Mcb Exam 1 - Enzymes

Front 1

Enzymes accelerate _____ and ______, but they do not change _____ and ______.

Back 1

accelerate: rxn rate & attaining equilibrium
do NOT change: equilibrium position & free energy of rxn

Front 2

What is velocity and what 2 factors does it depend on?

Back 2

change in [product] over time
depends on: [S] and rate constant (k)

Front 3

Rate Constant (k)

Back 3

ΔVo/Δ[S]
i.e. the slope of the initial velocity vs. [S] graph

Front 4

Rxns proceed through the formation of what 2 types of high energy, transient forms?

Back 4

intermediates
transition states

Front 5

activation energy

Back 5

ΔG to reach transition state
decreased by enzymes to accelerate rate of rxn

Front 6

What are the 2 general ways that enzymes lower activation energy

Back 6

1) lower energy of free reactants by pulling them out of solution (i.e. lower G of starting materials of rxn)
2) stabalize (lower G) the transition state

Front 7

What do K1 and K2 represent?

Back 7

K1 = enzyme binding to substrate
K2 = catalysis of ES complex

Front 8

What happens to Vo as [enzyme] increases?

Back 8

Vo increases

Front 9

Michaelis-Menton equation

Back 9

Vo = Vmax[S] / Km + [S]
causes a hyperbolic curve with enzyme saturation at Vmax

Front 10

Catalytic constant (Kcat)
(aka Turnover #)

Back 10

# of substrate converted to product per unit time for one active site
k2 is a good approximation; shown via Vmax

Front 11

Km

Back 11

[S] at 1/2 Vmax
Smaller Km = higher enzyme affinity for substrate

Front 12

Catalytic efficiency

Back 12

Kcat/Km
represents rate constant at biological conditions (i.e. when [S] is far below saturation concentrations)
indicates the "preferred substrate" of enzyme

Front 13

Catalytic proficiency

Back 13

(Kcat/Km) / rate constant of uncatalyzed rxn
shows how much faster the enzyme makes the rxn as compared to when the enzyme is absent

Front 14

Lineweaver-Burk Plot

Back 14

Double reciprocal of Michaelis-Menton (1/Vo vs 1/[S])
makes a straight line where 1/Vmax = y intercept
and -1/Km = x intercept
used to calculate Vmax and Km of an enzyme

Front 15

2 types of sequential displacement for enzymes with 2+ substrates

Back 15

Ordered - substrates bind in a specific order and release products in a specific order
Random - binding and releasing of substrates is random

Front 16

Double-displacement enzyme rxn

Back 16

enzyme removes a chemical group from first substrate to form a temporary "substituted enzyme intermediate" and adds this group to its next substrate
enables coupling of rxns to drive thermodynamically unfavorable rxns (ex: ATP hydrolysis)

Front 17

Catalytic strategy where enzyme forms a temporary covalent bond with substrate

Back 17

covalent catalysis

Front 18

Catalytic strategy where a molecule other than water serves as proton donor or acceptor

Back 18

General Acid-Base Catalysis

Front 19

Catalytic strategy where a metal ion acts a an electrophilic catalyst, base catalyst, or aids in substrate binding

Back 19

Metal Ion catalysis

Front 20

Catalytic strategy where enzymes fxn is to pull chemically reactive groups in substrates is close proximity and proper orientation

Back 20

Catalysis by approximation

Front 21

Types of Cofactors

Back 21

1) Inorganic Metal ions (called metalloenzymes if tightly bound)
2) Coenzymes - organic compounds either loosely bound (cosubstrates) or tightly bound (prosthetic groups)

Front 22

What are most vitamins considered as?
How does this tie into vitamin deficiencies?

Back 22

cofactors
deficiencies = impaired ability of enzyme to catalyze key metabolic pathways

Front 23

active site

Back 23

several aa's on enzyme's 3D structure that server to exclude water (pull substrate out of solution)
substrate may have complimentary shape (lock-and-key)
or cause a conformational change in enzmye upon binding (induced fit)

Front 24

Specificity and orientation of substrate in active site is dictated by what?

Back 24

reversible NONcovalent interactions b/w enzyme and substrate

Front 25

What determines the "functionalities" of an active site?

Back 25

functional groups on the amino acids found in the active site
cofactors may also play a role

Front 26

The ____ of amino acids in the active site determines the enzymes ability to participate in general acid-base mechanisms.

Back 26

pKa

Front 27

Which amino acid is most commonly found in an enzyme's active site?
Why?

Back 27

His - imidazole functional group has a pKa very close to physiological pH

Front 28

What is the advantage of an enzyme with a weak affinity for its substrate (i.e. large Km)

Back 28

can release its product more easily

Front 29

Catalytic RNA in ribosomes forms a peptide bone by pulling amino acids out of solution and positioning their reactive substrates close to one another. What type of enzyme mechanism is this an example of?

Back 29

catalysis by approximation

Front 30

In the enzyme Carbonic Anhydrase (the enzyme responsible for maintaining blood gases and pH), a zinc ion splits water in order to hydrate CO2. What type of enzyme mechanism is this an example of?

Back 30

Metal ion catalysis

Front 31

Explain the general structure of serine proteases' active sites and how each protease is able to recognize one specific amide bond substrate.

Back 31

Active site = "catalytic triad" = Ser, His, Asp
each protease contains a binding pocket that recognizes a specific R group shape/charge

Front 32

What is general catalytic mechanism common to serine proteases?

Back 32

1) His pulls an H+ from Serine to activate it to attack carboxy group on substrate (acid-base catalysis)
2) Asp stabilizes transition state
3) Ser covalently binds peptide group on subtrate (covalent intermediate)
4) amide group is removed (via collapse of intermediate)
5)Water is split by His to remove carboxyl group (acid-base catalysis)