Question

Describe what type of information the following views provide about protein structure determination?

a. Secondary structure:

b. Cartoon :

c. Composition

d. Hydrophobic/Polar

e. Charge

Answer 1

Secondary structure of protein:- The secondary structure of protein includes arrangement of peptie bonding or stretching of peptide bond for protein molecule. It can be done in two ways alpha helix & beta pleated sheet.

Alpha helix structure:- It is a right handed coiled strand. The side chain of amino acid groups are towards the outside of alpha helix. Hydrogen bonds form between the oxygen of the carbonyl group (>C=O) and the hydrogen atom of the N-H group of the peptide bond four amino acids below it in the helix. Hydrogen bonds give stability to the structure.

Beta pleated sheet structure:- In this either parallel or antiparallel depending on the directions of N-terminus to C-terminus on the same or opposite directions. The carbonyl oxygen of >C=O group hydrogen bonded with hydrogen atom of amino terminus.

Secondary Structure β pleated sheet он O H C-GN Examples of amino acid subunits C-H 、C-H N-H N-H α helix HC-R H-C-R H-C-R N-H Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings.

Cartoon:- It is useful in analysing and understanding complex protein folds.

Composition:- Proteins are made up of amino acids. Amino acids composition vary as it grouped as sulphur containging, basic amino acids, acidic amino acids, aromatic amino acids, imino group, branched chain. These gives protein differentiation for their structure, function.

Hydrophobic/polar:- Due to Hydrophobic nature proteins can be folded it gives compact shape to protein.

Chargge:- Depending on the charge of amino acid the interactions are takes place for folding the protein to give proper confirmation. It includes covalent interactions, Vander waals forces, hydrophobic interaction, disulfide bond these are involved and takes place in secondary and tertiary structure of protein.