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Lecture 2

Cell Biology - Lecture 2 - Video 3 - Notes

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CAS BI 203
Martin Steffen

Lesson 2 – Video 3 [00:00:00.00] 792 [00:00:01.16] SPEAKER 1: Hi. This will be the first of two lectures on protein structure. We've 793 been introduced to proteins as one of the four fundamental biopolymers. And now we'll learn 794 about them in a little bit more detail. 795 [00:00:13.65] Specifically, we'll talk about how proteins are made up of amino acids. It's a linear 796 string like beads on a necklace. We'll talk about the peptide bond which joins amino acids into 797 the protein. We'll talk about forces which govern the shape of folded proteins. And we'll talk 798 specifically about some misconceptions about hydrogen bonding that helps determine protein 799 structure. 800 [00:00:39.82] Before we get into that, I'd like to point these two pictures out to you. We 801 discussed in a previous lecture about how cells are made up of 70% of water, 30% biomolecules. 802 This bottom picture, in particular, is drawn to scale with the proper concentrations. 803 [00:00:58.40] And when you think of 70% water, you might not think about as crowded an 804 interior as that. There's a lot of molecules. This will affect diffusion. And most of the water in the 805 cell is, even though it's 70%, it's very close within, I think, six molecules of one of these 806 biomolecules. So there's not a lot of free water inside a cell. 807 [00:01:24.92] Another depiction of 70% water is up here in the protein-- these are various 808 pictures of protein crystals. We saw that sodium chloride crystal, that sort of makes some sense, 809 spears oppositely charge. But even complex shapes like proteins can crystallize. And that's pretty 810 amazing. And I think the pictures are pretty beautiful. 811 [00:01:47.88] I have about four or five slides of review just to remind you about things that 812 we've learned. The first was that opposite charges attract, like charges repel. We'll use that over 813 and over again. This is in regard to electrostatics. And remember, this is primarily an enthalpic 814 term of free energy. 815 [00:02:07.24] The second rule was that oil and water don't mix. And that is another simplified 816 way of stating the hydrophobic affect. And these are due mostly to entropic contributions to free 817 energy. 23 [00:02:22.87] And this is a review of what an amino acid l 818 ooks like. We have the amino group, 819 the alpha group, and the carboxylic acid, amino acid. Connected to the alpha carbon is the R 820 group. And we have 20 different R groups. All amino acids have this backbone, and this is where 821 the bonds will form for forming a protein structure. 822 [00:02:56.79] This is a reminder about the 20 amino acids. We're not memorizing structures, but 823 we are, again, remembering functional groups. We recall that there are five charged and polar 824 amino acids. There are five uncharged but polar amino acids. These are the amino acids that are 825 more likely to be involved with water or aqueous phases. 826 [00:03:21.82] These are hydrophobic amino acids. These 10 here. These side chains are nonpolar 827 and they will tend to cluster in either, for instance, the hydrophobic core of a protein or in the 828 hydrophobic section of a lipid bilayer. 829 [00:03:39.04] So here's an amino acid. They are joined together to form proteins. A protein is 830 nearly always a linear string of amino acids. And we'll see more about this, but again, this is 831 examples of amino acid one right here, side chain one, methionine. This is the peptide bond right 832 here. This is planar. We won't rotate around this. This is the second side chain, second amino 833 acid, third amino acid, fourth amino acid. 834 [00:04:15.20] When they're formed in linear, most of the time the side chains point in opposite 835 directions so that you can have two sides to a single protein. For instance, this side of the peptide 836 chain will be nonpolar, whereas up here it will be polar. So it's a property called ampthipathic. 837 [00:04:38.12] We do have rotation around two bonds. We have rotation between the amino 838 group and the alpha carbon. And we have rotation between the alpha carbon and the carboxyl 839 group. So this is, as depicted, this is an amino acid. In gray we have peptide bond one, gray 840 peptide bond two. Remember that these four atoms are planar. You do not have any rotation 841 around this single bond because it has a partial double bond character. 842 [00:05:07.84] So these phi and psi angles can take on characteristic values. And you can see 843 there's certain structures that are most common. This is a topographical map showing the most 844 common values. The red are the most common. So that the most likely angles for phi to adopt is 845 around minus 110. Here's zero. Here's minus 180. Around minus 110. 846 [00:05:31.82] And for psi, there's two structures that we'll learn about beta sheet and alpha helix. 847 If it's an alpha helix, psi will take on a value of minus 50. If it's a beta sheet, 150 will be a 848 common value. Any of these values are possible. These are just showing the most frequent found 849 in crystal structures of proteins. 850 [00:06:00.05] This is four different depictions of the same protein. This is a backbone only view. 851 It's sort of simple to see. But again, we get fooled to think that there might be some space there. 852 This is a space filling model where the atoms have their electronic radii filled in. And as we can 853 see, it's quite dense. It's closely packed. 24 [00:06:26.13] This is basically a backbone view also except 854 that you can see that we've added 855 some depictions of secondary structures. These arrows are beta sheets. This helix as an alpha 856 helix that helps our eyes draw attention to certain structural features in the protein. 857 [00:06:44.31] And here, this is in the bottom left hand corner, we have an all atom trace. This is 858 just the backbones up here. This is all the atoms being depicted. 859 [00:07:01.04] Now with regard to forces that help govern the shape of proteins, we've got three 860 re
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