This is still...not quite a promise, nor is it a delivery.

So...these are all the mechanisms of the enzymes in glycolysis. It is questionable whether the amino acid residues indicated are the correct ones. If you know that there is a certain mistake, please let me know. I won't give descriptions, I don't currently have time for that, but I noticed I haven't written anything in a while and I feel like I owe it to the internet to contribute.

This isn't a promise....

This is hard to see...but it is the entire mechanism of glycolysis. This may or may not be a promise that something good (great) may or may not be coming. Stay tuned.

This isn't Spring...

While it doesn't exactly look like I am going to be going to veterinary school this fall, which is totally okay, it does look like I've got some new stuff to talk about.

Just so you have a size comparison, that is Rem next to my new Biochemical Pathways posters that I received in the mail yesterday courtesy of Roche. I was absolutely thrilled because they were free and they are beautiful. Anyone interested in also getting free maps should take themselves here: https://www.roche-applied-science.com/shop/store/contact-us .. I guess if biochem is your thing, then you should get on that. I wrote to them about my newfound appreciation for all things chemistry and received the maps only a few weeks after I ordered them. 

This semester, I'm going to be talking about Biochem 2 and Advanced Cellular and Molecular Biology. I have found several really REALLy good videos on Glycolysis (what we started talking about in Biochem2), a few that I am sort of hesitant to "share with the class" or so to say...so I'll just give the link of the best possible one that I've found so that whoever is lost in the glycolysis land can find their way out....or in.

https://www.youtube.com/watch?v=BFxsJyzPPwY

In the next couple of whenevers I'm going to be watching dozens of glycolysis videos and combining them all into some great work of "art" which I may or may not share "with the class". So here's a toast to this upcoming semester and the VMCAS application that I will once again be crying over quite soon.

Microbiology Stuff

Tomorrow is my microbiology lab final. For the past couple weeks I've been memorizing 12 microorganisms and how they test in 12 different tests. Plus a few others. Here's some fun devices I've come up with for memorizing the activity of these particular organisms in these particular tests.

These are the culprits.

The first four tests we're going to talk about is the IMVC. The indole test tests for the ability of organisms to convert W into indole via reductive deamination. The final products you get are indole, pyruvic acid and ammonia. A positive indole gives you a red/violet color and a negative gives you yellow. 

The methyl red test is used to identify bacteria that produce stable acid end products by mixed acid fermentation of glucose. This includes enterics that metabolize pyruvic acid to other acids. When the pH of the medium is lowered, it turns the medium red. Neutral end products would give you a pH of about six with a yellow color.

The voges proskauer (sp?) is used to detect organisms that produce acetoin using the butanediol pathway. The color changes to red in a positive test and is yellow/brown in negative.

The simmons citrate agar has sodium nitrate as the only carbon source and ammonium phosphate as a nitrogen source. There's blue dye (that's green at pH 6.9, blue at 7.6) involved. The bacteria that survive in the medium and utilize citrate also convert ammonium phosphate to ammonia, making it alkaline. As the pH goes up the color changes from green to blue. A positive citrate is indicated by a blue color.

I memorized these twelves organisms' activity in IMVC by treating it as the group of testing that it is. You can first remember that in IMVC, E. coli and Shigella spp. both test as ++--

You then need to remember that Enterobacter cloacae tests the opposite of E. coli, along with two others. The way you remember the three that test as --++ is by calling them "mar-cl-polo" as in the photo above.

P. aeruginosa is the only one for IMVC that tests as ---+

The two proteus' test the same for IMVC with the exception of the citrate test.

And then I realized that P. mirabilis along with two others has the same pattern. The way that I memorized these three together is kind of silly, so I won't say it.

Then these two ^^ are the same for indole and citrate but switched for methyl red and VP.

Now, I also wanted to individually memorize all the tests individually. So I chose to memorize the +'s for some and -'s for others...when you're doing this you better make damn well sure that you know which ones you memorized the +'s for and which ones you memorized the -'s for. 

I'm particularly proud of this one. VP+ is almost the same thing as MeRed -. 

For VP, I came up with "Very pleased 2 know Ser. Marc E. Clar" as a device, and for the MeRed - I just remember to add aeruginosa to the list.

Couldn't really think of a good way to memorize simmons citrate...

The two decarboxylate tests were also kinda tricky. So for K-Decarboxylase (lysine...man I'm so glad I am taking biochem at the same time, it makes everything make more sense) I remember that since the letter for Lys is K, it has the 2 Klebsiella's and then their friends marc and sal. This test determines if a bacterium can use lysine as a carbon source. When it turns from yellow to purple, it's positive.

Cl a mm just made sense for this one to me. I don't know why I memorized it that easily. This determines if a bacterium can use ornithine as a carbon source. If so, there'll be an increase in pH and a change in color. At a low pH, it'll be yellow and it'll be purple in basic conditions. Positive is purple.

This one I only came up with tonight. It's a shitty one but it's all I got. For F (phenylalanine)-Deaminase...

"For dad: 2 Props: Salmon and Steak"

F-Deaminase: 2 Proteus', Salmonella, Stuartii

This determines if an organism can make F-Deaminase, needed to use phenylalanine as a carbon source. If it's positive, a product combines with iron to produce a green color.

The Urease I had to just kind of memorize, no fun here. The urease test determines if a bacteria can make the exoenzyme urease to hyrdolyze urea to ammonia and carbon dioxide. It'll come up as red in an acidic environment.

H2S tests for the reduction to gas. Either cysteine desulfurase will reduce cysteine to pyruvate or thiosulfate reductase catalyzes the reduction of sulfur in the electron transfer chain. In SIM medium, H2S gas combines with iron to form a black precipitate.

Since almost all the organisms are motile, I decided to memorize the three that aren't.

And I chose to memorize lac+ and suc- fermentors 

There will be more later on activity in agars (HE, EMB, MacConkey, etc) and some other stuff, but for now, the doge needs walking.

The snowy doge.

Protein folding and other things that are nice.

There's reasons for why proteins go from nice long strands of stuff to more compact folded things. The first part of it is conformational entropy... The -deltaS in this case makes a positive contribution because you're going from a very random thing to a much less random thing, which means entropy is technically working against folding.

But despite that, the thing still folds. That means deltaG must still be negative. So that means this happens because deltaH must be very negative, which comes from the nice interactions that happen between the amino acid side chains in the folded thing. 

Another thing going on in protein folding is charge-charge interactions. This comes from charged side chains that might form bridges. However, if pH changes, the side chains might lose their charge, breaking the ionic bonding between them, which would then contribute to denaturing the folded thing.

The next factor to look at is internal hydrogen bonding between side chain. Side chains with OH, NH2, etc are the ones that can participate in non-covalent *technically* bonding interactions.

If we go back far enough in our biochemistry memory map, we can maybe remember that neutral-neutral interactions (induced dipoles) are the strongest if the interaction is physically close enough, which is what I guess happens here. The non polar groups in the protein, when they pack in densely enough, will contribute to a more stable protein. The folding up of the protein also reduces any favorable interactions that the chains may have with solvent...the unfolded chain may have residues that CAN interact nicely with water.

So, looking at the enthalpy changes going from unfolded to folded, we see that the type of non covalent bonding changes..you go from interactions between the open chain and the solvent to interactions within the chain.

*Sort of * along those lines, there's disulfide bonds. They're usually the only covalent bonds that are going to form when a protein folds up, and the sentence is BLUE is very important because although disulfide bonds contribute to enthalpy, they have more entropic effects.

Final consideration for us is the hydrophobic effect. Myoglobin is actually stabilized by it.

When you have hydrophobic residues in contact with the solvent in open chain form, you get those CLATHRATES that we talked about in chapter...3? 2? oh, who remembers?

Anyway, when you form clathrates, water gets ordered around stuff that it doesn't really want to be around, which is bad for entropy. 

So when you have an unfolded protein with lots of crappy clathrates going to a folded thing where all the hydrophobic shit is inside...I'd say that frees up some of those unhappy water molecules. That's pretty good times.

Disulfide bonds are like the one girlfriend you had in high school..you're going to keep talking about her. In Bovine pancreatic trypsin inhibitor, we have three of them. BPTI is pretty hard to denature but putting it in really acidic stuff at temperatures above 100degreesC is going to get the job done. Eventually.

HOWEVER. If you cleave just ONE of those little suckers, you can start denaturing that shit at like...

...a much lower temperature !

And if you reduce all THREE of the disulfide bond, that shit is going to fall apart at room temperature.

In short, if you have disulfide bonds, you've got less conformational entropy in your unfolded state than if you don't have disulfide bonds....there's just less shapes for you to be in when you're all connected like that. Disulfide bonds are typically found in proteins that get taken out of the cell (RNase, BPTI, Insulin...)... In the cell you've got a reducing environment ... which...HELLO? Would reduce that shit. But outside the cell, you've got an oxidizing environment which is actually going to help stabilize those -S-S-'s

Chaperones keep proteins from getting into trouble..

Like this mess of an example..

A summary of what happens.

A short summary slide to help you remember which amino acids are going to be predominantly present in which things. I'm especially proud of the vampires.