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Proteins
• The word protein is derived from the Greek word
“proteios”. Which means primary or of prime
importance.
• Proteins are composed of long chains of amino acids
joined together via peptide bonds.
• A polypeptide with more than 100 amino acid residues,
having molecular mass more than 10,000u is called a
protein.
Amino Acids
Amino acids are derivatives of carboxylic acids
formed by substitution of -hydrogen for amino
functional group.
R
NH2
C COOH
H
•AA are optically active molecules due to the presence of a chiral
carbon (except in the case of glycine where the R-group is
hydrogen)
According new IUPAC nomenclature L- D- forms were
replaced for (S)- and (R)- system
Proteins play key roles in a
living system

Three examples of protein functions
– Catalysis:
Almost all chemical reactions in a living
cell are catalyzed by protein enzymes.
– Transport:
Some proteins transports various
substances, such as oxygen, ions, and so
on.
– Information transfer:
For example, hormones.
– Structural proteins: proteins with the
primary purpose of producing the
essential structural components of the
cell.
Alcohol
dehydrogenase
oxidizes alcohols
to aldehydes or
ketones
Haemoglobin
carries oxygen
Insulin controls
the amount of
sugar in the
blood
Amino acid: Basic unit of protein
R
NH2
C COOH
H
Different side chains, R, determin the properties
of 20 amino acids.
Zwitter Ion
A zwitter ion is a chemical compound that carries a
total net charge of 0 and is thus electrically neutral, but
carries formal charges on different atoms.
20 Amino acids
Glycine (G)
Alanine (A)
Valine (V)
Isoleucine (I)
Leucine (L)
Proline (P)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
Asparagine (N)
Glutamine (Q)
Serine (S)
Threonine (T)
Tyrosine (Y)
Cysteine (C)
Lysine (K)
Arginine (R)
Histidine (H)
Asparatic acid (D) Glutamic acid (E)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic
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
group with the release of a
water
H 2O
R1
R2
R3
NH3＋ C CO NH C CO NH C CO
H
A
F
Peptide
bond
G
N
S
Peptide
bond
H
T
D
K
G
H
S
A
The amino acid
sequence is called as
primary structure
Classification of Proteins
Globular Proteins
Proteins that consist of long chains of amino acids folded
up into complex shapes. Globular proteins serve as, or
form important components of, the following:
•
•
•
•
Enzymes
Hormones
Antibodies
Some structural proteins.
Structure of Insulin
Fibrous Proteins
Proteins that tend to be insoluble and strong and so play a
structural role in organisms for support or protection. They can be
subdivided into several different types:
•keratins, found in hair, fingernails, and bird feathers
•collagens – the most abundant proteins in a vertebrate body –
found in connective tissues such as cartilage
•elastins, found in ligaments, around blood vessels.
Structure of Keratin
DIFFERENCES BETWEEN GLOBULAR AND
FIBROUS PROTEINS
Globular
1. They are more or less spherical in
shape.
2. Globular proteins are usually
soluble in water.
Eg: insulin, albumins, etc.
Fibrous
1. They have polypeptide chains
which lie side by side, held
together by H-bonds and have
thread like structure.
2. Fibrous proteins are insoluble in
water.
Eg: keratin, myosin, etc.
Structure of Proteins
Each Protein has a unique
structure
Amino acid sequence
NLKTEWPELVGKSVEE
AKKVILQDKPEAQIIVL
PVGTIVTMEYRIDRVR
LFVDKLDNIAEVPRVG
Folding!
Basic Structural Units of Proteins
Primary Structure
The sequence in which the amino acids are
arranged in a polypeptide chain of a protein is
called the primary structure of the protein.
Secondary structure
There are two types of structural proteins:
• α-helix
The peptide chain coils and the turns of the coil are held
together by hydrogen bonds.
• β-pleated sheet
Here the protein chains are not coiled but are stretched out.
α-helix
β-sheet
Secondary structures, α-helix
and β-sheet, have regular
hydrogen-bonding patterns.
Tertiary Structure
Arises due to folding and coiling of secondary
proteins.
Quaternary Structure
Composed of two or more polypeptide chains.
Three-dimensional structure of
proteins
Tertiary
structure
Quaternary structure
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）
Close relationship between
protein structure and its function
Example of enzyme reaction
substrates
enzyme
A
enzyme
B
Matching
the shape
to A
enzyme
A
Binding to A
Digestion
of A!
Hormone receptor
Antibody
Protein structure prediction has
remained elusive over half a century
“Can we predict a protein structure
from its amino acid sequence?”
Now, impossible!
Native State
At normal pH and temperature, each protein
will take up a shape which is energetically most
stable. This shape is called the native state of a
protein.
Protein denaturation
 Denatured
state = unfolded state
 Native state = folded state
 Denaturation = heat, urea, salts
Summary





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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.
Thank You For Your
Attention