Protein Structure

and Function

Compiled & Edited by

Dr. Syed Ismail
VN Marathwada Agril. University
Parbhani
 DEFINITIONS OF PROTEIN

• Proteins are one of the essential

building blocks of the human body.
• They provide amino acids, which are a nutritional
requirement of the body to produce its own proteins
and a variety of nitrogen-based molecules.
• It is common for programs to recommend a minimum
of 50 grams of protein per day to maintain healthy
levels.
• Proteins vary in structure as well as function. They are
constructed from a set of 20 amino acids and have
distinct three-dimensional shapes.
 General Characteristics of Proteins
• They are the most complex and most diverse in chemical composition,
conferring upon the different tissues.
• Protein molecule contains elements of C, H, O,N, S, and P together with
traces of Fe, Cu, I, Mn, and Zn.
• It has a molecular weight of 5,000 to 3,000,000
• They are the most important of the biologic substances being the
fundamental constituent of cell cytoplasm.
• They supply not only heat and energy but also material for building and
repair.
• Unlike carbohydrates and lipids, only small amounts of protein is
temporarily stored in the body, and which can be quickly used up upon
demand.
FUNCTIONS OF PROTEIN
 FUNCTIONS OF PROTEIN
• Antibodies - are specialized proteins involved in defending the
body from antigens (foreign invaders). One way antibodies destroy
antigens is by immobilizing them so that they can be destroyed by
white blood cells.

• Enzymes - are proteins that facilitate biochemical reactions. They

are often referred to as catalysts because they speed up chemical
reactions. Examples include the enzymes lactase and pepsin.
Lactase breaks down the sugar lactose found in milk. Pepsin is a
digestive enzyme that works in the stomach to break down
proteins in food.

• Hormonal Proteins - are messenger proteins which help to

coordinate certain bodily activities. Examples include insulin,
Insulin regulates glucose metabolism by controlling the blood-
sugar concentration.
 FUNCTIONS OF PROTEIN
• Contractile Proteins - are responsible for movement. Examples include
actin and myosin. These proteins are involved in muscle contraction
and movement.
• Structural Proteins - are fibrous and stringy and provide support.
Examples include keratin, collagen, and elastin. Keratins strengthen
protective coverings such as hair, quills, feathers, horns, and beaks.
Collagens and elastin provide support for connective tissues such as
tendons and ligaments.
• Storage Proteins - store amino acids. Examples include ovalbumin and
casein. Ovalbumin is found in egg whites and casein is a milk-based
protein.
• Transport Proteins - are carrier proteins which move molecules from
one place to another around the body. Examples include hemoglobin
and cytochromes. Hemoglobin transports oxygen through the blood.
Cytochromes operate in the electron transport chain as electron carrier
proteins.
Classification of Proteins
Based on Composition:
• Simple proteins – composed of entirely amino acids
only.
Ex. Albumin, Globulin
• Complex or Conjugated proteins – made up of
amino acids and other organic compounds. The non-
amino acid group is termed as the prosthetic group.
Ex. Nucleoproteins, lipoproteins,
glycoproteins, metalloproteins
 Classification of Proteins
Based on Axial Ratio:
Axial ratio is the ratio of the length to the breath.
• Globular proteins – with axial ratio less than 10 but
not below 3 or 4. They are compactly folded and
coiled.
Ex. Insulin, plasma albumin, globulin,
enzymes
• Fibrous proteins – with axial ratio greater than 10.
They are spiral and helical and are cross linked by
disulfide and hydrogen bonds.
Ex. Keratin, myosin, elastin, collagen
Globular Proteins
• Globular proteins have
their axial ratio less
than 10 but not below 3
or 4. They are
compactly folded and
coiled.
• Examples are insulin,
plasma albumin,
globulin, enzymes
 Fibrous Proteins

• Fibrous proteins are

spiral and helical
and are cross linked
by disulfide and
hydrogen bonds
• Examples are
keratin, myosin,
elastin, collagen
 Based on Biological Functions
• Structural proteins: collagen, elastin, keratin, fibroin of silk
and webs
• Transport proteins: hemoglobin, myoglobin, lipoproteins
• Protective proteins: immunoglobulins, fibrinogen, thrombin,
snake venoms, bacterial toxins
• Contractile proteins: actin, myosin, tubulin
• Catalytic proteins: enzymes
• Regulatory proteins: hormones
• Storage proteins: ferritin, hemosiderin, gluten, casein,
ovalbumin
• Reception of Stimuli: rhodopsin, membrane receptor
proteins, acethylcholine, insulin
• Germicidal proteins: Polymyxin B1, Gramicidin S
 Shape = Amino Acid Sequence
• Proteins are made of 20 amino acids linked
by peptide bonds
• Polypeptide backbone is the repeating
sequence of the N-C-C-N-C-C… in the
peptide bond
• The side chain or R group is not part of the
backbone or the peptide bond
 Proteins
Composed of a chain of amino acids.

20 possible groups

R
|
H2N--C--COOH
|
H
 NH 3  C  COO -  NH 3  C  COO -

 NH 3  C  CO  NH  C  COO -  H2 0
 Different Amino Acid Classes
Alanine O O Cysteine
H2N C H2N C OH
OH
H C H C
C H Generic C H
H H HS H
Non-polar O Polar
Amine Acid
H2N C OH
O C O Histidine
Aspartic ?R
acid H C
H2N C H2N OH
OH
C H C
H
H C H
C
O C H C H
Basic
Acid OH NH
C
C
H+N
 Glycine O Non-Polar MethionineO
H2N C H2N C
C
OH
Amino Acids H C
OH

H H Valine O C H
Leucine O H
H2N C C H
Alanine O OH H2N C OH
H C S H
H2N C H C
OH C H H3C
C C H
H
H3C CH3
H TryptophanO
C H C H
H2N C OH
H H H3C CH3
H C
PhenylalanineO
H
C IsoleucineO C
H2N OH
C H
C H2N OH
H Proline O
H H3C C
C H2N+
H NH C OH
H H C
H2C C
C H
H2C CH2 H
H3C H
Protein Structure
 Polar Amino Acids
Serine O Threonine O Tyrosine O

H2N C H2N C H2N C OH

OH OH
C C H C
H H
H H C H
C H C
HO CH3 C OH H
H H

HO Glutamine O
Cysteine O Asparagine O
H2N C OH
H2N C OH H2N C OH H C
H C C
H C H
H H H
C C
C H
HS H O C H O C H
NH2
NH2
 Acidic Amino Acids

Aspartic O Glutamic O
acid acid
H2N C OH H2N C OH
H C H C
C H C H
H
O C H H
C
OH O C H
OH
 Basic Amino Acids
Histidine O
H2N C OH Lysine O
H C
H H2N C OH
C
H C Arginine O
C H
C H
NH H H2N C
C OH
H C H C
C H
H+N H C H H
H C
C H
H C H
+H N H
3 C H
N H
+H N
2 C H
NH2

Protein Structure
 Levels of Protein Organization
• Primary Structure - The sequence of amino
acids in the polypeptide chain
• Secondary Structure - The formation of 
helices and b pleated sheets due to hydrogen
bonding between the peptide backbone
• Tertiary Structure - Folding of helices and
sheets influenced by R group bonding
• Quaternary Structure - The association of more
than one polypeptide into a protein complex
influenced by R group bonding
 Levels of Protein Organization
Primary Structure

Met-Gly-Ala-Pro-His-Ile-Asp-Glu-Met-Ser-Thr-..

The sequence of amino acids in the primary structure determines the folding
of the molecule.

Protein Structure
 Protein Secondary Structure
• The peptide backbone has areas of positive
charge and negative charge
• These areas can interact with one another to
form hydrogen bonds
• The result of these hydrogen bonds are two
types of structures:
  helices
 b pleated sheets
H Protein Secondary Structure:
N  Helix
C H
C
O N
C H
C
H
O N +
C -
N C
H O H O
C H
O H N C N C OH
C
O N H C H C
C
O C H C H C H
H H HO H
H N
C
N C
C O
O
H Protein Secondary Structure:
N
C
C
H  Helix
O N
C
C
H
H
O
N - +
C C H O H O
N O
C H
H N C N C OH
C
O N H C H C
C
C H C H C H
O H H HO H
H N
C
N C
C O
O
 Protein Secondary Structure:
 Helix
R
R groups stick R
R
R
out from the  R
helix influencing R
R
higher levels of R
R
protein R
R
organization R
R
R
M
L Yeast Cytochrome C Oxidase
S
L
R
Subunit IV Leader
Q Neutral Non-polar
S The order of the amino acids
determines the hydrogen
Polar
I Basic
R bonding Acidic
F
F MLSLRQSIRFFKPATRTLCSSRYLL
K
P
T
A • This would localise specific classes of
R
amino acids in specific parts of the helix
T
L
C
S
S
R
Y
L
P
 Protein Secondary Structure:
b Pleated Sheet
O H O H O H O H
C C C C
C C N C C N C C N C C N
N C N C N C N C
H O H O H O H O

O H O H O H O H
C C N C C N C C N C C N
N C C N C C N C C N C C
H O H O H O H O
 Protein Secondary Structure:
b Pleated Sheet
O H O H O H O H
C C C C
C C N C C N C C N C C N
N C N C N C N C
H O H O H O H O

O H O H O H O H
C C N C C N C C N C C N
N C C N C C N C C N C C
H O H O H O H O

O H O H O H O H
C C C C
C C N C C N C C N C C N
N C N C N C N C
H O H O H O H O
 Levels of Protein Organization
Tertiary Structure
• Tertiary structure results from the folding
of  helices and b pleated sheets
• Factors influencing tertiary structure
include:
• Hydrophobic interactions
• Hydrogen bonding
• Disulphide bridges
• Ionic bonds
Hydrophobic interactions
Valine O
H2N C OH
H C
H Glycine O
C
CH3 H2N C OH
H3C
C
H H

Proline O
H2N+ C OH
H2C C
H2C CH2 H
 Hydrogen Bonding
Asparagine O Glutamine O

H2N C H2N C OH
OH
C H C
H
H C H
C H
O C H C H
NH2 O C H
NH2

N-------H (+) (-) O -------C

slightly slightly
 Disulphide bridges
Cysteine O
Cysteine O
H2N C OH
C H2N C OH
H
H H C
C
HS C H
H
Cysteine O S H
Cysteine O
H2N C OH
C H2N C OH
H
H H C
C
HS C H
H
S H
 Ionic Bonds
Glutamic O
acid
H2N C OH
H C
C H
H Arginine O
C H
H2N C OH
O C H
H C
O- H
H C
H C H
C H
N H
+H N
2 C H
NH2
e.g.G-3-P Dehydrogenase
Tertiary Structure
 Levels of Protein Organization
Quaternary Structure
• Quaternary structure results from the interaction
of independent polypeptide chains
• Factors influencing quaternary structure include:
• Hydrophobic interactions
• Hydrogen bonding
• The shape and charge distribution on amino
acids of associating polypeptides
 G-3-P Dehydrogenase
from Bacillus stearothermophilus
Protein structure
 Globular and Fibrous
• e.g. haemoglobin • e.g. collagen
• 3º structure normally • 2º structure does not
folds up in a ball fold up, form fibres
• hydrophilic R groups • not surrounded by
point outwards hydrophilic R groups
• Hydrophobic R
groups point inwards
• soluble • insoluble
• metabolic functions • structural functions
 Haemoglobin
• Haemoglobin is a globular protein with
a prosthetic ‘iron’ group b 
• In adults, hemoglobin is made up of 4
polypeptides (2  polypeptide chains
and 2 b polypeptide chains) Fe
• Each polypeptide surrounds a
prosthetic ‘haem’ group

• Hydrophobic interactions between side  b

groups pointing inwards maintain the
structure
• Hydrophilic side chains point outwards
making it soluble
Polypeptide
Backbone
 Amino Acids (magic 20)
You need to know these

Hydrophilic Hydrophobic
 Protein Folding
• The peptide bond allows for rotation
around it and therefore the protein can fold
and orient the R groups in favorable
positions
• Weak non-covalent interactions will hold
the protein in its functional shape – these
are weak and will take many to hold the
shape
Non-covalent Bonds in Proteins
 Globular Proteins

• The side chains will help determine the

conformation in an aqueous solution
 Hydrogen Bonds in Proteins

• H-bonds form between 1) atoms involved in the peptide bond;

2) peptide bond atoms and R groups; 3) R groups
 Protein Folding
• Proteins shape is determined by the
sequence of the amino acids
• The final shape is called the conformation
and has the lowest free energy possible
• Denaturation is the process of unfolding
the protein
– Can be done with heat, pH or chemical
compounds
– The chemical compound can be removed and
have the protein renature or refold
 Refolding

• Molecular chaperones are small proteins that help

guide the folding and can help keep the new
protein from associating with the wrong partner
 Protein Folding
• 2 regular folding patterns
have been identified –
formed between the bonds
of the peptide backbone
• -helix – protein turns like a
spiral – fibrous proteins
(hair, nails, horns)
• b-sheet – protein folds back
on itself as in a ribbon –
globular protein
b Sheets
• Core of many proteins is the b
sheet
• Form rigid structures with the H-
bond
• Can be of 2 types
– Anti-parallel – run in an
opposite direction of its
neighbor (A)
– Parallel – run in the same
direction with longer looping
sections between them (B)
 Helix
• Formed by a H-bond between
every 4th peptide bond – C=O to
N-H
• The  helix can either coil to the
right or the left
• Can also coil around each other –
coiled-coil shape – a framework
for structural proteins such as
nails and skin
Protein Structure
 Domains
• A domain is a basic structural unit of a
protein structure – distinct from those that
make up the conformations
• Part of protein that can fold into a stable
structure independently
• Different domains can impart different
functions to proteins
• Proteins can have one to many domains
depending on protein size
Domains
 Useful Proteins

• There are thousands and thousands of different

combinations of amino acids that can make up
proteins and that would increase if each one had
multiple shapes
• Proteins usually have only one useful
conformation because otherwise it would not be
efficient use of the energy available to the system
• Natural selection has eliminated proteins that do
not perform a specific function in the cell
 Protein
Families

• Have similarities in amino acid sequence and 3-D

structure
• Have similar functions such as breakdown
proteins but do it differently
 Proteins – Multiple Peptides
• Non-covalent bonds can form interactions
between individual polypeptide chains
– Binding site – where proteins interact with one
another
– Subunit – each polypeptide chain of large
protein
– Dimer – protein made of 2 subunits
• Can be same subunit or different subunits
Single Subunit Proteins
Different Subunit Proteins

•Hemoglobin
– 2  globin
subunits
– 2 b globin
subunits
Protein Assemblies
• Proteins can form very
large assemblies
• Can form long chains if
the protein has 2 binding
sites – link together as a
helix or a ring
• Actin fibers in muscles
and cytoskeleton – is
made from thousands of
actin molecules as a
helical fiber
 Types of Proteins

• Globular Proteins – most of what we have

dealt with so far
– Compact shape like a ball with irregular
surfaces
– Enzymes are globular
• Fibrous Proteins – usually span a long
distance in the cell
– 3-D structure is usually long and rod shaped
 Important Fibrous Proteins
• Intermediate filaments of the cytoskeleton
– Structural scaffold inside the cell
• Keratin in hair, horns and nails
• Extracellular matrix
– Bind cells together to make tissues
– Secreted from cells and assemble in long fibers
• Collagen – fiber with a glycine every third amino
acid in the protein
• Elastin – unstructured fibers that gives tissue an
elastic characteristic
Collagen and Elastin
 Stabilizing Cross-Links

• Cross linkages can be between 2 parts of a protein or

between 2 subunits
• Disulfide bonds (S-S) form between adjacent -SH
groups on the amino acid cysteine
 Proteins at Work
• The conformation of a protein gives it a unique
function
• To work proteins must interact with other
molecules, usually 1 or a few molecules from the
thousands to 1 protein
• Ligand – the molecule that a protein can bind
• Binding site – part of the protein that interacts
with the ligand
– Consists of a cavity formed by a specific arrangement
of amino acids
Ligand Binding
 Formation of Binding Site

• The binding site forms when amino acids from within

the protein come together in the folding
• The remaining sequences may play a role in regulating
the protein’s activity
 Antibody Family

• A family of proteins that can be created to

bind to almost any molecule
• Antibodies (immunoglobulins) are made in
response to a foreign molecule ie. bacteria,
virus, pollen… called the antigen
• Bind together tightly and therefore
inactivates the antigen or marks it for
destruction
 Antibodies
• Y-shaped molecules with 2 binding sites at
the upper ends of the Y
• The loops of polypeptides on the end of the
binding site are what imparts the
recognition of the antigen
• Changes in the sequence of the loops make
the antibody recognize different antigens -
specificity
Antibodies