Protein Function

Question 1

How does protein flexibility relate to function?

Answer 1

1. Fast and small scale motions tend to be associated with catalysis
2. Collective mid range spatial and temporal motions are associated with conformational changes upon binding or signaling
3. Slow and large scale motions associated with binding events

Question 2

Protein movement often involves:

Answer 2

1. The release of bound water molecules

2. Making/breaking of non-covalent interactions as the protein moves or subunits move relative to one another

Question 3

Triggered conformational changes are dependent on :

Answer 3

1. Unique structure of proteins

2. Inherent flexibility/ instability of molecules

Question 4

Molecular recognition depends on:

Answer 4

1. Complementarity of shape
2. Charge distribution between ligand and protein binding site
3. Formation of specialized microenvironments in the tertiary structure (ligand-binding sites/ enzyme active sites).

Question 5

Structure of binding sites

Answer 5

1. Lined with appropriate amino acids or binding elements which interact specifically with ligand
2. Higher than average amount of exposed hydrophobic groups
3. Can have different shapes

Question 6

For marcomolecules shape of binding site can be:

Answer 6

Concave, convex or flat and may be grooves

Question 7

For small molecules shape of binding site can be:

Answer 7

Clefts, pockets or cavities

Question 8

Catalytic active sites

Answer 8

Occur at the interface between subunits or domains in proteins.

Question 9

Weak interaction between ligand and protein

Answer 9

Favors easy exchange of molecules

Question 10

The energy for driving binding events is provided by

Answer 10

Displacement of water from ligand binding site

Question 11

Kd =

Answer 11

The equilibrium constant for the release of ligand

Question 12

[P.L]/[Po]

Answer 12

Proportion of protein that has ligand-bound

Question 13

Relationship between [P.L]/[Po] and [L]

Answer 13

Rectangular hyperbola

Question 14

Equation for ligand binding

Answer 14

[P.L]/[Po] = [L]/ [L] + [Kd]

Question 15

Units of Kd

Answer 15

Molar concentration e.g. Moles/litre

Question 16

The lower the value of Kd

Answer 16

The higher the affinity of the ligand for the protein