I have learned an important lesson

Tellurider · Post by **Tellurider** » Tue Mar 14, 2006 7:19 pm

I have a take-home final this week, and I have discovered something very important and, dare I say, profound.

DOING THE CROSSWORD PUZZLE INSTEAD OF TAKING NOTES IN CLASS IS A BAD IDEA.

I'm going to fail and it's all my fault. *sob!*

Keffria · Post by **Keffria** » Tue Mar 14, 2006 7:20 pm

Could be worse, you could be failing because you were playing sudoku, and then you'd be a failure AND a bandwagon-hopper.

*pat-pats you on the head*

Tellurider · Post by **Tellurider** » Tue Mar 14, 2006 7:21 pm

Actually I do the sudoku in my organometallics class, and then by bioinorganic I'm ready for the crossword puzzle. I also read the comics. And doodle.

Ahaugen · Post by **Ahaugen** » Tue Mar 14, 2006 7:23 pm

but it's take home and home has internet and Wikipedia. I'm sorry, but O fail to see the problem

Keffria · Post by **Keffria** » Tue Mar 14, 2006 7:23 pm

O_o

Well, then. Perhaps it's time to switch to something that interests you enough to distract you from the newspaper?

Ian Moulding · Post by **Ian Moulding** » Tue Mar 14, 2006 7:28 pm

Keffria wrote:O_o

Well, then. Perhaps it's time to switch to something that interests you enough to distract you from the newspaper?

Seriously. If your classes and labs, which cost many thousands of dollars, can't distract you from your newspaper, which costs one dollar, it's time to reconsider your investments.

Have you considered a career in homelessness and dumpster diving? I understand that path offers lots of time to read the paper.

Tellurider · Post by **Tellurider** » Tue Mar 14, 2006 7:30 pm

First problem:

"The redox potential of a metalloprotein reflects ist conformational state. The following table presents circular dichroism (CD) ellipticities (theta) for reduced (Fe2+ heme) and oxidized (Fe3+ heme) cytochrome c as a function of chemical denaturant concentration ([GdmHCl]) at 40 degrees C. The CD signal essentially measures the degree of secondary structure found in the protein. At low [GdmHCl] the protein is completely folded, at high GdmHCl it is denatured. Take theta as a probe of this transition.

a) With the data below find the difference in redox potential between the folded and unfolded states. (Hints: make use of the Gibbs equation and the Nernst equation to relate the equilibrium constant for folding at 0 M GdmHCl to the redox potential. Think in terms of a closed thermodynamic cycle of the states available to the protein)
b) What does the change in redox potential on unfolding (and/or differential stability of oxidized vs. reduced) tell you about the environment of the heme in the native state of this protein (Note that the porphyrin ring itself is dibasic)

YOU freakin' try googling that. And good luck finding anything on Wikipedia. I mean, what the fuck, redox potential? All I've got is E = 0.22V for the half reaction, how the hell does that relate to the protein folding, since you need to get two freakin' half reactions to get a whole one! How do I find the equilibrium constants for protein folding? What the hell are stability constants of complexes? AAAARGH!

(PS I posted the whole problem on the off chance anyone actually has an idea of how to do it - not the table though, that's ridiculously too much information)

EDIT: I would drop this class, except I'm a second-semester senior and need it to graduate. So tough beans for me.

Keffria · Post by **Keffria** » Tue Mar 14, 2006 7:33 pm

You lost me after "the"; I dropped chemistry after Grade 11.

Humand · Post by **Humand** » Tue Mar 14, 2006 7:44 pm

At least you can do the crossword puzzle. I don't even come close and then I have to resort to doing the girly wonderword to boost my confidence- So you should be alright.

Rkolter · Post by **Rkolter** » Tue Mar 14, 2006 8:46 pm

Tellurider wrote:"The redox potential of a metalloprotein reflects ist conformational state. The following table presents circular dichroism (CD) ellipticities (theta) for reduced (Fe2+ heme) and oxidized (Fe3+ heme) cytochrome c as a function of chemical denaturant concentration ([GdmHCl]) at 40 degrees C. The CD signal essentially measures the degree of secondary structure found in the protein. At low [GdmHCl] the protein is completely folded, at high GdmHCl it is denatured. Take theta as a probe of this transition.

a) With the data below find the difference in redox potential between the folded and unfolded states. (Hints: make use of the Gibbs equation and the Nernst equation to relate the equilibrium constant for folding at 0 M GdmHCl to the redox potential. Think in terms of a closed thermodynamic cycle of the states available to the protein)
b) What does the change in redox potential on unfolding (and/or differential stability of oxidized vs. reduced) tell you about the environment of the heme in the native state of this protein (Note that the porphyrin ring itself is dibasic)

Most of this is way beyond my knowledge of chemistry too. But I can maybe give you a nudge in the right direction...

Redox Potential of a substance is it's affinity for oxidizing (removing electrons) or reducing (adding electrons) to hydrogen. A high electronegativity means you are an oxidizer and have a positive redox potential; a low electronegativity means you are a reducer and have a negative redux potential. Likewise reduced substances have more electrons (reduced electronegativity) and oxidized substances have fewer electrons (enhanced electronegativity).

Circular Dichroism spectroscopy measures the differences in absorption between left and right handed polarized light in a substance due to its structure being asymmetrical. I suspect the chart you have is a CD ellipse of the protein between being folded and unfolded?

The Gibbs equation deals with the free energy available within a system; I looked around and found a good description of it here: http://library.thinkquest.org/C004970/thermo/gibbs.htm

I didn't know crud about the Nernst equation aside from that it existed, but did find an excellent resource here: http://www.science.uwaterloo.ca/~cchieh ... nsteq.html

You haven't studied for this class or paid attention? Good luck.

Sortelli · Post by **Sortelli** » Tue Mar 14, 2006 8:52 pm

See, this is why I dropped out of school so that I could work for a living.

Where the forums distract me from my job.

JTigerclaw · Post by **JTigerclaw** » Tue Mar 14, 2006 9:06 pm

How do you avoid chemistry and still go to college so you can say "Hey, I went to college, so I'm edjamacated"?

...You go to art college.

Btw, chemistry can suck my nuts hard.

McDuffies · Post by **McDuffies** » Tue Mar 14, 2006 10:01 pm

Hey, Rkolter, got something on database projecting? I'm a bit stuck with this exam.

Tellurider · Post by **Tellurider** » Wed Mar 15, 2006 5:32 am

Hey rkolter... thanks for the links. More resources = good.

See, not paying attention in class and not studying is how smart people act very, very stupid.

Dotty · Post by **Dotty** » Wed Mar 15, 2006 7:58 am

I can agree to that. I do have to ask, how can you spend thousands and thousands and thousands of dollars...and then not pay attention? I see people do it, I went to college too....I just don't understand it, and upon inquiry, they just mutter something about school sucking >_>

Jedster · Post by **Jedster** » Wed Mar 15, 2006 8:20 am

For a chemist I know surprisingly little about organometallics, and even less about bioinorganic... I prefer to stick to things like running Cl gas through a tube furnace at 1000 degrees C over a radioactive sample of bismuth, lead and polonium. Scares the crap out of the teaching staff.

Wish I could help a fellow Chemistry student in need, but I'm as stumped as you.

What you should really do are the chemistry crosswords/sudoku. It's a cunning way of disilusioning yourself by making you THINK you're doing chemistry, when in reality you're not.

Phact0rri · Post by **Phact0rri** » Wed Mar 15, 2006 8:38 am

I bet Lego could rock this stuff out.

Rkolter · Post by **Rkolter** » Wed Mar 15, 2006 8:42 am

phactorri wrote:I bet Lego could rock this stuff out.

I am kind of surprised by his absence from this thread. C'mon Lego - tell us a story about protein folding, electronegativity, and the free energy equation.

Jim North · Post by **Jim North** » Wed Mar 15, 2006 9:59 am

rkolter wrote:
phactorri wrote:I bet Lego could rock this stuff out.
I am kind of surprised by his absence from this thread. C'mon Lego - tell us a story about protein folding, electronegativity, and the free energy equation.

Aw, man, not another one!

Hollowghoul · Post by **Hollowghoul** » Wed Mar 15, 2006 2:54 pm

I should know this stuff, I passed an exam on that; unfortunately, it was some time ago and frankly I did not like it, that is to say I have learned a lot of things only to forget them after the exam...

However, the stabilty constant of a complex is "An equilibrium constant that expresses the propensity of a substance to form from its component parts. The larger the stability constant, the more stable is the species. The stability constant (formation constant) is the reciprocal of the instability constant (dissociation constant).
1997, 69, 1298 - IUPAC Compendium of Chemical Terminology"
So it seems that those things are the equilibrium constants of the reaction
A + B -> AB, being A the concentration of the unfolding element, B that of folded CytC and AB that of unfolded CytC. This constant is the reverse of that characterizing the inverse reaction.
The E= 0,22V is probably related to this constant via Gibbs, http://en.wikipedia.org/wiki/Gibbs_free_energy.
Since this is a metalloprotein its conformation influences the access of electrons to the heme, in ways I think you can deduce from those tables.

On second thought, still, the equation could be A -> B, a transition from a state to another (folded-unfolded) whose equlibrium depends on the concentration of the detergent...
Well, I surrender.
I hope I helped you, and I trust Lego to solve the riddle: from what I see, he is quite familiar with such problems, and I am now intrigued. I would really like to see the solution of this one.