Proteins lecture 10

1. Lecture 10
Proteins

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
 They form the fundamental basis of structure and
function of life

3. Origin
 The term protein is derived from a Greek word
Proteios, meaning holding the first place
 Mulder (Dutch chemist) in 1983 used the term
proteins for the higher molecular weight nitrogen-
rich and most abundant substances present in
animals and plants

4. Functions of proteins
 Static (structural) functions:
e.g. Elastin, collagen, α-Kertain
 Dynamic functions:
As enzymes, hormones, blood clotting factors,
immunoglobulin, membrane receptors, storage
proteins, muscle contraction, respiration (working
horses of cell)

5. Elemental composition of proteins
 Proteins are predominantly constituted by five
major elements in the following proportion
Carbon 50-55%
Hydrogen 6-7.3%
Oxygen 19-24%
Nitrogen 13-19%
Sulfur 0-4%
Beside these proteins also contain other elements
as P, Fe, Cu, I, Mg, Mn, Zn etc

6.  Proteins are polymers of amino acids and yield
L-α-amino acids on complete hydrolysis with
concentrated HCL for several hours

7. Standard amino acids
 As many as 300 amino acids occur in nature- of
these only 20-known as standard amino acids are
repeatedly found in the structure of proteins
isolated from different forms of life –animal, plant
and microbial
 This is because of the universal nature of the
genetic code available for the incorporation of
only 20 amino acids

8. Amino acids
 Amino acids are a group of organic compounds
containing two functional group
 Amino (-NH2)-basic
 Carboxyl (-C00H)-acidic

9. General structure
 The amino acids are termed as α-amino acids if both
the carboxyl and amino groups are attached to the same
carbon atom
 The Alpha carbon atom binds to side chain represented by
R which is different for each of the 20 amino acids

10. Classification of amino acids
 A. Classification based on the structure

11. B. Classification based on polarity
Four groups
1. Non-amino acids
These are also referred to as hydrophobic. They
have no charge on the “R” group
e.g. alanine, leucine, isoleucine
2. Polar amino acids with no charge on R group
They posses groups such as hydroxyl, sulfhydryl
and amide and participate in hydrogen bonding
of protein structure
Glycine, serine, threonine, cysteine,

12. 3. Polar amino acids with positive R group
e.g. lysine, arginine and histidine are included in
this group
4. Polar amino acids with negative R group
e.g. Aspartic acid and glutamic acid

13. c. Nutritional classification of amino
acids
1. Essential or indispensible amino acids
The amino acids that cannot be synthesized by the
body and therefore need to be supplied through
the diet
They are required for proper growth and
maintenance of individuals
e.g. PVT TIM HALL

14. 2. Non-essential or dispensable amino acids
The body can synthesize about 10 amino acids to
meet the biological needs hence they cannot be
consumed in the diet
e.g. Glycine, alanine, serine serine, cysteine,
aspartate, asparagine, glutamate, glutamine,
tyrosine, proline

15. D. Classification based on their
metabolic fate
The carbon skeleton of amino acids can serve as a
precursor for the synthesis of glucose
(glucogenic) or fat (ketogenic) or both
Three groups:
1. Glycogenic amino acids (alanine, aspartate,
glycine, methionine)
2. Ketogenic amino acids (leucine, lysine)
3. Glycogenic and ketogenic (isoleucine, phenyl
alanine, tryptophan, tyrosine)

16. Selenocysteine-the 21st amino acid
 It is found at the active site of various
enzymes/proteins (selenoproteins) eg Glutathione
peroxidase, glycine reductase
 It contain the trace element selenium in place of
the sulfur atom of cysteine
 Codon UGA

17. Physical properties of amino acids
1. Solubility:
Most of the amino acids are usually soluble in water
and insoluble in organic solvents
2. Melting point:
Generally melt at higher temperature often above
200o
C
3. Taste:
They may be sweet , tasteless or bitter

18. 4. Optical properties:
All the amino acids except glycine posses optical
isomers due to the presence o asymmetric
carbon atom
5. Amino acids as ampholytes
Amino acids contain both acidic (-COOH) and basic
(-NH2) groups. The can donate and accept a
proton
Zwitterion or dipolar ion

19. Chemical properties
The general reactions of amino acids are mostly
due to the presence of two functional groups
 Carboxyl group
 Amino group

20. Reactions due to –COOH group
1. Amino acids form salts with bases and esters
with alcohol
2. Amino acids undergo decarboxylation producing
corresponding amines (histamine, tyramine)
3. The carboxyl group of dicarboxylic amino acids
reacts with ammonia to form amide
Aspartic acid + NH3 Asparagine
Glutamic acid + NH3 glutamine

21. Reactions due to –NH2 group
1. The amino groups behave as bases and
combine with acids to form salt
2. The amino acids react with ninhydrin to form a
purple, blue or pink colour complex
(Ruhemann’s purple)
3. Colour reaction of amino acids: amino acids can
be identified by specific colour reactions
4. Transamination
5. Oxidative deamination

22. Non-standard amino acids
 Amino acid derivatives in proteins
e.g. Collagen, Histone, cystine
 Non-protein amino acids
They may be either alpha or non alpha amino acids
e.g. Ornithine, Citrulline, thyroxine
 D-amino acids
The vast majority of aa isolated from animals and plants
are of L-category. Certain D-amino acids are found in
the antibiotics.
D-alanine and D-glutamic acid are found in bacterial cell
wall
D-serine and D-aspartate are found in brain tissues

23. Structure of Proteins
The structure of proteins can be divided into four
levels of organization
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure

24. Primary structure of proteins
 Each protein has a unique sequence of amino acids
which is determined by the genes contained in a
DNA.
 The primary structure is largely responsible for its
function
 A vast majority of genetic disorders are due to
abnormalities in the primary structure of proteins
 Peptide bond
 Characteristics of peptide bonds
The peptide bond is rigid and planar with partial double
bond in character. Both –C=O and –NH groups of
peptide bonds are polar and are involved in hydrogen
bon formation

25. Writing of peptide structures:
 Conventionally the peptide chains are written with
the free amino end (N-terminal) at the left and the
free carboxyl end (C-terminal) at the right.
 The amino acid sequence is read from N-terminal
end to C-terminal end
 The protein synthesis also starts from the N-
terminal amino acid

26. Shorthand to read peptides:
The amino acids in a peptide or proteins are
represented by the 3-letter or one letter abbreviation.
This is chemical shorthand to write proteins
Naming of peptides:
The suffixes –ine, -an, -ate are changed to –yl with the
exception of C-terminal amino acid
H3N-glutamate-cysteine-glycine-COO-
E C G
Glu Cys Gly
Glutamyl Cysteinyl Glycine

27. Secondary structure of Protein