Ch 6

Question 1

characteristics of enzymes

Answer 1

1. powerful biological catalysts
2. high degree os specificity
3. contain specialized pockets called active sites and the molecule acted upon by the enzyme is called the substrate
4. catalytically powerful because a) they bind the most tightly to the transition state; b) they can carry out multiple catalytic mechanisms at the same time
5. are regulated

Question 2

cofactor

Answer 2

1+ inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+

Question 3

coenzyme

Answer 3

complex organic or metalloorganic molecule that act as transient carriers of specific functional groups

Question 4

prosthetic group

Answer 4

coenzyme or metal ion that is very tightly or covalently bound to the enzyme protein

Question 5

holoenzyme

Answer 5

complete catalytic active enzyme together with its bound coenzyme and/or metal ions

Question 6

apoenzyme or apoprotein

Answer 6

the protein part of a holoenzyme (not active if it’s an enzyme)

Question 7

class number 1
(class name and type of reaction catalyzed)

Answer 7

oxidoreductases
transfer of electrons (hydride ions or H atoms)

Question 8

class number 2
(class name and type of reaction catalyzed)

Answer 8

transferases
group transfer (PTMs - phosphorylation, ect)

Question 9

class number 3
(class name and type of reaction catalyzed)

Answer 9

hydrolases
hydrolysis (transfer of functional groups to water)

Question 10

class number 4
(class name and type of reaction catalyzed)

Answer 10

lysases
cleavage of C-C, C-O, C-N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds

Question 11

class number 5
(class name and type of reaction catalyzed)

Answer 11

isomerases
transfer of groups within molecules to yield isomeric forms

Question 12

class number 6
(class name and type of reaction catalyzed)

Answer 12

ligases
formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor

Question 13

class number 7
(class name and type of reaction catalyzed)

Answer 13

translocases
movement of molecules or ions across membranes or their separation within membranes

Question 14

ground state

Answer 14

starting point for either the forward or reverse reaction (more stable)

Question 15

transition state

Answer 15

the point at which decay or substrate or product are equally likely (higher energy, less stable)

Question 16

biochemical standard free energy change

Answer 16

the standard free energy change at pH 7.0

Question 17

activation energy

Answer 17

difference between the ground state energy level and the transition state energy level (ie the amount of energy needed to break the reaction barrier)
higher activation energy = slower reaction

Question 18

how do enzymes work?

Answer 18

catalysts lower the activation energy and increase the reaction rate

Question 19

reaction intermediate

Answer 19

any species on the reaction pathway that has a finite chemical lifetime
ex: ES and EP complexes

Question 20

rate limiting step

Answer 20

the step in a reaction with the highest activation energy that determines the overall rate of the reaction

Question 21

equilibrium constant, Keq

Answer 21

describes an equilibrium

Question 22

relationship between equilibrium constant and free energy change

Answer 22

a large negative value for free energy reflects a favorable reaction equilibrium (one in which there is more product than a substrate at equilibrium)

Question 23

first order reactions

Answer 23

rate depends only on the concentration of S

Question 24

second order reactions

Answer 24

rate depends on the concentration of two different compounds or the reaction is between two molecules of the same compound

Question 25

binding energy

Answer 25

energy derived from noncovalent enzyme substrate interaction mediated by hydrogen bonds, ionic interactions, and the hydrophobic effect

Question 26

specificity

Answer 26

the ability to discriminate between a substrate and a competing molecule

Question 27

barriers to reaction (activation energy)

Answer 27

1. the entropy of molecules in solution 2. the solvation shell of hydrogen bonded water that surrounds and stabilizes most biomolecules in aqueous solution 3. the distortion of substrates that must occur in many reactions 4. the need for proper alignment of catalytic functional groups on the enzyme

Question 28

entropy reduction

Answer 28

large restriction in the relative motions of two substrates that are to react binding energy constraints substrates in the proper orientation to maximize reaction

Question 29

desolvation

Answer 29

replacement of the solvation shell of structured water around the substrate with weak bonds between substrate and enzyme replaces most or all hydrogen bonds between the substrate and H2O

Question 30

distortion

Answer 30

binding energy involving weak interactions that are formed only in the reaction transition state helps to compensate thermodynamically for the unfavorable free-energy change associated with any distortion, primarily electron redistribution, that the substrate must undergo to react

Question 31

induced fit

Answer 31

mechanism by which the enzyme itself undergoes a conformational change when the substrate binds, induced by multiple weak interactions with the substrate

Question 32

catalytic functional group mechanisms

Answer 32

1. acid-base catalysis (specific/general) 2. covalent catalysis 3. metal ion catalysis

Question 33

inorganic ions as cofactors

Answer 33

stabilize protein structure and influence protein activity by binding to specific sites on the protein, often within the active site

Question 34

specific acid-baed catalysis

Answer 34

uses only the H+ (H3O+) or OH- ions present in water

Question 35

general acid-base catalysis

Answer 35

mediated by weak acids or bases other than water

Question 36

covalent catalysis

Answer 36

transient covalent bond forms between the enzyme and the substrate catalysis only results when the new pathway has a lower activation energy than the uncatalyzed pathway

Question 37

metal ion catalysis

Answer 37

1. help orient the substrate for reaction 2. stabilize charged reaction transition states 3. mediate oxidation-reduction reactions by reversible changes in the metal ion's oxidation state

Question 38

pre-steady state

Answer 38

Initial transient period during which ES builds up

Question 39

Steady state

Answer 39

Period during which [ES] and other intermediates remain constant

Question 40

Steady state kinetics

Answer 40

The traditional analysis of reaction rates

Question 41

Assumptions of steady state kinetics

Answer 41

- [S] >> [E] - ES complex formation happens quickly - [ES] is constant after the initial reaction time - formation of ES = loss or dissociation of ES

Question 42

Low [S]

Answer 42

Most of the enzyme is in the uncombined form

Question 43

High [S]

Answer 43

The enzyme concentration is very small

Question 44

Initial rate/initial velocity

Answer 44

Tangent to each curve taken at time = 0 Reflects the steady state

Question 45

Vmax

Answer 45

The reaction rate when the active site is completely bound by correctly oriented substrate

Question 46

Effect of [S] on the V0 of an enzyme catalyzed reaction

Answer 46

At low [S], V0 increases almost linearly with an increase in [S] At high [S], V0 increases by smaller and smaller amounts in response to increase in [S]

Question 47

Michaelis - Menten equation

Answer 47

Explains the relationship between substrate and reaction rate

Question 48

Km

Answer 48

The [S] specific to our circumstances, independent of enzyme concentration when [E] is limiting for the reaction Low Km means the enzyme has a high catalytic activity at low [S]

Question 49

Kcat (turnover number)

Answer 49

The number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated

Question 50

Kcat/Km

Answer 50

The catalytic efficiency or products formed for a particular substrate

Question 51

Catalytic perfection

Answer 51

10^8 to 10^9 M^-1s^-1

Question 52

Why study inhibition?

Answer 52

1. Enzymes catalyze virtually all cellular processes 2. Enzyme inhibitors are among the most pharmaceutical agents known 3. The study of enzyme inhibitors provides information about enzyme mechanisms and helps define some metabolic pathways

Question 53

Enzyme inhibitors

Answer 53

Molecules that interfere with catalysis, showing or halting enzymatic reactions

Question 54

Competitive inhibition

Answer 54

Competes with the substrate for the active site of an enzyme and creates an enzyme inhibitor complex instead of enzyme complex Increases the apparent Km of an enzyme, but the Vmax states the same

Question 55

Uncompetitive inhibition

Answer 55

Binds to a site distinct from the substrate active site and binds only to the ES complex Vmax and Km decreases

Question 56

Mixed inhibition

Answer 56

Binds to a site distinct from the substrate active site, but binds to either E or ES Binds to both active site and other site Vmax always decliens

Question 57

No competing inhibition

Answer 57

Alpha = alpha prime Km does not change

Question 58

Irreversible inhibitor

Answer 58

Bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme’s activity or form a height stable no covalent association

Question 59

Suicide inactivator

Answer 59

Not reactive until they bind to the active site of a specific enzyme

Question 60

Transition state analogs

Answer 60

Stable molecules designed to resemble transition states of proteins

Question 61

Transition state analogs

Answer 61

Stable molecules designed to resemble transition states of proteins