Notes from Ananta's review...

Notes from Ananta's Sunday review....

Remember to review sections 1 and 2
Know the Henderson Haselback eq.

You only need to know the L amino acids, but you better know the basic structure
(amine, cooh, H, R)
Each R group effects pka, and it matters where they are oriented in the chain.
pka is at half way between the two (equal parts)
Know which R groups are basic/acidic/hydrophobic/philic...
The zwitterion is the ion at pi (net neutral)

Structure:
1' amino acid sequence
2' alpha helixes, beta sheets, beta turns, etc
3' how the 2' comes together: alpha-beta-alpha
4' how monomers come together and attract each other: dimers, trimers, etc

2' is stabilized by H bonds (fig 4-4, 4-7)
alpha helix: polarity (dipole moment)
H bonding occurs between N-H----O=C

Beta sheets: parallel vs. antiparallel scheme... par is less stable/antipar is more stable because it is head on.
beta turn: fig 4-20 only possible for anit-par

Hemoglobin....
very like myoglobin
stucture is slightly different
binds O2, CO2, CO, BPG.
See fig 5-10
ph is analogous to how much CO2 in the signodal curve. (more CO2 at 7.2)
H+ protonates Histadine (fig 5-9) (see fig 5-16 too)
BPG at higher alts (fig 5-17) pg 172
At higher alts you bind less O2, but BPG helps you release more of it at a time so you end up with more in your bloodstream.
Hemoglobin forms 4' structures.
Read up on sickle cell anema.

Sugars:
It is an L sugar if the C4 is up, and R if it is down:
If it was LEFT UP to me, I would be DOWN RIGHT angry to have to learn this.

To know if a linkage is an alpha or a beta linkage:
Look at the one with the anameric carbon, and if C 1 and 4 are cis then it is alpha, and if it is trans, it is beta. (look at homework prob 2)

Nucleotides:
8.1, 8.2, and some of 8.3... KNOW IT WELL (fig 8.34)
a nucleotide has: a base, a sugar, and a phosphate group...
a nucleoside only has the first 2 'sides': a base and a sugar

Be sure to understand the logic of the experiments he talked about.

Puridines: A, G: 2 rings (2 H bonds)
Pyrimidines: C, T, U: 1 ring (3 H bonds) (more stable)
(the above may not be correct... so look it up, and make sure you know it)

DNA vs RNA
Make sure yo ukonw the chemical instability that results in RNA self-hydrolysis. (fig 8-8 and 8-4 and section 8.3)

Look at 8-33 thru 8-36 (mutations)