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Announcements:

Announcements:. I got caught checking my cell phone, so in order to avoid being labelled a hypocrite, you can text in class, just give me your attention when I lecture! No one wants to go to office hours on a Friday afternoon  should I change my hours? Quiz 3 average: 83%

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  1. Announcements: • I got caught checking my cell phone, so in order to avoid being labelled a hypocrite, you can text in class, just give me your attention when I lecture! • No one wants to go to office hours on a Friday afternoon  should I change my hours? • Quiz 3 average: 83% • Send me emails if you want help on anything but can’t attend office hours, if you’re still having trouble with the first weeks material, it isn’t going to get easier…

  2. How? Why? From strings to blobs

  3. From there to here • Week 3: How DNA can ‘mean’ anything; how it can pass that meaning on (replication) • Week 4: 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. What matters today? • How do we go from the ‘ticker tape’ of an mRNA to a machine? • machine = 3D object that does stuff • Who shapes proteins into their shapes? Terminology: ‘folding’ • How specific amino acids and protein shapes give rise to operational machines that perform body tasks

  5. Meet the building blocks • There are only about 5 ways molecular surfaces can be • What are they? • Amino acid easter egg hunt--find the one(s) that...

  6. How does it feel?

  7. http://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svghttp://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg

  8. Ooey gooey rich & chewy inside... • Protein folding, oil not mixing with water, and membrane formation all reflect the same principle • In protein folding, the constraint is that the individual units are all attached to a pair of neighbors • Many proteins need no further ‘instruction’ than their sequence & water to correctly assume their superhero identity

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

  10. If THIS is true… • Pencils made of…. • Paper made of…

  11. Question Authority • To your pencils, index cards & oil-water mixes! • Color one face of an index card with pencil • Cut out circles with hole puncher • Predict: what will happen? • Drop into oil/water bottles; mix

  12. Your turn • You ‘fold’ a protein: ProFolder (Bio181L_Go) • Show me each solution (Q. 3) • Leave the 2nd one on screen

  13. 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

  14. How does yours compare? 14

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

  16. Images of 3D Q. 4

  17. How? Why? Life’s blood: Hemoglobin

  18. Hemoglobin: overview http://www.youtube.com/watch?v=WXOBJEXxNEo&feature=related

  19. Small capillary (blood vessel) Tetramer: 4 protein chains (~145 amino acids) Heme: C34H32O4N4Fe Oxygen molecule 2 atoms Scale & role Image source: http://www.myoptumhealth.com/portal/ADAM/item/Sickle+cell+disease

  20. 1-2-3-4 protein! http://compbio.pbworks.com/w/page/16252897/Introduction-and-Basic-Molecular-Biology

  21. Hemoglobin: what is it? Image source:http://themedicalbiochemistrypage.org/hemoglobin-myoglobin.html

  22. What you’ll learn today • How hemoglobin’s amino acid sequence generates its structure • Why hemoglobin is a tetramer (gang of four)

  23. Todays assignments • 30% Worksheet: easter egg hunt • 60% points hemoglobin tutorial 10% points hemoglobin mini-research

  24. Adam Alice Anders Jillian Karl Montez Blake

  25. Hemoglobin_intro • Turn OFF Wi-Fi; QUIT safari (not close window) • Read... • the instructions on each question... • the instructions on the webpage... • all the words of each question... • Ask yourself: will you be the monkeys at the typewriter, or Shakespeare? • CLOSE EACH PAGE WHEN YOU’RE DONE WITH IT!

  26. On the relative likelihood of accidents...

  27. What specifically would it take for... • A lysine to become a glycine? • To your codon tables! (page 4-8 in lab manual) • How often is that going to happen?

  28. More on your disease! • Get into your Genetic Disease groups • Write up Part 2 of the assignment (view link on course homepage) • FOLLOW THE RUBRIC • Do you remember what disease you have? You should’ve written it down… If not, ask me. • EMAIL ME YOUR ANSWERS: jcumsky@email.arizona.edu • Provide your Genetic Disease Name in Subject

  29. Homework

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