Amino Acids

Amino Acids are the building units of proteins. Proteins are polymers of amino acids linked together by what is called “ Peptide bond” (see latter).

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

Structure of amino acids:

Each amino acid has 4 different groups attached to α- carbon ( which is C-atom next to COOH). These 4 groups are : α-amino group, COOH group, Hydrogen

atom and side Chain (R)

R

Classification of amino acids

1- Chemical classification: According to number of COOH and NH2 groups i.e. according to net charge on amino acid and

A- Monobasic, monocarboxylic amino acids i.e. neutral or uncharged:

R

According to chemical structure of R group, neutral amino acids are subclassified into:

I- Aliphatic, neutral amino acids: (6 amino acids)

1- Glycine (Gly): R= H

2- Alanine (Ala) R= CH3

3, 4, 5-Branched chain amino acids: valine, leucine and isoleucine R is branched Valine (Val): R= isopropyl group

Leucine (Leu): R= isobutyl gp

Isoleucine (Ile) R = is isobutyl

R is isobutyl in both leucine and isoleucine but branching is different: in leucine → branching occurs on γ carbon

in isoleucine→ branching occurs on β- carbon

6- Proline: In proline, amino group enters in the ring formation being α-imino group so proline is an α-imino acid rather than α-amino acid

Valine

Leucine

Isoleucine

II- Neutral Sulfur containing amino acids: 2 amino acids

1- Cysteine (Cys): R= CH2SH

What is cystine?

2- Methionine (Met):

III- Neutral, hydroxy amino acids: 2 amino acids 1- Serine (Ser): R= CH2OH

2- Threonine (Thr):

Formation of cystine

The bond S-S in cystine is called: disulfide bond

Serine

Threonine

Cysteine

Methionine

VI- Neutral aromatic amino acids: includes 3 amino acids

1- Phenyl alanine (Phe) :

It’s alanine in which one hydrogen of CH3 is substituted with phenyl group. So it’s called phenyl alanine.

2- Tyrosine (Tyr): - it is P- hydroxy phenyl alanine

- it is classified as phenolic amino acid

3- Tryptophan: contains indol ring

Phenylalanine

Tyrosine

Tryptophan

VI- Neutral amino acids with amide group in R (2):

1- Aspargine (Asn):

2- Glutamine (Gln):

• At physiological PH (7.4), in neutral amino acids, -COOH

group is dissociated forming a negatively charged

carboxylate ion (COO-) and amino group is protonated

forming positively charged ion (NH3+) forming Zwitterion

B- Basic amino acids: contain two or more NH2 groups or nitrogen atoms that act as base i.e. can bind proton. At physiological pH, basic amino acids will be positively charged.

a- Lysine( Lys)

b- Arginine(Arg): contains guanido group:

c- Histidine (His): contains imidazole ring.

guanido

C- Acidic Amino acids:

e.g. a- Aspartic acid (Asp) (aspartate),

b- Glutamic acid (Glu) (glutamate)

at physiological pH, acidic amino acids will carry negative charge .

Summary:

A- Neutral amino acids (15 amino acids)

Classified according to R into

- Aliphatic amino acids including glycine, alanine, valine, leucine,

isoleucine and proline

- Sulfur containing amino acids including: cysteine and methionine

- Hydroxy amino acids including serine and threonine

- Aromatic amino acids including phenylalanine, tyrosine and

tryptophan

- Amino acids containing amide group including aspargine and

glutamine

Lysine

Arginine

Histidine

Basic amino acids (3)

Aspartic acid

Glutamic acid

Acidic amino acids (2)

-At physiologic pH, neutral amino acids are present as Zwitterion

(carry equal positive and negative charges) so it is neutral (not

charged).

- At physiological pH, basic amino acids will be positively charged.

While acidic amino acids are negatively charged

So, Basic and acidic amino acids are called charged amino acids