1. AMINO ACIDS:
Introduction:
Asparagine(1806) found in asparagus,
first amino acid to be discovered.
Amino acids are small units of monomers
of proteins.
Proteins are made up of 20 amino acids
in different sequences and numbers.

2. Structure:
 All the standard amino acids except (glycine)
the α carbon is asymmetric.
 α carbon is bonded to four different
substituent groups:
 carboxyl group
 amino group
 R group
 hydrogen atom.

3. R (in red) represents the side
chain( different in each amino acid).
GLYCINE the α-carbon atom has four
different substituent groups.

4. Stereoisomerism:
Proteins Contain L-Amino Acids.
L-Amino acids are those with the αamino group on the left.
The naming of configurations of
both simple sugars and amino acids is
based on the absolute configuration
of glyceraldehyde.

6. CLASSIFICATION:
Classified based on the properties
of their R groups.
Tendency to interact with water at
biological pH (near pH 7.0).

7. ;those whose R groups are:
1)nonpolar and aliphatic
2)aromatic (generally nonpolar)
3) polar but uncharged
4) negatively charged
5) positively charged.
Within each class, there are
gradations of polarity, size, and
shape of the R groups.

8. 1) Nonpolar Aliphatic R group:
The hydrocarbon R groups are
nonpolar and hydrophobic.
The bulky side chains of alanine,
valine, leucine, and isoleucine,
promote hydrophobic
interactions within protein
structures.

9. Glycine :
Simplest amino acid structure.
Side chain( optically inactive) allows much
more structural flexibility than the other
amino acids.
Proline:
The secondary amino (imino) group is held
in a rigid conformation that reduces the
structural flexibility of the protein at that
point.

11. 2) Aromatic R Groups:
 Phenylalanine (Phe), tyrosine(Tyr), and
tryptophan (Trp), are relatively nonpolar.
 The OH group of tyrosine can form hydrogen
bonds, hence important functional group in the
activity of some enzymes.
 Tyrosine and tryptophan are more polar than
phenylalanine because of the tyrosine hydroxyl
group and the nitrogen of the tryptophan
indole ring.
 Tryptophan and tyrosine, and
phenylalanine(lesser), absorb ultraviolet light.

13. 3) Polar, Uncharged R Groups :
 Are more soluble in water than nonpolar
amino acids, because they contain functional
groups that form hydrogen bonds with water.
 Includes:
I. Serine(OH)
II. Threonine(OH)
III. cysteine( S)
IV.Methionine(S, sulphur atom)
V. Asparagine(NH2,amide group)
VI.glutamine. (NH2)

15. Asparagine and Glutamine are
easily hydrolyzed by acid or base.
 Cysteine has an R group (a thiol
group) that is acidic .
 It is readily oxidized to form
cystine, in which two cysteine
molecules are joined by a disulfide
bridge which stabilize the protein
structure.

17. 4) Negatively Charged (Acidic) R
Groups:
 Include:
1) aspartate
2) glutamate
 Each have a second carboxyl group.
 These are the parent compounds of
asparagine and glutamine.

19. 5) Positively Charged (Basic) R
Groups:
 Includes:
 lysine, has a second amino group at the e
position on its aliphatic chain;
 arginine, which has a positively charged
guanidino group; and
 Histidine, has an imidazole group.

standard amino acid having a side chain
with a pKa near neutrality.

21. GENERAL PROPERTIES OF
AMINO ACIDS:
1) Isomerism:
Two types: 1) L form
2) D forms.
a) stereo-isomerism: all amino acids except
glycine exist as D and L- isomers.
- In D-amino acids, -NH2 group (right). In
animals and plants.
- In L-amino acids (left) ,occur in bacteria.

22. b) Optical isomerism:
Dextro-rotatory and
Laevo-rotatory

23. 2) Ionization:
 Amino acids in aqueous solution are
ionized and can act as acids or bases.
 Those having a single amino group and
a single carboxyl group crystallize from
neutral aqueous solutions as fully
ionized species known as zwitterions
(German for "hybrid ions"), each having
both a positive and a negative charge.

24. Zwitterions: are electrically neutral
and remain stationary in an electric
field. The crystal lattice of amino acids
is held together by strong electrostatic
forces between positively and
negatively charged functional groups
of neighboring molecules, resembling
the stable ionic crystal lattice of NaCI.

26. 2)Amphoteric nature:
Amino Acids Can Act as Acids and
as Bases.
When a crystalline amino acid,
such as alanine, is dissolved in
water, it exists in solution as the
dipolar ion, or zwitterion, which
can act either as an acid (proton
donor),

28. or as a base (proton acceptor):

29. Substances having this dual
nature are amphoteric and are
often called ampholytes.

30. 3) Physical properties:
Colorless, crystalline substances.
 soluble in water(tyrosine in soluble
in hot water)
Melting point is higher than
200degrees Celsius.

31. 4) Undergo Characteristic
Chemical Reactions:
 Ninhydrin reaction:
 When amino acids are heated with excess
ninhydrin, all those having a free α-amino
group yield a purple product.
 Intensity of color produced proportional to the
amino acid concentration. Comparing the
absorbance to that of appropriate standard
solutions is an accurate and technically simple
method for measuring amino acid
concentration.

33. PEPTIDES:
 polymers of amino acids.
 Two amino acid molecules can be
covalently joined through a peptide
bond, to yield a dipeptide.
 linkage is formed by removal of the
elements of water from the α-carboxyl
group of one amino acid and the αamino group of another.

35. When a few amino acids are joined
in this fashion, the structure is
called an oligopeptide.
When many amino acids are joined,
the product is called a polypeptide.
The peptide bond is the most
important covalent bond linking
amino acids in peptides and
proteins.

36. Structure of the pentapeptide
serylglycyltyrosinylalanylleucine,

38. PROTEINS:
 Classification according to their functions:
 1) Enzymes :The most varied and highly
specialized proteins are those with
catalytic activity.
 They catalyze all the chemical reactions in
cells.
 Many thousands of different enzymes
have been discovered in different
organisms.

39. The light produced by fireflies is the result of a
light-producing reaction involving luciferin and ATP
that is catalyzed by the enzyme luciferase .

40. 2) Transport Proteins:
 Hemoglobin of erythrocytes binds oxygen
as the blood passes through the lungs,
carries it to the peripheral tissues, and there
releases it to participate in the energyyielding oxidation of nutrients.
 lipoproteins, which carry lipids from the
liver to other organs.

42. 3) Nutrient and Storage Proteins
 Ovalbumin, the major protein of egg
white.
 casein, the major protein of milk, is a
nutrient protein.
 The ferritin found in some bacteria and
in plant and animal tissues stores iron.

43. 4) Contractile or Motile Proteins
 Actin and myosin function in the
contractile system of skeletal muscle
and also in many non-muscle cells.
 Tubulin is the protein from which
microtubules are built.
 Microtubules act in concert with the
protein dynein in flagella and cilia to
propel cells.

44. The movement of cilia in protozoans
depends on the action of the protein dynein.

45. 5) Structural Proteins
 Give biological structures strength or
protection.
 collagen(tendons and cartilage), has very
high tensile strength.
 Ligaments contain elastin, capable of
stretching in two dimensions.
 Hair, fingernails, and feathers consist largely
of the tough, insoluble protein keratin. The
major component of silk fibers and spider
webs is fibroin .

47. 6) Defense Proteins:
 The Immunoglobulins/antibodies, made
by the lymphocytes of vertebrates, can
recognize and neutralize invading bacteria,
viruses.
 Fibrinogen and thrombin are bloodclotting proteins that prevent loss of blood
when the vascular system is injured.
 toxic plant proteins( ricin), also appear to
have defensive functions.

48. Castor beans contain a highly toxic protein called ricin.

49. 6) Regulatory Proteins:
regulate cellular or physiological
activity
E.g. insulin, which regulates sugar
metabolism.

50.  Growth hormones
(Somatotropin)
 Pituitary
hormone(prolactin)

51. Cancerous tumors are often made up of cells
that have defects involving one or more of the
proteins that regulate cell division.

52. Protein separation:
• properties such as charge, size, and solubility.
• binding properties.
• cells must be broken open and the protein
released into a solution called a crude extract.
• differential centrifugation( sucrose)

53. Methods used:
1. Paper chromatography:
 The physicochemical factors involved in
chromatography are adsorption, partition,
ion exchange, and molecular sieving.
 There are two phases in all types of
chromatography (i) stationary phase and
the (ii) mobile phase. In paper
chromatography, paper is the stationary
phase and organic solvent is the mobile
phase.

54. what Mann 1 or 3 filter paper is
used as supporting material for the
stationary phase.
An organic solvent layer of mixture
of butanol: acetic acid: water in
the ratio of 4:1:5 is used as solvent
or mobile phase.

55.  Retention value (Rf value): the ratio of
distance moved by a compound
(protein) to the distance moved by the
solvent front.
 When another solvent system in a
perpendicular direction is employed, it
is a two dimensional paper
chromatography that separates the
proteins more distinctively.

56. 1) Size-exclusion
chromatography/gel filtration.
 Separates proteins according to size.
 column contains a cross-linked polymer with
pores of selected size. Larger proteins
migrate faster than smaller ones, because
they are too large to enter the pores in the
beads.
 The smaller proteins enter the pores and are
slowed by the path they take through the
column.

58. 3) Affinity chromatography
 Separates proteins by their binding
specificities.
 The proteins retained on the column are those
that bind specifically to a ligand(a group or
molecule that is bound) cross-linked to the
beads.
 After nonspecific proteins are washed through
the column, the bound protein of particular
interest is eluted by a solution containing free
ligand.

61. 4) Electrophoresis
 Separation based on the migration of
charged proteins in an electric field.
 Different samples are loaded in wells at the
top of the polyacrylamide gel. The proteins
move into the gel when an electric field is
applied. The gel minimizes convection
currents caused by small temperature
gradients, and it minimizes protein
movements other than those induced by the
electric field.

62. (b) Proteins can be visualized by treating the gel
with a stain such as Coomassie blue, which
binds to the proteins.
Each band on the gel represents a different
protein: smaller proteins are found nearer the
bottom of the gel.
The first lane shows the proteins present in
the crude cellular extract. Successive lanes show
the proteins present after each purification step.
The purified protein contains four subunits, as
seen in the last lane on the right.

65. PROTEIN STRUCTURE

66. 1) Primary structure:
Is the linear sequence of amino acids held
together by peptide bonds.
Peptide bond form the backbone and side
chains of amino acid residues project outside
the peptide backbone.
The free –NH2 group is called N-terminal end
and –COOH group is C-terminal end.

67. 2) Secondary Structure
 regular, recurring arrangements in
space of adjacent amino acid residues
in a polypeptide chain.
 Types : α helix and the β conformation.
 makes up hair and wool (the fibrous
protein α-keratin) has a regular
structure that repeats every 0.54 nm.

68. α helix
 Is a helical structure (polypeptide chain with
its rigid peptide bonds but with the other
single bonds free to rotate)
 Polypeptide backbone is tightly wound
around the long axis of the molecule, and the
R groups of the amino acid residues protrude
outward from the helical backbone.
 The repeating unit is a single turn of the
helix, which extends about 0.56 nm along the
long axis.

70. 3) Protein Tertiary Structure
 Formed as a result of further folding, super
folding or twisting of Secondary structure.
 Occur in native protein.
 Amino acids located far apart are brought
closer.
 Bonds responsible are: a)hydrophobic
interactions: occur between nonpolar side
chains of amino acids such as alanine,
leucine etc.

71. b) Hydrogen bonds( polar side)
c) Ionic bonds( between oppositely
charged polar side chains of amino
acids)
d) Vander Waals forces( occur
between non polar side chains)
e) Disulphide bond(are S-S bonds
between –SH group of distance
cysteine residues.

72. heme group, present in myoglobin (protoporphyrin, to which is
bound an iron atom in its ferrous (Fe2+ ) state)

73. 4) Protein Quaternary Structure
 Constitute arrangement of proteins and
protein subunits in three-dimensional
complexes.
 multiple noncovalent interactions stabilize the
structure
 The assembly is called oligomer.
 Each constituent peptide chain is called
monomer.

74. Structure of Hemoglobin
 contains four polypeptide chains and
four heme groups, in which the iron
atoms are in the ferrous (Fe2+) state.
 Globin(protein portion), consists of two
α chains (141 residues each) and two β
chains (146 residues).
 hemoglobin molecule is roughly
spherical, with a diameter of about 5.5

75. α subunits(white and light blue); the β subunits( pink
and purple). heme groups( red), are far apart.