Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CHE 541 > 10 - Ligand Binding and Equilibria II > Flashcards

10 - Ligand Binding and Equilibria II Flashcards

1
Q

True or false: binding is a kinetic process

A

True: it depends on on and off rate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

True or false: all collisions lead to reactions

A

False: they need sufficient speed and orientation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the order of the association reaction?

A

2nd order (1/Ms)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the order of the dissociation reaction?

A

1st order (1/s)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

For a first order reaction, what is the equation for the half time?

A

t1/2 = ln(2)/k

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What does the association rate depend on?

A

Diffusion

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the fastest possible type of reaction?

A

A diffusion limited reaction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How does stopped flow work?

A

Two reactants are mixed, and it is measured how solution ages over time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

On what order does stopped flow work?

A

Reactions on order of seconds (mixing on order of ms)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is measured in stopped flow?

A

A change in absorbance or fluorescence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is calculated in stopped flow?

A

kon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How is kon calculated in stopped flow?

A

Measure the fluorescence over time for different [L] levels, then plot k vs L to find kon and koff.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

For stopped flow, what line is plotted?

A

kobs = (kon)[L]T + koff

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does SPR work?

A

A gold membrane is used to bind antibodies to receptor (immobilize protein), and change in density is measured

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is SPR used frequently for?

A

Protein/antibody, not protein/small molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How come SPR is used for protein/antibody?

A

Need a large change in molecular weight for detection

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How does FRET work?

A

Direct observation by a FRET signal (2 fluorophores close together)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the advantages of FRET?

A

Very sensitive, little background, very fast, small concentrations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What interactions can PDZ have?

A

Protein/protein (non-canonical) and protein/peptide (canonical)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

True or false: if two proteins have different kinetics, they must have different Kds

A

False: they can have different kinetics, but same Kd

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the kinetics for a protein/protein interaction?

A

Stay on for longer, slower kinetics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are the kinetics for a protein/peptide interaction?

A

Pop off very frequently, faster kinetics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the two major classes of protein/protein interactions?

A

Forming an interface, or peptide recognition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the typical protein/protein interface?

A

700-800 A^2, 10 H-bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the size of a typical protein?

A

100 A (largest dimension)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What percentage of a protein is an interface?

A

10%

27
Q

True or false: interfaces are based on one interaction

A

False: they are a mix of multiple interactions

28
Q

What two factors are needed for an interface?

A

Affinity and specificity

29
Q

What is the role of hydrophobic interactions in interfaces?

A

High affinity, low specificity

30
Q

What is the role of electrostatics in interfaces?

A

Give high specificity (positive and negative discrimination)

31
Q

What is the role of water in interfaces?

A

Can mediate contacts (solvation, or H-bond network)

32
Q

What is required for polar interactions?

A

Desolvation

33
Q

What is a positive delta G elec?

A

Repulsive

34
Q

What is a negative delta G elec?

A

Attractive

35
Q

Are electrostatics usually attractive or repulsive and why?

A

Repulsive, because desolvation is a big energy cost)

36
Q

Describe how forming a salt bridge is a repulsive electrostatic interaction

A

The surface is solvated, so there is a large enthalpic cost to desolvate. Not enough enthalpy is formed back when the salt bridge forms

37
Q

What are some examples of peptide recognition domains?

A

PTB, SH2, SH3, WW

38
Q

What is the purpose of combining modular domains?

A

Higher specificity and affinity

39
Q

How does the Kd change if two domains are joined?

A

The sum of the delta G’s can be used to find the overall Kd (Kd joined = product of Kds), and it should be lower than each individually (higher affinity)

40
Q

What is the MAGuK family?

A

Different scaffolds that can be combined together for different recognition

41
Q

What is the energetic cost for peptide recognition?

A

Entropic loss (less freedom), but enthalpic gain (bonding)

42
Q

Why is concentration required for specificity?

A

At low concentrations, there will be higher specificity than at higher concentrations

43
Q

What is alpha?

A

Specificity factor

44
Q

What is the formula for alpha?

A

alpha = [RoL]/sum([RiL]) (specific/non-specific)

45
Q

What happens to alpha if Kd(R0) < L < Kd (R1)

A

Alpha is high, only desired target, high specificity

46
Q

What happens to alpha if Kd(R0) < L = Kd(R1)?

A

Alpha decreases, more off target complexes

47
Q

What happens to alpha if Kd(R0) < Kd (R1) < L?

A

Alpha approaches one, everything is saturated

48
Q

What balance is needed with specificity?

A

Want concentration as low as possible for specificity (minimize off target effects), but need a certain amount to actually inhibit (bind to) target

49
Q

What is IC50%?

A

Inhibitor concentration for 50% inhibition

50
Q

What is Ki?

A

Dissociation constant for inhibitor

51
Q

What does IC50% depend on?

A

Concentration

52
Q

What interactions dominate DNA binding?

A

Electrostatic and polar interactions

53
Q

For DNA binding, what charge is the protein?

A

Positive (DNA is negative)

54
Q

How is dsDNA distinguished from dsRNA?

A

Differences in major/minor groove (complementary shape to specific protein in spacing of phosphates)

55
Q

How does DNA bending affect binding?

A

Contributes to affinity, but lacks specific constraints, and is energetically costly (loss of H bonds and base stacking)

56
Q

How do aromatic residues affect DNA binding?

A

These can lead to interactions beyond electrostatics

57
Q

What are the key determinants of DNA binding specificity?

A

H-bonds

58
Q

How can specificity be increased in DNA binding?

A

Tandem DNA binding domains

59
Q

What is an example of a tandem repeat for DNA binding?

A

Zinc finger

60
Q

What sequences do tandem domains recognize?

A

Palindromes (dimers)

61
Q

What cooperativity is present in DNA binding?

A

Protein complexes that also bind to DNA

62
Q

What is the problem of specificity in DNA binding?

A

Need to bind 20 bp in 10^9 bp sequence

63
Q

True or false: transcription factors always bind to the right site

A

False: there are so many sites, so they can bind to the wrong site

64
Q

What can be used to observe DNA binding and target searching?

A

Fluorescent microscopy (use a chip and fluorescence or FRET), and gel shift (have free DNA, and increase protein concentration leads to changes in mobility)

CHE 541 (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions