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s.
Function of proteins.
Proteins are very important in living organisms and take
on a variety of forms and functions:
Enzymes.
Antibodies.
Actin and myosin
Collagen.
Keratin
antigens
Amino acids.
Amino acids contain an amino group
(-NH) and a
carboxylic acid group
(-COOH).
Each amino acid has an R group.
There are 20 different R groups and this is the reason
for there being 20 different types of amino acids.
Amino
group
Carboxylic acid
group
F
I U
R
S C
T
Haveamine
groups
*Listedas
nonpolarby
sometexts
B A
A
S G
E
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG
SECONDBASE
Phe
Leu
Leu
AUU
AUC Ile
AUA
AUGMet/start
GUU
GUC
GUA
GUG
Val
UCU
UCC
UCA
UCG
CCU
CCC
CCA
CCG
ACU
ACC
ACA
ACG
GCU
GCC
GCA
GCG
Ser
UAU
UAC
UAA
UAG
Tyr
Pro
CAU
CAC
CAA
CAG
His
Thr
AAU
AAC
AAA
AAG
Asn
Ala
GAU
GAC
GAA
GAG
Stop
Gln
Lys
Asp
Glu
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG
Cys
Stop
Trp
Arg
Ser
Arg
Gly*
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
T
H
I
R
D
B
A
S
E
Different
Amino
Acid
Classes
O Cysteine
O
Alanine
H2 N
C
C
H
C OH
Nonpolar
H2 N
Generic
O
Amine
H2 N
O
Aspartic
acid
H2 N
C
H
C
Acid OH
C
HS
Polar
Acid
C OH
O Histidine
H2 N
C
C
O
C OH
?R
C OH
Basic
C
H+N
H
NH
C
C OH
H
Glycine O
C
Valine O
C OH
H2 N
C
C
H
H
C
CH3
H3C
H2N
C
C OH
H
C
H
CH3
Isoleucine O
H2 N
C
H3 C
C
H3C
C OH
C OH
H
C OH
H
C
H3 C
H
PhenylalanineO
C
C
H2 N
H
H2 N
Leucine O
C OH
H2 N
Alanine O
H
Non-Polar
Amino Acids
C OH
H2 N
MethionineO
C
H
H 3C
Tryptophan O
H 2N
C
C OH
H
C
H
Proline O
+
NH H2N
C OH
H2 C
C
H2 C
CH2 H
C OH
H2N
H
H2 N
C
H2 N
C
HS
Asparagine O
C OH
H
NH2
Glutamine O
HO
H 2N
C OH
C
O
H
NH2
C OH
H
C
O
H
Cysteine O
OH
C OH
H 2N
C OH
H
CH3
HO
Tyrosine O
Threonine O
Aspartic O
acid
C OH
H2N
C
H
H
C
C
H
OH
Glutamic O
acid
C OH
H 2N
C
H
H
C
H
C
O
H
OH
H2 N
C
C
H+N
H2 N
C
C
Lysine O
C
H
NH
C
H3 N
C
H
N
+
H2 N
C
NH2
C OH
H
H 2N
Arginine O
C OH
MetGlyAlaProHisIleAspGluMetSerThr...
A peptide
bond is
formed and
this results in
a dipeptide
What is a polypeptide?
A chain of amino acids is known as a polypeptide.
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
PRIMARY STRUCTURE
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
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)
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 a-helical and b-sheet
conformations.
Yellow areas : outer limit
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.
H bonding
2 types
Anti -Parallel
Parallel
N
SECONDARY STRUCTURE
EXAMPLES
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
beta-alpha-beta motif
-meander motif
Beta barrel
TERTIARY STRUCTURE
Tertiary structure is the threedimensional 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.
DOMAINS
Polypeptide chains containing more than ,200 residues usually
fold into two or more globular clusters known as domains.
Fundamental functional and 3 dimensional structure of
proteins.
Domains often have a specific function such as the binding of a
small molecule.
Many domains are structurally independent units that have the
characteristics of small globular proteins.
TERTIARY STRUCTURE
DETERMINATION OF TERTIARY
STRUCTURE
QUATERNARY STRUCTURE
The biological function of some
molecules is determined by multiple
polypeptide chains multimeric pro
teins.
Arrangement of polypeptide sub unit
is called quaternary structure.
Quaternary structure of hemoglobin.
Sub units are held together by non
covalent interactions.
Eg: Hemoglobin has the subunit
composition a2b2
Haem
group
Haemoglobin is
made up of 4
different
polypeptide
chains.
Haemoglobin molecule
Keratin is a secondary
structure protein. it has
a spiral shape and is
held in position by
hydrogen bonds.
Globular proteins.
Globular proteins have the following characteristics:
Irregular amino acid sequence
Sequence is highly specific and never varies between 2
examples of the same protein.
Polypeptides fold into a spherical shape.
Relatively unstable structure.
Metabolic functions.
Egs enzymes, hormones and haemoglobin.
Enzymes.
Denaturation of proteins.
The three dimensional shape of proteins is maintained by hydrogen
bonds and ionic bonds which are fairly weak.
Any agent such as heat, acids or alkalis will break these bonds and
cause a change in shape.
With a change in shape the protein can no longer carry out its
function.
Change in the tertiary/quartenary structure breakins of bonds
Denaturated proteins cannot play their role in cells
Denaturation is often irreversible (eg. fried egg yolk cannot be
unfried)
Denaturating agents include acids, bases, detergents, heavy metals
Protein denaturation