Introduction to Biochemistry, Cell and Molecular Biology...
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Introduction to Biochemistry, Cell and Molecular Biology I
Losiana NayakIndian Statistical Institutehttp://www.isical.ac.in/~losiana_t/
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Biochemistry:
Chemistry that deals with the chemical compounds and processes occurring in organisms. It deals with
“Molecular Basis of life”
Ref: http://www.britannica.com/
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Points to Study…
CarbohydratesProteinsLipidsNucleic acids
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Carbohydrates:
Functional unit- MonosaccharidesChemically they are aldehydes or ketones having two or more hydroxyl groups; hence divided into two categories:
Aldosesketoses
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The Aldoses
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The Ketoses
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Disaccharides
Contain two molecules of monosaccharide
Example:Sucrose [glucose + fructose]
Lactose [galactose + glucose]Maltose [glucose + glucose]
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Polysaccharides
Made up of multiple units of monosaccharide
Example:GlycogenStarchDextranCellulose
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Role of Carbohydrates in cellular environment
Serve as energy stores (Glycogen, Starch)Act as fuel (ATP is a phosphorylated sugar derivative)Metabolic intermediateStructural element in cell wallPlay key roles in cell-cell recognition process
[Fertilization begins with binding of sperm to a specific oligosaccharide on the surface of an egg]
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Special note:
Carbohydrates can exist in a complex form with proteins and lipids, i.e,
glycoproteins and glycolipids respectively.
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Lets go to Proteins…
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Origin of the word protein:
Derived from greek word proteios, which means “of the first rank”. Due to major role of this class of biomolecules in every aspect of life such a name was given to them. Jons J. Berzelius (1838) coined the term.
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Proteins:
Structural unit- amino acidR
H2N Cα COOH
H
Alpha Carbon
AcidGroup
Amino Group
Side chain
20 different type of amino acids make all the proteins!
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Aliphatic amino acids
Hydrophobic in nature.Glycine(R=H)- Simplest aaAlanine(R=CH3)ValineLeucineIsoleucineProline (Contains hetero atom N, hence less
hydrophobic in nature)
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Hydroxyl aliphatic amino acids
Hydrophilic in nature
Serine Threonine
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Aromatic amino acids
Hydrophobic in naturePhenylalanineTryptophanTyrosine
Presence of benzene ring is the
characteristic feature
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Basic amino acids
Polar and highly hydrophilicLysine, Arginine, Histidine
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Acidic Amino acids
Aspartic acidGlutamic acid
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Amides
Amino derivatives of aspartate and glutamate
AspargineGlutamine
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Amino acids containing sulpher
Cysteine
N.B. Cystine = Cysteine + Cysteine
Methionine
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Protein architecture10 structure- amino acid sequence
20 structure- alpha helices, beta sheets and random coils
30 structure- represent the folded protein
40 structure- More than one polypeptide chain exist .
Individual unit is known as motif or domain.
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How amino acids exist in a chain?
The answer is:Peptide linkage
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α1-carboxyl
group
α2-amino group
amino terminal
carboxy terminal
Peptide bond
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Polypeptide chain is…
A number of amino acids attached to each other by peptide linkage.
ATGHYKILQPRSWRHISAEDNSWQ
This form represents primary structure of a protein.
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Secondary structure of proteins
Does a polypeptide chain attain some periodic structures?
YES
Experimentally confirmed by scientists Pauling and Corey in 1951. Otherwise they are known as protein
secondary structures.
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Types of 20 structures: α-helix
Hydrogen bond exists between carboxy group of nth aa and amino group of (n+4)th aa.Each turn contains 3.6 aas
Gap between two aas is 1.5 A0
75% of Myoglobin and Hemoglobin are α-helix.
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Types of 20 structures: β-pleated sheets
Individual unit: β strand. Number of β strands are arranged like sheets of paper in a β-pleated sheet. Whole Structure is stabilized by hydrogen bonds between different strands. The strands can run in same or opposite direction. According the structure is named parallel or antiparallel β sheet. They are fully extended structures. Distance between
two successive aa is 3.5 A0.
Example: Silk fibroin
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Types of 20 structures: Random coils
They constitute intermediary stretches between αhelices and β sheets.
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Tertiary Structureexhibit one or more different type of
secondary structuredisulphide bonds and vanderwaal’s (weak) interactions come into picture. They enable protein foldingThe difference between secondary and tertiary structure is a very fine line and depend on matter of taste
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Quaternary structure
Represent association of polypeptide subunits in a defined geometric configuration
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Biological functions of Proteins
Enzyme catalysis (nearly all enzymes are proteins)Transport and storage (ex: Hemoglobin and
Myoglobin)Motion ( muscle movement: actin/myosin;
chromosome movement in mitosis;sperm movement etc.)
Mechanical support (ex: skin, bone)Immune protection (antibodies)Signal transfer (transmission of nerve impulses)Growth and differentiation in a controlled way (ex: growth factor proteins )
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Special note:
4o structure not required for all proteins to function- many proteins may have only 2o
or 3o structure.
Proteins can exist in a complex form with carbohydrates. (Proteoglycans)
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Welcome to the Lipid Arena
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Characteristics of lipids
Insoluble in water and soluble in organic solventsContain long aliphatic hydrocarbon chains or benzene rings as side chainsOverally divided into triglycerides and compound lipids
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Triglycerides
Triesters of fatty acidsNeutral fats, i.e., glycerol triesters (found in adipose tissue) and waxes, i.e., alcohol triesters (ex: beeswax) belong to this category
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Compound lipids
Phospholipids,Sphingolipids
Amphipathic in nature
Hydrophilic head
Hydrophobic tail
Alcohol
Fatty acids
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Biological significance of lipids
serve as structural components of biological membranesprovide energy reserves (9 kcal/mol), predominantly in the form of triacylglycerolsserve as vitamins and hormones
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The nucleic acids
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Introduction
They form the genetic material.DNA (deoxy ribo nucleic acid)RNA (ribo nucleic acid)
Difference between DNA and RNA?
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OH
OCH2
Sugar
H
HH
A NucleotideAdenosine Mono Phosphate (AMP)
NH2
N
N N
N
BaseP
O
OH
HO OPhosphate
NucleotideNucleoside
H+
2’3’
4’
5’
1’
OH
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SUG
AR
-PHO
SPHA
TE BA
CK
BO
NE
H
P
O
HO
O
O
CH2
HOH
P
O
O
HO
O
O
CH2
H
P
O
OH
HO
O
O
CH2
NH2
N
N
N
N
O
O
NH2N
NH
N
N
N O
NH2
N
B A
S E S
DDNNAA
OH
P
O
HO
O
O
CH2
HO
O
H 2NN
HN N
N H
H
P HO
O
O
CH2
OO
NO
H 2N
NH
H2O
H OH
P
O
HO
O
O
CH2
CH 3
O
O
HN N
H2O
STRAND
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Scientists James Watson and Francis Crick first proposed
the double helical structure of DNA in
1953.
Awarded Nobel Prize in 1962 for medicine
and physiology.
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Types of RNA
m- RNA (messenger RNA)
t- RNA (transfer RNA)
r- RNA (ribosomal RNA)
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Messenger RNA
The concept of mRNA was formulated by scientists Francois Jacob and Jacques
Monod in 1961.
3’ Untranslated Region5’ Untranslated Region
AAAAAG
3’ Poly A Tail5’ CapProtein Coding Region
Eukaryotic mRNA
5’ 3’
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Transfer RNA
Base sequence of yeast alanine tRNA was first determined by scientist Robert Holley (1965).
Most of the tRNAs are 73-93 nucleotides long and have complex folded structures.
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D Arm - Contains dihydrouridine
TψC arm - ψ stands for pseudouridine
Extra Arm - May vary in size
Anticodon
Transfer RNA (tRNA)
U*
9
262223Pu
1612Py 10
2520:1
G*
17:1
Pu
A20:2
1713
20G
A5051
656463G
6252
C Pu
59
ψ
A*
C
Py
T49
39
4142
31
2928
Pu*
43127
U35
38
36
Py*
34
4030 47:1
47:15
46
Py47:16
4544
47
73CCA
707172
66676869
321
7654
Amino Acid attachment siteAcceptor Arm - A specific amino acid is attached to the 3’ end
3’ OH
5’ P
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Ribosomal RNA
Present in ribosomeCritical for ribosomal architecture and functionHave role in protein synthesisThey are of three types, i.e., 5S, 16Sand 23S.
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EAP
Large subunit
Small subunit
50S
30S
23S rRNA
5S rRNA
16S rRNA
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Reference
1. Biochemistry by Lubert Stryer2. Cell and Molecular Biology by De
Roberties and De Roberties
Some Slides are taken from
Timothy G. Standish, Ph. D.