Presentation on theme: "1 ❖ If you have any food issues (allergies, reactions) don’t do any of this, please. I know of no significant risk, but I get paid less whenever someone."— Presentation transcript:
1 ❖ If you have any food issues (allergies, reactions) don’t do any of this, please. I know of no significant risk, but I get paid less whenever someone dies before the drop date. ❖ Use a friend’s observations ❖ Try some diet DP. Record observations; focus on sweetness ❖ Get a ‘lemon or lime kit’. When your mouth is totally free of other tastes, you may ‘suck a citrus’. Leave one section for later!! ❖ Record observations; await further instruction Keep an in-class experiential diary today* *You’ll need it for the homework
2 Oh, the weather outside There’s more to protein folding, structure, activity than just water & amino acid sequence. And it matters.
3 Atom parts ❖ What’s this? ❖ What happens when its electron gets ‘shared’ away? Freeman, Biological Science, Fig. 2-1
4 What happens when you... ❖ go outside and it’s raining? ❖ visit friends with a pet and not much cleaning up? An experimental demonstration of consequence of pH Step I: squeeze a lemon quarter into your mouth. Mmmmm Mmmmm good!
5 A word on nomenclature ❖ Hydrogen concentrations can vary a lot--like, 1,000,000,000,000-fold ❖ Inconvenient! We speak of ‘puissance d’hydrogene’ (‘power of hydrogen’, according to your text) or pH ❖ look to pure water (hydrogen ion concentration molar), extract the exponent (10 -7 ), positivize it & declare ‘pH 7’ ❖ Thus: pH = negative (logarithm of concentration H + ) ❖ i.e. pH = -log[H + ]
6 Causes cause effects ❖ Before: How does it feel as shown? ❖ After entering a proton rich (= ‘low pH’) zone? Consider this region H+H+ ❖ You get a proton! You get a proton! ❖ But it remains probabilistic never all or none
7 Watching H + (from tiny to tons) Fig x 100x 1,000x 10,000x 100,000x 1,000,000x 1/10 1/100 1/1,000 1/10,000 Relative More free H + Rarer free H + Clarity: An acid gives up its pH to become negatively charged, but the solution it’s in gains an H+ !
8 Amino acid balances of power Fig 2.16 Histidine sidechain 50% positive Glutamic acid sidechain 50% neutral Lysine sidechain 50% neutral Alert: This is a poorly thought out color scheme. Protons are more common at the bottom (alas, shown as red)
9 Picking on Histidine ❖ Fill in: while carbon makes __A__ [#] bonds b/c it has __B__ [#] outer shell electrons, nitrogen makes __C__ [#], oxygen _D_ [#] ❖ What are the 2 non-bonding electrons of nitrogen doing? the 2 PAIR of non-bonding electrons in oxygen? ❖ How do those pairs ‘feel’?
10 Sidechain ‘behavior’ Note: the image is linked from the homepage ‘sources’ menu as ‘aa sidechains’ pKa: the concentration of protons (pH) at which 50% of the group in question has an H + on board at pH 7, proton mostly gone. negative charge at pH 6, 1/2 neutral, 1/2 positive: in the balance! at pH 7, proton mostly loaded. positive charge
11 But who cares? Does pH matter? Argument I: Ever heard of ‘the flu’ ? Argument II: What happened to your lemon?
12 First, though... ONCE the lemon sourness gone, suck on your pill. Do not chew; goal is to coat tongue thoroughly
13 Background In the United States, seasonal influenza epidemics typically claim the lives of about 30,000 people each year and cause hospitalization of more than 100,000 (Reid & Tautenberger, 2003). Every two or three years, more virulent strains circulate, increasing death tolls by approximately 10,000 to 15,000 individuals*. These seasonal epidemics are the result of antigenic drift, a phenomenon caused by mutations in two key viral genes due to an error-prone RNA polymerase.*** ***Being small, it can get away with a ‘lesser’ nucleic acid (RNA) as its genome note that inevitable errors actually provide periodic advantage Clancy, S. (2008) Genetics of the influenza virus. Nature Education 1(1) *The one in 1918 killed million worldwide
14 ❖ Virus stick to cell surface protein ❖ Cell engulfs; creating vesicle (‘endosome’; first step in eating) ❖ Cell seeks to destroy by pumping in protons (cell thinks “I will destroy & eat!”) ❖ Virus fuses its membrane with vesicle, releasing genome (RNA) into cytoplasm!!! ❖ You sneeze for a week… or (occasionally) die Outside cell
18 So what? ❖ These are ways to influence a protein from without ❖...and ways for a cell to respond to environment
19 The rest of the demo When the pill is all gone --FIRST, have another swig of that delicious Diet DP! --NEXT try your other lemon slice What’s the difference? What has changed? What can you infer Assertion: pH + one or more histidines + stuff you can think your way through