Shaking hands with proteins

Let's talk a little more about proteins. The amino acids that make up proteins are going to have all sorts of different side chains unless it's a Poly-Amino Acid protein (synthetic). The side chains are what we talked about last time....they can be acidic, basic, hydrophobic, charged, etc. In the different regions of the protein that's all folded up and shit, the side chains are going to determine if certain areas of the protein are soluble/exposed to solvent, they're going to determine the folded structure of the protein (we'll see later that certain types of tertiary structures are going to be more likely to have certain amino acids in them), and the amino acids are going to determine the surface charges of the protein.

So...who the side chains be? Aliphatic is one of my least favorite non-words, because all it means is that the structure is open chain/non-aromatic form. Amino acids with aliphatic side chains are going to try to stay away from the solvent and therefore the outside surface of proteins. They're the non-polar things that we talked about before. They're going to try to be on the interior of the proteins so that like doesn't have to talk to non-like.

Then we have polar side chains. Like this. The stuff that has OH/S-groups in it. Paying attention to pKas, cysteine loses its hydrogen at pKa 8.3 and we usually call physiological pH around 6.5-8. Technically since it starts losing the hydrogen two units earlier than 8.3....maybe this means some of these suckers are charged at physiological pH and that's why they're happy talking to the solvent. 

I think I talked about talking about how cysteine residues can form disulfide bonds (two getting oxidized to a cystine), which give extra stability to proteins. As I learned in chapter 6...they're actually not that common... Which I'm still kind of confused about. When I first started learning about these suckers, I thought that they were kind of like essential for most proteins. Well, they are REALLY essential because breaking one disulfide bond will have crazy dramatic effects on denaturation of proteins...but apparently not all proteins have them.

As the bible (read: Biochem textbook) tells us, we can reduce that shit with betamercaptoethanol. Get your cysteine's back nice and fresh.

Aromatic amino acids like tyrosine, phenylalanine, and tryptophan absorb around 280 nm (remember how the stuff that makes up DNA absorbs around 260..) because of the aromatic regions and shit. This is helpful cause based on where it's absorbing, you can tell how much of what in reference to what is in your protein.

That's tyrosine (Tyr, Y). Our good friend whose side chain pKa we should probably know pretty well when we get asked a question about the charges on polypeptides at different pH's.

The basic amino acids are histidine, lysine, arginine. Histidine is the least basic, with the imidazole side chain having a pKa of 6. K & R are pretty basic, K's side chain pka is around 10 while R's is like 12.3. The guanidino group gives it that extra umph.

Since H's side chain has a pka pretty close to physiological pH, it has a role in enzyme activity, and it can participate as a proton donor/acceptor in proton transfers. 

Then we have the acidic amino acids (aspartic acid, glutamic acid) and their amides (asparagine and glutamine). D & E will be charged at physiological pH since the side chains get deprotonated around 3.9-4.

N & Q are also polar but they're uncharged at physiological pH.

And then there's this fucker. This big huge thing that puts turns into stuff. You would think that all that hydrophobic stuff doesn't want to be on the surface but....where inside are you going to fit that elephant?

I don't like this anymore. Initially this is what I came up with for remembering which amino acids are essential/non essential in mammals. But we can do better than this. 

For essentials: we can do.... WTF? Very High Resolution MILK 

(That's really no better but maybe a bit...)

For non-essentials we can do.... DYSPNEA CGQ ... When you're drawing Q, you start from something that looks like a C, then it gets to a G, then it's Q. But I mostly like DYSPNEA. 

That was a fantastic waste of time.

Here's some amino acids that you typically won't find in proteins. 

I mean...if you're going to choose to have slightly modified amino acids, you're going to modify the ones here. Alanine. Good structure. Not very sterically hindered. Can fit in most places. Glutamic Acid...nice and polar. Guess it's good times for cell walls since they're exposed to both the insides (liquidy) and outsides (also liquidy) of the cell. Cysteine...of course it's a precursor to methionine! All it needs is a methyl group. And then that last one...makes sense as well!

Two more. Look at the badass thyroid hormone. I should know all about that shit. Mad mad weirdness with my thyroid when I was a kid and now I'm always trying to protect it when restraining for radiographs.

This is kind of a small summary of pkas.

Here's two of the "other" amino acids that we've discussed before (I think?)

Pyrrolysine is a derivative of lysine. It's usually found in archeal enzymes.

Selenocysteine is the cysteine derivative where the sulfur is replaced with selenium. In prokaryotes it's involved in catabolic activity while in eukaryotes, the 25 selenoproteins are involved in anabolic activity and anti-oxidant catalysis. 

These guys are pretty important, especially the hydroxylated ones. We'll talk about this soon, too.

This is kind of a baby mechanism for forming a dipeptide. Dehydration reaction.

Also some modifications that may occur. The blocked N-termini are more common than the blocked C-terminus

To end off this short post, I'm going to briefly talk about how polypeptides can act as ampholytes/buffers and in the next post we'll try to finish off chapter 5. I really REALLY hope I have time to talk about translation today..

So that's a polypeptide. It has a few amino acid residues in it, all of which have different pkas. The differences in pkas from what they typically are in the lone amino acids are due to the local environments around the residues.

So for example, an amino acid like D has a pka of approximately 3.9. At physiological pH, it's going to hold a negative charge in a proteins. When you have that negatively charged residue in proximity to other negatively charged residues (another D or E) in comparison to having it near positively charged residues (like K or R), the pka is going to be higher when it's near a negatively charged residue than if it's near a positively charged residue. I think this deals with things not wanting to create too many of the same charges in proximity to another. 

So I guess that it would make sense that proteins are the least soluble when they're at their isolectric points. The overall charge on the peptide (or piece of peptide) is neutral and things won't repel each other, which will not bode will for your wanting to separate shit in ion exchange chromatography, which we'll also talk about later.

Last picture. Like DNA, proteins are kinetically stable and thermodynamically unstable. This just means that eventually they're going to get hydrolyzed, the universe wants them to get hydrolyzed, but it's going to happen slowly, or with the introduction of harsh conditions like high temperature, strong acids, or protease enzymes which we'll talk about next time.