Bch 201/Bch 211 (General biochemistry) Chemistry of biomolecules

Table of Content

Topics. Page number

1. Carbohydrates. 2
• Functions of carbohydrates
• Classification of carbohydrates
• Properties of monosaccharides

2. Protein and amino acids. 11

• Basic parts of amino acids
• Three and one -letter abbreviation’s of amino acids
• Classification of amino acids
• Peptides and Protein
• Structure of proteins(organization of protein)
3. The Nucleic acids. 18
• Composition of nucleotides
• Nucleosides and Nucleotides
• Structure of DNA(Watson-Crick)
• Various types of DNA conformation

4. Lipids and Fatty acids. 24

• Functions of lipids
• Classification of lipids
• Fatty acids
• Cholesterol
• Prostaglandins
5. Past Questions on each topics 31

Latest edition

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Mighty T

CARBOHYDRATES
Carbohydrates are aldehyde and ketone derivatives of polyhydroxy alcohols containing at least 3 carbon
atoms.
They can be regarded as compound that are composed of carbon, hydrogen and oxygen. In some cases, Sulphur
and Nitrogen compound are attached. They are the most abundant biomolecules on earth. Carbohydrates polymers
are called glycans.
The oxidation of a molecule of sugar provides about 4kcal of energy. The
general molecular formula of Carbohydrates is Cn(H 20)n.

Aldehyde group Ketone group

These are functional group of carbohydrates that Ketone groups have their carbonyl group at any
contain a carbonyl group at the end of the carbon chain. position within the carbon chain

The major difference between this two compounds is the attachment of a Hydrogen atoms to the carbonyl group
of an aldehyde group, which does not exist in the ketone group.

Functions of Carbohydrates
i. Carbohydrates are the main sources of energy in the body. Brain cells and Red blood cells are almost
wholly dependent on carbohydrates as the energy source.
ii. The oxidation of Carbohydrates is the central energy-yielding pathway in most non-photosynthetic cells.
iii. Glycans serve as structural and protective elements in the cell walls of bacteria and plants and in the
connective tissue of animals.
iv. Glycolipids and glycoproteins are components of cell membranes and receptors
v. Other carbohydrates polymers lubricate skeletal joints and participate in recognition and adhesion between
cells.
vi. The aldopentoses (D-ribose and 2 deoxy-D-ribose) are components of nucleotides and nucleic acids

Classification of Carbohydrates
Based on the number of sugar moeity, carbohydrates can be categorize as;
Monosaccharides
Disaccharides
Oligosaccharides
Polysaccharides

1. Monosaccharides(Simple sugar)
These are compounds that possess only one actual or potential sugar group.
They consist of a single polyhydroxy aldehyde or ketone unit. (Greek, Mono=one ; saccharide=sugar). They
cannot be further hydrolysed into smaller units. The most abundant monosaccharides in nature is the six
carbon sugar(Glucose).

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 Based on their functional group; monosaccharides that contain an aldehyde group is referred to as Aldose;
and those that contain a ketone group, a Ketose sugar.

• Depending on the number of carbon atoms, the monosaccharides are grouped as; Triose(C3),
Tetrose(C4), Pentose(C5), Hexose(C6), Heptose(C7) and so om

Common Monosaccharides
No. of carbon Generic name Aldoses(aldehyde group) Ketoses(Ketone group)
atoms
3 Triose Glyceraldehyde(aldotriose) Dihydroxyacetone(ketotriose)

4 Tetrose Erythrose (aldotetrose) Erythrulose(ketotetrose)

Xylose(aldopentose) ∆C3 Xylulose(ketopentose)
5 Pentose Ribose. . (aldopentose) Ribulose(ketopentose)
Arabinose (aldopentose)∆c2

6 Hexose Glucose.∆c3 (aldohexose) Fructose(ketohexose) ∆c3

Galactose(aldohexose) ∆C3,4
Mannose.(aldohexose) ∆C2,3
7 Heptose Glucoheptose(aldoheptose)∆c4 Sedoheptulose(ketoheptose)
Mannoheptulose(ketoheptose)

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Note:
Structure of triose and Tetrose exist in a straight chain, this is because of the presence of asymmetric
Centre. In nature, monosaccharides with more than 2 asymmetry center hardly exist in straight form. They rather
exist in cyclic form.
Asymmetric Centre(chiral Centre):can be defined as an atom that has 4-different groups attached to it. That is,
a carbon that has tetrahedral groups

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The configuration of Carbohydrates is based on two projection
• Emil Fischers(Straight form/linear structure)
• Walter Haworth (Ring form)

Configuration of Carbohydrates(Ring form)

The ring form of Carbohydrates structure are based on Walter Haworth projection
NB: Monosaccharides(aldoses or ketoses) with 5 or more carbons are most stable in their ring form.
I.e Monosaccharides with more than 2 asymmetry centers hardly exist in straight form; rather in their
cyclic form.
• Asymmetric Centre(Chiral Centre) is defined as an atom that has four different groups
attached to it. (a tetrahedral group).
In the ring form of Monosaccharides, the carbonyl carbon becomes covalently bound to another
OHgroup (majorly on the penultimate carbon) within the carbon chain. After cyclization, the carbonyl
carbon becomes the anomeric carbon.
• Anomeric carbon is the new asymmetric carbon formed when the carbonyl group(aldehyde or
ketone) in a Monosaccharide react with an alcohol group(usually OH group of penultimate
carbon) to form a cyclic compound. They contain free hemiacetal or hemiketal based on
aldehyde and ketone group respectively
• Penultimate carbon is the asymmetric carbon furthest away from the carbonyl group. I.e the
second to the last carbon

• Aldehyde reacts with alcohol group to form Hemiacetal

• Ketone reacts with alcohol group to form Hemiketal
Based on Haworth projection, there are two major forms of Carbohydrates ring configuration:
1. Pyranoses(6-membered ring)
A common example is glucose(a six-carbon atoms)
The ring structure of glucose is formed by a reaction between the carbonyl carbon(C-1) and the

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 OH group of the penultimate carbon (C-5 OH) to form a pyranose ring.

2. Furanoses(5-membered ring)
A common example is Ribose(a 5-carbon atoms. The ring structure is also formed by a reaction

between the C-1 and the penultimate carbon(C-4)

Now regarding the confusion on whether fructose is pyranose or Furanose;
Note: Although Fructose has 6-carbon atoms, yet it has a furan ring because it carbonyl group
group is at C-2. Therefore the reaction for cyclization takes places between C-2 and C-5(
instead of C-1 and C-5 like that of glucose).
Finally after cyclization, the anomeric OH-group can either be above or below the plane of
the ring
• alpha-D-Sugars have the OH group on the anomeric carbon below the plane of the ring
while the Beta-D-glucose have theirs above the plane of the ring

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Optical activity of monosaccharides

This is the ability of a sugar solution to rotate a beam of plane polarized light either to the left or right. .
When the beam of plane-polarized light is rotated to the right, it is called dextrorotatory(d) or (+) and to the left
is Levorotatory(l) or (-) . For instance, D-glucose is dextrorotatory but D-fructose is levorotatory.
Note: The D- and L-notation has no bearing with the optical activity
A racemic mixture is an equimolecular mixture of two optical isomers with no net rotation.

Stereoisomers
Compounds having the same structural formula, but differing in spatial configuration are known as stereoisomers.
While writing the molecular formula of monosaccharides, the spatial arrangements of H and OH groups are
important, since they contain asymmetric carbon atoms.The reference molecule is Glyceraldehyde which has a
single asymmetric carbon atom.

The configuration of H and OH groups at the second carbon atom of Glyceraldehyde may be noticed. The two
mirror forms are denoted as D- and L- varieties l. All monosaccharides can be considered as molecules derived
from Glyceraldehyde by the addition of carbon atoms.
The number of possible stereoisomers depends on the number of asymmetric carbon atoms by the
formula 2n where n is the number of asymmetric carbon atoms.
During stereoisomerism, one of a pair of stereoisomers produced that is the mirror image of the other are called
enantiomers, stereoisomers that are not mirror images are also Diastereoisomers.
• Enantiomers
Enantiomers are chiral molecules that are mirror images of one another. Furthermore, the molecules
are non-superimposable on one another. This means that the molecules cannot be placed on top of one
another and give the same molecule. With reference to the penultimate carbon, the configuration of
H and OH groups is changed and two mirror images are produced.

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 They are of D and L varieties. L isomers have the OH group attached to the left side of the asymmetric
carbon furthest from the carbonyl while D isomers have the OH group on the right side.
.

Epimerism
Two sugars that have different configuration with regard to a single carbon atom are called epimers. For
example,

glucose and mannose are an epimeric pair which differ only with respect to C-2. Similarly, galactose is the 4th
epimer of glucose.

Anomerism

This is a phenomenon exhibited by the sugars having the same molecular formula but differ in the arrangement
of H and OH around anomeric carbon atom.
This occurs when sugar solution shows a specific rotation of plane polarized light. This occurs as a result of spatial
configuration on the anomeric carbon.
During mutarotation, there is change in the specific rotation of a sugar solution that contains ketone or aldehyde
group. These anomers are produced by a change in configuration at C-1 of aldoses and C-2 of ketoses.
A phenomenon in which carbohydrates can change spontaneously between the alpha and beta configurations is
termed Mutarotation.

Anomerism is explained by the fact that D-glucose has two anomers, alpha and beta varieties.
• Alpha varieties have their OH group at the right hand side of the carbonyl group(anomeric carbon)

• Beta varieties posses an hydroxyl(OH) group at the left hand side.

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Note: Anomers unlike epimers deals with spatial configuration of H and OH around the carbonyl group(anomeric
carbon) that is, C-1 of aldoses and C-2 of ketoses.

Disaccharides
They consist of two monosaccharides joined covalently by a glycosidic bond(O-glycosidic bond). This
linkage exist between the hydroxyl(-OH) group of one sugar, typically cyclic and the anomeric carbon
of the other. (Anomeric carbon are carbon containing a free hemiacetal group(carbon with a free
hydroxyl group)
This reaction represents the formation of an acetal from a hemiacetal(such as glucopyranose) and an
alcohol(a hydroxyl group of the second sugar molecule).
N-glycosidic bonds join the anomeric carbon of a sugar to a Nitrogen atom in Glycoproteins.
Examples of Disaccharides include Maltose, Lactose and Sucrose.
• Reducing sugars are disaccharides containing a chain with a free anomeric carbon(one not involved
in a glycosidic bond) e.g Maltose, Lactose.
• Non-reducing sugars are sugars that do not possess a free anomeric carbon. A typical example is
Sucrose.

• Maltose(Glucose+Glucose)
The disaccharide(Maltose) contains two glucose residues joined by a glycosidic linkage between C-1(the
anomeric carbon) of one glucose residue and C-4 of the other.

The type of linkage present is alpha-1,4 glycosidic linkage. Due to the presence of free anomeric carbon
in Maltose; it is therefore a reducing sugar.

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 • Lactose(galactose + glucose)
Lactose(a sugar present in milk) contains a moeity of galactose and glucose joined by Beta-1,4
glycosidic bond. This glycosidic linkage exist between the C-1 of galactose and C-4 of glucose.

The anomeric carbon of the glucose residue is available for oxidation, and thus lactose is a reducing
sugar. Lactose is the major source of energy for newborn.

• Sucrose(glucose+fructose)
Sucrose(Table sugar) is a disaccharide formed from glucose and fructose. It is the sweetening agent
known as cane sugar. It is present in sugarcane and various fruits. It is formed by plants but not by
animals. The linkage between glucose and fructose moeity is the beta-1,2 glycosidic bond.

In contrast to Maltose and Lactose, Sucrose contains no free anomeric carbon atom; the anomeric
carbons of both monosaccharides units are involved in the glycosidic bond; sucrose is therefore a
nonreducing sugar.

3. Oligosaccharides:
These are compound that contain more than 2-sugar molecules but less than 10. They do not occur
naturally in human but are found in insect. (Greek, Oligo = a few) Examples are Maltotriose, Riabinose,
Riabinose(Raffin), Stachyose.

4. Polysaccharides:
These are polymerised products of many monosaccharides units (Greek, poly = many).
They are sugar that are composed of more than 10 monosaccharide units with no maximum number. It serves
as the storage form of sugar in nature. They are also linked together by glycosidic bond. These should be of
the Alpha and Beta configuration depending on the source. They are sometimes referred to as glycans.
Examples include Starch, cellulose, glycogen, agar, mucor, Chitin etc.
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Some polysaccharides are composed of a repeating unit of a monosaccharide and unit could be in straight
chain or branched chain.

They are catorized as Homopolysaccharides and Heteropolysaccharides.

a. Homopolysaccharides
Homoglycans are composed of a single kind of monosaccharides, e. g Starch, glycogen, cellulose,
inulin, dextran, chitin.

• Starch
Structure of starch
It is the reserve carbohydrate of plant kingdom. It is a polymer of glucose molecules linked together
by glycosidic linkage.
Sources: Potatoes, tapioca, cereals(rice, wheat) and other food grains.

Starch is composed of amylose and amylopectin.

Amylose(soluble part of starch) is made up of glucose units with alpha-1,4 glycosidic linkages to
form an unbranched long chain with a molecular weight 400,000 D or more.

Amylopectin(Insoluble part) is made up of glucose units, but it is highly branched with molecular
weight more than 1 million. The branching points are made by alpha-1,6 linkage.

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 Glycogen
It is the reserve carbohydrates in animals. It is stored in liver and muscle. About 5% of weight of
liver is made up by glycogen. Excess carbohydrates are deposited as glycogen. Glycogen is composed
of glucose units joined by alpha-1,4 links in the straight chains. It also has alpha-1,6 glycosidic
linkages at the branching points.

Molecular weight of glycogen is about 5million. Innermost core of glycogen contains a primer
protein, Glycogenin. Glycogen is more branched and more compact than amylopectin.

• Cellulose
It is the supporting tissues of plants. Cellulose constitutes 99% of cotton, 50% of wood and is the most
abundant organic material in nature.
It is made up of glucose units combined with beta-1,4 linkages. It has a straight line structure, with
no branching points. Molecular weight is in the order of 2 to 5 million.
Beta-1,4 bridges are hydrolysed by the enzyme cellobiase. But this enzyme is absent in animal and
human digestive system, and hence cellulose cannot be digested.
Herbivorous animals have large caecum, which harbor bacteria. These bacteria can hydrolysed
cellulose, and the glucose produced is utilised by the animal. White ants(termites) also digest cellulose
with the help of intestinal bacteria.
Cellulose has a variety of commercial applications, as it is the starting material to produce fibres,
celluloids, nitrocellulose and plastics.
Note: Cellulose is composed of beta-glucose units, compared to starch with alpha-glucose units.
• Inulin
It is a long chain homoglycan composed of D-fructose units with repeating beta-1,2 linkages. It is
the reserve carbohydrates present in various bulbs and tubers such as onion, garlic, dandelion etc. I it
clinically used to find renal clearance value and glomerular filtration rate.
Note: Inulin and Insulin are different!
Insulin is a polypeptide(protein) hormone, with wide ranging actions on carbohydrate and
lipid metabolism.
• Chitin
It is present in exoskeletons of crustacea and insects. It is composed of units N-acetyl-glucosamine
with beta-1,4 glycosidic linkages.
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b. Heteroglycans are composed of two or more different monosaccharides. Examples are Hyaluronic acid,
heparin, chondroitin sulphate.

• Agar
It is prepared from sea weeds. It contains galactose, glucose and other sugars. Agar cannot be digested
by bacteria and hence used widely as a supporting agent to culture bacterial colonies.
Agar is used as a supporting medium for immunodiffusion and immunoelectrophoresis. Agarose is
made up of galactose combined with 3,6-anhydrogalactose;it is used as matrix for electrophoresis.
• Mucopolysaccharides
Mucopolysaccharides or glycosamino glycans(GAG) are Heteropolysaccharides containing uronic
acid and amino sugars. Acetylated amino groups, sulfate and carboxyl groups are also generally
present. Mucopolysaccharides in combination with proteins form mucoproteins. Examples are
hyaluronic acid, chondroitin sulfate, dermatan sulfate and keratin sulfate.

 Hyaluronic acid: It is present in connective tissues, tendons, synovial fluid and vitreous
humor. It serves as a lubricant in joint cavities. It is composed of repeating units of N-
acetylglucosamine—>beta-1,4-Glucuronic acid —>beta-1,3-N-Acetyl glucosamine and so
on

 Heparin: It is an anticoagulant widely used when taking blood in vitro for clinical studies.
It is also used in vivo in suspected thromboembolic conditions to prevent intravascular
coagulation. It activates antithrombin III, which in turn inactivates thrombin, factor X and
factor IX.

 Chondroitin sulphate: It is present in ground substance of connective tissues widely

distributed in cartilage, bone, tendons, cornea and skin. It is composed of repeating units of
glucuronic acid —>beta-1,3-N-acetyl galactosamine sulphate—>beta-1,4 and so on.

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Mighty T

PROTEIN AND AMINO ACIDS

The human body has thousands of different proteins, all of which are necessary for staying alive and healthy.
Protein are the polymers of amino acids, with each amino acids residue joined to its neighbor by a specific type
of covalent bond(peptide bond). In other words, Amino acids are the building block of proteins I. e The unit form
of protein is amino acids.
Although about 300amino acids occur in nature, only 20 of them are seen in human body. Most of the amino
acids(except proline) are alpha amino acids, which means that the amino group is attached to the same carbon
atom to which carboxyl group is attached.

All amino acids include five basic parts:

1. a central carbon atom
2. an hydrogen atom
3. an amino groups (NH2 or NH3+) consisting of a nitrogen atom and two hydrogen atoms
4. a carboxyl group(COOH or COO-) consisting of a carbon atom, two oxygen atoms and one
hydrogen atom
5. an R-group or side chain consisting of varying atoms

Side chains

The R-group(side chain) is what makes each amino acid unique. Each of the 20 amino acids has a different side
chain structure. Side chains contain mainly Hydrogen(H), Carbon(C), Oxygen(O) atoms. Some amino acids have
sulfur or nitrogen atoms in their R-groups.
Note: All amino acids possess a chiral carbon- a carbon to which four different components are attached (except
glycine due to the presence of H atom as the R-group of glycine)
Because of the tetrahedral arrangement of the bonding orbitals around the alpha carbon atom, the four different
groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers. Since
they are nonsuperposable mirror images of each other,

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the two forms represent a class of stereoisomers called enantiomers.

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Classification of amino acids
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Amino acids can be classified based on:
• Nutritional requirements
• R-group(side chain)

1. Based on the nutritional requirements, amino acids are classified as;

a. Essential amino acids or Indispensable
b. Non-essential amino acids or dispensable

Essential amino acids

The amino acids may further be classified according to there essentially for growth. Thus Isoleucine, Leucine,
Threonine, Lysine, Methionine, Phenylalanine, Tryptophan and Valine are essential amino acids. Their carbon
skeleton cannot be synthesized by human beings and so such amino acids are to be taken in food for normal
growth. Histidine and Arginine are semi indispensable amino acids. Growing children require them in food,
but they are not essential for the adult individual.

Non-essential amino acids

The remaining 10 amino acids are non-essential, because their carbon skeleton can be synthesized by the body.
However they are also required for normal protein synthesis. All body proteins do contain all the non-essential
amino acids.

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2. Based on their R-group(side chain), amino acids can be classified as:
a. Nonpolar, Aliphatic R groups – Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine
b. Polar, uncharged R groups – Serine, Threonine, Cysteine, Proline, Asparagine, Glutamine
c. Aromatic R groups- Phenylalanine, Tyrosine, Tryptophan
d. Positively charged R groups – Lysine, Arginine, Histidine
e. Negatively charged R groups- Aspartate, Glutamate

Peptides and Proteins

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Peptides are chains of Amino acids
Two amino acids molecules can be covalently joined through a substituted amide linkage, termed a peptide bond,
to yield a dipeptide. Such a linkage is formed by the removal of the elements of water(dehydration) from the
alpha carboxyl group of one amino acid and the alpha amino group of another.

Peptide bond formation is an example of a condensation reaction, a common class of reactions in living cells.
Three amino acids can be joined by two peptide bond to form a tripeptide; Similarly, four amino acids can be
linked to form a tetrapeptide, five to form pentapeptide, and so forth. W a few amino acids are joined in this
fashion, the structure is called an oligopeptide. When many amino acids are joined, the product is called a
Polypeptide. Although the terms “proteins” and “polypeptide” are sometimes used interchangeably, molecules
referred to as polypeptides generally have molecular weights below 10,000 and those called proteins have higher
molecular weights.

Structure of Proteins(Organization of proteins)

Proteins have different levels of structural organisation;Primary, secondary, tertiary and quaternary.

• Primary Structure
Primary structure denotes the number and sequence of amino acids in the protein. The higher levels of
organisation are decided by the primary structure. Each polypeptide chain has a unique amino acid sequence
decided by the genes.

In a peptide, the amino acid residue at the end with a free alpha amino group is thee amino-
terminal(Nterminal) residue; the residue at the other end, which has a free carboxyl group, is the Carboxyl
Nterminal(N-terminal) residue.

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The primary structure is maintained by the covalent bonds of the peptide linkages . For
instance:
Gly-Ala-Val(1)
Gly-Val-Ala(2)
Both the tripeptides shown above contain the same amino acids; but their sequence is altered. When the
sequence is changed, the polypeptide is also different.
An example of the primary structure of a protein is that of insulin.

• Secondary structure
The term “secondary structure” denotes the configurational relationship between residues which are 3-4 amino
acids apart in the linear sequence. It refers to the regular, local structure of the protein backbone, stabilized
or preserved by noncovalent forces or bonds like hydrogen bonds, electrostatic bonds, hydrophobic
interactions and Van der Waals forces.
There are two common types of secondary structure of polypeptide chains described by Pauling and Corey.
a. Alpha helix
b. Beta-pleated sheet

a. The alpha-helix is the most common and stable conformation for a polypeptide chain. It is abundant
in proteins like hemoglobin and myoglobin.
The alpha-helix is a Spiral structure and its generally right handed. The polypeptide bonds form the
backbone and the side chains of amino acids extend outwards. The structure is stabilized by hydrogen
bonds between NH and C=O groups of the main chain.
Each turn is formed by 3.6 residues. The distance between each amino acid residue(translation) is
1.5armstrong.(A).

b. Beta-pleated sheet
A beta strand is a stretch of polypeptide chain, typically 3-10amino acids long with its backbone in an
almost fully extended conformation. The distance between the adjacent amino acids is 3.5armstrong(A).
It is stabilized by hydrogen bonds between NH and C=O groups of neighbouring polypeptide segments.
Two or more parallel or antiparallel adjacent polypeptide chains of beta strand stabilized by Hydrogen
bonds form a beta sheet.

Note: R-group does not contribute to the secondary structure of proteins

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• Tertiary structure

The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary
structure is primarily due to interactions between the R groups of the amino acids that make up the protein..

R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding,
dipoledipole interactions and London dispersion forces -basically the non-covalent bonds. For example,
R groups with like charges repel one another, while those with opposite charges can form an ionic bond.
Similarly, polar R groups can form hydrogen bond and other dipole-dipole interactions. Also important
to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R
groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outsiders

interact with surrounding water molecules.

Finally, there's one special type of covalent bond that can contribute to tertiary structure: the disulfide
bond. Disulfide bonds, covalent linkages between the sulfur-containing side chains of Cysteine are much
stronger than the other types of bonds that contribute to tertiary structure.

• Quaternary Structure

Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits. These
subunits may be the same (as in a homodimer) or different (as in a heterodimer). The quaternary structure
refers to how these protein subunits interact with each other and arrange themselves to form a larger
aggregate protein complex.
Depending on the number of monomers, the protein may be termed as dimer(2), tetramer(4), etc. Each
polypeptide chain is termed as subunits or monomer. For example, 2alpha chains and 2beta chains form
the Hemoglobin molecules. Similarly, 2 heavy chains and 2 light chains form one molecule of
immunoglobulins G. Creatinine kinase(CK) is a dimer. Lactate dehydrogenase(LDH) is a tetramer. The
final shape of the protein complex is once again stabilized by various interactions, including hydrogen-
bonding, disulfide-bridges and salt bridges.

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 Mighty T
The Nucleic acids

In 1868, Frederich Miescher isolated nucleic acid(then called nuclein) from pus cells.
Nucleotides are the precursors of nucleic acids(DNA(deoxy-ribonucleic acid) and
RNA(ribonucleic acid). In other words, Nucleic acids are the polymerised product(polymer) of
nucleotides. They contain monomers of nucleotides joined together by a phosphodiester bond.
The nucleic acids are concerned with storage and transfer of genetic information. The universal
currency of energy, namely ATP, is nucleotide derivative. Nucleotide are also component of
important coenzymes such as NAD+ and FAD, a metabolic regulators such as cAMP and cGMP.

Albrecht Kossel classified Nucleic acids into two major parts:

• Deoxy-ribonucleic acid(DNA) ;they are double stranded and contain a 2-deoxyribose
sugar. The nitrogenous base present in DNA includes adenine, guanine, cytosine, thymine.
• Ribonucleic acid(RNA) ; single stranded and contain ribose sugar. The nitrogenous bases
present includes adenine, guanine, cytosine, and uracil.
Note : In terms of nitrogenous bases, uracil is present in RNA but absent in DNA, also
thymine is present in DNA but absent in RNA.

COMPOSITION OF NUCLEOTIDES
A nucleotide is made up of 3 components:
a. Nitrogenous base, (a purine or a pyrimidine)
b. Pentose sugar, either ribose or deoxyribose;
c. Phosphate groups esterified to the sugar.

a. Nitrogenous base
Two types of nitrogenous bases; the purines and Pyrimidines are present in nucleotides.
• The Purine bases present in nucleotides(nucleic acids) includes Adenine and
guanine. Adenine is 6-amino purine and guanine is 2-amino, 6-oxypurine.

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 These purine bases are present both in RNA and DNA.
• The pyrimidine bases includes Cytosine, Thymine and Uracil. Cytosine is present
in both RNA and DNA. Thymine is present in DNA and Uracil is present in RNA.

Note: The structural difference between thymine and uracil is the presence of a methyl
group(CH3) at C-5 of thymine.

b. Pentose Sugar.
The aldopentoses(Ribose and 2-deoxyribose) are also one of the three major components
of nucleotides. The 5-carbon sugars; Ribose and 2-deoxyribose are present in nucleic acids.

Apart from the difference in their nitrogenous bases, the Pentose sugar present in RNA and
DNA also vary. The Pentose sugar- Ribose is present in RNA(Ribonucleic acid), while
DNA contains 2-deoxyribose and thus the name Deoxyribonucleic acid.

c. Phosphate group: This is the last component present in nucleic acids. The phosphate group
is the major difference between Nucleotide and Nucleoside.
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 That is, Nucleoside= Nucleotide – Phosphate group.

Corresponding Nucleoside mono, di, and tri- phosphates are formed by esterification of
further phosphate groups to the existing ones.

Nucleosides and Nucleotides

Nucleosides are formed when bases are attached to the Pentose sugar(D-ribose or 2-deoxyribose).
All the bases are attached to the corresponding Pentose sugar by a beta-1 – glycosidic bond
between the 1st carbon of the Pentose sugar and N9 of a purine or N1 of a pyrimidine. The
deoxy nucleosides are denoted by adding the prefix d- before the Nucleoside. The carbon atoms
of the Pentose sugar are denoted by using a prime number(e. g 3') to avoid confusion with the
carbon atoms of the purine or ring.

• Note: Nucleosides with purine bases have the suffix -sine, while pyrimidine
nucleotides end with -dine.
Uracil combines with ribose only; thymine with deoxy ribose only.

The addition of phosphate group to a nucleotide gives Nucleotide.

That is, Nucleotide=Nucleosides + Phosphate group. Note:
The phosphate groups can be mono-, di-, or tri-.
For example: Adenosine + monophosphate = adenosine monophospate

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 Tables showing possible nucleosides and nucleotides

Base Nucleoside (Base+sugar) Ribonucleosides Deoxyribonucleosides

Adenine Adenine + Adenosine d-adenosine

Ribose/deoxyribose
Guanine Guanine + Guanosine d-guanosine
Ribose/deoxyribose
Cytosine Cytosine + Cytidine d-cytidine
Ribose/deoxyribose
Thymine Thymine+deoxyribose Thymine does not d-thymidine
associate with ribose
Uracil Uracil + ribose Uridine Uracil does not associate
with 2-deoxyribose

Nucleotides Ribonucleotides Deoxyribonucleotides

(Nucleosides + (Ribonucleosides+phosphate) (Deoxyribonucleosides+phosphate)
phosphate)
Adenosine+ Phosphate Adenosine d-adenosine monophosphate (d-
monophosphate(AMP) AMP)
Guanosine+ Phosphate Guanosine d-guanosine monophosphate (d-
monophosphate(GMP) GMP)
Cytidine + Phosphate Cytidine d-Cytidine monophosphate (d-
monophosphate(CMP) CMP)
Thymidine+ Phosphate Thymine does not associate d-thymidine monophosphate (d-
with ribose sugar TTP)
Uridine + phosphate Uridine Uracil does not associate with
monophosphate(UMP) 2deoxyribose

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 Structure of DNA
Deoxyribonucleic acid(DNA) is composed of f Deoxyribonucleotides, that is, deoxyadenylate
Deoxyguanylate(G), deoxycytidylate( C), and deoxythymidylate(T).
These units are combined through 3' to 5' phosphodiester bonds to polymerised into a long
chain.
A phosphodiester bond (3’-5’) is a linkage that joins two successive nucleotides together.

The phosphodiester bridge occurs between the 3' hydroxyl of one sugar combined to the
5'hydroxyl of another sugar through a phosphate group. The nucleotide is formed by the
combination of base + sugar + phosphoric acid.
In the DNA, the base sequence is of paramount importance. The genetic information is coded
in the specific sequence of bases; if the base is altered, the information is altered.

Watson-Crick Model of DNA Structure

Elucidation of double helical structure of DNA by James Watson and Francis Crick in 1953 was
made visible by several pertinent research of other scientists.
Edwin Chargaff elicited the base pairing of the DNA. That most DNA possess a common and
possibly the same 3-dimensional pattern was suggested by the similarities in X-ray diffraction
pattern observed by Maurice Wilkins and Rosalind Franklin.
The salient features of Watson-Crick model of DNA are given below.

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 • Right handed double helix
DNA consists of two polydeoxyribonucleotide chains twisted around one another in a
right handed helix. The spiral of the helix are the deoxyribosyl residue linked by a
phosphodiester bond and the bases of the Deoxyribonucleotides project
perpendicularly to the Centre of the helix.
• The base pairing rule
Always the two strands are complimentary to each other. So, the adenine of one
strand will pair with thymine of the opposite strand, while guanine will pair with
cytosine. The base pairing(A with T; G with C) is called Chargaff's rule, which
states that the number of purines equal to the number od pyrimidines.
• Hydrogen bonding
The DNA strands are held together mainly by hydrogen bonds between the purine
and pyrimidines. There are two hydrogen bonds between A and T while there are 3
hydrogen bonds between G and C. The GC bond is therefore stronger than AT bonds.
• Antiparallel
The two strands in a DNA molecule run antiparallel which means that one strand
runs in 5'-3' direction, while the other is in the 3'-5' direction.
In the DNA, each strand acts as a template for the synthesis of the opposite strand
during replication process.

Types of structural conformations of DNA

Various forms of DNA conformation are named as;
1. A-DNA 2. B-DNA. 3. Z-DNA
Among these three types, the most abundant type of DNA is B-DNA, commonly known as

Features A-DNA B-DNA Z-DNA

Helix turn Right handed Right handed Left handed
Helical diameter 26A° 20A° 18A°
Height of helical 28.6A° 34A° 44A°
turns(helical pitch)
No of base pairs per 11.6 10 12
helical turn
Helical twist per base 31° 36° 9° or 51°
pair
Distance between 2.9A° 3.4A° 7.4A°
each base pair
Major grove Narrow & deep Wide and open Flat major grove
Minor grove Wide & shallow Narrow and deep Narrow and deep
Glycosidic bond Anti- Anti- Anti- for pyrimidine
formation and Syn- for purine
Watson-Crick model of DNA double helix.
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 A Comparison table of the structural features of A, B, and Z-DNA.

Lipids and Fatty acids

Lipids constitute a group of heterogeneous compounds of biochemical importance. Lipids may
be defined a compounds which are relatively insoluble in water, but freely soluble in nonpolar
organic solvents like benzene, chloroform, ether, hot alcohol, acetone, etc.

Functions of lipids
• Storage form of energy(triglycerides)
• Structural components of biomembranes (phospholipid and cholesterol)
• Acts as surfactants, detergents and emulsifying agents (amphiphatic lipids)
• Give shape and contour to the body and protect the internal organs by providing a
cushioning effect (pads of fat)
• Provide insulation against changes in external temperature (subcutaneous fat) • Help
in the absorption of fat soluble vitamins (A, D, E and K)

CLASSIFICATION OF LIPIDS

Based on the chemical nature, lipids are classified as

1.Simple lipids: They are esters of fatty acids with glycerol or other higher alcohols. Examples
include Triglycerides(Triacyl glycerol or neutral fat) – (esters of fatty acid and glycerol)

and Waxes(esters of fatty acid with alcohol other than glycerol)

2. Compound lipids: They are fatty acids esterified with alcohol; but in addition they contain
other groups. Depending on these extra groups, they are subclassified into ; a. Phosphorylated
lipid (Phospholipid) containing phosphoric acid
b. .Non-phosphorylated lipids

a. Phospholipid: These lipids contain fatty acid esterified with alcohol, and a phosphoric
group. That is
PPL=Fatty acid+alcohol(either glycerol or sphingosine) + Phosphoric acid
Based on the alcohol present, phospholipids can either be
• Glycerolphospholipid having glycerol as the alcohol, or
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 • sphingophospholipids with the alcohol (sphingosine). Example of
sphingophospholipids is Sphingomyelin.
The nitrogen containing glycerolphospholipid are Phosphatidylcholine(lecithin),
Phosphatidylethanolamine(Cephalin) and PS while the non-nitrogen glycerophosphatides are
phosphatidyl inositol, phosphatidyl glycerol, Diphosphatidyl glycerol (cardiolipin).

b. Non-phosphorylated lipid. They include:

• Glycosphingolipids (Glycolipids)
They are seen widely in nervous tissue. This group of lipids do not contain phosphoric
acid; instead they contain carbohydrate and ceramide. The alcohol present is sphingosine,
that is, glycerol is absent. E.g Cerebroside & ganglioside.

• Sulfolipids or sulfatides
These are formed when sulfate groups are attached to ceramide oligosaccharides. All these
complex lipids are important components of membranes of nervous tissue.

3.Derived lipids: They are compounds which are derived from lipids or precursors of lipids, e.g
fatty acids, steroids(cholesterol), prostaglandin, terpenes etc.

4. Lipids complexed to other compounds. E.g Proteolipids & lipoproteins.

Compound lipids (phospholipids)

They are polar ionic compounds that consist of an alcohol attached through a phosphodiester
bond to diacylglycerol or sphingosine. The backbone can be two(2);
• Glycerol (glycerolphospholipid).
• Sphingosine (sphingophospholipids).
Phospholipids in general are amphiphatic, particularly Lecithin. That is, they have both
hydrophobic and hydrophilic portion in their molecule.

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 The glycerol along with the phosphoric acid and choline constitute the polar “head”(hydrophilic
head) of a phospholipid molecules, whereas the hydrocarbon chains of the fatty acid represent the
nonpolar ‘tail’(hydrophobic tail).
The two classes of phospholipid as mentioned earlier based on the (alcohol) backbone are;
1-Glycerophospholipids 2-
Sphingophospholipids.

1.Glycerolphospholipid; They contain glycerol & are called glycerolphospholipid or

phosphoglyceride & constitute the major classes of phospholipids. These are derivatives of
phosphatidic acid which is the simplest phospholipid. All phosphoglycerate contain
phosphatidic acid.
• Phosphatidic acid is made up of one glycerol to which two fatty animals d residues are
esterified to carbon atom 1&2 (Diacylglycerol). The 3rd OH group is esterified to a

phosphoric acid.

The molecule has an asymmetric carbon atoms and therefore, exhibits optical isomerism.
Lisomer is found in nature.
Glycerolphospholipid are formed from phosphatidic acid and amino alcohol( Choline,
Serine, Ethanolamine).
The phosphate group on the phosphatidic acid can be esterified to another compound containing
an alcohol (amino alcohol) . For example;
• Phosphatidic + Ethanolamine – phosphatidyl Ethanolamine (Cephalin)

In phosphatidylethanolamine the phosphatidic add is esterified to the nitrogen base

(Ethanolamine). Cephalin is also found in biomembranes & possess amphiphatic properties.

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 • Phosphatidic + choline= Phosphatidyl choline or lecithin;
This is a nitrogen containing phospholipids. The word lecithin is derived from the Greek
word, lekithos=egg yolk. It contains glycerol.

The phosphoric acid is added to the third position to form phosphatidic acid. The phosphate
group is esterified to the quaternary nitrogen base, (choline).
• Phosphatidic + serine= Phosphatidyl Serine

In phosphatidylserine, the phosphatidic add is esterified to the nitrogen base (serine).

2.Sphingolipids: The sphingosine containing lipid is of 3 types, glycosphingolipids & sulfatides.

All sphingolipids have the long aliphatic amino alcohol sphingosine which is attached to a fatty
acid in amide linkage to form a ceramide. The fatty acid has a chain length varying from C18 to
C24.

Fatty acid (Derived lipid)

Fatty acid are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbon long (C4 to
C36). It is the most common component of lipids in the body.
Fatty acids are aliphatic carboxylic acids and have the general structural formula,
R-COOH, where COOH(carboxylic group) represents the functional group. Depending on
the R-groups (the Hydrocarbon chain), the fatty acids may vary.
Classification of fatty acids
Fatty acids can be classified depending on;
1.Total number of carbon atoms
a. Even chain (They have carbon atoms 2,4,6 & similar series)
b. Odd chain (They have carbon atoms 3,5,7 etc. They are odd numbered fatty acids are
seen in microbial cell walls. They are also present in milk) 2.Depending on length of
hydrocarbon chain
a. Short chain -with 2 to 6 carbon atoms
b. Medium chain- 8 to 14 carbon atoms
c. Long chain -16 & above, usually up to 24 carbon atoms
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 d. Very long chain fatty acids – (more than 24 carbon atoms)
3. Depending on nature of hydrocarbon chain
a. Saturated (They possess a single bond) e. g Laurie, myristic e. t. c
b. Unsaturated which may be monounsaturated ( having a single double bond) or
polyunsaturated with 2 or more double bonds. E.g Arachidonic, oleic and linoleic etc.

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 OMEGA FATTY ACID
The family of polyunsaturated fatty acids(PUFAs) with a double bond between the third and
the fourth carbon from the methyl(CH3)end of the chain are of special importance in human
nutrition. An alternative nomenclature is sometimes used for these fatty acids. The carbon of the
methyl group-that is, the carbon most distant from the carboxyl group-is called omega(w) carbon
and given number 1.
PUFAs with a double bond between C-3 and C-4 are called Omega-3(w-3)fatty acids, and those
with a double bond between C-6 and C-7 are omega-6(w-6) fatty acids.

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 Cholesterol (Derived lipid)
Cholesterol, the major sterol in animal tissues consist of three structural components which are

polar OH group, steroid nucleus and the branched aliphatic hydrocarbon group.

Due to the presence of a polar head group (the hydroxyl group at C-3) and a non-polar
hydrocarbon body (the steroid nucleus & the HC side chain at C-17), cholesterol is amphiphatic
in nature.
The steroid which are mostly of eukaryotic origin are derivatives of
CYCLOPENTANOPERHYDROPHENANTHRENE

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which consists of 4 fused rings lettered A-D (3 cyclohexane & 1 cyclopentane).
The much maligned cholesterol, is further classified as sterol due to the presence of -OH.
@C-3 & a branched aliphatic hydrocarbon @ C-17,with it’s properties of unsaturation shown at
C-5 of the steroid nucleus.
.

Prostaglandins
Prostaglandins contain a five carbon ring originating from the chain of arachidonic acid. Their
name derives from the prostate gland, the tissue from which they were first isolated from by

Bengt Samuelsson and Sune Bergstrom. Two types of prostaglandin were originally derived:
PGE(ether-soluble) and PGF(phosphate/fosfate).
Each group contains numerous subtitles, named PGE1,PGE2,PGF1 and so forth. PG have an array
of functions. Some stimulate contraction of the smooth muscle of the uterus during menstruation
and labor. Others affect blood flow to specific organs, the wake-sleep cycle, and the
responsiveness of certain tissues to hormones such as Epinephrine and glucagon. PG in a third
group elevate body temperature(producing fever) and cause inflammation and pain.

Past questions of macromolecules.

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Carbohydrates
• With the aids of appropriate structures, describe the following terms
a. Aldose sugar b. Ketose sugar c. Asymmetric Centre d. Ketotriose e. Aldopentose f.
Ketopentose
• Differentiate between alpha-D-glucopyranose and Beta-D-glucopyranose.
• Define the following terms: a. Isomerism b. Anomerism c. Epimerism d. Mutarotation
• Write a comprehensive note on polysaccharides
• What are Mucopolysaccharides and their significance
• Explain the term glycosidic bond and show structures • Explain (4) chemical properties of
monosaccharides.
• Give the structure of a. Sedoheptulose b. Mannose c. Glucose d. Dihydroxyacetone
Protein
• Write the single letter abbreviation for these amino acids: Asp-Arg-Val-Tyr-Ile-His-
ProPhe.
• What are peptide bonds and write on the structure of protein
• Write on the chemistry and classification of amino acids
• Name two proteins with quaternary structure and state their functions
• Discuss the various organisation of protein
• Give the structures of these amino acids: Asp, Phe, Ile, Gly, ser
• All amino (except glycine) possess a chiral carbon explain.
The Nucleic acid
• Write briefly in the following: a. Purine b. Pyrimidine c. Nucleoside d. Nucleotide
• Using typical structures, describe Deoxyribonucleic acid.
• Discuss in details the various forms of DNA
• Write on the Watson -crick structure of DNA
• State the difference between RNA and DNA Lipid • Draw the structure of the following :
a. Phosphatidylcholine b. Cholesterol c. ∆9 16:1 d. ∆9,12 18:2
• Write a comprehensive note on the structures and functions of membrane lipids
• Write short notes on the following a. Structure and functions of fatty acids b.
Prostaglandins
• Review the Biochemistry of prostaglandins and describe the structure of cholesterol
• Explain saturated and unsaturated fatty acids
• Write a short note on glycerolphospholipid
• Draw the structures of the fatty acids represented by w9,18:1 and w9,22:1

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