You are on page 1of 62

1

Cell biology Handout


Sources : - www.biologydaily.com
- www.biology.arizona.edu
Cell biology (also called cellular biology or cytology) is an academic discipline which
studies the physiological properties of cells, as well as their behaviours, interactions, and
environment; this is done both on a microscopic and molecular level. Cell biology
researches both single-celled organisms like bacteria and specialized cells in multicellular
organisms like humans.
Understanding the composition of cells and how cells works is fundamental to all of the
biological sciences. Appreciating the similarities and differences between cell types is
particularly important to the fields of cell and molecular biology. These fundamental
similarities and differences provide a unifying theme, allowing the principles learned from
studying one cell type to be extrapolated and generalized to other cell types. Research in
cell biology is closely related to genetics, biochemistry, molecular biology and developmental
biology.

Purification of cells and their parts

Purification of cells and their parts is achieved in the following ways:


Cell fractionation
Flow cytometry
Release of cellular organelles by disruption of cells.
Separation of different organelles by centrifugation.
Proteins extracted from membranes by detergents and salts.
The cell is the structural and functional unit of all living organisms. Some organisms, such
as bacteria, are unicellular, consisting of a single cell. Other organisms, such as humans,
are multicellular, (humans have an estimated 100,000 billion = 1014 cells). The cell theory,
first developed in the 19th century, states that all organisms are composed of one or more
cells; all cells come from preexisting cells; all vital functions of an organism occur within
cells and that cells contain the hereditary information necessary for regulating cell
functions and for transmitting information to the next generation of cells.
The word cell comes from the Latin cella, a small room. The name was chosen by Robert
Hooke because of the likeness he saw between cork cells and small rooms.
Each cell is a self-contained and self-maintaining entity: it can take in nutrients, convert
these nutrients into energy, carry out specialized functions, and reproduce as necessary.
Each cell stores its own set of instructions for carrying out each of these activities.
All cells share several abilities:

Reproduction by cell division.


Metabolism, including taking in raw materials, building cell components, creating
energy molecules and releasing by-products. The functioning of a cell depends upon
its ability to extract and use chemical energy stored in organic molecules. This
energy is derived from metabolic pathways.
Synthesis of proteins, the functional workhorses of cells, such as enzymes. A
typical mammalian cell contains up to 10,000 different proteins.
Response to external and internal stimuli such as changes in temperature, pH or
nutrient levels.
Traffic of vesicles.

2
Types of cells
One way to classify cells is whether they live alone or in groups. Organisms vary from
single cells (called single-celled or unicellular organisms) that function and survive
more or less independently, through colonial forms with cells living together, to
multicellular forms in which cells are specialized and do not generally survive once
separated. 220 types of cells and tissues make up the multicellular human body.
Cells can also be classified into two categories based on their internal structure.

Prokaryotic cells are structurally simple. They are found only in single-celled and
colonial organisms. In the three-domain system of scientific classification,
prokaryotic cells are placed in the domains Archaea and Eubacteria.

Eukaryotic cells have organelles with their own membranes. Single-celled

eukaryotic organisms are very diverse, but many colonial and multicellular forms
also exist. (The multicellular kingdoms, i.e., Animalia, Plantae and Fungi, are all
eukaryotic.)

Components of cells

Schematic of typical animal cell. Organelles: (1) nucleolus (2) nucleus (3) ribosome (4)
vesicle,(5) rough endoplasmic reticulum (ER), (6) Golgi apparatus, (7) Cytoskeleton, (8)
smooth ER, (9) mitochondria, (10) vacuole, (11) cytoplasm, (12) lysosome, (13) centrioles
All cells whether prokaryotic or eukaryotic have a membrane, which envelopes the cell,
separates its interior from the surroundings, strictly controls what moves in and out and
maintains the electric potential of the cell. Inside the membrane is a salty cytoplasm (the
substance which makes up most of the cell volume). All cells possess DNA, the hereditary
material of genes and RNA, which contain the information necessary to express various
proteins such as enzyme, the cell's primary machinery. Within the cell at any given time
are various additional biomolecules. This article will briefly overview these primary
components of the cell then continue to briefly describe their function.

Cell membrane - a cell's protective coat


The outer lining of a eukaryotic cell is called the plasma membrane. A form of plasma
membrane is also found in prokaryotes, but in this organism it is usually referred to as
the cell membrane. This membrane serves to separate and protect a cell from its
surrounding environment and is made mostly from a double layer of lipids (fat-like
molecules) and proteins. Embedded within this membrane are a variety of other
molecules that act as channels and pumps, moving different molecules into and out of
the cell.

Cytoskeleton - a cell's scaffold


The cytoskeleton is an important, complex, and dynamic cell component. It 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 moves parts of the cell in
processes of growth and motility. There are a great number of proteins associated with
the cytoskeleton, each controlling a cells structure by directing, bundling, and aligning
filaments.

Cytoplasm - a cell's inner space


Inside the cell there is a large fluid-filled space called the cytoplasm. This refers both to
the mixture of ions and fluids in solution within the cell, and the organelles contained in it
which are separated from this intercellular "soup" by their own membranes. The cytosol
refers only to the fluid, and not to the organelles.
In prokaryotes, the cytoplasm is relatively free of compartments. In eukaryotes, it
normally contains a large number of organelles, and is the home of the cytoskeleton. The
cytosol contains dissolved nutrients, helps break down waste products, and moves
material around the cell through a process called cytoplasmic streaming. The nucleus
often flows with the cytoplasm changing its shape as it moves. The cytoplasm also
contains many salts and is an excellent conductor of electricity, creating the perfect
environment for the mechanics of the cell. The function of the cytoplasm, and the
organelles which reside in it, are critical for a cell's survival.

Genetic material
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 a few
viruses have RNA as their genetic material. The biological information contained in an
organism is encoded in its DNA or RNA sequence. Note that RNA is also used for
information transport (mRNA) and enzymatic functions (like ribosomal RNA) in most
organisms.
Prokaryotic genetic material is organized in a simple circular DNA molecule (the bacterial
chromosome) that rests in the cytoplasm (more specifically in the nucleoid region).
Eukaryotic genetic material is more complex (DNA is condensed with proteins) and is
divided into different, linear molecules called chromosomes, which are found inside the
nucleus and can come in an haploid or diploid set. Besides some organelles have their own
genetic material, which is complemented by the nuclear genome (see endosymbiotic
theory).

4
Human genetic material, for example, is made up of two distinct components: the nuclear
genome and the mitochondrial genome. The nuclear genome (being diploid) is divided into
46 linear DNA molecules, each contained in a different chromosome. The mitochondrial
genome is a circular DNA molecule separate from the nuclear DNA. Although the
mitochondrial genome is very small, it codes for some very important proteins.

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. Organelles are found only in eukaryotes and are, with a few exceptions,
surrounded by a protective membrane.

Cell nucleus - a cell's 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 occur. The nucleus is spheroid
in shape 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 mRNA. This mRNA is then transported out of the nucleus, where it is
translated into a specific protein molecule. In prokaryotes, DNA processing takes
place in the cytoplasm.

Ribosomes - the protein production machine: Ribosomes are found in both


prokaryotes and eukaryotes. The ribosome is a large complex composed of many
molecules, including RNAs and proteins, and is responsible for processing the
genetic instructions carried by an mRNA. The process of converting an mRNA's
genetic code into the exact sequence of amino acids that make up a protein is
called translation. Protein synthesis is extremely important to all cells, and
therefore a large number of ribosomessometimes hundreds or even thousands
can be found throughout a cell.

Mitochondria and chloroplasts - the power generators: Mitochondria are


self-replicating organelles that occur in various numbers, shapes, and sizes in the
cytoplasm of all eukaryotic cells. As mentioned earlier, mitochondria contain their
own genome that is separate and distinct from the nuclear genome of a cell.
Mitochondria play a critical role in generating energy in the eukaryotic cell, and
this process involves a number of complex metabolic pathways.

Endoplasmic reticulum and Golgi apparatus - macromolecule managers::


The endoplasmic reticulum (ER) is the transport network for molecules targeted for
certain modifications and specific destinations, as compared to molecules that will
float freely in the cytoplasm. The ER has two forms: the rough ER and the smooth
ER. The rough ER is labeled as such because it has ribosomes adhering to its
outer surface, whereas the smooth ER does not. Translation of the mRNA for
those proteins that will either stay in the ER or be exported (moved out of the
cell) occurs at the ribosomes attached to the rough ER. Proteins to be exported
are passed to the Golgi apparatus, sometimes called a Golgi body or Golgi
complex, for further processing, packaging, and transport to a variety of other
cellular locations. The smooth ER serves for lipids synthesis, detoxification and as a
calcium reservoir.

Lysosomes and peroxisomes - the cellular digestive system: Lysosomes and


peroxisomes are often referred to as the garbage disposal system of a cell. Both
organelles are somewhat spherical, bound by a single membrane, and rich in
digestive enzymes, naturally occurring proteins that speed up biochemical
processes. For example, lysosomes can contain more than three dozen enzymes
for degrading proteins, nucleic acids, and certain sugars called polysaccharides.
Here we can see the importance behind compartmentalization of the eukaryotic
cell. The cell could not house such destructive enzymes if they were not contained
in a membrane-bound system.

Anatomy of cells
Eukaryotic cells are about 10 times the size of a prokaryote and can be as much as 1000

times greater in volume. The major and extremely significant 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 the presence of a nucleus, a membrane-delineated compartment that houses the
eukaryotic cells DNA. It is this nucleus that gives the eukaryoteliterally, true nucleus
its name. Eukaryotic organisms also have other specialized structures, performing
dedicated functions, the aforementioned organelles. Other differences include:

The cytoplasm of eukaryotes does not appear as granular as that of prokaryotes,


since an important part of the ribosomes are bound to the endoplasmic reticulum.
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 highly condensed (e.g. folded around histones). All
chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a
membrane. Some eukaryotic organelles can contain some DNA.
Eukaryotes can become mobile using cilia or flagella. The flagella are more
complex than those of prokaryotes.

Table 1: Comparison of features of prokaroytic and eukaryotic cells


Prokaryotes
Typical organisms
Typical size
Type of nucleus
DNA
RNA-/proteinsynthesis
Ribosomes

Cytoplasmatic

Eukaryotes

bacteria, archaea

protists, fungi, plants, animals

~ 1-10 m

~ 10-100 m (sperm cells, apart from the tail,


are smaller)

nucleoid region;

no

real nucleus

real nucleus with double membrane

circular (usually)

linear molecules (chromosomes) with histone

coupled in cytoplasm

RNA-synthesis inside the nucleus


protein synthesis in cytoplasm

50S+30S

60S+40S

very few structures

highly structured by endomembranes and a

proteins

cytoskeleton

6
structure
Cell movement

flagella made
flagellin

of

flagella and cilia made of tubulin

Mitochondria

none

one to several dozen (though some lack


mitochondria)

Chloroplasts

none

in algae and plants

Usually single cells

single cells, colonies, higher multicellular


organisms with specialized cells

Organization
Cell division

Binary fission

(simple

division)

Mitosis
Meiosis

Cell functions
Cell 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, where
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, via 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 Kreb's cycle, or citric acid cycle,
occurs inside the mitochondria and is capable of generating enough ATP to run all the cell
functions.

Making new cells


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. 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
Protein synthesis is the process in which the cell builds proteins. DNA transcription refers
to the synthesis of a messenger RNA (mRNA) molecule from a DNA template. This process

7
is very similar to DNA replication. Once the mRNA has been generated, a new protein
molecule is synthesized via the process of translation.
The cellular machinery responsible for synthesizing proteins is the ribosome. The
ribosome consists of structural RNA and about 80 different proteins. When the ribosome
encounters an mRNA, the process of translating an mRNA to a protein begins. The
ribosome accepts a new transfer RNA, or tRNAthe adaptor molecule that acts as a
translator between mRNA and proteinbearing an amino acid, the building block of the
protein. Another site binds the tRNA that becomes attached to the growing chain of
amino acids, forming the a polypeptide chain that will eventually be processed to become
a protein.

Origins of cells
The origin of cells has to do with the origin of life, and was one of the most important
steps in evolution of life as we know it. The birth of the cell marked the passage from
prebiotic chemistry to biological life.
If life is viewed from the point of view of replicators, that is DNA molecules in the
organism, cells satisfy two fundamental conditions: protection from the outside
environment and confinement of biochemical activity. The former condition is needed to
maintain the fragile DNA chains stable in a varying and sometimes aggressive
environment, and may have been the main reason for which cells evolved. The latter is
fundamental for the evolution of biological complexity . If freely-floating DNA molecules
that code for enzymes that are not enclosed into cells, the enzymes that advantage a
given DNA molecule (for example, by producing nucleotides) will automatically advantage
the neighbouring DNA molecules. This might be viewed as "parasitism by default".
Therefore the selection pressure on DNA molecules will be much lower, since there is not a
definitive advantage for the "lucky" DNA molecule that produces the better enzyme over
the others: all molecules in a given neighbourhood are almost equally advantaged.
If all the DNA molecule is enclosed in a cell, then the enzymes coded from the molecule
will be kept close to the DNA molecule itself. The DNA molecule will directly enjoy the
benefits of the enzymes it codes, and not of others. This means other DNA molecules
won't benefit from a positive mutation in a neighbouring molecule: this means that
positive mutations give immediate and selective advantage to the replicator bearing it,
and not on others. This is thought to have been the one of the main driving force of
evolution of life as we know it. (Note. This is more a metaphor given for simplicity than
complete accuracy, since the earliest molecules of life, probably up to the stage of cellular
life, were most likely RNA molecules, acting both as replicators and enzymes: see RNA
world hypothesis . But the core of the reasoning is the same.)
Biochemically, cell-like spheroids formed by proteinoids are observed by heating amino
acids with phosphoric acid as a catalyst. They bear much of the basic features provided
by cell membranes. Proteinoid-based protocells enclosing RNA molecules could (but not
necessarily should) have been the first cellular life forms on Earth.

Origin of eukaryotic cells


The eukaryotic cell seems to have evolved from a symbiotic community of prokaryotic
cells. It is almost certain that DNA-bearing organelles like the mitochondria and the
chloroplasts are what remains of ancient symbiotic oxygen-breathing bacteria and
cyanobacteria, respectively, where the rest of the cell seems to be derived from an
ancestral archaean prokaryote cell a theory termed the endosymbiotic theory.

8
There is still considerable debate on if organelles like the hydrogenosome predated the
origin of mitochondria, or viceversa : see the hydrogen hypothesis for the origin of
eukaryotic cells.

History

1632-1723: Antony 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.
...I could exceedingly plainly perceive it to be all perforated and porous, much like
a Honeycomb...these pores or cells, were not very deep, but consisted of a great
many little boxes... Hooke describing his observations on a thin slice of cork.
1839 : Theodor Schwann and Matthias Jakob Schleiden elucidate the principal that
plants and animals are made of cells, concluding that cells are a common unit of
structure and development, thus founding the Cell Theory.
The belief that life forms are able to occur spontaneously (generatio spontanea) is
contradicted by Louis Pasteur (1822-1895).
Rudolph 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.
1981: Lynn Margulis published Symbiosis in Cell Evolution detailing the
endosymbiotic theory.

Cell membrane
The selectively permeable cell membrane (or plasma membrane or plasmalemma) is
a thin and structured bilayer of phospholipid and protein molecules that envelopes the cell.
It separates a cell's interior from its surroundings and controls what moves in and out.
Cell surface membranes often contain receptor proteins and cell adhesion proteins. There
are also other proteins with a variety of functions. These membrane proteins are
important for the regulation of cell behavior and the organization of cells in tissues.

Transmembrane receptor
Transmembrane receptors are integral membrane proteins, which reside and operate
typically within a cell's plasma membrane, but also in the membranes of some subcellular
compartments and organelles. Binding to a signalling molecule or sometimes to a pair of
such molecules on one side of the membrane, transmembrane receptors initiate a
response on the other side. In this way they play a unique and important role in cellular
communications and signal transduction.
Many transmembrane receptors are composed of two or more protein subunits which
operate collectively and may dissociate when ligands bind, fall off, or at another stage of
their "activation" cycles. They are often classified based on their molecular structure, or

9
because the structure is unknown in any detail for all but a few receptors, based on their
hypothesized (and sometimes experimentally verified) membrane topology. The
polypeptide chains of the simplest are predicted to cross the lipid bilayer only once, while
others cross as many as seven times (the so-called G-protein coupled receptors).
Like any integral membrane protein, a transmembrane receptor may be subdivided into
three parts or domains.

E=extracellular space; I=intracellular space;


P=plasma membrane

The extracellular domain


The extracellular domain is the part of the
receptor that sticks out of the membrane on the outside of the cell or organelle. If the
polypeptide chain of the receptor crosses the bilayer several times, the external domain
can comprise several "loops" sticking out of the membrane. By definition. a receptor's
main function is to recognize and respond to a specific ligand, for example, a
neurotransmitter or hormone (although certain receptors respond also to changes in
transmembrane potential), and in many receptors these ligands bind to the extracellular
domain.

The transmembrane domain


In the majority of receptors for which structural evidence exists, transmembrane alpha
helices make up most of the transmembrane domain. In certain receptors, such as the
nicotinic acetylcholine receptor, the transmembrane domain forms a protein-lined pore
through the membrane, or ion channel. Upon activation of an extracellular domain by
binding of the appropriate ligand, the pore becomes accessible to ions, which then pass
through. In other receptors, the transmembrane domains are presumed to undergo a
conformational change upon binding, which exerts an effect intracellularly. In some
receptors, such as members of the 7TM superfamily, the transmembrane domain may
contain the ligand binding pocket (evidence for this and for much of what else is known
about this class of receptors is based in part on studies of bacteriorhodopsin, the detailed
structure of which has been determined by crystallography).

The intracellular domain


The intracellular (or cytoplasmic) domain of the receptor interacts with the interior of the
cell or organelle, relaying the signal. There are two fundamentally different ways for this
interaction:

The intracellular domain communicates via specific protein-protein-interactions


with effector proteins, which in turn send the signal along a signal chain to its
destination.
The intracellular domain has enzymatic activity. Often, this is a tyrosine kinase
activity. The enzymatic activity can also be located on an enzyme associated with
the intracellular domain.

10
Regulation of receptor activity
There are several ways for the cell to regulate the activity of a transmembrane receptor.
Most of them work through the intracellular domain. The most important ways are
phosphorylation and internalization (see ubiquitin).
Phosphorylation is the addition of a phosphate (PO4) group to a protein or a small
molecule. Its prominent role in biochemistry is the subject of a very large body of
research (the Medline database returns over 100,000 articles on the subject, largely on
protein phosphorylation).

Protein phosphorylation
Function
Protein phosphorylation is probably the most important regulatory event. Many enzymes
and receptors are switched "on" or "off" by phosphorylation and dephosphorylation.
Phosphorylation is catalyzed by various specific protein kinases, whereas phosphatases
dephosphorylate.
An example of the important role that phosphorylation plays is the p53 tumor suppressor
gene, whichwhen activestimulates transcription of gene that suppress the cell cycle ,
even to the extent that it undergoes apoptosis. However, this activity should be limited to
situations where the cell is damaged or physiology is disturbed. To this end, the p53
protein is extensively regulated. In fact, p53 contains more than 18 different
phosphorylation sites.
Upon the deactivating signal, the protein becomes dephosphorylated again and stops
working. This is the mechanism in many forms of signal transduction, for example the way
in which incoming light is processed in the light-sensitive cells of the retina.

Signaling networks
The network underlying phosphorylation can be very complex. In some cellular signalling
pathways, a protein A phosphorylates B, and B phosphorylates C, but A also
phosphorylates C directly, and B can phosphorylate D, which may in turn phosphorylate
A.

Types of phosphorylation
Within a protein, phosphorylation can occur on several amino acids. Phosphorylation on
serine is the most common, followed by threonine. Tyrosine phosphorylation is relatively
rare. However, since tyrosine phosphorylated proteins are relatively easy to purify using
antibodies, tyrosine phosphorylation sites are relatively well understood.
A protein kinase is an enzyme that can transfer a phosphate group from a donor
molecule (usually ATP) to an amino acid residue of a protein. The protein kinase
mechanism is used in signal transduction for the regulation of enzymes: phosphorylation
can activate (or inhibit) the activity of an enzyme. Although most protein kinases are
specialized for a single kind of amino acid residue, some exhibit dual kinase activity (they
can phosphorylate two different kinds of amino acids).

11

Other kinds
ATP, the "high-energy" exchange medium in the cell, is synthesized in the mitochondrion
by addition of a third phosphate group to ADP in a process referred to as oxidative
phosphorylation. ATP is also synthesized by substrate level phosphorylation during
glycolysis. Phosphorylation of sugars is often the stage of their catabolism. It allows cells

to accumulate sugars because the phosphate group prevents the molecules from diffusing
back across their transporter.
A tyrosine kinase is an enzyme that can transfer a phosphate group to a tyrosine
residue in a protein; these enzymes are a subgroup of the larger class of protein kinases.
Phosphorylation is an important function in signal transduction to regulate enzyme
activity. The hormones that act on tyrosine kinase receptors are generally growth
hormones and factors that promote cell division (e.g., insulin, insulin-like growth factor 1,
epidermal-derived growth factor).

A Fluid Mosaic
The basic composition and structure of the plasma membrane is the same as that of the
membranes that surround organelles and other subcellular compartments. The foundation
is a phospholipid bilayer, and the membrane as a whole is often described as a 'fluid
mosaic' - a two-dimensional fluid of freely diffusing lipids, dotted or embedded with
proteins which may function as channels or transporters across the membrane, or as
receptors. Some of these proteins simply adhere to the membrane (extrinsic or
peripheral proteins), while others might be said to reside within it or to span it (intrinsic
proteins -- more at integral membrane protein). Glycoproteins have carbohydrates
attached to their extracellular domains. Cells may vary the variety and the relative
amounts of different lipids to maintain the fluidity of their membranes despite changes in
temperature. Cholesterol molecules (in case of eukaryotes) or hopanoids (in case of
prokaryotes) in the bilayer assist in regulating fluidity.

12
Phospholipids are formed from four components: fatty acids, a negatively charged
phosphate group, an alcohol and a backbone. Phospholipids with a glycerol backbone
are known as phosphoglycerides. There is only one type of phospholipid with a
sphingosine backbone; sphingomyelin. Phospholipids are a major component of all
biological membranes, along with glycolipids and cholesterol.

Detailed Structure
In fact, not all lipid molecules in the cell membrane are "fluid," in the sense of free to
diffuse. Lipid rafts and caveolae are examples of more cohesive membrane regions. Across
the membrane globally, also many proteins are not entirely free to diffuse. The
cytoskeleton undergirds the cell membrane and provides anchoring points for integral
membrane proteins. Anchoring restricts them to a particular cell face or surface--for
example, the "apical" surface of epithelial cells that line the vertebrate gut--and limits how
far they may diffuse within the bilayer. Finally, rather than presenting always a formless
and fluid contour, the plasma membrane surface of cells may show structure. Returning
to the example of epithelial cells in the gut, the apical surfaces of many such cells are
dense with involutions, all similar in size. The finger-like projections, called "microvilli",
increase cell surface area and facilitate the absorption of molecules from the outside.
Synapses are another example of highly structured membrane.

Transport across membranes


As a lipid bilayer, the cell membrane is selectively permeable. This means that only some
molecules can pass unhindered in or out of the cell. These molecules are either small or
lipophilic. Other molecules can pass in or out of the cell, if there are specific transport
molecules.
Depending on the molecule, transport occurs by different mechanisms, which can be
separated into those that do not consume energy in the form of ATP (passive transport)
and those that do (active transport):

Passive transport
Passive transport is a means of moving biochemicals, and other atomic or molecular
substances, across membranes. Unlike active transport, this process does not involve
chemical energy (ATP). Passive transport is dependent on the permeability of the cell
membrane, which, in turn, is dependent on the organization and characteristics of the
membrane lipids and proteins. The four main kind of passive transport are diffusion,
facilitated diffusion, filtration and osmosis.

Diffusion
Diffusion is the net movement of material from an area of high concentration of that
material to an area with lower concentration. The difference of concentration between the
two areas is often termed as the concentration gradient, and diffusion will continue until
this gradient has been eliminated. Since diffusion moves material from area of higher
concentration to the lower, it is described as moving solutes "down the concentration
gradient" (compared with active transport, which often moves material from area of low
concentration to area of higher concentration, and therefore referred to as moving the
material "against the concentration gradient").

13
If and when the concentration gradient have been eliminated, no net exchange of
material occurs. Although material may move forth from one area to the other, it will be
balanced by movement of the same amount of material to the opposite direction.
Diffusion is biologically important because it enables the abolishment of concentration
gradients in the body. For example, metabolic activity will consume oxygen, which will
reduce its concentration in the bloodstream; diffusion of oxygen in the alveoli of the lungs
allows it to be replenished.

Facilitated diffusion
Facilitated diffusion is movement of molecules across the cell membrane via special
carrier proteins that are embedded within the cellular membrane. A lot of large
molecules, such as glucose, are insoluble in lipids and too large to fit through the
membrane pores. Therefore, it will bind with its specific carrier proteins, and the complex
will then be bonded to a receptor site and moved through the cellular membrane. Bear in
mind, however, that facilitated diffusion is a passive process, and the solutes still move
down the concentration gradient.

Filtration
Filtration is movement of water and solute molecules across the cell membrane due to
hydrostatic pressure generated by the cardiovascular system. Depending on the size of
the membrane pores, only solutes of a certain size may pass through it. For example, the
membrane pores of the Bowman's capsule in the kidneys are very small, and only albumin,
the smallest of the proteins, have any chance of being filtered through. On the other
hand, the membrane pores of liver cells are extremely large, to allow a veriety of solutes
to pass through and be metabolized.

Osmosis
Osmosis is basically diffusion of water molecules. Most cell membranes are permeable to
water, and since the diffusion of water plays such an important role in the biological
functioning of any living being, a special term has been coined for it -- osmosis.
Water molecules "stick" together via weak hydrogen bonds; therefore, unlike most
solutes, water molecules move around in large clumps, a phenomenon known as bulk
flow.

Active transport
Typically moves molecules against their electrochemical gradient , a process that would
be entropically unfavorable were it not stoichiometrically coupled with the hydrolysis of
ATP. This coupling can be either primary or secondary. In the primary active transport,
transporters that move molecules against their electrical/chemical gradient, hydrolyze
ATP. In the secondary active transport, transporters use energy derived from transport of
another molecule in the direction of their gradient, to move other molecules in the
direction against their gradient. This can be either symport (in the same direction) or
antiport (in the opposite direction).

14

Examples include:
1. endocytosis
2. exocytosis, in which molecules packaged in membrane vesicles are either
imported or exported, respectively. Molecular exchangers , transporters and
pumps represent other examples.
Active transport is the mediated transport of biochemicals, and other atomic/molecular
substances, across membranes. Unlike passive transport, this process requires chemical
energy. In this form of transport, molecules move against either an electrical or
concentration gradient (collectively termed an electrochemical gradient). This is achieved

by either altering the affinity of the binding site or altering the rate at which the protein
changes conformations.

Types
There are two main types, primary and secondary. In primary transport energy is directly
coupled to movement of desired substance across a membrane, independent of any other
species. Secondary transport concerns the diffusion of one species across a membrane to
drive the transport of another.

Primary
Primary active transport directly uses energy to transport molecules across a membrane.
Most of the enzymes that perform this type of transport are transmembrane ATPases. A
primary ATPase universal to all cellular life is the sodium-potassium pump, which helps
maintain the cell potential.
ATPases are a class of enzymes that catalyze the decomposition of adenosine
triphosphate (ATP) into adenosine diphosphate (ADP) and a free phosphate ion. This
dephosphorylation reaction releases energy, which the enzyme (in most cases) harnesses
to drive other chemical reactions that would not otherwise occur. Some such enzymes are
integral membrane proteins (anchored within biological membranes), and move solutes
across the membrane. (These are called transmembrane ATPases).
Transmembrane ATPases import many of the metabolites necessary for cell metabolism
and export toxins, wastes, and solutes that can hinder cellular processes. An important
example is the sodium-potassium exchanger (or Na+/K+ATPase), which establishes the
ionic concentration balance that maintains the cell potential.

Secondary

15
In secondary active transport, there is no direct coupling of ATP; instead, the
electrochemical potential difference created by pumping ions out of cells is used. The two
main forms of this are counter-transport (antiport) and co-transport (symport).

Counter-transport
In counter-transport two species of ion or other solute are pumped in opposite directions
across a membrane. One of these species is allowed to flow from high to low
concentration, which yields the entropic energy to drive the transport of the other solute
from a low concentration region to a high one. An example is the sodium-calcium
exchanger or antiporter, which allows three sodium ions into the cell to transport one
calcium out.
Many cells also posses a calcium ATPase, which can operate at lower intracellular
concentrations of calcium and sets the normal or resting concentration of this important
second messenger. But the ATPase exports calcium ions more slowly: only 30 per second
versus 2000 per second by the exchanger. The exchanger comes into service when the
calcium concentration rises steeply or "spikes" and enables rapid recovery. This shows
that a single type of ion can be transported by several enzymes, which need not be active
all the time (constitutively), but may exist to meet specific, intermittent needs.

Co-transport
Co-transport also uses the flow of one solute species from high to low concentration to
move another molecule against its preferred direction of flow; but here, both solutes
move in the same direction across the membrane. An example is the glucose symporter,
which cotransports two sodiums for every molecule of glucose it imports into the cell.

Movement of proteins
Proteins are synthesized by ribosomes in the cytoplasm. This process is also known as
protein biosynthesis or simply protein translation . Some proteins, such as those to be
incorporated in membranes (membrane proteins), are transported into the ER during
synthesis and further processed in the Golgi apparatus. From the Golgi, membrane
proteins can move to the plasma membrane, to other subcellular comparments 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 constant flux of proteins through these compartments. ER and
Golgi-resident proteins associate with other proteins and remain in their respective
compartments. Other proteins "flow" through the ER and Golgi to the plasma membrane.
From the plasma membrane, proteins destined to be degraded move back into
intracellular compartments where they are broken down to their individual amino acids.

16

Summary of the different methods by which molecules can enter cells.

Cell adhesion

Schematic of cell adhesion


Cells are often not found in isolation, rather they tend to stick to other cells or non-

cellular components of their environment. A fundamental question is: what makes cells
sticky? Cell adhesion generally involves protein molecules at the surface of cells, so the
study of cell adhesion involves cell adhesion proteins and the molecules that they bind to.

Cell adhesion proteins (or Cell adhesion molecules, CAMs)


Cell adhesion proteins are often transmembrane receptors. Transmembrane cell adhesion
proteins extend across the cell surface membrane and typically have domains that extend
into both the extracellular space and the intracellular space. The extracellular domain of a
cell adhesion protein can bind to other molecules that might be either on the surface of
an adjacent cell (cell-to-cell adhesion) or part of the extracellular matrix (cell-to-ECM
adhesion). The molecule that a cell adhesion protein binds to is called its ligand. There

17
are families of cell adhesion proteins that can be characterized in terms of the structure
of the adhesion proteins and their ligands. Adhesion between two copies of the same
adhesion protein is called "homophilic" binding. Adhesion between an adhesion protein
and some other molecule is "heterophilic" binding.

Major Cell Adhesion Protein Families


Family

ligands

interactions

Selectins

Carbohydrates

heterophilic

Integrins

Extracellular matrix

heterophilic

Ig superfamily proteins heterophilic


Ig superfamily proteins Integrins

heterophilic

Ig superfamily proteins homophilic


Cadherins

Cadherins

homophilic

Cytoskeletal interactions
For a cell adhesion protein like the one shown in the diagram, the intracellular domain
binds to protein components of the cell's cytoskeleton. This allows for very tight
adhesion. Without attachment to the cytoskeleton, a cell adhesion protein that is tightly
bound to a ligand would be in danger of being ripped out of the fragile cell membrane.
Often the connection between the cell adhesion proteins and the cytoskeleton is not as
direct as shown in the diagram. For example, cadherin cell adhesion proteins are typically
coupled to the cytoskeleton by way of special linking proteins called "catenins".

Importance of cell adhesion


Cell adhesion proteins are important for the normal functioning of living organisms. Cell
adhesion proteins hold together the components of solid tissues. They are also important
for the function of migratory cells like white blood cells. Regulation of cell adhesion
proteins is important during embryonic development for the process of morphogenesis.
Some people have "blistering diseases" that result from inherited molecular defects in
genes for adhesion proteins. Some cancers involve mutations in genes for adhesion
proteins that result in abnormal cell-to-cell interactions and tumor growth. Cell adhesion
proteins are also important for interactions that allow viruses and bacteria to cause
damage to humans. Cell adhesion proteins hold synapses together and the regulation of
synaptic adhesion is involved in learning and memory. In Alzheimer's disease there is
abnormal regulation of synaptic cell adhesion.

18
Desmosome

Cell adhesion in desmosomes


A desmosome (also known as macula adherens) is a cell structure specialized for cellto-cell adhesion. Desmosomes are molecular complexes of cell adhesion proteins and
linking proteins that attach the cell surface adhesion proteins to intracellular keratin
cytoskeletal filaments. The cell adhesion proteins of the desmosome are members of the
cadherin family of cell adhesion molecules. They are transmembrane proteins that bridge
the space between adjacent epithelial cells by way of homophilic binding of their
extracellular domains to other desmosomal cadherins on the adjacent cell. The
desmosomal linking proteins such as desmoplakin bind to the intracellular domain of
cadherins and form a connecting bridge to the cytoskeleton.

Blistering diseases
If the desmosomes connecting adjacent epithelial cells of the skin are not functioning
correctly, layers of the skin can pull apart and allow abnormal movements of fluid within
the skin, resulting in blisters and other tissue damage. Blistering diseases such as
Pemphigus Vulgaris can be due to genetic defects in desmosomal proteins or due to an
autoimmune response. These patients are often be found to have antibodies that bind to
the desmosomal cadherins and disrupt the desmosomes.

Hemidesmosomes
When visualized by electron microscopy, hemidesmosomes are similar in appearance to
desmosomes. Rather than linking two cells, hemidesmosomes attach one cell to the
extracellular matrix. Rather than using cadherins, hemidesmosomes use integrin cell
adhesion proteins.

19
Cytoskeleton
The cytoskeleton is a cellular "scaffolding" or "skeleton" contained within the cytoplasm.
It is a dynamic structure that maintains cell shape, enables some cell motion (using
structures such as flagella and cilia), and plays important roles in both intra-cellular
transport (the movement of vesicles and organelles, for example) and cellular division.
Eukaryotic cells contain three kinds of cytoskeletal filaments.

Actin Filaments
Actin is a globular protein that polymerize helicaly forming actin filaments (or
microfilaments), which like the other two components of the cellular cytoskeleton form a
three-dimensional network inside an eukariotic cell. Actin filaments provide mechanical
support for the cell, determine the cell shape, enable cell movements (through
pseudopods); and participate in certain cell junctions, in cytoplasmic streaming and in
contraction of the cell during cytokinesis. In muscle cells they play an essential role, along
with myosin, in muscle contraction. In the cytosol, actin is predominantly bound to ATP, but
can also bind to ADP. An ATP-actin complex polymerizes faster and dissociates slower
than an ADP-actin complex. Actin is also one of the most highly conserved proteins,
differing by no more than 5% in species as diverse as algae and humans.

Microfilaments assembly
The globular Actin is known as G-actin, while the filamentous polymer composed of Gactin subunits (a microfilament), is called F-actin. The microfilaments are the thickest of
the cytoskeleton, with only 7nm in diameter. Much like the microtubules, actin filaments
are polar, with the plus (+) end elongating approximately 10 times faster than the minus
(-) end. The process of actin polymerization, nucleation, starts with the association of
three G-actin monomers into a trimer. ATP-actin then binds the plus (+) end, and the ATP
is subsequently hydrolyzed, which reduces the binding strength between neighboring
units and generally destabilizes the filament. ADP-actin dissociates from the minus end
and the increase in ADP-actin stimulates the exchange of bound ADP for ATP, leading to
more ATP-actin units. This rapid turnover is important for the cells movement.
The protein cofilin binds to ADP-actin units and promotes their dissociation from the
minus end and prevents their reassembly. The protein profilin reverses this effect by
stimulating the exchange of bound ADP for ATP. In addition, ATP-actin units bound to
profilin will dissociate from cofilin and are then free to polymerize. Another important
component in filament production is the Arp2/3 proteins, which serve as sites for
nucleation, stimulating the formation of G-actin trimers. All of these three proteins are
regulated by cell signaling mechanism.
Actin filaments are assembled in two general types of structures: bundles and networks.
Actin-binding proteins dictate the formation of either structure since they cross-link actin
filaments. Actin filaments have the appearance of a double-stranded helix.

Bundles
There are two types of actin bundles: parallel and contractile bundles. In parallel bundles,
the filaments are spaced 14nm apart by the actin-bundling proteins fimbrin. Parallel
bundles are responsible for the supporting a cells microvilli. In vertebrates, the actinbundling protein villin is almost entirely found in the microvilli of intestinal cells.
Together with myosin filaments actin it forms Actomyosin, which provides the mechanism
for muscle contraction. Actin uses ATP for energy. The ATP allows, through hydrolysis, the
myosin head to extend up and bind with the actin filament. The myosin head then
releases after moving the actin filament in a relaxing or contracting movement by usage
of ADP.

20
In contractile bundles, the actin-bundling protein actinin separates each filament by
40nm. This increase in distance allows the motor protein myosin to interact with the
filament, enabling deformation or contraction. In the first case, one end of myosin is
bound to the plasma membrane while the other end walks towards the plus end of the
actin filament. This pulls the membrane into a different shape relative to the cell cortex.
For contraction, the myosin molecule is usually bound to two separate filaments and both
ends simultaneously walk towards their filament's plus end, sliding the actin filaments
over each other. This results in the shorterning, or contraction, of the actin bundle (but
not the filament). This mechanism is responsible for muscle contraction and cytokinesis,
the division of one cell into two.

Networks
Actin networks, along with their actin-binding protein, filamin , form the cells cortex. This
underlies the plasma membrane and is responsible for the shape of the cell.

Intermediate Filaments
These 8 to 11 nanometers in diameter filaments are the more stable (strongly bound)
and heterogenous constitutents of the cytoskeleton. They organize the internal
tridimensional structure of the cell (they are structural components of the nuclear
envelope or the sarcomeres for example). Their size is intermediate between that of
microfilaments and microtubules. They are assembled from several different proteins. IFs
crisscross the cytosol from the nuclear envelope to the cell membrane. They also
participate in some cell-cell and cell-matrix junctions.
Different intermediate filaments are:

vimentins, being the common structural support of many cells.


keratin, found in skin cells, hair and nails.
Neurofilaments of neural cells.
Lamin, giving structural support to the nuclear envelope.

Microtubules
They are hollow cylinders of about 25 nm., formed by 13 protofilaments which, in turn,
are polymers of alpha and beta tubulin (a potein). They have a very dynamic behaviour,
binding GTP for polymerization, they are organized by the centrosome.
They play key roles in:

Intracellular transport (asociated with dyneins and kinesins they transport


organelles like mitochondria or vesicles.)
the axoneme of cilia and flagella
the mitotic spindle

Microtubules are part of a structural network (the cytoskeleton) within the cell's
cytoplasm, but in addition to structural support microtubules are used in many other
processes as well. They are capable of growing and shrinking in order to generate force,
and there are also motor proteins that move along the microtubule. A notable structure
involving microtubules is the mitotic spindle used by eukaryotic cells to segregate their

21
chromosomes correctly during cell division. Microtubules are also responsible for the
flagella of eukaryotic cells (prokaryote flagella are entirely different).

Dynamic Instability
Tubulin binds GTP in order to assemble onto the (+) end of a microtubule. Shortly after

assembly, the GTP is hydrolyzed to GDP. A GDP-bound tubulin subunit at the tip of a
microtubule will fall off, though a GDP-bound tubulin in the middle of a microtubule
cannot spontaneously pop out. Since tubulin adds onto the end of the microtubule only in
the GTP-bound state, there is generally a cap of GTP-bound tubulin at the tip of the
microtubule, protecting it from disassembly. When hydrolysis catches up to the tip of the
microtubule, it begins a rapid depolymerization and shrinkage. This switch from growth to
shrinking is called a catastrophe. GTP-bound tubulin can begin adding to the tip of the
microtubule again, providing a new cap and protecting the microtubule from shrinking.
This is referred to as rescue.
The drug taxol, used in the treatment of cancer, blocks dynamic instability by stabilizing
GDP-bound tubulin in the microtubule. Thus, even when hydrolysis of GTP reaches the tip
of the microtubule, there is no depolymerization and the microtubule does not shrink
back. Colchicine has the opposite effect: it blocks the polymerization of tubulin into
microtubules.

Motor Proteins
In addition to movement generated by the dynamic instability of the microtubule itself,
the fibers are substrates along which motor proteins can move. The major microtubule
motor proteins are kinesin and dynein.

Cilium
A cilium (plural cilia) is a fine projection from a cell. There are two types of cilia: (1)
motile cilium, which constantly beats in one direction, and (2) non-motile cilium, which
cannot beat and usually serves as a sensor.
Cilia are structurally identical to eukaryotic flagella, and the two terms are often used
interchangeably. In general, though, the term cilia is used when they are numerous,
short and coordinated while flagella is used when they are relatively sparse and long. The
name cilium may also be used to emphasize their differences from bacterial flagella.
Motile cilia are almost never found alone, usually being present on a cell's surface in large
numbers that beat coordinately in unified waves. In humans, for example, motile cilia are
found in the lining of the trachea or windpipe, where they sweep mucus and dirt out of
the lungs. In the oviducts, the beating of cilia moves the ovum from the ovary to the
uterus.
Opposite to the motile cilia, non-motile cilium usually exists as one cilium per cell. The
outer segment of the rod photoreceptor cell in the human eye is connected to its cell
body with a specialized non-motile cilium. The terminal fiber of the olfactory neuron is
also a non-motile cilium, where the odorant receptors locate. Almost all types of the
mammalian cells have a single non-motile cilium called "Primary cilium" that has been
neglected for a long time. Recent studies led scientists to re-evaluate its physiological
role(s) in the cell signaling and the control of cell growth and development.
A cilium has an outer membrane that surrounds a core called an axoneme, which
contains nine pairs of microtubule doublets and other associated proteins. Motile cilia
have a central core with two additional microtubule singlets and dynein motor proteins
which are attached to the outer microtubule doublets. Biologists refer to this organization

22
as a cononical "9 + 2" structure. The non-motile cilia do not have the two central
microtubule singlets and do not have dyneins. This configuration of axoneme is referred
as a "9 + 0" type. At the base of the cilium is its microtubule organization center called a
basal body. Basal body is structurally identical to and functionally interchangeable with
centriole in the animal cells. The region between the basal body and axoneme is a short
transition zone which is less studied.
A defect in the cilium can cause human disease. The best known cilia-related disorder is
Primary Ciliary Dyskinesia (PCD). In addition, a defect of the primary cilium in the renal
tube cells can lead to polycystic kidney disease (PKD). In another genetic disorder called
Bardet-Biedl syndrome (BBS), the mutant gene products are the components in the basal
body and cilia.

Dynein

Dynein is a class of protein and can be divided into two groups: cytoplasmic dynein and

axonemal dynein.
The axonemal dynein acts to activate a sliding within flagellar microtubules, whereas the
cytoplasmic dynein is implicated in moving toward the negative end of a microtubule.

Kinesin

Kinesins typically consist of two large globular heads that allow attachment to
microtubules, a central coiled region, and a region termed light-chain, which connects the

kinesin to the intracellular component to be moved.

Kinesin and Dynein belong to Microtubule Associated Proteins (MAPs). These motor MAPs
attach both to intracellular components, and to microtubles (MTs), and by moving along
the MT they are able to transport the intracellular components, which could be organelles,
or vesicles, to where they are required.

Cytoplasm
Cytoplasm is the colloidal, semi-fluid matter contained within the cell's plasma
membrane, in which organelles are suspended. In contrast to the protoplasm, the
cytoplasm does not include the cell nucleus, the interior of which is made up of
nucleoplasm.

Components of the cytoplasm


The aqueous component of the cytoplasm (making up 80 percent of it) is composed of
ions and soluble macromolecules like enzymes, carbohydrates, different salts and
proteins, as well as a great proportion of ARN. The cytoplasm's watery component is also
known as hyaloplasm .
The watery component can be more or less gel-like or liquid depending on the milieu's
conditions and the activity phases of the cell. In the first case, it is named cytogel and is
a viscid solid mass. In the second case, called cytosol, is a liquid in movement. In
general, margin regions of the cell are gel-like and the cell's interior is liquid.
The insoluble constituents of the cytoplasm are organelles (such as the mitochondria, the
lysosomes, peroxysomes, ribosomes), several vacuoles, cytoskeletons as well as complex
membrane structures (e.g. endoplasmic reticulums or the golgi apparatus).

23
Function
The cytoplasm plays a mechanical role, i.e. to maintain the shape, the consistency of the
cell and to provide suspension to the organelles. It is also a storage place for chemical
substances indispensable to life. Vital metabolic reactions take place here, for example
anaerobic glycolysis and proteic synthesis.

Cytosol
The cytosol (as opposed to cytoplasm, which also includes the organelles) is the internal
fluid of the cell, and a large part of cell metabolism occurs here. Proteins within the
cytosol play an important role in signal transduction pathways, glycolysis, and they act as
intracellular receptors and ribosomes. In prokaryotes, all chemical reactions take place in
the cytosol. In eukaryotes, the cytosol contains the cell organelles. The cytosol is not a
"soup" with free-floating particles, but is highly organized on the molecular level. The
cytosol also contains the cytoskeleton. This is made of fibrous proteins (microfilaments,
microtubules, and intermediate filaments) and (in many organisms) maintains the shape
of the cell, anchors organelles, and controls internal movement of structures, e.g.,
transport vesicles.
As the concentration of soluble molecules increases within the cytosol, an osmotic
gradient builds up toward the outside of the cell. Water flows into the cell, making the cell
larger. To prevent the cell from bursting apart, molecular pumps in the plasma
membrane, the cytoskeleton, the tonoplast or the cell wall (if present), are used to
counteract the osmotic pressure.
Details
The cytosol is 20% to 30% protein.
Normal human cytosolic pH is (roughly) 7.0 (i.e. neutral), whereas the pH of the
extracellular fluid is 7.4.

Vesicle
A vesicle is a relatively small and enclosed compartment, separated from the cytosol by
at least one lipid bilayer. Vesicles store, transport, or digest cellular products and wastes.
This biomembrane enclosing the vesicle is the same as that of the outer (cellular)
membrane. Thus, because of the separation, the intravesicular environment can be made
to be different from the cytosolic environment. Vesicles are a basic tool of the cell for
organizing metabolism, transport, enzyme storage, as well as being chemical reaction
chambers. Many vesicles are made in the Golgi apparatus, but also in the endoplasmic
reticulum, or are made from parts of the plasma membrane.
Lysosomes (membrane-bound digestive vesicles) can digest macromolecules (break them

down to small compounds) that were taken in from the outside of the cell by an endocytic
vesicle. This is the basic way for a cell to feed (except for photosynthesis in plants, which
don't have lysosomes). The membrane of the lysosome is impermeable for lysozyme, the
enzyme that does the actual digestion, to protect the cell interior from being digested by
its own enzyme. Lysosomes are made in the Golgi apparatus.
Neurons store neurotransmitters in synaptic vesicles located at presynaptic terminals.

24
Transport vesicles
Transport vesicles can move molecules between locations inside the cell, e.g., proteins
from the endoplasmic reticulum to the Golgi apparatus, and from there to the outer cell
membrane, where they are secreted. They do this by budding off from one compartment
and joining to another.
Anterograde transport vesicles : These are forward-moving vesicles.
Retrograde transport vesicles : These vesicles move from later to earlier cisterna.
Vesicles can be used as reaction chambers for chemical reactions that could damage the
cell if they would occur in the cytosol. For example, peroxisomes are detoxifiers of
hydrogen peroxide (H2O2), a toxic byproduct of cell metabolism. Large storage vesicles
are known as vacuoles.

Mechanisms
Assembly of a protein coat drives vesicle formation and selection of cargo molecules.

Vesicle coat
The vesicle coat serves to sculpt the curvature of a donor membrane, and to select
specific proteins as cargo. It selects cargo proteins by binding to sorting signals . In this
way the vesicle coat clusters selected membrane cargo proteins into nascent vesicle
buds.

Organelle
An organelle is one of several structures with specialized functions, suspended in the
cytoplasm of a eukaryotic cell. Organelles were historically identified through the use of
some form of microscopy and were also identified through the use of cell fractionation.
Organelles include:

mitochondrion
endoplasmic reticulum
golgi apparatus
lysosome
myofibril
centriole
nucleus
peroxisome
ribosome
vacuole
vesicle

25
Mitochondria
A mitochondrion (from Greek mitos thread + khondrion granule) is an organelle found
in most eukaryotic cells, including those of plants, animals, fungi. Usually a cell has
hundreds or thousands of mitochondria. The exact number of mitochondria depends on
the cell's level of metabolic activity: more activity means more mitochondria.
Mitochondria can occupy up to 25% of the cell's cytosol.
Mitochondria are sometimes described as "cellular power plants", because their primary
function is to convert organic materials into energy in the form of ATP.

Mitochondrion structure

Cross-section of a mitochondrion, showing: (1) inner membrane, (2) outer


membrane, (3) cristae, (4) matrix
Depending on the cell type, mitochondria can have very different overall structures. At
one end of the spectrum, the mitochondria can resemble the standard sausage-shaped
organelle pictured to the right, ranging from 1 to 4 m in length. At the other end of the
spectrum, mitochondria can appear as a highly branched, interconnected tubular
network. Observations of fluorescently labelled mitochondria in living cells have shown
them to be dynamic organelles capable of dramatic changes in shape. Finally,
mitochondria can fuse with one another, or split in two.
The outer boundary of a mitochondrion contains two functionally distinct membranes: the
outer mitochondrial membrane and the inner mitochondrial membrane. The outer
mitochondrial membrane completely encloses the organelle, serving as its outer
boundary. The inner mitochondrial membrane is thrown into folds, or cristae, that project
inward. The cristae surface houses the machinery needed for aerobic respiration and ATP
formation, and their folded form increases that capacity by increasing the surface area of
the inner mitochondrial membrane.
The membranes of the mitochondrion divide the organelle into two distinct
compartments: one within the interior of the mitochondrion, called the matrix, and a
second between the inner and outer membranes, called the intermembrane space.

The mitochondrial membranes


The outer and inner membranes are composed of phospholipid bilayers studded with
proteins, much like a typical cell membrane. The two membranes, however, have very
different properties. The outer mitochondrial membrane, which encloses the entire
organelle, is composed of about 50% phospholipids by weight and contains a variety of
enzymes involved in such diverse activities such as the oxidation of epinephrine
(adrenaline), the degradation of tryptophan, and the elongation of fatty acids.

26
The inner mitochondrial membrane, in contrast, contains more than 100 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). Additionally, the inner membrane is rich in
a an unusual phospholipid, cardiolipin , which is usually characteristic of bacterial plasma
membranes.
The outer mitochondrial membrane contains numerous integral proteins called porins,
which contain a relatively large internal channel (about 2-3 nm) and allow ions and small
molecules to move in and out of the mitochondrion. Large molecules, however, cannot
traverse the outer membrane. The inner membrane does not contain porins, however,
and is highly impermeable; almost all ions and molecules require special membrane
transporters to enter or exit the matrix.

The mitochondrial matrix


In addition to various enzymes, the mitochondrial matrix also contains ribosomes and
several molecules of DNA. Thus, mitochondria possess their own genetic material, and
the machinery to manufacture their own RNAs and proteins. (See: protein synthesis).
This nonchromosomal DNA encodes a small number of mitochondrial peptides (13 in
humans) that are integrated into the inner mitochondrial membrane, along with
polypeptides encoded by genes that reside in the host cell's nucleus.

Mitochondrial functions
Although the primary function of mitochondria is to convert organic materials into cellular
energy in the form of ATP, mitochondria play an important role in many important
metabolic tasks, such as:

Apoptosis
Glutamate-mediated excitotoxic neuronal injury

Cellular proliferation
Regulation of the cellular redox state
Heme synthesis
Steroid synthesis
Heat production (enabling the organism to stay warm)

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 a variety of mitochondrial diseases.

Energy conversion
As stated above, the primary function of the mitochondria is the production of ATP. This is
done by metabolizing the major products of glycolysis, pyruvate and NADH (glycolysis is
performed outside the mitochondria, in the host cell's cytosol). This metabolism can be
performed in two very different ways, depending on the type of cell and the presence or
absence of oxygen.
Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the
"molecular currency" of intracellular energy transfer; that is, ATP is able to store and
transport chemical energy within cells. ATP also plays an important role in the synthesis

27
of nucleic acids. ATP molecules are also used to store the energy plants make in cellular
respiration.

Chemical properties
Chemically, ATP consists of adenosine and three phosphate groups. It has the empirical
formula C10H16N5O13P3, and the chemical formula C10H8N4O2NH2(OH)2(PO3H)3H, with a
molecular mass of 507.184 u. The phosphoryl groups starting with that on AMP are
referred to as the alpha, beta, and gamma phosphates. The biochemical name for ATP is
9--D-ribofuranosyladenine-5'-triphosphate.

Synthesis
ATP can be produced by various cellular processes, most typically in mitochondria by
oxidative phosphorylation under the catalytic influence of ATP synthase. The main fuels
for ATP synthesis are glucose and fatty acids. Initially glucose is broken down into
pyruvate in the cytosol. Two molecules of ATP are generated for each molecule of
glucose. The terminal stages of ATP synthesis are carried out in the mitochondrion and
can generate up to 36 ATP.

ATP in the human body


The total quantity of ATP in the human body is about 0.1 mole. The energy used by
human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that
each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be
stored, hence its synthesis must closely follow its consumption.

Other triphosphates
Living cells also have other "high-energy" nucleoside triphosphates, such as guanosine
triphosphate. Between them and ATP, energy can be easily transferred with reactions
such as those catalyzed by nucleoside diphosphokinase : Energy is released when
hydrolysis of the phosphate-phosphate bonds is carried out. This energy can be used by a
variety of enzymes, motor proteins , and transport proteins to carry out the work of the
cell. Also, the hydrolysis yields free inorganic phosphate and adenosine diphosphate,
which can be broken down further to another phosphate ion and adenosine
monophosphate. ATP can also be broken down to adenosine monophosphate directly, with
the formation of pyrophosphate. This last reaction has the advantage of being an
effectively irreversible process in aqueous solution.

Reaction of ADP with GTP


ADP + GTP

ATP + GDP

There is talk of using ATP as a power source for nanotechnology and implants. Artificial
pacemakers could become independent of batteries.

Pyruvate: the Krebs cycle

28
Each pyruvate molecule produced by glycolysis is actively transported across the inner
mitochondrial membrane, and into the matrix where it is combined coenzyme A to form
acetyl CoA. Once formed, acetyl CoA is fed into the Krebs cycle, also known as the
tricarboxylic acid (TCA) cycle or citric acid cycle. This process creates 3 molecules of
NADH and 1 molecule of FADH2, which go on to participate in the electron transport
chain. With the exception of succinate dehydrogenase, which is bound to the inner
mitochondrial membrane, all of the enzymes of the Krebs cycle are dissolved in the
mitochondrial matrix.

NADH and FADH2: the electron transport chain


This energy from NADH and FADH2 is transferred to oxygen (O2) in several steps involving
the electron transfer chain. The protein complexes in the inner membrane (NADH
dehydrogenase, cytochrome c reductase, cytochrome c oxidase) that perform the transfer
use the released energy to pump protons (H+) against a gradient (the concentration of
protons in the intermembrane space is higher than that in the matrix). An active
transport system (energy requiring) pumps the protons against their physical tendency
(in the "wrong" direction) from the matrix into the intermembrane space.
As the proton concentration increases in the intermembrane space, a strong diffusion
gradient is built up. The only exit for these protons is through the ATP synthase complex.
By transporting protons from the intermembrane space back into the matrix, the ATP
synthase complex can make ATP from ADP and inorganic phosphate (Pi). This process is
called chemiosmosis and is an example of facilitated diffusion. Peter Mitchell was awarded
the 1978 Nobel Prize in Chemistry for his work on chemiosmosis. 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.

Use in population genetic studies


Because eggs (ovum) destroy the mitochondria of the sperm that fertilize them, the
mitochondrial DNA of an individual derives exclusively from the mother. Individuals inherit
the other kinds of genes and DNA from both parents jointly. Because of the unique
matrilineal transmission of mitochondrial DNA, scientists in population genetics and
evolutionary biology often use data from mitochondrial DNA sequences to draw
conclusions about genealogy and evolution.

The endosymbiotic theory

Mitochondria are unusual among organelles in that they contain ribosomes and their own
genetic material. Mitochondrial DNA is circular and employs characteristic variants of the
standard eukaryotic genetic code.
These and similar pieces of evidence motivate the endosymbiotic theory that
mitochondria originated as prokaryotic endosymbionts. Essentially this widely accepted
hypothesis postulates that the ancestors of modern mitochondria were independent
bacteria that colonized the interior of the ancient precursor of all eukaryotic life.

29

Ribosome

Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). Side
and front view.
(1) Head. (2) Platform. (3) Base. (4) Ridge. (5) Central protuberance. (6) Back. (7) Stalk.
(8) Front.

A ribosome is an organelle composed of rRNA (synthesized in the nucleolus) and


ribosomal proteins. It translates mRNA into a polypeptide chain (e.g., a protein). It can
be thought of as a factory that builds a protein from a set of genetic instructions.
Ribosomes can float freely in the cytoplasm (the internal fluid of the cell) or bind to
another organelle called the endoplasmic reticulum. Since ribosomes are ribozymes, it is
thought that they might be remnants of the RNA world.
Ribosomes consist of two subunits (Figure 1) that fit together (Figure 2) and work as one
to translate the mRNA into a polypeptide chain during protein synthesis (Figure 3). Each
subunit consists of one or two very large RNA molecules (known as ribosomal RNA or
rRNA) and multiple smaller protein molecules. Experiments have shown that the rRNA are
the crucial components in protein synthesis, and that one aspect of the process, peptide
transfer, can occur in the presence of rRNA alone, albeit at a slower rate. This suggests
that the protein components of ribosomes act as a scaffold that may enhance the ability
of rRNA to synthesise protein.
The structure and function of ribosomes, and their attendant molecules, known as the
translational apparatus, has been of ongoing research interest since the mid 20th century
on through the early 21st century. A triennial conference is held to discuss the ribosome.
In 1999, the conference was held in Elsinore, Denmark. The 2002 conference was held in
Queenstown, New Zealand [1].

30

Figure 2 : Large (1) and small (2) subunit fit together

Free ribosomes
Free ribosomes occur in all cells, and also in mitochondria and chloroplasts in eukaryotic
cells. Several free ribosomes can associate on a single mRNA molecule to form a
polyribosome or polysome. Free ribosomes usually produce proteins that are used in the
cytosol or in the organelle they occur in.

Membrane bound ribosomes


When certain proteins are synthesized by a ribosome, it can become "membrane-bound",
associated with the membrane of the nucleus and the rough endoplasmic reticulum (in
eukaryotes only) for the time of synthesis. They insert the freshly produced polypeptide
chains directly into the ER, from where they are transported to their destinations. Bound
ribosomes usually produce proteins that are used within the cell membrane or are
expelled from the cell via exocytosis.
The ribosomal subunits of prokaryotes and eukaryotes are quite similar. However,
prokaryotes use 70S ribosomes, each consisting of a (small) 30S and a (large) 50S
subunit, whereas eukaryotes use 80S ribosomes, each consisting of a (small) 40S and a
bound (large) 60S subunit.[The unit S means Svedberg units, a measure of the rate of
sedimentation of a particle in a centrifuge, where the sedimentation rate is associated
with the size of the particle. Svedberg units are not additive - two subunits together can
have Svedberg values that do not add up to that of the entire ribosome.]

Figure 3 : Translation (1) of mRNA by a ribosome (2) into a polypeptide chain (3). The mRNA
begins with a start codon (AUG) and ends with a stop codon (UAG).

In Figure 3, both ribosomal subunits (small and large) assemble at the start codon (the 5'
end of the mRNA). The ribosome uses tRNA (transfer RNAs which are RNA molecules that
carry an amino acid and present the matching anti-codon, according to the genetic code,
to the ribosome) which matches the current codon (triplet) on the mRNA to append an
amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the
ribosome moves towards the 3' end of the mRNA. Usually, several ribosomes are working
parallel on a single mRNA.

31
Endoplasmic reticulum
The endoplasmic reticulum or ER (endoplasmic means "within the cytoplasm",
reticulum means "little net") modifies proteins, makes macromolecules, and transfers
substances throughout the cell. Prokaryotic organisms do not have organelles and thus do
not have an ER. ER's base structure and composition is similar to the plasma membrane,
though it is an extension of the nuclear membrane. The ER is the site of the translation and
folding of and transport of proteins that are to become part of the cell membrane (e.g.,
transmembrane receptors and other integral membrane proteins) as well as proteins that
are to be secreted or "exocytosed" from the cell (e.g., digestive enzymes).

Structure

Figure 1 : Image of nucleus, endoplasmic reticulum and Golgi apparatus.


(1) Nucleus. (2) Nuclear pore. (3) Rough endoplasmic reticulum (RER). (4) Smooth
endoplasmic reticulum (SER). (5) Ribosome on the rough ER. (6) Proteins that are
transported. (7) Transport vesicle. (8) Golgi apparatus. (9) Cis face of the Golgi
apparatus. (10) Trans face of the Golgi apparatus. (11) Cisternae of the Golgi apparatus.
The ER consists of an extensive membrane network of tubes and cisternae (sac-like
structures). The membrane encloses a space, the cisternal space (or internal lumen) from
the cytosol. This space is acting as a gateway. Parts of the ER membrane are continuous
with the outer membrane of the nuclear envelope, and the cisternal space of the ER is
continuous with the space in between the two layers of the nuclear envelope.
Parts of the ER are covered with ribosomes (which assemble amino acids into proteins
based on instructions from the nucleus). Their rough appearance under electron
microscopy led to their being called rough ER (RER), other parts are free of ribosomes
and are called smooth ER (SER). The ribosomes on the surface of the rough ER insert the
freshly produced proteins directly into the ER, which processes them and then passes
them on to the Golgi apparatus (Fig. 1). Rough and smooth ER differ not only in
appearance, but also in function.

32
Rough ER
The coarse ER manufactures and transports proteins destined for membranes and
secretion. It synthesizes membrane, organellar, and excreted proteins. Minutes after
proteins are synthesized most of them leave to the Golgi apparatus within vesicles. The
rough ER also modifies, folds, and controls the quality of proteins.

Smooth ER
The smooth ER has functions in several metabolic processes. It takes part in the
synthesis of various lipids (e.g., for building membranes such as phospholipids), fatty
acids and steroids (e.g., hormones), and also plays an important role in carbohydrate
metabolism, detoxification of the cell (enzymes in the smooth ER detoxify chemicals), and
calcium storage. It also is a large transporter of nutrient found in each cell.

Functions
The endoplasmic reticulum serves many general functions, including the facilitation of
protein folding, and the transport of proteins. Correct folding of newly made proteins is
made possible by several ER proteins including: PDI, Hsc70 family , calnexin , calreticulin,
and the peptidylpropyl isomerase family . Only properly folded proteins are transported
from the RER to the Golgi complex.

Transport of proteins
Secretory proteins are moved across the ER membrane. Proteins that are transported by
the ER and from there throughout the cell are marked with an address tag that are called
a signal sequence. Gnter Blobel was awarded the 1999 Nobel Prize in Physiology or
Medicine for his discovery of these signal sequences in 1975. The N-terminus (one end)
of a polypeptide chain (e.g., a protein) contains a few amino acids that work as an
address tag, which are removed when the polypeptide reaches its destination. Proteins
that are destined for places outside the ER are packed into transport vesicles and moved
along the cytoskeleton towards their destination. The ER is also part of a protein sorting
pathway.

Other functions

Insertion of proteins into the ER membrane. Integral proteins need to be


inserted into the ER membrane after they are synthesized. Insertion into the ER
membrane requires the correct topogenic sequences.
Glycosylation. Glycosylation involves the attachment of oligosaccharides.
Disulfide bond formation and rearrangement. Disulfide bonds stabilize the
tertiary and quaternary structure of many proteins.
Sarcoplasmic reticulum. The endoplasmic reticulum found in muscle fibers is
called sarcoplasmic reticulum.

Golgi apparatus

33
The Golgi apparatus (Golgi body, Golgi complex, or dictyosome) is an organelle
found in most eukaryotic cells, including those of plants and animals (but not most fungi).
The name comes from Italian anatomist Camillo Golgi, who identified it in 1898. Its primary
function is to process proteins targeted to the plasma membrane, lysosomes or
endosomes and those that will be secreted from the cell, and sort them within vesicles.
Thus, it functions as a central delivery system for the cell.
Most of the transport vesicles that leave the endoplasmic reticulum (ER), specifically rough
ER, are transported to the Golgi apparatus, where they are modified, sorted and shipped
towards their final destination. The Golgi apparatus is present in most eukaryotic cells, but
tends to be more prominent where there are a lot of substances, such as enzymes, being
secreted.

Structure

Figure 1: Image of nucleus, endoplasmic reticulum and Golgi apparatus: (1) Nucleus, (2)
Nuclear pore, (3) Rough endoplasmic reticulum (RER), (4) Smooth endoplasmic reticulum
(SER), (5) Ribosome on the rough ER, (6) Proteins that are transported, (7) Transport
vesicle, (8) Golgi apparatus, (9) Cis face of the Golgi apparatus, (10) Trans face of the
Golgi apparatus, (11) Cisternae of the Golgi apparatus, (12) Secretory vesicle, (13)
Plasma membrane, (14) Exocytosis, (15) Cytoplasm, (16) Extracellular space.
The structure and internal function of the Golgi apparatus is quite complex and is the
subject of scientific dispute. The Golgi apparatus consists, like the ER, of membranous
structures. It is made up of a stack of flattened cisternae and similar vesicles. The cis
face is the side facing the ER, the medial region is in the middle while the trans face is
directed towards the plasma membrane (Fig. 1). The cis and trans faces have different
membranous compositions.

Function
The transport vesicles from the ER fuse with the cis face of the Golgi apparatus (to the
cisternae) and empty their protein content into the Golgi lumen. The proteins are then
transported through the medial region towards the trans face and are modified on their
way.
The transport mechanism itself is not yet clear; it could happen by cisternae progression
(the movement of the apparatus itself, building new cisternae at the cis face and
destroying them at the trans face) or by vesicular transport (small vesicles transport the
proteins from one cisterna to the next, while the cisternae remain unchanged). Lately, it

34
is also proposed that the cisternae are interconnected and the transport of cargo
molecules within the Golgi is due to diffusion, while the localisation of Golgi resident
proteins is achieved by an unknown mechansim.
Once the proteins reach the trans face, they are embedded into coated transport vesicles
and brought to their final destinations. An example is the modification of glycoproteins
(used in cell membranes). Vesicles from the ER contain simplified glycosylated proteins.
In the Golgi Apparatus, carbohydrates are attached and removed from these
glycoproteins, creating a diversity of carbohydrate structures on the proteins. After they
have been secreted in to the cell the vesicles fuse to the cell membrane and release their
contents.
As well as protein modification, Golgi apparatus is involved in the transport of lipids
around the cell as well creating lysosomes -- organelles involved in digestion.

Lysosome
Lysosomes are organelles that contain digestive enzymes to digest macromolecules. They
are built in the Golgi apparatus. At pH 4.8, the interior of the lysosomes is more acidic
than the cytosol (pH 7). The lysosome single membrane stabilizes the low pH by pumping
in protons (H+) from the cytosol, and also protects the cytosol, and therefore the rest of
the cell, from the degradative enzymes within the lysosome. The digestive enzymes need
the acidic environment of the lysosome to function correctly. All these enzymes are
produced in the endoplasmic reticulum, and transported and processed through the Golgi
apparatus. The Golgi apparatus produces lysosomes by budding.
The most important enzymes in lysosomes are:

Lipase, which digests lipids,

Carbohydrases , which digest carbohydrates (e.g., sugars),


Proteases, which digest proteins,
Nucleases, which digest nucleic acids.

The lysosomes are used for the digestion of macromolecules from phagocytosis (ingestion
of cells), from the cell's own recycling process (where old components such as worn out
mitochondria are continuously destroyed and replaced by new ones, and receptor proteins
are recycled), and for autophagic cell death, a form of programmed self-destruction of the
cell, which means that the cell is digesting itself. Other functions include digesting foreign
bacteria that invade a cell and helping repair damage to the plasma membrane by serving
as a membrane patch, sealing the wound.
There are a number of illnesses that are caused by the malfunction of the lysosomes or
one of their digestive proteins, e.g., Tay-Sachs disease, or Pompe's disease. These are
caused by a defective or missing digestive protein, which leads to the accumulation of
substrates within the cell, resulting in impaired cell metabolism. Broadly, these can be
classified as mucopolysaccharidoses, GM2 gangliosidoses , lipid storage disorders ,
glycoproteinoses , mucolipidoses , or leukodystrophies .
The constant pH of 4.8 is maintained by hydrogen ion pumps and Cl- ion channels.

Peroxisome

35
Peroxisomes consist of a single membrane that separates them from the cytosol (the
internal fluid of the cell). Peroxisomes were discovered by Christian de Duve in 1965.
Unlike lysosomes, which are formed in the Golgi apparatus, peroxisomes usually selfreplicate by enlarging and then dividing, although there is some indication new ones may
be formed directly. They also have membrane proteins that are critical for various
functions, such as for importing proteins into their interiors and to proliferate and
segregate into daughter cells.
Peroxisomes function to rid the cell of toxic substances, such as hydrogen peroxide, or
other metabolites and contain enzymes concerned with oxygen utilization such as D-amino
acid oxidase and urease oxidase . The peroxisome contains the enzyme catalase which
converts H2O2 (hydrogen peroxide, a toxic byproduct of cellular metabolism) to H2O and
O2, with 4H2O2 4H2O + 2O2.
In humans, high numbers of peroxisomes can be found in the liver, where toxic
byproducts are known to accumulate. All of the enzymes found in a peroxisome are
imported from the cytosol. Each enzyme transferred to a peroxisome has a special
sequence at one end of the protein, called a PTS or peroxisomal targeting signal , that
allows the protein to be taken into that organelle, where they then function to rid the cell
of toxic substances.
Peroxisomes also degrade fatty acids and toxic compounds and catalyze the first two
steps in the synthesis of ether phospholipids, which are later used to build membranes.
Peroxisomes are responsible for oxidation of long-chain fatty acids and thereby generating
acetyl groups.

Vacuole
Vacuoles are large membrane-bound compartments within some eukaryotic cells where
they serve a variety of different functions: capturing food materials or unwanted
structural debris surrounding the cell, sequestering materials that might be toxic to the
cell, maintaining fluid balance (called turgor) within the cell, exporting unwanted
substances from the cell, or even determining relative cell size. The cavity that is the
vacuole is considered nonprotoplasmic and the contents classified as ergastic according to
some authors (Esau, 1965). Vacuoles are especially conspicuous in most plant cells.
Vacuoles are typically filled with a liquid called cell sap, the composition of which can
vary (even between vacuoles in the same cell), but is principally water. Water tends to
move along concentration gradients into vacuoles. Vacuoles perform different roles in
different organisms and these functions include the capture of food, the maintenance of
internal hydrostatic pressure (store water), the containment of waste products, the
maintenance of an acidic internal pH, the storage of small molecules and finally can
enable a cell to elongate rapidly.

Cell nucleus

36
The nucleus (from Latin nucleus or nuculeus, kernel) contains most of the cell's genetic
material. Nuclei have two primary functions: to control chemical reactions within the
cytoplasm and to store information needed for cellular division.
The nucleus, being the largest organelle, varies in diameter from 10 to 20 micrometres.
It is enclosed by a double membrane called the nuclear envelope. The inner and outer
membrane fuse at regular intervals, forming nuclear pores. The nuclear envelope
regulates and facilitates transport between the nucleus and the cytoplasm, while
separating the chemical reactions taking place in cytoplasm from reactions happening
within the nucleus. The outer membrane is continuous with the rough endoplasmic
reticulum (RER) and may be studded with ribosomes. The space between the two
membranes (called the "perinuclear space") is continuous with the lumen of the RER.

Drawing of nucleus and the endoplasmic reticulum.


(1) Nuclear envelope. (2) Ribosomes. (3) Nuclear pore complexes. (4) Nucleolus.
(5) Chromatin. (6) Nucleus. (7) Endoplasmic reticulum. (8) Nucleoplasm.
The whole structure is surrounded by cytoplasm. (Drawing is based on ER images.)

Inside the nucleus is one or several nucleoli surrounded by a fibrous matrix called the
nucleoplasm. The nucleoplasm is a liquid with a gel-like consistency (similar in this
respect to the cytoplasm), in which many substances are dissolved. These substances
include nucleotide triphospates, enzymes, proteins, and transcription factors. Genetic
material (DNA) is also present in the nucleus, the DNA is present as a DNA-protein
complex called chromatin. The DNA is present as a number of discrete units known as
chromosomes.
There are two types of chromatin: euchromatin and heterochromatin. Euchromatin is the
least compact form of DNA, and the regions of DNA which constitute euchromatin contain
genes which are frequently expressed by the cell.

37
In heterochromatin, DNA is more tightly compacted. Regions of DNA which constitute
heterochromatin generally contain genes which are not expressed by the cell (this type of
heterochromatin is known as facultative heterochromatin) or are regions which make up
the telomeres and centromeres of the chromosomes (this type of heterochromatin is
known as constitutive heterochromatin). In multicellular organisms, cells are highly
specialised to perform particular functions, hence different sets of genes are required and
expressed. Therefore, the regions of DNA that constitute heterochromatin vary between
cell types.
Nucleoli are densely-stained structures at which ribosome subunits are assembled.

Nuclear envelope
Synonyms: karyotheca, nuclear membrane, nucleolemma, perinuclear envelope
The nuclear envelope refers to the double membrane of the nucleus that encloses
genetic material in eukaryotic cells. It separates the contents of the nucleus (DNA in
particular) from the cytosol. The space between the two membranes that make up the
nuclear envelope is called the perinuclear space, and is usually about 20 - 100 nm wide.
The outer membrane is continuous with the rough endoplasmic reticulum.
Numerous nuclear pores are present on the nuclear envelope to facilitate and regulate
the exchange of materials (for example, proteins and mRNA) between the nucleus and
the cytoplasm.
The inner membrane is erected upon the nuclear lamina, a network of intermediate
filaments made of lamin. This network of filaments is essential for the disarrangement of
the nuclear envelope into vesicles during mitosis or meiosis, and its posterior reassembly.
When, during the cell cycle, a certain cyclin-dependent kinase complex phosphorylates
the lamins they undergo a conformational change that triggers the disassembly of the
nuclear envelope. After the chromosomes have migrated to each pole, dephosphorylation
of lamins causes the nucleus to reassemble. The nuclear envelope may also play a role in
the disposition of chromatin inside the nucleus.

Nucleolus
The nucleolus is, strictly speaking, a "suborganelle" of the cell nucleus. It is a
consequence of ribosomal RNA (rRNA) synthesis: nucleolar organizers , special regions on
some chromosomes that contain multiple copies of the genes encoding for rRNA (which is
involved in protein biosynthesis), gather themselves in the same region where they
transcribe the rRNA genes. Thus it can be said the nucleolus consists basically of
nucleolar organizers and the transcribed rRNA (plus associated proteins). Following
synthesis, rRNA molecules are attached to proteins, forming ribosomal subunits, which
leave for the cytosol through nuclear pores.
Function: it creates ribosomes.

38

APPENDIX
1. Cell theory
The cell theory says that:
1.
2.
3.
4.

All organisms are composed of one or more cells.


All cells come from preexisting cells.
All vital functions of an organism occur within cells.
Cells contain the hereditary information necessary for regulating cell functions and
for transmitting information to the next generation of cells.

2. Cell metabolism
Cell metabolism is the process (or really the sum of many ongoing individual processes)
by which living cells process nutrient molecules and maintain a living state. Metabolism
has two distinct divisions: anabolism, in which a cell uses energy and reducing power to
construct complex molecules and perform other life functions such a creating cellular
structure; and catabolism, in which a cell breaks down complex molecules to yield
energy and reducing power. Cell metabolism involves extremely complex sequences of
controlled chemical reactions called metabolic pathways.

Anabolism
Anabolism is a constructive metabolic process whereby energy is consumed to
synthesize or combine simpler substances, such as amino acids, into more complex
organic compounds, such as enzymes and nucleic acids.

Catabolism
Catabolism is a type of metabolic process occurring in living cells by which complex
molecules are broken down to produce energy and reducing power. On balance, catabolic
reactions are normally exothermic.

Carbohydrate catabolism
Main article: Carbohydrate catabolism
Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. The
empirical formula for carbohydrates, like that of their monomer counterparts, is
CX(H2YOY). Carbohydrates literally undergo combustion to retrieve the large amounts of
energy in their bonds. Read more about mitochondria to find out more about the reaction
and how its energy is secured in ATP.

Fat catabolism
Main article: Fat catabolism

39
Fat catabolism, also known as lipid catabolism, is the process of lipids or phospholipids
being broken down by lipases. The opposite of fat catabolism is fat anabolism, involving
the storage of energy, and the building of membranes.

Protein catabolism
Main article: Protein catabolism
Protein catabolism is the breakdown of proteins into amino acids and simple derivative
compounds, for transport into the cell through the plasma membrane and ultimately for
the polymerisation into new proteins via the use of ribonucleic acids (RNA) and ribosomes.

3. Metabolic pathway
A metabolic pathway is a series of chemical reactions occurring within a cell, catalyzed by
enzymes, and resulting in either the formation of a metabolic product to be used or
stored by the cell (metabolic sink ), or the initiation of another metabolic pathway (then
called a flux generating step).

Overview
Most metabolic pathways have these common properties:

They are irreversible, usually because the first step is a committed step that only
runs in one direction.
The pathways are regulated, usually by feedback inhibition .
Anabolic and catabolic pathways in eukaryotes are separated by either
compartmentation or by the use of different enzymes and cofactors.

Major metabolic pathways


Cellular respiration
Main article: Cellular respiration
Several distinct but linked metabolic pathways are used by cells to transfer the energy
released by breakdown of fuel molecules to ATP:
1.
2.
3.
4.

Glycolysis
Anaerobic respiration
Krebs cycle / Citric acid cycle
Oxidative phosphorylation

Other pathways

Fatty acid oxidation (-oxidation)


Gluconeogenesis
HMG-CoA reductase pathway (cholesterol, isoprene prenylation chains)
Pentose phosphate pathway (hexose monophosphate shunt)
Porphyrin synthesis (or heme synthesis) pathway

40

Urea cycle

4. Cellular respiration
Cellular respiration is, in its broadest definition, the process in which the chemical
bonds of energy-rich molecules such as glucose are converted into energy usable for life
processes. Oxidation of organic materialin a bonfire, for exampleis an exothermic
reaction that releases a large amount of energy rather quickly. The overall equation for
the oxidation of glucose is:
C6H12O6 + 6O2 6CO2 + 6H2O + energy
In cellular respiration, this oxidation process is broken down into two basic metabolic
pathways: glycolysis, anaerobic respiration or aerobic respiration.

Glycolysis
Glycolysis is a metabolic pathway that is found in all living organisms and does not
require oxygen. The process converts one molecule of glucose into two molecules of
pyruvate, and makes energy in the form of two molecules of ATP. Glycolysis takes place
in the cytoplasm of the cell. The overall reaction can be expressed this way:
Glucose + 2 NAD+ + 2 ADP + 2 Pi 2 NADH + 2 pyruvate + 2 ATP + 2 H2O + 4 H+
The individual steps of the conversion of glucose into pyruvate are (in brief):
1. A glucose molecule from the hydrolysation of starch or glycogen is phosphorylated
using one ATP molecule to give glucose-6-phosphate.
2. The glucose-6-phosphate is converted to fructose-6-phosphate by isomerisation.
3. Fructose-6-phosphate is again phosphorylated to give fructose-1,6-diphosphate
with the use of another ATP molecule.
4. Next, the fructose-1,6-diphosphate is then lysed into two molecules of 3-carbon
sugar (dihydroxyacetone phosphate and glyceraldehyde-3-phosphate) which are
interconvertible.
5. The 3-carbon sugars are dehydrogenated and inorganic phosphate is added to
them, forming two molecules of 1,3 diphosphoglycerate.
6. The hydrogen is used to oxidise two molecules of NAD, a hydrogen carrier, to give
NADH+H+. NADH+H+ later proceeds to the mitochondria for use in the electron
transport chain.
7. The two molecules of 1,3 diphosphoglycerate lose two phosphate groups to form
two molecules of glycerate-3-phosphate (3-phosphoglycerate), converting two
molecules of ADP to ATP.
8. The two molecules of glycerate-3-phosphate again lose phosphate forming two
molecules of pyruvate, with the production of another two ATP molecules (for a
net gain of 2 ATP).

Breakdown of pyruvate
There are now two ways to break down the resulting pyruvate:

Aerobic respiration (Cellular Respiration)

41

Aerobic respiration requires oxygen. It is the preferred method of pyruvate breakdown. A


molecule of pyruvate acid travels into a mitochondrion entering the Krebs cycle. In this
process it is broken down producing energy in the form of ATP (which travels to the cell),
NADH and FADH2 which travel to the electron transport chain. In this process, an electron
is transferred from an energy-rich atom (such as a carbon atom in an organic molecule)
to an oxygen atom, via an electron transport chain. Oxygen serves as the "terminal
electron acceptor" in the electron transport chain. In the process, it yields 36 ATP
molecules via the diffusion of hydrogen atoms through an ATP synthase, as well as
carbon dioxide and water. This makes for a total gain of 38 ATP molecules during cellular
respiration under optimal conditions; however, such conditions are generally not realized
due to such losses as the cost of moving pyruvate into mitochondria. This takes place in
the mitochondria in eukaryotic cells, and at the cell membrane in prokaryotic cells.

Anaerobic respiration (Fermentation)


"Anaerobic respiration" It does not require oxygen. True anaerobic respiration involves an
electron acceptor other than oxygen. Bacteria are capable of using a wide variety of
compounds as terminal electron acceptors in respiration: nitrogenous compounds (such
as nitrates and nitrites), sulfur compounds (such as sulfates, sulfites, sulfur dioxide, and
elemental sulfur), carbon dioxide, iron compounds, manganese compounds, cobalt
compounds, and uranium compounds.
However, none of these alternative electron acceptors yields as much energy from
respiration as does oxygen. In environments where oxygen is present, typically only
aerobic respiration will occur.
Fermentation is a process in which pyruvate is partially broken down, but there is no
Krebs cycle and no production of ATP by an electron transport chain. Fermentations of
various kinds produce a number of different compounds. Textbook examples of
fermentation products are ethanol (drinkable alcohol), lactic acid, and hydrogen.

42
However, more exotic compounds can be produced by fermentation, such as butyric acid
and acetone.
Although fermentation produces no ATP, it is useful to the cell because it regenerates
nicotinamide adenine dinucleotide (NAD+), which is consumed by glycolysis.

Ethanol fermentation (done by yeast and some types of bacteria) breaks the
pyruvate down into ethanol, carbon dioxide, and water. It is important in bread
making, brewing, and wine making.
Lactic acid fermentation breaks the pyruvate down into lactic acid, carbon dioxide,
and water. It occurs in the muscles of animals when they need energy faster than
the blood can supply oxygen. It also occurs in some bacteria. It is this type of
bacteria that convert lactose into lactic acid in yogurt giving it its sour taste.

Fermentation products contain chemical energy that cannot be further broken down by
fermentation, making fermentation less efficient than respiration. Fermentation releases a
total of two ATP molecules per molecule of glucose (compare to the approximately 38 of
aerobic respiration).

5. Protein biosynthesis
Protein biosynthesis is the process in which cells build proteins. The term is sometimes
used to refer only to protein translation but more often it refers to a multi-step process,
beginning with transcription and ending with translation. Protein biosynthesis although
very similar, differs between prokaryotes and eukaryotes.

Transcription
Main article: Transcription
Transcription only requires one strand of the DNA double helix. This is called the coding
strand. The transcription starts with initiation. RNA polymerase, an enzyme, binds to a
specific region on the DNA, marking the starting point, called the promoter. As the RNA
polymerase binds on to the promoter, the DNA strands are beginning to unwind.
The second process is known as elongation. As the RNA polymerase travels through the
strand that is opposite to the coding strand (the cell wants a copy of the coding strand, so
it needs to copy that from the DNA that is the opposite of the coding strand), it matches
corresponding mRNA nucleotides to the DNA.
As the polymerase reaches the termination stage, modifications are required for the
newly transcribed mRNA to be able to travel to the other parts of the cell, including
cytoplasm and endoplasmic reticulum. A 5 cap is added to the mRNA to protect it from
degradation. A poly-A tail is added on the 3 end for protection and as a template for
further process.

Translation
Main article: Translation

43
During translation, the message of mRNA is decoded to make proteins. Initiation and
elongation occur when the ribosome recognizes the starting codon on the mRNA strand
and binds to it. The ribosome has sites, which allow another enzyme, tRNA to bind to the
mRNA. On tRNA, there is an anticodon that is used to match the codon on the mRNA.
tRNA also has a single unit of amino acid attached to it.
As the ribosome travels down the mRNA one codon at a time, another tRNA is attached to
the mRNA at one of the ribosome site. The first tRNA is released, but the amino acid that
is attached to the first tRNA is now moved to the second tRNA, and binds to its amino
acid. This translocation continues on, and a long chain of amino acid (protein), is formed.
When the entire unit reaches the end codon on the mRNA, it falls apart and a newly
formed protein is released. This is the termination. It is important to know that during
this process, many enzymes are used to either assist or facilitate the whole procedure.

Events following biosynthesis


The events following biosynthesis include protein folding and post-translational modification.
During and after synthesis, polypeptide chains often fold to assume, so called, native
secondary and tertiary structures. This is known as protein folding.
Many proteins undergo post-translational modification. This is may include the formation
of disulfide bridges or attachment of any of a number of biochemical functional groups,
such as acetate, phosphate, various lipids and carbohydrates. Enzymes may also remove
one or more amino acids from the leading (amino) end of the polypeptide chain, leaving a
protein consisting of two polypeptide chains connected by disulfide

6. Transcription (genetics)
Transcription is the process through which a DNA sequence is enzymatically copied by
an RNA polymerase to produce a complementary RNA. In the case of protein-encoding
DNA, transcription is the beginning of the process that ultimately leads to the translation
of the genetic code (via the RNA intermediate), into a functional peptide or protein.
Transcription has some proofreading mechanisms, but they are fewer and less effective
than the controls for DNA; therefore, transcription has a lower copying fidelity than DNA
replication.
Transcription proceeds in the 5' 3' direction, and is divided into 3 stages: initiation,
elongation and termination.

Eukaryotic transcription
Eukaryotes have evolved much more complex transcriptional regulatory mechanisms than
prokaryotes. For instance, in eukaryotes the genetic material (DNA), and therefore
transcription, is localized to the nucleus, where it is separated from the cytoplasm (where
translation occurs) by the nuclear membrane. This allows for the temporal regulation of
gene expression through the sequestration of the RNA in the nucleus, and allows for
selective transport of RNAs to the cytoplasm, where the ribosomes reside.

44
Adding to this complexity, eukaryotes have three RNA polymerases, each with distinct
roles and properties:

RNA Polymerase I is located in the nucleolus and transcribes ribosomal RNA


(rRNA).
RNA Polymerase II is localized to the nucleus, and transcribes messenger RNA
(mRNA).
RNA Polymerase III transcribes transfer RNA (tRNA) and other small RNAs.

Further complexity is added by the multitude of transcripton factors and signaling


pathways that may interact in combination to mediate cell-type and developmental
transcriptional regulation.
The basal eukaryotic transcription complex includes the RNA polymerase and additional
proteins that are necessary for correct initiation and elongation.
Primary (initial) mRNA transcripts in eukaryotic cells are synthesized as larger precursor
RNAs that are processed by splicing out introns (non-coding sequences) and ligating exons
(non-contiguous coding sequences) into the mature mRNA. Primary transcripts for some
genes can be large. The primary transcripts of the neurexin genes, for instance, are as
large as 1.7 megabases (1,700,000 bases), while the mature (processed) neurexin
mRNAs are under 10 kilobases (10,000 bases), with as many as 24 exons and thousands
of possible alternative splice variants that produce proteins with different activities.
Gene expression in eukaryotes is also controlled by complex interactions between cis-acting
sites within the regulatory regions of the DNA, and trans-acting factors that include
transcription factors and the basal transcription complex.

Initiation
The core promoter of protein-encoding genes contains binding sites for the basal
transcription complex and RNA polymerase II, and is normally within about 50 bases
upstream of the transcription initiation site. Further transcriptional regulation is provided
by upstream control elements (UCEs), usually present within about 200 bases upstream
of the transcription initiation site. The core promoter for RNAP II normally (though not
always) contains a TATA box, the highly conserved DNA sequence
T A T A T/A A
A similar sequence, though not as highly conserved, is found in the INR (initiator)
element, part of the some RNAP II promoters.
Some genes also have enhancer elements that can be thousands of bases upstream or
downstream of the transcription initiation site. Combinations of these upstream control
elements and enhancers regulate and amplify the formation of the basal transcription
complex.

Measuring and detecting transcription


Transcription can be measured and detected in a variety of ways:

45

Northern blot

RNase protection assay


RT-PCR

In vitro transcription
In situ hybridization

History
RNA synthesis by RNA polymerase had been established in vitro by several laboratories
by 1965; however, the RNA synthesized by these enzymes had properties that suggested
the existence of an additional factor needed to terminate transcription correctly.
By the late 1960s several papers that came out of the Harvard University Biological
Laboratories established the basic mechanics of gene expression in bacteria.

7. Translation (genetics)
Translation is the second process of protein biosynthesis (part of the overall process of
gene expression). In translation, messenger RNA is decoded to produce a specific
polypeptide according to the rules specified by the genetic code. Translation is invariably
preceded by transcription. Similarly to transcription, translation proceeds in three phases:
initiation, elongation and termination (all describing the growth of the amino acid chain,
or polypeptide that is the product of translation). The capacity of disabling or inhibiting
translation in protein biosynthesis is used by antibiotics such as: anisomycin,
cycloheximide , chloramphenicol and tetracycline.

Basic mechanisms
The mRNA carries the genetic information from the chromosomes to the ribosomes.
Harboured on the ribosome (structures containing rRNA and a protein base), the mRNA
information is matched (through hydrogen bonds) to the specific tRNA (tRNA is a small
RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing
polypeptide chain at the ribosomal site of protein synthesis). The information sequence is
tranferred in triplets of nucleotides. Each of those triplets is linked to an amino acid. Each
three mRNA nucleotides are called a codon and their three complementary tRNA
nucleotides are called its anti-codon. Aminoacyl tRNA synthetase is the enzyme that
catalyzes the binding of a specific amino acid to a tRNA to form an aminoacyl-tRNA.

Eukaryotic translation
In eukaryotes, transcription occurs in the nucleus, then the mRNA moves to the cytoplasm
for the translation to occur. The mRNA is spliced with 5' cap and 3' poly-A-tail and then
transported. Initiation is described below, elongation and termination proceed similarly to
that in prokaryotes.

Initiation
Initiation of translation involves the small ribosomal subunit binding to the 'start' codon on
the mRNA, which indicates where the mRNA starts coding for the protein. In eukaryotes

46
and archaea, the amino acid encoded by the start codon is methionine. The initiator tRNA
charged with Met forms part of the ribosomal complex.

Translation by hand
It is also possible to translate either by hand (for short sequences) or by computer (after
first programming one appropriately), this allows biologists and chemists to draw out the
chemical structure of the encoded protein on paper.
First, convert each DNA base to its RNA complement:

DNA
A
T
G
C

-> RNA
-> U
-> A
-> C
-> G

Then split into triplets, and see:Genetic code for the code table used by ribosomes. Note
that there are 3 translation "windows" depending on where you start reading the code.
Finally, use the table at Amino acid to translate the above into a structural formula as used
in chemistry.
This will give you the primary structure of the protein. However, proteins tend to fold,
depending in part on hydrophilic and hydrophobic segments along the chain. Secondary
structure can often still be guessed at, but the proper tertiary structure is often very hard
to determine, though chemical simulations currently are able to guess right about 70% of
the time.

8. Molecular biology
Molecular biology is the study of biology at a molecular level. The field overlaps with
other areas of biology, particularly genetics and biochemistry. Molecular biology chiefly
concerns itself with understanding the interactions between the various systems of a cell,
including the interrelationship of DNA, RNA and protein synthesis and learning how these
interactions are regulated.

Relationship to other "molecular-scale" biological sciences

Schematic relationship between biochemistry, genetics and molecular biology

47
Researchers in molecular biology use specific techniques native to molecular biology (see
Techniques section later in article), but increasingly combine these with techniques and
ideas from genetics, biochemistry and biophysics. There is not a hard-line between these
disciplines as there once was. 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.
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 which lack one or more functional components with
respect to the so-called "wild type" or normal phenotype. Genetic interactions
such as epistasis can often confound simple interpretations of such "knock-out"
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.

Much of the work in molecular biology is quantitative, and recently much work has been
done at the interface of molecular biology and computer science in bioinformatics and
computational biology. As of the early 2000s, the study of gene structure and function,
molecular genetics, has been amongst the most prominent sub-field of molecular biology.
Increasingly many other fields of biology focus on molecules, either directly studying their
interactions in their own right such as in cell biology and developmental biology, or
indirectly, where the techniques of molecular biology are used to infer historical attributes
of populations or species, as in fields in evolutionary biology such as population genetics
and phylogenetics. There is also a long tradition of studying biomolecules "from the
ground up" in biophysics.

Techniques of molecular biology


Since the late 1950s and early 1960s, molecular biologists have learned to characterise,
isolate, and manipulate the molecular components of cells and organisms. These
components include DNA, the repository of genetic information; RNA, a close relative of
DNA whose functions range from serving as a temporary working copy of DNA to actual
structural and enzymatic functions as well as a functional and structural part of the
translational apparatus; and proteins, the major structural and enzymatic type of
molecule in cells.

Expression cloning
One of the most basic techniques of molecular biology to study protein function is
expression cloning. In this technique, DNA coding for a protein of interest is cloned (using
PCR and/or restriction enzymes) into a plasmid (known as an expression vector). This
plasmid may have special promoter elements to drive production of the protein of
interest, and may also have antibiotic resistance markers to help follow the plasmid.
This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into
bacterial cells is called transformation, and can be effected by several methods, including

48
electroporation, microinjection and chemically. Introducing DNA into eukaryotic cells,
such as animal cells, is called transfection. Several different transfection techniques are
available, including calcium phosphate transfection, liposome transfection, and
proprietary transfection reagents such as Fugene. DNA can also be introduced into cells
using viruses as a carrier. In such cases, the technique is called viral transduction, and
the cells are said to be transduced.
In either case, DNA coding for a protein of interest is now inside a cell, and the protein
can now be expressed. A variety of systems, such as inducible promoters and specific
cell-signaling factors, are available to help express the protein of interest at high levels.
Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell.
The protein can be tested for enzymatic activity under a variety of situations, the protein
may be crystallized so its tertiary structure can be studied, or, in the pharmaceutical
industry, the activity of new drugs against the protein can be studied.

Polymerase chain reaction (PCR)


Main article: Polymerase chain reaction
The polymerase chain reaction is an extremely versatile technique for copying DNA. In
brief, PCR allows a single DNA sequence to be copied (millions of times), or altered in
predetermined ways. For example, PCR can be used to introduce restriction enzyme sites,
or to mutate (change) particular bases of DNA. PCR can also be used to determine
whether a particular DNA fragment is found in a cDNA library.

Gel electrophoresis
Gel electrophoresis is one of the principal tools of molecular biology. The basic principle is
that DNA, RNA, and proteins can all be separated using an electric field. In agarose gel
electrophoresis, DNA and RNA can be separated based on size by running the DNA
through an agarose gel. Proteins can be separated based on size using an SDS-PAGE gel.
Proteins can also be separated based on their electric charge, using what is known as an
isoelectric gel...

Western blotting and immunochemistry


Main article: Western blot
Antibodies to most proteins can be created by injecting small amounts of the protein into
an animal such as a mouse, rabbit, sheep, or donkey. These antibodies can be used for a
variety of analytical and preprative techniques.
In Western blotting, proteins are first separated by size, in a thin gel sandwiched between
two glass plates. This technique is called SDS-PAGE (for Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis). The proteins in the gel are then transferred to a PVDF,
nitrocellulose, nylon or other support membrane. This membrane can then be probed
with solutions of antibodies. Antibodies that specifically bind to the protein of interest can
then be visualized by a variety of techniques, including chemoluminescence or
radioactivity.
Antibodies can also be used to purify proteins. Antibodies to a protein are generated and
are often then coupled to "beads". After the antibody has bound to the protein of
interest, this antibody-protein complex can be separated from all other proteins by

49
centrifugation. During centrifugation, the beads, to which the antibody is coupled, will
pellet (bringing the protein of interest down with it) whereas all other proteins will remain
in the solution. Alternatively, antibodies coupled to a solid support matrix like Sephadex
or Sepharose beads, for example, can be used to remove a protein of interest from a
complex solution. After washing unbound and non-specifically bound materials away from
the "beads", the protein of interest is then eluted from the matrix, usually by adding a
solution with a high salt concentration, or by varying the pH of the solution in which the
matrix is contained. The beads can either be suspended in solution (batch processing) or
packed into a tube (column processing).

History
Molecular biology was established in the 1930s, the term was first coined by Warren
Weaver in 1938 however. Warren was director of Natural Sciences for the Rockefeller
Foundation at the time and believed that biology was about to undergo a period of
significant change given recent advances in fields such as X-ray crystallography. He
therefore channeled significant amounts of (Rockefeller Institute) money into biological
fields.

9. Biomolecule

A representation of the 3D structure of myoglobin, showing coloured alpha helices. This


protein was the first to have its structure solved by X-ray crystallography by Max Perutz
and Sir John Cowdery Kendrew in 1958, for which they received a Nobel Prize in
Chemistry.
A biomolecule is a chemical compound that naturally occurs in living organisms.
Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen,
phosphorus and sulfur. Other elements sometimes are incorporated but these are much
less common.
Biomolecules are necessary for the existence of all known forms of life. For example,
humans possess skin and hair. The main component of hair is keratin, an agglomeration
of proteins which are themselves polymers built from amino acids. Amino acids are some
of the most important building blocks used, in nature, to construct larger molecules.
Another type of building block is the nucleotides, each of which consists of three
components: either a purine or pyrimidine base, a pentose sugar and a phosphate group.
These nucleotides, mainly, form the nucleic acids.

50
Besides the polymeric biomolecules, numerous small organic molecules are absorbed or
synthesised by living systems. Many biomolecules may be useful or important drugs.

Types of biomolecules
A diverse range of biomolecules exist, including:

Small molecules:
o Lipid, Phospholipid, Glycolipid, Sterol
Vitamin
Hormone, Neurotransmitter
Carbohydrate, Sugar
Disaccharide
Monomers:
o Amino acid
o Nucleotide
o Phosphate
o Monosaccharide
Polymers:
o Peptide, Oligopeptide, Polypeptide, Protein
o Nucleic acid, i.e. DNA, RNA
o Oligosaccharide, Polysaccharide
Macromolecules:
o Prion

o
o
o
o

Nucleosides and nucleotides


Nucleosides are molecules formed by attaching a nucleobase to a ribose ring. Examples
of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine.
Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides,
which are the molecular building blocks of DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid).

Saccharides
Monosaccharides are carbohydrates in the form of simple sugars.
Disaccharides are formed from two monosaccharides joined together. Monosaccharides
and disaccharides are sweet, water soluble, and crystalline. Examples of
monosaccharides include the hexoses (glucose, fructose, and galactose) and pentoses
(ribose, deoxyribose). Examples of disaccharides include sucrose, maltose, and lactose.
Polysaccharides are polymerized monosaccharides, complex unsweet carbohydrates. They
are, generally, large and often have a complex, branched, connectivity. They are insoluble
in water and do not form crystals. Examples include starch, cellulose, and glycogen.
Shorter polysaccharides, with 2-15 monomers, are sometimes known as
oligosaccharides.

51

Lipids
Lipids are chiefly fatty acid esters, and are the basic building blocks of biological
membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids
consist of a polar or hydrophilic head and one to three nonpolar or hydrophobic fatty acid
tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of
carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both
single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon
groups long.
For lipids present in biological membranes, the hydrophilic head is from one of three
classes:

Glycolipids, whose heads contain an oligosaccharide with 1-15 saccharide


residues.
Phospholipids, whose heads contain a positively charged group that is linked to
the tail by a negatively charged phosphate group.
Sterols, whose heads contain a planar steroid ring, for example, cholesterol.

Hormones
Hormones are produced in the endocrine glands, where they are excreted into the
bloodstream. They perform a wide range of roles in the various organs including the
regulation of metabolic pathways and the regulation of membrane transport processes.
Hormones may be grouped into three structural classes:

The steroids are one class of such hormones. They perform a variety of functions,
but they are all made from cholesterol.
Simple amines or amino acids.
Peptides or proteins.

Amino acids
Amino acids are molecules that contain both amino and carboxylic acid functional groups.
( In biochemistry, the term amino acid is used when referring to those amino acids in
which the amino and carboxylate functionalities are attached to the same carbon, plus
proline which is not actually an amino acid).
Amino acids are the building blocks of long polymer chains. With 2-10 amino acids such
chains are called peptides, with 10-100 they are often called polypeptides, and longer
chains are known as proteins. These protein structures have many structural and
functional roles in organisms.
There are twenty amino acids that are encoded by the standard genetic code, but there
are more than 500 natural amino acids. When amino acids other than the set of twenty
are observed in proteins, this is usually the result of modification after translation

52
(protein synthesis). Only two amino acids other than the standard twenty are known to
be incorporated into proteins during translation, in certain organisms:

Selenocysteine is incorporated into some proteins at a UGA codon, which is


normally a stop codon.
Pyrrolysine is incorporated into some proteins at a UAG codon. For instance, in
some methanogens in enzymes that are used to produce methane.

Besides those used in protein synthesis, other biologically important amino acids include
carnitine (used in lipid transport within a cell), ornithine, GABA and taurine.

Protein structure
The particular series of amino acids that form a protein is known as that protein's primary
structure. Proteins have several, well-classified, elements of local structure and these are
termed secondary structure. The overall 3D structure of a protein is termed its tertiary
structure. Proteins often aggregate into macromolecular structures, or quaternary
structure.

Metalloproteins
A metalloprotein is a protein that contains a metal cofactor. The metal may be an isolated
ion or may be coordinated with an nonprotein organic compound, such as the porphyrin
group found in hemoproteins. In some cases, the metal is coordinated with both a side
chain of the protein and an inorganic nonmetallic ion. This type of protein-metalnonmetal structure is found in iron-sulfur clusters.

Vitamins
A vitamin is a compound that can not be synthesized by a given organism but is
nonetheless vital to its survival or health. These compounds must be absorbed, or eaten,
but typically only in trace quantities.

10. DNA

53
DNA replication
Deoxyribonucleic acid (DNA) is a nucleic acid which is capable of carrying genetic
instructions for the biological development of all cellular forms of life and many viruses.
DNA is sometimes referred to as the molecule of heredity as it is inherited and used to
propagate traits. During reproduction, it is replicated and transmitted to offspring.
In bacteria and other simple cell organisms, DNA is not separated from the cytoplasm by
a nuclear envelope. In the complex cells that make up plants, animals and in other multicelled organisms, by contrast, most of the DNA is located in the cell nucleus. The energygenerating organelles known as chloroplasts and mitochondria also carry DNA, as do
many viruses.

DNA in brief
This section presents a brief and simple overview of DNA.

Genes can be loosely viewed as the organism's "cookbook";


A strand of DNA contains genes, areas that regulate genes, and areas that either
have no function, or a function we do not (yet) know;
DNA is organized as two complementary strands, head-to-toe, with bonds
between them that can be "unzipped" like a zipper, separating the strands;
DNA is encoded with four interchangeable "building blocks", called "bases", which
can be abbreviated A, T, C, and G; each base "pairs up" with only one other base:
A+T, T+A, C+G and G+C; that is, an "A" on one strand of double-stranded DNA
will "mate" properly only with a "T" on the other, complementary strand;
The order does matter: A+T is not the same as T+A, just as C+G is not the same
as G+C;
However, since there are just four possible combinations, naming only one base
on the conventionally chosen side of the strand is enough to describe the
sequence;
The order of the bases along the length of the DNA is what it's all about, the
sequence itself is the description for genes;
Replication is performed by splitting (unzipping) the double strand down the
middle via relatively trivial chemical reactions, and recreating the "other half" of
each new single strand by drowning each half in a "soup" made of the four bases.
Since each of the "bases" can only combine with one other base, the base on the
old strand dictates which base will be on the new strand. This way, each split half
of the strand plus the bases it collects from the soup will ideally end up as a
complete replica of the original, unless a mutation occurs;
Mutations are simply chemical imperfections in this process: a base is accidentally
skipped, inserted, or incorrectly copied, or the chain is trimmed, or added to; all
other basic mutations can be described as combinations of these accidental
"operations".

DNA in crime
Forensic scientists can use DNA located in blood, semen, or hair left at the scene of a
crime to identify a possible suspect, a process called DNA profiling or genetic
fingerprinting. In DNA profiling the relative lengths of sections of repetitive DNA, such as
short tandom repeats and minisatellites are compared. DNA profiling was developed in
1984 English geneticist Alec Jeffries, and was first used in 1986 in the Enderby murders
case in Leicestershire, England. Many jurisdictions require convicts of certain types of

54
crimes to provide a sample of DNA for inclusion in a computerized database. This has
helped investigators solve old cases where the perpetrator was unknown and only a DNA
sample was obtained from the scene (particularly in rape cases between strangers). This
method is one of the most reliable techniques for identifying a criminal, but is not always
perfect, for example if no DNA can be retrieved, or if the scene is contaminated with the
DNA of several possible suspects.

Overview of molecular structure


Although sometimes called "the molecule of heredity", pieces of DNA as people typically
think of them are not single molecules. Rather, they are pairs of molecules, which
entwine like vines to form a double helix (see the illustration at the right).
Each vine-like molecule is a strand of DNA: a chemically linked chain of nucleotides, each
of which consists of a sugar, a phosphate and one of four kinds of nucleobases ("bases").
Because DNA strands are composed of these nucleotide subunits, they are polymers.
The diversity of the bases means that there are four kinds of nucleotides, which are
commonly referred to by the identity of their bases. These are adenine (A), thymine (T),
cytosine (C), and guanine (G).
In a DNA double helix, two polynucleotide strands can associate through the hydrophobic
effect. Specificity of which strands stay associated is determined by complementary
pairing. Each base forms hydrogen bonds readily to only one other -- A to T and C to G -so that the identity of the base on one strand dictates the strength of the association; the
more complementary bases exist, the stronger and longer-lasting the association.
The cell's machinery is capable of melting or disassociating a DNA double helix, and using
each DNA strand as a template for synthesizing a new strand which is nearly identical to
the previous strand. Errors that occur in the synthesis are known as mutations. The
process known as PCR mimics this process in vitro in a nonliving system.
Because pairing causes the nucleotide bases to face the helical axis, the sugar and
phosphate groups of the nucleotides run along the outside; the two chains they form are
sometimes called the "backbones" of the helix. In fact, it is chemical bonds between the
phosphates and the sugars that link one nucleotide to the next in the DNA strand.

The role of the sequence


Within a gene, the sequence of nucleotides along a DNA strand defines a protein, which
an organism is liable to manufacture or "express" at one or several points in its life using
the information of the sequence. The relationship between the nucleotide sequence and
the amino-acid sequence of the protein is determined by simple cellular rules of
translation, known collectively as the genetic code. The genetic code is made up of threeletter 'words' (termed a codon) formed from a sequence of three nucleotides (e.g. ACT,
CAG, TTT). These codons can then be translated with messenger RNA and then transfer
RNA, with a codon corresponding to a particular amino acid. Since there are 64 possible
codons, most amino acids have more than one possible codon. There are also three 'stop'
or 'nonsense' codons signifying the end of the coding region.
In many species of organism, only a small fraction of the total sequence of the genome
appears to encode protein. The function of the rest is a matter of speculation. It is known
that certain nucleotide sequences specify affinity for DNA binding proteins, which play a

55
wide variety of vital roles, in particular through control of replication and transcription.
These sequences are frequently called regulatory sequences, and researchers assume
that so far they have identified only a tiny fraction of the total that exist. "Junk DNA"
represents sequences that do not yet appear to contain genes or to have a function.
Sequence also determines a DNA segment's susceptibility to cleavage by restriction
enzymes, the quintessential tools of genetic engineering. The position of cleavage sites
throughout an individual's genome determines one kind of an individual's "DNA
fingerprint".

DNA replication
Main article: DNA replication
DNA replication or DNA synthesis is the process of copying the double-stranded DNA prior
to cell division. The two resulting double strands are generally almost perfectly identical,
but occasionally errors in replication can result in a less than perfect copy (see mutation),
and each of them consists of one original and one newly synthesized strand. This is called
semiconservative replication. The process of replication consists of three steps: initiation,
replication and termination.

Mechanical properties relevant to biology


Strands association and dissociation
The hydrogen bonds between the strands of the double helix are weak enough that they
can be easily separated by enzymes. Enzymes known as helicases unwind the strands to
facilitate the advance of sequence-reading enzymes such as DNA polymerase. The
unwinding requires that helicases chemically cleave the phosphate backbone of one of the
strands so that it can swivel around the other. The strands can also be separated by
gentle heating, as used in PCR, provided they have fewer than about 10,000 base pairs
(10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments
difficult to separate.

Circular DNA
When the ends of a piece of double-helical DNA are joined so that it forms a circle, as in
plasmid DNA, the strands are topologically knotted. This means they cannot be separated
by gentle heating or by any process that does not involve breaking a strand. The task of
unknotting topologically linked strands of DNA falls to enzymes known as topoisomerases.
Some of these enzymes unknot circular DNA by cleaving two strands so that another
double-stranded segment can pass through. Unknotting is required for the replication of
circular DNA as well as for various types of recombination in linear DNA.

Great length versus tiny breadth


The narrow breadth of the double helix makes it impossible to detect by conventional
electron microscopy, except by heavy staining. At the same time, the DNA found in many
cells can be macroscopic in length -- approximately 5 centimetres long for strands in a
human chromosome. Consequently, cells must compact or "package" DNA to carry it
within them. This is one of the functions of the chromosomes, which contain spool-like
proteins known as histones, around which DNA winds.

56

Different helix geometries


The DNA helix can assume one of three slightly different geometries, of which the "B"
form described by James D. Watson and Francis Crick is believed to predominate in cells.
It is 2 nanometres wide and extends 3.4 nanometres per 10 bp of sequence. This is also
the approximate length of sequence in which the double helix makes one complete turn
about its axis. This frequency of twist (known as the helical pitch) depends largely on
stacking forces that each base exerts on its neighbors in the chain.

Supercoiled DNA
The B form of the DNA helix twists 360 per 10.6 bp in the absence of strain. But many
molecular biological processes can induce strain. A DNA segment with excess or
insufficient helical twisting is referred to, respectively, as positively or negatively
"supercoiled". DNA in vivo is typically negatively supercoiled, which facilitates the
unwinding of the double-helix required for RNA transcription.

Conditions for formation of A and Z helices


The two other known double-helical forms of DNA, called A and Z, differ modestly in their
geometry and dimensions. The A form appears likely to occur only in dehydrated samples
of DNA, such as those used in crystallographic experiments, and possibly in hybrid
pairings of DNA and RNA strands. Segments of DNA that cells have methylated for
regulatory purposes may adopt the Z geometry, in which the strands turn about the
helical axis like a mirror image of the B form.

Non-helical forms
Other, including non-helical, forms of DNA have been described, for example a side-byside (SBS) configuration. Indeed, it is far from certain that the B-form double helix is the
dominant form in living cells.

Direction of DNA strands


The asymmetric shape and linkage of nucleotides means that a DNA strand always has a
discernible orientation or directionality. Because of this directionality, close inspection of a
double helix reveals that nucleotides are heading one way along one strand (the
"ascending strand"), and the other way along the other strand (the "descending strand").
This arrangement of the strands is called antiparallel.

Chemical nomenclature (5' and 3')


For reasons of chemical nomenclature, people who work with DNA refer to the
asymmetric ends of each strand as the 5' and 3' ends (pronounced "five prime" and
"three prime"). DNA workers and enzymes alike always read nucleotide sequences in the
"5' to 3' direction". In a vertically oriented double helix, the 3' strand is said to be
ascending while the 5' strand is said to be descending.

Sense and antisense

57
As a result of their antiparallel arrangement and the sequence-reading preferences of
enzymes, even if both strands carried identical instead of complementary sequences,
cells could properly translate only one of them. The other strand a cell can only read
backwards. Molecular biologists call a sequence "sense" if it is translated or translatable,
and they call its complement "antisense". It follows then, somewhat paradoxically, that
the template for transcription is the antisense strand. The resulting transcript is an RNA
replica of the sense strand and is itself sense.

An exception: viruses
Some viruses blur the distinction between sense and antisense, because certain
sequences of their genomes do double duty, encoding one protein when read 5' to 3'
along one strand, and a second protein when read in the opposite direction along the
other strand. As a result, the genomes of these viruses are unusually compact for the
number of genes they contain, which biologists view as an adaptation.

As viewed by topologists
Topologists like to note that the juxtaposition of the 3' end of one DNA strand beside the
5' end of the other at both ends of a double-helical segment makes the arrangement a
"crab canon".

Single-stranded DNA (ssDNA) and repair of mutations


In some viruses DNA appears in a non-helical, single-stranded form. Because many of the
DNA repair mechanisms of cells work only on paired bases, viruses that carry singlestranded DNA genomes mutate more frequently than they would otherwise. As a result,
such species may adapt more rapidly to avoid extinction. The result would not be so
favorable in more complicated and more slowly replicating organisms, however, which
may explain why only viruses carry single-stranded DNA. These viruses presumably also
benefit from the lower cost of replicating one strand versus two.

The history of DNA research

James Watson in the Cavendish Laboratory at the University of Cambridge


The discovery that DNA was the carrier of genetic information was a process which
required many earlier discoveries. The existence of DNA was discovered in the mid 19th
century. However, it was only in the early 20th century that researchers began
suggesting that it might storeb genetic information. This was only accepted after the

58
structure of DNA was elucidated by Watson and Crick, which they published in 1953.
Watson and Crick proposed the central dogma of molecular biology in 1957, describing
the process whereby proteins are produced from nucleic DNA.

First isolation of DNA


Working in the 19th century, biochemists initially isolated DNA and RNA (mixed together)
from cell nuclei. They were relatively quick to appreciate the polymeric nature of their
"nucleic acid" isolates, but realized only later that nucleotides were of two types--one
containing ribose and the other deoxyribose. It was this subsequent discovery that led to
the identification and naming of DNA as a substance distinct from RNA.
Friedrich Miescher (1844-1895) discovered a substance he called "nuclein" in 1869.
Somewhat later, he isolated a pure sample of the material now known as DNA from the
sperm of salmon, and in 1889 his pupil, Richard Altmann , named it "nucleic acid". This
substance was found to exist only in the chromosomes.

Discovery of the structure of DNA


In the 1950s, only a few groups made it their goal to determine the structure of DNA.
These included an American group led by Linus Pauling, and two groups in Britain. At the
University of Cambridge, Crick and Watson were building physical models using metal
rods and balls, in which they incorporated the known chemical structures of the
nucleotides, as well as the known position of the linkages joining one nucleotide to the
next along the polymer. At King's College, London, Maurice Wilkins and Rosalind Franklin
were examining X-ray diffraction patterns of DNA fibers.

Discovery that DNA is helical


A key inspiration in the work of all of these teams was the discovery in 1948 by Pauling
that many proteins included helical (see alpha helix) shapes. Pauling had deduced this
structure from X-ray patterns. Even in the initial crude diffraction data from DNA, it was
evident that the structure involved helices. But this insight was only a beginning. There
remained the questions of how many strands came together, whether this number was
the same for every helix, whether the bases pointed toward the helical axis or away, and
ultimately what were the explicit angles and coordinates of all the bonds and atoms. Such
questions motivated the modeling efforts of Watson and Crick.

59
11. Chromosome

Figure 1: Chromosome. (1) Chromatid. One of the two identical parts of the
chromosome after S phase. (2) Centromere. The point where the two chromatids touch,
and where the microtubules attach. (3) Short arm. (4) Long arm.
A chromosome (in Greek chroma = colour and soma = body) is, minimally, a very long,
continuous piece of DNA, which contains many genes, regulatory elements and other
intervening nucleotide sequences. In the chromosomes of eukaryotes, the uncondensed
DNA exists in a quasi-ordered structure inside the nucleus, where it wraps around
histones (structural proteins, Fig. 1), and where this composite material is called
chromatin. During mitosis (cell division), the chromosomes are condensed and called
metaphasic chromosomes. This is the only natural context in which individual
chromosomes are visible with an optical microscope. Prokaryotes do not possess histones
or nuclei. In its relaxed state, the DNA can be accessed for transcription, regulation, and
replication. Chromosomes were first observed by Karl Wilhelm von Ngeli in 1842 and
their behavior later described in detail by Walther Flemming in 1882. In 1910, Thomas
Hunt Morgan proved that chromosomes are the carriers of genes.

Chromosomes in eukaryotes
Eukaryotes possess multiple linear chromosomes contained in the cell's nucleus. Each
chromosome has one centromere, with one or two arms projecting from the centromere.
The ends of the chromosomes are special structures called telomeres. DNA replication
begins at many different locations on the chromosome.

Chromatin
Two types of chromatin can be distinguished:

Euchromatin, which consists of DNA that is active, e.g., expressed as protein.


Heterochromatin, which consists of mostly inactive DNA. It seems to serve
structural purposes during the chromosomal stages. Heterochromatin can be
further distinguished into two types:
o Constitutive heterochromatin, which is never expressed. It is located
around the centromere and usually contains repetitive sequences.
o Facultative heterochromatin, which is sometimes expressed.

60

Figure 2: Different levels of DNA condensation. (1) Single DNA strand. (2) Chromatin
strand (DNA with histones). (3) Chromatin during interphase with centromere. (4)
Condensed chromatin during prophase. (Two copies of the DNA molecule are now
present) (5) Chromosome during metaphase.
In the early stages of mitosis, the chromatin strands become more and more condensed.
They cease to function as accessible genetic material and become a compact transport
form. Eventually, the two matching chromatids (condensed chromatin strands) become
visible as a chromosome, linked at the centromere. Long microtubules are attached at
the centromere and two opposite ends of the cell. During mitosis, the microtubules pull
the chromatids apart, so that each daughter cell inherits one set of chromatids. Once the
cells have divided, the chromatids are uncoiled and can function again as chromatin. In
spite of their appearance, chromosomes are highly structured (Fig. 2). For example,
genes with similar functions are often kept close together in the nucleus, even if they are
far apart on the chromosome. The short arm of a chromosome can be extended by a
satellite chromosome that contains codes for ribosomal RNA.

Figure 3: Karyogram of human female

Karyotype
To determine the (diploid) number of chromosomes of an organism, cells can be locked in
metaphase in vitro (in a reaction vial) with colchicine. These cells are then stained (the
name chromosome was given because of their ability to be stained), photographed and
arranged into a karyotype (an ordered set of chromosomes, Fig. 3), also called
karyogram. Like many sexually reproducing species, humans have special gonosomes

61
(sex chromosomes, in contrast to autosomes for body functions). These are XX in
females and XY in males. In females, one of the two X chromosomes is inactive and can
be seen under a microscope as Barr bodies.

Human chromosome

Chromosome

Genes

Bases

Determined bases*

1 2968 245,203,898

218,712,898

2 2288 243,315,028

237,043,673

3 2032 199,411,731

193,607,218

4 1297 191,610,523

186,580,523

5 1643 180,967,295

177,524,972

6 1963 170,740,541

166,880,540

7 1443 158,431,299

154,546,299

1127 145,908,738

141,694,337

9 1299 134,505,819

166,880,540

10 1440 135,480,874

115,187,714

11 2093 134,978,784

130,709,420

12 1652 133,464,434

129,328,332

13

748 114,151,656

95,511,656

14 1098 105,311,216

87,191,216

15

81,117,055

1122 100,114,055

16 1098

89,995,999

79,890,791

17 1576

81,691,216

77,480,855

18

766

77,753,510

74,534,531

19 1454

63,790,860

55,780,860

20

927

63,644,868

59,424,990

21

303

46,976,537

33,924,742

22

288

49,476,972

34,352,051

1184 152,634,166

147,686,664

62
Y

231

50,961,097

22,761,097

unplaced various

25,263,157

25,062,835

* Human Genome Project goals called for determination of only the euchromatic portion
of the genome. Telomeres, centromeres, and other heterochromatic regions have been
left undetermined, as have a small number of unclonable gaps. [1]

Chromosomal aberrations
Some chromosome abnormalities do not cause disease in carriers, such as translocations,
or chromosomal inversions, although it may lead to a higher chance of having a child with
an chromosome disorder. Abnormal numbers of chromosomes or chromosome sets,
Aneuploidy, may be lethal or give rise to genetic disorders. Genetic counseling is offered
for families that may carry a chromosome rearrangement. The gain or loss of
chromosome material can lead to a variety of genetic disorders. Examples include:

Cri du chat syndrome, which is caused by the deletion of part of the short arm of
chromosome 5. Victims make high-pitched cries that sound like a cat. They have
wide-set eyes, a small head and jaw and are mentally retarded.
Wolf-Hirschhorn syndrome, which is caused by partial deletion of the short arm of
chromosome 4. It is characterized by severe growth retardation and mental
defect.
Down syndrome (extra chromosome 21). This is also known as mongolism or
trisomy 21. Symptoms are decreased muscle tone, asymmetrical skull, slanting
eyes and mental retardation.
Edward's syndrome is the second most common trisomy after Down's Syndrome.
It is a trisomy of chromosome 18. Symptoms include mental and motor
retardation.
Patau Syndrome, also called D-Syndrome or trisomy-13. Symptoms somewhat
similar to those of trisomy-18.
Jacobsen syndrome , also called the terminal 11q deletion disorder. A very rare
disorder. More information at http://www.11q.org/.
Klinefelters syndrome (XXY). Men with Klinefelter syndrome are usually sterile.
They tend to have longer arms and legs and tend to be taller than their peers.
Other common symptoms are fatigue, apathy, lack of emotion, and an increased
tendency to develop psychiatric disorders.
Turner syndrome (X instead of XX or XY). In Turner syndrome, female sexual
characteristics are present but underdeveloped. People with Turner syndrome
often have a short stature, low hairline, abnormal eye features and bone
development and a "caved-in" appearance to the chest.
XYY syndrome
Triple-X syndrome