bioinformatics education presentation

1. STRUCTURE OF
PROTEINS
Shumail Ayub Qureshi
MPhil zoology
Molecular biology

2. Protein / Amino Acids
Amino acids are the building block of proteins.
There are a total of 21 amino acid types based on their different
R groups. 12 of these can be synthesized in the body, while the
other 9 must be consumed in the diet and are termed essential
amino acids.
Their structure consists of three main groups namely
the amino group or N terminus, the carboxyl group or
C terminus, and the R group which contains the
functional component of the amino acid. The R group
gives the amino acid specific features according to its
polarity and charge, which then affect the chemical and
biological properties of the protein.

4. Structure of protein
There are basically 4 types of proteins structure are as ,
I. Primary structure
II. Secondary structure
III. Tertiary structure
IV. Quaternary structure

6. Primary structure of protein
 linear sequences of amino acids in entire protein molecule.
 It is stabilized by covalent bond due to which its shows its perfect structure even at 180℃
 This is the first structural level of proteins during protein structure formation, and it also
shows the final structural level of proteins when a protein is subjected to complete
denaturation.
 Based on this polarity, the ends of the primary structure are represented as N- terminus
(α-amino group side) and C- terminus (carboxylic end).
• The amino acid sequence of this structure also determines the codon sequence in the
coding gene of a particular protein.
• Any alterations in the codon sequence of the gene can affect the primary structure of a
protein by changing the amino acid sequence.

8. Secondary Structure
Local folding at primary level
Closely arranged regions form a weak H-bonding.
It is level where protein fulfill its functional characteristics of protein.
H-bond present –COOH group oxygen of the peptide bond and
amino hydrogen of another peptide bond.
It will reduced polarity so, higher ordered structure will obtained.
CD Spectroscopy and Ramachandran plot.

9. The formation of fold,regular and irregular pattern is called as Helical formation.
• Its has 2 parts helix and beta pleated sheet.
• Alpha-helix – a coil formed by hydrogen bonds between the carbonyl group
and the amino group of different amino acids. The strong bonds and stability
of this structure give it a strong tensile strength, which allows it to form the
shape seen in DNA.
• Beta-pleated sheet – formed by hydrogen bonds between the carboxyl group
of one amino acid on one sheet and the hydrogen molecule of an amino acid
on another sheet. The sheets can be in parallel or antiparallel.
There are 3 types of helical formation,
1. ∝-helix
2. 3-10 helix
3. Π helix

10. ∝ helix
Intra chain hydrogen bonding
3.6 amino acid residue per turn.
100° turn helix after every 5 turns or 18 amino acids.
3-10 helix
3 amino acids per turn.
120° at helical turns.
Π helix
Evolutionary adaptation.
4.4 amino acid per turn.

11. Beta pleated sheet
Opposite to ∝ helix.
H-bonding will be in two different chains.
Two chains involved in β-strands. Based on the beta strands arrangement it divided into
2 types,
I. Parallel
 Arranged in same direction.
 Amnio terminus of 1 strand closed to amino terminus of opposite strand.
I. Anti parallel
 2 beta strands in opposite direction.
 Amino group is closely related to carboxyl group terminus of ither strand.

13. Tertiary structure
3-D structure of protein
Native structure of protein
Takes place in catalytic activity.
Covalent (Sulphur containing amino acid)+ non covalent interaction(
hydrophobic )
Hydrophobic portion in tertiary structure is called as nucleation center.

15. Quaternary Structure
More than one polypeptide chain interchain and intrachain interaction knowns
as quaternary structure.
Stabilized by both non covalent and covalent interaction.
Dimer of cro-protein ( DNA binding protein) of bacteriophage is type of
quaternary structure.
For example; Antibodies,haemoglobin.