Amino acids

• Organic molecules that are the building block of

proteins.

• There is 20 α-amino acids commonly found in proteins

• They have a carboxyl group and an amino group bonded

to the same carbon atom [the α-carbon]).

• Amino acids differ from each other in their side chains

(R-group) which vary in structure, size, and electric

charge and which influence the solubility of the amino

acids in water.

• All amino acids have free α-carboxyl group.

• All amino acids except proline have free unsubstituted α-

amino group.

• The common amino acids of proteins have been assigned

three-letter abbreviations and one letter symbols.

Example:

Alanine: Ala

Serine : Ser

Classification on the basis of their R-group: depend on the polarity

of their R-groups [tendency to interact with water at biological PH

(near PH 7.0)]

• The polarity of the R-groups varies widely from non-polar and

hydrophobic (water-insoluble) to highly polar and hydrophilic

(water-soluble).

1) Amino acids with non-polar (hydrophobic) R-groups.

2) Amino acids with aromatic R-groups .

3) Amino acids with polar, uncharged R-group

4) Amino acids with positively charged (basic) R-group.

5) Amino acids with negatively charged (acidic) R-group.

Optical activity of amino acids

• All standard amino acids except glycine have an asymmetric

carbon atom [α-carbon atom bound to four different substituent

groups (i.e., a carboxyl group, amino group, R-group, and a

hydrogen atom).

• The asymmetric α-carbon atom is thus a chiral centre.

• Because amino acids that obtained from the hydrolysis of proteins

have one or more asymmetric carbon atoms

so all amino acids except glycine are optically active.

The α-carbon atom of all amino acids except glycine is

asymmetric, and thus amino acids exist in two stereoisomeric

forms: L-isomer, D-isomer.

• L- and D-isomer of amino acid depend on the configuration

of the four different substituents around the asymmetric

carbon atom.

Example:

Alanine

• Nearly all biologically occurring compounds containing

asymmetric carbon atom are found in nature in only one

stereoisomers form either D or L.

• Except for glycine, the amino acids present in protein

molecules are L-stereoisomers.

• When a compound has two or more asymmetric carbon

atom, it has 2n possible stereoisomers (n = number of

asymmetric carbon atoms).

Peptides

• Two or more amino acids covalently joined by peptide bonds.

• Two amino acid molecules can be covalently joined by

peptide bond to yield dipeptide.

• This linkage is formed by removal of the element of H2O

from the α-carboxyl group of one amino acid and the α-

amino group of the other by the action of strong reducing

agents.

• Three amino acids can be joined by two peptide bonds to form

a tripeptide. Similarly we have tetrapeptides and

pentapeptides. When there are many amino acids joined in the

same way (the structure is called a polypeptide).

• The amino acid residue at the end of peptide having a free α-

amino group is the amino terminal residue (N-terminal

residue).

• The residue at the opposite end, which has a free carboxyl

group, is the carboxyl terminal residue (C-terminal residue).

• Peptides contain only one free α-amino group and one free α-

carboxyl group at their terminal residues.

Proteins

• Proteins are made up of large numbers of amino acids

linked into chains by peptide bonds joining the amino

group of one amino acid to the carboxyl of the next.

• The number of amino acids present varies from about a

hundred to several thousands in different proteins.

• Some proteins are composed of only one polypeptide chain

while others are composed of two or more polypeptide

chains (multi-subunit proteins) held together by non-

covalent bonds.

Classification of proteins:

A) proteins can be classified

on the basis of the chemical

composition.

B) proteins can be classified

on the basis of shape.

C) proteins can be

classified on the basis

of their biological

function.

A) proteins can be classified on the basis of the chemical

composition:

a) Simple proteins b) conjugated proteins

a) Simple proteins:

are those proteins which upon hydrolysis give only amino acids.

Example:

ribonuclease A, chymotrypsin.

b) Conjugated proteins:

are proteins which yield upon hydrolysis organic or

inorganic components in addition to the amino acids.

•The non-protein part is called the prosthetic group.

•Conjugated proteins are classified on the basis of the

chemical nature of their prosthetic groups:

i) nucleoproteins

ii) glycoproteins

iii) lipoproteins

iv) hemoproteins

v) metalloproteins

vi) phosphoproteins

B) proteins can be classified on the basis of shape:

a) Globular proteins b) Fibrous proteins

a) Globular proteins:

• They are generally soluble in water.

• The polypeptide chains are tightly folded into a globular shape.

Example:

enzymes, hemoglobin, myoglobin

b) Fibrous proteins:

• They are insoluble in water

• Their polypeptide chains are arranged in long

strands (elongated in the form of fibers).

Example:

Collagen, keratin

C) proteins can be classified on the basis of their

biological function:

i) enzymes

ii) Transport proteins

[e.g., hemoglobin iii) Nutrient and

lipoprotein] storage proteins

[e.g., casein

ferritin] iv) contractile or

mobile proteins

(e.g., actin, myosin)

v) structural

proteins

vi) defense proteins (e.g., α-keratin,

[e.g., immunoglobulins(antibodies) collagen)

fibrinogen and thrombin]

vii) Regulatory proteins

(protein hormones)