Protein Function and Regulation

Question 1

Ligand

Answer 1

Any molecule, other than an enzyme substrate, that binds tightly and specifically to a macromolecule, usually a protein, forming a macromolecule-ligand complex; sometimes causes a change in shape of a protein

Question 2

Specificity

Answer 2

The ability of immune cells or their products to distinguish between structurally closely related molecules

Question 3

Affinity

Answer 3

The tightness or strength of binding, usually expressed as the dissociation constant (Kd)

Question 4

Molecular Complementarity

Answer 4

Lock-and-key kind of fit between the shapes, charges, hydrophobicity, and/or other physical properties of two molecules or portions thereof that allow formation of multiple non covalent interactions between them at close range

Question 5

Antibodies

Answer 5

Proteins that circulate in the blood and are made by the immune system in response to antigens (macromolecules present in infectious agents or other foreign substances)

Question 6

Active Site

Answer 6

Specific region of an enzyme that binds a substrate molecule(s) and promotes a chemical change in the bound substrate

Question 7

Induced Fit Model

Answer 7

The substrate-binding site is not rigid, but flexible, and that substrate binding induces the enzyme to change shape and consequently bind most strongly to the transition state, thereby optimizing catalysis

Question 8

Maximal Velocity

Answer 8

Parameter that describes the maximal velocity of an enzyme-catalyzed reaction or other process such as protein-mediated transport of molecules across a membrane; value is directly proportional to the amount of enzyme present in the reaction mixture

Question 9

Enzyme-Substrate Complex

Answer 9

The binding of substrate molecules to a fixed and limited number of sites on the enzyme

Question 10

Michaelis Constant (Km)

Answer 10

A parameter that describes the affinity of an enzyme for its substrate and equal the substrate concentration that yields the half-maximal reaction rate; smaller Km, more effective the enzyme is at making product from dilute solutions of substrate, and the lower the substrate concentration needed to reach half-maximal velocity

Question 11

Enzymatic Catalysis Key Features

Answer 11

1. Enzyme catalytic sites have evolved to stabilize the binding of a transition state, thus lowering the activation energy and accelerating the overall reaction
2. Multiple side chains, together with the polypeptide backbone, carefully organized in three dimensions, work together to chemically transform substrate into product, often by multistep reactions
3. Acid-base catalysis mediated by one or more amino acid side chains is often used by enzymes, resulting in only a particular ionization state of one or more amino acid side chains in the catalytic site to be compatible with catalysis (enzyme activity may be pH dependent)

Question 12

Cofactor / Prosthetic Group

Answer 12

Nonpolypeptide small molecule or ion that is bound in the active site and plays an essential role in the reaction mechanism

Question 13

Enzyme Inhibitors

Answer 13

Small molecules that can bind to active sites and disrupt catalytic reactions

Question 14

Metabolic Coupling

Answer 14

Mechanism for bringing enzymes in a common pathway into close proximity to overcome slowness of diffusion