Question

1. Ramachandran plot is useful in telling which of the following property of a protein: (with explaination)
A. sequence
B. structure
C. function
D. modification

2. SDS is used in protein electrophoresis because? (with explaination)
A. it denatures proteins
B. it stains protein
C. it provides protein with charges
D. it makes the size of protein different.

3. Whichnof the following is not a mechanism for altering the flux of metabolities through the rate-determinating step of a pathway?
A. allosteric control of the enzyme activity.
B. Diffusional coupling between adjacent active sites
C. lower affinity for proton
D. higher affinity for proton

Answer 1

The Ramachandran plot is usually exploited by the Structural biologists to help them with the structure of a protein validated. These structural biologists plot the dihedral angles or torsion angles of a polypeptide such as & and find out whether or not the structure of a predicted protein is allowed. You have to understand that the bonds between two atoms rotate and these rotations generate these torsion angles. The bonds that we are talking about are the ones that are formed between the amino acids. Remember that these aminoacids will further join in a chain and form a protein. So these & plots will further help find the allowed conformation that a protein can largely take. If the data falls at the region that is not permissible on a Ramachandran plot that means that there is a steric hindrance in the rotation of the bonds amongst the basic monomeric subunits, amino acids, and that particular protein structure cannot be stable or acceptable or allowed. Thus this plot is used to validate a structure of a protein.

SDS or Sodium Dodecyl Sulfate is an anionic detergent that is used in the Polyacrylamide gel electrophoresis experiment. SDS PAGE is a routine experiment in which proteins are separated based on their molecular weight on a polyacrylamide gel under the constant current or electric field. For these protein molecules to separate solely on the basis of their molecular weight they are subjected to the reducing environment and given a net negative charge. SDS comes in the picture where the net negative charge is to be given to the protein molecules. These proteins or polypeptides will now migrate towards the anode(+vely charged pole) due to the net negative charge because of SDS and separate on the basis of their weight. They can thus be separated and identified by running a molecular weight marker/ladder.

Flux in terms of metabolites can be defined as the turnover rate of the metabolites through a metabolic network. In simpler terms, it is the rate of the passage or replacement of the metabolites through a pathway. This could be altered through all the options mentioned above but not through the diffusional coupling between adjacent active sites.