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Lecture 2

Cell Biology - Lecture 2 - Video 2.2 - Notes

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Boston University
CAS BI 203
Martin Steffen

Lesson 2 – Video 2b [00:00:00.00] 675 [00:00:01.09] PROFESSOR: All right. In this video, we will resume our survey of biopolymers. 676 And we'll talk about proteins first, which are made up of amino acids. Here, we can see the basic 677 structure of amino acid-- amino acid because it has an amino group on one end and a carboxylic 678 acid on the other, amino acid. 679 [00:00:25.20] In between those two groups, there's an alpha carbon. And connected to that is the 680 side chain often talked about just as an R group. Now, every amino acid is going to have this 681 same backbone. And every amino acid is going to have a different side chain. So that's what's 682 going to give them their different properties. 683 [00:00:48.28] Now, in aqueous solution, amino acids exist as zwitterions, meaning doubly684 charged molecules with a positively-charged amino group and a negatively-charged carboxylic 685 group. And in the next couple of videos, we'll be talking about some of the consequences for its 686 zwitterionic form. This is, again, two other depictions of the same molecule, ball and chain and a 687 space filling model with the amino group, the alpha carbon, and the carboxylic acid. 688 [00:01:22.53] Now, proteins are linear chains of amino acids. And so that we're going to have to 689 connect amino acid one to amino acid two, we're going to do that by a type of reaction called a 690 condensation reaction, where we'll lose a molecule of water but we're going to connect the 691 carboxylic group to an amino group of the second protein. So here is amino acid one. Here is 692 amino acid two. They're joined between those groups in this gray box by a bond called the 693 peptide bond. 694 [00:01:57.35] This peptide bond, there's nothing special about peptide bonds compared to other 695 bonds. But it's a convenient way to refer to that. Now, peptide bonds do have some properties 696 that some of these other bonds don't. Even though this is a single bond, it has partial double bond 697 character. So these four atoms will be planar. We will not rotate around these bonds, whereas 698 these single bonds we can rotate freely. 699 [00:02:21.79] Down here, we see three amino acids connected to it. This is the amino terminus, 700 because we have the free amino end. This is the carboxy terminus. We have a histidine, a 701 cystine, and a valine amino acid. Now, you won't have to memorize the amino acids. As you can 702 see, I struggled a bit on that. But we will need to know a little bit about amino acids, and we'll 703 get to that in a second. 704 [00:02:50.18] Important point about the synthesis of proteins-- we'll see this a couple times-- is 705 that proteins are synthesized from the amino terminus to the carboxy terminus, sometimes 706 depicted as N to C. Here, we have the amino group. This amino acid was before searing 707 glutamine and lysine. If we're going to add another amino acid, we're going to connect it to the C 708 terminus, so that the amino terminus is always the first part of a peptide that is synthesized. 20 [00:03:23.99] Now I'm going to run through different types of amino a 709 cids. We'll talk about-- I'll 710 just flip through charged amino acids, uncharged polar amino acids, and nonpolar or 711 hydrophobic. So we're going to have to remember these three groups. Here are the charged 712 amino acids. Lysine, arginine, and histidine-- these are all positively charged on their side chain. 713 Histidine can be neutral or positively charged. 714 [00:03:52.37] Acidic side chains, aspartic acid, and glutamic acid-- these are all charged so these 715 will tend to have certain properties that you will need to be able to deduce and reason about 716 when talking about that. For instance, just as a preview, you would never find a charged amino 717 acid buried inside the hydrophobic interior of a lipid membrane. But we'll get to that. 718 [00:04:25.78] The second main category of amino acids are polar, like the charged amino acids. 719 But they themselves are not charged. We have asparagine and glutamine that have carboxamide 720 side groups. And we have three types of amino acids that have hydroxyl groups-- serine, 721 threonine, tyrosine. These also tend to be exposed towards the aqueous solvent. These will not be 722 buried inside the hydrophobic interior of proteins. 723 [00:05:02.41] These three amino acids with their hydroxyl groups could all be phosphorylated. 724 And that will play a major role in cell signaling. We'll see those. 725 [00:05:12.95] The third type of amino acids are the hydrophobic amino acids. There are 10 of 726 them. They are primarily hydrocarbons-- as you can see here, methyl groups, hydrocarbons, we 727 have a methionine with the sulfur group, and the largest amino acid, tryptophan, with an amino 728 functionality. There are two special types of amino acids here. 729 [00:05:39.49] Proline-- this is technically not an amino acid, you don't need to know this. But it's 730 called an imino acid. And this has a side chain that is connected to both the alpha carbon and the 731 amino group. So we're not going to be able to rotate a
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