OC2 - general characteristics of binding sites

Question 1

binding site

Answer 1

a region of protein, DNA, or RNA that a ligand forms a temporary none-covalent chemical bond with, as it has complementary shape
crevices in the 3D structure where a ligand can bind
they exclude water so are surrounded by hydrophobic (non-polar) amino acids

Question 2

chemical specificity

Answer 2

a measure of the types of ligands that will bind

Question 3

affinity

Answer 3

a measure of the strength of the chemical bond

Question 4

ligand

Answer 4

a molecule which interacts with a protein by specific binding

Question 5

ligand binding

Answer 5

the ligand must bind to the protein before any chemical changes occur
ligand binding is reversible
the ligand will bind to the protein at a specific site which has complementary shape

Question 6

lock and key model

Answer 6

the substrate binds to the enzymes active site exactly as they are complementary in shape to each other

Question 7

induced fit model

Answer 7

binding of a substrate to an enzymes active site induces a conformational change in the enzymes active site to bind the substrate more tightly
reactions can only take place after induced fit has occurred
the bonds in the enzyme-substrate complex are under stress as the conformation of the enzyme has been altered, this lowers the activation energy required for the reaction to proceed.
allows the possibility that more than one specific substrate can bind to one enzyme
e.g. hexokinase and citrate synthase.

Question 8

hexokinase

Answer 8

performs the first step in glycolysis using an ATP molecule to start the process.
it transfers a phosphate from ATP to glucose forming glucose-6-phosphate.
hexokinase then changes shape by induced fit (after glucose and ATP binding) to form the enzyme-substrate complex, closing over the ATP and glucose substrates.

Question 9

citrate synthase

Answer 9

oxaloacetate binds first inducing a conformational change and creating a binding site for acetyl CoA. oxaloacetate and acetyl CoA are now in close proximity to each other and citrate synthase can catalyse the condensation reaction between them.

Question 10

evolutionary conservation of crucial residues

Answer 10

a conserved region refers to identical or similar sequences of DNA/RNA or amino acids that occur in different or the same species over generations
a conserved region shows no changes or trace changes in their sequence over generations
a significant sequence similarity between two molecules suggests that they are likely to have the same evolutionary origin and therefore the same 3D structure, function and mechanism.