2. Groups for semester project Carly, Alexandra, Lindsay Natalia, Cara, Tyler Rachyl, Candice. Nicole, Angel Michaela, Jacob, Katherine Jessica, Jordann, Hailey Keionna, Tamilla, Kathryn

3. Groups for semester project Kelly, Gina, Samuel Wesley, Alexia, Clayton May, Philip, Gustavo Christopher, Colby, Benjamin Neal, Donald, Taylor Marissa, John, Nicole Jennifer, Karling

4. Some words on group projects ‘Divide and conquer’ is fine, BUT everyone in your group MUST read and approve the entire final submission If you name is on it, it means that you contributed to the work as much as any other group member

5. Things to clarify/review for translation (questions about these will be on next week’s quiz) What is the role of diffusion/Brownian motion - Are the molecules ‘seeking’ partners, or is just random chance? What exactly is the role of the Ribosome? Who/what determines if a tRNA matches the codon on the mRNA? (Hint – think about ‘feels’ WHAT is the termination factor?

6. Strings to Blobs Hemoglobin (chains of amino acids -> folded proteins)

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

8. 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

9. “Building Blocks” There are ~ 4 ways molecular surfaces can ‘feel’ What are they? Amino acid ‘Easter egg hunt’ – find the one(s) that… Homepage -> “Sources” Internet

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

12. 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

13. How does yours compare?

14. 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

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

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

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

18. Again, WHY was this the best?

19. 19 Other ‘rules’ of folding (for last question on W.S.) (+) (-)

20. How to hydrogen interactions (H-bonds) contribute to alpha-helix and beta-sheet?

21. 21 Other ‘rules’ of folding (+) (-)

22. 22 Mutation--not always bad While the comparison is often made, proteins are not sentences An amino acid is a collection of properties; changing from one to another changes a region of the protein by (little/some/a lot/completely) It ’ s an exaggeration, but think of amino acids more like different vacuum cleaner nozzles

23. Now let’s “Hemoglobin”

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. 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

26. 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

27. 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

28. 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

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

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

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

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

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

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

35. 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?

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

37. 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?

38. 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

39. Hemoglobin

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

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

42. 30% Worksheet – Easter egg hunt 60% Hb Tutorial 10% Hb mini research What today will look like:

43. 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

44. Do it with ‘feeling’

45. 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”

46. Genetic disease part 2 Follow the rubric Your Disease

47. Things you already “know”