Exercise planning

Put only TWO numbers on each genome--one for your first child; one for you second

Make it clear we’re staying with RNA genome; no changes to T

Fully disperse the group before having them go to ‘shuffled’ positions

2Anfinsen

A1) each molecule more or less instantly goes to fully correct form. It’s a ‘snowball rolling down hill’ model, where each correct association greatly enhances the subsequent. So my 2nd bond is quicker than your 1st. Predicts precise tracking of disulfides formed vs. achieved activity

3Anfinsen A1

A1) each molecule more or less instantly goes to fully correct form. It’s a ‘snowball rolling down hill’ model, where each correct association greatly enhances the subsequent. So my 2nd bond is quicker than your 1st. Predicts precise tracking of disulfides formed vs. achieved activity

4Anfinsen A2

A2) Only correct bonds form, but with different rates for different bonds--so there is an order and timing of bond formation that is the same for all molecules. So A-A’ might form quickly; B-B’ slowly, etc.

5Deadline = line + dead

deadline |ˈdedˌlīn|noun1 this definition not relevant2 historical a line drawn around a prison beyond which prisoners were liable to be shot.

think about it

Does it really make sense to designate that period at the end as the target as opposed to that at the

beginning?

Is it really the case that your schedule is such that all available times just happen to fall at the last minute?

66

Beating TamifluBeating TamifluThemes:

Evolution: then and nowamino acids, mutations, folding: they

matter

Themes: Evolution: then and now

amino acids, mutations, folding: they matter

7How evolution happens

• Good ideas are rewarded not sought/planned

• There’s no mechanism for foresight, so it cannot be that way

8How the flu happens

http://www.ch.ic.ac.uk/local/projects/sanderson/images/lifecyc.gif

9Just passin’ through

http://www.ch.ic.ac.uk/local/projects/sanderson/images/lifecyc.gif

10

Just passin’ through

http://www.ch.ic.ac.uk/local/projects/sanderson/images/lifecyc.gif

11

Just passin’ through

http://www.ch.ic.ac.uk/local/projects/sanderson/images/lifecyc.gif

12Midterm

• There will be one

• Periodic Table, Hemoglobin, DNA, proteins, Anfinsen

• Study TOPIC guide will appear

• Oct. 18

13

Tamiflu: you shall not pass!

http://en.wikipedia.org/wiki/File:Oseltamivir-3D-balls.png

a.k.a. oseltamivir

14

And it goes like this...

http://www.ks.uiuc.edu/Research/influenza/

Note: this is modeled, not a crystal structure

15Fluorescence

http://web.uvic.ca/ail/techniques/epi-fluorescence.html

Scorpion Scorpion glows in glows in the dark!the dark!

16

Cell sorting

• Laser is like a black light--molecules GLOW a different color than they are being hit with

• In our case, GFP (green) and cherry (you guess)

17

GFP: paint by numbers

Tsien lab GFPs!

“Inward-facing sidechains of the barrel induce specific cyclization reactions in the tripeptide Ser65–Tyr66–Gly67 that induce ionization of HBI to the phenolate form and chromophore formation. This process of post-translational modification is referred to as maturation.[22] The hydrogen-bonding network and electron-stacking interactions with these sidechains influence the color, intensity and photostability of GFP and its numerous derivatives.”

Not the words, but the sense

--Wikipedia, “GFP”

*

18Shadowboxing

http://www.whudat.de/shadow-sculptures-made-of-rubbish-12-pictures/

19What you’ll see

‘illuminated’ from left shows

how much green

‘illuminated’ from below shows how

much red

20Vocab & Paper

• This is a challenge--and I’m not ashamed of that

• Challenges require a combination of EFFORT and THINKING

21Phylogenetic trees

• Participants: to your spot on the tape!

• Observers: watch & predict outcome and what it’s good for

Each round:Copy any changes your parent already hasDetermine position of your new change by adding #s (0 = none)Randomly change to new base & mark (A, G, C, U)Turn to your kids & repeat

22Derived rules

• Better ‘trees’ = trees with the fewest total changes from neighbor to neighbor

• We can infer missing ancestors by comparing the kids

• Older mutations appear in more of the children (and all of the children derived from the initiator

23

Which makes sense?

Or this?Or this?Or this?Or this?

2424

SupplementalSupplementalStuff you might find usefulStuff you might find useful

25Supplemental

• Cartoon of infections & tamiflu action (contr. Katie F12)

• http://www.youtube.com/watch?v=0qCTyKrhVWc

26

27Now what???

What information allows you to make good inferences about who is most related?

Who gave rise to whom?

28How about this?