Proteins lecture 11

1. Lecture 11
Proteins

2. 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

3. 4. Optical properties:
All the amino acids except glycine posses optical
isomers due to the presence of 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

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

5. 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

6. 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

7. 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

8. 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

9. 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
bond formation

10. 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

11. 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

12. Secondary structure of Protein
 The conformation of polypeptide chain by twisting
or folding is referred to as secondary structure
 The amino acids are located close to each other
in their sequence
 Two types of secondary structures, alpha helix an
beta sheet are mainly identified
 Indian scientist Ramachandran made a significant
contribution in understanding the spatial
arrangement of polypeptide chains

13. Alpha helix
 α-helix is the most common spiral structure or
proteins. It has a rigid arrangement of polypeptide
chain
 α-helical structure was proposed by Pauling and Corey
(1951)

15. Salient features
 1. the alpha helix is tightly packed coiled structure
with amino acid side chains extending outwards
from the central axis
 The alpha helix is stabilized by extensive
hydrogen bonding. It is formed between H atom
attached to peptide N, and O atom attached to
peptide C. the hydrogen bonds are individually
weak but collectively they are strong enough to
stabilize the helix
 All the peptide bonds except the first and last in
polypeptide chain participate in hydrogen bonding

16.  Each turn of alpha helix contains 3.6 amino acids
and travel a distance of 0.54 nm. The spacing of
each amino acid is 0.15 nm
 Alpha helix is a stable conformation formed
spontaneously with the lowest energy
 The right handed helix is more stable than the left
handed helix
 Certain amino acids disrupt the alpha helix
(proline, basic and acidic amino acids)

17. Beta pleated sheets
 They are composed of two or more segments of
fully extended peptide chains
 In the beta sheets the hydrogen bonds are
formed between the neighboring segments of
polypeptide chains

21. Tertiary structure
 The three dimensional arrangement of protein
structure is referred to as tertiary structure.
 It is a compact structure with hydrophobic side
chains held interior while the hydrophilic group on
the surface of protein molecule
 Besides the hydrogen bond, disulphide bond,
ionic interaction, hydrophobic interactions and
Vander wall forces also contribute to the tertiary
structure of proteins

23. Quaternary structure
 A great majority of proteins are composed of
single polypeptide chains
 Some of the proteins however consists of two or
more polypeptides which may be identical or
unrelated. Such proteins are termed as oligomers
and possess quaternary structure
 The individual polypeptide chains are known as
monomers, protomers or subunits
 A dimer consists of two polypeptide chains while
tetramer has four

24. Bonds
 The monomeric subunits are held together by non
covalent bonds namely hydrogen bonds, ionic
bonds

25. Importance
 These proteins play a significant role in the
regulation of metabolism and cellular functions
 Examples
Hemoglobin, aspartate tanscarbomylase, lactate
dehydrogenase.