Chapter 7

Question 1

what are the 2 models to describe how enzymes and substrates fit together? what is the reality?

Answer 1

1. lock and key
2. induced fit
   in reality is likely a mixture of both

Question 2

what is the lock and key model? what does it rely heavily upon?

Answer 2

there is a perfect substrate for every enzyme; relies heavily on conformational selection

Question 3

what is the induced fit model? what is it dependent upon?

Answer 3

says that enzyme and substrate change a little bith to fit together; depends upon noncovalten interactions but allows more freedom

Question 3

what is the active site?

Answer 3

the area inside the enzyme where the REACTION HAPPENS

Question 4

give an example of a reaction site

Answer 4

where a ligand binds to a protein

Question 5

does hemoglobin have an active site?

Answer 5

NO! although O2 binds, no reaction occurs

Question 6

what is a substrate?

Answer 6

the reactant the enzyme binds (AKA the ligand)

Question 7

what is rate?

Answer 7

reactions per unit time; bigger is better

Question 8

what is rate enhancement?

Answer 8

catalyzed rate divided by uncatalyzed rate; bigger is better

Question 9

what is rate enhancement used for?

Answer 9

to compare enzymes

Question 10

what are the 3 ways to change the rate of a reaction? how do these ways do this?

Answer 10

1. temperature: via conformational selection and diffusion
2. concentrationn: shifts equilibrium
3. catalysts: lower activation energy

Question 11

what are the 2 types of catalysts?

Answer 11

1. enzymatic: biological catalysts
2. nonenzymatic

Question 12

what allows enzymes to bind with high affinity and selectivity?

Answer 12

the creation of an active site environment that is optimal for substrate binding

Question 13

what does susbtrate binding do to the enzymes conformation? how (2)

Answer 13

substrate binding changes the enzyme’s conformation by
1. nonbonded interactions broken and formed
2. new conformation favors product formation

Question 14

in what 2 ways is enyzme activity heavily regulated in cells?

Answer 14

1. bioavailability
2. signaling

Question 15

what is a transition state?

Answer 15

a high energy intermediate state formed during conversion of substrate to product

Question 16

how many molecules are in the transition state simultaneously?

Answer 16

only a few

Question 17

is the transition state easy to isolae through conventional methods?

Answer 17

nope

Question 18

describe how transition state relates to the path from reactant to product

Answer 18

reactions have to take a certain path from reactants to products; the transition state is at the height of the path

Question 19

describe the energy and stability of the transition state

Answer 19

high energy, low stability

Question 20

what is delta G double dagger?

Answer 20

the activation energ, or the difference between reactant ground state energy and transition state energy

Question 21

what do catalysts do to the transition state?

Answer 21

stabilize transition state to lower associated energy and make transition state more favorable

Question 22

can a catalyst affect overall delta G? why or why not?

Answer 22

no; because cannot affect equilibrium

Question 23

give 4 things that help enzymes catalyze reactions

Answer 23

1. amino acid side chains in active site
2. cofactors
3. coenzymes
4. prosthetic groups

Question 24

what are cofactors?

Answer 24

small molecules that aid in catalysis (Fe2+, Cu2+, Mg2+)

Question 25

what are coenzymes?

Answer 25

cofcators that have organic components and include vitamin-derived species such as NAD+/NADH and FAD/FADH2

Question 26

what are prosthetic groups?

Answer 26

coenzymes that are permanently attached to enzymes like heme and biotin

Question 27

what are the 6 classes of enzymes?

Answer 27

1. oxidoreductase 2. transferase 3. hydrolase 4. lyase 5. isomerase 6. ligase

Question 28

what do oxidoreductases do?

Answer 28

oxidation-reduction; transfer of H or O atoms

Question 29

give 2 examples of oxidoreductases

Answer 29

oxidases, dehydrogenases

Question 30

what do transferases do?

Answer 30

trasnfer of functional groups like methyls, acyls, aminos, phosphoryls

Question 31

give 2 examples of transferases

Answer 31

kinases, transaminases

Question 32

what do hydrolases do?

Answer 32

formation of two products by hydrolyzin a substrate

Question 33

give two examples of hydrolases

Answer 33

peptidases, lipases

Question 34

what do lyases do?

Answer 34

cleavage of C-C, C-O, C-N, and other bonds by means other than hydrolysis or oxidation

Question 35

give two examples of lyases

Answer 35

decarboxylases, carboxylases

Question 36

what do isomerases do?

Answer 36

intramolecular rearrangements, transfer of groups within molecules

Question 37

give 2 examples of isomerases

Answer 37

mutases, isomerases

Question 38

what do ligases do?

Answer 38

formation of C-C, C-O, C-S, or C-N bonds using ATP cleavage

Question 39

give an example of a ligase

Answer 39

synthetases

Question 40

list and describe 3 methods of catalysis

Answer 40

1. stabilize transition state: lower activation energy (barrier height) via interactions with involved molecules 2. provide an alternate path for product formation via formation o stable intermediates (like base camp to rest before continue climb) 3. orient substrates for reaction to occur and reduce entropy

Question 41

what is the active site microenvironment?

Answer 41

a small subenvironment away from other things for the reaction to occur

Question 42

what 3 things can an enzyme to in the active site microenvironment?

Answer 42

1. induce geometric fit via altering protein conformation 2. use cahrged residues on amino acid side chains 3. exlusion of solvent via a hydrophobic core

Question 43

list the 3 enzyme mechanisms

Answer 43

1. acid-base catalysis 2. covalent catalysis 3. metal ion catalysis

Question 44

describe the acid base catalysis enzyme mechanism (4)

Answer 44

1. protons transferred between protein and substrate 2. requires an ionizable aino acid 3. enzyme always regenerated at the end 4. pH dependent mechanism

Question 45

give an example and describe an amino acid involved in acid base catalysis enzyme mechanism

Answer 45

histidine, has a pKa of approximately 7, meaning it is readily found in either acid or base form at body pH; can act as proton donor or acceptor

Question 46

what is a nucleophile?

Answer 46

a reactant that donates an electron pair to form a bond

Question 47

what is an electrophile?

Answer 47

accepts an electron pair

Question 48

describe covalent catalysis as an enzyme mechanism

Answer 48

involves formation of a transient covalent bond between enzyme and substrate to form an unstable intermediate

Question 49

what 5 amino acids are typically involved in covalent catalysis enzyme mechanisms?

Answer 49

1. serine 2. tyrosine 3. cysteine 4. lysine 5. histidine

Question 50

describe metal ion catalysis enzyme mechanism

Answer 50

positively charge metal ions stabilize negatively charged intermediated

Question 51

what are the 2 types of enzymes involved in metal ion catalysis? describe

Answer 51

1. metal activated enzymes: loosely bound metal ions 2. metalloenzymes: tightly bound metal ions

Question 52

what 2 amino acids are typically involved in metal ion catalysis?

Answer 52

1. cysteine 2. histidine

Question 53

describe enzyme binding affinity for the transition state

Answer 53

high

Question 54

why is the transition state so unstable?

Answer 54

free energy is high

Question 55

describe enzyme bindning affinity for products low and result of this

Answer 55

enzyme has low binding affinity for products, so products dissociate and enzyme regenerated