1.

0 Proteins
Dr. Kinjalka Ghosh
MBBS, MD Biochemistry.
Assistant Professor, Dept. of Biochemistry,
Seth G.S.M.C & KEM Hospital, Mumbai

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What are proteins?

A group of nitrogenous compounds of high molecular
weight that are essential constituents of all living
organisms. They consist of one or more chains of amino
acids linked by peptide bonds and are folded into a
specific three-dimensional shape maintained by further
chemical bonding

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Origin of the word:

The word protein that I propose to you . . . I would wish to
derive from proteios, because it appears to be the
primitive or principal substance of animal nutrition that
plants prepare for the herbivores, and which the latter
then furnish to the carnivores.
J. J. Berzelius, letter to G. J. Mulder, 1838
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Function of proteins.
Proteins are very important in living organisms and take
on a variety of forms and functions:

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Enzymes.
Antibodies.
Actin and myosin
Collagen.
Keratin
Antigens
Nuceloproteins
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The structure & composition of

proteins.
Proteins are made up of carbon, hydrogen, oxygen and
nitrogen. Sometimes sulphur is present.
Proteins are polymers made up of the monomers called
amino acids.
There are 20 different amino acids.
Amino acids can join up in any order and form an
infinite number of protein molecules.

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Protein structure can be described at

four levels.
Primary structure: Amino acid sequence.
Secondary structure: Conformation
adopted by local regions of the polypeptide
chain.

Tertiary structure: Overall folding of the

polypeptide chain.

Quaternary structure: Specific

association of multiple polypeptide chains to
form multisubunit complexes.
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Different Levels of Protein Structure

NH2
Lysine
Histidine
Valine
Arginine
Alanine
COOH

Primary

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Seconda
ry

Tertia
ry

Quaternary

Amino Acids
Amino Acids Share Common Structural Features
All 20 of the common amino acids are -amino acids.
They have a carboxyl group and an amino group
bonded to the same carbon atom (the - carbon)
They differ from each other in their side chains, or R
groups, which vary in
1.
2.
3.
4.
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Structure,
Size,
electric charge, and
Solubility of the amino acids in water.
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General structure of an amino

acid.
This structure is common to all but one of the -amino
acids. (Proline, a cyclic amino acid, is the exception.)
The R group or side chain attached to the carbon is
different in each amino acid.
R
Group

Amino
group

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Carboxylic
acid group

How do two amino acids join together ?

Two amino acids join together by condensation to form
a dipeptide .

A peptide bond
is formed and
this results in a
dipeptide

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What is a polypeptide?
A chain of amino acids is known as a polypeptide.

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Formation of a Polypeptide:

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Primary Structure
The Peptide Bond Is Rigid and Planar
Protein ArchitecturePrimary Structure Covalent
bonds also place important constraints on the
conformation of a polypeptide.
In the late 1930s, Linus Pauling and Robert Corey
embarked on a series of studies that laid the foundation
for our present understanding of protein structure.
The carbons of adjacent amino acid residues are
separated by three covalent bonds, arranged as C-C-NC.
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Primary Structure
This indicated a resonance or partial sharing of two pairs of
electrons between the carbonyl oxygen and the amide nitrogen.
The oxygen has a partial negative charge and the nitrogen a
partial positive charge, setting up a small electric dipole. The six
atoms of the peptide group lie in a single plane, with the
oxygen atom of the carbonyl group and the hydrogen atom of
the amide nitrogen trans to each other.

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 From these findings Pauling and Corey concluded that the peptide C-N
bonds are unable to rotate freely because of their partial double-bond
character.
Rotation is permitted about the N-C and the C-C bonds. The backbone
of a polypeptide chain can thus be pictured as a series of rigid planes with
consecutive planes sharing a common point of rotation at C
The rigid peptide bonds limit the range of conformations that can be
assumed by a polypeptide chain.
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PRIMARY STRUCTURE

The primary structure of protein refers to the sequence of amino acids present in the
polypeptide chain.
Amino acids are covalently linked by peptide bonds.
Each component amino acid in a polypeptide is called a residue or moiety
By convention, the 10 structure of a protein starts from the amino-terminal (N) end and ends
in the carboxyl-terminal (C) end.

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IMPORTANCE OF PRIMARY STRUCTURE

To predict 20 and 30 structures from sequence homologies with related proteins. (Structure
prediction)
Many genetic diseases result from abnormal amino acid sequences.
To understand the molecular mechanism of action of proteins.
To trace evolutionary paths.

METHODS OF AMINO ACID SEQUENCE DETERMINATION

End group analysis Edman degradation.
Gene sequencing method.

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SECONDARY STRUCTURE
Localized arrangement of adjacent amino acids formed as the polypeptide chain folds.

It consists of

-helix
-pleated sheet
-bends
Non repetitive structures
Super secondary structures

Linus Pauling proposed some essential features of peptide units and polypeptide backbone. They
are:
The amide group is rigid and planar as a result of resonance. So rotation about C-N bond is not feasible.
Rotation can take place only about N- C and C C bonds.
Trans configuration is more stable than cis for R grps at C

From these conclusions Pauling postulated 2 ordered structures helix and sheet
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POLYPEPTIDE
CHAIN CONFORMATIONS
The only reasonably free movements are rotations
around the C-N bond (measured as ) and the
C-C bond (measured as ).
The conformation of the backbone can therefore be
described by the torsion angles (also called
dihedral angles or rotation angles)

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Animation showing Phi angle rotation at Psi = 0.

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Animations showing Psi angle rotation at Phi = 0.

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ALPHA HELIX
Spiral structure
Tightly packed, coiled polypeptide backbone
core.
Side chain extend outwards
Stabilized by H bonding b/w carbonyl oxygen
and amide hydrogen.
Amino acids per turn 3.6
Pitch is 5.4 A
Alpha helical segments are found in many
globular proteins like myoglobins, troponin- C
etc.

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H bonding

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BETA PLEATED SHEET

Formed when 2 or more polypeptides line up side by
side.
Individual polypeptide - strand

Each strand is fully extended.

They are stabilized by H bond b/w N-H and carbonyl

grps of adjacent chains.

2 types
Anti -Parallel

Parallel
N

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SECONDARY STRUCTURE

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EXAMPLES

The collagen triple helix.

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Silk fibroin beta sheet.

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BETA BENDS
Permits the change of direction of the peptide chain to
get a folded structure.
It gives a protein globularity rather than linearity.
H bond stabilizes the beta bend structure.
Proline and Glycine are frequently found in beta turns.
Beta turns often promote the formation of antiparallel
beta sheets.
Occur at protein surfaces.
Involve four successive aminoacid residues

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NON REPETITIVE STRUCTURES

A significant portion of globular proteins
structure may be irregular or unique.
They include coils and loops.
Segments of polypeptide chains whose
successive residues do not have similar and
values are called coils.
Almost all proteins with more than 60 residues
contain one or more loops of 6 to 16 residues,
called loops.
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Space-filling model of an loop

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RAMACHANDRAN PLOT
A Ramachandran plot (also known as a Ramachandran diagram or a [,] plot),
originally developed in 1963 by G. N. Ramachandran.

White regions : Sterically disallowed for all

amino acids except glycine.
Red regions : allowed regions namely the ahelical and b-sheet conformations.
Yellow areas : outer limit
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Secondary Structure
Table 10

Phi & Psi angles for Regular Secondary

Structure Conformations
Structure
Antiparallel -sheet
Parallel -Sheet
Right-handed -helix
310 helix
helix
Polyproline I
Polyproline II
Polyglycine II

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Phi ( )
-139
-119
+64
-49
-57
-83
-78
-80

Psi( )
+135
+113
+40
-26
-70
+158
+149
+150

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SUPER SECONDARY STRUCTURES (MOTIFS)

Certain combinations of secondary structural elements are called motifs.

beta-alpha-beta motif

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-meander motif

Greek key motif

Beta barrel

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TERTIARY STRUCTURE
Tertiary structure is the three-dimensional
conformation of a polypeptide.
The common features of protein tertiary structure
reveal much about the biological functions of the
proteins and their evolutionary origins.
The function of a protein depends on its tertiary
structure. If this is disrupted, it loses its activity.

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TERTIARY STRUCTURE

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DETERMINATION OF TERTIARY STRUCTURE

The known protein structures have come to light through:
X-ray crystallographic studies

Nuclear Magnetic Resonance studies

The atomic coordinates of most of these structures are deposited in a database known
as the Protein Data Bank (PDB).
It allows the tertiary structures of a variety of proteins to be analyzed and compared.

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Every protein has a three-dimensional

structure that reflects its function.
Protein structure is stabilized by multiple weak interactions.
Hydrophobic interactions are the major contributors to stabilizing the globular form of

most soluble proteins.

Hydrogen bonds and ionic interactions are optimized in the specific structures that are

thermodynamically most stable.

The nature of the covalent bonds in the polypeptide backbone places

constraints on structure.
The peptide bond has a partial double-bond character that keeps the entire six-atom

peptide group in a rigid planar configuration.

The N-C and C -C bonds can rotate to assume bond angles of and , respectively.
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TIM Barrel (Triosephosphate

IsoMerase)
The eight-stranded / barrel (TIM barrel)
The most common tertiary fold observed in high
resolution protein crystal structures
10% of all known enzymes have this domain

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Summary:
Proteins Are Built from a Repertoire of 20 Amino Acids.
Proteins are linear polymers of amino acids. Each amino acid consists of a central
tetrahedral carbon atom linked to an amino group, a carboxylic acid group, a
distinctive side chain, and a hydrogen atom.
These tetrahedral centers, with the exception of that of glycine, are chiral; only the
L- isomer exists in natural proteins.
All natural proteins are constructed from the same set of 20 amino acids. The side
chains of these 20 building blocks vary tremendously in size, shape, and the
presence of functional groups.
They can be grouped as follows:
(1) Hydrophobic side chains, including the aliphatic amino acidsglycine, alanine,
valine, leucine, isoleucine, and aromatic side chainsphenylalanine, and tryptophan;
(2) polar side chains, including OH-containing side chainsserine, threonine and
tyrosine; the SH-containing cysteine; and carboxamide-containing side chains
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asparagine and glutamine;

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Summary:

Primary Structure:

Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains.

The amino acids in a polypeptide are linked by amide bonds formed between the carboxyl
group of one amino acid and the amino group of the next.
This linkage is called a peptide bond, has several important properties.
First, it is resistant to hydrolysis, and so proteins are remarkably stable kinetically.
Second, the peptide group is planar because the C-N bond has considerable double-bond character.
Third, each peptide bond has both a hydrogen-bond donor (the NH group) and a hydrogen-bond
acceptor (the CO group).
Hydrogen bonding between these backbone groups is a distinctive feature of protein structure.

Finally, the peptide bond is uncharged, which allows proteins to form tightly packed globular
structures having significant amounts of the backbone buried within the protein interior.
Because they are linear polymers, proteins can be described as sequences of amino acids.
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Such sequences are written from the amino to the carboxyl terminus.

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Summary:

Secondary Structure:

Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the
Beta Sheet, and Turns and Loops Two major elements of secondary structure are
the a helix and the b strand.
In the a helix, the polypeptide chain twists into a tightly packed rod.
Within the helix, the CO group of each amino acid is hydrogen bonded to the NH
group of the amino acid four residues farther along the polypeptide chain.
In the b strand, the polypeptide chain is nearly fully extended. Two or more b
strands connected by NH-to-CO hydrogen bonds come together to form b sheets.
The strands in b sheets can be antiparallel, parallel, or mixed.
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Summary:

Tertiary Structure:

Water-Soluble Proteins Fold into Compact Structures with Nonpolar

Cores
The compact, asymmetric structure that individual polypeptides
attain is called tertiary structure.
The tertiary structures of water-soluble proteins have features in
common:
(1) an interior formed of amino acids with hydrophobic side chains and
(2) a surface formed largely of hydrophilic amino acids that interact with the
aqueous environment.
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Summary:
Some proteins that exist in a hydrophobic environment,
such as in membranes, display the inverse distribution
of hydrophobic and hydrophilic amino acids.
In these proteins, the hydrophobic amino acids are on
the surface to interact with the environment, whereas
the hydrophilic groups are shielded from the
environment in the interior of the protein
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Thank You!
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