Friday, September 24, 2004

sulfur-containing and secondary amino group-containing amino acids, thermodynamics

Cysteine (Cys, C)
Gly-CH2-SH

Methionine (Met, M)
Gly-CH2-CH2-S-CH3

Proline (Pro, P)
[weird circular thing: Gly-NH2-CH2-CH2-CH2-]

------------------------------------------

I confess to be intimidated by thermodynamics, especially since we were required to take 2 semesters worth of it in college. Moreso, since I cannot recall a single thing that I've learned from that class, except that take-home exams are cool and that you make sure that Barney is around during the study group/copying answers sessions. However, thermodynamics in biochemistry seems to be a lot simpler than I once thought. It is basically concerned with determining if a reaction can proceed spontaneously or if it requires some energy. The key term here if free energy or Gibb's free energy, [delta G].

Reactions are:

spontaneous if and only if [delta G] is negative.

at equilibrium if [delta G] = 0.

NOT spontaneous if [delta G] is positive, i.e., it needs some free energy input to drive reactions.



Furthermore, transport is likewise dependent on [delta G]:

passive transport if [delta G] is negative

active transport if [delta G] is positive


notes:
[delta G] is path independent, e.g., the value of [delta G] of a specific rxn is the same if the reaction proceed in one step or in a hundred steps. Hence, the [delta G] gives no information about the reaction rate.

Important: Gibbs free energy, [delta G] should not be mistaken with Standard free-energy change [delta G not]. The latter is the free-energy at standard conditions and is NOT a true indicator of spontaneous rxns. So, having a negative value for [delta G not] does not necessarily mean that the rxn is spontaneous.

[delta G not] is useful in this way:
Say you have a rxn:

A + B <=> C + D

then:

[delta G] = [delta G not] + RT loge ( [C][D] / [A][B] )


But at standard conditions,

K'eq = [C][D] / [A][B]


and,

[delta G not]' = -RT loge K'eq


we know that: loge = 2.303 log10

so,

[delta G not]' = -2.303RT log10 K'eq


solving for K'eq,

K'eq = 10^( -[delta G not]' / 1.36 )



Finally, the overall [delta G not]' of a reaction = sum of [delta G not]' of the steps. This is seen in energy coupling rxns. Say you have a reaction:

A <=> B + C [delta G not]'= +5 (not spontaneous)
B <=> D [delta G not]'= -8 (spontaneous)
----------------------------------------------------
A <=> C + D [delta G not]'= -3 (spontaneous)

So, you can have a reaction happen spontaneously even if not all the steps do. For example, energy (ATP) can be produced in one of the steps that drives the "non-spontaneous" rxn.

Hmm...I just said earlier that the [delta G not] is not an indicator of sponteneity but Stryer and Zubay use them as such. WTF?!?!

------------------------------------

Drinking in the middle of the day is generally not a good idea. Two co-workers at work decided to celebrate their recent birthday by going out for drinks at 1:30 pm last wednesday. Seeing as my boss is out all day for a job interview I decided to go join them. We found ourselves (once again) at the Squealing Pig. The food this time was actually good. I got fries -- not those soggy, curry fries like last time. For alcohol I got a Mike's Hard Lemonade and 2 bottles of Paulaner Haffeweisen.

Going back to work we passed by a biomedical vendor fair where one of my co-workers scored 5 free t-shirts earlier in the morning. I lucked out.

now playing: diet coke with lime fizzing