Lecture 10: Substrate binding

Question 1

Oxidoreductases and carriers

Answer 1

Move electrons in redox reactions

NADH, NADPH, FADH2, FMNH2

Question 2

Transferases ATP and pyridoxal phosphate

Answer 2

Transfer phosphate functional groups

Question 3

Transferases SAM, THF, 5’-DAC

Answer 3

Transfer methyl groups

Question 4

Hydrolases

Answer 4

Break a chemical bond by added water across it (hydrolysis)

Question 5

Isomerases

Answer 5

Rearrange order of atoms in a molecule (isomerization)

Question 6

Lyases

Answer 6

Break a chemical bond without using water

Question 7

Ligases

Answer 7

Paste two pieces together using ATP

Question 8

TPP

Answer 8

+/- aldehyde group

Question 9

CoASH, lipoamide

Answer 9

+/- Acyl group

Question 10

Biotin

Answer 10

+/- CO2 group

Question 11

Carbonyl condensation

Answer 11

Change number of carbons

Question 12

Elimination

Answer 12

Increase bond order

Question 13

Active site structure

Answer 13

Only consists of a few residues out of the protein

3-D pocket creating unique microenvironment

Question 14

How does active site determine specificity and what type of interactions occur

Answer 14

Specificity determined by size and charge

Contacts substrate through non-covalent interactions

Question 15

Allosteric binding

Answer 15

Does NOT occur at the active site, but follows same rules

Involves second substrate that can be inhibitor or activator

Question 16

Apoenzymes

Answer 16

Incomplete
Inactive
Lack cofactor/coenzyme

Question 17

Holoenzymes

Answer 17

Whole
Active
Contain cofactor/coenzyme
Require allosteric activation

Question 18

Kd

Answer 18

Dissociation constant for E x Sn complexes
Equal to the concentration of ligand where 1/2 the available binding sites are full
When the receptor is half-saturated

Question 19

Hill equation (n=1)

Answer 19

Y= [S] / Kd + [S]

Question 20

When Y= 0.5, what does [S] equal

Answer 20

Kd

Question 21

When n=1 what are the values of the slope, y-intercept and x-intercept

Answer 21

Slope= -1/Kd
y-intercept= 1/Kd
x-intercept= [E]t

Question 22

Cooperativity

Answer 22

Binding of each subsequent ligand influences the affinity of the next ligand to bind active site

Question 23

Hill equation (n>1, perfectly cooperative)

Answer 23

0(with dash through middle) =
[S]^n / (Kd + [S]^n)
n= number of binding sates

Question 24

Slope and y-intercept values for Hill plot when n>1

Answer 24

Slope= n(h)
y-intercept= log(1 / Kd)

Question 25

Interpretations of hill equation n(h)=1 n(h)>1 0 < n(h) < 1

Answer 25

nh=1 means no cooperativity (sites are independent) nh>1 means positive cooperativity (affinity increases) 1