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Cell Bio > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q

How many proteins in an e.coli cell

A

approx 10^6 proteins

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2
Q

Molecules diffuse

A

All particles exhibit this random motion. Atoms continually bombarding themselves.

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3
Q

Diffusion

A

A random walk; result of random motion of molecules.

In 2D, the probability of moving to the right is exactly the same as to the left. Particles spread out over time. On average, they go nowhere. Diffusion broadens the distribution around the original site of particles.

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4
Q

Diffusion time =?

A

T = x^2 / 6D

x = radius (distance travelled)
D = diffusion coefficient.

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5
Q

Diffusion and entropy

A

Diffusion maximises entropy.

An isolated system will move towards
the macroscopic state that can occur
in the largest number of microscopic
ways (i.e. has the highest entropy, S).

S = kB ln(W)

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6
Q

Diffusion coefficient

A

*Viscosity
*Collisions
*Binding

The property of diffusing particle and medium.

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7
Q

Diffusion coefficient for a small globular protein

A

approx 5nm in diameter, coefficient is approx 10um^2/s.

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8
Q

Guessing diffusion coefficients

A

If dealing with a large protein or organelle, can make assumptions about being a couple of orders of magnitude larger; the diffusion coefficient would be between 1-2 orders of magnitude smaller; calculate the diffusion time with these two orders of magnitude and that’ll give you a range of time.

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9
Q

Typical protein half life in e.coli cell

A

Minutes scale

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10
Q

How long will it take a small protein to diffuse
across an E. coli cell?

A

Milliseconds. Approx 10ms.

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11
Q

Biological structure as a competition between
entropy and enthalpy

A

==> Gibbs free energy. DG = DH - TDS

–> an interplay between energies of binding (enthalpic terms) and the multiplicity of states associated with the unbound state (an entropic term).

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12
Q

Free energy

A

∆G = - kBT ln(C/Co)

where Co is the concentration of the reactant at equilibrium

DG < 0: energetically favorable
DG > 0: energetically unfavorable
DG = 0: equilibrium

Changes are additive.

Delta G also depends on reactant concentrations; in low concentration regions, there are many micro states available to diffusing ligands. The higher the concentration, the lower the entropic costs.

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13
Q

Biological systems and equilibrium

A

Biological systems are not at equilibrium.

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14
Q

FtsZ

A

FtsZ localises to the division plane prior to division. ==> correlation. (Visualising that under the microscope with fluorescently tagged FtsZ).

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15
Q

FtsZ - necessity

A

FtsZ is necessary for bacterial cell division - when FtsZ is depleted, cells are growing but not dividing. So, localisation pattern correlates to site of division AND protein is necessary for division.

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16
Q

FtsZ reaction diffusion mechanism

A

FtsZ forms Z ring at site of division. Pinches mother cell into two daughter cells.

MinD binds to ATP (ATPase) and binds to the membrane at the cell pole.

MinC binds to MinD. MinC is an FtsZ inhibitor, so Z ring cannot form anywhere MinC is present. MinC cannot bind directly to the membrane. Z ring can’t be at the pole.

MinE forms a ring of proteins that oscillates back and forth inside of the cell. When it encounters MinD at the pole, it binds and promotes ATP hydrolysis activity of MinD and causes MinD to be released from the membrane (refractory period where it’s been kicked off and cannot localise to membrane). So MinC isn’t attached either.

Free minD can re-acquire ATP and bind to the membrane at the opposite pole (can’t do so at the other end because of the MinE ring). So the cycle is repeated. MinC is recruited to the membrane at the opposite pole by MinD. The membrane localisation of MinC, which inhibits FtsZ. MinE reforms in the middle of the cell and will move the other way. So MinE keeps the MinCD complex from acting in the midcill region, and its oscillation keeps the zone of MinCD inhibition at the poles.

Z ring forms where you have no inhibition of FtsZ (so where there is no MinC-MinD) which is the middle of the cell.

17
Q

FtsZ and Min system - correlation: Do the relative levels of constituent elements fluctuate (over time and/or space) in a predictable fashion?

A

The model predicts: MinD localizes to the membrane first, followed by MinE.

18
Q

FtsZ and Min system - causation:Is one element necessary for the
localization/activity/etc of another? ==> Min oscillations?

A

MinD is necessary for MinE to localize to
the membrane.
MinE is necessary for MinD to localize to
the membrane
MinE is necessary for MinD oscillations.

In vitro reconstitution experiments: purify components –> mix pure components together in various combinations –> assay to determine if oscillations can be measured.

==> MinD, MinE, ATP, and a lipid bilayer are sufficient for Min oscillations.

this isn’t a perfect reconstitution of Min oscillations in E. coli because the scale (50um instead of 10um) is much larger than in vivo.

19
Q

Min oscillations in bacterial cells - sufficiency experiment

A

In vitro reconstitution of
Min oscillations in bacterial-
shaped bathtubs.

MinC + Min D + MinE + FtsZ-mts are sufficient.

20
Q

Turing patterns

A

Reaction-diffusion mechanisms generate “Turing patterns”

21
Q

How long will it take a small protein
to diffuse across a neuron?

A

Motor neuron axon is approx 1m.
D = 10um^2/sec

Would take about 500 years.

22
Q

Size of mRNA vs protein

A

mRNA is 10x bigger; so an order of magnitude bigger. So its diffusion coefficient is about an order of magnitude smaller (approx 1um^2/s)

23
Q

How long will it take an mRNA
to diffuse across a neuron?

A

Approx 5,000 years.

24
Q

Typical mRNA half life in human cell

A

Hours.

25
Q

How long will it take a small protein
or mRNA to diffuse across a smaller
neuron?

A

D 1-10 μm2/s. x = 100um.
On the minutes scale. (3-30 mins).

26
Q

Summary

A

*The cytoplasm is crowded
*Diffusing molecules explore the cytoplasm via an unbiased random walk, maximizing entropy
*Diffusion times scale with distance squared
*Biological order is a competition between entropy and enthalpy
*Diffusion-to-capture and reaction-diffusion mechanisms pattern cells
*Classes of evidence: correlation and causation
*Major experimental approach: in vitro reconstitution

Cell Bio (15 decks)

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