Proteins and Amino Acid

Proteins are the most abundant organic molecule of the living system .

They occur in every part of the cell and constitute about 50% of the cellular weight.

The term protein is derived from a Greek word Proteios, meaning holding the first place.

Function of protein:

1 Static( structural ) function: Certain protein perform brick and mortar roles and are primarily responsible for structure and strength of body.

these include collagen and elastin found in bone matrix, vascular system and other organs α- keratin present in epidermal tissue.

Dynamic function: These include protein acting as Enzymes, hormones, blood clotting factor, immunoglobulin, membrane receptors, storage protein , beside their function in genetic control, muscle contraction, respiration etc.

Protein performing dynamic function are appropriately regarded as the working horses of cell.

Composition of protein:

Carbon: 50 - 55%

Hydrogen: 06- 7.3%

Oxygen: 19 - 24%

Nitrogen: 13 - 19%

Sulfur: 0 - 4%

• Proteins on hydrolysis with concentrated HCl for several hours yield L- α- Amino acid. Therefore, protein are the polymer of L- α- Amino acid.

• Standard amino acids: as many as 300 amino acids occur in nature of these , only 20 known as standard amino acid are repeatedly found in the structure of protein, isolated from different form of life animal, plant and microbial.

What is an amino acid?• Twenty different kinds of amino acids are used by living organisms to produce proteins• An amino acid is a molecule containing an amine (-NH2) an acid (-COOH) and a third chemical group (-R) that defines the amino acid. In glycine, the simplest amino acid, R is –H, or a hydrogen atom. In alanine, R = -CH3. The R groups give specific properties to each amino acid, and to the proteins composed of amino acids.

R |

Structure of an amino acid: H2N – C – COOH H

• Amino Acid:

COOH

NH2

COOH

H2NH H R D- L-

naturally-occurring amino acids are generally L-series

Classification of Amino Acids

C C

O

O –

RR

H

H3N+

• The amino acids obtained by hydrolysis of proteins differ in respect to R (the side chain).

• The properties of the amino acid vary as the structure of R varies.

Amino acid containing hydroxyl group (-OH)

Amino acid containing Sulfur group

Acidic amino acid and their amides

Basic amino acid

Aromatic amino acid

Imino acid

• Proline is the only amino acid that contains a secondary amine function. Its side chain is nonpolar and cyclic.

Amino Acid classification based on polarity

27- 15

Non-Polar

Polar

UnchargedCysteineProlineSerine

GlutamineAsparagine

HydrophobicTryptophan

PhenylalanineIsoleucineTyrosineLeucineValine

Methionine

AmbivalentGlycine

ThreonineAlanine

ChargedArginine (+)

Glutamic acid (-)Aspartic Acid (-)

Lysine (+)Histidine (+)

Amino acid classification based on metabolic fat

• The carbon skeleton of amino acid can serve as a precursor for the synthesis of glucose (glycogenic) , or fat (ketogenic).

1. Glycogenic amino acid: these amino acid can serve as precursors for the formation of Glucose or Glycogen.

e. g. Alanine, Aspartate, glycine, Metheionine

2. Ketogenic Amino Acid: fat can be synthesized from these Amino acids. Two amino acid Leucine and Lysine.

3. Glycogenic and Ketogenic Amino Acid: the four amino acids isoleucine, phenylalanine, trytophan, tyrosine are precursor for the synthesis of glucose and fat.

Selenocystein – the 21st amino acid: it is found that the active sites of certain enzymes /protein (selenoprotein) e.g. Glutathion peroxidase, glycine reductase, thioredoxine reductase. Selenocystein is an unusual amino acid containing the trace element Selenium in place of sulfur atom of cysteine.

Cysteine Selenocystein

Essential AA Nonessential AAHistidine AlanineIsoleucine Arginine **Leucine AsparagineLysine Aspartic AcidMethionine Cysteine **Phenylalanine Glutamic acidThreonine Glutamine **Tryptophan Glycine **Valine Proline **

SerineTyrosine **

Properties of Amino Acid• Physical properties:• Solubility: most of the amino acids are soluble in water

and insoluble in inorganic solvent:• Melting point: amino acids are generally melt at higher

temperature , often above 200°C • Taste : amino acids may be sweet (Gly, Ala, Val),

tasteless (Leu) or bitter (Arg, ILe).• Monosodium Glutamate (Ajinomoto) is used as

flavouring agent in food industry, chinese foood to increase taste and flavour.

27- 20

CHO

H OH

CH2OH

CHO

HO H

CH2OH

D - L -

=

R

C CO2HH

H2N

(L) - Amino Acids(-) -

=

CHO

CH2OHH

HO

(S) - Glyceraldehyde(-) -

R

CHH2N CO2H

All DNA encoded aa are

All are chiral, except GlycineR = HAll DNA

encoded aa are usually L-

Amino acids as ampholytes: amino acid containing both acidic (-COOH ) and basic (-NH2) groups. They can donate proton and accept proton.

Zwitterions or dipolar ion

• The name Zwitter derived from the German word which mean hybrid. Zwitter ion is a hybrid molecule containing positive and negative ionic group.

• The amino acids rarely exists in a neutral form with free carboxylic (-COOH ) and free amino (-NH2) groups.

• In strongly acidic pH the amino acid are positively charged, while in strongly alkaline pH it is negatively charged.

• Each amino acid has a characteristics pH at which it carries both positive and negative charge and Exist as Zwitterions.

Isoelectric pH• pH at which amino acids exist as the zwitterion

(neutral) and carries no net charge. Thus molecule is electrically neutral.

• The pl value can be calculated by taking the average pKa values corresponding to the ionizable groups. For example leucine has two ionizable groups , and its pl value can be calculated as follows.

• Leucine exists as cation at pH below 6 and anion at pH above 6. at the ispelectric pH leucine is found as Zwitterions .

• Titration curve of Amino acid: in the graphical representation of Leucine titrarion at low pH , Leucine exists in fully protonated forms as cation. As the titration proceeds with NaOH, Leucine loses its protons and at isoelectric pH its become Zwitterions. Further titration results in formation of anionic form of Leucine.

The isoelectric point (pI) of an amino acid is the pH atwhich it has no net charge

Structure and pH

Chemical properties• Reaction due to –COOH group

1. Amino acid form salts (-COONa) with base, and Ester (-COOR) with alcohol.

2. Decarboxylation: Amino acid undergo deacarboxylation to produce amines.

this reaction assumes significance in the living cell due to the formation of many biologically important amine. These include histamine, tyramine, γ-amino butyric acid from the amino acid histidine, tyrosine and glutamate respectively.

3. Reaction with ammonia: the carboxyl group of dicarboxylic amino acid reacts with NH3 to form amide. Aspartic acid + NH3

Aspargine

Reaction due to NH2

4. The amino acid behave as bases and combine with acids to form salts.

5. Reaction with ninhydrine: the α- Amino acidreact with ninhydrine to form a purple , blue or pink color complex(Ruhemann’s purple)

Amino acid + ninhydrine keto acid+NH3+

CO2+ Hydrindantin

Hydrindantin+ NH3+Ninhydrine

Ruhemann’s purple

6. Colour reaction

7. Transamination

8. Oxidative deamination

Non – standard amino acidA. Amino acid derivatives in proteins: some of these

amino acid undergo specific modification after the protein synthesis occurs. These derivatives of amino acids are very important for protein structure.

• Collagen: the most abundant protein in mammals contain 4- hydroxyproline and 5- hydroxylysine.

• Histones: the protein found in association with DNA- contain many methylated and phosphoraylated amino acid.

• γ- Carboxyglutamic acid is found in certain plasma protein involved in blood clotting.

A mixture of amino acids can also be separated on thebasis of polarity