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CHE 541 > 11 - Allostery > Flashcards

11 - Allostery Flashcards

1
Q

What does allostery do?

A

It alters affinity response

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2
Q

What does a 100 fold change in ligand concentration lead to?

A

9 fold change in fractional occupancy

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3
Q

What is a graded response?

A

Continuum

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4
Q

What is a linear response?

A

Stepwise

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5
Q

What does an ultrasensitive response look like?

A

It is steeper (10 fold change in input for 9 fold change in fractional occupancy)

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6
Q

On a linear scale, what do graded and ultrasensitive responses look like?

A

Graded response is hyperbolic, while ultrasensitive response is sigmoidal

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7
Q

What is a graded response similar to?

A

A dimer

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8
Q

What is an ultrasensitive response similar to?

A

A switch

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9
Q

What is cooperativity?

A

Binding of one ligand molecule changes the affinity for the second ligand binding

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10
Q

What is allostery?

A

Binding occurs at a different site (not the active site)

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11
Q

What is needed for allostery?

A

More than one binding site

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12
Q

True or false: all cooperative binding is allosteric

A

False: not all cooperative binding is allosteric

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13
Q

What is an example of cooperative binding that is not allosteric?

A

2 binding sites on DNA for transcription factors, can increase or decrease binding

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14
Q

Why is allosteric feedback common at the beginning of biochemical pathways?

A

Can regulate whether the pathway proceeds or not (it has the proper substrates)

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15
Q

What is the MWC model of allostery?

A

Induced fit model, change conformation of active site

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16
Q

In a plot of E vs conformation, what would the MWC model predict?

A

The graph would shift to the right (conformational shift)

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17
Q

What is the KNF model of allostery?

A

Transient formation of low and high state, binding shifts equilibrium

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18
Q

In a plot of E vs conformation, what would the KNF model predict?

A

A narrower curve (population shift)

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19
Q

True or false: ligand binding changes protein dynamics

A

True: this affects the jiggles and wiggles of the protein

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20
Q

How does bacterial chemotaxis work?

A

When bound to a repellant, CheY is phosphorylated, causing clockwise rotation and tumbling

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21
Q

What type of response is pCheY?

A

Ultrasensitive response

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22
Q

What is the general structure of a protein kinase?

A

N lobe, C lobe, and ATP pocket

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23
Q

What is found in the N lobe of a protein kinase?

A

DFG motif (activation loop)

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24
Q

What regulates the DFG motif in a kinase?

A

Helix alpha C

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25
Q

What does the P loop do in a kinase?

A

Covers ATP product

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26
Q

What does a kinase cycle between?

A

Active and inactive states

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27
Q

What happens when the activation loop is phosphorylated?

A

It locks the kinase into the active configuration

28
Q

How does helix alpha C regulate the kinase?

A

It can either break salt bridge, or flip DFG motif

29
Q

What are kinase cascades an example of?

A

An ultrasensitive switch (multiply system output)

30
Q

Is the response of MAPK3 shallow or steep and why?

A

Shallow (initial protein in cascade)

31
Q

Is the response of MAPK shallow or steep and why?

A

Steep (amplification by enzyme activity)

32
Q

What affects the steepness of the response?

A

Cooperativity

33
Q

What is positive cooperativty?

A

Increases affinity (Kd1 > Kd2)

34
Q

What is negative cooperativity?

A

Decreases affinity (Kd1 < Kd2)

35
Q

How does positive cooperativity change the slope steepness?

A

It increases it

36
Q

How does negative cooperativity change the slope steepness?

A

It decreases it

37
Q

What is the significance of negative cooperativity?

A

Wide range of sensitivity (extend dynamic range, better at detecting high vs. low)

38
Q

How does oxygen transport work?

A

Load hemoglobin with high O2 in lungs, release with low O2 in tissues

39
Q

What is the importance of myoglobin?

A

It scavenges O2 away from hemoglobin to keep O2 levels low

40
Q

What is the structure of hemoglobin?

A

4 subunits

41
Q

What happens when O2 binds to a hemoglobin subunit?

A

It causes a conformational change, and increases affinity

42
Q

How does hemoglobin give rise to cooperativity?

A

Switch between different states of affinity

43
Q

What is the high affinity state in hemoglobin?

A

R

44
Q

What is the low affinity state in hemoglobin?

A

T

45
Q

If hemoglobin goes from R to T, what cooperativity is this?

A

Negative

46
Q

If hemoglobin goes from T to R, what cooperativity is this?

A

Positive

47
Q

What is the response to switch between 2 affinity states?

A

A sigmoidal response

48
Q

What happens at f/(1-f) = 1?

A

f = 0.5, Kd = L

49
Q

How can you find Kd from f/(1-f) and L?

A

Plot f/(1-f) and log(L), and log(Kd) is when f/(1-f) = 1

50
Q

What happens if two isotherms are far apart?

A

There is stronger cooperativity?

51
Q

What quantifies binding cooperativity?

A

Hill coefficient (slope in log (f/(1-f)) vs log(L) plot at half ligand saturation)

52
Q

What is the formula for hill coefficient?

A

nH = 2/(1+sqrt(Kd2/Kd1))

53
Q

What happens if nH > 1?

A

Positive cooperativity (slope > 1)

54
Q

What happens if nH < 1?

A

Negative cooperativity (slope < 1)

55
Q

What is the maximum of nH?

A

2

56
Q

What is the minimum of nH?

A

0

57
Q

What does the maximum value of nH represent?

A

The minimum number of interacting binding sites

58
Q

What is the max nH for hemoglobin?

A

4

59
Q

What happens if Kd1 = Kd2?

A

nH = 1, no cooperativity (no change in affinity)

60
Q

What is the structure of deoxyhemoglobin?

A

It has a twisted heme group

61
Q

What happens when deoxyhemoglobin becomes oxygenated?

A

The heme group is flattened, changing the conformation and changing affinity states (rotation)

62
Q

What does biphosphoglycerate do?

A

It stabilizes deoxyhemoglobin

63
Q

What do BPG and CO2 have in common?

A

They reduce oxygen affinity binding

64
Q

What is allosteric regulation?

A

Stabilize low affinity state

65
Q

What is the Bohr effect?

A

Fine tune O2 transport by decreases in pH

66
Q

Which has the higher pH: lungs or tissues?

A

Lungs

67
Q

How does CO2 impair oxygen affinity?

A

It interacts with K40 and D94 to disrupt salt bridge

CHE 541 (20 decks)

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