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Lecture 6

Cell Biology - Lecture 6 -Video 2.1 - Notes

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CAS BI 203
Martin Steffen

Lesson 6 – Video 2a [00:00:00.00] 65 [00:00:00.95] OK, this is the first of two videos on translation, a 2354 s we continue our discussion of 2355 gene expression-- which is turning specific genes on-- and translation, specifically, the act of 2356 making protein out of RNA. We'll learn that when we read the mRNA, the reading frame is 2357 crucial. That codons of three nucleotides specify amino acids. 2358 [00:00:24.62] We'll be introduced to tRNAmolecules, which are the adapter molecule between 2359 the nucleic acid code and the protein code. We'll emphasize that proteins are synthesized in the 2360 amino to carboxy direction, also written as N to C. 2361 [00:00:42.83] In the second video we'll be introduced to the fact that the ribosome is the 2362 molecular machine of many proteins and RNAmolecules, that it's responsible for making 2363 proteins, and it's quite a remarkable machine. 2364 [00:00:57.16] And we will learn the four step process of making proteins from amino acids. 2365 [00:01:07.40] In this slide we want to emphasize a major difference between eukaryotes and 2366 prokaryotes. For making proteins in eukaryotes here in the nucleus, in the white circle, DNAis 2367 transcribed into RNA. The RNA is spliced and capped. It'll be exported out of the nucleus into 2368 the cytosol. And here is where the protein is made from the mRNA, the separation of where the 2369 RNAis made, and where the protein is made. 2370 [00:01:36.59] Prokaryotes don't have a nucleus, so DNAis made to RNA, and protein's made 2371 from RNAin the same compartment, and it can happen even at the same time. While the is RNA 2372 polymerase is making part of the mRNA molecule, the ribosomes may have already hopped on 2373 the other end and started to make protein. 2374 [00:02:00.54] Now on this slide we see the beginning of mRNA being converted into protein. 2375 And the first thing you'll notice is that there are three nucleotides, C-U-C in this case, coding for 2376 a single amino acid, leucine. Now you might ask, why should that be? So I want you to just 2377 pause the video and think about it for a few seconds. Why you need three nucleotides to code for 2378 one amino acid? 2379 [00:02:27.94] OK, I hope you gave that some thought. The answer is, that's the smallest number 2380 of nucleotides which can be used. If you only used one nucleotide-- well there's four different 2381 nucleotides that could be there-- you could only code for four different amino acids. 2382 [00:02:43.18] So if you used two nucleotides, you have four that could go here, four that could 2383 go here, that's 16 different combinations. You can only code for 16 amino acids then. It's only by 2384 using the third, in which case you have four by four times four-- or 64 different possibilities-- 2385 that you have enough coding potential to code uniquely for 20 amino acids. 2386 [00:03:10.64] The second important thing to notice is, the way you group the three nucleotides is 2387 crucial. You can see that different groupings of the same nucleotide sequence-- I'll say the first 2388 five bases-- C-U-C-A-G, C-U-C-A-G, C-U-C-A-G-- so this is the same sequence, just grouped 2389 differently. In this case we're grouping the first three, in this case we grouping two three and 66 four, in this case we're grouping nucleotides three, four, and five. The 2390 y code for different amino 2391 acids, leucine, serine, glutamine. 2392 [00:03:46.53] Normally the cell, and you, when presented with a sequence would have to figure 2393 out what the reading frame is. We'll see later in the course some of the tricks for doing that, or 2394 computational approaches for doing that. For this class, for now, you can always assume that 2395 when you're given a mRNA sequence.And you have to convert to protein, you can always 2396 assume the first three is a codon, and then four, five, and six is a codon, and seven, eight, nine. 2397 [00:04:23.27] Now here we see the 64 different codons, the 64 ways of taking three nucleotides 2398 at a time. They're organized by the 20 amino acids, and there are three special codons that code 2399 for stop codons. This is the signal to the ribosome to stop making the protein. I'll just mention 2400 that these three codons have special names, sometimes you'll see in the literature amber, ochre, 2401 and opal. I don't know which is which, you don't need to know that either. 2402 [00:05:01.85] We can also see here that this is the three letter code for the various amino acids. 2403 Underneath we have the one letter code for amino acids. If you plan on going on in biological or 2404 biomedical research, you might as well learn the single letter codes, but you're not required to for 2405 this class. You do need to know the three letter codes. 2406 [00:05:30.63] And as we mentioned earlier, what class of amino acid they are.Alanine is a 2407 hydrophobic amino acid.Arginine is a positively charged amino acid.Aspartic acid is a 2408 negatively charged amino acid, and so on. 2409 [00:05:47.63] Now let's focus in on alanine. There are four different ways to code for alanine. G2410 C-A, G-C-C, and G-C-U. You'll notice that in all cases the first two codons are G-C. This is 2411 generally typical of all the variation in the coding system. It's in the third position where it's 2412 tolerant of any base. For this reason, the third position is called the wobble position, and its 2413 generally less important for specifying an amino acid. 2414 [00:06:28.64] The first two being the same doesn't always hold. For instance, there's six different 2415 ways of doing serine. The first two can either beA-G or U-C. 2416 [00:06:41.14] Let's talk about the six different ways of coding for leucine. In principle, all six of 2417 these are interchangeable. The cell can use any of these at any time, and they will always specify 2418 leucine. Now in practice, in actuality, the cell uses different codons at different times. 2419 [00:07:02.73] Sort of the most prominent example is, some of these codons are used in highly 2420 abundant proteins. They have highly abundant tRNAs, they are incorporated quickly int
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