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dipolar. Since water has got opposite charges on two points and due to large difference in
electronegativity of hydrogen and oxygen the hydrogen of water molecules are attracted to
unshared pairs of electrons of another molecule. This non-covalent relationship is called
hydrogen bond, which is due to strong electrostatic action rather than a true bond.
In addition to hydrogen bonds, the water interact with other molecules through three more
types of non-covalent interactions. The electrostatic interaction causes hydration of ions and
solvation of charged species in water. Van der waals forces are weak transient electrostatic
interactions between permanent or induced dipoles. Hydrophobic interactions when water mixed
with non-polar substances, they coalesce into droplets because water-water interactions are
stronger than non-polar interactions. Water has a variety of unusual properties because of
attractions between two polar regions. The slightly negative regions of one molecule are attracted
to the slightly positive regions of nearby molecules, forming a hydrogen bond. Each water
molecule
can
form
hydrogen
bonds
with
up
to
four neighbors.
HYDROGEN BONDS
It hold water molecules together, each water molecule can form a maximum of 4 hydrogen
bonds. The hydrogen bonds joining water molecules are weak, about 1/20 th as strong as covalent
bonds. They form, break, and reform with great frequency. Extraordinary Properties that are a
result of hydrogen bonds.
Cohesive behavior
Resists changes in temperature
High heat of vaporization
Expands when it freezes
Versatile solvent
Water is most dense at 4oC, expands from 4oC to 0oC, water becomes locked into a
crystalline lattice and solidifies. As ice starts to melt, some of the hydrogen bonds break and
some water molecules can slip closer together than they can while in the ice state. Ice is about
10% less dense than water at 4oC.
Most biochemical reactions involve solutes dissolved in water. There are two important
quantitative properties of aqueous solutions-Concentration and pH. Water is called as an
Universal solvent because large variety of ionic and polar substances can dissolve in it since
water has very large dielectric constant .
Dissociation of Water Molecules
Occasionally, a hydrogen atom shared by two water molecules shifts from one molecule to
the other. The hydrogen atom leaves its electron behind and is transferred as a single proton - a
hydrogen ion (H+). The water molecule that lost a proton is now a hydroxide ion (OH-). The
water molecule with the extra proton is a hydronium ion (H3O+).
A simpler way to view this process is that a water molecule dissociates into a hydrogen ion and a
hydroxide ion:
H2O <=> H+ + OHThis reaction is reversible. At equilibrium the concentration of water molecules greatly exceeds
that of H+ and OH-. In pure water only one water molecule in every 554 million is dissociated. At
equilibrium, the concentration of H+ or OH- is 10-7M (25C) .
ELECTROLYTES
Electrolytes & Non-electrolytes
Electrolytes forms ions in water & conduct electric current while non-electrolytes dissolve as
molecules in water, do not produce ions in water & do not conduct electric current.
Strong Electrolytes
Strong electrolytes dissociates in water, producing positive and negative ions. It also dissolves in
water will conduct an electric current . Equations show the formation of ions in aqueous (aq)
solutions
Learning Check
Complete each of the following equations for strong electrolytes dissolving in water.
Solution
Complete each of the following equations for strong electrolytes dissolving in water.
Weak Electrolytes
A weak electrolyte dissociates only slightly in water and forms a solution of a few ions and
mostly undissociated molecules.
Stereoisomers
Compounds with the same molecular formula but only differ in the spatial arrangement of
their constituent atoms or groups.
Enantiomers
Stereoisomers which are non-superimposable mirror images of one another
Diastereoisomers
Stereoisomers which are not mirror images of each other.
Chiral molecules
Molecules that are capable of existing in mirror image forms but can not be super imposable
in their mirror images . A carbon atom has 4 different substituent attached to it forming an
asymmetric molecule, the carbon is said to be chiral or a centre of chirality. For eg- all amino
acids except glycine have four different groups attached to central carbon atom.
Chiros Greek Handed
Stereoisomers of Ibuprofen
H
H
(CH3)2CHCH2
CH3
H3C
COOH HOOC
(-)-(R)-ibuprofen
(+)-(S)-ibuprofen
Stereoisomers of Phenylpropanolamine
CH2CH(CH3)2
CARBOHYDRATES
The most abundant organic molecules in nature which Provides a significant fraction of the
energy in the diet of most organisms. Important source of energy for cells act as a storage form
of energy. Structural components of many organisms and Cell-membrane components mediates
intercellular communication. As a cell-surface antigens, the Part of the bodys extracellular
ground substance associates with proteins and lipids. Part of RNA, DNA, and several coenzymes
(NAD+, NADP+, FAD, CoA).
Monosaccharides
Simple sugars which have 3 to 9 carbon atoms attached to Polyhydroxy aldehydes or ketones
that cant easily be further hydrolyzed.
Disaccharides
Disaccharides are glycosides that are composed of 2 monosaccharide units found in abundance
in nature, disaccharides provide a significant source of calories in many human diets. On
hydrolysis they release two molecules of monosaccharides.
Examples: Sucrose, Lactose, fructose
Oligosaccharides
Hydrolyzable polymers of 2-10 monosaccharide units. These small polymers are most often
found attached to polypeptides in glycoproteins and in some glycolipids.
Polysaccharides
They are composed of large numbers of monosaccharide units connected by glycosidic linkages.
Most commonly occurring polysaccharides are large molecules containing from 100s to
thousands of sugar units. They may linear structure (cellulose, Amylose) or branched (glycogen
amylopactin)
Homopolysaccharides:
Polymer of a single type of monosaccharide
Examples: Starch,Glycogen, Cellulose
Heteropolysaccharides:
Polymer of two or more different types of monosaccharide
Example: Glucosaminoglycans.
Reducing sugars
Carbohydrate with a free or potentially free aldehyde or ketone group
Dietary carbohydrates
Only monosaccharides are absorbed into the bloodstream from the gut. Digestion of
carbohydrates involves their hydrolysis into monosaccharides.
Digestive Enzymes
Enzymes for carbohydrate digestion
LIPIDS
Capacity to polymerize
Amino acids are mostly having the central carbon chiral except for glycine. The structure of
20 amino acids that are commonly found in proteins or reffered to a standard amino acids to
distinguish them from non standard amino acids which are not found in proteins but are
chemically modified after their incorporation in to polypeptides and amino acids that occur in
living organisms.
Aromatic (3)
The Three Letter Code Naming starts from the N-terminus and the Sequence is written as:
Ala-Glu-Gly-Lys. Sometimes the one-letter code is used as AEGK.
amanitin (mushrooms)
chlorotoxin (scorpions)
Proteins
Polypeptides (covalently linked -amino acids) + possibly are said to be
cofactors,
coenzymes,
prosthetic groups,
other modifications
Cofactor is a general term for functional non-amino acid component
Metal ions or organic molecules
Coenzyme is used to designate an organic cofactors
NAD+ in lactate dehydrogenase
Nitrogen Bases
The nitrogen bases in nucleotides consist of two general types. Purines: adenine (A) and guanine
(G) and Pyrimidines: cytosine (C), thymine (T) and Uracil (U)
Pentose Sugars
There are two related pentose sugars. RNA contains ribose and DNA contains deoxyribose. The
sugars have their carbon atoms numbered with primes to distinguish them from the nitrogen bases
Nucleosides are named by changing the the nitrogen base ending to -osine for purines and idine for
pyrimidines. A nucleotide is a nucleoside that forms a phosphate ester with the C5 OH group of ribose
or deoxyribose. Nucleotides are named using the name of the nucleoside followed by 5-monophosphate
Transfer RNA
Transfer RNA translates the genetic code from the messenger RNA and brings specific amino acids to
the ribosome for protein synthesis. Each amino acid is recognized by one or more specific tRNA . tRNA
has a tertiary structure that is L-shaped and its one end attaches to the amino acid and the other binds to
the mRNA by a 3-base complimentary sequence.
end of a polypeptide chain. The amino acid sequence of a protein can be determined by reading the
triplets in the DNA sequence that are complementary to the codons of the mRNA, or directly from the
mRNA sequence. The entire DNA sequence of several organisms, including humans, have been
determined, however, only primary structure can be determined this way that doesnt give tertiary
structure or protein function.
mRNA Codons and Associated Amino Acids
ENZYMES
Chemical reactions in biological systems rarely occur in the absence of a catalyst. These catalysts are
specific proteins called enzymes. Enzymes accelerate reactions by factors of at least a million.
Indeed,most reactions in biological systems donot occur at perceptible rates in the absence of enzymes.
Enzymes are highly specific,both in the reaction catalyzed & in their choice of reactants, which are
called substrates. An enzyme usually catalyzes a single chemical reaction or a set of closely related
reactions.
In many biochemical reactions, the energy of the reactants is converted into a different form with
high efficiency. For eg: In photosynthesis, light energy is converted to chemical bond energy. An
enzyme is a catalyst and consequently, it cannot alter the equilibrium of a chemical reaction. This
means, that an enzyme accelerates forward and reverse reaction by precisely the same factor. The
making and breaking of chemical bonds by an enzyme are preceded by the formation of an enzymesubstrate complex. The substrate is bound to a specific region of the enzyme called active site.
COFACTORS
The non protein component of an enzyme either an inorganic ion or a coenzyme is termed as Cofactors.
Cofactors
Prosthetic groups
Dissociable cofactors
Metal cofactors
Many Fe Cofactors
How much Iron in a Human?
Typically in an adult human there is 4-5 grams of Fe comprising.
hemoglobin - 2.6 g (65%)
myglobin - 0.13 g (6%)
transferrin - 0.007 g (0.2%)
ferritin - 0.52 g (13%)
hemosiderin - 0.50 g (12%)
catalase - 0.004 g (0.1%)
Ancient Fe Cofactors
Heme Metabolism
The largest repository of heme in the human body is in red blood cells, which have a life span of
about 120 days. There is thus a turnover of about 6 g/day of hemoglobin, which presents 2 problems.
First, the porphyrin ring is hydrophobic and must be solubilized to be excreted. Second, iron must be
conserved for new heme synthesis. Heme is oxidized, with the heme ring being opened by the
endoplasmic reticulum enzyme, heme oxygenase. The oxidation step requires heme as a substrate, and
any hemin (Fe3+) is reduced to heme (Fe2+) prior to oxidation by heme oxygenase. The oxidation
occurs on a specific carbon producing the linear tetrapyrrole biliverdin, ferric iron (Fe3+), and
carbon monoxide (CO). This is the only reaction in the body that is known to produce CO. Most of
the CO is excreted through the lungs, with the result that the CO content of expired air is a direct
measure of the activity of heme oxygenase in an individual.
In the next reaction a second bridging methylene (between rings III and IV) is reduced by biliverdin
reductase, producing bilirubin. Bilirubin is significantly less extensively conjugated than biliverdin
causing a change in the color of the molecule from blue-green (biliverdin) to yellow-red (bilirubin).
The latter catabolic changes in the structure of tetrapyrroles are responsible for the progressive
changes in color of a hematoma, or bruise, in which the damaged tissue changes its color from an
initial dark blue to a red-yellow and finally to a yellow color before all the pigment is transported out of
the affected tissue.
in
Vitamins
Definition and Classification
An organic molecule required by organisms in minute quantities for proper functioning. Some vitamins
are used in the synthesis of some coenzymes required for the function of cellular enzymes. The vitamins
can be fat or water soluble.
Fat soluble vitamins are found in the fats and oils of food. Absorbed into the lymph and carried in blood
with protein transporters = chylomicrons. *Stored in liver and body fat and can become toxic if large
amounts are consumed.
Water soluble vitamins are found in vegetables, fruit and grains, meat. Absorbed directly into the
blood stream and is stored in the body and toxicity is rare. Alcohol can increase elimination, smoking,
etc. cause decreased absorption.
Fat Soluble Vitamins
Vitamin A (precursor beta carotene) are of 3 forms: retinol (stored in liver), retinal, retinoic acid.
Roles in body:
Regulation of gene expression
Part of the visual pigment rhodopsin, maintains clarity of cornea (yes eating carrots is good for your
eyesight).
Required for cell growth and division - epithelial cells, bones and teeth.
Promotes development of immune cells, especially Natural Killer Cells
Antioxidant.
Deficiencies cause:
Night blindness, xerophthalmia (keratin deposits in cornea), macular degeneration.
Skin and mucous membrane dryness and infection, keratin deposits.
Anemia
Developmental defects bones, teeth, immune system, vision
Toxicities (RetinA/Accutaine, single large doses of supplements, eating excessive amounts of liver)
cause:
Fragile RBCs, hemorrhage
Bone pain, fractures
Abdominal pain and diarrhea
Blurred vision
Dry skin, hair loss
Liver enlargement
DRI: 700(women)-900(men) micrograms/day, UL 3000 micrograms
Source snapshot given below.
HORMONES
Hormones are chemical messengers that coordinate the activities of different cells. The term
hormone was first used in 1904 by William Bayliss and Ernest Starling to describe the action of
secretin, a molecule secreted by duodenum that stimulates the subsequent flow of pancreatic juice.
Hormones are molecules synthesized by specific cells, tissues (glands) that influence the function of
distant target cells. A number of hormones, produced by certain cells, are secreted directly into the
blood which carries them to their site of action.and they specifically alter the activities of certain
responsive tissues, target cell or target organs. The hormones are produced by specialized in the
glands called as endocrine glands. These glands are ductless and release the hormones directly to
blood.
Hormones are chemically reverse. Some hormones, such as epinephrine and thyroxine,
are small molecules that are derived from amino acids. Others, such as oxytocin, insulin and thyroidstimulating hormones are polypeptides or proteins. A third group of hormones consists of the
steroids, which are derived from cholesterol. The molecular bases of the actions of some hormones
are now being elucidated.
Hormones can exert their specific effects in three ways: (1) by influencing the rate of
synthesis of enzymes and other proteins, (2) by affecting the rate of enzymatic catalysis, and (3) by
altering the permeability of cell membranes. It is interesting to note that no known hormone is an
enzyme or coenzyme. Rather hormones act by regulating preexisting processes.