bio/essential-cell-bio/01.markdown @ ba56d8b4c9b5

Chapter 1
=========

Questions
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### Q 1-1

* Person: 7
* Potato: 7
* Vacuum: 3

### Q 1-2

No, because a mistake in producing a shoe will usually result in it being thrown
out.  In a rare case of a beneficial mistake, the one who notices the mistake
(the eventual wearer) is probably not in a position to give feedback that would
let the improvement be incorporated back into the shoes, unless they happen to
work at the factory (unlikely).

### Q 1-3

It doesn't prove you've generated life, it could easily be contamination from
airborne microorganisms.  You would need to filter or at least sterilize the air
first to remove microorganisms.

Pasteur did it by using long, bent-neck flasks, assuming that the organisms
wouldn't be able to fight gravity and make it up the neck of the tube.  I guess
it worked, but that seems iffy to me — I could easily imagine an errant air
current managing to push a dust speck into the neck.

### Q 1-4

    10e-12 g * (N₀ * 2^(t/20 min)) = 6e24 kg
    10e-12 g * ( 1 * 2^(t/20 min)) = 6e27 g
    2^(t/20min) = 6e27 g / 10e-12 g
    2^(t/20min) = 6e38
    log₂(2^(t/20min)) = log₂(6e38)
    t/20min = 128.818
    t ≈ 43 hours

    set logscale y
    set xlabel "Time (hours)"
    set ylabel "Biomass (kg)"
    plot [0:44][] ((2**(x/0.333333)) * 10.0**-15)

It's not a paradox because in reality the bacteria are resource-constrained long
before they approach the mass of Earth.

### Q 1-5

Certain substances are harmful if they get into the cell, while others are
helpful (and some can be either, depending on what else it happening in the
cell).  Having a membrane that can selectively import specific substances allows
a cell to keep out the bad stuff but allow the good stuff.

### Q 1-6

Light microscopy is cheaper, usually less labor intensive, and allows studying
of living cells.  Electron microscopy allows much higher
magnification/resolution.

* Living skin cell: must be done with light, electron cannot image living cells.
* Yeast mitochondrion: probably requires the magnification of electron.
* Bacterium: light is probably sufficient.
* Microtubule: required electron magnification.

### Q 1-7

Many genes are similar between humans and yeast.  Studying a particular gene in
yeast can be many times more efficient than trying to study it in humans, so her
money goes much further.

### Q 1-8

A. Cytosol: subset of the cytoplasm that is not contained inside an organelle.
   A gel where many of the chemical reactions inside the cell happen.
B. Cytoplasm: everything inside the cell membrane and outside the nucleus.
   Does… lots of different things.
C. Mitochondria: small organelles where cellular respiration happens ("the
   powerhouse of the cell").  Originated from a bacteria being engulfed by an
   ancestral cell (Margulis' endosymbiont hypothesis).  Have their own genomes,
   though many genes have been lost/relocated to the nuclear genome.  The
   compatibility between a mitochondrial genome and nuclear genome is important:
   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981548/
D. Nucleus: membrane-surrounded organelle that contains the cell's DNA.  Site of
   DNA→ RNA transcription and DNA replication.  Only found in eukaryotes (by
   definition).
E. Chloroplasts: plant organelles where photosynthesis happens.  Thought to be
   another endosymbiont.  Also have their own genomes.  Is chloroplast/nuclear
   genome compatibility also important?
F. Lysosomes: small organelles that digest food particles and break down other
   unwanted particles.
G. Chromosomes: packaged DNA (includes e.g. histones, etc).  Condense during
   cell division so they can line up along the metaphase plate and microtubules
   can attach to the kinetochores and pull apart/sort them.
H. Golgi Apparatus: organelle that modifies/packages things to be moved around
   inside of or out of the cell.
I. Peroxisomes: small vesicles used for reactions where hydrogen peroxide is
   used to inactivate something toxic.
J. Plasma Membrane: phospholipid bilayer separating the cell from the world.
   Selectively permeable to things, studded with various things (e.g. channel
   proteins, receptors, etc).
K. Endoplasmic Reticulum: extension of the nuclear membrane.  Partly studded
   with ribosomes (rough ER), partly not (smooth ER).  Site where parts of the
   cell membrane and things destined for outside the cell are made.
L. Cytoskeleton: three kinds of proteins (actin, intermediate filaments,
   microtubules) in the cytosol that act as the internal structure/scaffolding
   of the cell.
M. Ribosome: small machine made of RNA and protein, used to translate RNA into
   protein.

### Q 1-9

A. No, it's passed by DNA.
B. Yes, bacteria are prokaryotes and don't have a nucleus.
C. No, plants are eukaryotes.
D. Pretty much always yes.
E. No, the cytosol is everything that's NOT an organelle.  The cytoplasm
   includes the organelles.
F. Yes.
G. No, protozoans are unicellular.
H. Yes (if you count digested food particles as "unwanted").

### Q 1-10

A. Nucleus
B. Vacuole
C. Cell wall
D. Chloroplast

### Q 1-11

Actin
Intermediate filaments
Microtubules

Muscle cells have a lot of actin.

Skin would probably have more microtubules (helpful for communication).

### Q 1-12

    1e6 * 2^(t/20) = 1 * 2^(t/15)
    1e6 = (2^(t/15) / 2^(t/20))
    1e6 = 2^(t/15 - t/20)
    log₂(1e6) = log₂(2^(t/15 - t/20))
    20 ≈ t/15 - t/20
    20 ≈ t * (1/15 - 1/20)
    20 ≈ t * (1/60)
    1200 minutes ≈ t
    20 hours ≈ t

    set logscale y
    set xlabel "Time (hours)"
    set ylabel "Population"
    plot [0:24][] (1.0e6 * 2**(x/0.333333)), (1 * 2**(x/0.25))

### Q 1-13

Eventually one bacterium may acquire a mutation that resists the antibiotic.
Selection pressure will rapidly cause its descendants to take over the
population, at which point it continues growing normally.

### Q 1-14

    10^13 = 1 * 2^(t/24)
    2^43 = 2^(t/24)
    43 = t/24
    43 * (24 hours) = t
    43 days = t