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Four ‘ bonds ’ (review)

Covalent: like a dowel. Arises from? Ionic: like a rare earth magnet. Arises from? Hydrogen: like a wimpy old fridge magnet. Arises from? (we will talk about this again today extensively) Hydrophobic: like nothing else. Arises from?. Four ‘ bonds ’ (review).

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Four ‘ bonds ’ (review)

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  1. Covalent: like a dowel. Arises from? Ionic: like a rare earth magnet. Arises from? Hydrogen: like a wimpy old fridge magnet. Arises from? (we will talk about this again today extensively) Hydrophobic: like nothing else. Arises from? Four ‘bonds’(review)

  2. Why is one of these the genetic code?

  3. Instructions for the parts of living things DNA Why the instructions for you are stored as hydrogen interactions between ringy things http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

  4. Why care about DNA? DNA http://jennifersaylor.files.wordpress.com/2006/08/dna.jpg

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

  6. 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 • key is in H-bonding donor/acceptor pairing • its structure IS its function

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

  8. Primary goals for today • Make leap from Chemistry to Biology: how can you get ‘you’ from C, H, O, N and P (finish next week) • Describe HOW/WHY A goes with T and G with C (and ‘not’ G with T) • Discuss what took ‘them’ so long • Mutations happen ALL THE TIME! • Begin investigation into genetic diseases

  9. Is today ‘science’?Are these ‘investigations’? • The goal of science is to create simplifying worldview that is predictive and explanatory. • 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 • We are working with MODELS today

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

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

  12. Party hats on- • Starting point: • BLUE hats – L hand out, palm down • GREEN hats – L hand out, palm out (shake) • YELLOW hats – L hand out, palm up • RED hats – L hand out, palm out (shake) • START with a strand of GGTT ,‘right hand’ on neighbor’s shoulder • Make a matching strand (dbl-stranded DNA) • Why do bases go together? • Each strand ‘count off’ from their L to R, how do the two directions compare? Gua = Green Cyt = Red Ade = Blue Thy = Yellow

  13. Separate strands; who partners with whom? What external info do we need to re-create the missing strand? • Restart; RED hat turns hand palm up (put on purple hat) • it’s undergone chemical change… replicate &…? Gua = Green Cyt = Red Ade = Blue Thy = Yellow GGGTT

  14. Why do atoms make bonds? DNA

  15. Why do atoms make bonds? • What types of ‘bonds’ are there? DNA

  16. Why do atoms make bonds? • What types of ‘bonds’ are there? • Not all atoms play fair DNA

  17. Hydrogen bond/interaction DNA

  18. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ DNA

  19. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ • Based on electronegativity DNA

  20. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ • Based on electronegativity • Why not Carbon-Hydrogen? DNA

  21. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ • H-Bond Donors DNA

  22. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ • H-Bond Donors • Positive charge (Hydrogen) DNA

  23. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ • H-Bond Donors • Positive charge (Hydrogen) • H-Bond Acceptors DNA

  24. Hydrogen bond/interaction • When H bonds with ‘O’ or ‘N’ • H-Bond Donors • Positive charge (Hydrogen) • H-Bond Acceptors • Negative charge (O, N) DNA

  25. Oregano Basil Garlic Salt

  26. Oregano Basil Garlic Salt

  27. Oregano Basil Garlic Salt

  28. Guanine Adenine Thymine Cytosine

  29. First look • Touching, feeling bases

  30. Blinding you with science (jargon) • Pyrimidine (single ring), Purine (double) • PURAs Gold • Big base gets the little name • Hydrogen interaction, H-bond: O-H :N- • Donor: the group possessing the H, sharing it • Acceptor: the partial (-) atom partaking of the H

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

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

  33. 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

  34. Building block

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

  36. Rubrics • Homepage = > my instructor link => this week => BasePairer rubric • http://blc.arizona.edu/courses/181Lab/Rubrics/BasePairer_rubricF12.pdf

  37. Basepairer • Launch ‘BasePairer’ • Homepage = > my instructor link => this week => Activity guide • 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 tautomer in your lab notebook

  38. Base Pairer Rubric

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

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

  41. What to do with your piece of paper • Look at the paper I handed out again • Explore the tautomer that is on your paper now that we have talked about what a tautomer is • Write down the tautomer on your piece of paper in your lab notebook because that is the one you will need to use for your homework

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

  43. “Rather than believe that Watson and Crick made the DNA structure, I would rather stress that the structure made Watson and Crick.... what I think is overlooked in such arguments is the intrinsic beauty of the DNA double helix. It is the molecule which has style, quite as much as the scientists.” —F. H. C. Crick

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

  45. Back to the little sheet of paper again • make a note of your group name & genetic disease in your lab notebook • Make sure all of your names are on the back of that sheet of paper and that you TURN IT IN TODAY or no credit

  46. This exercise... • Spans the next 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. 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

  48. The task • Over the coming weeks, you’ll characterize a genetic disease • Symptoms and distribution • DNA mutation, amino acid change • Your ideas about influence on protein structure • Then you’ll share your findings with the class

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