Protein Structure Flashcards
Fibrous proteins
They are insoluble in water
They play a structural role
Examples include alpha keratin and collagen
Globular proteins
They are soluble in water
They play functional role
All enzymes are globular proteins
Importance of protein
Protein may be broken down to provide energy or provide raw materials for the synthesis of other macromolecules
What are the levels of protein structure
Primary structure
Secondary structure
Tertiary structure
Quanternary structure
Primary structure
Is the sequence of amino acid in a protein in which a peptide bond connects the alpha carboxyl group of each amino acid to the alpha amino group of the next chain
Secondary structure
It refers to the repeating patterns formed by the backbone of at least part of a polypeptide chain which is stabilized by hydrogen bonding
Tertiary structure
These are structure with single three dimensional structure and stabilized by bonding between amino acids
Quaternanry structure
It is the complete three dimensional structure including the interaction between the component polypeptide chains
Bonds involved in the maintenance of protein structure
Hydrogen bond
Disulphide bridges
Van DER Waals bonds
Co ordinate bonds
How to determine a primary structure
By the isolation of polypeptide chain i.e to determine the number of different N terminal amino acid and the number of different C terminal amino acids in a polypeptide chain
What reagent is used to identify N terminal amino acids
Dansyl chloride
Sanger’s reagent (1-fluoro-2,4-dinitrobenzene)
Edman’s reagent
What added advantage does dansyl cloride has when it reacts with alpha amino groups
Dansyl amino acids are highly fluorescent and can be identified in very small quantities by HPLC
How is the c terminal amino acid identified
1.It is identified by treating the protein with a reagent that attacks the free carboxyl group e.g sodium borohydride
2.it can also be treated with anhydrous hydrazine at high temperature for several hours in the presence of a catalyst.
What happens when the protein is treated with anhydrous hydrazine
Each free carboxyl group react to form a hydrazide
What happens when protein is treated with sodium borohydride
The side chain carboxyl group will be reduced with the subsequent production of amino alcohols
Ways by which the linkages between various polypeptide chain may be broken
Disulphide bridges maybe broken by treatment with performic acid
Non covalent bond is broken by extremes of pH at high salt concentration or in presence of reagents
Determination of the amino acid composition of each polypeptide chain
- By determining the molecular weight of the polypeptide by the use of size exclusion chromatography then the polypeptide is then completely hydrolysed to it’s component amino acid and the concentration of each determined
- By ion exchange chromatography in which the eluate is mixed with a reagent such as ninhydrin which reacts with the most amino acid to give blue purple colour.
Enzymes used to split long polypeptide chain
Cyanogen bromide which breaks the bond of methionine
Trypsin which breaks the bond on lysine or arginine side chain
Chymotrypsin which breaks the bond on phenylalanine, tryptophan and tyrosine side chain
What are the effects of the enzymes on polypeptide chain
It produces a number of peptide fragments which are separated from each other by chromatography or electrophoresis
Peptides consisting up to 25 amino acid residues maybe separated directly by means of
Tandem mass spectrometry
