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Lecture 2

Cell Biology - Lecture 2 - Video 4 - Notes

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CAS BI 203
Martin Steffen

Lesson 2 – Video 4 [00:00:00.00] 931 [00:00:01.20] DR. MARTIN STEFFEN: Hi. In the second video about protein structure, we'll 932 continue our discussion about protein structure. We'll talk about four levels of protein structure 933 that scientists talk about when discussing protein structure-- that being primary, secondary, 934 tertiary, and quaternary. We'll spend a fair bit of time talking about two special types of 935 secondary structure-- alpha helix and beta sheet. 936 [00:00:24.62] We'll give examples about how related protein sequences can produce related three 937 dimensional structures. And in turn, the proteins will have related functions, not necessarily the 938 same. We're going to go into greater detail about binding interactions for protein. And then, 939 we're going to talk about a structural way that proteins control their activity. 940 [00:00:47.17] So we're already going to start talking about sort of a high level of regulation of 941 the protein. And it's pretty amazing about the way it happens automatically. I think you'll like 942 that. 943 [00:00:59.43] OK, so the first level of protein structure is called the primary structure. And all it 944 is is the linear sequence of amino acid. It's nothing besides just telling the amino acid sequence. 945 So the primary structure of this tetra peptide is methionine, aspartic acid, leucine, and tyrosine. 946 Secondary structure of a protein is common regular folds that we'll see over and over. And 99% 947 of what we're going to talk about are alpha helices and beta sheets. 948 [00:01:43.24] These are common folding patterns that proteins adopt. This is a couple different 949 pictures of an alpha helix. As you can see over here on the right, it's a right-handed helix. And in 950 a little more detail in section B, there are 3.6 amino acid residues per turn. 951 [00:02:05.50] Each amino acid has an angle of about 100 degrees. So four amino acids would be 952 400 degrees. So it's a little bit more than a full turn. And 5.4 angstroms between a turn, so that's 953 the pitch of the helix. 954 [00:02:22.76] One of the really important things that happens, if you look at the backbone atoms, 955 the carbonyl oxygen and the hydrogen attached to one of the nitrogens, these form a series of 956 hydrogen bonds. So as we talked in the previous lecture, an alpha helix is a straightforward way 957 of satisfying all the hydrogen bonding possibilities of these backbone atoms. And that's one of 958 the reasons that it has such a high propensity for appearing in a folded protein structure. 959 [00:02:59.83] Alpha helices are one simple way that proteins can cross lipid bilayers, 960 membranes. And that's because you can have a string of about 20 amino acids here that are only 961 the 10 hydrophobic amino acids so that they can interact with the hydrophobic lipid membrane 962 tails. You could not bury a charged amino acid here in this portion of the alpha helix. 27 [00:03:33.70] So that means you can computationally identify regions 963 of proteins that are likely 964 to cross a membrane. Whenever you see 20 amino acids in a row that are hydrophobic, then you 965 have a good hint that this is one possible folding structure it could take. And so you might guess 966 that it's a membrane protein. Another thing to point out-- that the amino acids above and below 967 those 20 will often be hydrophilic. Because they're interacting with the hydrophilic heads of the 968 lipids and also the aqueous environment out here. 969 [00:04:12.13] Now, let's imagine what happens-- and this sort of anchors the protein-- if you're 970 moving the peptide either up or down here. As soon as you start to pull it down a little bit, you'll 971 be pulling these hydrophilic residues down into the hydrophobic interior. And this hydrophilic 972 amino acid is going to resist being pulled down here. It's energetically unfavorable. So these 973 hydrophilic residues will prevent the peptide from slipping downward. 974 [00:04:51.68] Similarly, these hydrophilic residues will not want to be pulled up into this thing. 975 So it's going to keep it from slipping upwards. So by positioning hydrophilic residues on the 976 edge of this hydrophobic run, you are anchoring the alpha helix in the membrane in exactly the 977 location you would like it to. 978 [00:05:17.44] Here, we see another type of secondary structure, a beta sheet, schematized by 979 arrows. In this case, it's an anti-parallel beta sheet with the direction of one going up. Again, this 980 would be the amino end. This would be the carboxy end. For this strand, it would be the amino 981 end. This would be the carboxy end, and then an amino end and a carboxy end. 982 [00:05:42.52] The beta sheets can also be parallel where all these arrows are going in the same 983 direction. This is the backbone atoms, the alpha carbon, the nitrogen, and the carboxylic acid. 984 And they adopt this sort of pleated sheet here. And they will line up. And once again, we see, 985 when we look at the hydrogen bonding between the carbonyl oxygen and the hydrogens on the 986 amino groups that they are all satisfied. So this is, again, a common way of solving the problem 987 of having all the backbone hydrogen bonds being satisfied. 988 [00:06:22.29] So you also notice that you have two sides of this sheet. You have some R groups 989 that are below, also here, also here below the sheet. And then, you have another set of R groups 990 that are above the sheet. So you could, just like with an alpha helix, have one side being 991 hydrophobic or hydrophilic. In this case, the beta sheet can have different characters on the 992 different sides. 993 [00:06:47.71] Moving up a level of organization is the tertiary structure. And this is the complex 994 final fold of a monomer subunit where that includes all the alpha helices-- I'm sorry, here-- all 995 the beta sheets, the way the various domains, sort of sections of proteins, folds next to each 996 other, and also disordered regions that are just sort of random loops or linker regions. So the 997 tertiary structure is the final folded structure of a monomer. 998 [00:07:26.56] And the last level of protein structure is the quaternary structure. And this is the 999 interaction of different subunits. Here's a monomer green subunit and a monomer red subunit. 1000 And the way they interact and gives rise to this overall protein complex, that is called quaternary 1001 structure. 28 [00:07:51.42] In this case, you can see that the green s 1002 ubunit and the red subunit look very 1003 similar. If they are in fact similar, this could be a homodimer. These could also be related 1004 molecules, heterodimers, if there are some slight differences between the red subunit and the 1005 green subunit. 1006 [00:08:10.19] Now, there's one additional aspect of protein structure th
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