Wed @ 11 meeting: Andrea - Sara-Ryan Lynn - Bob Steve Katie - Heidi Leslie Aleksi - Deborah

1. Pics: homepage => Instructors Wed @ 11 meeting: Andrea- Sara-Ryan Lynn - Bob Steve Katie- Heidi Leslie Aleksi- Deborah Emily- Sarah Jing Tyler- Candice Jessica

2. Grading • Movie: BruceStuff => Tutorial Movies => ‘Grading Tao” • taProg: BruceStuff => TA Software • Must have VPN client running (available same page) • They (and you!) can see their grades from the homepage grade link • Master_of_Patterns; DNA walk-throughs posted • Emily will contact you about PMaster write-up conferences (guidance in rubric interpretation)

3. Expectations • Surface tension is a word. • “Billions of interlinings creating a tight mesh that doesn’t readily separate” is an explanation • It truly is exactly like popping the water balloon • stuff pulls back from the introduced point of weakness • See ‘TA_Guide’ for this type of walk through • Answers should be mechanistic, cause-effect!

4. Building Quizzes • See the QuizBank; it has examples and point distros • New as a 181L instructor? Please send your quiz draft to me 24-48 hours before you intend to distro

5. New • Party hats & replication, mutation demo • Desk drawing bases, charges • Paired homework • Nucleobases argument map (ID the claims & their support)

6. What is teaching? • How is it different from teaching a parrot to say words?

7. All the news that’s fit to print A goes with T G goes with C

8. Spider dance! • Now that’s‘information’!

9. How? Why? DNA: instructions for the parts of living things • Why the instructions for you are stored as hydrogen interactions between ringy things

10. Who cares about DNA? • It’s what’s in you (and every other living thing) • It’s (part of) the magical interface between chemistry and life • It is perhaps the single most easily understood biomolecule you’ll ever meet • doesn’t ‘do’ anything, its more or less inert • key is in Hydrogen interaction pairing • its structure IS its function

11. Green = Guanine Red = Cytosine Blue = Adenine Yellow = Thymine Use: GGGTT

12. Primary goals • Consider the necessary properties of a chemical (DNA) that ‘is’ information • Understand HOW the bases go together • See how base pairing is replication • See how mutations arise • and why they cannot (always) be prevented • Genes in (in)action: genetic diseases

13. Is today ‘science’?Are these ‘investigations’? • The goal of science is to create simplifying worldview that is predictive and explanatory. • We’re working with computers today: You’ll never feel the pull of electronegativity, the ‘pH-ey’ presence of a proton. But thinking in this way helps you explain, predict? • That’s what we’re going for today in this way of looking at the bases

14. Life: gimme adjectives • What’s the difference between you, the bench top, a rock, a candle flame?

15. Review: bonds and “interactions” • A few more pieces of review

16. Four ‘bonds’/’interactions’ • Covalent: like a dowel. Arises from? • Hydrogen interactions: like a wimpy old fridge magnet. Arises from? • Hydrophobic interaction/exclusion: like nothing else. Arises from? • Ionic: like a rare earth magnet. Arises from?

17. H-bond donors and acceptors • Hydrogen interaction, H-bond: R-O-H - - - :N-R • Donor (+): the group possessing the H, sharing it • Acceptor (-): the partial (-) atom partaking of the H

19. Which one of these is a part of the genetic code? Why

20. Which one of these is a part of the genetic code? Why MonomersPolymers Nucleotide Nucleic acid Amino Acid Protein

21. Building block

22. Oregano Basil Garlic Salt http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

23. Guanine Adenine Thymine Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

24. Blinding you with science (jargon) • Pyrimidine (single ring), Purine (double) • PURAs Gold • Big base gets the little name

25. Green = Guanine Red = Cytosine Blue = Adenine Yellow = Thymine Use: GGGTT

26. Pas de deux* Gua = Green Cyt = Red Ade = Blue Thy = Yellow GGGTT • Party hats on--we’re going to do some line dancing! • Starting point: a double strand of DNA, each base facing partner with their ‘right hand’ on neighbor’s shoulder • Each strand ‘count off’ from their L to R, how do the two directions compare? • Separate strands; who partners with whom? What external info do we need to re-create the missing strand? • Restart; ‘Mask’ one with a purple hat; it’s undergone chemical change • replicate &…? *Dictionary.com: a dance by two persons

27. Fantastic plastic • Each group gets GC or AT pair. Investigate. • Superimposability of GC, CG, AT, TA pairs • High crimes & misdemeanors

28. Anatomy of a basepair Ornaments: -NH2 =O -H -OH =NH H ----- Dashed lines indicate double bonds present in some purines or pyrimidines

29. Hydrogen bonds form between G-C pairs and A-T pairs. Hydrogen bonds 5′ 3′ Guanine Cytosine Sugar-phosphate backbone Adenine Thymine DNA contains thymine,whereas RNA contains uracil 5′ 3′ Freeman, Biological Science, 4.6b Grow your own--make GC or AT Text

30. Closer look:Pairing Bases • the Truth about the Code

31. BasePairer • Homepage = > my instructor link => this week => BasePairer rubric • ‘Activity Guide’ is also on the web page

32. Basepairer • Launch ‘BasePairer’ • Don’t log in; that’s for homework • Write your names on the paper I hand out; return it at end of class or zero credit • make a note of your group name & genetic disease in your lab notebook

33. DNA • What properties of DNA… • Make it a good molecule to store info? • Make it easy to copy?

34. Precision & Pickiness • H-bonds: because weak, picky • Combined with stiff bases: it’s all right or it it’s wrong

35. Chemistry Happens II • Dr. Base & Mr. Tautomer • Why Chargaff’s rules didn’t => the structure

36. Stuff happens (baaaad stuff) http://www.nature.com/scitable/nated/content/ne0000/ne0000/ne0000/ne0000/97271/pierce_17_11_FULL.jpg

37. Bad things happen to good bases

38. Deamination Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

39. DeAMINation Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

40. Deamination NH3 H2O just add water… and heat Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

41. Deamination Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

42. Deamination THIS Hmmm, this is IDENTICAL to Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

43. Deamination We started with Cytosine Deaminated it to URACIL Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

44. Deamination Thymine Uracil Cytosine http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

45. Genetic Diseases • Why mutations matter • What loss of genetic information looks like

46. This exercise... • Spans the next month – same groups all month! • Lets you apply your learning and thinking to an actual disease • What is most important is that you think well and integrate what you are learning; being ‘right’ is secondary

47. The task • Over the coming weeks, you’ll characterize a genetic disease • Symptoms and distribution (DUE AT END OF THIS LAB!) • DNA mutation, amino acid change • Your ideas about influence on protein structure • Then you’ll share your findings with the class

48. Google & Wikipedia • GOOGLE.com (or Blackle.com) • search several terms • “phrases in quotes” • google.com/advanced_search • Wikipedia.org • User contributed • User policed • But pretty good! Caveat emptor! The web is a wonderful, rich source of information. ***But anybody can have a webpage*** If you want to Bing, I’m not stopping you

49. My sources • Wikipedia: I generally trust it based on personal experience and b/c it is community edited and putting up lies about science just isn’t that interesting • NIH: Federally funded science & health professionals, I judge it generally very trustworthy • Campbell textbook: textbook authors are not experts in every area of content, they consult with experts and their work is critically read by thousands, so I trust it

50. Due today! • Genetic disease part 1, from today on calendar • Handed in to me with all group member names on it • An example: hemoglobin/sickle cell anemia • Sufferers: one in 12 African Americans has the TRAIT; overall, 1/5000 Americans suffer • Common in areas with malaria • symptoms: shortened lifespan (48-52), see next slide”