Important Notes:
The Ch. 17 Quiz has been moved to MONDAY
Test Corrections for the last test are due Monday at 3:05
Today in class we did a lot of learning! Starting with a discussion of the concepts from yesterday's assignment on DNA From the Beginning (dnaftb.org). From Concept 21 I focused on making sure students understand the differences between DNA and RNA, the composition of a ribosome, and the attachment of amino acids to a specific transfer RNA (tRNA) molecule by an enzyme. From Concept 22 I chose to highlight the 3-letter codon and how to use a codon chart, as well as the basic structure of tRNA. I will not be collecting this assignment.
Students were asked to make a long notes sheet by attaching two pieces of paper end-to-end. The paper should have the Central Dogma drawn at the top (DNA --> mRNA --> protein) with lots of space. I asked students to create 5 columns, corresponding to the sections of the Central Dogma. The first column will stay blank. The second column is titled "Transcription" the third column "Transcript Processing" the fourth column "Translation" and the fifth column "Post-Translational Modification."
Transcription
Watch the video below and then construct your understanding of transcription by applying the following terms in a written explanation: Promoter, TATA box, Transcription Unit, Transcription Factors, RNA polymerase, Termination. The other terms used in the animation are beyond the scope of this course.
Transcript Processing
Watch the two videos below and then construct your understanding of transcript processing by applying the following terms in a written explanation: 5' cap, 3' poly-A tail, spliceosome, intron, exon. The other terms used in the animation are beyond the scope of this course, as are the specific mechanisms for removal of nucleotide segments.
Your homework tonight is to complete the handout from class using the Bioflix animation on the texbook website. http://wps.aw.com/bc_campbell_biology_7 Look in the left column for Bioflix. It is the one for Chapter 17 Protein Synthesis. If you need the handout you can print your own from the animation site. It is listed as the Study Sheet. If you cannot access the textbook link you can fill out the handout using your textbook (but the animation is really helpful and clear!)
By mistake, I posted a long, important comment about the transcription cartoon above on the "Protein Synthesis Part 2" blog entry. Please read it!
ReplyDeleteEven though I work on gene regulation now, my Ph.D. thesis was about introns, so I was very interested to hear this part of your class. The cartoons about transcript processing are very nice! One thing I found a little confusing from the cartoons, though, was the order in which things happen. Maybe I can shed a little light on that...but first I'm going to talk about something else, and afterward something else too. :)
ReplyDeleteA big difference between bacteria and eukaryotes is that bacteria don't have a nucleus, but eukaryotes do. The nucleus separates the process of transcription (inside the nucleus) from the process of translation (outside the nucleus). In bacteria, however, there is nothing separating these two processes. In bacteria, the same RNA molecule is often under construction (via transcription) and in use (via translation). In eukaryotes, however, transcription ends before translation begins.
All of the things that happen to an mRNA in the eukaryotic nucleus (transcription, capping, splicing, and polyadenylation) can happen AT THE SAME TIME...so long as the part of the RNA molecule that's involved has been transcribed. As shown in the cartoon, the mRNA is capped almost immediately. Splicing can happen as soon as the RNA of the intron has all been transcribed, so some of the mRNA may get spliced out while another part is still being transcribed.
One of the big mysteries about introns is how the proteins in the nucleus recognize exactly what part of the mRNA is "intron" and what part is "exon". The cartoon shows the intron contains four signals: a "GU" at the beginning of the intron, a branchpoint "A" somewhere in the middle, a polypyrimidine tract near the end (pyrimidines are C and U nucleotides, so a "polypyrimidine tract" is an RNA sequence that is mostly C and U), and finally an "AG" at the end of the intron.
Now, I hate to break it to you, but all the letters you get in an RNA are A, C, G, or U. If you try writing these four letters at random for a while, you'll notice that sometimes you write "GU", and other times you'll write "AG". Are those the start and end of an intron?
Even worse, suppose a gene has two introns (most human genes do; if I recall correctly the average is around five introns, and some actually have more than a hundred!). Both start with "GU" and both end with "AG", and both have branchpoint "A"s and polypyrimidine tracts. So how does the cell figure out to match up the start and end of the first intron, rather than matching up the start of the first intron with the end of the second???
Unfortunately I can't give you a simple, complete answer to that. Part of the answer is that the signal at the start isn't just "GU". The best signal for "an intron starts here" is "AG|GUAAGU", where the start of the intron is shown as "|"; but only the "GU" is (almost) always required. Likewise, the end of the intron is usually "CAG|", but only the "AG" is always there.
There is a lot more to it than that. There are proteins that bind other RNA sequences inside the introns, and other proteins that bind RNA sequences inside the exons (my Ph.D. thesis was about some of the sequences inside the exons). The only sequences that are used FOR EVERY INTRON are the ones that were mentioned in the cartoon, but there are _hundreds_ of proteins as well as a handful of RNA molecules (in addition to the mRNA that is being spliced) that are involved in splicing. And there is still a lot that we don't know yet about splicing. (And by "we", I mean everyone in the whole world.)
I imagine it would be possible to have a whole course dedicated to transcription and mRNA processing.
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