Biochem Test 2

Front 1

Quaternary structure of hemoglobin

Back 1

Tetramer consisting of two alpha-beta dimers
ab-ab

Front 2

Heme definition

Back 2

Prosthetic group, consisting of an organic portion called porphyrin and an inorganic portion, a Fe atom in the center

Front 3

Iron in center can form 6 bonds:

Back 3

4 with the nitrogens of the porphyrin, 2 on either side of plane.

Hemoglobin: Histidine on one, o2 on the other

myoglobin: histidine on one, O2 on other, and distal histidine w/ hydrogen bond to stabilize and prevent superoxide anion O2-

Front 4

Short term name for normal hemoglobin

Back 4

Hb or Hbg

Front 5

Shape of the curve for 02 binding hemoglobin

Back 5

sigmoidal, yo

Front 6

Deoxyhemoglobin is in what state?
Oxyhemoglobin is in what state?

Back 6

T state
R state

Front 7

Sickle Cell Anemia:
specifics

Back 7

Mutation in B globin chain
A to T sub in 6th codon of B globin chain

Glutamic acid --> Valine

Code word: HbS

Front 8

Loci for B chain: how many?
Loci for A chain: How many?

Which thalassemia is more common?

Back 8

2 (one gene)
4 (two genes)

B, because if you fuck up only 2, you're fucked. gotta fuck up four for A thal

Front 9

BPG

Back 9

stabilizes the T state of hemoglobin, so that it will release the oxygen to the tissues

Front 10

Thalassemia

Back 10

A-thalassemia - hemoglobin tetramers of B form (HbH), because A chains are not produced

B-Thalassemia - B chains are not produced. A chains become insoluble aggregates. Blood cell loss.

Front 11

Fetal hemoglobin makeup and function

Back 11

2 alpha chains and 2 gamma chains.

why so oxygen greedy? bpg does not bind as well due to the y chain change in binding site

Front 12

All enzymes are proteins. true or false

Back 12

FALSE. ribozymes

Front 13

Definitions:
1. Cofactor
2. Apoenzyme
3. Holoenzyme
4. Prosthetic group

Back 13

1. Small molecules that aid in enzyme function
a) metals
b) coenzymes
2. enzyme without cofactor
3. enzyme with cofactor
4. Tightly bound cofactor

Front 14

What exactly does trypsin cleave?

What exactly does chymotrypsin cleave?

Back 14

C terminal side of lysine and arginine
maybe histidine?

tryptophan, tyrosine, phenylalanine, leucine, and methionine. C end

Front 15

Gibbs free energy

Back 15

Free energy difference between product and reactant.

Front 16

Is Gibbs Free energy affected by enzymes?

Back 16

No.

Front 17

Do enzymes accelerate the attainment of equilibria?

Do they shift the position of equilibria?

Back 17

Yes

No

Front 18

Rate is determined by the energy required to...

Back 18

initiate conversion of reactants to products

Front 19

Specificity of an enzyme is determined by its...

Back 19

3d structure

Front 20

Michaelis Menten equation

Back 20

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

Front 21

MM equation when [s] = Km

MM equation when [s] >> Km

MM equation when [s] << Km

Back 21

V = vmax/2

V = vmax

V = vmax[S]/Km

Front 22

When [E] is constant V is...

Back 22

linearly proportional to [S] when [S] is small

when [S] is large, it's in excess of the enzyme, and V is independent of S

Front 23

V equals

Back 23

the number of moles of product formed per second

Front 24

The Michaelis Constant

Back 24

Km - the [substrate] at V = Vmax/2

Front 25

What is the Km used for?

Back 25

Used to define the affinity that an enzyme has for its substrate

higher the Km, the lower the affinity.

lower the Km, the higher the affinity

Front 26

What does the Vmax depend on?

Back 26

enzyme concentration

Front 27

Kcat

Back 27

The turnover rate
reactions/second

Kcat = Vmax/[E]t
enzyme is fully saturated with substrate

Front 28

Lineweaver-Burk double rec plot
1. x axis:
2. y axis:
3. slope:
4. x intercept:
5. y intercept:

Back 28

1. 1/[S]
2. 1/Vo
3. Km/Vmax
4. -1/Km
5. 1/Vmax

Front 29

Reversible inhibition

Back 29

substance that binds to an enzyme to inhibit it, but can be released.

Front 30

3 kinds of reversible inhibition

Back 30

1. Competitive inhibition: an enzyme can bind to either a substrate [ES] but not both.
Can be relieved by increasing [S]

2. Uncompetitive inhibition - inhibitor binds to a site that is only present when E binds to S

3. Noncompetitive inhibition - inhibitor binds to place other than active site

Front 31

double-reciprocol plot for different inhibitors, and what happens:
1. competitive inhibition
2. noncompetitive inhibition
3. uncompetitive inhibition

Back 31

1. Vmax unchanged
Km goes up
so, y intercept is the same,
x intercept increases

2. km stays the same
Vmax decreases
so, x intercept stays the same
y intercept decreass (it looks like it's going up)
3. Km goes down
Vmax goes down
both x and y intercepts decrease
slope remains the same

Front 32

Reaction rate in noncompetitive inhibition increases more ...... at low [s] in comparison with uncompetitive inhibitor

Back 32

slowly

Front 33

In noncompetitive inhibition, why is Vmax decreased while Km remains unchanged?

Back 33

The inhibitor lowers the concentration of functional enzyme. Since the pool of free enzyme is lower in presence of inhibitor, Vmax will be lower.

Front 34

Irreversible inhibition

Back 34

inhibitor covalently bonds with enzyme. attachment often occurs at the active site.

Front 35

DIPF - what does it dooo

Back 35

inactivates acetylcholinesterase, causes paralysis and death.

Front 36

Penicillin - what does it dooo

Back 36

messes with the peptidoglycan cell wall.

Suicide inhibitor!

Front 37

Cyanide - what does it doo

Back 37

binds to transitional metals used as cofactors

Front 38

Catalytic strategies: (4)

Back 38

Covalent catalysis
Acid-Base catalysis
Catalysis by approximation
Metal Ion Catalysis

Front 39

Covalent catalysis

Back 39

Active site contains a reactive group, usually a powerful nucleophile, that becomes temporarily covalently attached to a part of the substrate in the course of catalysis

ex: chymotrypsin

Front 40

General acid-base catalysis

Back 40

A molecule other than water plays the part of proton donor or acceptor.

ex: chymotrypsin, using a histidine residue as a base catalyst to enhance the nucleophilic power of serine

Front 41

General Acid catalysis

Back 41

Enzyme donates a proton to substrate.
Enzyme must be protonated

Front 42

General Base catalysis

Back 42

Enzyme accepts protons from base.
Enzyme must be deprotonated.

Front 43

Metal Ion catalysis
Ways metals ions can function catalytically

Back 43

1. Facilitate the formation of nucleophiles, such as hydroxide ion by direct coordination.
ex: Zinc(II) in carbonic anhydrase

2. metal ion may serve as an electrophile, stabilizing a negative charge on a reaction intermediate
ex: magnesium in EcoRV

3. metal ion may serve as a bridge between enzyme and substrate, increasing the binding energy and holding the substrate in a conformation appropriate for catalysis.
ex: all enzymes that use atp as a substrate

Front 44

metalloenzymes

Back 44

contain tightly bound metal cofactors such as fe2+, fe3+, Cu2+...

Front 45

Serine proteases

Back 45

A family of proteolytic enzymes that have an active site w/ serine

Front 46

digestive enzymes trypsin, chymotrypsin and elastase are similar how?
different how?

Back 46

1. with respect to their 3d structure and catalytic mechanism
2. specificity

Front 47

specificity of elastase

Back 47

C-t side of small, neutral amino acids

Front 48

chromogenic substrate

Back 48

upon catalysis, product generates color which can be used to measure enzyme kinetics

Front 49

mechanism of chymotrypsin
(2 steps)

Back 49

1. acylation
serine protease hydroxyl group (OH) acts as a nucleophile and covalently bonds with substrate. burst phase.
2. deacylation - water reacts with acyl-enzyme intermediate to free the product

Front 50

Catalytic Triad of chymotrypsin
Residues and Numbers

Back 50

Aspartic Acid 102
Histidine 57
Serine 195