Biochemistry of Amino Acid

Dr.Manoranjan Shrestha,
MBBS,MD
Department of
Biochemistry
Introduction of Amino Acid-
Protein- polymer of amino acid
Amino acid-

 Defination
 In nature, > 300 AA but only 20 are standard AA found in
structure of protein.
 Peptide Bond

 Peptide chain read/write with N-terminal to C-terminal eg-

polypeptide hormone insulin (51 AA).

 Function
Classification of amino acids:

Base on:

 The Structural and Chemical nature.

 Nutritional requirement !!!
 Metabolic fate etc !!!
Classification base on the structural and chemical nature.
Classification base on the structural and chemical nature.
Classification base on Nutritional requirement
1. Essential- 10 AA
(VITTAL H LMP)
• Arginine, Valine, Histidine, isoleucine, Leucine, Lysine,
Methionine, Phenylalanine, Threonine, Tryptophan.
• Ah….. Semiessential

2. Non-essential- 10 AA
Classification base on Metabolic fate:
I. Glucogenic AA-

II. Ketogenic AA- Leucine and Lysine.

III.Glucogenic and ketogenic AA- PITT

 Isoleucine
 Phenylalanine
 Tryptophan
 Tyrosine
Protein-
Protein- polymer of amino acid
Peptide bond-

Peptide chain read/write with N-terminal to C-terminal eg- polypeptide

hormone insulin (51 AA).

Peptide- short chain of AA.

Polypeptide- > 10 AA or longer chain of AA
Function of protein in human body:
 Catalytic eg- enzymes (Glucokinase/hexokinase, lipase)
 Transporting eg- Hb, albumin.
 Receptor eg- insulin receptor
 Metabolic eg- glycogenin
 Hormonal eg- ADH, oxytocin, TRH
 Hemostatic eg- coagulation factors
 Protective eg-antibodies (defense against disease)
 Contractile proteins in muscles for movement eg- actin,
myosin
 Structural protein eg- collagen, elastin
Structure of proteins
Four levels of protein structure:

1) Primary structure
2) Secondary structure
3) Tertiary structure
4) Quaternary structure
Primary structure of protein:
AA sequence in a polypeptide chain linked via peptide bond.

 Determine overall 3D structure.

 Read from N C terminus.

Secondary structure of protein:

 α-helix, β-pleated sheet/strand.

α-helix

 Spiral or helical structure.

 Side chain are extending outward from
central axis.
 H-bond between the peptide bond of
carbonyl oxygen and amide hydrogen,
extend up and parallel.
 Each turn contains 3.6 AA.
β-pleated sheet/strand

 Composed of two or more peptide chains

which are fully extended and adjacent to
each other.
 H-bond are perpendicular to the polypeptide
backbone.
 Two or more polypeptide chain arranged
either parallel or antiparallel.
 single polypeptide chain folds on itself.
Tertiary structure of protein:
The polypeptide chain is folded in unique 3D structure
which is determine by primary AA sequence.

The most important factor/driving force for folding to

occur is due to formation of-
1. Hydrophobic bonds
2. Disulfide bonds
3. Hydrogen bonds
4. Electrostatic/ ionic bonds
Quaternary structure of protein:
The arrangement of more than one polypeptide subunits held
together by noncovalent interaction is called quaternary
structure.
RECALL- Structure of protein
Classification of Protein-

 Several ways-

Classification based on function-

 Catalytic protein eg- enzymes

 Structural protein eg- collagen, elastin
 Contractile protein eg- actin, myosin
 Transport protein eg- hemoglobin, albumin
 Regulatory hormones protein eg- insulin, ACTH
 Protective protein eg- immunoglobulin, clotting factors
Classification based on composition and solubility

I. Simple protein-
 Albumin- soluble in water and coagulated by heat.
 Globulin- soluble in dilute salt solution and coagulated by
heat

II. Conjugated protein-

 Glycoprotein
 Lipoprotein
 Metalloprotein

III. Derived protein-

 Degradation products of native proteins
 Protein  peptides  amino acids
Classification based on nutritional value-
I. Complete protein-
Contain all ten essential amino acid. Eg- egg, casein of milk

II. Incomplete protein-

Lack one or more essential amino acid. Eg- pulses, deficient of
methionine, cereals lack in lysine

III. Poor protein-

Lack in many essential amino acid.