2. 2 Future regrets (again) At the end of every semester, some students ask: “is there anything I can do to raise my grade” The answer is always: Go back in time and be more committed, go to office hours, earn higher scores You are at that time now. Grab it before it goes by

3. Your questions Partial charges and “feels” Assessors and Programs Lab reports vs. write-ups

4. Strings to Blobs Hb One

5. How do we go from ‘string’ of mRNA to a MACHINE? How do you build a machine that builds a machine? Machine = 3D object that does stuff How do we get the shape? What Matters Today?

6. From there to here Week 2: How DNA can ‘mean’ anything; how it can pass that meaning on (replication) Week 3: How DNA can send out a ‘message’ (transcription); how that ‘message’ can be ‘translated’ into amino acids Now: How a string of amino acids is formed into a functional shape

7. “Building Blocks” There are ~ 5 ways molecular surfaces can ‘feel’ What are they? Amino acid ‘Easter egg hunt’ – find the one(s) that… Homepage -> “Sources” Interweb

9. Your Turn You ‘fold’ a protein: ProFolder (Bio181L_Go) Show me each solution (Q3) Leave 2 nd on screen

10. Profolder Features Destinations (lower right) => Folding Top: amino acid string Squares: places amino acids could go. Note ‘Undo last’ button Two spots--use one to improve upon what you did in the other Bottom: note that when you mouseOver an amino acid, it’s structure & ‘feel’ are shown

11. How does yours compare?

12. Inside and Outside Protein folding, oil/water, m-brane formation all same principle Protein folding- individual units attached to a pair of neighbors Many proteins need no further ‘instruction’ than sequence & water

13. Question Authority Pencils, paper, water, and oil

14. If THIS is true… Pencils made of…. http://www.nano-enhanced-wholesale- technologies.com/faq/carbon-forms.htm

15. If THIS is true… Pencils made of…. Paper made of…

16. If THIS is true… Pencils made of…. Paper made of… Oil and water… Pencils, paper, oil, water…

18. Now let’s “Hemoglobin”

19. Where we are Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+diseasehttp://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease

20. Where we are Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+diseasehttp://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Hb made of four protein chains

21. Where we are Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+diseasehttp://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Hb made of four protein chains 2 alpha chains 2 beta chains

22. Where we are Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+diseasehttp://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Each Hb molecule has four Heme groups

23. Where we are Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+diseasehttp://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Oxygen IS molecular, so TWO oxygen atoms

24. Where we are Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+diseasehttp://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease

25. Hb made of four Protein chains 2 alpha chains 2 beta chains

26. You’ve seen this before: http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

27. You’ve seen this before: Amino Acid sequence http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

28. You’ve seen this before: Amino Acid sequence http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology How is this determined?

29. You’ve seen this before: Amino Acid sequence Alpha Helix http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

30. You’ve seen this before: Amino Acid sequence Alpha Helix http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology How is this determined?

31. You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

32. You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology How is this determined?

33. You’ve seen this before: Amino Acid sequence Alpha Helix Folded peptide Aggregation of peptides http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

34. Hemoglobin

35. How hemoglobin’s amino acid sequence generates its structure Hemoglobin

36. How hemoglobin’s amino acid sequence generates its structure Why hemoglobin is a tetramer (gang of four) Hemoglobin

37. 30% Worksheet – Easter egg hunt 60% Hb Tutorial 10% Hb mini research What today will look like:

38. Turn OFF Wi-Fi; QUIT safari (not close window) READ the instructions on the intro... READ the instructions on each question... READ the instructions on the webpage... READ all the words of each question... Running the Tutorial

39. Do it with ‘feeling’

40. Spend about 10 minutes on your question I need a ‘link’ 2-3 sentence summary of findings Search words that were most affective Brief comment on ‘interestingness’ and accessibility “Mini Research”

41. On the relative likelihood of accidents…

42. What specifically would it take for… A lysine to become a glycine? To your codon tables! How often is that going to happen?

43. Genetic disease part 2 Follow the rubric Your Disease

44. Things you already “know”