the development of new and innovative approaches for glycan isolation, characterization and synthesis. Research in bacterial glycomics could lead to the development of novel drugs, bioactive glycans and glycoconjugate vaccines.[8]

Horizontal gene transfer
Horizontal gene transfer (HGT) is a highly significant phenomenon amongst single-celled organisms. The evolution of bacteria and archaea often results from the acquisition of new genes through horizontal transfer rather than by modification of vertically inherited genes. Horizontal or lateral gene transfer is a major factor in the spread of bacterial antibiotic resistance and other adaptive traits of microorganisms and is particularly significant in microbial communities. HGT may also play a substantial role in the emergence of novel infections and opportunistic pathogens.[9]

Viruses
Viruses are important pathogens of humans and animals.[10] Their genomes are relatively small. For these reasons they were among the first organisms to be fully sequenced. The complete DNA sequence of the Epstein-Barr virus was completed in 1984.[11][12] Bluetongue virus (BTV) has been in the forefront of molecular studies for last three decades and now represents one of the best understood viruses at the molecular and structural levels.[13][14] Other viruses such as Papillomavirus,[15] Coronavirus,[16] Caliciviruses,[17] Paramyxoviruses[18] and Influenza virus[19][20] have also been extensively studied at the molecular level. Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and diverse entities in the biosphere. Bacteriophages, or "phage", have been fundamental in the development of the science of molecular biology and became "model organisms" for probing the basic chemistry of life.[21] The first DNA-genome project to be completed was the phage Φ-X174 in 1977. Φ29 phage, a phage of Bacillus, is a paradigm for the study of several molecular mechanisms of general biological processes, including DNA replication and regulation of transcription.[21][22]

Gene Therapy
Some viruses are used as vectors for gene therapy. Virus vectors have been developed that mediate stable genetic modification of treated cells by chromosomal integration of the transferred vector genomes. Gammaretroviral and lentiviral vectors, for example, can be utilized in clinical gene therapy aimed at the long-term correction of genetic defects, e.g., in stem and progenitor cells. Gammaretroviral and lentiviral vectors have so far been used in more than 300 clinical trials, addressing treatment options for various diseases.[23][24]

Molecular microbiology

284

RNAi and viruses
The new technology of RNAi is emerging as a powerful modality for battling some of the most notoriously challenging viral clinical targets. In particular, this technology is being developed as a new therapeutic tool for fighting specific viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV) and respiratory viruses.[25]

Fungi
Yeasts and molds are eukaryotic microorganisms classified in the kingdom Fungi.

Neurospora
Neurospora is the leading model for the study of the genomics and molecular biology of filamentous fungi. The ease of culture, amenability to genetic and molecular genetic analysis, and the close correlation between genetic and biochemical traits are some of its advantages. Research with Neurospora has provided insights unachievable from work with simpler systems and difficult to extract from more complicated ones. The application of modern high throughput analyses had led to increased information on the genomics and molecular biology of Neurospora in recent years.[26]

Technology
Polymerase chain reaction[27][28][29] (PCR) is used in microbiology to amplify (replicate many times) a single DNA sequence. If required, the sequence can also be altered in predetermined ways. Real-time PCR [30] is used for the rapid detection of microorganisms and is currently employed in diagnostic clinical microbiology laboratories, environmental analysis, food microbiology, and many other fields.[31] The closely related technique of quantitative PCR (qPCR) permits the quantitative measurement of DNA or RNA molecules and is used to estimate the densities of the reference pathogens in food, water and environmental samples. qPCR provides both specificity and quantification of target microorganisms.[29] Loop-mediated isothermal amplification (LAMP) is a relatively new DNA amplification technique that is simple, rugged and low cost. In LAMP, the target sequence is amplified at a constant temperature using either two or three sets of primers and a polymerase with high strand displacement activity. LAMP is used in organizations engaged in combating infectious diseases such as tuberculosis, malaria, and sleeping sickness in developing regions and has been proposed for the detection of waterborne pathogens.[5] Gel electrophoresis is used routinely in microbiology to separate DNA, RNA, or protein molecules using an electric field by virtue of their size, shape or electric charge. Southern blotting, northern blotting, western blotting and Eastern blotting are molecular techniques for detecting the presence of microbial DNA sequences (Southern), RNA sequences (northern), protein molecules (western) or protein modifications (Eastern). DNA microarrays are used in microbiology as the modern alternative to the "blotting" techniques. Microarrays permit the exploration of thousands of sequences at one time. This technique is used in molecular microbiology to detect the presence of pathogens in a sample (air, water, organ tissue, etc.). It is also used to determine the genetic differences between two microbial strains.[32] DNA sequencing and genomics have been used for many decades in molecular microbiology studies. Due to their relatively small size, virus and bacterial genomes were the first to be completely analysed by DNA sequencing. A huge range of sequence and genomic data is now available for a number of species and strains of microorganisms. Lab-on-a-chip (LOC) devices integrate and scale down laboratory functions and processes to a miniaturized chip format. Many LOC devices are used in a wide array of biomedical and other analytical applications including rapid

Molecular microbiology pathogen detection, clinical diagnosis, forensic science, electrophoresis, flow cytometry, blood chemistry analysis, protein and DNA analysis. LOC devices can be fabricated from many types of material including various polymers, glass, or silicon, or combinations of these materials. A broad variety of fabrication technologies are used for LOC device fabrication. LOC systems have several common features including microfluidics and sensing capabilities. Microfluidics deals with fluid flow in tiny channels using flow control devices (e.g. channels, pumps, mixers and valves). Sensing capabilities, usually optical or electrochemical sensors, can also be integrated into the chip.[32][33] RNA interference (RNAi) was discovered as a cellular gene regulation mechanism in 1998, but several RNAi-based applications for gene silencing have already made it into clinical trials. RNA interference (RNAi) technology has formed the basis of novel tools for biological research and drug discovery.[25][34] Nanotechnology, the engineering and art of manipulating matter at the nanoscale (1-100 nm), offers the potential of novel nanomaterials with applications in microbiology, in particular environmental microbiology.[35]

285

References
[1] Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2. [2] Fratamico PM and Bayles DO (editor). (2005). Foodborne Pathogens: Microbiology and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-00-4. [3] Mayo, B; van Sinderen, D (editor) (2010). Bifidobacteria: Genomics and Molecular Aspects. Caister Academic Press. ISBN 978-1-904455-68-4. [4] Miller, AA; Miller, PF (editor) (2011). Emerging Trends in Antibacterial Discovery: Answering the Call to Arms. Caister Academic Press. ISBN 978-1-904455-89-9. [5] Sen, K; Ashbolt, NK (editor) (2010). Environmental Microbiology: Current Technology and Water Applications. Caister Academic Press. ISBN 978-1-904455-70-7. [6] Spiro, S; Dixon, R (editor) (2010). Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition. Caister Academic Press. ISBN 978-1-904455-69-1. [7] Locht, C; Simonet, M (editor) (2012). Bacterial Pathogenesis: Molecular and Cellular Mechanisms. Caister Academic Press. ISBN 978-1-904455-91-2. [8] Reid, CW; Twine, SM; Reid, AN (editor) (2012). Bacterial Glycomics: Current Research, Technology and Applications. Caister Academic Press. ISBN 978-1-904455-95-0. [9] Francino, MP (editor) (2012). Horizontal Gene Transfer in Microorganisms. Caister Academic Press. ISBN 978-1-908230-10-2. [10] Mettenleiter TC and Sobrino F (editors). (2008). Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. [11] Baer et al. (1984). "DNA sequence and expression of the B95-8 Epstein—Barr virus genome". Nature 310 (5974): 207–211. doi:10.1038/310207a0. PMID 6087149. [12] Robertson ES (editor). (2005). Epstein-Barr Virus. Caister Academic Press. ISBN 978-1-904455-03-5. [13] Roy P (2008). "Molecular Dissection of Bluetongue Virus". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. [14] Roy P (2008). "Structure and Function of Bluetongue Virus and its Proteins". Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-21-9. [15] Campo MS (editor). (2006). Papillomavirus Research: From Natural History To Vaccines and Beyond. Caister Academic Press. ISBN 978-1-904455-04-2. [16] Thiel V (editor). (2007). Coronaviruses: Molecular and Cellular Biology. Caister Academic Press. ISBN 978-1-904455-16-5. [17] Hansman, GS (editor) (2010). Caliciviruses: Molecular and Cellular Virology. Caister Academic Press. ISBN 978-1-904455-63-9. [18] Samal, SK (editor) (2011). The Biology of Paramyxoviruses. Caister Academic Press. ISBN 978-1-904455-85-1. [19] Kawaoka Y (editor). (2006). Influenza Virology: Current Topics. Caister Academic Press. ISBN 978-1-904455-06-6. [20] Wang, Q; Tao, YJ (editors) (2010). Influenza: Molecular Virology. Caister Academic Press. ISBN 978-1-904455-57-8. [21] Mc Grath S and van Sinderen D (editors). (2007). Bacteriophage: Genetics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-14-1. [22] Graumann P (editor). (2007). Bacillus: Cellular and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-12-7. [23] Kurth, R; Bannert, N (editors) (2010). Retroviruses: Molecular Biology, Genomics and Pathogenesis. Caister Academic Press. ISBN 978-1-904455-55-4. [24] Desport, M (editors) (2010). Lentiviruses and Macrophages: Molecular and Cellular Interactions. Caister Academic Press. ISBN 978-1-904455-60-8. [25] Martinez, MA (editor) (2010). RNA Interference and Viruses: Current Innovations and Future Trends. Caister Academic Press. ISBN 978-1-904455-56-1. [26] Kasbekar, DP; McCluskey, K (editor) (2013). Neurospora: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-908230-12-6.

Molecular microbiology
[27] Logan J, Edwards K, Saunders N (editors) (2009). Real-Time PCR: Current Technology and Applications. Caister Academic Press. ISBN 978-1-904455-39-4. [28] Kennedy, S; Oswald, N (editor) (2011). PCR Troubleshooting and Optimization: The Essential Guide. Caister Academic Press. ISBN 978-1-904455-72-1. [29] Filion, M (editor) (2012). Quantitative Real-time PCR in Applied Microbiology. Caister Academic Press. ISBN 978-1-908230-01-0. [30] http:/ / www. horizonpress. com/ pcr [31] Mackay IM (editor). (2007). Real-Time PCR in Microbiology: From Diagnosis to Characterization. Caister Academic Press. ISBN 978-1-904455-18-9. [32] Herold, KE; Rasooly, A (editor) (2009). Lab-on-a-Chip Technology: Biomolecular Separation and Analysis. Caister Academic Press. ISBN 978-1-904455-47-9. [33] Herold, KE; Rasooly, A (editor) (2009). Lab-on-a-Chip Technology: Fabrication and Microfluidics. Caister Academic Press. ISBN 978-1-904455-46-2. [34] Morris, KV (editor) (2008). RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Caister Academic Press. ISBN 978-1-904455-25-7. [35] Cloete, TE (editor) (2010). Nanotechnology in Water Treatment Applications. Caister Academic Press. ISBN 978-1-904455-66-0.

286

External links
• Microbiology (http://www.horizonpress.com/gateway/micro.html) • University of Washington Medicine | Molecular Microbiology Division (http://depts.washington.edu/ molmicdx/) • John Innes Centre | Molecular Microbiology Department (http://www.jic.ac.uk/corporate/ science-departments/mol-micro.htm)

Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural [1][2][3][4][5][6][7] features. This includes aspects of the outward appearance (shape, structure, colour, pattern)[8] as well as the form and structure of the internal parts like bones and organs. This is in contrast to physiology, which deals primarily with function. Morphology is a branch of life science dealing with the study of gross structure of an organism or Taxon and its component parts.

Term
The word "morphology" is from the Greek μορφή, morphé = form and λόγος, lógos = word, study, research. The biological concept of morphology was developed by Johann Wolfgang von Goethe (1790) and independently by the German anatomist and physiologist Karl Friedrich Burdach (1800).

Morphology of a male Caprella mutica

In English-speaking countries, the term "molecular morphology" has been used for some time for describing the structure of compound molecules, such as polymers. [9] and RNA. The term "gross morphology" refers to the collective structures or an organism as a whole as a general description of the form and structure of an organism,

Morphology (biology) taking into account all of its structures without specifying an individual structure.

287

Branches of morphology
• Comparative Morphology is analysis of the patterns of the locus of structures within the body plan of an organism, and forms the basis of taxonomical categorization. • Functional Morphology is the study of the relationship between the structure and function of morphological features. • Experimental Morphology is the study of the effects of external factors upon the morphology of organisms under experimental conditions, such as the effect of genetic mutation. The field of morphology is divided into two distinct branches. • "Anatomy" is the study of the form and structure of internal features of an organism. • "Eidonomy" is the study of the form and structure of the external features of an organism.

Morphology and classification
Most taxa differ morphologically from other taxa. Typically, closely related taxa differ much less than more distantly related ones, but there are exceptions to this. Cryptic species are species which look very similar, or perhaps even outwardly identical, but are reproductively isolated. Conversely, sometimes unrelated taxa acquire a similar appearance as a result of convergent evolution or even mimicry. A further problem with relying on morphological data is that what may appear, morphologically speaking, to be two distinct species, may in fact be shown by DNA analysis to be a single species. The significance of these differences can be examined through the use of allometric engineering in which one or both species are manipulated to phenocopy the other species.

References
[1] [2] [3] [4] [5] [6] [7] [8] [9] "Morphology" (http:/ / www. askoxford. com/ concise_oed/ morphology?view=uk). http:/ / www. askoxford. com. . Retrieved 2010-06-24. "Morphology" (http:/ / www. merriam-webster. com/ medical/ morphology). Merriam Webster.com. . Retrieved 2010-06-24. "Morphology" (http:/ / dictionary. cambridge. org/ dictionary/ british/ morphology). dictionary.cambridge.org. . Retrieved 2010-06-24. "Morphology" (http:/ / encarta. msn. com/ encnet/ features/ dictionary/ DictionaryResults. aspx?lextype=3& search=morphology). encarta.msn.com. . Retrieved 2010-06-24. "Morphology" (http:/ / www. medterms. com/ script/ main/ art. asp?articlekey=4432lextype=3& search=morphology). www.medterms.com. . Retrieved 2010-06-24. "Morphology" (http:/ / dictionary. reference. com/ browse/ morphology). dictionary.reference.com. . Retrieved 2010-06-24. "Morphology" (http:/ / www. dictionary. net/ morphology). http:/ / www. dictionary. net/ . . Retrieved 2010-06-24. "morphology" (http:/ / www. britannica. com/ EBchecked/ topic/ 392797/ morphology). Encyclopædia Britannica. . Retrieved 2009-04-09. "Polymer Morphology" (http:/ / www. eng. uc. edu/ ~gbeaucag/ Classes/ Morphology. html). http:/ / www. ceas. uc. edu/ . . Retrieved 2010-06-24.

Mucin

288

Mucin
Mucins are a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most metazoans.[1] Mucins' key characteristic is their ability to form gels; therefore they are a key component in most gel-like secretions, serving functions from lubrication to cell signalling to forming chemical barriers.[1] They often take an inhibitory role.[1] Some mucins are associated with controlling mineralization, including nacre formation in molluscs,[2] calcification in echinoderms[3] and bone formation in vertebrates.[4] They bind to pathogens as part of the immune system. Overexpression of the mucin proteins, especially MUC1 is associated with many types of cancer.[5]

Micrograph showing cells with prominent mucin-containing intracytoplasmic vacuoles. Pap stain.

Although some mucins are membrane-bound due to the presence of a hydrophobic membrane-spanning domain that favors retention in the plasma membrane, most mucins are secreted onto mucosal surfaces or secreted to become a component of saliva.

Genes
At least 19 human mucin genes have been distinguished by cDNA cloning — MUC1, MUC2, MUC3A, MUC3B, MUC4, MUC5AC, MUC5B, MUC6, MUC7, MUC8, MUC12, MUC13, MUC15, MUC16, MUC17, MUC19, and MUC20.[6] The major secreted airway mucins are MUC5AC and MUC5B, while MUC2 is secreted mostly in the intestine but also in the airway.

Protein structure
Mature mucins are composed of two distinct regions: • The amino- and carboxy-terminal regions are very lightly glycosylated, but rich in cysteines. The cysteine residues participate in establishing disulfide linkages within and among mucin monomers. • A large central region formed of multiple tandem repeats of 10 to 80 residue sequences in which up to half of the amino acids are serine or threonine. This area becomes saturated with hundreds of O-linked oligosaccharides. N-linked oligosaccharides are also found on mucins, but in less abundance than O-linked sugars.

Mucin

289

Glycosylation and aggregation
Mucin genes encode mucin monomers that are synthesized as rod-shape apomucin cores that are post-translationally modified by exceptionally abundant glycosylation. The dense "sugar coating" of mucins gives them considerable water-holding capacity and also makes them resistant to proteolysis, which may be important in maintaining mucosal barriers. Mucins are secreted as massive aggregates of proteins with molecular masses of roughly 1 to 10 million Da. Within these aggregates, monomers are linked to one another mostly by non-covalent interactions, although intermolecular disulfide bonds may also play a role in this process.

Secretion
Upon stimulation, MARCKS (myristylated alanine-rich C kinase substrate) protein coordinates the secretion of mucin from mucin filled vesicles within the specialized epithelial cells.[7] Fusion of the vesicles to the plasma membrane causes release of the mucin, which as it exchanges Ca2+ for Na+ expands up to 600 fold. The result is a viscoelastic product of interwoven molecules which, combined with other secretions (e.g., from the airway epithelium and the submucosal glands in the respiratory system), is called mucus.[8] [9]

Clinical significance
Increased mucin production occurs in many adenocarcinomas, including cancers of the pancreas, lung, breast, ovary, colon and other tissues. Mucins are also overexpressed in lung diseases such as asthma, bronchitis, COPD or cystic fibrosis. Two membrane mucins, MUC1 and MUC4 have been extensively studied in relation to their pathological implication in the disease process.[10][11][12] Mucins are under investigation as possible diagnostic markers for malignancies and other disease processes in which they are most commonly over- or mis-expressed. Abnormal deposits of mucin are responsible for the non-pitting facial edema seen in untreated hypothryoidism. This edema is seen in the pretibial area as well.[13]

References
[1] Marin, F.; Luquet, G.; Marie, B.; Medakovic, D. (2007). "Molluscan Shell Proteins: Primary Structure, Origin, and Evolution". Current Topics in Developmental Biology Volume 80. Current Topics in Developmental Biology. 80. pp. 209. doi:10.1016/S0070-2153(07)80006-8. ISBN 9780123739148. [2] Marin, F.; Corstjens, P.; De Gaulejac, B.; De Vrind-De Jong, E.; Westbroek, P. (2000). "Mucins and molluscan calcification. Molecular characterization of mucoperlin, a novel mucin-like protein from the nacreous shell layer of the fan mussel Pinna nobilis (Bivalvia, pteriomorphia)". The Journal of Biological Chemistry 275 (27): 20667–20675. doi:10.1074/jbc.M003006200. PMID 10770949. [3] Boskey, A. (2003). "Biomineralization: an Overview". Connective Tissue Research 44 (1): 5–9. doi:10.1080/713713622. PMID 12952166. [4] RJ Midura, VC Hascall (1996). "Bone sialoprotein–a mucin in disguise?". Glycobiology 6 (7): 677–81. doi:10.1093/glycob/6.7.677. PMID 8953277. [5] Niv Y (April 2008). "MUC1 and colorectal cancer pathophysiology considerations". World J. Gastroenterol. 14 (14): 2139–41. doi:10.3748/wjg.14.2139. PMC 2703837. PMID 18407586. [6] Perez-Vilar, J; Hill, RL (2004). "Mucin Family of Glycoproteins". Encyclopedia of Biological Chemistry (Lennarz & Lane, EDs.) (Oxford: Academic Press/Elsevier) 2: 758–764. [7] Li, Y; Martin, LD; Spizz, G; Adler, KB (November 2, 2001). "MARCKS protein is a key molecule regulating mucin secretion by human airway epithelial cells in vitro". J Biol Chem 276 (44): 40982–90. doi:10.1074/jbc.M105614200. PMID 11533058. [8] Rogers, DF (September 2007). "Physiology of airway mucus secretion and pathophysiology of hypersecretion". Respir Care 52 (9): 1134–1146. PMID 17716382. [9] Perez-Vilar, J (20087). "Mucin granule intraluminal organization". Am J Respir Cell Mol Biol 36 (2): 183–190. doi:10.1165/rcmb.2006-0291TR. PMC 2176109. PMID 16960124. [10] Singh AP, Moniaux N, Chauhan SC, Meza JL, Batra SK (January 2004). "Inhibition of MUC4 expression suppresses pancreatic tumor cell growth and metastasis.". Cancer Research 64 (2): 622–30. doi:10.1158/0008-5472.CAN-03-2636. PMID 14744777. [11] Singh Ajay P., Chauhan Subhash C., Bafna Sangeeta, Johansson Sonny L., Smith Lynette M., Moniaux Nicolas, Lin Ming-Fong, Batra Surinder K. (March 2006). "Aberrant expression of transmembrane mucins, MUC1 and MUC4, in human prostate carcinomas". The Prostate

Mucin
66 (4): 421–429. doi:10.1002/pros.20372. PMID 16302265. [12] Singh A. P., Chaturvedi P., Batra S. K. (January 2007). "Emerging Roles of MUC4 in Cancer: A Novel Target for Diagnosis and Therapy". Cancer Research 67 (2): 433–436. doi:10.1158/0008-5472.CAN-06-3114. PMID 17234748. [13] Hanberg, Allen "Medical Surgical Nursing: clinical management for positive outcomes" Black and Hawk (Eds.). ElSevier 2009.

290

• Ali M, Hutton D, Wilson J, Pearson J (September 2005). "Major Secretory Mucin Expression in Chronic Sinusitis". Otolaryngology - Head and Neck Surgery 133 (3): 423–428. doi:10.1016/j.otohns.2005.06.005. PMID 16143194.

External links
• Mucins (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Mucins) at the US National Library of Medicine Medical Subject Headings (MeSH) • " Mucin (http://web.archive.org/web/20090616022448/http://www.mercksource.com/pp/us/cns/ cns_hl_dorlands_split.jsp?pg=/ppdocs/us/common/dorlands/dorland/five/000067870.htm)" at Dorland's Medical Dictionary

Mycology
Mycology (from the Greek μύκης, mukēs, meaning "fungus") is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, medicinals (e.g., penicillin), food (e.g., beer, wine, cheese, edible mushrooms) and entheogens, as well as their dangers, such as poisoning or infection. From mycology arose the field of phytopathology, the study of plant diseases, and the two disciplines remain closely related because the vast majority of "plant" pathogens are fungi. A biologist who studies mycology is called a mycologist.

Mushrooms are a kind of fungal reproductive structure

Historically, mycology was a branch of botany because, although fungi are evolutionarily more closely related to animals than to plants, this was not recognized until a few decades ago. Pioneer mycologists included Elias Magnus Fries, Christian Hendrik Persoon, Anton de Bary and Lewis David von Schweinitz. Many fungi produce toxins, antibiotics and other secondary metabolites. For example the cosmopolitan (worldwide) genus Fusarium and their toxins associated with fatal outbreaks of alimentary toxic aleukia in humans were extensively studied by Abraham Joffe. Fungi are fundamental for life on earth in their roles as symbionts, e.g. in the form of mycorrhizae, insect symbionts and lichens. Many fungi are able to break down complex organic biomolecules such as lignin, the more durable component of wood, and pollutants such as xenobiotics, petroleum, and polycyclic aromatic hydrocarbons. By decomposing these molecules, fungi play a critical role in the global carbon cycle. Fungi and other organisms traditionally recognized as fungi, such as oomycetes and myxomycetes (slime molds), often are economically and socially important as some cause diseases of animals (such as histoplasmosis) as well as plants (such as Dutch elm disease and Rice blast). Field meetings to find interesting species of fungi are known as 'forays', after the first such meeting organized by the Woolhope Naturalists' Field Club in 1868 and entitled "a foray among the fungi."

Mycology Some fungi can cause disease in humans or other organisms. The study of pathogenic fungi is referred to as medical mycology.[1]

291

History
Humans probably started collecting mushrooms as food in Prehistoric times. Mushrooms were first written about in the works of Euripides (480-406 B.C.). The Greek philosopher Theophrastos of Eressos (371-288 B.C.) was perhaps the first to try to systematically classify plants; mushrooms were considered to be plants that were missing certain organs. It was later Pliny the elder (23–79 A.D.), who wrote about truffles in his encyclopedia Naturalis historia. The Middle Ages saw little advancement in the body of knowledge about fungi. Rather, the invention of the printing press allowed some authors to disseminate superstitions and misconceptions about the fungi that had been perpetuated by the classical authors.[2]

Fungi and truffles are neither herbs, nor roots, nor flowers, nor seeds, but merely the superfluous moisture or earth, of trees, or rotten wood, and of other rotting things. This is plain from the fact that all fungi and truffles, especially those that are used for eating, grow most commonly in thundery and wet weather.


[3]

—Jerome Bock (Hieronymus Tragus), 1552

The start of the modern age of mycology begins with Pier Antonio Micheli's 1737 publication of Nova plantarum genera.[4] Published in Florence, this seminal work laid the foundations for the systematic classification of grasses, mosses and fungi. The term mycology and the complementary mycologist were first used in 1836 by M.J. Berkeley.[5]

Medicinal mycology
For centuries, certain mushrooms have been documented as a folk medicine in China, Japan, and Russia.[6] Although the use of mushrooms in folk medicine is largely centered on the Asian continent, people in other parts of the world like the Middle East, Poland and Belarus have been documented using mushrooms for medicinal purposes.[7][8] Certain mushrooms, especially polypores like Reishi were thought to be able to benefit a wide variety of health ailments. Medicinal mushroom research in the United States is currently active, with studies taking place at City of Hope National Medical Center,[9][10] as well as the Memorial Sloan–Kettering Cancer Center.[11] Current research focuses on mushrooms that may have hypoglycemic activity, anti-cancer activity, anti-pathogenic activity, and immune system enhancing activity. Recent research has found that the oyster mushroom naturally contains the cholesterol-lowering drug lovastatin,[12] mushrooms produce large amounts of vitamin D when exposed to UV light,[13] and that certain fungi may be a future source of taxol.[14] To date, penicillin, lovastatin, ciclosporin, griseofulvin, cephalosporin, ergometrine, and statins are the most famous pharmaceuticals which have been isolated from the fungi kingdom.

Mycology

292

Notes
[1] San-Blas G; Calderone RA (editors). (2008). Pathogenic Fungi (http:/ / www. horizonpress. com/ pat2). Caister Academic Press. . . [2] Ainsworth, p. 13. [3] De stirpium maxime earum quae in Germania nostra nascuntur, usitatis nomenclaturis. Strasbourg. In Ainsworth, p. 13, quoting Buller, AHR. (1915). Micheli and the discovery of reproduction in fungi. Transactions of the royal Society of Canada, series 3 9: 1–25. [4] Ainsworth, p. 4. [5] Ainsworth, p. 2. [6] Smith JE, Rowan NJ, Sullivan R (May 2002). "Medicinal Mushrooms: Their therapeutic properties and current medical usage with special emphasis on cancer treatments" (http:/ / sci. cancerresearchuk. org/ labs/ med_mush/ med_mush. html). Cancer Research UK. p. 5. . [7] Sarfaraz Khan Marwat, Mir Ajab Khan, Muhammad Aslam Khan, Mushtaq Ahmad, Muhammad Zafar, Fazal-ur-Rehman and Shazia Sultana (2009). "Vegetables mentioned in the Holy Qura’n and Ahadith and their ethnomedicinal studies in Dera Ismail Khan, N.W.F.P., Pakistan" (http:/ / scialert. net/ fulltext/ ?doi=pjn. 2009. 530. 538). Pakistan Journal of Nutrition 8 (5): 530–538. . Sahih Muslim, Book 23, Chapter 27, Hadiths [8] Shashkina MIa, Shashkin PN, Sergeev AV (October 2006). "[Chemical and medicobiological properties of Chaga (review)]". Farmatsevtychnyĭ zhurnal 40 (10). doi:10.1007/s11094-006-0194-4. [9] Di Rado, Alicia (July 2008). "A salad fixin' with medical benefits?" (http:/ / www. cityofhope. org/ about/ publications/ eHope/ 2008-vol-7-num-7-july-29/ Pages/ a-salad-fixin-with-medical-benefits. aspx). EHope (City of Hope National Medical Center) 7 (7). . [10] Di Rado, Alicia (November 2008). "Can a mushroom help fight lung cancer?" (http:/ / www. cityofhope. org/ about/ publications/ eHope/ 2008-vol-7-num-11-november-26/ Pages/ can-a-mushroom-help-fight-lung-cancer. aspx). EHope (City of Hope National Medical Center) 7 (11). . [11] Deng G, Lin H, Seidman A (September 2009). "A phase I/II trial of a polysaccharide extract from Grifola frondosa (Maitake mushroom) in breast cancer patients: immunological effects". Journal of Cancer Research and Clinical Oncology 135 (9): 1215–21. doi:10.1007/s00432-009-0562-z. PMID 19253021. [12] Gunde-Cimerman N, Cimerman A. (Mar 1995), "Pleurotus fruiting bodies contain the inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A reductase-lovastatin.", Exp Mycol. 19 (1): 1–6, doi:10.1006/emyc.1995.1001, ISSN 0147-5975, PMID 7614366 [13] Bowerman, Susan (March 31, 2008), "If mushrooms see the light" (http:/ / articles. latimes. com/ 2008/ mar/ 31/ health/ he-eat31), The Los Angeles Times, [14] Ji, Y; Bi; Yan; Zhu (Jan 2006), "Taxol-producing fungi: a new approach to industrial production of taxol" (http:/ / toxnet. nlm. nih. gov/ cgi-bin/ sis/ search/ r?dbs+ hsdb:@term+ @rn+ 33069-62-4) (Free full text), Sheng wu gong cheng xue bao = Chinese journal of biotechnology 22 (1): 1–6, ISSN 1000-3061, PMID 16572833,

References
Ainsworth, G. C. (1976). Introduction to the History of Mycology. Cambridge, UK: Cambridge University Press. ISBN 0-521-21013-5.

External links
• Professional organizations • BMS: British Mycological Society (http://www.britmycolsoc.org.uk/) (United Kingdom) • MSA: Mycological Society of America (http://www.msafungi.org) (North America) • Amateur organizations • Mycological Society of San Francisco (http://www.mssf.org/) • North American Mycological Association (http://namyco.org/clubs/index.html/) (list of amateur organizations in North America) • Puget Sound Mycological Society (http://psms.org/) • Oregon Mycological Society (http://www.wildmushrooms.org/) • Miscellaneous links • Online lectures in mycology (http://media.med.sc.edu/microbiology2007/) University of South Carolina • The WWW Virtual Library: Mycology (http://mycology.cornell.edu/) • MykoWeb links page (http://www.mykoweb.com/links.html) • Mycological Glossary at the Illinois Mycological Association (http://www.mushroomthejournal.com/ greatlakesdata/Terms/TermsFrame.html)

Mycology • FUNGI Magazine (http://www.fungimag.com/) for professionals and amateurs - largest circulating U.S. publication concerning all things mycological] • Fungal Cell Biology Group (http://129.215.156.68/index.html) at University of Edinburgh, UK. • Mycological Marvels (http://exhibits.mannlib.cornell.edu/mycological/) Cornell University, Mann Library

293

Myofibril
Myofibril

1. Axon 2. Neuromuscular junction 3. Muscle fiber 4. Myofibril Latin MeSH Code myofibrilla Myofibrils
[1] [2]

TH H2.00.05.0.00007

A myofibril (also known as a muscle fibril) is a basic rod-like unit of a muscle.[3] Muscles are composed of tubular cells called myocytes, also known as muscle fibers, and these cells in turn contain many chains of myofibrils. Myofibrils are composed of long proteins such as actin, myosin, and titin, and other proteins that hold them together. These proteins are organized into thin filaments and thick filaments, which repeat along the length of the myofibril in sections called sarcomeres. Muscles contract by sliding the thin (actin) and thick (myosin) filaments along each other. Actomyosin motors are important in muscle contraction (relying in this case on "classical myosins") as well as other processes like retraction of membrane blebs, filiopod
A diagram of the structure of a Myofibril

Myofibril

294

retraction, and uropodium advancement (relying in this case on "nonclassical myosins").

Structure
The filaments of myofibrils, myofilaments, consist of two types, thick and thin:

Sliding filament model of muscle contraction

• Thin filaments consist primarily of the protein actin, coiled with nebulin filaments. • Thick filaments consist primarily of the protein myosin, held in place by titin filaments. The protein complex composed of actin and myosin is sometimes referred to as "actomyosin." In striated muscle, such as skeletal and cardiac muscle, the actin and myosin filaments each have a specific and constant length on the order of a few micrometers, far less than the length of the elongated muscle cell (a few millimeters in the case of human skeletal muscle cells). The filaments are organized into repeated subunits along the length of the myofibril. These subunits are called sarcomeres. The muscle cell is nearly filled with myofibrils running parallel to each other on the long axis of the cell. The sarcomeric subunits of one myofibril are in nearly perfect alignment with those of the myofibrils next to it. This alignment gives rise to certain optical properties which cause the cell to appear striped or striated. In smooth muscle cells, this alignment is absent, hence there are no apparent striations and the cells are called smooth.

Appearance
The names of the various sub-regions of the sarcomere are based on their relatively lighter or darker appearance when viewed through the light microscope. Each sarcomere is delimited by two very dark colored bands called Z-discs or Z-lines (from the German zwischen meaning between). These Z-discs are dense protein discs that do not easily allow the passage of light. The T-tubule is present in this area. The area between the Z-discs is further divided into two lighter colored bands at either end called the I-bands, and a darker, grayish band in the middle called the A band. The I bands appear lighter because these regions of the sarcomere mainly contain the thin actin filaments, whose smaller diameter allows the passage of light between them. The A band, on the other hand, contains mostly myosin filaments whose larger diameter restricts the passage of light. A stands for anisotropic and I for isotropic, referring to the optical properties of living muscle as demonstrated with polarized light microscopy. The parts of the A band that abut the I bands are occupied by the both actin and myosin filaments (where they interdigitate as described above). Also within the A band is a relatively brighter central region called the H-zone (from the German helle, meaning bright) in which there is no actin/myosin overlap when the muscle is in a relaxed state. Finally, the A band is bisected by a dark central line called the M-line (from the German mittel meaning middle).

Myofibril

295

Action
The myosin heads form cross bridges with the Actin filaments, this is where they carry out a 'rowing' action along the actin. when the muscle fibre is relaxed (before contraction) the myosin head has ADP + pi bound to it. When a nerve impluse arrives, Ca2+ ions cause troponin to change shape, this moves the troponin+tropomyosin complex away from the myosin binding site. The Myosin head can now bind to the actin filament and tilts it through 45 degree angle so the actin is pulled along, the myosin head tilts the ADP+pi are released allowing ATP to attach to the myosin head. The myosin head hydrolyses the ATP to ADP+Pi (presence of Ca2+ ions activate the myosins ATPase) the energy produced by this is used to detach the myosin head from the actin The myosin head now flips back to the cocked position and is ready to bind to the actin again. And once the muscle relaxes the troponin and tropomyosin complex covers the myosin binding site once more. When a muscle contracts, the actin is pulled along myosin toward the center of the sarcomere until the actin and myosin filaments are completely overlapped. The H zone becomes smaller and smaller due to the increasing overlap of actin and myosin filaments, and the muscle shortens. Thus when the muscle is fully contracted, the H zone is no longer visible (as in the bottom diagram, left). Note that the actin and myosin filaments themselves do not change length, but instead slide past each other. This is known as the sliding filament theory of muscle contraction.

References
[1] http:/ / www. nlm. nih. gov/ cgi/ mesh/ 2011/ MB_cgi?mode=& term=Myofibrils [2] http:/ / www. unifr. ch/ ifaa/ Public/ EntryPage/ ViewTH/ THh200. html [3] McCracken, Thomas (1999). New Atlas of Human Anatomy. China: Metro Books. pp. 1-120. ISBN 1-5866-3097-0.

External links
• Nismat (http://www.nismat.org/physcor/muscle.html) • MsJensen (http://msjensen.cehd.umn.edu/1135/Links/Animations/Flash/0008-swf_sarcomere_shor.swf) (animation of sarcomeres contraction)

Nerve

296

Nerve
A nerve is an enclosed, cable-like bundle of axons (the long, slender projections of neurons) in the peripheral nervous system. A nerve provides a common pathway for the electrochemical nerve impulses that are transmitted along each of the axons to peripheral organs. In the central nervous system, the analogous structures are known as tracts.[1][2] Neurons are sometimes called nerve cells, though this term is potentially misleading since many neurons do not form nerves, and nerves also include non-neuronal Schwann cells that coat the axons in myelin. Each nerve is a cordlike structure that contains many axons. These axons are often referred to as "fibres". Within a nerve, each axon is surrounded by a layer of connective tissue called the endoneurium. The axons are bundled together into groups called fascicles, and each fascicle is wrapped in a layer of connective tissue called the perineurium. Finally, the entire nerve is wrapped in a layer of connective tissue called the epineurium.

Anatomy
Nerves are categorized into three groups based on the direction that signals are conducted: • Afferent nerves conduct signals from sensory neurons to the central nervous system, for example from the mechanoreceptors in skin.
Nerves (yellow)

• Efferent nerves conduct signals from the central nervous system along motor neurons to their target muscles and glands. • Mixed nerves contain both afferent and efferent axons, and thus conduct both incoming sensory information and outgoing muscle commands in the same bundle. Nerves can be categorized into two groups based on where they connect to the central nervous system: • Spinal nerves innervate much of the body, and connect through the spinal column to the spinal cord. They are given letter-number designations according to the vertebra through which they connect to the spinal column. • Cranial nerves innervate parts of the head, and connect directly to the brain (especially to the brainstem). They are typically assigned Roman numerals from 1 to 12, although cranial nerve zero is sometimes included. In addition, cranial nerves have descriptive names.

Nerve

297

Each nerve is covered externally by a dense sheath of connective tissue, the epineurium. Underlying this is a layer of flat cells, the perineurium, which forms a complete sleeve around a bundle of axons. Perineurial septae extend into the nerve and subdivide it into several bundles of fibers. Surrounding each such fiber is the endoneurium. This forms an unbroken tube which extends from the surface of the spinal cord to the level at which the axon synapses with its muscle fibers, or ends in sensory receptors. The endoneurium consists of an inner sleeve of material called the glycocalyx and an outer, delicate, Cross-section of a nerve meshwork of collagen fibers. Nerves are bundled along with blood vessels, since the neurons of a nerve have fairly high energy requirements. Within the endoneurium, the individual nerve fibers are surrounded by a low protein liquid called endoneurial fluid. The endoneurium has properties analogous to the blood–brain barrier, in that it prevents certain molecules from crossing from the blood into the endoneurial fluid. In this respect, endoneurial fluid is similar to cerebro-spinal fluid in the central nervous system. During the development of nerve edema from nerve irritation or (injury), the amount of endoneurial fluid may increase at the site of irritation. This increase in fluid can be visualized using magnetic resonance neurography, and thus MR neurography can identify nerve irritation and/or injury.

Physiology
A nerve conveys information in the form of electrochemical impulses (known as nerve impulses or action potentials) carried by the i