1. Strings to Blobs Hb One

2. How do we go from ‘string’ of mRNA to a MACHINE? –machine = 3D object that does stuff How do proteins get the shape? –Term: ‘folding’ How specific aminos and protein shapes = operational machines What Matters Today?

3. 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

4. “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

6. Freeman, Scott. Biological Science. 4 th Edition.

7. Your Turn You ‘fold’ a protein: ProFolder (Bio181L_Go) Show me each solution (Q4) Leave 2 nd on screen

8. 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

9. How does yours compare?

10. Other ‘rules’ of folding (+) (-)

11. Images of 3D Q. 4

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

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

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

16. Now let’s “Hemoglobin”

17. 17 Scale & role Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease Small capillary (blood vessel) Tetramer: 4 protein chains (~145 amino acids) Oxygen molecule 2 atoms Heme: C 34 H 32 O 4 N 4 Fe

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

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

20. You’ve seen this before: What is it? http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

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

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

23. 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?

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

25. 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?

26. 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

27. How hemoglobin’s amino acid sequence generates its structure What will we learn about Hb?

28. How hemoglobin’s amino acid sequence generates its structure Why hemoglobin is a tetramer (gang of four) What will we learn about Hb?

29. 30% Worksheet – Easter egg hunt 60% Hb Tutorial 10% Hb mini research What today will look like:

30. 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 (Hemo one)

31. 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 (Hemo one)

32. Do it with ‘feeling’

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

34. Genetic disease part 2 Follow the rubric Your mutations linked on course calendar Your Disease

35. Things you already “know”