PROTEIN

STRUCTURE & FUNCTION

DESAK MADE
WIHANDANI
Proteins play key roles in a
living system
Alcohol
dehydrogen
Three examples of protein ase
functions oxidizes
alcohols to
aldehydes
Catalysis: or ketones
Almost all chemical reactions in a
living cell are catalyzed by
protein enzymes.
Haemoglobin
Transport: carries
Some proteins transports oxygen
various
substances, such as oxygen, ions,
and so on.
Insulin
Information transfer: controls the
amount of
For example, hormones. sugar in the
blood
Functional group of protein
Carrier
Enzymes
Mechanical functions
Energy production
Oxygen carriage
Regulatory signals
Protein synthesis
Protection molecule
Building blocks
Precursors of Neurotransmitters, hormones
Source of energy from the diet and during
fasting
Carrier protein
Function : move mol within and between cells or
between blood stream and the lymphatic system.
Located : in the blood, lymph and cells
Example : albumin (transfer of fatty acid), Hb
(transport oxygen), lipoprotein (cholesterol),
transferin (iron)
The ability of hem to bind oxygen reversibly is the
function of globin protein.
In fact alone hem cannot bind oxygen reversibly
Incidentally CO, NO, H2S are toxic because they
bind to the hem of Hb, myoglobin, and
cytochrome where oxygen normally does.
Enzymes
Is protein specific catalyst/organic catalyst.
Until recently all known enzyme were
protein, but Thomas Chech and Sidney
Altman found that two other type of mol
have enzyme activity r-RNA and RNAse
(ribozymes)
Function: increase rate of chemical reactions,
without themselves being consumed.
Over than 1000 protein enzymes are known
and each are capable of carrying out a
unique chemical transformation
Protection molecule
Function : to protect the body against microbial
invasion or against the toxins of some of these
microorganism which themselves are protein (such
as tetanus, botulinum, and diphteria toxins)
Location : animal fluids (saliva, tears) contain an
enzyme called lysozyme digest the cell walls of
bacteria.
Properdin protein found in serum attaches to
bacterial cell membrane and cause disruption of
killing the bacterial cell
Interferon a group of protein produce by many
cell type of human bodies in responds to viral
infections.
 Interferon, as the name suggest, interfere
with the viral multiplication and also
stimulate cells of the immune system to
respond to the infections.
Antibodies/immunoglobulin : the most
important protection molecules
The receptors on immune system cells
The Interleukins. Both together above, are
designed to inactivate or to destroy
microorganism and to neutralize their
toxins.
The interleukins are chemical messengers
or informational molecule need for
communications between and among the
cells, of the immune system.
Protein Architecture
Proteins are polymers consisting of amino
acids
linked by peptide bonds
each amino acid consists of
a central carbon atom
an amino group
a carboxyl group
a side chain
Differences in side chains distinguish
different
amino acid
 Amino acid: Basic unit of
protein
R Different side
chains, R,
NH3 +
C COO - determin the
properties of 20
Amino group Carboxylic
acid group amino acids.
H
An amino
acid
Peptide Bonds
Amino Acids
Amino acids are building blocks for proteins
They have a central -carbon, -amino and
-carboxyl group
20 different amino acids
Same core structure,but different side group
(R)
AMINO ACIDS
20 amino acids (essential & non ess.)
SMALL A.A: Gly, Ala
AROMATIC: Phe, Tyr, Trp, His
BRANCHED-CHAIN: Val, Ile, Leu
BASIC A.A: Arg, Lys
ACIDIC A.A: Glu, Asp
SULPHUR-CONTAINING: Cys, Met
HYDROXY A.A: Ser, Thr
Amino Acid Side Chains
 20 Amino acids

Glycine Alanine (A) Valine Isoleucine (I) Leucine (L)

(G) (V)

Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine

(N)

Glutamine (Q) Serine Threonine (T) Tyrosine (Y) Cysteine (C)

(S)

Asparatic acid (D)Glutamic acid (E) Lysine (K) Arginine (R) Histidine (H)

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

Proteins are linear polymers
of amino acids
R1 R2

NH3 C COO
NH3 C COO

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

H Peptide H Peptide H
bond bond
The amino acid
sequence is
F T D
A G N S K A called as primary
G S
structure
Each Protein has a unique
structure
Amino acid
sequence
NLKTEWPELVGKSV
EEAKKVILQDKPEAQ
IIVLPVGTIVTMEYRI
DRVRLFVDKLDNIAE
VPRVG
Folding!
Hierarchical nature of
protein structure
Primary structure (Amino acid sequence)

Secondary structure -helix, -sheet

Tertiary structure Three-dimensional
structure formed by assembly of secondary
structures

Quaternary structure Structure formed by
more than one polypeptide chains
Levels of Description
Basic structural units of
proteins: Secondary structure
-helix -sheet

Secondary structures, -helix and

-sheet, have regular hydrogen-
bonding patterns.
Three-dimensional
structure of proteins

Tertiary
structure
Quaternary structure
Levels of Description
Amino acid sequence is
encoded by DNA base
sequence in a gene
DNA DNA base
sequence
molecule G C
C G
G C
C G
T A
T
A
A
A
T
T
G C
C G
G C
C G

Gene is proteins blueprint,
genome is lifes blueprint
DNA Genome

Gene Gene Gene Gene Gene

Gene Gene Gene
Gene Gene Gene
Gene Gene Gene
Protein Gene

Protein
Protein Protein
Protein
Protein Protein Protein
Protein Protein
Protein
Protein Protein
Protein Protein
Gene is proteins blueprint,
genome is lifes blueprint
Glycolysis network Genome

Gene Gene Gene Gene

Gene Gene Gene
Gene Gene Gene
Gene Gene Gene
Gene

Protein
Protein Protein
Protein
Protein Protein Protein
Protein Protein
Protein
Protein Protein
Protein Protein
 In 2003, Human genome
sequence was deciphered!
Genome is the complete set of genes of a living thing.
In 2003, the human genome sequencing was completed.
The human genome contains about 3 billion base pairs.
The number of genes is estimated to be between 20,000
to 25,000.
The difference between the genome of human and that
of chimpanzee is only 1.23%!

3 billion base pair => 6 G letters

&
1 letter => 1 byte
The whole genome can be
recorded in just 10 CD-ROMs!
DNA
Gene Expression
Gene structure and its biological
activity

Gene encode the information

that determine the structure of
protein.
In turn the protein structure
determine its biological
activity.
Through the biological activity of
protein the cells physiological
role is determined.
Genotype and phenotype
Any changes in DNA, such as mutation,
affect the cells through changes in
protein structure
Ultimately the cell will be affected
because altered the protein structure
and than alters protein biological activity.
So the cells genotype it is store of
information determines the cells
phenotype--- the expression of the
genotype via proteins
 Close relationship between
protein structure and its
function
Example of enzyme Hormone receptor Antibody
reaction
substrate
s
A
enzym enzym
e e

Matching
Digestion
the shape
of A!
to A enzym
e
A

Binding to A
 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.