Amino acid sdk (biochem)

AMINO ACID SDK

February 2, 2013

Amino Acids, Peptides, ProteinsOBJECTIVES

• What are Amino acids• Structure and naming of amino acids• Standard and Non-standard amino acids• What is peptide bond and peptides• Ionization behavior of amino acids and peptides• Structure and properties of peptides

AMINO ACIDS

ØAmino acids are organic acids containing an amine group, they are

the building units of proteins.

ØThere are about 300 amino acids occur in nature. Only 20 of them

occur in proteins.

Structure of amino acids:

ØEach amino acid has 4 different groups attached to α- carbon ( which is C-atom next toCOOH).

ØThese 4 groups are :

ØAmino Group,

ØCOOH Group

ØHydrogen Atom

ØSide Chain (R)

COOH|

H2N—C — H|R side chain

Structure of amino acids:

• The most common amino acids are alpha-amino(a-amino acids) acids and the most common aminoacids are the L- alpha-amino acids.

• Biochemical designation: start from α-carbon andgo down the R-group

Structure of amino acids:

D & L Amino Acids

At physiological PH (7.4), COOH group is dissociated forming a

negatively charged carboxylate ion (COO-) and H2N amino

group is protonated forming positively charged ion (NH3+)

forming Zwitter ion

Amino Acids Physiological PH

• Both the –NH2 and the –COOH groups in an amino acid undergo ionization in water.

• At physiological pH (7.4), a zwitterion forms – Both + and – charges

– Overall neutral

– Amphoteric• Amino group is protonated

• Carboxyl group is deprotonated

• Soluble in polar solvents due to ionic character

• Structure of R also influence solubility

Zwitterions

Classification of Amino acids

Amino acids are classified on following bases1. On the basis of protein formation2. On the basis of Side chain3. Nutritional classification4. On the basis of polarity

• The building blocks of proteins

• These 20 A.A. are the only A.A. coded for by DNA .• Each amino acid (except proline) has a carboxyl group, an amino group, and a

distinctive side chain “R-group” bonded to the α -carbon atom.

• Proline has imino (NH)group

Standard & Nonstandard amino Amino Acids:

Nonstandard amino acids are not coded for protein synthesis

by DNA. eg. Ornithine, Citrulline

Non-standard amino acids

↕collagen

Myosin

Ca2+ binding proteins

Ca2+

Elastin

Redox Proteins

Classification on the basis of side chain

• Acidic side chain • Basic side chain • Neutral

– Aliphatic side chain – Aromatic side chain

• Hetero cyclic– Hydrocarbon side chain – Hydroxylic side chain– Sulphur – containing side chain – Imino side chain

Sulfur containing•Cysteine•Methionine

Neutral Acidic•Aspartic•Glutamic•Asparagine•Glutamine

Basic•Arginine•Lysine

Aliphatic Aromatic•Phynylalanine•Tyrosine

Heterocyclic•Tryptophan•Proline•Histidine

With a hydrocarbon side chain

•Glycine•Alanine•Valine•Leucine•Isoleucine

Hydroxyl containing

•Serine•Threonine

1. Chemical classification of amino acids

Sulfur containing•Cysteine•Methionine

Neutral Acidic•Aspartic•Glutamic•Asparagine•Glutamine

Basic•Arginine•Lysine

Aliphatic Aromatic•Phynylalanine•Tyrosine

Heterocyclic•Tryptophan•Proline•Histidine

With a hydrocarbon side chain

•Glycine•Alanine•Valine•Leucine•Isoleucine

Hydroxyl containing

•Serine•Threonine

1. Chemical classification of amino acids

Aliphatic Side Chain • Glycine , Alanine , Valine Leucine Isoleucine

C

COOH

H

H2N H C

COOH

H

H2N CH3

Glycine Alanine

Aromatic Side Chain

• Phenylalanine Tryptophan & tyrosine

C

COOH

H

H2N CH2

N

HTryptophan

Sulphur – Containing Side Chain• Cysteine Methionine

C

COOH

H

H2N CH2 CH2 S CH3

C

COOH

H

H2N CH2 SH

Methionine

Cysteine

Cystine

C

COOH

H

H2N CH2 S S CH2 C

H

NH2

COOH

Acidic Side Chain

C

COOH

H

H2N CH2 C

O

O-

C

COOH

H

H2N CH2 CH2 C

O

O-

Aspartic acid

Glutamic acid

Basic Side Chain

C

COOH

H

H2N CH2 CH2 CH2 CH2 NH3+

C

COOH

H

H2N CH2 CH2 CH2 NH C

NH2+NH2

C

COOH

H

H2N CH2

HN N

Lysine

Arginine

Histidine

Amide Side Chain

C

C O O H

H

H2N C H2 C

ON H2

C

COOH

H

H2N CH2 CH2 C

ONH2

Asparagine

Glutamine

Hydroxylic Side Chain

C

COOH

H

H2N CH2 OH

C

COOH

H

H2N CH CH3

OH

Serine

Threonine

Imino Side Chain

C

COOH

H

N

CH2CH2

CH2

H

Proline

2. Nutritional Classification

• Essential amino acid/ Indispensable amino acid

• Nonessential amino acid/ Dispensaable amino

acid.

Classification of amino acids based on their nutritional value

1-Essential amino acids ;They are those amino acids that cannot be synthesized in the body thus they are essential in the diet.

Essential amino acids include the following amino acids ;

MATT VIL PHLY2- Non-essential amino acids; They are those amino acids that can be synthesized in

the body thus they are non-essential in the diet.

3-Classification according to the polarity of the side chain R.

a)Non-polar amino acids.Each of these amino acids has a non-polar side chain that does not bind or give

off protons or participate in hydrogen or ionic bonds.

b)Polar amino acids 1-Polar uncharged amino acids These amino acids have zero net charge at neutral pH2-Polar charged amino acids Ø Polar acidic or positively charged amino acids.The amino acids acid are proton donors Ø Polar basic or negatively charged amino acidsThe side chains of the basic amino acids accept protons

Peptide Bond

• Acid amide linkage. • α-carboxyl group of one amino acid join with

the α-amino group of another amino acid.• It is covalent linkage

C

H

C

R1

H2N

O

OH + C

H

C

R2

H2N

O

OH C

H

C

R1

H2N

O

N C

H

C

H

R2

O

OH + H2O

Peptide bond

Characteristic of Peptide bonds • Peptide bonds are not broken by conditions that denature

proteins, such as heating or high concentrations of urea.• Prolonged exposure to a strong acid or base at elevated

temperatures is required to hydrolyze these bonds non-enzymatically.

• The peptide bond has a partial double-bond character, that is, it is shorter than a single bond,

• It is rigid and planar.• The peptide bond is generally a trans bond

Peptide bond formation

Make sure you clearly indicate whether water is a product or reactant!

Zwitterion form

Formation: dehydration reaction

Highlight the peptide bond

• More amino acids can be added using the same condensation reaction– oligopeptide/polypeptide/protein

Peptides and Proteins

Fig 3-14

R1 R2 R3 R4 R5

C

H

C O O HH2N

C H3

+

+ H2O

C

H

C O O HH2N

H

C

H

C O O HH2N

C H2O H

+

Glycine ( Gly )Alanine ( Ala ) Serine (Ser )

2C

H

CH2N

C H3

O

N

H

C

H

H

C

O

N

H

C

H

C H2O H

C

O

O H

Alanylglycylserine (Ala-Gly-Ser)

Peptide Bond

Clinical Importance

1. Synthesis of body proteins. 2. Synthesis of essential nitrogen compounds e.g ( Histamine,

DNA,RNA).3. Synthesis of glucose, fat, energy.4. Synthesis of hormones(Thyroid Hormones) 5. Synthesis of neurotransmitters(dopamine, epinephrine,

norepinephrine, serotonin, and histamine)

Thank you