1 00:00:08,466 --> 00:00:09,316 >> Dude: Hey Sally. 2 00:00:09,556 --> 00:00:10,226 >> Sally: Hmmm? 3 00:00:10,226 --> 00:00:12,546 >> Dude: How come Buddy is green and I'm not? 4 00:00:12,766 --> 00:00:13,356 >> Sally: Well Dude. 5 00:00:13,356 --> 00:00:16,786 Your parents aren't green and I'm guessing that Buddy's parent was. 6 00:00:16,896 --> 00:00:20,206 >> Dude: That's not what I mean...like, what makes him green? 7 00:00:20,466 --> 00:00:20,966 >> Sally: Envy? 8 00:00:21,346 --> 00:00:23,796 >> Dude: Fine, I'll figure it out myself. 9 00:00:25,156 --> 00:00:27,526 Alright! Here it is. 10 00:00:27,666 --> 00:00:30,046 Hey Sally, check this out. 11 00:00:30,266 --> 00:00:31,876 All of Buddy's DNA is online. 12 00:00:31,966 --> 00:00:34,516 Now all I have to do is find the part that makes him green. 13 00:00:35,526 --> 00:00:38,636 What a nightmare. 14 00:00:37,066 --> 00:00:38,036 It all looks the same. 15 00:00:38,036 --> 00:00:39,846 Just Gs, As, Ts, and Cs. 16 00:00:39,846 --> 00:00:42,026 How am I suppose to know what's what? 17 00:00:42,376 --> 00:00:44,656 Someone needs to write a manual. 18 00:00:44,926 --> 00:00:47,376 >> Sally: We are writing one, but it's a work in progress. 19 00:00:47,676 --> 00:00:48,876 Why is Buddy green? 20 00:00:48,966 --> 00:00:52,266 Well, it's probably because he makes a protein or two that turn him green. 21 00:00:52,566 --> 00:00:57,336 We can figure that out, because sequences that code for proteins have a few things in common. 22 00:00:57,976 --> 00:00:59,626 >> Dude: Oh I remember now. 23 00:00:59,826 --> 00:01:05,046 They all start with ATG then call out for amino acids using three bases at a time. 24 00:01:05,316 --> 00:01:07,676 >> Sally: Those 3 bases are called triplet codons. 25 00:01:08,016 --> 00:01:10,916 Here's a look up table with the genetic code for Buddy. 26 00:01:11,336 --> 00:01:14,836 It tells you which amino acids are encoded by each triplet codon. 27 00:01:15,076 --> 00:01:16,436 >> Dude: OK I got it now. 28 00:01:16,726 --> 00:01:22,366 Here's an ATG for the methionine start, then I see a TAT, that translates to tyrosine, 29 00:01:22,546 --> 00:01:25,696 then TAG that will make a ...stop? 30 00:01:26,296 --> 00:01:27,606 That's only two amino acids. 31 00:01:27,906 --> 00:01:29,876 That seems too short to do anything in the cell. 32 00:01:30,136 --> 00:01:32,536 >> Sally: You've just figured out something really important. 33 00:01:32,696 --> 00:01:34,496 Not every ORF will make a protein. 34 00:01:34,946 --> 00:01:39,956 As a rule of thumb, people consider 100 amino acids the minimum to produce a protein, 35 00:01:40,326 --> 00:01:43,266 even though there are lots of proteins we know that contain fewer. 36 00:01:43,556 --> 00:01:47,436 >> Dude: Did you say ORF or did you just burp? 37 00:01:47,856 --> 00:01:49,056 >> Sally: didn't burp! 38 00:01:49,376 --> 00:01:51,246 ORF stands for open reading frame. 39 00:01:51,376 --> 00:01:57,406 It's a register for reading the section of DNA that starts with ATG, uses 3 letters at a time 40 00:01:57,406 --> 00:02:02,776 to call for amino acids and then uses one or more of the stop codons to close the reading. 41 00:02:03,056 --> 00:02:06,746 >> Dude: So in this DNA sequence there are 3 reading frames that I have to look through? 42 00:02:07,256 --> 00:02:08,386 That will take me forever. 43 00:02:08,756 --> 00:02:13,506 >> Sally: Actually it will take you forever times two since there are 6 reading frames. 44 00:02:13,616 --> 00:02:18,036 Remember DNA is double stranded and the bottom strand, the one you're not seeing here, 45 00:02:18,076 --> 00:02:20,076 might also have ORFs that make proteins. 46 00:02:20,176 --> 00:02:23,076 >> Dude: Please tell me there are computer programs to help me with this. 47 00:02:23,166 --> 00:02:26,776 >> Sally: There are lots of good ones, but once you find all the ORFs what will you do? 48 00:02:27,186 --> 00:02:29,046 >> Dude: Yeah...then what? 49 00:02:29,166 --> 00:02:31,786 How will I know which of the ORFs really make proteins? 50 00:02:31,786 --> 00:02:32,866 And what if I've missed a bunch? 51 00:02:32,976 --> 00:02:36,766 Maybe some proteins that turn Buddy green are only a few amino acids long. 52 00:02:36,836 --> 00:02:37,526 >> Sally: Nice! 53 00:02:37,526 --> 00:02:40,166 You've got the start of a really interesting project here. 54 00:02:40,536 --> 00:02:44,146 But remember that discovering important proteins is only part of your job. 55 00:02:44,516 --> 00:02:48,536 If you really want to engineer biology you'll have to refine the genetic material 56 00:02:48,766 --> 00:02:50,306 so you and others can build with it. 57 00:02:50,626 --> 00:02:53,436 Before Buddy wakes up, can I show you one great example?