Exam 2 M7

Question 1

define allostery

Answer 1

how a molecule binding to one site on a protein can affect that protein’s activity at distal sites unrelated to where that molecule is binding to

Question 2

how do cells control enzymatic activity

Answer 2

availability
physical env
substrate availability
allostery
physical/chemical changes
effectors

Question 3

is there significant secondary structure change upon allosteric binding

Answer 3

no

Question 4

T/F: allostery dec sensitivity of enzyme to substrate

Answer 4

F

Question 5

inhibitors bind to and stabilize

Answer 5

T state

Question 6

activators bind to and stabilize

Answer 6

R state

Question 7

does M-M apply to allosteric enzymes

Answer 7

no

Question 8

ATCase is involved in

Answer 8

first step of biosynthesis of pyrimidines

Question 9

structure of ATCase

Answer 9

multisubunit; 6 catalytic and 6 regulatory

Question 10

does ATCase have cooperative substrate binding

Answer 10

yes

Question 11

allosteric inhibitor of ATCase

Answer 11

CTP

Question 12

allosteric activator of ATCase

Answer 12

ATP

Question 13

substrates of ATCase

Answer 13

carbamoyl phosphate and aspartate

Question 14

substrates for ATCase are _____ charged

Answer 14

negatively

Question 15

ATCase has a ____ velocity curve

Answer 15

sigmoidal

Question 16

does ATCase obey M-M?

Answer 16

no

Question 17

ATCase: catalytic trimers can be isolated and are active; ___ greater than holoenzyme

Answer 17

Vmax

Question 18

ATCase: dimer of trimers plus trimer of dimers

Answer 18

(c3)2(r2)3

Question 19

ATCase: allosteric regulators bind to ___ and substrate binds to ____

Answer 19

regulatory dimers; catalytic trimers

Question 20

ATCase: catalytic trimers are high catalytically active and even ___ active than intact full enzyme w 12 subunits

Answer 20

more

Question 21

ATCase: ____ slows down enzyme

Answer 21

regulatory subunits

Question 22

ATCase: what happens when substrate binds

Answer 22

pushes catalytic trimers apart and separates them out and gives substrate more room to bind active site

Question 23

ATCase: driving to R state

Answer 23

substrate binding to 1 monomer of catalytic subunit drives formation of R state in all single monomers; only need 1 monomer to be bound and then all other monomers are locked into R state w higher binding affinity

Question 24

ATCase: In T state, steric hindrances prevent ___ binding domain from rotating into favorable position for substrate binding

Answer 24

Asp

Question 25

ATCase: ___ binding drives structural changes that remove barrier to rotation

Answer 25

CP

Question 26

ATCase: once CP binds, the two substrate binding domains reorient in each catalytic subunit to give___state with more accessible substrate binding sites

Answer 26

R

Question 27

ATCase: concerted ___ and ___ conf changes

Answer 27

tertiary; quaternary

Question 28

ATCase: T to R state transition requires ___

Answer 28

catalytic trimers to push away from each other, induced by substrate binding

Question 29

ATCase: each catalytic monomer has

Answer 29

2 domains

Question 30

ATCase: in R state, the 2 domains are

Answer 30

closer together/pinched together

Question 31

ATCase: 2 mvmts upon substrate binding that drives cooperativity

Answer 31

1)trimers push away from each other which gives more space for substrate to come in and bind 2)pinching in of domains so 2 substrates come in close proximity to each other so they can react

Question 32

ATCase has __ allosteric effectors

Answer 32

2

Question 33

ATCase: CTP binds to __ state where active sites are compressed

Answer 33

T

Question 34

ATCase: ATP binds to __ state where catalytic trimers are farther away from each other that allows substrate binding

Answer 34

R

Question 35

PFK: involved in

Answer 35

glycolysis

Question 36

substrates for PFK

Answer 36

F6P and ATP

Question 37

products of PFK

Answer 37

FBP, ADP

Question 38

inhibitor of PFK

Answer 38

ATP

Question 39

Activators of PFK

Answer 39

ADP, AMP

Question 40

PFK structure

Answer 40

tetramer

Question 41

PFK: for each subunit, there is a __ and ___

Answer 41

substrate binding site; allosteric regulatory site

Question 42

PFK: ATP is both __ and ___

Answer 42

substrate and allosteric inhibitor

Question 43

PFK: each subunit has ___ ATP binding sites

Answer 43

2; regualatory and substrate

Question 44

PFK: at substrate binding site, F6P binds to enzyme in __ state

Answer 44

R

Question 45

PFK: at substrate binding site, ATP binds to enzyme in ___ state

Answer 45

T or R

Question 46

PFK: at regulatory binding site, ATP binds enzyme in __ state

Answer 46

T

Question 47

PFK: at regulatory binding sites, AMP and ADP bind to __ state

Answer 47

R

Question 48

T/F: ATP levels are always constant

Answer 48

T

Question 49

PFK: ATP serves as a product ___

Answer 49

inhibitor

Question 50

PFK: R state helix is

Answer 50

full wound up and end has charged neg Glu

Question 51

PFK: R state Arg is in

Answer 51

substrate binding site

Question 52

PFK: Arg is in substrate binding site so that it

Answer 52

makes an ion pair w substrate and inc affinity btwn enzyme substrate in R state

Question 53

PFK: in T state, alpha helix is

Answer 53

not fully wound so neg Glu now in substrate binding site and Arg is over yonder and can't form ionic interactions w substrate to inc stability

Question 54

PFK: In T state, neg Glu in substrate

Answer 54

repels neg charged F6P

Question 55

PFK: allosteric molecules bind to regulatory site causes ___

Answer 55

conf change that results in residue switch (+Arg in r state which favors interaction w F6P; -Glu in T state repels F6P)

Question 56

glycogen phosphorylase structure

Answer 56

dimer in 2 forms: A = phosphorylated at Ser14 B = unphosphorylated

Question 56

PFK: need to be in __ state for catalysis to happen

Answer 56

R

Question 57

glycogen phosphorylase function

Answer 57

cleaves glycosidic bonds in glycogen

Question 58

glycogen phosphorylase: regulated by

Answer 58

allostery and phosphorylation (promotes R form)

Question 59

glycogen phosphorylase: phosphorylation of Ser14 transitions from __ to ___

Answer 59

T; R

Question 60

glycogen phosphorylase: what happens when N term gets phosphorylated

Answer 60

It swings out and tower helix tilts, moving green loop out of way of active site and Arg residues in active site reorient to bind substrate

Question 61

glycogen phosphorylase activator

Answer 61

AMP

Question 62

glycogen phosphorylase: AMP binds to __ state

Answer 62

R