Introduction Basic structure of protein Types- - primary structure - secondary structure - tertiary structure - quaternary structure

1. STRUCTURE OF PROTEINS
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. SYNOPSIS
Secondary structure of protein
 Introduction
 Basic structure of protein
Types- - primary structure
- secondary structure
- tertiary structure
- quaternary structure
Conclusion
References

3. INTRODUCTION
DEFINITION- Proteins are polymers of
amino acids with each amino acid residue
joined to it’s neighbor by a specific type of
covalent bond.
 Proteins are most abundant macromolecules
found in all cells.
 Proteins are formed on ribosomes as linear
polymers of amino acids.
 Protein play a crucial role in virtually all
biological process.

4. BASIC STRUCTURE OF
PROTEIN
Proteins are built from repertoire of 20
amino acids.
 Amino acids are the basic structural unit of
protein.
 An α- amino acid consists of an amino group,
a carboxyl group, a hydrogen atom & a
distinctive R group bonded to a carbon atom.

5.  In proteins, the α-carboxyl group of one amino
acid is joined to the α-amino group of another
amino acid by a peptide bond (amide bond). In
peptide bond formation loss of water molecule
takes place.

6.  The tetrahedral array of 4 different groups
about α-carbon confers optical activity on
amino acid. The 2 mirror images forms are L-
isomer & D-isomer.

7. Types of protein structure
1) Primary structure –
 It refers to the covalent structure, which
includes amino acid sequence and
location of disulfide bond.
 The main mode of linkage in primary
structure is peptide bond.
 Linus Pauling & Robert Corey in late
1930s demonstrated that α-carbon of
adjacent amino acid are separated by 3
covalent bond.

8. Cα—C—N—Cα
 They indicate the presence of resonance/partial
sharing of 2 pairs of electrons between
carbonyl oxygen & amide nitrogen.
 The 4 atoms of peptide bond lies in a single
plane in such a way that oxygen of carbonyl
group & hydrogen of amide group lie trans to
each other.

9.  Thus the peptide C—N bonds are unable to
rotate freely because of their partial double
bond character.
 Limited rotation is permitted about N—Cα
& Cα—C bonds.
The bond angles resulting from rotation are
labeled phi(Φ) for N—Cα & psi(Ψ) for
Cα—C bond.

11. 2)Secondary structure- it refers to local
folding of polypeptide backbone into helical,
pleated sheet or random conformations.
3) Tertiary structure- it includes the
conformational relationship in space of side
chain & geometric relation between distant
regions of polypeptide.
4) Quaternary structure- the structure
formed by several polypeptide subunits
(protein molecules) into a multisubunit protein
/single protein complex.

13. Stereochemistry of peptide chains
 All proteins are made up of AA of L-
configuration. This fixes the steric
arrangement at α- C atom.
 The peptide bond which is an imide
(substituted amide) bond has a planar structure
 The 6 atoms within the plane are related to
each other by bond lengths & angles that vary
little from AA residue to AA residue.
 Only 3 of these bonds are part of peptide chain
per se : the α-C to carbonyl C, the C—N bond
& the imide N to α-C bond.

14.  Since the double bond character of C—N bond
limits rotation about it, only the 1st & last
allow rotation.
 The rotation angles Ψ & Φ establish the
relative position of any 2 successive amide
planes along the polypeptide chains.

15. Secondary structure of proteins
 The term secondary structure refers to the
local conformation of some part of
polypeptide.
 It focuses on regular pattern of polypeptide
backbone.
Types of secondary structure
1. The α- helix
2. The β-pleated sheet

17. 1) The α- helix structure –
 It is a rod like structure, deduced by Linus
Pauling & Robert Corey.
 The simplest arrangement, the polypeptide
chain could assume with it’s rigid planar
peptide bonds is α- helical structure, which
Pauling & Corey called α- helix.
 In this the polypeptide chain is tightly wound
around on imaginary axis drawn
longitudinally through middle of helix.
 R group of amino acid residue protrude
outward from helical background.

18.  The repeating unit is a single turn of the
helix, which extends about 5.4A˚ about long
axis (pitch=5.4A˚).
 Each helical turn includes 3.6 amino acids
residues.
 Spacing per amino acid residue=
5.4/3.6=1.5A˚.
 The amino acid residue in an a- helix have
conformation psi=-45 degree & phi=-60
degree.

21.  The α helix can be of two types
1) right handed (clockwise)
2) left handed ( anticlockwise)
 The α helix is stabilized by H bonds between
the NH & CO groups of the main chain.
 Each successive turn of the α helix is held to
adjacent turns by 3-4 H bonds.
 Although H bonds are weak but since they are
numerous they maintain a stable structure
(intramolecular H –bonding).

22. Amino acid sequence affects α helix
stability
 the 5 different kinds of constraints affect
stability of α helix:-
1) electrostatic attraction or repulsion between
successive amino acid residues with charged R
groups.
2) the bulkiness of adjacent R groups.
3) the interactions between R groups spaced ¾
residues apart.
4) the occurrence of proline & glycine residues

23. 5) The interaction between AA residues at ends
of helical segment & electric dipole inherent to
α helix.
 AA with bulky side chains are less frequent in
helices. E.g. tyrosine (big phenyl side chain).
 Proline is a helix breaker because it has lno
backbone NH to H-bond. InN atom is a part of
rigid ring & rotation about N—Cα is not
possible.
 Negatively charged carboxyl groups of
adjacent Glu residues repel each other strongly
that they prevent formation of α helix.

24.  Main criterion for α helix preference is that
AA side chain should cover & protect
backbone H-bonds in core of helix.
 The α helix preference order –
alanine> leucine > methionine >
phenylalanine> glutamic acid > glutamine >
histidine > cysteine > arginine
 Glycine occurs infrequently in α helix because
it has more conformational flexibility than
other AA residues.

26. Solvent induced distortion in α helix
 Solvent exposed helices are often bent away
from solvent region, because exposed CO
groups tend to point towards solvent to
maximize their H-bonding capacity,resulting
into bend in helix axis.

27. 2) The β- pleated sheet
Linus pauling & Robert corey(1953) identified a
2nd type of repetitive stable conformation
named β pleated sheet .
 Formation of β pleated sheet depends upon
intermolecular H-bonding.
 The backbone of polypeptide chain is extended
in a zigzag manner.
 The R groups of constituent AA in one
polypeptide chain alternately project above &
below the plane of sheet.

28.  The 2 types of β pleated sheet are parallel &
antiparallel β pleated sheet.
1)Parallel β pleated sheet
 A sheet is parallel when N-terminal ends of
all the participating polypeptide chains lie on
same edge of sheet, with all C-terminal ends
on opposite edge.
2)Antiparallel β pleated sheet
 A sheet is anti parallel if alternate chains are
oriented in same direction.
 This structure permits maximum H-bonding.

31.  It is significantly stable due to well aligned H-
bond.
 Example of β pleated sheet is β keratin/fibroin
found in spider & silk moth silk.
The β turns
 In globular protein, which have a compact
folded structure, nearly 1/3rd of the AA
residues are in turns or loop where the
polypeptide chain reverse direction.
 These are connecting element that link
successive runs of α helix or β conformation.

32.  Common β turns are those that connect the
ends of 2 adjacent segments of an anti parallel
β sheet.
The structure is 180˚ turn involving 4
AA residues, with carbonyl O of 1st residue
forming a H-bond with amino group H of 4th.
 Gly & pro residue often occur in β turns, the
former because it is small & flexible & the
latter because peptide bonds involving imino N
of proline readily assume a cis-configuration, a
form that is particularly amenable to a tight
turn.

33.  The β turns are often found near the surface of
a protein where the peptide groups of central 2
AA residues in the turn can H-bond with
water.
 The β turns are known as reverse turn or
hairpin bends.

34. Comparison between α helix & β pleated
sheet
The α helix The β pleated
sheet
1) Polypeptide
chain is tightly
coiled
Polypeptide chains
(β strand) have
fully extended
conformation
2) Axial distance
b/w adjacent
AA=1.5 A˚
Axial distance b/w
adjacent AA=1.5 A˚
3) Intramolecular
H-bonding
Intermolecular H-
bonding

35.  The α helix may be considered as default state
for secondary structure although P.E. is not as
low as for β sheet, H-bond formation is intra
strand, so there is an entropic advantage over β
sheet where H-bonds form from strand to
strand.

37. Super secondary structures
 Also called “motifs” or simply “folds”. These
are particularly stable arrangements of several
elements of secondary structure & connections
b/w them.
 They can be simple or complex.
 Domains-Are polypeptides with a more than
few 100 AA residues often fold into 2 or more
stable globular units.
 E.g β turns, ω loops etc.

38. What is the tertiary structure of a protein?
 In very general terms the tertiary structure of a protein can be thought of as
the overall, unique, three dimensional folding of a protein.
 The diagram above represents the tertiary structure of a protein. In this
diagram you should recognize the (ribbons with arrows) and alpha helical
region (barrel shaped structure)
Tertiary Structure of Proteins

40. Forces that give rise to tertiary structure

41.  The forces that give rise to the tertiary structure
of a protein are
 Ionic bond
 hydrogen bond
 hydrophobic interaction
 disulphide bond

42. Properties of hydrogen bond
 How are they formed?
 Strength
 What classes of compound can form hydrogen bond?
 Importance
Hydrogen Bonds

44.  ionic bonds are forces of attraction between ions of opposite
charge (+and -).
 any kind of biological molecule that can form ions.
 An example of a functional group that can enter into ionic
bonds is shown below. The carboxyl group is shown.
Ionic Bonds

45.  They play an important role in determining the shapes
(tertiary and quaternary structures) of proteins
 They are involved in the process of enzyme catalysis
 they are important in determining the shapes of chromosomes.
 They play a role in muscle contraction and cell shape
What function do ionic bonds have in
biology

46. Hydrophobic InteractionsHydrophobic interactions are more
correctly called hydrophobic exclusions.

47. What is a disulfide bond?
a single covalent bond between the sulfur atoms to two
amino acids called cysteine.
Disulfide bond

48.  It is a covalent bond, the disulfide bond can be considered as
part of the primary structure of a protein.
 they are very important in determining the tertiary structure of
proteins
 they are very important in determining the quaternary
structure of some proteins. An very prominent example would
be the role of disulfide bonds in the structure of antibody
molecules.
What is the significance of disulfide
bonds?

49. These examples show how 2o structure is used as a framework,
and show the importance of hydrophobic interactions.
Myoglobin
 This protein binds and stores oxygen in muscle. It consists of
153 amino acids, which fold into 8 a-helices of differing
lengths.
 The helices have non-polar side chains on one side
(green=Valine) and polar side chains on the other (red =
glutamate, lilac = histidine). They are described as
"amphipathic" helices.
Example

51.  This protein hydrolyses RNA. It is made from 124 amino acids and folds
into a b-sheet (3 b-strands) and 3 a-helices. Ribonuclease has several
disulphide bonds stabilizing its tertiary structure. Use the popup menu in
the structure frame to turn disulphide bridges on (in the "Options"
Submenus).
Ribonuclease

52. QUATERNARY STRUCTURE:
 Quaternary structure is the three-dimensional
structure of a multi-subunit protein.
 the quaternary structure is stabilized by the
same non-covalent interactions and disulfide
bonds as the tertiary structure.
 Complexes of two or more polypeptides are
called multimers.

53. PROTIEN LEVELS

54. FORCES INVOLVE IN
QUATERNARY STRUCTURE
 Disulfide Bonds:
 Hydrogen Bonding:
 Non-Polar Hydrophobic Interactions:
 Protien-protien interaction:
 Peptide bond

55. Disulphide bond

56. Hydrogen bonding

57. Hydrophobic interaction

58. PROTEIN-PROTEIN
INTERACTION
 Proteins are capable of forming very tight
complexes.
For example, ribonuclease inhibitor binds to
ribonuclease A with a roughly dissociation
constant. Other proteins have evolved to bind
specifically to unusual moieties on another
protein, e.g., biotin groups (avidin),
phosphorylated tyrosines (SH2 domains) or
proline-rich segments (SH3 domains).

59. Peptide bond

61. TYPES OF QUATERNARY
PROTEIN
 1 FIBROUS
 2 GLOBULAR
 FIBROUS PROTEIN-
 The final beta-pleated sheet structure of silk is
the result of the interaction of many individual
protein chains. Specifically, hydrogen bonding
on amide groups on different chains is the
basis of beta-pleated sheet in silk proteins.

62. FIBROIN

63. Silk protein

64.  GLOBULAR PROTEIN-
 globular proteins may have a combination of the
above types of structures and are mostly clumped
into a shape of a ball.
 Have compact 3-D structures
 More common in the cell than fibrous proteins
 Ex. Myoglobin (Mb), hemoglobin (Hb),
antibodies, CD4 cell-surface protein,
ribonuclease, PRP protein, enzymes,

65. EXAMPLES OF GLOBULAR
STRUCTURE
 HAEMOGLOBIN-

66.  Haemoglobin is found in red blood cells
 The haemoglobin molecule is a tetramer
consisting of 4 polypeptide chains, known as
globins, which are usually:
 2 alpha chains that are each 141 amino acids long
 2 beta chains that are each 146 amino acids long
 Attached to each chain is an iron-containing
molecule known as haem

67. INSULIN

68.  Human insulin contains two protein chains
with a total of 51 amino acids.
The chains are connected by two disulfide
bonds.
 Insulin is classified as a hormone and is
needed for the proper utilization of glucose
 Diabetics must take insulin injections to
maintain health.

69.  As a enzyme or biocatalyst
 As a carrier molecules
 As a hormones ,like- Insulin
 Provide energy
 Help in transmission of heredity material
 In blood clotting
 Cell’s made by protein
Function of protein

70.  Protein structures evolved to function in
particular cellular environment.
 Condition different from those in the cell can
result in protein structural changes ,large and
small
 A loss of three dimensional structure sufficient
to cause loss of function is called denaturation.
Denaturation of protein

71. CONCLUSIONS
 Proteins serve a variety of functions within
cells. Some are involved in
structural support and movement, others in
enzymatic activity, and still others in
interaction with the outside world. Indeed, the
functions of individual proteins are as varied
as their unique amino acid sequences and
complex three-dimensional physical structures.

72. References
Books:
• Biochemistry by Lehninger (Nelson & Cox)
• Biochemistry by Lubert Stryer
• Biochemistry by J.L.Jain
Internet:
• www.wikipedia.com
• www.tutorvista.com

73. Ask your queries…