Biochem Exam 2

Front 1

Catalysis depends on what structure of the enzyme?

Back 1

depends on tertiary structure or the 3-D structure.

Front 2

Kinetic vs. thermodynamics

Back 2

Kinetic - reaction rates, how fast the reaction takes place
Thermo - energetic of a reaction, deta G.

these two are independent of each other.

Front 3

Effect of catalytic amounts of enzyme on delta G.

Back 3

small catalyst had on effect on delta G or the spontenaity of the reaction.

the catalyst is not consumed, therefore it can be cancelled out.
K = [B]c/[A]c
K is not affected, therefore, the delta G is alos not affected.

Front 4

Activation energy

Back 4

determines the rate of the reaction.
a catalyst lower the activtation barrier, allowing the reaction to proceed quicker.

Front 5

How does a catalyst lower the transition state?

Back 5

catalyst stabalizes the intermediate and lowers the amount of energy need to reach that intermediate.

Front 6

Give an example of a unimolecule reaction.

Back 6

radioactive decay.

Front 7

Lock and Key vs. Induced fit model

Back 7

Lock and Key - the substrate binds to a complementary active site. The exact fit of enzyme and substrate is a very stable structure, lowering the energy and causeing for an even greater need of energy to start the reaction.

Induced Fit - binding of sub. causes conf. change in active site of enzyme. This conf. change gives the transition state a higher energy.
The change in the substrate also helps activate the reaction.

Front 8

Chymotrypsin as a model enzyme.

Back 8

chymotrypsin catalyses the hydrolysis of peptide bonds as well as ester bonds.
Rate of the reaction gives a hyperbolic curve.

Front 9

ATCase

Back 9

allosteric enzyme catalyst - gives a sigmoidal curve.
reation rate depends on the concentration of aspartate and forms CTP and UTP.

Front 10

Michaelis-Menten equation

Back 10

E+S = ES = E+P

Front 11

Simplification of the M-M equation:

Back 11

assume steady state
assume a catalytic amount of enzyme
assume that E and P do not react backwards to form ES

Front 12

M-M graph equation

Back 12

Vo = Vmax [S]/Km + [S]

Front 13

M-M graph equation simplifications.

Back 13

[S]>>Km - Vo=Vmax (zero order)

S<<Km - Vo = Vmax [S]/Km
(first order)

S=Km - Vo=Vmax/2 constant

Front 14

How does Km affect affinty between enzyme and substrate.

Back 14

the lower the Km - the more affinity the enzyme has for the substrate.

Front 15

The M-M approach is for nonallosteric enzymes!

Back 15

!

Front 16

Lineweaver-Burk equation

Back 16

1/Vo = (Km/Vmax)(1/[S] + (1/Vmax)

1/Vmax = at the + y axis
1/Km = at the - x axis

Front 17

Slope of L-B equation

Back 17

slope = Km/Vmax

Front 18

How is Vmax related to the turn over number?

Back 18

Vmax=Kcat[E]

Front 19

the turn over number

Back 19

the number of moles of substrate the react to form product per mole of enzyme.

Kcat is equal to the turnover number.

the turnover number represents the efficency of the catalyst.

Kcat= Vmax/[E]
because Vmax=Kcat[E]

Front 20

2 way to inhibit ezyymatic reaction.

Back 20

through reversible or irreversible inhibitors.

Front 21

inhibitors

Back 21

reduce rate of enzyme.

molecules that interact with enzyme to reduce their rate.

Front 22

Reversible inhibitors

Back 22

can bind and then dissociate.

Competitive and Noncompetitive inhibitors.
Competative bind to active site - therefore, have structural similarities to the substrate.
Noncompetative:
bind to allosteric site and don't have similar strucutre to the substrate.
binding inactivates the enzyme.

Front 23

Competative inhibitors:

(reversible)

Back 23

competative inhibitor can be overcome by increasing the amount of substrate.
The Km value increases because you need more substrate to reach 1/2 V0.
Vmax is unaffected because you retain the same amount of enzyme.

the hyperbolic curve is lower in the presence of the competative inhibitor.

L-B plot - the lines with intersect at diff point on the x axis - giving diff. Km values.

Front 24

Noncompetative inhibitors:

(reversible)

Back 24

the inhibitor binds to the allosteric site. Therefore substrate cannot be increased to overcome this affect.

The Km value doesnot change. You still need the same amount of substrate to reach 1/2 Vo.

The Vmax value decreases because enzyme is being "removed" by the inhibitor. So, in effect you have less enzyme available.

Front 25

Myoglobin and Chymotrypsin
Vs.
ATCase and Hemoglobin

Back 25

Myo. Chym - hyperbolic

Hb, ATCase - sigmoidal.

Front 26

ACTase

Back 26

ATP actitives
CTP inhibits

Front 27

Enzymes exist in 2 conf.

Back 27

R- bind substrate tightly and is active
T-binds substrate lossely and is not-active.

Front 28

Concerted Model

Back 28

complete change from R to T.

lock and key

Front 29

Sequential

Back 29

induced fit.
changing of one subunit affects the other subunits.
change to one subunit makes it easier for sequential changing to that subunit.

Front 30

Allosteric systems have K system and V system.

Back 30

K system - equivalent to competative inhibitors.
-the Km is lowered and the Vmax stays the same.

V system - noncompetative inhibitors.
the Vmax changes and the Km stays the same.

Front 31

Sequential model has what coopertivity

Back 31

S model has negative coopertivity that is unique to this model.

Front 32

Cofactors
Apoezyme-
Holofactor-

Back 32

Apoenzyme - an ezyme that is missing its cofactor
Holofactor - enzyme that has its cofactor.

Cofactors are inorganic.
Coenzymes are organic.

Front 33

Prostetic groups

Back 33

tightly bound cofactors.

Front 34

Coenzyme:
Biotin

Back 34

biotin - cofactor for pyruvate carboxylase and the reaction is carboxylation.

Vitamen precursor is biotin.

Front 35

Coenzyme A

Back 35

reaction type is acyl transfer.
involved in PDHC

vitamen precursor is pantophenic acid.

Lipoic acid - involved in acyl transfer.
had 2 sulfures that can make disulfide bonds.

Front 36

Flavin coenzymes
Nicatinamide adinin

Back 36

both ozidation/reduction .

nicatinamide comes form niacin
flavin come from favin.

Front 37

TPP
thyminpyrophosphate

Back 37

aldehyde transfer.
involved with pyruvate dehydrogenase.

derived from thymine - vit. B1

Front 38

NAD structure.

Back 38

adenine
2 ribose
nicotinamide - vit portion

joined by a phosphoanhydride bond.

nicotinamide is the portion that is reduced.

Front 39

Chemical reactions that occur in the active site

Back 39

1. nucleophile
2. acid-base reactions
3. metal ion catalyst.

Front 40

Metal ion catalyst

Back 40

act as lewis acids and accept electrons for the carbonyl ozygen.
Make cabonyl carbon have detla positive and avaliable for nucleophillic attach.

Carboxypeptidase has a metal ion that aids in cleavage of the peptide bond at the C-terminus.