bio/essential-cell-bio/02.markdown @ 8159c14ffbb8

Chapter 2
=========

Questions
---------

### Q 2-1

Number of molecules in the ocean:

    1.5e24 cm³ = 1.5e24 g = 1.5e24 g * 6e23 molecules = 9e37
                            ^^^^^^^^^^^^^^^^^^^^^^^
    Not sure if this is right -- do I need the divide by the molecular weight of
    water here?

Picking up a mole of water means you have 6e23 shots at getting one of the
original molecules, each with a (roughly) 6e23/9e37 chance (1/150000000000000)
of success, or 149999999999999/150000000000000 chance of failure:

    1 - ((1 - 6e23/9e37) ^ 6e23)

    set logscale x
    plot [1:600000000000000000000000][] (1 - (0.9999999999999933 ** x))

The chance is almost 100%.

### Q 2-2

A. Number: 6.  Weight: 12.
B. 6.
C. 4.  It can form covalent bonds with up to 4 other atoms.
D. It has 2 additional neutrons.  It will eventually radioactively decay, but
   otherwise acts like Carbon.

### Q 2-3

This seems like a reasonable statement to make.

### Q 2-4

True.  In water molecules the O atom has a partial negative charge δ⁻, so it
will be attracted to the positively charged Na⁺ cations and will repelled from the
negatively charged Cl⁻ anions.

### Q 2-5

Yes, at a concentration of 10⁻⁷ M/L.  They're formed by protons moving between
water molecules.

### Q 2-6

Using two separate types of amino acids would require separate versions of all
the various translation machinery for no benefit, and it's simpler to just use
one kind of machinery for everything.

### Q 2-7

The polarity of a chemical bond is referring to electrical polarity (+/-).  When
the word is used for a polypeptide it's just referring to the general
asymmetry/directionality of the different ends, not electrical charge.

### Q 2-8

Having a single type of reaction mechanism means enzymes can be reused for
multiple purposes, instead of having to build many different types of metabolism
pathways.  Condensation/hydrolysis is nice because water is already so abundant
in the cell.

### Q 2-9

Covalent bonds are much harder to break apart when finished than noncovalent
bonds.

Because covalent bonds are very strong, a single covalent bond might be enough
to hold macromolecules together.  But this is not necessarily a good thing
— requiring multiple noncovalent bonds allows more specificity and lets
a molecule be more selective about the other molecules it binds to.

### Q 2-10

A. Usually, although H sometimes has no neutron.
B. If it does, it's an ion (an anion).
C. True.
D. No, different isotopes have different number of neutrons.
E. True (but is it the *only* factor?  not sure).
F. True.
G. True.

### Q 2-11

C     12
H      2
O     16
Total 30

A. 12/30 * 5 * 6e23 = 1.2e24
B. I'm not really sure what they're asking here.
C. 2e-10 * n = 0.07e-3
   n = 350,000

### Q 2-12

A. 4, 8, 8
B.
              Gain Lose
    Helium    0    0
    Oxygen    2    6
    Carbon    4    4
    Sodium    7    1
    Chlorine  1    7

C. Helium is not very reactive.  Sodium and Chlorine are well suited to bonding
   with each other.

### Q 2-13

Oxygen is much more electronegative than Sulfur (3.44 > 2.58).  This means H₂O
is a much more polar molecule than H₂S, so water molecules have much more
hydrogen bonding between themselves which helps keep water liquid at higher
temperatures than H₂S.

### Q 2-14

Glycine + Alanine
H₅NC₂O₂ + H₇NC₃O₂ = H₂O + H₁₀N₂C₅O₄