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CHE 541 > 7 - Time > Flashcards

7 - Time Flashcards

1
Q

What is the importance of motion in enzyme catalysis?

A

Need motion to figure out how an enzyme works

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2
Q

What does a hinging motion do?

A

It can open and close a cleft to allow for binding or removal of bulk water

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3
Q

What is the time scale for vibrations?

A

10^-15 to 10^-12 s

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4
Q

What is the time scale for rotations?

A

10^-12 to 10^-9 s

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5
Q

What is the time scale for translations?

A

10^-6 s

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6
Q

What happens if small motions are tracked over long time scales?

A

These small motions give rise to larger motions, such as opening and closing of a cleft

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7
Q

How are vibrations measured?

A

Through infrared or Raman spectroscopy

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8
Q

How are rotations measured?

A

Through NMR or fluorescence anisotropy

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9
Q

How are translations measured?

A

Through NMR or fluorescence

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10
Q

What are the types of vibrations?

A

Stretch, bend, and torsion

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11
Q

What is a normal mode?

A

A combination of vibrations such that the center of mass does not change

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12
Q

What law is used to model vibration frequency?

A

Hooke’s law

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13
Q

Using Hooke’s law, how can molecules be modeled?

A

As masses attached to springs

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14
Q

What is the formula for vibration frequency?

A

v = 1/2pi (k/u)^1/2

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15
Q

For vibration frequency, what is v?

A

Vibration frequency

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16
Q

For vibration frequency, what is k?

A

Spring constant

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17
Q

For vibration frequency, what is u?

A

Reduced mass (m1m2/m1+m2)

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18
Q

If mass is increased, what happens to the frequency?

A

It decreases

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19
Q

If frequency is decreased, what happens to the energy?

A

It decreases

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20
Q

What is the range of high frequency vibrations?

A

3000-4000 1/cm

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21
Q

What are examples of high frequency vibrations?

A

C-H, N-H, and O-H stretches

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22
Q

What is usually the focus of vibrational spectroscopy?

A

C-C (1000 1/cm) and C=C (1500 1/cm) stretches

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23
Q

How come low frequency vibrations are not mentioned frequently?

A

They are hard to measure

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24
Q

What is the importance of low frequency vibrations?

A

Involve many atoms, lead to “breathing” of proteins

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25
Q

What are some examples of low frequency vibrations?

A

Heme protein, hemoglobin, and GFP

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26
Q

How does heme protein use low frequency vibration?

A

By leading to electron transport

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27
Q

How does hemoglobin use low frequency vibration?

A

Lead to diatomic binding of oxygen

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28
Q

How does GFP use low frequency vibration?

A

Drives reaction of fluorescence (proton transfers)

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29
Q

What is the time scale for GFP?

A

3-10 ps

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30
Q

What is the molecules used for GFP proton transfer?

A

Chromophore, water, Ser205, and Glu222

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31
Q

What are MD simulations?

A

Put energy into atoms and see how they fold (through vibrations)

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32
Q

What does MD simulation stand for?

A

Molecular dynamics simulation

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33
Q

What are the forces underlying MD simulations?

A

Coulomb’s law and Hooke’s law

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34
Q

What files are needed for an MD simulation?

A

Coordinate file and parameter file

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35
Q

What information is in a coordinate file?

A

Geometry (distances, angles, and coordinates)

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36
Q

How does one get a coordinate file?

A

From a protein data bank (PDB)

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37
Q

What information is in a parameter file?

A

Spring constants, partial charges, and dielectric constant

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38
Q

What do large scale motions involve?

A

Many normal modes

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39
Q

What is the time scale for large scale motions?

A

100 us to 1 ms

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40
Q

How are large scale motions usually modeled?

A

By connecting two crystal structures through a low energy pathway

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41
Q

How does a myristol switch protein work?

A

The myristol (hydrophobic) group hides in the membrane when calcium is present

42
Q

What are the four (basic) steps of the Ca2+ ATPase?

A

E1, E1-P, E2-P, and E2

43
Q

What is the rate of the Ca2+ ATPase?

A

~30 Ca2+ per sec, or 66 msec per cycle

44
Q

How come the Ca2+ ATPase is slower than the Na+/Ca2+ exchange pumps?

A

Ca2+ ATPase requires ATP and large conformational changes

45
Q

What happens in E1 for the Ca2+ ATPase?

A

2 Ca2+ are bound, cytoplasmic gate allows ATP to bind and close the gate

46
Q

What happens in E1-P for the Ca2+ ATPase?

A

Phosphoryl transfer leads to Ca2+ binding disruption and opening of lumenal gate

47
Q

What happens in E2-P for the Ca2+ ATPase?

A

Ca2+ is released to lumen, and lumenal gate is closed

48
Q

What happens in E2 for the Ca2+ ATPase?

A

Ca2+ binds through affinity tunnel

49
Q

What amino acids coordinate Ca2+ in the Ca2+ ATPase?

A

Deprot Asp and Glu

50
Q

How is Ca2+ released from the Ca2+ ATPase?

A

Asp and Glu become prot

51
Q

How does Asp and Glu become prot in the Ca2+ ATPase?

A

They are moved to a hydrophobic environment (in the membrane) (destabilize A-, decrease Ka, increase pKa)

52
Q

What does ATP do in the CA2+ ATPase?

A

It causes the hinging motion of two domains (Pac-man)

53
Q

How does ATP lead to release of calcium?

A

ATP hinge motion causes rotation of helix into membrane, protonating Asp and Glu

54
Q

How does ATPsynthase work?

A

A proton gradient is used to rotate central stalk to force subunits to open/close (pac-man in reverse)

55
Q

How does kinesin use ATP?

A

It uses ATP as Pac-man clamps to walk along microtubules

56
Q

What closes the pac-man clamp?

A

ATP hydrolysis

57
Q

What opens the pac-man clamp?

A

Conversion to ADP

58
Q

What is an example of translational motion?

A

Diffusion

59
Q

What is diffusion?

A

How fast/far can it travel

60
Q

What is a diffusion limited enzyme?

A

An enzyme working as fast as it can (saturated - RDS)

61
Q

What is the rate of a kinesin molecule?

A

1.6 um/sec, 160 A/sec, 1 sec = 100 steps, 1 step = 10 ms

62
Q

What is the RDS of kinesin?

A

Hydrolysis of ATP

63
Q

If a cell moves 10 um in 10 ms by actin polymerization, how fast is actin polymerization?

A

Say width of actin = 10 nm. Need 1000 to cover 10 um. Thus, it takes 10 us to hydrolyze ATP (10 us * 1000 = 10 ms)

64
Q

What is the conclusion of the actin polymerization math?

A

It cannot use a pac-man mechanism (too fast)

65
Q

What is the mechanism for actin polymerization?

A

Membrane has ATP bound G-actin, which can polymerize without ATP

66
Q

How is ATP like a clock?

A

It can be used to regulate other proteins by controlling the rate of ATP hydrolysis

67
Q

How far can a molecule diffuse in solution in 1 us?

A

100 A

68
Q

How far can a molecule diffuse in solution in 1 ms?

A

1000 A

69
Q

How quick is light detection by rhodopsin?

A

13 ms (was 100 ms)

70
Q

How is light detection so quick?

A

It uses myelin electrical impulses (not diffusion)

71
Q

What is the equation for diffusion coefficient?

A

D = kT/f

72
Q

What does D describe?

A

How fast/far something can diffuse

73
Q

What does f describe?

A

Size/shape of molecule

74
Q

What is the equation for frictional coefficient?

A

f = 6pin(solvent)r

75
Q

What is the distance for diffusion in n-D?

A

x^2=2nDt

76
Q

What is important to consider in column chromatography?

A

Diffusion, shape, MW

77
Q

What does MW stand for?

A

Molecular weight

78
Q

What shape has the smallest f for a given weight?

A

Sphere

79
Q

What is a prolate ellipsoid?

A

Z axis is longer (football)

80
Q

What is an oblate ellipsoid?

A

Z axis is shorter (pancake)

81
Q

In biology, which ellipsoid is most common?

A

Prolate ellipsoid

82
Q

What limits diffusion in a cell?

A

All of the stuff in the cell

83
Q

True or false: diffusion is a random walk process

A

True

84
Q

How can diffusion be biased?

A

Through an electrochemical gradient

85
Q

How can diffusion be increased?

A

By restricting the diffusion to 1D or 2D

86
Q

What is an example of restricting to 1D diffusion?

A

Diffuse along DNA

87
Q

What is an example of restricting to 2D diffusion?

A

Diffuse along membrane surface

88
Q

What type of process is diffusion?

A

A flux process

89
Q

If there is a bigger gradient, what happens to D?

A

It increases (higher flux)

90
Q

What are the units of D?

A

cm^2/sec

91
Q

What is a flux?

A

The number of molecules that pass through a square patch in a given time

92
Q

What is an analytical ultracentrifuge used for?

A

Know how big, shape, or how fast a molecule is diffusing

93
Q

Besides analytical ultracentrifugation, what can also be used to measure diffusion?

A

NMR spectroscopy

94
Q

What are the two types of analytical ultracentrifugation?

A

Velocity sedimentation and equilibrium sedimentation

95
Q

How does velocity sedimentation work?

A

Spin source, and pass light to measure concentration change over time

96
Q

What information does velocity sedimentation give you?

A

The size and shape (how fast to pellet)

97
Q

How does equilibrium sedimentation work?

A

Spin at a slower speed to have centripetal force counteract diffusion force

98
Q

What forces are balanced in equilibrium sedimentation?

A

Centripetal force towards center, and diffusive force outward (down concentration gradient)

99
Q

What information does equilibrium sedimentation give you?

A

MW (oligomers), and how they are distributed throughout a sample

100
Q

What would be used to measure equilibrium between a monomer and dimer?

A

Equilibrium sedimentation

101
Q

What is the equation for rotational correlation time?

A

tr = 3Vn(solvent)/kT

CHE 541 (20 decks)

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