Metabolism of Biomolecules

(SBT104 Unit 1)

Prepared and presented

by

Dr. Amee K Nair

Institute of Science,
Nirma University, Ahmedabad
 Proteins are linear polymers of amino acids

R1 R2
NH3 ＋ C COO ＋ NH3 ＋ C COO ＋
ー ー
H H A carboxylic acid
H 2O condenses with an amino
H2 O
group with the release of a
R1 R2 R3 water

NH3 ＋ C CO NH C CO NH C CO
H Peptide H Peptide H
bond bond
The amino acid
F T D sequence is called as
A G N S K A
G S primary structure
 Protein

Protein from the Greek proteios, meaning primary.

What is their role?
They play key roles in metabolic pathways,
constructing and maintaining living cells.
Where do they come from ?
Our genes code for proteins.
What are they formed off ?
They are polymers of amino acids.
Polypeptides are covalently linked α-amino acids

Cofactors are non-amino acid components

e.g. metal ions like Zn 2+ in carboxypeptidase

Coenzymes are organic cofactors

e.g. nucleotides in lactate dehydrogenase

Prosthetic groups are covalently attached cofactors

e.g. heme in myoglobin
 Roles played by proteins

Enzymes (biological catalysts)

Alcohol dehydrogenase oxidizes alcohols

to aldehydes or ketones

Transport proteins
Haemoglobin carries oxygen
Hormones (information transfer)

Alcohol dehydrogenase oxidizes alcohols

to aldehydes or ketones

Building Blocks
cell shape and support.
eg. Tubulin, Actin, Collagen
 Four Levels of Protein Structure

• Primary structure -The particular sequence of amino acids that

is the backbone of a peptide chain or protein - amino acid linear
sequence
• Secondary structure - regions of regularly repeating
conformations of the peptide chain,
α-helices and β-sheets
• Tertiary structure - describes the shape of the fully folded
polypeptide chain
• Quaternary structure - arrangement of two or more
polypeptide chains into multisubunit molecule
 Hierarchical nature of protein structure

Primary structure (Amino acid sequence)

↓
Secondary structure （ α-helix, β-sheet ）
↓
Tertiary structure （ Three-dimensional structure
formed by assembly of secondary structures ）
↓
Quaternary structure （ Structure formed by
more than one polypeptide chains ）
- Helix
 Stereo view of right-handed  helix

All side chains project outward from helix axis

Prentice Hall c2002

-Sheets (a) parallel, (b) antiparallel

Prentice Hall c2002

 Globular proteins

• Usually water soluble, compact, roughly spherical

• Hydrophobic interior, hydrophilic surface
• Globular proteins include enzymes,carrier and regulatory
proteins

Fibrous proteins
• Provide mechanical support
• α-Keratins: major components of hair and nails
• Collagen: major component of tendons, skin, bones and
teeth
 Tertiary Structure
• Specific overall shape of a protein
• Examples of cross links between R groups of
amino acids in chain
disulfide –S–S– +
ionic –COO– H3N–
H bonds C=O HO–
hydrophobic –CH3 H3C–
 Quaternary Structure

Proteins with two or more chains

Example is hemoglobin
Carries oxygen in blood
Four polypeptide chains
Each chain has a heme group to
bind oxygen
 Protein Structure

Prentice Hall c2002

Hemoglobin – Primary Structure

NH2-Val-His-Leu-Thr-Pro-Glu-Glu-
Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-
Gly-Lys-Val-Asn-Val-Asp-Glu-Val-
Gly-Gly-Glu-…..
beta subunit amino acid sequence
Hemoglobin – Secondary Structure

alpha helix
Hemoglobin – Quaternary Structure

Two alpha subunits and two beta subunits

(141 AA per alpha, 146 AA per beta)
 Protein Hydrolysis

• Break down of peptide bonds

• Requires acid or base
• Gives smaller peptides and amino acids
• Similar to digestion of proteins using
enzymes
• Occurs in cells to provide amino acids to
synthesize other proteins and tissues
 Denaturation

Disruption of secondary, tertiary and quaternary

protein structure by:
1. Heat/organics
2. Acids/ bases
3. Heavy metal ions
4. Agitation
Basically the protein is unfolded without changing the
primary structure resulting in the protein changing its’
physical properties.
 Frying or boiling an egg
 Ironing or curling your hair
 Alcohol on cuts to denature proteins in
bacteria
 Cooking food to denature proteins in
bacteria
 SUMMARY

• Proteins are building blocks in our living systems.

• Proteins are polymers consisting of 20 kinds of
amino acids.
• Each protein folds into a unique three-dimensional
structure defined by its amino acid sequence.
• Protein structure has a hierarchical nature.
• Protein structure is closely related to its function.