Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Upcoming❖Molecular World tutorial: due 10 p.m. before your Molecular World tutorial: due 10 p.m. before your lablab❖Atoms+Molecules vocab: dittoAtoms+Molecules vocab: ditto1What was that?❖Science: figuring out; shrinking Science: figuring out; shrinking the Universe.the Universe.❖The Periodic Table… live & in-The Periodic Table… live & in-personperson❖An example of ‘when it clicks’An example of ‘when it clicks’❖Why not Biology?Why not Biology?23FYI…Vocabulary❖bondbond❖polarpolar❖covalentcovalent❖shellshell❖orbitalorbital❖hydrogen interactionhydrogen interaction4Where are we?❖Looked at the Looked at the principlesprinciples behind science & discovery behind science & discovery❖Heading toward the Heading toward the machines that run the cellmachines that run the cell❖Need solid grounding in Need solid grounding in the the piecespieces from which they’re built from which they’re built❖Note that all of biology springs 6 MAJOR atomsNote that all of biology springs 6 MAJOR atoms ( (CC, , HH, , OO, , NN, , SS, , PP) and a sprinkling of others (P, Ca, Mg, ) and a sprinkling of others (P, Ca, Mg, Fe…)Fe…)❖We need We need onlyonly 2-3 simple properties, mainly Lust for 2-3 simple properties, mainly Lust for ELECTRONSELECTRONS5MoleculesMoleculesWhat happens when atoms get togetherWhat happens when atoms get together6Art by Bruce7http://www.green-planet-solar-energy.com/images/neon-bohr.gifWhat’s wrong here?8http://www.green-planet-solar-energy.com/images/fluorine-bohr.gifOK, here?9http://www.green-planet-solar-energy.com/images/oxygen-bohr.gifOoops....10http://www.green-planet-solar-energy.com/images/sodium-bohr.gifMore to the storyMore to the story11Losing one, I become helium-likeSo close!Just 1 more, please!Am I perfect or what?The Bond seriesThe Bond seriesA franchise built upon stupid nomenclatureA franchise built upon stupid nomenclature12A word on words...❖Using them is often handier than pointing & gruntingUsing them is often handier than pointing & grunting❖‘‘bonds’ is not one of those times. Pay attention--the bonds’ is not one of those times. Pay attention--the entire scientific community is seeking to confuse you!entire scientific community is seeking to confuse you!❖‘‘bond’ used for bond’ used for wholly differentwholly different phenomena. I’ll re- phenomena. I’ll re-label some and attempt to be careful in usage. Filter label some and attempt to be careful in usage. Filter carefully!!carefully!!13*There is a general phenomenon where a term in a specific context is VERY different from every day. ‘Theory’ is a classicBond... covalent bond14❖Sharing of electronsSharing of electrons❖Each atom gets to Each atom gets to ‘count’ ‘count’ both both sharedshared electrons towards its electrons towards its goal of eight (two if goal of eight (two if hydrogen)hydrogen)electron collecting: Pieces of Eight15--Hydrogen fills with only two--in all cases, outer shell, not totalFig 2-8SHARING counts the same as HAVING-1-2-3-4+1+2Sharing, and… sharing❖Remember ‘sharing’ toys with friends & siblings?Remember ‘sharing’ toys with friends & siblings?❖Atoms are like that… some of them share ‘not so much’Atoms are like that… some of them share ‘not so much’16❖Let location be your guide❖And handily colored here!Molecule: Four views of WaterH2OHOHSee lab manual, p. 0-5; memorize it.(Study hint:this will be on Big Check #1)++-17These things are real--and they have real shapes18Molecule geometry matters. It’s why snowflakes look like snowflakeshttp://www.its.caltech.edu/~atomic/snowcrystals/photos/photos.htmBond... ionic bond*19Important: Charge interactions are directionless, and can be felt (decreasingly) over a distance.*I’ll use ‘ionic interaction’++--http://www.snohomishcounty.redcross.org/Volunteer.phpheart source:++--It’s a continuum, mon20NiceNaughtyWinner!loserCovalent bonds are all relatively strong.A full outer shell is not something atoms give up lightly!!Nomenclature: those greek deltas signify partial charge: plus-ish, minus-ishBond... hydrogen bond*21❖Note that it’s about (partial) Note that it’s about (partial) chargescharges playing nice playing nice❖in H-bonds, atoms, in H-bonds, atoms, electronselectrons stay with the ones stay with the ones that brung ‘emthat brung ‘em❖They are picky--both distance & geometry (note They are picky--both distance & geometry (note linear arrangement of the 3 atoms in ‘b’linear arrangement of the 3 atoms in ‘b’Cultural referencecauseeffect*We try to use ‘hydrogen interaction’Nomenclature22❖The words kinda suckThe words kinda suck❖The hydrogen is never ‘given away’; the ‘owner’ is The hydrogen is never ‘given away’; the ‘owner’ is the ‘donor’the ‘donor’❖MemorizeMemorize these names & relationships. Really.these names & relationships. Really.Cultural referenceH-bond acceptorH-bond donorThe War with Chemistry:a cautionary tale23❖TheyThey care about a lot more environments than care about a lot more environments than wewe dodo❖Living organisms are 50-95% waterLiving organisms are 50-95% water❖IN WATER, covalent bonds dominate.IN WATER, covalent bonds dominate.❖IN WATER, individual hydrogen bonds count for IN WATER, individual hydrogen bonds count for little (you can always throw over your partner for a little (you can always throw over your partner for a nearby water!!)nearby water!!)❖This is true for ionics as wellThis is true for ionics as wellBond?... hydrophobic exclusion*❖It’s what’s going on when oil & water don’t mixIt’s what’s going on when oil & water don’t mix❖Weird as it is, it really, Weird as it is, it really, reallyreally matters in biology matters in biology❖It is It is notnot about about❖the attraction of two oily thingsthe attraction of two oily things❖anybody being afraid of (phobic of) wateranybody being afraid of (phobic of) water❖It It is is aboutabout❖water’swater’s desire to dance free & grope other waters desire to dance free & grope other waters24*b/c really it’s water indirectly excluding hydrophobic surfaces. And it mattersOil & water25++-Rules vs. Reasons26❖Like