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Lecture 3

Cell Biology - Lecture 3 - Video 2 - Notes

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CAS BI 203
Martin Steffen

Lesson 3 – Video 2 [00:00:00.00] 1190 [00:00:00.86] SPEAKER 1: Hi. In this video, we'd like to continue discussing enzymes. In 1191 particular, we want to focus on the mechanisms whereby an enzyme will reduce the activation 1192 energy of a reaction.And then we'll end up talking a little bit about protein folding. 1193 [00:00:18.04] In this first slide, we see in blue an enzyme called lysozyme which acts upon 1194 polysaccharides which are strings of sugars which are shown in red. The reaction cleaves a 1195 longer polysaccharide into two smaller fragments.And here you can see some of the detail. You 1196 have a glycocidic bond between two sugar molecules. You have two amino acids-- glutamic acid 1197 and aspartic acid-- making a simultaneous attacks on the glycosidic bond proceeding to a 1198 covalent intermediate with this sugar. 1199 [00:01:04.10] And then we have hydrolysis of a water molecule adding a proton to the glutamic 1200 acid and putting a hydroxyl group on the carbon cleaving this ester bond which is an 1201 intermediate.And that's pretty nice, but I feel it's still fairly complicated.And so I'd like to help 1202 build your intuition about a kind of enzyme mechanism.And really the only rule you need to 1203 know is that opposite charges attract, like charges repel. 1204 [00:01:38.26] This figure from the book shows three mechanisms of enzyme catalysis. The first 1205 is undeniably important. It's simply an enzyme which will hold the reactants in the proper 1206 orientation near each other, giving them plenty of time to react and not relying on fleeting 1207 interactions, collisions in solution based on diffusion. 1208 [00:02:03.94] The second mechanism is one we'll talk about more, and that is electronic 1209 stabilization of the transition state. However, this picture is somewhat flawed as you don't see a 1210 transition state. You have a charged molecule. What you see is electronic stabilization of a 1211 molecule itself.And we'll talk about that. 1212 [00:02:24.54] And finally, I think I disagree with this third mechanism of physically squeezing 1213 or bending a molecule, but perhaps I don't understand exactly what they're talking about. So now 1214 we'll talk more about mechanism two and we'll also use that to discuss some features of protein 1215 structure in a little greater detail. 1216 [00:02:46.14] Now let's talk a little bit more about an amino acid. In solution, we've talked about 1217 it being a zwitterion with a positively charged amino group and a negatively charged carboxyl 34 group. And here is a peptide bond with the C-alpha carbon, 1218 another amino group here and 1219 another carboxyl end here. If we look along these four atoms in the peptide bond, there's actually 1220 a fairly significant dipole moment where we have excess electron density at the oxygen end and 1221 relative electron deficiency at the proton. So that results in a dipole moment of about 3.5 Debye, 1222 which is quite large. 1223 [00:03:37.99] And I should just mention that-- for whatever reason, who knows-- in biology, the 1224 convention is different from physics. In biology, the arrow points towards the positive end of the 1225 dipole. That's opposite what you may have learned in physics class. 1226 [00:03:54.76] So now I'm going to talk about what happens to those dipole moments for each of 1227 these peptide bonds in the helix. Unfortunately, the orientation is upside down here. But what we 1228 have for those hydrogen bonds, if we can look, here is a peptide bond. We have the oxygen, the 1229 alpha carbon, the amino group, the hydrogen.And so we have, in this case, a dipole, but it's 1230 pointing almost along the alpha helix axis.And we can see many of those. Here's another one 1231 pointing up. Here's another one. 1232 [00:04:38.67] Now in this slide, it's emphasizing all the different dipole moment of the 1233 individual peptide bonds or amino acids, however you want to think about it.And these will sum 1234 into a fairly significant vector that points down the alpha helix. This has the effect of creating 1235 fairly significant electric fields at either end of the alpha helix. 1236 [00:05:02.78] Now let's imagine a hypothetical active site where there's going to be a molecule 1237 reacting in here.And we have four alpha helices lined up pointing towards the active site. It's not 1238 at all unusual to have this sort of orientation, although, it would be spread out in three 1239 dimensions rather than in two. 1240 [00:05:24.98] Now to understand a little bit more about the stabilization of the transition state, 1241 we need to think about a molecule in a generic transition state.And I've just drawn a molecule 1242 with five atoms here, and we're going to pretend that this enzyme is going to cleave between 1243 bond three and four.As it goes towards the transition state, so here's the starting material, normal 1244 bond between three and four. Here is the product, a broken bond between three and four.And the 1245 transition state is starting to stretch bond three and four longer and longer on its way to being 1246 broken. 1247 [00:06:05.00] Because you have a certain amount of electron density between atoms three and 1248 four, stretching it out over a longer distance means there's going to be less electron density in the 1249 transition state relative t
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