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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.

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Presentation on theme: "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."— Presentation transcript:

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 2 From strings to blobs How?Why?

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 3

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 4

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... 5

6 How does it feel? 6

7 7 http://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 8

9 If THIS is true… Pencils made of…. http://www.nano- enhanced-wholesale- technologies.com/faq/carbo n-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 11

12 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 13

14 14 How does yours compare? 14

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

16 Images of 3D 16 Q. 4

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

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

19 19 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

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

21 21 Hemoglobin: what is it? Image source: http://themedicalbiochemistrypage.org/hemoglobin-myoglobin.html 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) 22

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

24 24 Karl Jillian Alice Blake Adam Anders Montez

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! 25

26 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? 27

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.edujcumsky@email.arizona.edu Provide your Genetic Disease Name in Subject 28

29 29 Homework

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