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Announcements

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”.

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Announcements

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  1. 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” 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. Thursday, 4 pm, Rm 141 Loomis– Physics Colloquium—Me!

  2. the gain or loss • Ionic bonds are formed by ________________of electrons by an atom. Covalent bonds form by ________________ of electrons. • 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 sharing Quiz #2: ECB Chpt 2 Sugars nucleotides fatty acids amino acids 1. 2. 3. An energy source Storage of information Signalling lipid condensation

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

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

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

  12. Original DNA target region Heat Heat Heat Cool Cool … PCR (Polymerase Chain Reaction) Copies DNA Exponentially through Multiple Thermal Cycles Oligo’s DNA Polymerase dNTP 1 copy 2 copies 4 copies In 32 cycles at 100% efficiency, ?? copies are created 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.

  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.

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