JKW Lab

Cell Bio Assignments for Next Wednesday

jkwlab — Tue, 04 Nov 2008 20:20:50 +0000

WPR Corrections (30 points). Append to your WPR #2 the corrections and citations. This does not need to be pretty, but it does need to be legible. E.g. On problem 3 the answer should be “D”. Taq is the DNA polymerase from a thermophilic organism and it’s used because the protein won’t denature/unfold at high temperatures in the PCR reaction. Source: lesson 16 slides and lecture and the DNAtube movie from the lesson objective handout.
Central Dogma Assignment (30 points, 3 problems, 10 each): Start with each of the following DNA and show how it undergoes semi-conservative replication, the transcription of each product, and the translation of each product just as we did in problem H on the WPR (mutations in DNA 1 is a G-to-A transition and in DNA 2 is a depurination):

Mobility Assignment (30 points): In your own handwriting, draw a combined figure of Figures 15-19 and 15-20 from the book. Include a brief but descriptive discussion on event sequence, affinity, specificity, and all the components including the lipid bilayer, adaptin, clathrin, dynamin, cargo receptor(s), cargo molecule(s), v-SNARE(s), t-SNARE(s). Ensure you label the cytosol side of a membrane and name the starting and ending compartments. Make it neat o/w your grade will reflect.

Wednesday Fun (or what you need to focus on)

jkwlab — Mon, 27 Oct 2008 20:16:13 +0000

These are the topics that you should really own during your prep for the exam:

PCR – be able to talk me through a PCR reaction.
Quiz #7 (not Restriction Enzyme problem)
Restriction enzmes
membranes – what they composed of, what crosses a lipid bilayer, what needs channels/pores
Genetic control: DNA level
Know the Trp Operon figure and be able to brief me on it
Know the Lac Operon figure and be able to brief me on it
Know the differences between DNA and RNA polymerases
Know flavors of diffusion/transport across membranes
Cytoskeleton: know the 3 types, the subunits, the polarity/direction, what marks + vs. – ends, what engines move toward + vs – ends.
Know 1, 2, 3, and 4 structure in proteins. Know the IMF and covalent interactions that drive these levels of structure.

Time will be an issue. There will not be time to ponder my intent on wording etc – so no tricks, just up the middle definitions and concepts.

See me for AI if the Quiz 7 is not clear.

Good Luck.

Why It’s Tough to Accept New Scientific Data that Conflicts With our Learned Beliefs

jkwlab — Mon, 20 Oct 2008 01:30:37 +0000

Check out this absolutely amazing review in Science magazine:

Abstract

If you cannot get the full text let me know and I’ll send it out individually.

Btw, these psychologists cite Francis Crick. Amazing. The guy was an absolute giant.

Virus Research Paper

jkwlab — Thu, 09 Oct 2008 20:47:39 +0000

The course website has been updated so that the Research Paper hyperlink works. Read the document to get an idea of what is expected of you.
Trustworthy sources — the best is PubMed, although our library’s subscription list is spotty at best so many of the papers you will try and access will be unavailable. But that shouldn’t stop you from trying as most everything on PubMed is infinitely more trustworthy than standard Google fare.

If the lack of subscriptions is annoying you can go to PubMed Central, an online repository of public-accessible journal articles. It’s basically PubMed without some of the newest articles.

You want to stick with reviews, at least at first (click the tab titled “Review” or include the word “review” in your search parameter, e.g. “smallpox review vaccine” or “HIV AZT review”). Find a couple of review titles that interest you and then sit down and read them. The danger here is that many of these reviews are very well written and you might find yourself adopting phrases and sentences rather than just adopting the ideas presented and fashioning your own interpretation and presentation of the material.

Also think of figures that you might generate to help describe the virus, the cell biology, and the biochemistry involved with that virus. You might also choose to concentrate on therapeutics for a particular virus. What are they? What is the mechanism? What is the target? Give us molecular details.

Hope this helps.

Cell Bio Course Update

jkwlab — Sun, 28 Sep 2008 13:09:27 +0000

Greetings all,

Given the terrible mass email program available, I’m using this method for commo instead.

I sent out an attached xls file earlier today with your grade data and (if you scroll down in excel) some charts including a histogram. Hopefully this will assuage any anxiety about the exam and whether it was fair.

The course website has been updated for lessons 14-16. These next lessons are set up to be direct extensions of our nucleic acids lessons. First we get into mutations at the nucleic acids level and we’ll study the response at the peptide level. Then we’ll get into manipulating DNA in the laboratory.

WPR #1 Cell Bio

jkwlab — Wed, 24 Sep 2008 20:54:51 +0000

There’s a lot of material. But if you ensure you understand these major points that we’ve covered, then you ought to be doing pretty well.

Drop me a line with Q’s.

- Proks vs. Euks – differences and similarities

- Kind of chemical bonds that define or are distinctive for a given class of biological macromolecule.

- Reaction energy diagrams (RED)

- Enzymes and what they do (think RED)

- Delta G and DeltaGo

- Know primary classes of biological macromolecules, their monomer units and be able to identify them from a picture

- Scientific Method

- Microscope

- DNA replication: you need to be able to talk over a movie and describe each step, the players, and the chemistry behind the operation.

- DNA packing: DNA, histone-DNA string, histone-DNA fiber, diffuse chromatid material, condense into chromosomes.

- Genetic Code: total codons, codons encoding amino acids, understand the wobble position.

- Base pairs: understand that G can pair with U (the wobble pair) to give flexibility to the genetic code.

- Know Mitosis and Meiosis

The movies and cartoons I linked to in the lessons will really help you out for this exam.

Good luck and see you tomorrow!

Nucleic Acids crew: In vitro selection and SELEX and your next papers

jkwlab — Sun, 14 Sep 2008 15:41:33 +0000

Some links to get you started:

Ensure you understand PCR. Here are some resources:

DNA PCR Tutorial (Click on Amplification Tutorial)
Here’s a great YouTube video of PCR

Famalouk’s page on SELEX: http://www.lmb.uni-muenchen.de/groups/famulok/SELEX.html

SELEX wiki

The next review paper you need to read (it’s more digest-able than the Breaker review). Click on PDF.

The next data paper you need to read. It involves the reselection of a known ATP aptamer for high affinity and specificity. Click on PDF.

Online Cuttlefish Resources

jkwlab — Sun, 14 Sep 2008 15:06:38 +0000

Some Links to get you started on your cuttlefish journey are as follows:

http://www.cephalopod.org/

http://en.wikipedia.org/wiki/Cuttlefish

http://www.pbs.org/wgbh/nova/camo/

http://www.tonmo.com/cephcare/cuttlefishcare.php

http://marinebio.org/species.asp?id=540

http://www.thecephalopodpage.org/

A basic news story about cuttles from National Geographic.

Polymerization – a caveat to Condensation

jkwlab — Fri, 29 Aug 2008 14:30:18 +0000

I remember that I did not make the point that a condensation reaction requires the production of a small molecule and that the molecule doesn’t have to be water. In the case of nucleic acid polymerization, inorganic pyrophosphate, or PPi (the beta and gamma phosphates from the triphosphate precursor), is produced as the NMP is incorporated into the nascent chain.

Check out this transcription video but take care to note that this is a cartoon and the authors chose to show DNA as a tube rather than a double helix that gets separated in a transcription bubble as the polymerase proceeds.

The Scientific Method: Inductive and Deductive

jkwlab — Tue, 26 Aug 2008 20:30:06 +0000

Check out this brief summary of the scientific method and what goes into it.

Brief Summary #2.

Brief Summary #3.