Chapter 5: Protein Function

Question 1

Ligand

Answer 1

a molecule bound by a given protein; can be any kind of molecule, including nucleic acid or another protein; transient nature of protein-ligand interaction is essential

Question 2

Binding Site

Answer 2

a specific site on the protein at which the ligand binds; complementary to the ligand in size, shape, charge, and hydrophobic or hydrophilic character; one protein may have multiple sites

Question 3

Conformational Flexibility

Answer 3

changes may be subtle or dramatic; frequently essential to protein function

Question 4

Induced Fit

Answer 4

conformational change in a protein that alters a binding site so that it becomes more complementary to the ligand, making tighter binding

Question 5

Cooperativity

Answer 5

when a conformational change in one subunit (triggered by the binding of a ligand) can increase or decrease affinity of neighboring protein for same ligand

Question 6

Regulation of Protein activity

Answer 6

usually accomplished through specific interactions with one or more additional ligands

Question 7

Equilibrium Expression

Answer 7

a way to describe the reversible binding of a protein and a ligand
P+LPL

Question 8

Helix-turn-Helix Motif

Answer 8

DNA binding motif crucial to the interaction of many bacterial regulatory proteins with DNA

Question 9

Cofactor

Answer 9

additional chemical component that allows an enzyme to complete its activity

Question 10

Coenzyme

Answer 10

complex organic or metallo-organic molecule called a coenzyme; acts as a transient carrier of specific functional groups; most derived from vitamins

Question 11

Prosthetic Group

Answer 11

coenzyme or inorganic cofactor that is tights or covalently bonded to the enzyme protein

Question 12

Holoenzyme

Answer 12

complete, catalytically active enzyme with bound coenzyme or cofactor

Question 13

Apoenzyme/Apoprotein

Answer 13

the protein part of a holoenzyme

Question 14

Binding Energy (delta Gb)

Answer 14

energy derived from the enzyme-substrate interaction; major source of free energy used by enzymes to increase the rates of reactions; stabilizes enzyme-substrate interaction

Question 15

Transition State

Answer 15

a transient moment when the alteration in the substrate has reached a point corresponding to the highest energy in the reaction coordinate diagram

Question 16

Activation Energy

Answer 16

difference between energy of ground state and transition state

Question 17

Enzyme Kinetics

Answer 17

determining the rate of a reaction and how it changes in response to changes in experimental parameters

Question 18

Competitive Inhibitor

Answer 18

reversible; competes with a substrate for the active site of an enzyme; usually structurally similar to substrate

Question 19

Uncompetitive Inhibitor

Answer 19

reversible; binds at a site distinct from the substrate active site; binds to ES

Question 20

Mixed Inhibitor

Answer 20

reversible; binds at a site distinct from the substrate active site, but binds E or ES

Question 21

Covalent Modification

Answer 21

a way of modulating protein activity by binding a group to one or more AA residues

Question 22

Protein Kinase

Answer 22

catalyzes the attachment of phosphoryl groups to specific AA residues of a protein

Question 23

Protein Phosphatase

Answer 23

catalyzes the removal of phosphoryl groups

Question 24

Proteolytic Cleavage

Answer 24

inactive precursor protein is cleaved to form the active protein

Question 25

Proprotein/Proenzyme

Answer 25

a larger, uncleaved precursor proteins before proteolytic cleavage