Fundamentals I: Mon-Fri 10:00 12:00 Scribe: Tiffany Luke
Fundamentals I: Mon-Fri 10:00 – 12:00 Scribe: Tiffany Luke
8-10-2010 Proof Read by: Heather Thigpen
DeLucas Amino Acids and Their Proteins Page 8 of 8
1. Amino Acids: The Building Blocks for Proteins [S1]
a. Look at protein structure using x-ray crystallography so at some point in this week I’ll tell you a little bit about that technique along with other ways you can look at structure.
b. You will learn a little bit about techniques in my next lecture coming up.
2. Amino Acids Used in Living Organisms [S2]
a. Today we will focus on chapter 4, which is basically something all of you have had over and over, but the fundamental aspect of what makes up proteins, amino acids.
b. There are 20 naturally occurring amino acids. That means we don’t need to eat anything to get these.
c. I’ll talk a little bit about the unique properties of these. These amino acids can lead to other amino acids with some derivation of these.
d. You will see a couple of examples of those. One of the most important features of amino acids is the fact that they have a tetrahedral Carbon atom.
3. Amino Acids: Building Blocks of Proteins [S3]
a. Today we know from the sequencing of the human genome that there are about 35,000 genes in the human genome. But, in terms of protein, we don’t know.
b. There are anywhere from probably 600,000 to 1 million different proteins in our cells and bodies.
i. It’s because these genes can rearrange and one portion of one gene and another can come together to make a new protein that you have many more combinations of proteins.
c. When you think about it, if there are that many proteins, how is it that they can all be so different? Well, it’s all based on the fact that Carbon has 4 different positions that substituents can come off of, you can create, as these amino acids build the protein, in 3D structures that are tremendously varied.
d. That’s probably the most important aspect of that tetrahedral nature as you’ll see.
4. Amino Acids Can Join Via Peptide Bonds [S4]
a. Another aspect is that these amino acids can polymerize. One can bind to another to form what’s called a peptide bond. I’ll show you that interaction in a few slides here. That’s how we build the protein.
5. What is Fundamental Structural Pattern in Proteins? [S5]
a. That’s how we build the protein. It’s not stable for that reaction to occur. It’s unstable and so for it to occur, we have to give it energy and in fact these are made on a ribosome in eukaryotes and transfer RNA has to carry each amino acid and it’s bound to one at a time and it sits on that ribosome in a specific way.
6. The Peptide Bond [S6]
a. Because of all the stereochemistry, the ribosome of course is a complex of many proteins, the way these are built is amino acids are made in the N to C terminal direction. So from the N terminus of the amino acid, that’s the beginning and then we build on it adding Carbons to the C double bond O end.
b. I talked about tetrahedral nature, the Carbon that has the 4 branch points coming off of it is called the C alpha Carbon.
7. The Peptide Bond Figure [S7]
a. You can see that for these amino acids, you always have an amino group, a carboxyl group and then an R side chain group. That is what gives you the distinction between one amino acid and another. This part is the same for all these amino acids except for two exceptions – Gly and Val.
b. So, you can make this as a ball and stick arrangement, but you can see it is a tetrahedron. So now, things that hook on here and here can branch in different directions and there’s some rotational freedom about these as you go to build that protein.
c. Two of these combine to form what’s called the peptide bond and when they do a water molecule is dissociated. The C double bond O group here sits here and it binds with the Nitrogen group and that bond has partial double bond character. That’s another important aspect of this is that you think the double bond is all right here - the Carbon to the double bond O and if it were, that would have a certain distance because most C double bond O’s the length of that bond is a very specific number, but when you add this what happens is you have a sharing of electrons across here and it creates a planar environment. It cannot rotate and as a result, this double bond is a little bit longer than you would normally think and this one which normally would be a single bond is a little bit shorter.
8. What is the Fundamental Structural Pattern in Proteins (a)? [S8]
a. That once again just shows you the chemistry and the area where this planar area occurs is right here and so right here and right here you have rotational freedom. So, imagine this part as being a plane and then this part can twist around in and out of the plane of the board and the same with this one so that the R-group could be coming out toward you or going back into the board, same with that one and these R-groups are again what in part the uniqueness of each amino acid and some of them are quite large. So, in addition to having rotational freedom, what constrains what those rotations are is the actual size of that R-group, the charge of that R-group because as you build a protein, this will interact even with these proteins here in certain areas and so it has constraints and there was an Indian scientist way back named Rahmashandran that actually looked at just Alanine along the peptide chain all the possible ways these areas could rotate.
b. An alpha helix, one geometry can have once you build this peptide along it’s backbone. Or for other structures like a Beta turn or Beta sheet and as he did this, he found unique areas where most of these could fit and if it twisted too much you would have steric interference and so it’s called a Rahmashandran plot. Look at that and see the angles that most of these can assume. Just based on Ala, but now it’s been done of course for all different combinations of amino acids. If you had two next to each other about how much they could twist.
c. All that today is used by modelers that used to use super computers. Now you can do this with a desktop computer and you can actually predict to some extent protein structure. So, you can take any primary sequence today and there’s programs free right on the Web you can input that sequence and predict the 3D confirmation – how all these things will twist to give you protein, but it’s not at all accurate. It’s very inaccurate. The goal today of the NIH is to have one example of every way a protein can possibly fold, just one based on crystallography and to some extent NMR. If you had that and you give that to a modeler, then if they have a homologous structure something that’s just 30% homologous in terms of the sequence of the amino acids, now today we can predict the structure of some unknown protein, but it’s 30% or more homologous with a 3Angstrom accuracy. That was when we realized that we’d be able to do that, it became a major goal in NIH to try to determine these structures as quickly as possible and there have been literally about ½ a billion dollars now spent in the last decade to come up with a very rapid ways to determine structures so where are we? We know about ½ of the possible folds today and the ones that we don’t know are rare and are proteins that are more difficult to isolate and do the structure. It has dramatically helped modeling.
9. What is the Fundamental Structural Pattern in Proteins (b)? [S9]
a. Question from audience . . . .
b. One thing I didn’t say is because of this partial double bond character, the Nitrogen is not quite as positive as you would expect and the O negative end of this molecule is a little bit less negative than you’d expect because they are sharing these electrons. Again, here’s all the numbers and I don’t expect you to really know this, I do expect you to know that this can exist in two different confirmations. This is the trans or open and stretched out confirmation. You can twist this around and there would be a cup-like or cis confirmation and it can exist two different ways. Which one exists in a protein just depends on the stereochemistry of everything around it. So, generally you don’t see an all trans situation like this because there would be too much interference.
10. What is the Fundamental Structural Pattern in Proteins (c)? [S10]
a. Again, this kind of just talks about what’s happening in terms of the double bond bondedness of these and the sharing and where that plane is along here to form the peptide plane where you don’t have rotational freedom. Then, between here and the next group close to it, you would and the same with over here.
11. What is the Fundamental Structural Pattern in Proteins (coplanar relationship)? [S11]
a. I don’t think I need to dwell on that, but here’s a nice image of the bond and then where you end up having rotational freedom on these ends. As we start talking about primary structure, you’ll see how one of these hooks to another and I’ll show you how these R groups can get in the way of each other. Also how it dictates what kind of configuration is the most stable. Another portion of what dictates that is as you build the protein structure, there are interactions between these amino acids in terms of Hydrogen-bonding. There are even ionic interactions and those play a critical role. That is the reason why the alpha helical arrangement is one of the most stable ones. You’ll see that in a couple of days when we talk about primary structure.
12. 20 Amino Acids in Proteins [S12]
a. There are 20 naturally occurring amino acids and they can be grouped many different ways, but a common way is to talk about the ones that are non-polar vs polar, but uncharged and then again polar, but charged.
13. Figures – Nonpolar (hydrophobic) [S13]
a. Those are the groups that I usually refer to when we talk about amino acids and so if you look at a non-polar case here like Leucine, you can see there are no charges here and it doesn’t have a polar end group anywhere and so this tends to be not very water soluble and of course, it’s not charged.
14. Figures – Nonpolar (hydrophobic cont’d) [S14]
a. More for you to look at. You should absolutely know the three letter and the single letter code for these so that is one thing that you’ll see as you read papers. (decided to not require this in a later lecture)
b. As far as knowing the structure of these, you probably should know what they look like, but again, I don’t expect you to know all the structures, but you probably should know some of the key ones like Histidine that is so important in terms of acid/base chemistry and some of the others that react like Serine is very important.
15. Figures – Polar, uncharged [S15]
a. As we get to amino acids like these that are polar, but uncharged – they often are involed in enzymatic reactions because the hydrodgen bond can interact with the substrate. These are examples. There’s a whole category of enzymes called Serine proteases, there’s another category called Cystine proteases. Because of that O-H group in this case that it’s important and it’s part of what’s called the catalytic triad for those proteases.
16. Figures – [S16]
a. Here is the Histidine that I talked about and one thing that makes this very important is the R-group for it has a pKa of 6.4 and that means that it’s close to physiological pH – 7.4 and it means it’s going to be partially hydrated and so it’s not too difficult to pull that hydrogen off or put it back on and that is the one amino acid that has a pKa that close to physiological pH. For that reason, Histidine plays a very prominent role in a lot of physiological reactions that occur in our cells.
17. Figures – Polar, acidic [S17]
a. Then we get to the polar acidic amino acids like Aspartic acid and Butamic acid. If we’re at pH 7.0, this is going to be the negative form and the same with that. Because the pKa of these are fairly low. The pKa of that group is even lower. You’ll see as we go forward why that’s important and why it’s important to know the general pKa numbers for the different R-groups vs the substituents that are bound to the C-alpha Carbon.
18. Figures – Polar, basic [S18]
a. Again, we have polar, but instead of negatively charged, positively charged amino acids. These are listed here. This one is the one that I told you that is kind of partially charged – Histidine. Whereas, these, if you look at their pKa, it’s up by 9.0.
19. Amino Acid R Groups [S19]
a. Take home points – one thing I didn’t mention is that those non-polar amino acids play a very important role in protein folding as the protein’s being made in the ribosome. Because they are non-polar, they don’t like an aqueous environment, so they’re going to try to interact with themselves and you generally find a lot of non-polar amino acids the backbone of the peptide within the internal part of a protein away from the water. The part that’s more on the outside of that protein is going to be polar or charged. There’s always exceptions. There’s non-polar ones on the outside and actually non-polar ones on the surface can play a very important role in one protein docking with another one. Because again, to shield themselves from water, they tend to interact with each other so it can be a way to have two proteins interact charge-wise, but if the stereochemistry isn’t right because there are non-polar patches on many molecules, they still won’t interact. So two things need to play a role: the stereochemistry and also the polarity or the charge of a protein.