ASSIGNMENT

PRESENTED TO: Dr. ATIF ALI HASHMI

TOPIC: PROTEIN & AMINO ACIDS
BY: FARAH IQBAL LODHI
FROM: 2nd yr 1ST SEMESTER. CC
AMINO ACID

INTRODUCTION:-

 Aminoacids are building blocks of proteins.

 Proteins are composed of 20 different amino acids.
 Their chemical structure influences three dimensional structure of protein.
 They are important intermediates in metabolism.
 They can have hormonal and catalytic function.

DEFINITION:-

An organic compound containing an amino group (NH2), a carboxylic acid group

(COOH), and any of various side groups, especially any of the 20 compounds that
have the basic formula NH2CHRCOOH, and that link together by peptide bonds to
form proteins or that function as chemical messengers and as intermediates in
metabolism.

The amino acids differ from each other in the particular chemical structure of their R
group.

CLASSIFICATION OF AMINO ACIDS:-

On the basis of R group the most helpful point is to separate amino acids into:

1) Non-polar (Hydrophobic)
a. Aliphatic side chain
b. Aromatic side chain
2) Polar (Hydrophillic)
a. Positively charged R group
b. Negatively charged R group
c. Un charged R group

1) NON-POLAR AMINO ACIDS:-

 Only carbon & hydrogen in their side chain.

 Generally unreactive.
 Determining 3-D structure of proteins (as they tend to cluster on the inside of
molecule).

 Glycin is the simplest amino acid having single H atom as its side chain.

 Alanine, Valine, Leucine & Isoleucine have saturated hydrocarbon R groups

(i-e: they only have Hydrogen & Carbon linked by single covalent bonds).

 Leucine & Isoleucine are isomers of each other.

  Proline is rather an imino acid than amino acid because its side chain is
bonded to the backbone Nitrogen as well as to the alpha Carbon.

 The side chain of Methionine includes a Sulphur atom but remains

Hydrophobic in nature.

 Phenylalanine & Alanine with an extra benzene group on the end some times
called Phenyl group. Phenylalanine is highly hydrophobic & is found buried
within globular proteins.

alanine
phenylalanine
  Tryptophan is highly hydrophobic & structurally related to Alanine, but with 2
ring indole group added in place of the single aromatic ring found in
Phenylalanine.

POLAR HYDROPHILLIC R-GROUP:-

 Tyrosine is polar, very weakly acidic Phenylalanine with an extra OH group

attached.
 Serine & Threonine play important role in enzymes which regulate
phosphorylation & energy metabolism.

 Cysteine has sulphur containing side group. It tends to be more reactive. It is

not very polar.

• Cysteine is more important for its ability to link to another cysteine via
sulphur atom to form a covalent Di-sulfide bridge.

 Asparagine & Glutamine are amide derivatives of Aspartate (Aspartic acid) &
Glutamate ( Glutamic acid).
NEGATIVELY CHARGED R-GROUP:-

 Two amino acids with negatively charged side chains ASPARTATE (Aspartic
acid) & GLUTAMATE (Glutamic acid).
 They confer a –ve charge on the protein of which they are a part.
POSITIVELY CHARGED R-GROUP:-

 Lysine & Arginine (pK: 10) are +vely charged at neutral pH.
 Histidine (pK: 6.5) can be uncharged or +vely charged depending on its local
environment. It has important role in catalytic mechanism of enzymes.
CLASSIFICATION BASED ON CHEMICAL
CONSTITUTION:-

 Small amino acids: Glycin & Alanine.

 Branched amino acids: Valine, Leucine & Isoleucine
 Hydroxyl amino acids: Serine & Threonine
 Sulphur amino acids: Cysteine & Methionine
 Aromatic amino acids: Phenylalanine, Tyrosine & Tryptophan
 Acidic amino acids & their derivatives: ASPARTATE, Asparagine &
GLUTAMATE , Glutamine.
 Basic amino acids: Lysine, Arginine & Histidine
 Imino acids: Proline

ESSENTIAL AMINO ACID:

 Required in diet.
 They must come from food or amino acid supplements.

1 Isoleucine*
2 Leucine*
3 Lysine
4 Methionine
5 Phenylalanine
6 Threonine
7 Tryptophan
8 Valine*

Food Sources: Fish - meat - poultry - cottage cheese - peanuts - lentils

*= BCAA, Branched-Chain Amino Acids, all important in muscle
recovery.
NON-ESSENTIAL AMINO ACID:-

 Not required in diet.

 The body can make these amino acids from the above essential amino acids.

1 Alanine
2 Arginine*
3 Asparagine
Aspartic
4
Acid
5 Cysteine
Glutamic
6
Acid
7 Glutamine
8 Glycine
9 Histidine*
10 Proline
11 Serine
12 Tyrosine

*= These are Essential for infants, since their bodies cannot produce them yet.
STRUCTURE OF PROTEIN:-
1) PRIMARY STRUCTURE:

The sequence of amino acid in a polypeptide chain.

2)SECONDARY STRUCTURE:-

Within the long protein chains there are regions in which the chains are organized into
regular structures known as alpha-helices (alpha-helixes) and beta-pleated sheets.
These are the secondary structures in proteins.

(A) ALPHA HELIX:

In an alpha-helix, the protein chain is coiled like a loosely-coiled spring.

(B) BETA PLEATED:

In a beta-pleated sheet, the chains are folded so that they lie alongside each other.
3) TERTIARY STRUCTURE:-

The folding back of a molecule upon itself and held together by disulfide bridges and
hydrogen bonds. This adds to the proteins stability.

4) QUATERNARY STRUCTURE:

Complex structure formed by the interaction of 2 or more polypeptide chains.

HEMOGLOBIN STRUCTURE:-

 A hemoglobin molecule consists of four polypeptide chains.

 Two alpha chains, each with 141 amino acids and two beta
chains, each with 146 amino acids.
 The protein portion of each of these chains is called "globin".
 The alpha and beta globin chains are very similar in structure.
 Each alpha or beta globin chain folds into 8 helical segments
(A- H) which, in turn, fold to form globular tertiary structures .
 The folded helices form a pocket that holds the working part of
each chain, the heme.
 A heme group is a flat ring molecule containing carbon,
nitrogen and hydrogen atoms, with a single Fe2+ ion at the
center.
 In a heme molecule, the iron is held within the flat plane by
four nitrogen ligands from the porphyrin ring.

Hemoglobin
COLLAGEN:-
A collagenous fiber is a bundle of many macrofibrils. Each macrofibrilis in turn a
bundle of numerous microfibrils. The microfibril is composed of many tropocollagen
helices. Each of these assembled from three polypeptide chains twisted together.

STRUCTURE OF COLLAGEN:-

1) AMINO ACID SEQUENCE:-

Collagen is rich in praline and glycin, both of which are important in the formation of
the triple-stranded helix. Glycin is found in every third position of the polypeptide
chain.

2) TRIPLE-HELICAL STRUCTURE:-

Collagen has an elongated, triple-helical structure that places many of its amino acid
side chains on the surface of the triple-helical molecule.

3) HYDROXYPROLINE & HYDROXYLYCIN:-

Collagen contains hydroxyproline (hyp) and hydroxylycine (hyl) which are not
present in many other proteins. Hydroxyproline is important in stabilizing the triple-
helical structure of collagen because it maximizes interchain hydrogen bond
formation.

4) GLYCOSYLATION:-

Most commonly, glucose and galactose are sequentially attached to the poly peptide
chain prior to triple-helix formation.

Collagen