1. Last time: I assigned you read “Predictable Packaging,” by Tim Richmond Commentary about Widom et al, Nature, 2006 and to write-up a ½-1 page summary! (Due next Monday). Do NOT do this. Instead focus on: Due on Monday: Your article on what you will give your talk and research paper. Turn in the original research paper; also turn in the title of a review paper that gives background on the general subject; also, the title(s) a general (biophysics) book/web pages (e.g. Wikipedia pages) that gives a more general background. In general, an original research article has LOTS of terminology that you must learn first, before you even have a hope of understanding it! You can pick articles from Nature, Science, Cell. You do NOT need to pick from these, but it does assure you that the article is important ½ pg write-up. Including why it’s of interest to you, why it’s generally of “widespread” interest. Announcements Today (Wednesday) – quiz on Chpt 2 of ECB HW #3, Assigned today, due next Wednesday; Chpt 3 of ECB Today’s Lecture: Anne on Ribosome; Paul on Applications of DNA: Forensics, FISH, DNA “chips” Thursday, 4 pm, Rm 141 Loomis– Physics Colloquium—Me!

2. Quiz #2: ECB Chpt 2 1. Ionic bonds are formed by ________________of electrons by an atom. Covalent bonds form by ________________ of electrons. 2. Cells contain four major families of small organic molecules, what are they? 1.____________ 2. __________________3. ________________4. __________ 3. Each family in question #2 (above) can be used for 3 things. They are: __________________________________________________________ 4. The __________ bilayer forms the structural basis for all cell membranes. 5. In order to make long polymers of sugar, two monomers can be brought together by enzymes such that their hydroxyl groups (-OH) couple together. This catalysis is an example of a ____________________ reaction. the gain or loss the sharing lipid condensation Sugars nucleotides fatty acids amino acids 1. 2. 3. Storage of information Signalling An energy source

3. Translation Anne Cai, my TA, presents on Translation and the Ribosome

4. Stages in translation Initiation Elongation Termination Recycling

5. Initiation mRNA binds to small subunit of the ribosome (30S) fMet-tRNA binds to the P site of the ribosome Initiation factors (IF1, IF2 and IF3) help to assemble the initiation complex.

6. Elongation

7. Termination and Recycling Ref: Thomas A. Steitz, A structural understanding of the dynamic ribosome machine. Natue Reviews Molecular cell biology, Volume 9, 243. (2008)

8. IF1, IF2 and IF3: initiation factors EF-Tu and EF-G: elongation factors RF1, RF2 and RF3: release factors RRF: ribosome recycling/release factor GTP: Guanosine triphosphate Discussion of movie on translation: (Venki Ramakrishnan's, 2009 Nobel Prize Winner) home page. http://www.mrc- lmb.cam.ac.uk/ribo/homepage/mov_and_overview.html The movie is actually pretty long including the initiation, elongation, termination and recycling stage.

9. (Paul’s turn:) Intro to DNA Forensics Every person has their own, unique DNA (except for twins). A person can be “tagged” with their DNA. If your blood, semen is found  you’re in trouble. Your genes found in a kid  parent. You’re killed in war/car accident and can only recognize you from your DNA. Don’t have to completely sequence their DNA. Can find certain regions. Just enough –say 13 different ones– that chances that another person has exactly the same set is 1 in a trillion.

10. DNA in the Cell chromosome cell nucleus Double stranded DNA molecule Individual nucleotides PCR, stands for? Polymerase Chain Reaction.what is it? Invented 1990; Nobel Prize in 1993: Kary Mullis Target Region for PCR

11. Make copies (extend primers) Starting DNA Template 5’ 3’ 5’ 3’ Add primers (anneal) 5’ 3’ 5’ Forward primer Reverse primer DNA Amplification with the Polymerase Chain Reaction (PCR) Separate strands (denature) 5’ 3’

12. In 32 cycles at 100% efficiency, ?? copies are created PCR (Polymerase Chain Reaction) Copies DNA Exponentially through Multiple Thermal Cycles Original DNA target region Heat Cool Heat DNA Polymerase dNTP Oligo’s 1 copy 2 copies Cool 4 copies Heat … 1.07 billion To work, what property of DNA polymerase have to have? Heat stable so don’t have to add in new polymerase for every cycle Thermostable organisms, e.g. living in Yellowstone Geysers have this. New Scientists (1998)…Yellowstone's bugs land up in court... Microorganisms from hot springs are especially valuable because their enzymes are not easily destroyed by heat....

13. Class evaluation 1. What was the most interesting thing you learned in class today? 2. What are you confused about? 3. Related to today’s subject, what would you like to know more about? 4. Any helpful comments. Answer, and turn in at the end of class.