Enzymes

Question 1

Lock-and-key hypothesis

Answer 1

Substrate-binding site exists in absence of substrate + fits chemically/geometrically w/enzyme’s substrate

Question 2

Induced-fit hypothesis

Answer 2

Substrate binding triggers change in enzyme conformation to form final conformation of substrate-binding site - substrate engulfed by enzyme closing in on substrate

Question 3

Active site

Answer 3

Substrate converted to product here

Question 4

Cofactors

Answer 4

Assist enzymes when they act as catalysts - contain inorganic molecules or organic molecules (which makes them coenzymes)

Question 5

Apoenzyme

Answer 5

Inactive form of enzyme observed before cofactor association

Question 6

Holoenzyme

Answer 6

Active enzyme-cofactor complex

Question 7

Prosthetic groups

Answer 7

Make up electron transport chain + tightly bound to proteins

Question 8

5 ways enzymes can participate directly in the reaction mechanism

Answer 8

1. Acid-base catalysis
2. Covalent catalysis
3. Metal ion catalysis
4. Electrostatic catalysis
5. Proximity + orientation effects

Question 9

What explains the reaction rates achieved by enzymes along with the direct involvement of amino acid side chains in complex reaction mechanisms?

Answer 9

Enzymes preferentially bind to the activation complex X*

Question 10

Steady-state assumption

Answer 10

Michaelis-Menten complex concentration is constant during rxn measurement time

Question 11

Transient phase

Answer 11

Short initial time period required for initial diffusion of substrate to binding site

Question 12

Turnover number (k2)

Answer 12

Number of rxns that each active site can catalyze /unit time once substrate has already been bound

Question 13

Ligands

Answer 13

Molecules that attach to proteins via reversible non-covalent interactions - ligand bonding/covalent modifications of proteins causes shift in tertiary/quaternary structure of proteins

Question 14

Enzyme regulators

Answer 14

Alter catalytic activity of enzymes

Question 15

Enzyme activators

Answer 15

Increase catalytic activity upon binding the protein

Question 16

Enzyme inhibitors

Answer 16

Decrease enzymatic activity upon binding

Question 17

Feedback inhibition

Answer 17

Reduces flux through glycolysis pathway when end-product of pathway reaches elevated concentrations

Question 18

Allosteric regulators

Answer 18

Don’t bind to active site of protein but change its activity by interacting w/remote site - act as activators/inhibitors

Question 19

Homotropic

Answer 19

Term for allosteric effects if ligand at remote site is same as ligand at active site

Question 20

Heterotropic

Answer 20

Term for allosteric effects if two ligands are different

Question 21

Competitive inhibition

Answer 21

Reduces catalytic rates by competing w/substrate to enter + interact w/substrate-binding site

Question 22

Uncompetitive inhibition

Answer 22

When inhibitors only have high affinity for enzyme-substrate complex

Question 23

Mixed inhibition

Answer 23

When inhibitors can bind at allosteric sites both on free enzyme/on enzyme-substrate complex

Question 24

Michaelis constant (Km)

Answer 24

Measurement of affinity of enzyme for substrate - higher Km leads to lower stability of ES complex

Question 25

How do competitive inhibitors impact enzyme affinity for substrate + Vmax?

Answer 25

They decrease enzyme affinity for substrate + don't alter Vmax

Question 26

How do uncompetitive inhibitors affect the apparent Vmax and the apparent Km?

Answer 26

Decrease in apparent Vmax and Km - decrease in max rxn rate + increase in enzyme affinity for substrate

Question 27

How do mixed inhibitors affect the apparent values of Km and Vmax?

Answer 27

Km apparent depends on the alpha/alpha' ratio and Vmax apparent is decreased

Question 28

Tense state vs relaxed state

Answer 28

Relaxed state has higher affinity to bind ligands/higher capacity to catalyze reactions than the tense state

Question 29

Cooperative ligand binding

Answer 29

Change in affinity of 1 protein subunit for a given ligand depending on previous ligand-binding events occurring on other subunits - typically allosteric effect due to change in quaternary structure of protein

Question 30

Positive cooperativity

Answer 30

Effect observed if binding a given ligand locks the protein in a relaxed state that increases binding affinity of protein for further ligands - more common than negative cooperativity

Question 31

Negative cooperativity

Answer 31

Effect observed if affinity of protein for further ligands decreases after binding a 1st ligand

Question 32

Hemoglobin

Answer 32

Protein that undergoes positive homotropic cooperative ligand binding - involved in oxygen transport from site where oxygen exchange occurs to other tissues + has 4 subunits including 2 alpha and 2 beta (subunits are analogous to myoglobin so 1 hemoglobin can bind 4 oxygen molecules in comparison to myoglobin that can only bind 1)

Question 33

Myoglobin

Answer 33

Monomeric oxygen binding protein - its secondary structure has many alpha helices that fold together to form water soluble globular protein + contains 8 right-handed alpha helices that form compact structure

Question 34

Heme group

Answer 34

- Compact structure in myoglobin contains this - hydrophobic pocket that tightly + non-covalently binds this - Contains cyclic structure (porphyrin)

Question 35

How does oxygen binding change the state of a protein?

Answer 35

Pressures a change from a tense (T) to a relaxed (R) state - T has lower oxygen binding affinity and R has higher so oxygen binding is cooperative (oxygen binding promotes further oxygen binding by pushing TR equilibrium towards R state - Perutz mechanism)

Question 36

Fractional saturation

Answer 36

Ratio of occupied ligand-binding sites divided by total # of ligand-binding sites - in case of infinite cooperativity ignore the "ligand" term

Question 37

What if Hill constant is greater than 1? Equal to 1? Less than 1?

Answer 37

- Greater: ligand binding is positively cooperative - Equal: binding is non-cooperative - Less: ligand binding to 1 subunit hinders binding to subsequent subunits

Question 38

Intrinsic dissociation constant in the Adair model

Answer 38

Corresponds to dissociation constant of ith binding rxn between a ligand and an individual subunit

Question 39

Macroscopic dissociation constant in the Adair model

Answer 39

Dissociation constant of ligand from any subunit on protein at ith binding step

Question 40

How do changes in ki values in the Adair model indicate cooperativity?

Answer 40

Decrease of ki values as a function of i indicates positive cooperativity - increase of ki values as function of i indicates negative cooperativity + if k1 = k2= ... kn then binding is non-cooperative