Lesson 2 – Video 3
792 [00:00:01.16] SPEAKER 1: Hi. This will be the first of two lectures on protein structure.
793 been introduced to proteins as one of the four fundamental biopolymers. And now we'll
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
796 string like beads on a necklace. We'll talk about the peptide bond which joins amino
797 the protein. We'll talk about forces which govern the shape of folded proteins. And we'll
798 specifically about some misconceptions about hydrogen bonding that helps determine
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%
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
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
808 pictures of protein crystals. We saw that sodium chloride crystal, that sort of makes
809 spears oppositely charge. But even complex shapes like proteins can crystallize. And
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
812 we've learned. The first was that opposite charges attract, like charges repel. We'll use
813 and over again. This is in regard to electrostatics. And remember, this is primarily an
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
816 way of stating the hydrophobic affect. And these are due mostly to entropic contributions
[00:02:22.87] And this is a review of what an amino acid l 818 ooks like. We have the amino
819 the alpha group, and the carboxylic acid, amino acid. Connected to the alpha carbon is
820 group. And we have 20 different R groups. All amino acids have this backbone, and this
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
823 we are, again, remembering functional groups. We recall that there are five charged and
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
827 and they will tend to cluster in either, for instance, the hydrophobic core of a protein or in
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,
831 examples of amino acid one right here, side chain one, methionine. This is the peptide
832 here. This is planar. We won't rotate around this. This is the second side chain, second
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
835 directions so that you can have two sides to a single protein. For instance, this side of
836 chain will be nonpolar, whereas up here it will be polar. So it's a property called
837 [00:04:38.12] We do have rotation around two bonds. We have rotation between the
838 group and the alpha carbon. And we have rotation between the alpha carbon and the
839 group. So this is, as depicted, this is an amino acid. In gray we have peptide bond one,
840 peptide bond two. Remember that these four atoms are planar. You do not have any
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
843 there's certain structures that are most common. This is a topographical map showing
844 common values. The red are the most common. So that the most likely angles for phi to
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
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
849 in crystal structures of proteins. 850 [00:06:00.05] This is four different depictions of the same protein. This is a backbone
851 It's sort of simple to see. But again, we get fooled to think that there might be some
852 This is a space filling model where the atoms have their electronic radii filled in. And as
853 see, it's quite dense. It's closely packed.
[00:06:26.13] This is basically a backbone view also except 854 that you can see that we've
855 some depictions of secondary structures. These arrows are beta sheets. This helix as
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.
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