5. Protein function and regulation

Question 1

ligand

Answer 1

molecule to which a protein binds

Question 2

ligand-induced conformational changes

Answer 2

integral to mechanism of action, caused by ligand

Question 3

2 important properties of ligand binding

Answer 3

• specificity: ability of protein to bind only one ligand
• affinity: strength og binding (Kd)

Question 4

binding

Answer 4

interaction between complementary molecular surfaces: many weak interactions are collectively strong

Question 5

Complementarily Determining Region (CDR)

Answer 5

antigen-binding surface on antibody with a highly variable amino acid sequence

Question 6

enzymes

Answer 6

diverse class of catalytically active proteins whose ligands include the substrate of reactions they catalyse

Question 7

Vmax

Answer 7

maximal rate of catalysis given saturating amounts of substrate

Question 8

what does Vmax depend on

Answer 8

number of enzymes and how fast they work

Question 9

Km

Answer 9

substrate concentration that supports a rate of catalysis equal to 1/2 Vmax
-> measures affinity

Question 10

what does Km depend on

Answer 10

enzyme-substrate type

Question 11

lower Km =

Answer 11

higher binding affinity

Question 12

trypsin

Answer 12

serine protease which cleaves peptide bonds

Question 13

what defines enzyme specificity?

Answer 13

differences in their substrate recognition pocket

Question 14

serine protease trypsin mechanism

Answer 14

1. cleavage of peptide bond through formation of covalent substrate-enzyme complex as oxygen attacks carbon, breaking its bond with nitrogen
2. hydrolysis of acyl enzyme complex: cleavage of peptide bond

Question 15

amino acid side chains involved in Trypsin mechanism (3):

Answer 15

• Asp-102
• His-57
• Ser-195

Question 16

pH optima of enzymes reflect

Answer 16

• active site acid-base chemistry
• sensitivity of overall protein conformation to charge distribution

Question 17

allosteric effects

Answer 17

binding at one site on a protein leading to conformational changes that affect the binding of another ligand at a different site

Question 18

allosteric regulations

Answer 18

conformation switch in regulatory proteins in response to ligand binding or post-translational modification

Question 19

examples of allosteric regulation (2):

Answer 19

• non covalent binding of Ca2+
• non covalent binding of GTP

Question 20

non-covalent binding of Ca2+

Answer 20

• Ca2+ binding to calmodulin changes its conformation –> allows calmodulin to bind to target peptides
• regulates target protein structure + activity as protein is packed
• protein becomes inactive when Ca2+ falls off

Question 21

non-covalent binding of GTP

Answer 21

• G-proteins switched on/off depending on protein interactions
• switching off: facilitated by GAP through phosphorylation of GTP to GDP -> GDP bound to GTPase
• switching on: facilitated by GEF which removes GDP, allowing GTP to bind to GTPase

Question 22

post-translational modification

Answer 22

rapidly reversible covalent modification of protein structure

Question 23

protein kinase

Answer 23

phosphorylates ATP to ADP to activate target protein, aka addition of phosphate

Question 24

protein phosphatase

Answer 24

dephosphorylates H20 to Pi to inactivate target protein

Question 25

cascade effect

Answer 25

permits amplification of a signal and many levels of fine-tuning

Question 26

molecular complementarity

Answer 26

complementation between shape and chemical properties of a ligand molecule to a bind gsite

Question 27

examples of enzyme specificity

Answer 27

• elastase obstructed by bulky valine side chains –> prefers small side chains (alanine, glycine)
• chemotrypsin allows for large uncharged side chains

Question 28

phosphorylation

Answer 28

reversible covalent addition of a phosphate group from ATP to an OH on serine, threonine or tyrosine