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BCH 201 - Ibbul - 2017
BCH 201 - Ibbul - 2017
BCH 201
General BiochemistryI
I. Introduction
II. Stereoisomerism
C 0.19% Mg 0.01%
All important biological molecules contain carbon. All molecules that contain carbon are
called organic (except for CO2). Carbon has the unique ability to form a virtually infinite
number of compounds as a result of its capacity to make as many as four highly stable
covalent bonds (including single, double, and triple bonds) combined with ability to form
covalently linked C-C chains of unlimited extent.
The number of biological molecules is extremely large. However, the number of building
blocks used to make these molecules is surprisingly small. Most biological molecules have a
core made of carbon and hydrogen. Molecules differ in structure and function, in part,
because of different functional groups.
Biomolecules are the organic compounds which form the basis of life, i.e., they build up the
living system and responsible for their growth and maintenance.
The major classes of biological molecules that are important for all living things are
carbohydrates, lipids, proteins, and nucleic acids. Large biological molecules are called
macromolecules. Macromolecules are built by combining smaller building blocks into
polymers.
Isomers are classified into structural or constitutional or positional isomers, which occur
when atoms and groups are linked together in different ways; and stereo- or
configurational isomers, which occur when atoms and groups are connected in the same
way, yet having different arrangements in space.
Constitutional isomers:
different IUPAC names;
the same or different functional groups;
different physical properties, so they are separable by physical techniques such as
distillation; and
different chemical properties. They behave differently or give different products in
chemical reactions.
The two most common types of isomers in biological systems are cis-trans isomers and
isomerism due to the presence of a chiral carbon.
Other molecules are like socks. Two socks from a pair are mirror images that are
superimposable. One sock can fit inside another, aligning toes and heels, and tops and
bottoms. A sock and its mirror image are identical. A molecule (or object) that is
superimposable on its mirror image is said to be achiral. Achiral molecules usually contain a
plane of symmetry but chiral molecules do not. A plane of symmetry is a mirror plane that
cuts a molecule in half, so that one half of the molecule is a reflection of the other half.
Chirality is very important to discuss because biomolecules for the most part chiral and the
different chiral forms differ from each other in two aspects: How they affect light and how
To determine how a particular form affects light, it is necessary to use plane polarized light,
in which all the light waves vibrate in the same plane. Chiral compounds have the ability to
rotate plane polarized light (PPL), and this property has been used historically to
differentiate between enantiomers; when an enantiomer turns the PPL to the right it is
called dextrorotatory and, when it turns it to the left it is called levorotatory and
designated as (+) and (-) respectively. The dextrorotatory and levorotatory forms are
stereoisomers and are optically active. When a solution contains equivalent amounts of the
two enantiomers, it is referred to as a racemic mixture.
Many stereochemical descriptors are found which has nothing to do with the optical
activity, as they only describe how different groups are distributed around the chiral centre
(e.g.. D and L, R and S, E and Z). Nowadays their importance has lessened somewhat with
the development of powerful NMR and chiral chromatographic methods.
Although one enantiomer had the desired therapeutic effect, the other enantiomer was
responsible for thousands of catastrophic birth defects in children born to women who took
the drug during pregnancy.
2. Draw the mirror image of each compound below. Label each molecule as chiral or
achiral.
3. Locate any stereogenic center in the given molecules. (Some compounds contain no
stereogenic centers.)
a. CH3CH2CH(Cl)CH2CH3
b. (CH3)3CH
c. CH3CH(OH)CH=CH2
d. CH3CH2CH2OH
e. (CH3)2CHCH2CH2CH(CH3)CH2CH3
f. CH3CH2CH(CH3)CH2CH2CH3
OCCURENCE
Carbohydrates are the single most abundant class of organic molecules found in nature,
they constitute more than 50 % of the total biochemical matter. Energy from the sun
captured by green plants, algae, and some bacteria during photosynthesis converts more
than 250 billion kilograms of CO2 into carbohydrates every day on earth. They are widely
distributed in plants, animals and microbes. Animals have no way of synthesizing
carbohydrates from carbon dioxide and rely on plants for their supply. The carbohydrates
are then converted into other organic materials by a variety of biosynthetic pathways.
Metabolic/Nutritional
1. Chief source of energy (4 kcal/g). The biological breakdown of carbohydrates (often
spoken of as "combustion") supplies the principal part of the energy that every
organism needs for various processes.
2. Reserve or storage forms of energy in plants (starch, inulin) and animals (glycogen).
3. Carbohydrate fibre in our meals helps to keep bowel function going smooth.
4. Carbohydrates add on to the taste and appearance of food item
Structural
5. Insoluble carbohydrate polymers serve as structural and protective elements in the
cell walls of of certain microorganisms (peptidoglycans), exoskeleton of some insects
and crustacea (chitin) and in plant cell wall (cellulose).
6. They form a major portion of the supporting tissue and in the connective tissues of
animals (mucopolysaccharides).
Communications
7. Glycosaminoglycans as polymers of derivatives of carbohydrates are of critical
importance in intercellular communication in organisms. They are involved in cell
recognition, contact inhibition and also have antigenic properties of blood group
substances.
8. Some carbohydrate polymers lubricate skeletal joints and participate in recognition
and adhesion between cells
Description Classes
Carbohydrates can be classified based on complexities into three main groups as: a)
Monosaccharides (and their derivatives), b) Oligosaccharides and c) Polysaccharides, based
on number of monomeric sugar units present.
Oligosaccharides (Greek Oligo 'few') contain from two to ten monosaccharide units joined
through glycosidic linkage or bond. They are hydrolyzable into constituent monosaccharide
units.
MONOSACCHARIDES
The term ‘monosaccharide’ denotes a single sugar unit without glycosidic connection to
other such units. Chemically, monosaccharides are either polyhydroxyaldehydes or aldoses
(e.g., glucose) or polyhydroxyketones or ketoses (e.g., fructose). I.e. they contain a short
chain of carbon atoms with one carbonyl group, each of the remaining carbon atoms
bearing a hydroxyl group. The suffix –ose is often used in describing and naming carbohydrates.
The simplest aldose is glyceraldehyde, and the simplest ketose is dihydroxyacetone. These
two simple sugars are termed trioses because they each contain three carbon atoms.
General Properties
Some of the general properties of monosaccharides are summarized below:
Stereochemistry
All the monosaccharides except dihydroxyacetone contain one or more asymmetric carbon
atom(s). If a molecule has more than one asymmetric carbon atom, it can exist in 2 n
stereoisomeric forms, where 'n' represents the number of asymmetric carbon atoms
present. Thus, aldotrioses. aldotetroses. aldopentoses and aldohexoses have 1, 2,3 and 4
asymmetric (chiral) carbon atoms and exist in 2, 4, 8 and 16 stereoisomeric forms
respectively.
The D- and L-glyceraldehydes are used as reference or parent compounds for designating
the absolute configuration of all stereoisomeric compounds.
Assignment:
1. Glyceraldehyde
2. Dihydroxyacetone
If the rotation of the beam of plane-polarized light is clockwise (to the right or rectus as the
observer looks towards the light source), the enantiomer is designated as dextrorotatory
(dextro, 'd' or '+' symbols) and if it is anticlockwise (to the left or sinister), the enantiomer is
designated as levorotatory (levo, 'l' or '-' symbols). For example, the specific rotation of a-D-
glucose is + 112.2o (dextrorotatory) and that of D-fructose is -930 (levorotatory). Thus, the
symbol '+' and '-' refer to the direction of rotation of the beam of plane-polarized light but
not the absolute configuration.
The D-and L-stereoisomers of any given compound have identical physical properties and
identical chemical reactivities, with two exceptions: (a) they rotate the plane of plane-
polarized light equally but in opposite directions and (b) they react at different rates with
reagents that are themselves asymmetric. The equimolar mixture of the D- and L-
stereoisomers, known as racemic mixture or racemate (designated as D L-) is optically
inactive as the asymmetric carbon atom passes through a symmetrical intermediate during
chemical reaction.
Enantiomers: Aldoses and ketoses of the L-series are mirror-images of their D-counterparts.
These two D- and L- forms of a sugar are known as enantiomers. L- sugars are found in
nature, but they are not so abundant as D-sugars.
Diastereoisomers: Two sugars having the same molecular formulae but not the mirror
images of each other are known as diastereoisomers. e.g. D-glucose and D-mannose.
The Kiliani–Fischer synthesis proceeds through through cyanohydrin and aldonic acid
lactone intermediates. The process is based upon the addition of HCN to the carbonyl group
of aldehydes (or ketones) of the sugars forming cyanohydrin (Reaction-1). This reaction
creates a new asymmetric carbon atom. Thus, two compounds differing in conformation
about the newly-formed asymmetric carbon atom are formed. The cyanohydrin resulting
from this addition is heated in water, which hydrolyzes the cyanide into a carboxylic acid
group that quickly reacts with itself to form a more stable lactone. (Reaction2) which are
later converted to γ-lactones or inner esters (Reaction-3). Finally, the lactones are reduced
to the corresponding aldoses, containing one carbon atom more than their parent sugar
(Reaction-4). The process can be repeated and the 4 isomeric D-pentoses may be produced;
and from these the 8 isomeric D-hexoses would also result.
The same way aldehydes and ketones react with alcohols to form hemiacetals and
hemiketals, respectively, carbohydrates react intermolecularly to form rings. When forming
a ring 5 or 6 membered ring is most favorable and will only be formed. The Carbon 1 will be
attacked by either the Carbon 5 or Carbon 6 hydroxyl group to form a 5 or 6 membered
(respectively) carbohydrate ring.
Up to this point we have been representing the sugars as "linear" molecules. In reality the
linear form is normally a minor species (often less than 0.1%). In the solid state and in
solution monosaccharides exist in a cyclic hemiacetal form, ring closure corresponding to
reaction between the aldehyde group and either the C-4-OH or C-5OH. Cyclization involving
O-4 results in a five membered ring structurally related to furan and therefore designated as
a furanose, whilst hemiacetal formation with O-5 gives rise to an essentially strain-free,
hence sterically more favored, six-membered ring, a derivative of pyran, hence termed a
pyranose.
Either ring formation generates a new asymmetric carbon atom at C-1, the anomeric center,
thereby giving rise to diastereomeric hemiacetals which are called and labeled α and β.
In aqueous solution, many monosaccharides act as if they have one more asymmetric center
than is given by the open chain structural formulae. D-glucose may exist in two different
isomeric forms differing in specific rotation, αD-glucose, for which [α]D20 = + 112.2°, and
β-D-glucose, for which [β]D20 = +18.7°. These two sugars do not differ in elementary
composition but differ in physical and chemical properties. When the α and β-isomers of D-
glucose are dissolved in water, the optical rotation of each gradually changes with time and
approaches a final equilibrium value of [αD20 = +52.7°. This change, called mutarotation is
due to the formation of an equilibrium mixture consisting of about one-third α-D-glucose
and two thirds β-D-glucose at 20°C. The ring forms of the sugars are the ones that
predominate in solution. For example, the proportion of the straight-chain form of glucose
is quite small, about 0.1% of the total molecules. Glucose slowly inter converts between the
three structures (half time ~ 1 hour).
Less common is attack by the C4 -OH which leads to the sterically strained, 5-membered
furanoside. In ketohexoses the C=O is at C2 and so attack by C5 still yields a 5-membered
ring. The cyclic sugars are normally represented using Haworth structures; in this
representation the lines denote -OH and there is an implicit -H on the other end.
pyranoside fuanoside
Haworth formulae may be used to indicate the ring forms of monosaccharides. The
substituents on the carbon atoms are represented as extending above or below the plane of
the ring. The lower half of the ring is thickened to indicate that it is the portion of the ring
that is directed out of the plane of the paper towards the reader.
1. If the ring closes on a -OH which is on the right of the Fischer's projection, the
hydroxymethyl group (-CH20H 'tail') points up; if it closes on a -OH group on the left,
the tail points down
2. The ring -OHs points down if they are on the right in the Fisher's projection, and up if
they are on the left
3. The -OH group on the anomeric carbon atom in the D-series will be down if it is α- and
up if β-
Anomers
From various chemical considerations it has been deduced that the α- and β- isomers of D-
glucose are not open-chain structures in aqueous solution but six-membered ring structures
formed by the reaction of the alcoholic hydroxyl group at carbon atom 5 with the aldehydic
carbon atom 1 to form a hemiacetal which renders another chiral center at carbon atom 1,
also known as carbonyl carbon atom or anomeric carbon atom. Isomeric forms of
monosaccharides that differ from each other only in configuration about the carbonyl
carbon atom are known as anomers. Thus, D-glucose will have two anomers designated as
α-D-glucose and β-D-glucose.
In the case of fructose, the hemiketal is formed by reaction of the hydroxyl group on carbon
atom 5 with the carbonyl group at carbon atom 2 to yield a five-membered ring. The five-
membered ring forms of sugars are called furanoses as they are derivatives of heterocyclic
compound, furan as suggested by Haworth. The systematic name for the ring form of α-D-
fructose is α-D-fructofuranose.
Sugar Conformation
Conformation denotes the arrangement in space of atoms in a molecule which can be
achieved by rotation about single bonds. Although, the Haworth formulae give a better
indication of the true structures of sugars than do the straight chain forms, they do not
represent the actual conformations. Hexoses and pentoses that have converted into
pyranoses or furanoses take on either chair, boat, or
envelope conformations due to the tetrahedral
geometry of their carbons. Pyranose rings can form
either chair or boat conformational isomers
(conformers) while furanose rings take on the
envelope (also called half-boat) conformation which
are comparatively stable.
Reactions of Sugars
The carbohydrates, because of the various reactive groups present in the molecule, undergo
a large number of chemical reactions. Although monosaccharides exists predominantly as
hemiacetals, enough aldehyde or ketone is present at equilibrium that the sugars give most
of the reactions of these functional groups. In addition, monosaccharides exhibit reactions
of alcohol.
2. Reducing property of sugars: The enediols formed above are reactive species. They
are good reducing sugars. When glucose is heated with an alkaline solution of Cu2+
ions, the Cu2+ is reduced to Cu+ which is precipitated as Cu2O. This is the basis for
the estimation of reducing sugars.
3. Reduction to alcohols: The carboxyl group of monosaccharides can be reduced by
hydrogen gas in the presence of metal catalysts or by sodium amalgam in water to
form the corresponding sugar alcohols. For example, D-glucose on reduction yields
D-glucitol (also called L-sorbitol) while D-mannose yields D-mannitol. Sugar alcohols
occur in nature, particularly in plants. One such alcohol, glycerol is an essential
component of lipids. Myo-inositol, a stereoisomer of inositol is found as a
component of phosphoglycerides and also in phytic acid, the hexaphosphoric ester
of inositol.
4. Reactions with carbonyl reagents: The carbonyl group of monosaccharide reacts
with carbonyl reagents like hydrazine, phenyl hydrazine, hydroxylamine or
semicarbazide to yield crystalline hydrazone, phenylhydrazone, oxime or
Assignment:
1. Sugar acids
2. Sugar phosphates
OLIGOSACCHARIDES
These sugars consist of a short chain of 2 to 8 or 10 monosaccharide units linked by the
glycosidic bond (s) with the elimination of water molecule (s). The glycosidic bond is formed
most frequently between the anomeric carbon of one sugar residue and a hydroxyl group of
the other sugar residue. Depending on the number of monosaccharide units that are linked,
the oligosaccharides are further classified as disaccharides (two sugar units), trisaccharides
(three sugar units), tetrasaccharides (four sugar units), etc. Amongst these, disaccharides
are the most important class because of their biological role and relative abundance in
natural products.
Disaccharides (C12H22O11)
These are a group of compound sugars composed of two monosaccharides linked by the
glycosidic bond with the elimination of one molecule of water.
1. Those with potentially a free aldehyde or a ketone group can reduce Fehling's
solution, hence are called reducing disaccharides.
The most abundant disaccharides in nature are maltose, sucrose and lactose.
Assignment:
Trisaccharides (C18H34O17):
A naturally occurring trisaccharide is raffinose [α-D-galactopyranosyl-O-( 1,6-α-D-
glucopyranosyl-O-(1,2) –β-D-fructofuranoside] found in sugar beet, coffee and other plant
materials. It is a non-reducing sugar. Melezitose [O-α-O-D-glucopyranosyl(1->3)-O-β-D-
fructofuranosyl(2,1)-α-D-glucopyranoside] is found in the sap of some coniferous trees.
POLYSACCHARIDES (C5H10O5)n
These are complex carbohydrates which are polymerized anhydrides of a large but
undetermined number of the simple sugars which are joined by glycosidic bonds. Those
found in nature contain either five or six carbon monosaccharide units. The bulk of carbon
found in nature exists in the form of polysaccharides. These are involved in the majority of
biological processes although free monosaccharides and disaccharides occur in many
biological fluids and plants.
Classification
Polysaccharides can be classified in many ways:
A. Based on function:
1. Structural polysaccharides: These polysaccharides serve as structural components of
living organisms. e.g. cellulose (plant cell wall), chitin (exoskeleton of some insects),
etc.
2. Storage/ reserve / nutrient polysaccharides: These polysaccharides function as
reserve or storage form of fuel in living organisms e.g. starch (plants), glycogen
(animal cells) etc.
B. Based on composition
1. Homopolysaccharides: These are made up of single kind of monosaccharide
residues or their derivatives. e.g. Starch, glycogen, cellulose, chitin, inulin, etc.
2. Heteropolysaccharides: These are made up of two or more different kinds of
monosaccharide units or their derivatives. e.g. Hyaluronic acid, heparin, pectins,
gums, mucilages, chondroitins, etc.
Polysaccharides are often called as glycans. Those containing glucose are called as glycans
(starch and glycogen); those containing mannose are called mannans and those containing
galactose units are called galactans.
Structural polysaccharides
Cellulose: It is the most abundant organic compound of our planet accounting for about 50
per cent of all carbon. It is the principal constituent of cell walls in higher plants forming the
main structural element. It is a linear homopolymer of glucose units linked by β-1,4
glycosidic bonds. It is insoluble in water and all organic solvents. It dissolves in conc. H 2SO4,
on diluting the solution and boiling, glucose is formed as final product. Partial hydrolysis of
cellulose yields cellobiose, a disaccharide. Cellulase, a β-glucosidase produced by many
bacteria and fungi, hydrolyzes cellulose. The large amount of glucose present in cellulose is
not available as a source of energy for humans due to the lack of enzymes capable of
Storage polysaccharides
Starch: It is a principal storage homopolysaccharide of the plant kingdom, made up of D-
glucose as repeating units. It is a mixture of two components amylose (about 20%) and
amylopectin (about 80%) Amylose consists of long unbranched chains of D-glucose units
which are linked by α-1, 4 glycosidic bonds. Its molecular weight ranges from a few
thousands of about 500,000. It gives blue colour with iodine due to the iodine- amylose
complex in which iodine molecule is occupying a position in the interior of the helical coil.
Dextrans: These are storage polysaccharides of some yeasts and bacteria. They consist of D-
glucose units joined by α-1, 6 glycosidic bonds primarily with cross linkages through α- 1,2
and and α-1, 3 linkages.
Assignment:
Lipids are a diverse group of fatty substances found in all living organisms. Lipids are any of a
diverse group of organic compounds including fats, oils, hormones, and certain components
of membranes that are grouped together because they do not interact appreciably with
water. Lipids can thus be defined fatty acids and their derivatives, and substances related
biosynthetically or functionally to these compounds.
They are the components of living systems consisting of basically carbon, hydrogen and
oxygen; in addition some have nitrogen and phosphorus. Fats and oils are widely distributed
in nature in both plant and animal tissues. They occur in relatively high concentration in
seeds of certain plants (oilseeds) where they function to supply food for use of the growing
seedlings. Animals store deposits of fats in their adipose tissues; these stored fats constitute
a reserve which can be used as the source of energy.
5. Intense biological activity – some have profound biological activity; they include
some of the vitamins and hormones
GENERAL PROPERTIES
Although the properties vary form one class to other, some of the general properties of
lipids are:
Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 31
1. Soluble in nonpolar solvents but only sparingly soluble in water
2. Greasy or fat-like in nature and show translucent properties
3. Polar lipids are amphipathic i.e., one end of a lipid molecule, the head, is polar or
ionic and therefore, hydrophilic the other end, the tail (hydrocarbon) is nonpolar
and therefore hydrophobic.
4. Most lipids contain fatty acids. The glyceride esters of saturated fatty acids are
usually liquids at room temperature and
5. Fats and oils containing unsaturated fatty acids slowly become rancid when
exposed to light, heat, moisture and air.
CLASSIFICATION
Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of
lipids called triglycerides. Biological lipids originate entirely or in part from two distinct
types of biochemical subunits or "building-blocks": ketoacyl and isoprene groups.
There are eight categories of lipids defined by the LIPID MAPS Consortium, which classifies
them by their chemically functional backbones. The eight categories - fatty acyls,
glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids,
saccharolipids, and polyketides - are then further divided into classes and subclasses. Based
on their reactivity with strong bases, lipids are classified into two major classes; saponifiable
and non-saponifiable lipids. The nonsaponifiable classes include the "fat-soluble" vitamins
(A, E) and cholesterol. The major saponifiable lipids are triacylglycerides,
glycerophospholipids, and the sphingolipids. The saponifiable lipids contain long chain
carboxylic acids, or fatty acids, esterified to a “backbone” molecule, which is either glycerol
or sphingosine. Saponification is the process that produces soaps from the reaction of lipids
and a strong base.
Lipids can also be broadly classified into simple lipids, complex lipids, derived lipids and
miscellaneous lipids based on their chemical composition
A. Simple Lipids
These lipids are the esters of fatty acids with alcohols. They are of two types.
1. Triglycerides (fats and oil): Found in adipose tissue, butterfat, lard, suet, fish oils,
olive oil, corn oil, etc. Esters of three molecules of fatty acids plus one molecule of
2. Waxes: beeswax, head oil of sperm whale, cerumen, carnauba oil, and lanolin.
Composed of esters of fatty acids with alcohol other than glycerol; of industrial and
medicinal importance.
Saturated Unsaturated
Common Melting Melting
Formula Formula Common Name
Name Point Point
CH3(CH2)10CO2H lauric acid 45 ºC CH3(CH2)5CH=CH(CH2)7CO2H palmitoleic acid 0 ºC
Assignment:
Proteins are complex organic nitrogenous substances found in the cells of the living beings.
Proteins are the most functionally diverse class of biomolecules. Protein diversity is the
basis of the diversity of life. Everything that organisms are composed of - all parts - are
made of, or by proteins. They are most abundant intracellular macro-molecules and
constitute over half the dry weight of most organisms. “Proteins occupy a central position in
the architecture and functioning of living matter.
Proteins serve for enzyme catalysis, defense, transport, support, motion, regulation and
storage.
Some proteins serve as important structural elements of the body, for example, as hair,
wool, fibrin which forms blood clots and collagen, an important constituent of connective
tissue. Proteins also serve as circulatory transporters such as haemoglobin and myoglobins,
and membrane transporters such as glucose transporters. Proteins such as immunoglobulins
and surface antigens serve as defence systems. Actin and mysosin which are protein
muscles participate in muscular contraction. other proteins may be enzymes, or regulators
such as osmotic proteins, gene regulators and hormones. Still other proteins, such as
camoldulin, ferritin and casein are storage proteins.
The constituent elements of proteins are carbon, hydrogen, oxygen, nitrogen and very
rarely sulphur also. In certain complex proteins, phosphorus occurs as well. All proteins are
macromolecules because of their very high molecular weights. They are polymers i.e., chain-
like molecules produced by joining a number of small units called monomers. The units
(monomers) that make up protein polymers are called amino acids.
AMINO ACIDS
Amino acids are the building blocks of proteins. The general formula of an amino acid is:
Only L-amino acids are constituents of proteins. Amino acids in solution at neutral pH exist
predominantly as dipolar ions (also called zwitterions). In the dipolar form, the amino group
is protonated (–NH3+) and the carboxyl group is deprotonated (–COO--). The ionization state
of an amino acid varies with pH. In acid solution (e.g., pH 1), the amino group is protonated
(–NH3+) and the carboxyl group is not dissociated (–COOH). As the pH is raised, the
carboxylic acid is the first group to give up a proton. The dipolar form persists until the pH
approaches 9, when the protonated amino group loses a proton. Thus, the zwitterionic form
predominates near physiological pH.
Although over 100 amino acids have been shown to be present in various plants and
animals, only 20 of them (L-isomers) are found as constituent of most proteins. These 20
amino acids of proteins are often referred to as proteigenic, standard, primary or normal
amino acids, to distinguish them from others. Their side chains vary in size, shape, charge,
hydrogen- bonding capacity, hydrophobic character, and chemical reactivity. Indeed, all
proteins in all species—bacterial, archaeal, and eukaryotic—are constructed from the same
set of 20 amino acids.
Assignment:
Draw the structures of all the 20 amino acids listed above
List 10 non-standard and non-protein amino acids each
Acid-Base Properties
1. Amino acids form zwitterions (dipolar ions) at neutral pH.
2. Amino acids are all weak polyprotic acids.
3. Amino acids react with both acids and bases. Hence, they are amphoteric in nature.
Substances having this dual nature are often called ampholytes (from “amphoteric
electrolytes”).
Chemically, proteins are unbranched polymers of amino acids linked head to tail, from
carboxyl group to amino group, through formation of covalent peptide bonds. Peptide bond
formation results in the release of H2O.
Function of Proteins
1. Establishment and maintenance of structure:- Structural proteins are responsible for
the shape and stability of cells and tissues. Histones are examples of structural
proteins. They organize the arrangement of DNA in chromatin.
2. Transport:- A well-known transport protein is hemoglobin in the erythrocytes. It is
responsible for the transport of oxygen and carbon dioxide between the lungs and
tissues.
3. Protection and defence:- The immune system protects the body from pathogens and
foreign substances. An important component of this system is immunoglobulin G.
4. Control and regulation:- In biochemical signal chains, proteins function as signalling
substances (hormones) and as hormone receptors.
5. Catalysis:- Enzymes, with more than 2000 known representatives, are the largest
group of proteins in terms of numbers
6. Movement:- The interaction between actin and myosin is responsible for muscle
contraction and cell movement.
7. Storage:- Plants contain special storage proteins, which are also important for
human nutrition. In animals, muscle proteins constitute a nutrient reserve that can
be mobilized in emergencies.
Protein Structure
Four basic structural levels of organization of proteins based on the degree of complexity of
their molecule have been recognized. The basic primary structure of a protein is relatively
simple and consists of one or more linear chains of a number of amino acid units. This linear,
unfolded structure or the polypeptide chain often assumes a helical shape to produce the
secondary structure. Secondary structure in a protein refers to the regular folding of regions
of the polypeptide chain. The two most common types of secondary structure are the α-
helix and the β-pleated sheet. The α-helix is a cylindrical, rod-like helical arrangement of the
amino acids in the polypeptide chain which is maintained by hydrogen bonds parallel to the
helix axis. In a β-pleated sheet, hydrogen bonds form between adjacent sections of
polypeptides that are either running in the same direction (parallel β-pleated sheet) or in
the opposite direction (antiparallel β-pleated sheet). The secondary structure, in turn, may
fold in certain specific patterns to produce the twisted three-dimensional or the tertiary
structure of the protein molecule. Finally, certain other proteins are made up of subunits of
similar or dissimilar types of the polypeptide chains. These subunits interact with each other
in a specific manner to give rise to the so-called quaternary structure of the protein.
Whereas the primary structure of a protein is determined by the covalently linked amino
acid residues in the polypeptide backbone, secondary and higher orders of structure are
Assignment:
How do the chemical bonds discussed above help to stabilise the various levels of
protein structures?
PROTEINS CLASSIFICATION
Proteins are classified based on the following criteria:
Chemical Properties
1. Hydrolysis: Proteins are hydrolysed by a variety of hydrolytic agents:
a. By acidic agents. Proteins, upon hydrolysis with conc. HCl (6–12N) at 100–
110°C for 6 to 20 hrs, yield amino acids in the form of their hydrochlorides.
Undesirable side-effects of acid hydrolysis includes Asparagine and glutamine
are deamidated to aspartate and glutamate respectively; Tryptophan, serine
and threonine are destroyed.
b. By alkaline agents. Proteins may also be hydrolyzed with 2N NaOH. Alkaline
hydrolysis is, however, less used as it is highly disadvantageous because it
leads to the destruction of certain amino acids like arginine, cysteine, cystine,
serine, threonine etc. and It also causes loss of optical activity (or
racemization) of the amino acids.
c. By proteolytic enzymes. Under relatively mild conditions of temperature and
acidity, certain proteolytic enzymes like pepsin and trypsin hydrolyze the
proteins. Enzyme hydrolysis is used for the isolation of certain amino acids
like tryptophan, but it requires prolonged incubation and hydrolysis is
incomplete.
2. Reactions Involving COOH Group
a. Salt formation. The carboxylic group of amino acids can release a H+ ion with
the formation of carboxylate (COO—) ions. These may be neutralised by
cations like Na+ and Ca2+ to form salts. Thus, amino acids react with alkalies
to form salts.
b. Esterification. Carboxylic acids reacts with alcohols and corresponding esters
are produced. The esters, so obtained, are volatile in contrast to the free
amino acids.
c. Amino acids react with amines to form amides
3. Reactions Involving NH2 Group
a. Salt formation. When either free amino acids or proteins are treated with
acids like HCl, the acid salts are formed. The basic amino acids, arginine and
lysine react with CO2 in the presence of air to form carbonate salts.
INTRODUCTION
Serving an even more central biological purpose are the nucleic acids, the elements of
heredity and the agents of genetic information transfer. Nucleic acids are high molecular
weight biopolymers of nucleotides as repeating units which are linked by characteristic 3’-5’
phosphodiester bonds. Nucleic acids are one of the major components of all cells, making
up from 5 to 15 per cent of their dry weight. They are also present in viruses. They are
responsible for the storage and transmission of genetic information and translation of this
information for a precise synthesis of proteins characteristics of the individual cell. Like the
letters in this sentence, the orderly sequence of nucleotide residues in a nucleic acid can
encode information. The two basic kinds of nucleic acids are deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA).
Based on the nature of sugar moiety and the nitrogenous bases present, two types of
nucleic acids are recognized: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Although the name nucleic acid suggests their location in the nuclei of cells, certain of them
are, however, also present in the cytoplasm. Complete hydrolysis of nucleic acids by acids,
bases or specific enzymes yields three characteristics components: (a) heterocyclic bases (b)
sugar and (c) phosphoric acid.
Pentose Sugar
The two types of nucleic acids are distinguished primarily on the basis of the 5-carbon keto
sugar or pentose which they possess. One possesses D-2-deoxyribose, hence the name
deoxyribose nucleic acid or deoxyribonucleic acid, while the other contains D-ribose, hence
the name ribouncleic acid. Both these sugars in nucleic acids are present in the furanose
form and are of β configuration.
NUCLEOSIDES
The nucleosides are compounds formed by linking purine and pyrimidine bases to either D-
ribose or 2'-deoxy-D-ribiose in a N--glycosidic bound. The point of attachment of the bases
to the sugar is N-9 of the purines or N- 1-of the pyrimidines to C-1 or D-ribose or 2'-deoxy-D-
ribose. The carbon atoms of the sugar are designated by prime numbers (i.e., C-1’, C-5’),
while the atoms in the bases lack the prime sign. Nucleosides are named by adding the
ending –idine to the root name of a pyrimidine or –osine to the root name of a purine. The
common nucleosides are thus cytidine, uridine, thymidine, adenosine, and guanosine.
Nucleosides are more water soluble than the free bases, because of the hydrophilicity of the
pentose.
NUCLEOTIDES
A nucleotide results when phosphoric acid is esterified to a sugar -OH group of a nucleoside.
The nucleoside ribose ring has three -OH groups available for esterification, at C-2’, C-3’, and
C-5’ (although 2’-deoxyribose has only two). The vast majority of monomeric nucleotides in
the cell are ribonucleotides having 5’-phosphate groups. Therefore, 2’, 3’ or 5’
ribonucleoside monophosphate and 3’ or 5’ deoxyribonucleoside monophosphtes can be
formed. However, the 5’ position is most commonly phosphorylated.
METABOLIC FUNCTIONS
1. Role in energy metabolism: ATP is the main form of chemical energy available to the
cells. It is generated in cells by oxidative phosphorylation and substrate level
phosphorylation .
2. Monomeric units of nucleic acids: The nucleic acids, DNA and RNA are composed of
monomeric units of the nucleotides as building-blocks.
6. Allosteric effectors: Many of the regulated steps of the metabolic pathways are
controlled by the intracellular concentrations of nucleotides.
DNA
The DNA isolated from different cells and viruses characteristically consists of two
polynucleotide strands wound together to form a long, slender, helical molecule, the DNA
double helix (exceeding 2 x 109 in molecular weight). The strands run in opposite directions;
that is, they are antiparallel. The two strands are held together in the double helical
structure through inter-chain hydrogen bonds. An important feature of the double helix is
the specificity of the pairing of bases. Pairing always occurs between adenine and thymine
and between guanine and cytosine
DNA occurs in various forms in different cells. The single chromosome of prokaryotic cells is
typically a circular DNA molecule. In diploid eukaryotic cells nearly all the DNA molecules
are present in the cell nucleus, where they are combined with s class of arginine- and lysine-
rich basic proteins called histones.
2. DNA content: The DNA content of a cell is remarkably constant for each species
3. Base composition: DNA isolated from different tissues of the same organism has the
same base composition
4. Effect of pH: DNA is a polybasic acid due to the presence of phosphate groups which
are fully ionized at physiological pH.
6. Absorbance: The purine and pyrimidine bases found in the DNA and also RNA
strongly absorb ultraviolet radiation of wave-length at 260 nm. This property is used
to identify and estimate nucleic acids.
Biological role
1. It contains the genetic information that is transmitted from generation to
generation, which is achieved by self-replication of DNA during cell growth and
division so that two daughter double helical molecules of DNA are obtained, each
identical to parent DNA.
2. It expresses it encoded genetic information for the synthesis of RNA and proteins for
metabolic function and control of all cellular activities.
The genetic information is carried in the form of genes and expressed at appropriate
times. A gene is defined as a sequence of bases in DNA which specifies the complete
amino acid sequence of polypeptide chain or the base sequence of an RNA molecule
(rRNA, tRNA).
RNA
RNA occurs in all prokaryotic and eukaryotic cells and in some viruses. RNA is present mainly
in the cytosol. Unlike DNA, RNA is essentially a single stranded molecule. Although DNA is
the primary genetic material within the cells, many RNA molecules participate in the
processes by which this genetic information is expressed.
Types of RNA
Based on cellular location and function, three major types of RNA have been identified in all
cells:
mRNA: This is also known as a template RNA. Messenger RNA (mRNA) serves to carry the
information or “message” that is encoded in genes to the sites of protein synthesis in the
cell, where this information is translated into a polypeptide sequence. That is mRNA
molecules are transcribed copies of the protein-coding genetic units of DNA. It has a primary
structure complementary to a portion of one of the stands of DNA; In bacterial cells, mRNA
is highly unstable i.e., it is constantly being degraded and re-synthesized. In eukaryotic cells,
the turnover rate of mRNA is much lower.
rRNA: This is also known as a high- molecular RNA and constitutes up to 65 per cent of the
mass of ribiosomes. The major portion of the total RNA of a cell is ribiosomal RNA. The
different species of rRNA are generally referred to according to their sedimentation
coefficients. There are three types of rRNA; 5S, 15S and 23S in prokaryotic cells and four
types – 5S, 5.8S, 18S and 28S in eukaryotic cells. The rRNA is presumed to play a role in
maintenance of structure of ribosomes.
The orderly course of metabolic processes is only possible because each cell is equipped
with its own genetically determined set of enzymes. It is only this that allows coordinated
sequences of reactions. An important point about enzymes is that they are very specific
about what they can catalyse. Even small changes in the reactant molecule can stop the
enzyme from catalysing its reaction. The reason for this lies in the active site present in the
enzyme
Almost all enzymes are proteins, with the exception of a few catalytically active ribonucleic
acids (catalytic RNA molecules), or ribozymes. Their catalytic activity depends on the
integrity of their native protein conformation. If an enzyme is broken down into its
component amino acids, its catalytic activity is always destroyed. Thus the primary,
secondary, tertiary, and quaternary structures of protein enzymes are essential to their
catalytic activity.
Some enzymes require no chemical groups for activity other than their amino acid residues.
Others require an additional chemical component called a cofactor - either one or more
inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+, or a complex organic or metalloorganic
molecule called a coenzyme. Cofactors are generally stable to heat while the enzyme
protein loses its activity on heating.
Coenzymes are non-protein, organic molecules that facilitate the catalysis, or reaction, of its
enzyme. Coenzymes are one of two types of cofactors used by enzymes in these enzymatic
reactions. The other types of cofactors are inorganic ions.
Coenzymes work by binding to the active side of the enzymes, the side that works in the
reaction. Since enzymes and coenzymes are non-metal organic molecules, they bind
together by forming covalent bonds. The coenzymes share electrons with the enzymes,
rather than lose or gain electrons. When they form this bond, they only help the reaction to
occur by carrying and transferring electrons through the reaction. Coenzymes do not
become integral parts of the enzymatic reaction. Instead, the covalent bonds are broken at
the end of the reaction, and the coenzyme returns back to free circulation within the cell
until it is used again.
Taking vitamins, whether from eating foods or in supplement form, increases the amount of
coenzymes in the body. Some vitamins help the body produce coenzymes, such as folic acid
and some of the B vitamins, while other vitamins directly act as coenzymes, such as vitamin
C. Without vitamins, the body would be unable to produce coenzymes. A vitamin is defined
as an organic compound that is required in the diet in small amounts for the maintenance of
normal metabolic integrity. There are two types of vitamins; fat-soluble and water-soluble,
Riboflavin (B2)
Thiamine (B1)
Vitamin A (retinol) is the precursor of retinal, the light-sensitive group in rhodopsin and
other visual pigments. Retinoic acid, which contains a terminal carboxylate in place of the
alcohol terminus of retinol, serves as a signal molecule and activates the transcription of
specific genes that mediate growth and development.
Important Coenzymes
Coenzymes fall into two groups: