Structural Organisation

of Proteins

Dr. Mohammad Akram

Metabolic Laboratory

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Objectives

Purpose of the lecture

 This session will describe what are
proteins.
 Behavior of proteins in living organisms.
 Classification of protein functions.
 At the conclusion of this session, you
should understand the proteins and its
classification.

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History of protein
study
 The word PROTEIN comes from Greek
language (prota) which means "of
primary importance". This name was
introduced by Jons Jakob Berzelius in
1838 for large organic compounds with
almost equivalent empirical formulas.
This name was used because the studied
organic compounds were primitive but
seems to be very important for nutrition.

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Protein in living
organisms

Proteins are responsible for many

different functions in the living cell. It
is possible to classify proteins on the
basis of their functions. Very often,
proteins can carry few functions and
such proteins can be placed into
different groups, but despite this, it is
possible to assign main group for
each protein.

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Protein Architecture

1. proteins are polymers consisting of amino

acids linked by peptide bonds
2. each amino acid consists of
a central carbon atom
an amino group NH2
a carboxylic group COOH
a side chain
Difference in side chains distinguish
different amino acids

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Amino acid: Basic unit
of protein
Different side chains, R, determine
the properties of 20 amino acids.

R
NH3+ C COO-
H
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Peptide Bonds
Amino Side Carboxyl group
group Chain

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Each amino acid has
specific properties

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The Protein Folding

The function of a protein is determined

by its 3D shape (fold, conformation)

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Type of structures

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Type of Structure

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 Structural Levels of Proteins

Primary – linear sequence of amino acids

composing the polypeptide chain (strand of amino
acid “beads”)

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Structural Levels of
Proteins
Secondary – alpha helix or beta
pleated sheets

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Both stabilized by Hydrogen bonds

α-helix
A common feature in the
secondary structure of proteins, the
alpha helix (α-helix) is a right- or
left-handed coiled conformation,
resembling a spring, in which every
backbone N-H group donates a
hydrogen bond to the backbone C=O
group of the amino acid four residues
earlier ( hydrogen bonding).

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Beta helix

A beta helix is a protein

structure formed by the
association of parallel
beta strands in a helical pattern
with either two or three faces.

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Two-stranded helices

The simplest beta helix contains

two "layers" of beta sheets
connected by glycine-rich six-
residue loops that contain an
aspartate to bind one calcium ion
per loop.

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Structural Levels of
Proteins
Tertiary – superimposed folding of secondary
Structures producing a ball-like or globular
molecule

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Structural Levels of
Proteins
Quaternary – polypeptide chains
linked together in a specific
manner

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Protein Denaturation
 The activity of a protein depends on its three-
dimensional structure.

 Intramolecular bonds, especially hydrogen

bonds, maintain the structure.

 Hydrogen bonds may break when the pH

drops or the temperature rises above normal

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Denaturisation process
When protein unfolds and loses its three
dimensional shape

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Protein Functions
1) Enzymatic catalysis. (e.g., enzymes)
2) Transport and storage. (e.g., Hemoglobin & Myoglobin)
3) Muscle motion.
4) Mechanical support .
5) Immune protection (e.g., Antibodies)
6) Generation and transmission of nerve impulses a
photoreceptor protein in retinal rod cell, which can be
triggered by acetylcholine, is responsible for transmitting
nerve impulses at synapses (i.e., at junctions between
nerve cells)
7) Control of growth and differentiation (e.g., Nerve growth
factor)

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Summary
 Proteins are key players 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.
 Protein structure prediction is a grand challenge of
computational biology.

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THANK YOU

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