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Notes from Meeting with Bio Faculty

Page history last edited by Ben Dreyfus 8 years ago

Notes from 1/31/2012 meeting with intro bio faculty

Joe's Audio: InterdiscMeeting 1-31-12-Audio.mp4


Wow, BD's notes are a lot better than mine. I've got generalities. I'm putting them at the bottom of this page. - VS


Present:  Joe Redish, Joelle Presson, Chandra Turpen, Ben Geller, Vashti Sawtelle, Kaci Thompson, Ben Dreyfus, Arthur LaPorta, Arnaldo Vaz, Mike Keller (lab coordinator, BSCI 105), Richard Payne (teaches cell bio, neurophys), John Buchner (lecture faculty in CBMG, teaching intro micro and genetics 412), Lee Friedman  (lecture faculty in biochem), Bonnie Dixon (organic chem and gen chem), Patty Shields (course coordinator for genetics; teaches 105), Spencer Benson (105)

Via Skype: Julia Svoboda, Wolfgang Losert


(BD in these notes is Bonnie Dixon, not Ben Dreyfus)


BD:  no Gibbs in chem 131, only in 271.

LF:  in 131, heat transfer and enthalpy, from calorimetry standpoint, potential energy stored in bonds.  Gibbs and entropy introduced in 271.

JR: Potential energy stored in bonds?

LF : in chem, energy is stored in bonds.  put atoms together, release energy.

JR: But that sounds like the opposite.

LF: yeah, i know what you're saying.


PS: it's a waste to wait until senior year to take this!

CT: coordinate with counselors


MK:  in 105 we all teach the same material, but focus on different things to different degrees.  enthalpy, Gibbs free energy, metabolism, bidirectional, why you need enzymes, energy of activation.  free energy diagram - here's what an enzyme is doing.  how do enzymes make things go - they don't change the laws of thermo.  a lecture on energy.  change in free energy.  how many calories stored in glucose molecule, but that leads to misconceptions.  enthalpy is just there to lead to delta G.

JR: is this in the textbook?

PS: yes, Campbell textbook, chapter on energy.  students can't wrap their heads around negative value in delta G, or negative enthalpy, or increasing entropy.  it blows their minds.  many moons ago, tried deriving from formulas, but it was too much for them.

JR: this is what we want to do.  my students have issues with negative PE, binding energy, so we've written this series of problems to work them through it.

PS: changing my whole approach to teaching entropy.

MK: just getting to the negative and positive.

JP: context in metabolism?

PS: breakdown of molecules, buildup of molecules.  they see these as violations of laws of thermo, since they don't see that it's about universe (not system under consideration).  get into systems.  picture in textbook (Campbell p. 147)

MK: students are confused by extracting energy from breaking down molecules.  ATP - why it's so valuable and funky.  they've learned about electronegativity, why oxygens don't play well together.  why do we need ATP, why can't we just burn sugar.

PS:  coupling (p. 150, figure 8-10) - breakdown of ATP to take positive and turn overall reaction into negative delta G.

LF: glycolysis?

PS: here, making an amino acid.

BD: we only talk about enthalpy, but we use reaction coordinate diagrams, it would help to use a common language.  exothermic = more stable in the end.  I don't say going down, going up, just more stable, that's why energy is released.

PS: we talk about exothermic and endothermic, but common terms would be great.

JR: if we can use the same language, that's a goal of the project, to learn your language.

JP: do you say negative delta G?

BD: yes, but we don't focus on the sign, just on exo vs. endo.

LF: I focus on the sign, we calculate delta S, etc.


RP: Still on enthalpy.  In 300-level course, delta H is in terms of change in chemical reaction, not about energy being stored, negative delta H = energy to break bonds < energy released by making bonds.  stability.  phosphate in ATP reaction.  confusion b/c switching from language of bonds made/broken to language of stability.

LF: I hate the word stability.  I ask students why does a reaction happen, they say products are more stable than reactants.  Duh.  That's why anything happens.  Common language is ok as long as we get into why the words are there.

JR: see the physical system, not a string of words.


WL: in chem/bio, are phosphorylation and ATP introduced at macro or molecular viewpoint?

JP: what do you mean? we don't use those words

WL: do you draw the molecule?  or a reaction equation?

RP:  molecular concept.  ATP molecule is drawn out.  opposing negative charges in tail, phosphate has resonance structure that allows double bond to rotate among hydroxyl groups so it's stable.  micro perspective.  BUT free energy change that ATP generates -- free energy is measure of amount of work a biological reaction can perform.  2nd law tells you which way a reaction can proceed spontaneously, and how much work it takes.  coupled reactions, pumping ions across a membrane.

WL: chemistry model of bonds to introduce how ATP works?

RP: yes

PS: I introduce that high-energy phosphate bond, with other high-energy phosphate molecules?

JR: does high-energy mean weakly bound, or strongly bound?

PS: breaking bond yields energy

JR: but breaking bond takes energy

RP: you create something more stable

LF: if you have ATP in a vacuum, it will stay intact and you have to put in energy to break the bond.  but here it releases energy.

JR: how?

RP: periodic table

JR: you're binding those parts to something else.

BD: you still have to put energy in, and you get other energy out.

JR: further down to more strongly bound state.  it's not the bond, it's what it goes to.

LF: activation barrier

JR: so by high-energy bond you mean more weakly bond than what it's going to.

all: yes.

BD: you have to look at whole system, not just that bond.

MK: this confuses the students.  energy put in at step where you break that phosphate, you get more out of it.

PS: that energy can drive a cellular system

SB: in bio systems, this is driven by enzymes, not in free solutions.

PS: that phosphate stays as inorganic phosphate, until it's bound to another ADP.

JR: does it bind to something else? and that gives you the energy?

PS: no

ALP: water in solution

LF: electrons in phosphate. there's an activation barrier

JR: attraction

LF: confusing me with your language.

JR: activation energy makes me think of a metastable state.  not truly bound, but can go to something deeper

MK: i talk about ATP as a player.  we talk about phosphorylation, destabilizes.  oxygen-rich.  transferring from one molecule to another, altering entire molecule's stability.

JR: going to more stable state, get energy out

all: ehhh, I don't know.

MK: you need energy to snap that bond, but oxygens repel each other, so it lowers the activation energy and doesn't take much to snap that bond.

BD: JR's point is about the language - in bio, people don't know what "high-energy bond" means.  like in chemistry "resonance energy" is a misnomer, since it's the stability that resonance brings.

PS: we should stop saying high energy bond.  what should we say instead?

JP: it's used in relation to ATP.

LF: weak bonds in chemistry that are easily broken.  peroxide, O-O.

JR: explosives?

LF: yeah.  high-energy.


LF: it's a weak bond. with ATP you're forcing things that don't want to be together together. 

LF: but not metastable - that sounds like it's on the verge of falling apart

MK: you can have powdered ATP sitting on your shelf indefinitely

RP:  "high-energy bonds" is used specifically for ATP, like one of those newspaper stories.  NADH is an energy carrier that works totally differently - redox reaction.  when oxidized, releases 4x energy as ATP.  56 vs 7 kJ.  and sugar, on table won't go anywhere.  but free energy is released when sugar is oxidized.

MK: we put this up front with

BD: doesn't metabolism go up a few steps then start running down?

RP: activation energy and free energy change have very different consequences.  can't use activation energy to do work.  free energy change can be used to do work.  change activation energy -> don't change equilibrium.  can't get energy out of enzymes.  application of energy to equilibria, we do in 300-level courses.

MK: we do too.  we use these as stepping stones to oxidative respiration.

JR: when i ask, they're not familiar with the basics.


JR: what does reaction coordinate mean?

ALP: that's from physics

BD: progress of reaction as bonds are broken, to transition state, and bonds are formed

ALP: just parameterizes going from here to there.

LF: just plotting activation energy, etc., numerically

JR: so particular slope has no meaning.  axis has no units.

LF: not technically true - if you go into transition state theory, rxn coord has some parameter like bond length. people think of it as a movie.  early vs late transition state.  not arbitrary.

JR: what units on axis? distance?

ALP: distance

MK: time

BD: degree of bond formation

JR: if it's distance, i can make sense of that.

ALP: reaction rate is well-modeled as diffusion on that landscape.


JR: we think of molecule in frictionless vacuum

LF: molecules in solvent stabilize transition state.  if it's in a vacuum, rxns wouldn't happen fast enough.

ALP: when you say physicist, you mean particle physicist

WL: ditto

RP: there are desperate fudges.  ditching chemical activities, replaced by concentration.

LF: i tried doing that with my students, it was a disaster.  should have just taught concentrations.  most of the time, you can get away with that.  too complicated.  not in the textbook.

MK: students look at it as you have a million molecules, in the middle half have gone through reaction, at the end all have.

PS: or "and then a miracle happens".

MK: a single molecule, they would expect it to go ka-chunk.  they're thinking bulk reaction perspective.

ALP: single-molecule perspective might be helpful.  model of protein folding or rxn, thermal fluctuations.

RP: disadvantages: omitting the solvent comes back to bite you.  students think any rxn involving formation of macromolecule involves decreasing in entropy, increase in order.  not necessarily, if in making the polymer you throw out water.

JP: we're doing that problem this week with membrane formation!


JR: entropy in 105: how?

MK: with evolution, you can't violate entropy.  at the beginning, how do you recognize if something is alive.  increasing/decreasing order.  living organisms are good at increasing entropy on a universal scale.  in the process of making things, we're creating a lot of chaos.

JR: you're using language of entropy as measure of order.

MK: entropy as global measure of order.

JR: not Q/T

PS: no way

LF: that's what i do, in 271.  To get to thermo law, i introduce chemistry like most intro chemistry texts - maximizing probability of distribution of molecules across some system.  2 boxes, 4 molecules, most likely state is 2+2.  then apply that to a larger thing.  then delta S = Qrev/T, reversibility.

JR: then how do you get to T delta S?

MK: see this, don't worry about it.

RP: i stay clear of what entropy is.

MK: i say they'll learn it in chemistry.

RP: the price you have to pay.  make and break bonds, and if you keep delta G negative overall, you can decrease your entropy.  this is what organisms do for a living.  they throw heat out.

PS: heat is the big thing.

MK: heat as a waste product.

JR: increasing entropy of world

MK: even though you're building something, you give off heat.

SB: people use "systems" across all of these, and students can't do that.  everyone calibrated to that system, students can't.

JR: we do this even when we're doing Newton & forces.

MK: some cool molecules.  ATP, all the things to unwind DNA then it self-assembles again.  hydrogen bonding we talk about 8000 times.  hydrogen bonding rules 105.  base-pairing just happening blows their minds.

RP: whole discussion of dynamics, not encouraged by textbooks.

WL: any discussion of emergent properties in 105?

everyone: yeah

MK: why can't i predict what a peptide will do?

WL: in a physics class, simple examples of emergent properties?

MK: yes.  self-assembly.

JR: we brought it up with diffusion.

MK: tubulin

ALP: paradox of high-energy bond would go away if you say high-energy state.  (nodding in the room)

MK: yeah b/c high-energy bond sounds like it should take more energy to break.



VS Notes:


People I don't know:

Arthur Laporta – biophysics single molecule

Mike Keller – lab coordinator for Bio

Richard Payne – cell bio, neurophysiology research in phototransduction

John Bachner – lecture faculty in Cell Bio Molecular Genetics (CBMG)

Lee Freedman – intro sequence

Bonnie Dixon – biochem, organic and general chem

Wolfgang Losert – faculty in biophysics, in the fall he’s going to teach

Patty Shields – course coordinator for genetics, teaches Bio 105 (freshman)

Spencer Benson – 105 – intro bio, director of center for teaching excellence


Open discussion on the way the biologists/chemists use discuss entropy, enthalpy, Gibb’s: 10 – 15 minutes of background on what we’ve done.


131: no Gibb’s but they do in 271


Broken gen chem into 2 semesters and put orgo in the middle


Intro chem: enthalpy & heat transfer from a calorimetry perpesctive. In chemistry we put the energy in bonds. In chem 4 is where they get to Gibb’s.


Patty Shields – doesn’t want this course to be done in the senior year of college. Likes that we’re targeting sophomores and juniors.


Mike Keller – in 105 (intro?)

-                    talk about enthalpy, Gibb’s free energy. Metabolism and directionality. Why things are spontaneous.

-                    What the role of enzymes play. (Lots of agreement from the faculty that students have trouble with this.

  • o    (free energy diagrams – what are these?).
  • o   Particularly what are enzymes for. It’s not changing the role of thermodynamics.

-                     Lecture on energy = why are somethings “negative” (wait! he just used free energy so maybe when he says energy is he thinking free energy?)

-                    talk about enthalpy mostly to get to delta-G, gateway to metabolism

-                    Really focusing on the “negative” and on increasing entropy

  • o   “just sort of throw it up there” (don’t know what “it” is, entropy?), because students really struggle with these ideas

-                    Context of metabolism: the break down of molecules,

  • §  The buildup of molecules and the breakdown of molecules must violate the laws of thermodynamics
  • §  Going back to systems
  • §  Harp on these diagrams (pg 147 in Campbell’s)
  • o   Proposed example
    • §  You can extract energy from breaking bonds, and the example they go to is ATP
    • §  Why do we need ATP, not just sugar?
    • §  (pg 150) is another figure, to beat them over the head with


-                    Talk about entropy (?) through enthalpy

-                    Common language: when something is exothermic it’s more stable than it was (**it’s more stable**) so it releases energy when it’s exothermic

  • o   **Biologists say they do endo and exo too

-                    Don’t focus as much on the sign, b/c it just says endo or exo (so neg is exo?)

  • o   ??, they do a lot of the entropy calculation when they’re thinking about delta-G from an entropy perspective


Enthalpy (Richard Payne)

-                    delta H, comes in terms of the change, he makes a statement I didn’t quite catch, but everyone seems to agree it’s correct

-                    stability: phosphate, flicker of confusion, switching between bonds being formed and broken, confusion

  • o   The other chemist makes a bid for avoiding the “stability” because he doesn’t want it to just be an automatic


Wolfgang: Chemistry/Biology phosphorylation of ?? is it done on the micro or macro model that is introduced?

-                    Draw the molecule? Or draw a reaction equation

-                    For ATP it’s introduced as a molecular concept (ATP is drawn out with the opposing charges on the tail) something about hydroxyl or something or other

  • o   BUT the delta-G (the measure of the amount of work that a reaction can perform – everyone is nodding) it tells you how which way a reaction will proceed spontaneously, but it also tells you how much work can be used for work from that reaction

-                    “high energy phosphate bonds” and now thinking about “phosphate bonds”

  • o   If you have a molecule of ATP in a vacuum, then you’d have to put energy in, but ATP doesn’t exist in a vacuum
  • o   Can’t just look at the one bond (the energy that you put in to break off that original phosphate, you get back more when go and bind it with the other one)
  • o   In Bio this is also being driven by enzymes. Payne is saying no, no.

-                    Chemist says: that’s why we talk about delta-G and delta-H


Chem - Resonance energy: the amount of stability that resonance bring


High energy bond: the change in the energy from what you put in and then you get back out when the process is finished, mostly used for ATP and other high-energy phosphate molecules


Weak bonds in chemistry that are easily broken bonds


NADH – oxidation releases energy (free energy), the free energy that’s released when it’s oxidized


Activation energy and the free energy change. The free energy change can be used to do work. But when you change the activation energy it doesn’t do anything to change the equilibrium. But you can’t get energy out of enzymes.


The application of free energy to enzymes is in the 300 level biology.




Question about the representation (the hill, with the reaction cooling in the middle) – the progress of free energy change as the reaction progresses (b/c the reaction the really doesn’t happen in steps, it happens all at once), horizontal axis is the bond distance

- Bowl of sugar: a million molecules of something, you get the reaction going, and then it’s just a miracle happens and the rest go


The solvents are important in chemistry b/c they are what stabilize the intermediates in the reactions

-                    Omitting the solvent comes back to bite you

-                    Students start to believe that when you create bonds, you must be decreasing the entropy


“Activities” get ditched in preference of concentrations – most of the time you can “get away with” concentration


In 105 entropy: (both biologists nod at this)

-                    evolution and violate entropy

-                    expectation of increasing/decreasing order, and living organisms are great at “increasing disorder” chaos, disorder


In Chem (?) 271 entropy, maximizing probability. Molecules in boxes. And then they do reversibility and S = Q/T


Bio: stay clear of what entropy is. Stop at the concept of free energy. Entropy is a component of a free energy change. It’s an inconvenience. Something you have to deal with. Making and breaking bonds, (delta-H) and so if you can keep the delta-H high enough, then you can decrease entropy.


Spraying out the heat is the way of increasing the entropy of the universe. Heat happens. That’s the way we can talk about this. The system is an important piece of this.


“Energy” = enthalpy = gibb’s = heat


System identification! Needs to be more important.


Unwinding DNA, and then it goes back together again. Heat flow.


A discussion of dynamics. The textbooks don’t help. Because they show blobs.


Emergent properties = enzymes, experiments to determine what a protein does.


They say “self-assembly” and “emergent properties” could be brought up more.



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