blargh......*with added footnotes?

[coffee_moon]

So it's been like a month since I last updated, which in retrospect isn't too bad since I've gone MONTHS between posts before. Hard to believe that we're already in the last week of January....which of course can only mean one thing - exams in February. Oh joy. I should count myself lucky that I came back from Princeton Review early today (for the

Comments

[darkenedminds]

I'm currently doing my Biochem prelab, remembered running into you last week, and remembered that I promised to forward to you someone named Karl's essay: (censored last name)

Message no. 8
Author: Karl **
Date: Thursday, January 22, 2009 8:42am

Hi Bernice,

Professor Haro gave us the website where you can download Pymol at the beginning of
class. It is: http://delsci.com/ep
User name is 09dec31, and the password is mol2view

As for lecture itself. most of it is found in his lecture 1 and beginning of lecture 2 notes
(we stopped at the slide about the effect of creation of charge on acidity for H3PO4). His
slides about basic chemistry (bonding and orbitals) are not on the website yet, but I
believe he will be posting them soon. Here is a summary of the lecture if you need it:

Professor Haro began by discussing Stanley Miller's famous prebiotic soup experiment,
and how it was able to synthesize a number of amino acids out of basic reagents such as
water, methane, and nitrogen. There wasn't much he wanted us to know about that other
than that basic molecules, subjected to electrical shocks, can create the basic building
blocks of life.

He then moved on to basic chemistry. First was an overview of subatomic particles
(proton, neutron, electron), and the types of atomic orbitals that electrons form (1s, 2s,
2p, etc.). Then, he went on to how the atomic orbitals can interact to form molecular
orbitals (bonding). The most basic is the sigma bond, where two atomic orbitals overlap.
Next to be formed are pi bonds, where p orbitals align themselves in the same direction
for double and triple bonds.

Then he moved on to hydrogen bonding, and its high heat of formation that makes water
molecules have a high affinity for one another. Because of the unequal sharing of
electrons in water, ions are attracted to the partial charges in water molecules, and are
hence highly soluble in water. Indeed, a number of functional groups make molecules
more water soluble (such as the hydroxyl groups in sugar). On the other hand,
hydrocarbons tend to be very hydrophobic (as seen in lipids).

There is a quote in the Lecture 2 powerpoint that Professor Haro felt was really important.
"Biology is dominated by the chemistry of the noncovalent bond." While I highly doubt the
quote itself needs to be memorized, do know that he finds this quote to be a nice
summary.

Next, we briefly discussed the various types of intermolecular interactions. While you do
not have to memorize the specific numbers, do know what they are and their strengths
relative to one another. Intermolecular forces help stabilize a number of macromolecules,
and the greater the number of intermolecular forces interacting, the tougher it is to break
molecules apart.

Finally, we discussed water's ability to self-ionize, forming H3O+ and OH-, leading to the
topic of pH. Know that the identity of the central atom that is losing a proton in part
determines its acidity (for example, pKa of methane (CH4) >> water (H2O)), and that the
more negative the charge is on a molecule, the harder it will be for it to lose another
proton.

Karl

Reply Reply privately Quote Download
Message no. 9
Author: Karl **
Date: Thursday, January 22, 2009 8:47am

Oh, one more thing. While you do not have to know the exact pKa values of molecules, you
should know the approximate range of the acidity of various functional groups (I believe
he'll go into greater detail about this later). For example, carboxylic acids are on the order
of pKa ~ 4-5, amines are ~9-10, alcohols are ~18-19, sp3 carbon ~<50, so forth.

Karl

[coffee_moon]

Um, wow. Can you really say anything to something like that? He seems to be a really helpful classmate though. I never even check webct unless it's to get something the teacher posted.

[darkenedminds]

Helpful my ass >:( I asked for help and he didn't reply! I wonder if he recognized my name or something.

[coffee_moon]

Are you serious? He actually might have since he seemed to think me someone familiar when we exchanged our 1-sec eye-contact. If you really wanted to you could try mailing him directly through webct. He would actually have to reply then. Unless he holds some monstrous grudge on you from like, what almost 8 years ago? Ha, that would be strange.

[darkenedminds]

I don't really care enough to try; maybe, though. I just can't remember if I was mean to him or not. I mostly just want to borrow his photographic memory to repeat all of the crap the professor says in easy words (my prof is the vaguest mofo ever).

--

Why are we awake, checking LJ?

[coffee_moon]

Well I'm sure there are other people in your class besides Karl and Jafar that you could ask. Also, text book. And ppt notes if he ever puts any up.

I'm actually studying for a test but left lj open. Kinda feels like r e a l l y s l o w instant messaging.

[darkenedminds]

*whine, whine* but his essay was sooo concise! And my damned book hasn't come in! /ok, so I use the library's like a diligent little nerd, but let me whine. give me cheese to go with it, ruthless, i'm hungry.

I'm giving up my studying, because I just realized that this online embryology course I'm in has the test available for several more days than I thought. Procrastination! I'd stay to distract you more with our r e a l l y s l o w instant messaging, but I'm off to bed and work in 8 hours. Good luck on your test!