amino acid by LODHI

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.

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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

4

Aspartic Acid

5

Cysteine

6

Glutamic 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 triplehelical 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