L10: Substrate Binding

Question 1

standard 6 classes of enzymes

Answer 1

1. oxidoreductases
2. transferases
3. hydrolases
4. lyases
5. isomerases
6. ligases

Question 2

the active site

Answer 2

1. few residues out of protein
2. 3D pocket, unique
3. determines substrate specificity by various properties
4. makes contact w/ substrate thru noncovalent interactions

Question 3

allosteric interactions

Answer 3

1. does not occur in active site – yet follows same rules
2. involves a 2nd substrate
   - —which can be an activator or inhibitor

Question 4

activators vs inhibitors

Answer 4

will either activate an enzyme or inhibit enzyme activation thru conformational change

Question 5

apoenzymes

Answer 5

an incomplete, inactive enzyme

requires a cofactor/coenzyme to be activated

Question 6

cooperativity

Answer 6

quaternary structure of proteins can have multiple active/allosteric sites
—results in cooperativity

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

affinity = strength of interaction

Question 7

the Hill Plot

Answer 7

used to make a linear plot for cooperative binder where n >1

slope = n
y-intercept = log(1/Kd)

Question 8

biotin is ?

Answer 8

vitamin B7

Question 9

biotin is ?

Answer 9

vitamin B7

Question 10

nucleophilic substitution/addition results in ?

Answer 10

swapping or addition of functional groups

Question 11

carbonyl condensation results in ?

Answer 11

change in # of carbons

Question 12

elimination rxns results in ?

Answer 12

increase in bond order

Question 13

Redox rxns result in ?

Answer 13

mvt of electrons (e-)

Question 14

substrate binding depends on ?

Answer 14

shape
charge
complementarity

Question 15

competitive inhibitor

Answer 15

binds to active site to prevent substrate binding

Question 16

allosteric inhibitor

Answer 16

binds to allosteric site induces a conformational change

which does not allow substrate to fit in active site

Question 17

allosteric activator

Answer 17

binds to allosteric site

inducing conformational change

substrate is not able to bind active site

Question 18

allosteric activator

Answer 18

binds to allosteric site

inducing conformational change

substrate is not able to bind active site

Question 19

can we have competitive activators ?

Answer 19

no

Question 20

Ka= ?

Answer 20

affinity/association constant
(coming together)

= 1/Kd

Question 21

Kd = ?

Answer 21

dissociation constant
–breaking apart

= 1/Ka

Question 22

Kd = ?

Answer 22

dissociation constant
–breaking apart

= 1/Ka

Question 23

define fractional saturation

Answer 23

what fraction of active sites have ligands bound

= Y

Question 24

possible values for Y when n = 1

Answer 24

n = # binding sites

0 means no ligand bound
1 = full saturation
0.5 = half saturation

Question 25

for Y = 0.5, by definition ?

Answer 25

[substrate] = Kd

Question 26

fractional saturation when n >1

Answer 26

now called theta, v or b or degree of binding or Y

but still defined as fraction of protein molecules that contain ligand

instead of this math we will consider cooperativity instead

Question 27

fractional saturation when n >1

Answer 27

now called theta, v or b or degree of binding or Y

but still defined as fraction of protein molecules that contain ligand

instead of this math we will consider cooperativity instead

Question 28

in terms of cooperativity, we interpret Hill coefficients in what way?

Answer 28

n = 1
means no cooperativity
sites are independent

n >1 positive cooperativity
affinity increases as each ligand binds

0< n <1 negative cooperativity
affinity decreases as each new ligand binds