Long term-2023-Medical-Biology

CHAPTER - 9
BIOMOLECULES
PROTEINS
Proteins are heteropolymer of 20 types of amino acids
Proteins are the most complex, most abundant and most diverse biomolecule
Functional classification of proteins
1. Enzymes : Pepsin, Trypsin, hexokinase, succinate dehydrogenase, RuBisCo etc. RuBisCo
is the most abundant protein in biosphere
2. Hormones : GH, PRL, insulin, Glucagon, OT, VP .....
OT & V.P are nona peptide hormones
3. Transporters : Hb, Albumin, GLUT-4....
4. Receptors : Sensory Receptors, hormonal receptors .......
5. Defense proteins : Antibodies
6. Contractile proteins : Myosin > Actin > Titin ........
7. Genetic proteins : Histones
8. Structural proteins : Keratin, Collagen etc. Collagen in the most abundant protein in
mammals
Amino acids
General Structure :
Amino acids are substituted methane (CH4)

NH2 C COOH R : Alkyl group


R

 - Amino acids are most common

Classification of Amino acids based on nature of ‘R’ (Alkyl group)
I. Aliphatic / Hydrophobic Acids

1. Glycin  H C  simplest Aa  only Aa without asymmetric carbon and optically inactive

2. Alanin  CH3 C

3. Valine  Essential Aa
4. Leucine  Essential Aa
5. Isoleucine  Essential Aa

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II. Hydroxyl Containing Aminoacids

6. Serine CH2 C  Most common Aa present at active site of enzyme

OH
7. Threonine  Essential Aa
III. Sulphur Containing Aa’s

8. Cysteine  CH2 C

OH
(It is only Aa involve in formation of Disulphide bonds in Proteins)
9. Methionine  Essential Aa
IV. Acidic Amino acids and Amides
O

10. Aspartic acid HO C CH2 C

11. Glutamic acid HO C (CH2)2 C

12. Asparagine NH2 C CH2 C

13. Glutamine NH2 C (CH2)2 C

V. Basic/+ve Charge Aminoacids

14. Lysine : NH3 (CH2)4 C  Essential Aa

15. Arginine  Semi-essential Aa

Lysine and Arginine are most abundant in histone proteins and gives ve charge
16. Histidine  Semi-essential Aa
 involve synthesis of histamine which is inflammatory molecule
VI. Aromatic Amino acids

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17. Phenylalanine : CH2 C  Essential Aa

18. Thyrosine : It involve in synthesis of hormones like T3, T4, epinephrine, norepinephrine and pigment
melanin

Phenylalanine
CH2 C   HO CH2 C
Hydroxylase

Phenylalanine Thyrosine
19. Tryptophan : Essential Aa
 involve in synthesis of melatonin, seratonin and IAA

20. Protein : Amino acid

N COOH
H

D and L forms of Amino acids

It relates to spatial arrangement of –NH2 group around ‘  ’ Carbon. If NH2 is at right side called D-
Aminoacid and if it is at left side called L-Aminoacids.
 Naturally occuring aminoacids are L-Aminoacids.

H
O H
NH2 C COOH HOC C NH2
R
R

L-Aminoacid D-Aminoacid

Zwitter / Dipolar ion :

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NH2 C COOH

R L-Aa
ent Al
ol v ka
ic s lin
aci d e
H+ pH
+
H
H H

NH2 C COO
NH3 C COOH

R R
Cation Anion

I
P

NH3 C COO

Zwitter ion

Iso electric pH (pI) : It is particular pH where particular Aa (or) protein is exist as Zitter ion. pI of most
aminoacids around ‘7’.
Structure of Proteins : There are 4 levels of protein structure include 1o, 2o, 3o and 4o.
Primary structure : It is linear sequence of Aminoacid Residues linked by Peptide bond.

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H H

NH2 C COOH + HNH C COOH

R1 R2 Aa - 2

Aa - 1

H2O [dehydration]

H O H
NH2 C C N C COOH

R1 H R2

Peptide bond

 Peptide bond is formed by Carboxyl group of first Aa react with Amino group of next Aa with release
of H2O, mediated by enzyme Peptidyl Transferase.
 Peptide bond fixation is example of dehydration.
 G. N. Ramachandran discovered triple helical structure of Collagen.
Secondary structure : It is intermediate folding of polypeptide stabilized by H-bonds.
 It include   Helix and   sheet. Helix include both right and left handed. Right handed   Helix
is the most common secondary structure in cell.
Tertiary structure : It is completely folded 3D structure of proteins stabilized by Disulphide bond
formed by Cysteine.
 It is natural and functional form of simple proteins - made up of only one polypeptide chain.
ex. Myoglobin, Albumin, etc.
Quarternary structure : If a protein is made up of more than one polypeptide chain, called Multimeric
proteins.
 These proteins function in 4o structure ex. Hb - A -  22
Bonds Responsible for stabilising protein structure
1. Peptide bond
2. H - bond
3. Disulphide bond
4. Hydrophobic bonds

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Denaturation of Proteins
 Disorganization of protein structure from Tertiary to Primary..
 During this proteins lose 3o and 2o structures but 1o structure or peptide bonds remain same.
 During denaturation proteins lose there function.
eg. At high temperature enzymes lose function by denaturation.
Enzymes
Definition : Enzymes are organic catalyst increases rate of reaction, mostly proteins, heat sensitive
and specific reaction.
 Inorganic catalyst work at high temperature and pressure where as enzymes work at physiological
conditions of organisms.
 Most of enzymes are proteins except Ribozyme -RNA with enzyme activity..
 Most of enzymes are heat sensitive except those associated with thermophiles.
ex. Taq DNA polymerase use in PCR
 The specificity of enzymes due to shape of substrate and active site of enzymes are complement
(or) opposite.
Components of Holo enzyme
Holo enzyme = Apo enzyme + Co-factor
(complete functional enzyme) (Protein part) (Non-protein part)
 Co factors are of 3 types, include
a) Prosthetic group : These are organic cofactors permanently (or) covalently associated with
Apoenzyme.
ex. Haem is possible group of enzymes like catalases and peroxidases
b) Co-enzymes : These are also organic cofactors but temporary (or) loosely (or) non covalently
associated with apo enzymes.
 Many of co-enzymes synthesis from vitamins
ex : NAD+/NADP+ - Coenzyme synthesize from vitamin Niacin (Vitamin B3)
 Coenzyme FMN and FAD synthesize from vitamin Riboflavin (Vitamin B2)
c) Metal ion : Most common cofactors covalently associated with Apoenzyme.
ex. Zn+2 is required for enzymes like carboxy peptidase, carbonic anhydrase
 Molybdenum (Mo) and Iron (Fe) required for enzyme Nitrogenase complex.
Classification of Enzymes : All enzymes are classified into 6 classes based on type of reaction they
catalyse.
Class 1 : Oxido Reductases (or) Dehydrogenases.
Definition : Mediate Redox Reactions.
A(red)  B(oxi)  A(oxi)  B(red)
Class 2 : Transferases
Definition : Mediate transfer of simple groups like phosphate, amino group etc.
AgB ABg
Class 3 : Hydrolases
Definition : Mediate breakdown of bonds with addition of H2O.

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A  B  H 2 O  A  H  B  OH
Class 4 : Lyases
Definition : There enzymes cause breakdown of bonds without Hydrolysis by leaving double bond
between carbon atoms.
X Y

C C C C+X Y
Class 5 : Isomerases :
Definition : Mediate inter conversion of optical (or) Geometrical isomers.
A  A
Class 6 : Ligases
Definition : Mediate joining of molecules with energy.
ATP
A  B  A B
Factors effecting enzyme activity
A) Effect of Substrate Concentration :

 Initially rate of reaction is directly proportional to substrate concentration. A particular substrate

concentrates where enzyme giving maximal velocity (Vmax) called Saturation point. If substrate
concentration increases further rate of reaction become independent.
Km(Micheals - Constant) : It is substrate concentration where enzyme gives half of maximal velocity.
1
Km 
enzyme affinity to substrate
B) Effect of Temperature :

* Optimal temperature for most of enzymes is around 40oC.

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C) Effect of pH

* Optimal pH for most of enzymes is around 7

Steps involve in Enzyme action :
Step 1 : Substrate binds with active site of enzymes
Step 2 : Substrate causes conformational changes in enzyme result enzyme substrate complex
Step 3 : Enzymes causes breakdown of old bonds and cause formation of new bonds results enzyme
- Product complex.
Step 4 : Enzyme release product and ready to binds with another substrate.

E+S [ES] [EP] E+P

Enzyme inhibition
 It is broadly classified into reversible and irreversible.
 Reversible enzyme inhibition is again classified into
a) Competative
b) Non competative / Allosteric
c) Uncompetative
a) Competative Enzyme inhibition
In which substrate and inhibitor are structurally similar. So both substare and inhibitor compete for
binding to active site of enzyme. It results rate of reaction gets decrease.
 During this inhibition Km value is increase and Vmax is same.

E+S [ES] [EP] E+P

+
I

[EI]

ex. Malonate is competative inhibitor of enzyme, Succinate dehydrogenase.

b) Allosteric Enzyme inhibition : In which structure of substrate and inhibitor are different. Inhibitor
combines with other than active site of enzyme called Allosteric site.
 During this inhibition Km value is same but Vmax is decrease.

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E+S [ES] [EP] E+P

+ +
I I

[EI] [ESI]

C) Uncompetative Enzyme inhibition :

In which inhibitor binds with only Enzyme - Substrate complex.
 During this both Km and Vmax are reduce.

E+S [ES] [EP] E+P

+
I

[ESI]

Mechanism of Enzyme action :

 Enzyme increase rate of a reaction by decreases in activation energy [Ea]

 While a substrate convert into product, it should cross transient unstable intermediate.
 The above graph is representation of an exothermic reaction. Some of exothermic reactions are
spontaneous.
NUCLEIC ACIDS :
Function : Nucleic acid is acts as genetic material responsible for inheritance.
 Nucleic acid is polymer of Nucleotides linked through phosphodiester bond. RNA is polymer of
Ribonucleotides and DNA is polymer of deoxyribonucleotides.
Nucleoside = N2 base + Pentose sugar [ie, Ribose in RNA / 2/ Deoxyribose in DNA]
Nucleotide = N2 base + Pentose sugar + minimum one (or) maximum 3 phosphates
N2 base Nucleoside Nucleotide
RNA / DNA RNA / DNA
1. Adenine  Adenosine / deoxy adenosine  Adenylic acid / deoxy adenylic acid
2. Guanine  Guanosine / deoxy Guanosine  Guanylic acid/deoxy guanylic acid
3. Cytosine  Cytidine / deoxy cytidine  Cytidilic acid / deoxy cytidilic acid
4. Uracil  Uridine /  Uridylic acid /
5. Thymine  / Thymidine  / Thymidylic acid 9
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Structure of Nitrogen bases

Adenine Guanine

NH2 O

N N
N HN

N N NH2 N N
H H

Cytosine Uracil Thymine

NH2 O O

CH3
N HN HN

O O N O N
N
H H H

RNA

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 Polymer of ribonucleotides
 Contains Ribose as sugar
 Mostly exist as single stranded molecule (ss)
 Do not follow chargaff’s rule
 Contain A, G, C and U
 Base pairing  A = U and G  C
Functions
 Genetic material  Most of virus ex. TMV, HIV
 Enzyme  Ribozyme
 Messenger  m-RNA  least abundant
 Adaptor  t-RNA
 Ribosome  r-RNA  Most abundant
DNA
 Polymer of deoxyribonucleotide
 Contain 2/ Deoxy ribose sugar
 Mostly exist as double stranded molecule (ds)
 Follow Chargaff’s rule / A = T ; G = C / A + G = T + C
 Contain N2 bases like A, G, C and T
 Base pairing  A = T and G  C
Function
DNA is genetic material in both Prokaryotes and Eukaryotes.
General Structure of Nucleoside Triphosphate

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Secondary Structure of B-DNA

 The structure was discovered by Watson and Crick based on X-ray diffraction done by Franklin
and Wilkins.
 B - DNA is Right handed double helical structure stabilised by Hydrogen bonds. Each strand is
polymer of deoxyribonucleotides linked through phosphodiester bond.
 Both strands of DNA are complement and antiparallel.
 In B-DNA, length of one turn is 34 Ao/3.4nm, distance between 2 pair is 3.4 Ao/0.34 nm, and diameter
is 20Ao/2nm.
 At each step of Ascent, strand turns 36o.
CARBOHYDRATES
Functions
1. Carbohydrates are energy storing substances.
ex. Starch in plants and Glycogen in Animals.
2. These are structural components of cell wall.
ex. Peptidoglycon in bacteria
Chitin in Fungi
Cellulose in Plants
Structure of Some Monosaccharides

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Glucose Fructose Galactose

CHO CH2 OH CHO

H C OH C O H C OH

HO C H HO C H HO C H

H C OH H C OH HO C H

H C OH H C OH H C OH

CH2 OH CH2 OH CH2 OH

Classification of Carbohydrates
Carbohydrates are classified into 3 types include :
A) Monosaccharides
B) Disaccharides
C) Polysaccharides
A) Monosaccharides
 These are simplest carbohydrates
 Based on functional group, these are classified into 2 types include :
a) Aldoses - Contain aldehyde functional group present at first carbon
b) Ketoses - Contain keto functional group present at second carbon
 Based on number of carbon atoms, mono saccharides classified into following types.
a) Trioses  contain 3C
 simplest Monosaccharides
b) Tetroses  Contain 4C
c) Pentoses  5C
d) Hexoses  6C
Aldoses Family
 Aldotriose  ex. Glyceraldehyde
 Aldotetrose  ex. Erythrose
 Aldopentose  ex. Ribose
 Aldohexoses  ex. Glucose, Galactose, Mannose
Ketoses Family

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 Ketotriose  DHA (Dihydroxy Acetone)

 Ketotetrose  Erythrulose
 Ketopentose  Ribulose
 Keto Hexose  Fructose
D and L forms of Monosaccharide
 It is spatial arrangement of ‘OH’ group around last asymmetric carbon. If ‘OH’ group on last
asymmetric is at right side, it is called D-sugar and if it is left side called L-Sugar.
 Most common sugars are D-sugar..

CHO CHO

H C OH H C OH

HO C H HO C H

H C OH H C OH

H C OH HO C H

CH2 OH CH2 OH

D-Glucose L-Glucose

Cyclic forms of Monosaccharide

 There are 2 types of cyclic structures include pyranose and furanose.
 Ring number has to start with functional carbon number
 If it is   anomer. ‘OH’ group on function carbon represent towards down and if it is   anomer,,
represent towards up.
 on 2o Hydroxyl carbon, if ‘OH’ group is at right represent towards down and if it is left side represent
towards up.
  D-Glucopyranose   D-Glucopyranose

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6 CH2 OH 6 CH2 OH
O O
5 5 OH
4 1 1
4
OH OH
OH 3 2 OH OH 3 2

OH OH

  D-Galactopyranose   D-Galactopyranose

6 CH2 OH 6 CH2 OH
O O
OH 5 OH 5 OH
4 1 4 1
OH OH
3 2 OH 3 2

OH OH

  D-Fructofurnanose   D-Fructofurnanose

6 6
CH2 OH O 1 CH2 OH O
CH2OH OH

5 2 5 2
OH OH OH CH2OH
4 3 4 3 1
OH OH

Disaccharides : Two monosaccharide residues are linked by Glycosidic bond. These are of 2 types include:
a) Reducing Disaccharides - eg. Maltose, Lactose
b) Non Reducing Disaccharides - eg. Sucrose
a) Reducing Disaccharide
1. Maltose - It consist of 2 Glucose molecules linked by (1  4) Glycosidic bond.

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CH2OH
6 CH2 OH
O
O
5
4 1 1
OH OH OH
OH 3 2 OH HO 4

OH OH

  D-Glucopyranose   D-Glucopyranose
  H 2 O[dehydration]

CH2OH CH2OH
O O

1 1 Maltose
OH O OH OH
OH 4 4

OH OH

(1  4) Glycosidic bond

Lactose : It consists of   D  Galactopyranose linked with   D  Glucopyranose by (1  4) Glyco-
sidic bond.

CH2OH CH2OH

O O
OH OH OH

1 1
4
OH OH OH
4

OH OH

  D-Galactopyranose H2O   D-Glucopyranose

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CH2OH CH2OH

O O
OH OH
O 4 1
4 1
OH OH

OH OH

(1  4) Glycosidic bond

Non Reducing Disaccharide
Sucrose : It consists of   D  Glucopyranose links with   D  Fructo furanose by 1  2 Glyco-
sidic bond.

CH2OH CH2OH
O O

4 1 1
OH OH
OH OH OH
O
D-Glucopyranose OH OH
O
H2O CH2OH
O
CH2OH OH 2
OH
OH CH2 OH
4 CH2 OH
2
OH
OH
Sucrose
-D-Fructo furanose

Polysaccharides : It consists of number of Monosaccharide residues linked through Glycosidic bond.

It include Homo and heteropolysaccharides.
Homo polysaccharides : Made up of same type of sugar (or) monosaccharide.
1. Starch
 Is stored polysaccharide in plants
 It consists of amylose and amylopectin
 Amylose is linear polymer of   D  Glucopyronse linked through  (1  4)Gly cos idic bond

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CH 2 OH CH 2 OH CH 2 OH
O O O

OH OH OH
OH O O OH
OH OH OH
n

(1  4)
 Amylopectin is branched polymer of   D  Glyucopyranose linked by (1  4) Glycosidic bond
and (1  6) Glycosidic bond at branch point.

O  (1 4)

OH CH2 OH

HO O

O  (1 6) Glycosidic bond

CH2 OH CH2 CH2 OH

O O O

OH OH OH
OH O O OH

OH OH n OH

 Starch gives blue color with I2 because it contains complex helical structure.
 In a polysaccharide left end is non reducing and right end is reducing.
2. Glycogen
 Stored polysaccharide in Animals
 Also called Animal starch
 It is branched polymer of   D  Glucopyranose like Amylopectin.
3. Cellulose
 It is cell wall of plants
 Most abundant carbohydrate
 It is linear polymer of   D  Glucopyranose linked through (1  4) Glycosidic bond.
 It can not gives blue colour with I2 bcz it is not having helical structure.
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4. Chitin
 Cell wall of fungi
 Second most abundant carbohydrate present as exo skeleton of invertebrates
 It is linear polymer of N-Acetyl - Glucosamine linked through (1  4) Glycosidic bond.
5. Inulin
 It is polymer of Fructose
 Shortest homopolysaccharide used in detection of Glomerular filtration rate (GFR)
Heteropolysaccharides
1. Peptido Glycan
2. Agar
3. Heparin
4. Hyaluronic acid
5. Chondriotin sulfate
FATTY ACIDS AND LIPIDS
Functions of lipids
1. Phospholipids are major structural components of plasma membrane
2. Triglycerides (or) fat is the major energy storing substance.

Ester bond
O
O
CH2 O C R1
CH2 OH HO C R1
O
O
3H2O CH O C R2
CH OH + HO C R2
O
O
CH2 O C R3
CH2 OH HO C R3

Glycerol Triglycerides / Fat / oil

(or) 3 x Fatty acids
Tri (OH) propane

Fatty acids
 These are long aliphatic acids
 These are of 2 types based on number of carbon atoms include
a) even number  Most common
b) Odd number
ex. for even number fatty acids.
1. Palmitic acid (16 : 0) = CH3 CH2 COOH
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2. Stearic acid (18 : 0) = CH3 CH2 COOH

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 Based on saturation, fatty acids are of 2 types include :

a) Saturated
are equally present
b) Unsaturated

If a fatty acid contains more than one double bond called polyunsaturated fatty acid.
Essential Fattyacids
1. Linoleic acid (18 : 2)
2. Linolenic acid (18 : 3)
3. Arachidonic acid (20 : 4)
Phospholipids
Lecithin

CH2 O C R1
O

CH O C R2
O

CH2 O P O CH2 CH2 N (CH3)3

Sterols
Cholesterol
 Most common Animal sterol
Functions
 These are membrane stabilising molecules
 Cholesterol involve in synthesis of steroid hormones like Testosterone, Estrogen
Structure of Cholesterol

HO

Classification of Lipids

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Organic analysis of Tissue

Comparison between polysaccharides, proteins, nucleic acids with lipids.

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Polysaccharides, Proteins, Lipids (Phospholipids)
Nucleic acids
 Hydrophilic  Hydrophobic (Amphipathic)
 Polymer  Monomer