Notes

Department of Biochemistry University of Karachi
Introduction to Biochemistry-1
Course NO: Bio-311

Credit hours (2+1)
Khwaja Ali Hasan

Lecturer
Department of Biochemistry
References and Books
(1) Modern Concepts In Biochemistry (R C Bohinski) 5th Edition

(2) Principles of Biochemistry (Lehinger) by David L. Nelson and Michael M. Cox, 5-7th Edition
(3) Fundamentals of Biochemistry (Donald Voet, Judith G. Voet and Charlotte W. Pratt) 3rd Edition
(3) Molecular Biology of the Cell. Alberts B, Johnson A, Lewis J, et al. New York: Garland Science;
2002. 4th edition.
Amino acids
• Amino acids are organic compounds which contain at least one
amino group (-NH2) and a carboxy (-COOH) group.
• In the human genome, 20 amino acids are created to build

proteins and therefore termed proteinogen.
• Besides this, there are approximately 250 amino acids which do

not form proteins
• The 20 proteinogen amino acids are also called standard amino

acids, which can be divided into three groups according to
nutritional requirements :
• Essential, Semi-essential and Non-essential.

• Essential amino acids as the body cannot produce them by
themselves, and they have to be supplied externally.
• These are: isoleucine, leucine, lysine, methionine,

phenylalanine, threonine, tryptophan and valine.
• Arginine and histidine form the group of so-called semi-

essential amino acids. They have to be consumed in the diet
under certain circumstances.
• The ten non-essential amino acids are able to be produced

in the body. The following amino acids fall into this
category:
• Slanine, asparagine, aspartic acid, cysteine, glutamine,

glutamic acid, glycine, proline, serin and tyrosine.
Essential amino acids
• Out of 20 standard amino acids, essential
amino acids are 10 in number and can be
remembered as PTV HIM TALL:
• Phenylalanine, tyrosine, valine, histidine,

isoleucine, methionine, tryptophan, arginine,
leucine and lysine.
2° 2°
Selenocysteine: the 21st amino acid

Sec or U
Enzymes: Glutathione Peroxidases; Glycine Reductases

Stereoisomerism in α-amino acids
The two stereoisomers of
alanine,
L- and D-alanine, are
nonsuperposable mirror
images of each other
(Enantiomers)
• In perspective formulas: The solid wedge-
shaped bonds project out of the plane of the
paper, the dashed bonds behind it
• In projection formulas: The horizontal bonds

are assumed to project out of the plane of the
paper, the vertical bonds behind
• Amino acids having same
molecular mass differs in their P.I
and hydropathy index
Behavior of Amino acids
Condensation Reaction of amino acid
and Di-peptide Formation
Calculate the pI When the Side
Chain is Ionizable
• Identify species that carries a net zero charge
• Identify pKa value that defines the acid
strength of this zwitterion: (pK2)
• •Identify pKa value that defines the base
strength of this zwitterion: (pK1)
• •Take the average of these two pKa values.
What is the pI of histidine?
Weak Interactions
• Ionic (Electrostatic interaction)

• Hydrogen bonds
• Hydrophobic (Greek, “water-fearing”), and
• van der Waals interactions
• These weak interactions are individually weak, but
collectively they have a very significant influence
on the three-dimensional structures of proteins,
nucleic acids, polysaccharides, and membrane
lipids.
Side Chains (R group) of Amino Acids involved in Non-Covalent Interactions
Weak Interactions are Driving force in
Enzyme Catalysis
• Polar Biomolecules dissolve readily in water
because they can replace water-water
interactions with more energetically favorable
water-solute interactions.
• Nonpolar Biomolecules interfere with water-
water interactions but are unable to form
water-solute interactions— consequently,
nonpolar molecules are poorly soluble in
water.
• In aqueous solutions, non-polar molecules tend

to cluster together.
Kosmotrope and Chaotrope
The solutes that stabilized, proteins and membranes

or other Macromolecules Kosmotrope (order-
maker).
Kosmotropes stabilize proteins and hydrophobic

aggregates in solution and reduce the solubility of
hydrophobes.
Chaotrope
The solutes that destabilized proteins and
membranes or other Macromolecules
Chaotrope' (disorder-maker)
Chaotropes unfold proteins, destabilize

hydrophobic aggregates and increase the
solubility of hydrophobes
Peptide to Proteins
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Biological Significance of Peptides and Protein
Chemotactic peptides (N-formylated tripeptide): Acts on neutrophils
formyl peptide G protein coupled receptor (FPR)
Peptide Antibiotics and Immunosuppressant
Scorpion and Snake venom peptides
Hormones
Enzyme
Cell surface Receptors (Cell signaling and communication)
Antigens and Antibodies
Antiviral and Antibacterials

Primary Structure
Primary Structure determines tertiary structure

Peptide or
Amide Bond
Condensation Reaction
or
Dehydration Synthesis
Dihedral Angles
Dihedral Angles
Configuration and Conformation
Trans Peptide
Cis Peptide
Peptide (Naming)
Disulphide Bond
Weak Interactions are Core Deterinants
Secondary Structure
α-Helix
1) 3.6 Amino acid residue per turn
α-Helix 2) Hydrogen bonds are located in

side the helix
3) The vertical rise per residue
(0.15nm)
4) The oxygen atom on carbonyl
group of residue n forms a
hydrogen bond with hydrogen atom
of the N-H group of residue n + 4.
Proline and glycine have least
tendency to fit in helix
D-Amino acid L-Amino acid

Secondary Structure, Intra and Inter Molecular Interaction
β-sheet
β-turn and loops
• Turns and loops connects α-Helical and β-
strands segments with in a protein allowing the
polypeptide backbone to fold back upon it self
and reverse the direction
• Glycine and proline are commonly present in
beta turns
• Glycine is conformationally flexible to fit in
turns
• Proline steric constraints are also well situted to
β-turn
• Loops contain five or more residues, tend to be
quite flexible, and lack define structure
Super Secondary Structure
Motifs
1) Combinations of secondary
structure called super secondary
structure or folding motifs
Domain
Tertiary Structure
Quaternary Structure
Virion Assembly
Protein Denaturation
Aggregation
Precipitation

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Department of Biochemistry University of Karachi

Course NO: Bio-311

Khwaja Ali Hasan

References and Books

(1) Modern Concepts In Biochemistry (R C Bohinski) 5th Edition

• In the human genome, 20 amino acids are created to build

• Besides this, there are approximately 250 amino acids which do

• The 20 proteinogen amino acids are also called standard amino

• Essential, Semi-essential and Non-essential.

• These are: isoleucine, leucine, lysine, methionine,

• Arginine and histidine form the group of so-called semi-

• The ten non-essential amino acids are able to be produced

• Slanine, asparagine, aspartic acid, cysteine, glutamine,

• Phenylalanine, tyrosine, valine, histidine,

Selenocysteine: the 21st amino acid

Enzymes: Glutathione Peroxidases; Glycine Reductases

• In projection formulas: The horizontal bonds

• Ionic (Electrostatic interaction)

• In aqueous solutions, non-polar molecules tend

The solutes that stabilized, proteins and membranes

Kosmotropes stabilize proteins and hydrophobic

Chaotropes unfold proteins, destabilize

Peptide Antibiotics and Immunosuppressant

Scorpion and Snake venom peptides

Cell surface Receptors (Cell signaling and communication)

Antigens and Antibodies

Antiviral and Antibacterials

Primary Structure determines tertiary structure

α-Helix 2) Hydrogen bonds are located in

D-Amino acid L-Amino acid

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