Amino acids and proteins

1. Proteins and Amino Acids

2. Introduction
• Proteins are the most abundant organic molecules of the living
system.
• They occur in every part of the cell and constitute about 50% of the
cellular dry weight.
• Proteins form the fundamental basis of structure and function of life.

3. Introduction…
• The functions of proteins are grouped as
1. Structural functions:
Example: collagen and elastin found in bone matrix, vascular system and other organs and
α-keratin present in epidermal tissues
2. Dynamic functions:
Example: enzymes, hormones, blood clotting factors, immunoglobulins, membrane
receptors, storage proteins
• Proteins are polymers of amino acids

4. Amino acids
• Amino acids are a group of organic compounds containing two functional
groups— amino and carboxyl
• The amino acids are termed as α-amino acids, if both the carboxyl and amino
groups are attached to the same carbon atom
• The amino group (—NH2) is basic while the carboxyl group (—COOH) is acidic
in nature.

5. Amino acids
• There are about 300 amino acids occurring in nature but only
20 of them occur In proteins.
• The 20 amino acids are different in the R group.
• The amino acids (except glycine) possess optical isomerism.
• Contain asymmetric carbon atom (attached to four different groups)
• The amino acids of the proteins are L-α-amino acids (α-amino
group is on the left side configuration).

6. Amino acids…
• One of the 20 amino acids called proline is not an amino acid.
• It is an imino acid as It contains imino group (-NH).

7. Amino acids…
• At physiological pH (approximately pH=7 .4) the carboxyl group is
dissociated forming a negatively charged carboxylate ion (-COO-) and
the amino group is protonated, forming positively charged ion (-NH3
+)

8. Abbreviations and symbols of amino acids

9. Classification of amino acids
A. Amino acid classification based on the structure
A. Nutritional classification of amino acids
A. Amino acid classification based on their metabolic fate

10. A. Amino acid classification based on the structure
• Amino acids are classified according to the side chain:
a. Nonpolar, Aliphatic R Groups
b. Aromatic R Groups
c. Polar, Uncharged R Groups
d. Positively Charged (Basic) R Groups
e. Negatively Charged (Acidic) R Groups

11. A. Amino acid classification based on the structure

12. B. Nutritional classification of amino acids
• Based on the nutritional requirements, amino acids are grouped into
two classes:
1. Essential or indispensable amino acids:
• Cannot be synthesized by the body and need to be supplied through the diet
• These are 10 amino acids: Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine,
Methionine, Phenylalanine, Threonine, Tryptophan.(A.V. HILL, MP., T. T.)
• arginine and histidine are semi-essential amino acids
2. Non-essential or dispensable amino acids:
• The body can synthesize and need not be consumed in the diet
• These are 10 amino acids: glycine, alanine, serine, cysteine, aspartate, asparagine,
glutamate, glutamine, tyrosine and proline

13. C. Amino acid classification based on their
metabolic fate
• From metabolic view point, amino acids (carbon skeleton of amino
acids) are divided into three groups
1. Glycogenic amino acids
• These amino acids can serve as precursors for the formation of glucose or glycogen.
• Example: alanine, aspartate, glycine, methionine etc
2. Ketogenic amino acids
• Fat can be synthesized from these amino acids.
• Two amino acids leucine and lysine are exclusively ketogenic.
3. Glycogenic and ketogenic amino acids
• The four amino acids isoleucine, phenylalanine, tryptophan, tyrosine are precursors for
synthesis of glucose as well as fat

14. STRUCTURE OF PROTEINS
• Proteins are the polymers of L-α-amino acids linked together by
peptide bond
• The structure of proteins can be divided into 4 levels of organization:
1. Primary structure :
• The linear sequence of amino acids forming the backbone of proteins (polypeptides).
2. Secondary structure :
• The spatial arrangement of protein by twisting of the polypeptide chain.
3. Tertiary structure :
• The three dimensional structure of a functional protein.
4. Quaternary structure :
• proteins composed of two or more polypeptide chains (subunits)

15. STRUCTURE OF PROTEINS

16. STRUCTURE OF PROTEINS
• The term protein is generally used for a polypeptide containing more
than 50 amino acids.
• Some authors use ‘polypeptide’ even if the number of amino acids is
a few hundreds.
• They prefer to use protein to an assembly of polypeptide chains with
quaternary structure

17. PRIMARY STRUCTURE OF PROTEIN
• Each protein has a unique sequence of amino acids which is
determined by the genes contained in DNA.
• The amino acid composition of a protein determines its physical and
chemical properties
• The amino acids are held together in a protein by covalent peptide
bonds or linkages
• It is when the amino group of an amino acid combines with the carboxyl
group of another amino acid
• Conventionally, the peptide chains are written with the free amino
end (N-terminal residue) at the left, and the free carboxyl end (C-
terminal residue) at the right

18. PRIMARY STRUCTURE OF PROTEIN
Formation of a peptide bond.
Use of symbols in representing a peptide

19. SECONDARY STRUCTURE OF PROTEIN
• It is the conformation of polypeptide chain by twisting or folding
• Two types of secondary structures, α-helix and β-sheet