Amino Acids: Building Blocks of Proteins

• The peptide bond is formed when the OH group

from the carboxyl group of one of the amino acids
is removed and a hydrogen from the other amino
acid is removed. The OH and H bond to from
water.
• The formation of water from the two amino acids
is called dehydration synthesis.
• The covalent linkage that is formed is known as a
peptide bond, and the molecule that is formed by
the linking of amino acids is called polypeptide.
 Example of an Amino Group
R Group
Carboxyl
Amino Group Group

Central Carbon
Amino Acids: Building Blocks of Proteins
Amino Acid Amino Acid
R R

H N C C OH H N C C OH

H H O H H O

H2O

Dipeptide
R R

H N C C N C C OH

H H O H H O
 Proteins are Very Large Molecules

• Some proteins consist of a single polypeptide

chain and others called multisubunit proteins,
have two or more.
• Individual polypeptide chains in a multisubunit
protein may be identical or different. If at least
some are identical, the protein is sometimes
called an oligomers protein and the subunits
themselves are referred to as protomers.
 Levels of Protein Organization
• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary structure
PROPERTIES OF AMINO ACIDS
A. Isomerism: Two types of isomerism are shown by
amino acids basically due to the presence of asymmetric
carbon atom. Glycine has no asymmetric carbon atom
in its structure hence is optically inactive.
(a) Stereoisomerism: All amino acids except glycine exist
in D and L isomers.

In D-amino acids– NH2 group is on the right hand while

in L-amino acids it is oriented to the left.
Natural proteins of animals and plants
generally contain L-amino acids.

D-amino acids occur in bacteria.

 Optical activity - The ability to rotate plane - polarized
light
Asymmetric carbon atom

Chirality - Not superimposable

Mirror image - enantiomers

(+) Dextrorotatory - right - clockwise

Operational definition
(-) Levorotatory - left counterclockwise only cannot predict

}
absolute
Na D Line passed through polarizing filters. configurations
 Stereoisomers
Stereoisomers
One or many chiral centers

N chiral centers 2N possible stereoisomers and 2N-1 are

enantiomeric
For N = 2
there are 4 possible sterioisomers
of which 2 are enatiomers
and 2 are diastereomers

Diastereomers are not mirror images and have

different chemical properties.
 The Fischer Convention
Absolute configuration about an asymmetric carbon

related to glyceraldehyde
(+) = D-Glyceraldehyde
(-) = L-Glyceraldehyde
All naturally occurring amino acids that make up
proteins are in the L conformation

In the Fischer projection all bonds in the horizontal

direction is coming out of the plane if the paper, while
the vertical bonds project behind the plane of the
paper
The CORN method for L
isomers: put the hydrogen
towards you and read off
CO R N clockwise
around the Ca This works
for all amino acids.
An example
An example of
of an
an amino
amino acid
acid with
with two
two
asymmetric carbons
asymmetric carbons
 Cahn - Ingold - Prelog system
Can give absolute configuration nomenclature to multiple
chiral centers.

Priority

Atoms of higher atomic number bonded to a chiral center

are ranked above those of lower atomic number with
lowest priority away from you R highest to lowest =
clockwise, S highest to lowest = counterclockwise

SH>OH>NH2>COOH>CHO>CH2OH>C6H5>CH3>H
The major advantage of the CIP or RS system is
that the chiralities of compounds with multiple
asymmetric centers can be unambiguously
described
B. Amphoteric Nature and Isoelectric pH: The -NH2
and -COOH groups of amino acids are ionizable
groups. Further, charged polar side chains of few
amino acids also ionise.

Depending on the pH of the solution these groups act

as proton donors (acids) or proton acceptors (bases).
This property is called as amphoteric and
therefore amino acids are called as
ampholytes.

At a specific pH the amino acid carries both

the charges in equal number and exists as
dipolar ion or “Zwitterion”.
At this point the net charge on it is zero
The pH at which amino acid occurs without any
charge on it is called pI or isoelectric pH.
On the acidic side of its pI amino acids exist as a
cation by accepting a proton and on alkaline as anion
by donating a proton.
C. Physical Properties: They are
Colorless
Crystalline substances
more soluble in water than in polar solvents
They have high melting point usually more than 200°C.
They have a high dielectric constant.
They possess a large dipole moment.
D. Chemical Properties
I. Due to Carboxylic (—COOH) Group
1. Formation of esters: They can form esters with
alcohols. The COOH group can be esterified with
alcohol.
[Link] to amino alcohol: This is achieved in
presence of lithium aluminium hydride.
3. Formation of amines by decarboxylation:

In vivo, the amino acids can be decarboxylated by

the enzyme decarboxylase and forms the
corresponding amines.
4. Formation of amides:
II. Properties Due to Amino (–NH2) Group
1-Salt formation with acids: The basic amino group
reacts with mineral acids such as HCl to form salts like
hydrochlorides
2. Formation of acyl derivatives:
hippuric acid is an acyl glycine formed by the
conjugation of benzoic acid with glycine This is one of
the mechanisms of detoxication in which glycine is
used and this also forms the basis of one of the liver
function tests. Hippuric acid is a normal component of
urine and is typically increased with increased
consumption of phenolic compounds (tea, fruit juices)
3. Oxidation: Potassium permanganate or H2O2
oxidises the NH2 group and converts the amino acid
into imino acid which reacts with water to form NH3
and α-ketoacid.
4. Reaction with HNO2: the amino acids except
proline and hydroxyproline react with HNO2
(nitrous acid) libering N2 from NH2 group.
5. Reaction with CO2: The amino acid anion present in
an alkaline solution may react with CO2 through NH2
group to form a carbamino acid anion.
6. Reaction with formaldehyde: Formaldehyde reacts
with the-NH2 group to form a methylene compound.
III. Properties of Amino acids Due to Both NH2
and COOH Groups
In addition to the property of reacting with both
cation and anion, the amino acids form
chelated, co-ordination complexes with certain
heavy metals and other ions.
These include Cu++, Co++, Mn++ and Ca++.
Levels of Protein Organization
 1. Primary Structure

 1-A. Sequence of amino acids in proteins

 Primary structure denotes the number and sequence of
amino acids in the protein. The higher levels of
organisation are decided by the primary structure. Each
polypeptide chain has a unique amino acid sequence
decided by the genes.
 The primary structure is maintained by the covalent peptide
bonds
 Sequence both are different.
 Gly - Ala - Val (1)
 Gly - Val - Ala (2)
 Primary Structure
• Covalent bonds between amino acids and is
normally defined by the sequence of peptide-
bonded amino acids and locations of disulfide
bonds.
• The relative spatial arrangement of the linked
amino acids is unspecified.
• Similarly A chain 20th cysteine and B chain 19th
cysteine are connected. There is another intrachain
disulphide bond between 6th and 11th cysteine
residues of A chain.

• iii. The species variation is restricted to amino

acids in position 8, 9 and 10 in A chain and in C-
terminal of B chain
• The porcine insulin and human insulin are
structurally similar, except the terminal amino
acid in B chain (Thr → Ala)
 [Link] Structure of protein
• The term "secondary structure" denotes the
configurational relationship between residues which
are about 3–4 amino acids apart in the linear
sequence

• Secondary and tertiary levels of protein structure are

preserved by noncovalent forces or bonds like
hydrogen bonds, electrostatic bonds, hydrophobic
interactions and van der Waals forces
 Secondary Structure
• Refers to regular recurring arrangements in
space of adjacent amino acid residues in a
polypeptide chain.
• There are few common types of secondary
structure, the most prominent being the α
helix & β conformation.
 Secondary structure

• The regular folding and twisting of polypeptide chain

into ordered structure, maintained by hydrogen
bonding .
 Secondary structure includes:
- -helix
- - pleated sheet
- collagen helix
- B-bend or B- turn
- Disordered region
 2-A. Alpha helix
 Pauling (Nobel prize, 1954) and Corey described the alpha-
helix and beta-pleated sheet structures of polypeptide chains
in 1951.

 i. The alpha-helix is the most common and stable

conformation for a polypeptide chain.

 In proteins like hemoglobin and myoglobin, the alpha-helix

is abundant, whereas it is virtually absent in chymotrypsin.

 ii. The alpha helix is a spiral structure .The polypeptide

bonds form the back-bone and the side chains of amino
acids extend outward
 The structure is stabilized by hydrogen bonds between NH and C=O
groups of the main chain.
• The helix is rod like structure, stabilized by hydrogen
bonds between hydrogen of amide (NH) group and oxygen
of carbonyl group (CO).

 iv. Each turn is formed by 3.6 residues. The distance between each
amino acid residue (translation) is 1.5 Å.

 v. The alpha-helix is generally right handed. Left handed alpha helix is

rare, because amino acids found in proteins are of L-variety, which
exclude left handedness. Proline and hydroxy proline will not allow the
formation of alpha-helix.
• Disulfide bonds formed between polypeptide(adjacent),
chain having cysteine residues ,enhance strength
of structure.

Structural importance
• Several - helix can coil round one another like a twisted
twined cable forming, strong stiff bundles of fibers and
give mechanical support.
Eg.
(a)Fibrous protein:
Eg. - keratin of hair, nail, skin.
Myosin and tropomyosin muscles.
Fibrin of blood.
(b) Globular protein:
Eg. Haemoglobin – 80% - helix str.

• Helix destabilizing amino acids.

• Glycine & proline – “helix breakers.”
 2-B. Beta-pleated sheet

• i. The polypeptide chains in beta-pleated

sheet is almost fully extended. The distance
between adjacent amino acids is 3.5Å.

• ii. It is stabilized by hydrogen bonds between

NH and C=O groups of neighboring
polypeptide segments
 -pleated structure
The surface of -sheet appear ‘pleated’-called “-
pleated sheet” .
Differ from -helix in that,
• Sheet rather than rod.
• It is extended rather than tightly coiled as in -helix.
• Unlike, -helix, composed of two or more
polypeptide chains.
• Structure stabilized by hydrogen bonds between NH
and C=O in different or the same polypeptide chain.
• Hydrogen bonds are perpendicular to the
polypeptide backbone [parallel in -helix] .
 Parallel pleated sheet
• The polypeptide are side by side and lie in the same
direction (with respect to –N & C-terminal)& stabilized
by hydrogen bond.
Anti-parallel sheet
• Polypeptide chains lie in opposite directions N-terminal
of one is next to C-terminal of other (N-terminal faces
to C-terminal).
Eg. Found in both fibrous and globular proteins.
• Best example in nature silk fibrion, in human tissues
amyloid, a protein accumulates in amyloidosis and
Alzheimer’s disease.
 ALPHA HELIX
 Spiral structure
 Tightly packed, coiled polypeptide backbone
core.
 Side chain extend outwards
 Stabilized by H bonding b/w carbonyl H bonding
oxygen and amide hydrogen( 1-4, 2- 5)
 Same peptide chain
 Amino acids per turn – 3.6
 Pitch is 5.4 A
 All bonds are paralled
 Right handed common and stable
 Proline never in alpha helix
 Glycine disrupts alpha helix
 Alpha helical segments are found in many
globular proteins like myoglobins, troponin-
C etc.
 BETA PLEATED SHEET
 Formed when 2 or more polypeptides
line up side by side.
 Individual polypeptide - β strand
 Each β strand is fully extended.
 They are stabilized by H bond b/w N-H
and carbonyl grps of adjacent chains.

2 types

Parallel Anti -
Parallel
N C N C

N C C N

 Glycine main amino acid, produces

kinks
 [Link] Structure
• Secondary structure denotes the configurational
relationship between residues which are about 3-4
amino acids apart; or secondary level defines the
organization at immediate vicinity of amino acids.

• The tertiary structure denotes three dimensional

structure of the whole protein.
• The tertiary structure defines the steric relationship of
amino acids which are far apart from each other in the
linear sequence, but are close in the three-dimensional
aspect.
 Tertiary Structure
• The spatial relationship among all amino acids
in a polypeptide.
• It is the complete 3D structure of the
polypeptide.
 Tertiary structure
• Three dimensional folded compact and
biologically active conformation of protein is
known as its tertiary structure.
Eg. Myoglobin
• Structure stabilized by:
- Hydrogen bonds.
- Hydrophobic interactions.
- Van der waals forces.
- Disulfide bond.
- Ionic bond or salt bridge.
 Quaternary Structure
• Proteins with several polypeptide chains have
one more level of structure referred to at the
quaternary structure.
• Refers to the spatial relationship of the
polypeptides, or subunits, within the protein
 Quaternary structure of protein
• The arrangement of many polypeptide subunits in three
dimensional complexes is called quaternary structure of
protein.
• Stabilizing forces are hydrophobic interactions, hydrogen
bond & ionic bond.
Eg. Glycolytic enzymes
- Aldolase
- Lactate dehydrogenase
- Pyruvate dehydrogenase etc
Hb
Creatine kinase
Alkaline phosphatase
• For example, 2 alpha-chains and 2 beta-chains
form the Hemoglobin molecule.

• Similarly, 2 heavy chains and 2 light chains

form one molecule of immunoglobulin G.

• Creatine kinase (CK) is a dimer. Lactate

dehydrogenase (LDH) is a tetramer.
 Proteins
• provide structure, catalyze cellular reactions
and carry out other tasks.
• have multiple biological functions
• classified according to their biological roles.
 Types of proteins and their function

Enzymes
• Most varied and specialized proteins with
catalytic activity.
• All chemical reactions of organic biomolecules
in cells are catalyzed by enzymes.
 Types of proteins and their function

Transport Proteins
• Bind and carry molecules or ions to organs in
the blood plasma.
• Lipoproteins in blood plasma carries lipids
from the live to other organs.
 Types of proteins and their function

Nutrient and Storage Proteins

• Seeds of many plants store nutrient proteins
required for the growth of the germinating
seedlings.
• Ovalbumin, the major protein of egg white,
and casein the major protein of milk are
examples of nutrient proteins.
 Types of proteins and their function

Contractile or Motile Proteins

• Some proteins endow cells and organisms
with the ability to contract, to change shape,
or to move about.
• Tubulin is the protein from which
microtubules are built.
 Types of proteins and their function

Structural Proteins
• Many proteins serve as supporting filaments,
cables, or sheets, to give biological structures
strength or protection.
• Major component of tendons and cartilage is
the fibrous protein collagen, which has very
high tensile strength.
• Ligaments contain elastin, a structural
protein.
 Types of proteins and their function
Defense Proteins
• Defend organisms against invasion by other
species or protect them
• Immunoglobulin or antibodies, are made by the
lymphocytes of vertebrates and can recognize &
precipitate or neutralize invading bacteria
• Fibrinogen and thrombin are blood clotting
proteins
 Types of proteins and their function

Regulatory Proteins
• Help regulate cellular or physiological activity.
• The cellular response to many hormonal signals
is often mediated by a class of GTP-binding
proteins called G proteins.
 Denaturation of Proteins

• Mild heating, treating with urea, salicylate, X-

ray,ultraviolet rays, high pressure, vigorous shaking
and similar physico-chemical agents produce
denaturation.

• There will be non-specific alterations in secondary,

tertiary and quaternary structures of protein
molecules.
• Primary structure is not altered during
denaturation
• In general, during the process the solubility is
decreased while precipitability of the protein is
increased. It often causes loss of biological
activity.

• Native proteins are often resistant to proteolytic

enzymes, but denatured proteins will have more
exposed sites for enzyme action. Since cooking
leads to denaturation of proteins, cooked foods
are more easily digested.
• Denatured proteins are sometimes re-natured when the
physical agent is removed. Ribonuclease is a good example for
such reversible denaturation.

• Immunoglobulin chains are dissociated when treated with

urea. When the urea is removed by dialysis, the subunits are
reassociated and biological activity of immunoglobulin is
regained.

• But many proteins undergo irreversible denaturation.

For example, albumin once heated, cannot be
renatured by cooling
Denaturation of proteins
 Coagulation
• Semi-solid viscous precipitates-coagulum.
• Permanently disordered protein or irreversible
denaturation.
Eg. Coagulated egg white of boiled egg.

Flocculation
it’s a process of precipitation of protein at
its iso electric pH – precipitate is flocculum
Biologically important Peptide:
• Naturally occuring small polypeptide/ oligopeptides.
• Important biological activities.
1. Insulin: Pancreatic hormone, two polypeptide chain.
2. Glucagon: Pancreatic hormone, 29 residues, oppose
action of insulin.
3. Thyrotropin releasing hormone (TRH):
• Hypothalamic, 3 amino acids.
• Glu – His – Pro (Glu, Pro modified).
• Stimulate release of thyrotropin from anterior pitutary.
4. Oxitocin:
• Nanopeptide (9 amino acids).
• Posterior pitutary.
• Stimulates uterine contractions.
5. Glutathione:
• tripeptide glutamate, cysteine, glycine.
• γ – peptide bond not attacked by peptidase.
• glutamate linked to cysteine through γ – carboxyl
rather α – carboxyl group.
• Found in all cells except neurons.
• Exist as GSH & G-SSG so play role in oxidation-
reduction.
• Keep enzyme in active state.
• -SH functional group.
6. Vasopressin:
• 9 amino acids.
• Posterior pitutary.
• Increases blood pressure.
• Antidiuretic action.
 7. Angiotensin: Angiotensinogen protein synthesis by
liver present in blood.

Angiotensinogen Angiotensin I (10 a.a)

ACE

• Vasoconstrictor, hypertensive Angiotensin II (8 a.a)

• Elevates arterial pressure.

• Promotes synthesis of steroid hormone aldosterone.

Sodium retension

Captopril & enalapril - ACE

Hypertension & CCF
8. Gramicidins: antibiotic, 10 amino acids, Bacillus brevis.
9. Bradykinin:
• 9 amino acids, vasodilator.
• Formed under certain conditions.
• Contraction of smooth muscle.
• Responsible for intense pain by stimulating pain
receptors.
10. Enkepalins:
• Peptides formed in CNS.
• Binds to receptors in certain cells of brain and induce
analgesia.
11. Aspartame:
• dipeptide L- Aspartyl phenylalanyl methyl ester.
• unsuitable for phenylketonurias.
• Low calorie sweetner.