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CHE 541 > 7 - Time > Flashcards

7 - Time Flashcards

(101 cards)

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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
What are some examples of low frequency vibrations?
Heme protein, hemoglobin, and GFP
26
How does heme protein use low frequency vibration?
By leading to electron transport
27
How does hemoglobin use low frequency vibration?
Lead to diatomic binding of oxygen
28
How does GFP use low frequency vibration?
Drives reaction of fluorescence (proton transfers)
29
What is the time scale for GFP?
3-10 ps
30
What is the molecules used for GFP proton transfer?
Chromophore, water, Ser205, and Glu222
31
What are MD simulations?
Put energy into atoms and see how they fold (through vibrations)
32
What does MD simulation stand for?
Molecular dynamics simulation
33
What are the forces underlying MD simulations?
Coulomb's law and Hooke's law
34
What files are needed for an MD simulation?
Coordinate file and parameter file
35
What information is in a coordinate file?
Geometry (distances, angles, and coordinates)
36
How does one get a coordinate file?
From a protein data bank (PDB)
37
What information is in a parameter file?
Spring constants, partial charges, and dielectric constant
38
What do large scale motions involve?
Many normal modes
39
What is the time scale for large scale motions?
100 us to 1 ms
40
How are large scale motions usually modeled?
By connecting two crystal structures through a low energy pathway
41
How does a myristol switch protein work?
The myristol (hydrophobic) group hides in the membrane when calcium is present
42
What are the four (basic) steps of the Ca2+ ATPase?
E1, E1-P, E2-P, and E2
43
What is the rate of the Ca2+ ATPase?
~30 Ca2+ per sec, or 66 msec per cycle
44
How come the Ca2+ ATPase is slower than the Na+/Ca2+ exchange pumps?
Ca2+ ATPase requires ATP and large conformational changes
45
What happens in E1 for the Ca2+ ATPase?
2 Ca2+ are bound, cytoplasmic gate allows ATP to bind and close the gate
46
What happens in E1-P for the Ca2+ ATPase?
Phosphoryl transfer leads to Ca2+ binding disruption and opening of lumenal gate
47
What happens in E2-P for the Ca2+ ATPase?
Ca2+ is released to lumen, and lumenal gate is closed
48
What happens in E2 for the Ca2+ ATPase?
Ca2+ binds through affinity tunnel
49
What amino acids coordinate Ca2+ in the Ca2+ ATPase?
Deprot Asp and Glu
50
How is Ca2+ released from the Ca2+ ATPase?
Asp and Glu become prot
51
How does Asp and Glu become prot in the Ca2+ ATPase?
They are moved to a hydrophobic environment (in the membrane) (destabilize A-, decrease Ka, increase pKa)
52
What does ATP do in the CA2+ ATPase?
It causes the hinging motion of two domains (Pac-man)
53
How does ATP lead to release of calcium?
ATP hinge motion causes rotation of helix into membrane, protonating Asp and Glu
54
How does ATPsynthase work?
A proton gradient is used to rotate central stalk to force subunits to open/close (pac-man in reverse)
55
How does kinesin use ATP?
It uses ATP as Pac-man clamps to walk along microtubules
56
What closes the pac-man clamp?
ATP hydrolysis
57
What opens the pac-man clamp?
Conversion to ADP
58
What is an example of translational motion?
Diffusion
59
What is diffusion?
How fast/far can it travel
60
What is a diffusion limited enzyme?
An enzyme working as fast as it can (saturated - RDS)
61
What is the rate of a kinesin molecule?
1.6 um/sec, 160 A/sec, 1 sec = 100 steps, 1 step = 10 ms
62
What is the RDS of kinesin?
Hydrolysis of ATP
63
If a cell moves 10 um in 10 ms by actin polymerization, how fast is actin polymerization?
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
What is the conclusion of the actin polymerization math?
It cannot use a pac-man mechanism (too fast)
65
What is the mechanism for actin polymerization?
Membrane has ATP bound G-actin, which can polymerize without ATP
66
How is ATP like a clock?
It can be used to regulate other proteins by controlling the rate of ATP hydrolysis
67
How far can a molecule diffuse in solution in 1 us?
100 A
68
How far can a molecule diffuse in solution in 1 ms?
1000 A
69
How quick is light detection by rhodopsin?
13 ms (was 100 ms)
70
How is light detection so quick?
It uses myelin electrical impulses (not diffusion)
71
What is the equation for diffusion coefficient?
D = kT/f
72
What does D describe?
How fast/far something can diffuse
73
What does f describe?
Size/shape of molecule
74
What is the equation for frictional coefficient?
f = 6pi*n(solvent)*r
75
What is the distance for diffusion in n-D?
x^2=2nDt
76
What is important to consider in column chromatography?
Diffusion, shape, MW
77
What does MW stand for?
Molecular weight
78
What shape has the smallest f for a given weight?
Sphere
79
What is a prolate ellipsoid?
Z axis is longer (football)
80
What is an oblate ellipsoid?
Z axis is shorter (pancake)
81
In biology, which ellipsoid is most common?
Prolate ellipsoid
82
What limits diffusion in a cell?
All of the stuff in the cell
83
True or false: diffusion is a random walk process
True
84
How can diffusion be biased?
Through an electrochemical gradient
85
How can diffusion be increased?
By restricting the diffusion to 1D or 2D
86
What is an example of restricting to 1D diffusion?
Diffuse along DNA
87
What is an example of restricting to 2D diffusion?
Diffuse along membrane surface
88
What type of process is diffusion?
A flux process
89
If there is a bigger gradient, what happens to D?
It increases (higher flux)
90
What are the units of D?
cm^2/sec
91
What is a flux?
The number of molecules that pass through a square patch in a given time
92
What is an analytical ultracentrifuge used for?
Know how big, shape, or how fast a molecule is diffusing
93
Besides analytical ultracentrifugation, what can also be used to measure diffusion?
NMR spectroscopy
94
What are the two types of analytical ultracentrifugation?
Velocity sedimentation and equilibrium sedimentation
95
How does velocity sedimentation work?
Spin source, and pass light to measure concentration change over time
96
What information does velocity sedimentation give you?
The size and shape (how fast to pellet)
97
How does equilibrium sedimentation work?
Spin at a slower speed to have centripetal force counteract diffusion force
98
What forces are balanced in equilibrium sedimentation?
Centripetal force towards center, and diffusive force outward (down concentration gradient)
99
What information does equilibrium sedimentation give you?
MW (oligomers), and how they are distributed throughout a sample
100
What would be used to measure equilibrium between a monomer and dimer?
Equilibrium sedimentation
101
What is the equation for rotational correlation time?
tr = 3Vn(solvent)/kT

CHE 541 (20 decks)

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