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Physical Chemistry > Quiz 5: Chapter 8: Motions of Biological Molecules > Flashcards

Quiz 5: Chapter 8: Motions of Biological Molecules Flashcards

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1
Q

Under what conditions does diffusion of molecules occur?

A

occurs if there is a concentration gradient dc/dx

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2
Q

What is net flux of molecules? (Diffusion)

A
  • Flux is J, has units mol m^-2 s^-1
  • it is the moles of molecules that moves through an area per second
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3
Q

What is Fick’s first law of diffusion?

A
  • The net flux of molecules (J) is proportional to the gradient (dc/dx), the constant of proportionality is the diffusion coefficient D
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4
Q

What is the negative sign is Fick’s first law due to?

A

The negative sign is due to the flux being in the opposite direction of the gradient

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5
Q

What is the graph of a concentration gradient of a membrane between two reservoirs?

A
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6
Q

What is Fick’s second law of diffusion?

A
  • relates the time dependent concentration change to the spatial variation of the concentration at that time point
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7
Q

What does Fick’s Second Law of Diffusion allow us to assume about this diagram?

A
  • consider the slab with cross section A and thickness L (the slap extends from x to x + L)
  • the number of molecules in moles that enter the slab in a time interval (dt) from the left is J(x)Adt
  • Dividing this number by the volume AL gives the concentration change per time interval as:
    dc/dt = (JAdt) / (ALdt) = J / L
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8
Q

*****What is the solution to Fick’s second law equation?

A
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9
Q

How does the solution to the diffusion equation change with time?

A

The solution of the equation for the diffusion from a point source is a Gaussian function that broadens with time

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10
Q

Describe Fick’s second law equation (order)?

A

Fick’s second law is a second-order differential equation in space and first order in time.

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11
Q

What is terminal velocity?

A

terminal velocity:
the limiting velocity due to friction with the air or for an object sinking in water

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12
Q

Why are calculated frictional coefficients lower than measured frictional coefficients?

A
  • the hydrodynamic volume of macromolecules in the water (effective volume as they diffuse) is increased by tightly bound water molecules adhering to their surface (shell of hydration)
  • spheriodal or ellipsoidal proteins have larger frictional coefficients than spheres of the same volume
  • irregularities and clefts on the protein surface retard translational and rotational diffusion
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13
Q

What are the probability and average equations for a discrete variable?

A
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14
Q

What does a high diffusion coefficient mean?

A

diffuses quickly?

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15
Q

What is the average value of squared displacement for one dimensional diffusion?

A

x^2 = 2 D t

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16
Q

What is the average value of squared displacement for 3D diffusion?

A

d^2 = 6 D t

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17
Q

Flux is always___________

A

in the opposite direction of the gradient

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18
Q

What are the influx and outflux equations?

A
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19
Q

What does THE SOLUTION of Fick’s second law describe the behavior of?

A

diffusion of particles from a point source

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20
Q

What is Fick’s first law for?

A

steady state diffusion

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21
Q

What is Fick’s second law for?

A

time dependent concentration at position x

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22
Q

What is probability density?

A

probability of X falling in the interval between Xo to Xo + dx

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23
Q

What is the average equation for a continuous variable?

A
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24
Q

What is the friction coefficient equal to?

A
  • r = radius of the sphere
  • n = viscosity
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25
Q

What is a diagram illustrating stoke’s law?

A
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26
Q

How does the friction coefficient relate to force imbalance? For a pebble moving through water at CONSTANT velocity?

A
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27
Q

What is the equation for Ff?

A

Ff = (6 π n r) vt
Ff = f Vt
Force of friction = friction coefficient x terminal velocity

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28
Q

What is the equation for flux due to diffusion?

A
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29
Q

What is the equation for flux due to Fext?

A
30
Q

What is the general equation for Fext? (always applies)

A
31
Q

What are the units of J?

A

(this is FLUX)
mol / (m^2 s)

32
Q

What are the units of v?

A

m / s

33
Q

What should the units of concentration be in the flux and diffusion equations?

A

mol / m^3

34
Q

What equations can you assume if two fluxes balance each other? No net flux?

A
35
Q

What is an additional equation for flux due to external forces?

A

Jext = c x (Vt)

36
Q

What do high and low concentrations indicate?

A

High or low potential energy

37
Q

What are the units of the diffusion coefficient?

A

(m^2/s)

38
Q

What is an equation for D?

A
39
Q

What is the equation for the volume of a sphere?

A
40
Q

What is D proportional to?

A
41
Q

What proportional relationship is relevant to spheroids?

A
42
Q

What are the forces involved in sedimentation?

A
43
Q

What is bouyant force?

A

the weight of the solvent displaced by the particle

44
Q

What is partial specific volume? What equation is it relevant to?

A
  • relevant to bouyant force
45
Q

What are the equations for buoyant force?

A
46
Q

What is the equation for external force due to gravitation? (No frictional force) (Think about the sedimentation diagram)

A
47
Q

What are the possible units of s?

A

-sedimentation coefficient
- svedbergs (S)
- 1 svedberg = 10 ^ -13 seconds

48
Q

How does acceleration change in a centrifuge?

A

acceleration isnt g it is Arot

49
Q

What are the angular rotation equations?

A
50
Q

What is the first s equation?

A
51
Q

What is X1/2?

A

the distance from the midpoint of the boundary to the center of the rotor

52
Q

What is the second s equation?

A
53
Q

What is the analytical centrifugation graph? Axes? Slope? What equation is it based off of?

A
54
Q

How does diffusion affect centrifugation patterns?

A
  • as the boundary migrates outward as a result of centrifugal force, diffusion causes the sharp step it forms at the beginning (b/c of sharpness of the solution air boundary) to be smeared out by diffusion
  • sharp boundary - small D
  • smeared boundary - large D
    (in a graph of c vs x)
55
Q

What is the equation for the standard sedimentation coefficient and what is is based on?

A
56
Q

What can we assume if the values for s are significantly different from each other?

A

the macromolecule has different conformations in the two solvents

57
Q

Long equation, relates x and c

A
58
Q

Case 1

A
59
Q

Case 2

A
60
Q

What is viscosity?

A

net effect of retardation of momentum/ aka the rate of momentum transfer per unit time

61
Q

What is an equation involving the viscosity coefficient?

A
62
Q

What is electrophoretic mobility?

A

(u) the terminal velocity per unit electric field

63
Q

What is the electrophoretic mobility equation?

A
64
Q

What is the terminal velocity equation for electrophoresis?

A
65
Q

What does net flux = 0 mean?

A
66
Q

What is the equation for molar mass of the solute? (Mb)

A
67
Q

List conversion equation

A

1 cm^3 = 1 mL = (1 x 10^-6) m^3

68
Q

What is sedimentation? What determines its rate?

A
  • in a gravitational field particles tend to settle towards the bottom in a column of solution
  • the rate of this process is determined by the strength of the field, the shape and mass of the particles, and the solvent viscosity
69
Q

What is the unit of viscosity?

A

n = Pa s or Ns/m^2

70
Q

What is Jp?

A

flux of the x component of the momentum

71
Q

What are two ways to experimentally measure viscosity?

A
  • fill cylinder with known liquid, drop a bead in and bead travels with vt
  • use vt and frictional coefficient equations to solve for n
  • Oswald Viscometer

Physical Chemistry (6 decks)

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