Editing 11/13/06

*Exam 2: cofactors through energy charge
**Constants are given

<h2>Transport (continued)</h2>

<h3>Example: ATP ADP Exchange protein</h3>
*On mitochondrial inner membrane
*ATP sent into cytoplasm to be used by the cell.
*We have to pump ATP out and ADP in (so the ADP can be turned into ATP).
*Bonkrekate and Atricate are two poisons that shut down this process
**Bonkrekate competes with ATP on inside of inner membrane to bind in the protein.
**Atricate competes with ADP on outside of inner membrane to bind in the protein.
*Scientists determined how this protein worked partly by cleaving off normal and inverted cristae to observe which side the protein faces and which molecule (ADP or ATP) reacts with each side.
**Cristae are the highly folded surface of the inner membrane.

<h3>Summary of Transport</h3>
*Two models: Mobile Carrier Model, Pore Model.

<h4>Mobile Carrier Model</h4>
*This is the idea that a protein binds its substrate, flips across the membrane and releases the substrate onto the other side of the membrane.
*This is '''not''' how it works.
*Thermodynamically this is nearly impossible and the flip flop rate of proteins is ''way'' too slow.
*Exception: ionophores work this way, though, because they are small (so this only works for very small things).

<h4>Pore Model</h4>
*This is what we've been talking about (see ATP ADP Exchange protein example), and this is how it actually works.

<h2>Bioenergetics</h2>
*Bioenergetics is how a cell can make ATP: the energy currency
*ATP -> ADP + Pi is the reaction that yields free energy to be used.  This is the cleaving off of a terminal phosphate group.
**This reaction gives -7.3 Kcal of energy
**The actual amount of energy depends on conditions of cutting environment (so it isn't always exactly -7.3).
**If the amount of energy given off when drawing energy from a given compound is more negative than -7.3 (e.g. -7.9 kcal) it is a ''high energy'' compound.  If more positive, the compound is called a ''low energy'' compound.

<h3>How do we make ATP</h3>
*Two ways: substrate level phosphorylation, oxidative phosphorylation.

<h4>Comparison of the two methods</h4>
*~6 ATP are made via substrate level phosphorylation in the round of glycolysis and Krebs cycle.
**Anaerobic organisms have only substrate level phosphorylation
**This type occurs twice in gylcolysis and once in the Krebs cycle.
*34 ATP per glucose molecule are made via oxidative phosphorylation. 
*This occurs in the Krebs cycle.

<h4>Substrate Level Phosphorylation</h4>
*There are three of these types of these reactions: one in glycolysis, two in Krebs cycle.
*We have substrates that have more than -7.3 kcal potential energy in them so we break them down to release that energy and put it into making an ATP.

*The three substrate level phosphorylations:
<h5>1,3, diphosphogylcerate</h5>
*Occurs in glycolysis
*1,3, diphosphogylcerate is hydrolyzed via phosphoglycerate kinase to give 3 phosphoglycerate
*Yields -11.8 kcal.
<h5>Phosphoenolpyruvate</h5>
*Occurs in glycolosis
*Hydrolyses Phosphoenolpyruvate via pyruvate kinase to give pyruvate (which goes to the Krebs cycle) and -14.8 kcal free energy.
**Note that there is enough energy to produce two ATP, '''but it doesn't'''.
<h5>Succinyl-CoA</h5>
*Occurs in Krebs cycle.
*Succinyl-CoA -> succinate (succinic acid) via succinyl thiokinase
*Note the thio ester on succinyl-CoA which is the energy residing bond.
*Does not involve direct phosphorylation.
*GDP is phosphorylated to GTP, then the Pi is transferred to ADP to make ATP.
*We have to put Pi on Succinyl-CoA first (no so sure about this...?)


<h4>Oxidative Phosphorylation</h4>
*Here, energy is trapped in bonds (C-O, C-C, C-H); we move this energy into an ATP molecule via oxidizing the C-O, C-C, C-H bonds.
*The most reduced carbons are in alkanes.
*Alkanes are oxidized to alkenes
**Then we add water, so as not to be stuck with a double bond
**This is an hydration, not an oxidation.
**This gives an alcohol.
*We want to transduce energy and we do this in two ways: autotrophic (photosynthesis) and heterotrophic (plants, animals, energy obtained from chemical bonds).
*There are three (3) uses of energy (ATP)
#Mechanical
#Osmotic
#Synthesis
*General mechanism: A + B <-> C + D
**dG = dg' + RTLn([c][d]/[a][b]) 
***dG' is a constant; a characteristic of the reaction; the standard free energy exchange; found in books, can't be changed.
**([c][d]/[a][b]) = Keq so dG = dG' + RTLn(Keq)
***If [a]=[b]=[c]=[d] then Keq = 1 and Ln(Keq) = 0 so dG = dG'
***At equilibrium, dG = 0, so dG' = -RTLn(Keq) == -2.3(1.982x10^-3)*(298K)*Log(10)(Keq)

<h5>Example: dihydroxy acetone phosphate</h5>
*dihydroxy acetone phosphate -> glyceraldehyd 3-phosphate (G3P) via triosphosphate isomerase.
*Test Tube vs. ''in vivo''
**Test tube:
***Keq = products / reactants = G3P / DHAP = Keq = 0.0475
***So the previous reaction goes the wrong way because we want to make G3P for glycolosis!
***dG' = -2.3*RT*Log(0.0475) = +1.8 kcal
**''in vivo''
***Remember that dG' is a constant
***dG = dG' + 2.3*RT*Log ([G3P]/[DHAP]) where glycolosis is depleting the G3P causing the [G3P] to decrease.
***[DHAP] = 2x10^-4 Molar
***[G3P]  = 3x10^-5 Molar
***dG = 1.8 + 2.3*RT*Log(3x10^-5 / 2x10^-4) = 0.07 kcal
****Therefore, the reaction goes forward.

<h5>Two types of Reactions</h5>
*Exergonic (releases energy, dG is < 0, equilibrium constant is > 1) and endergonic (takes energy, dG > 0, Keq < 1)
*Remember that we look at the net dG over the course of a pathway of reactions to know if the pathway will proceed.
*We often see that exergonic reactions force endergonic reactions to occur.

<h3>ATP</h3>
*We don't store ATP, we don't have much in our body at any given time, but we're always cycling through it.
*Found in 1941 by Fritz.
*We have less than 0.1 Mols of ATP, yet we use more than 200 mols per day!
*We consume 88 pounds of ATP per day
**When exercising, we can use up to 1.1 pounds of ATP per minute!
*While running a marathon one can use 140 pounds of ATP!

<h4>The energy of ATP</h4>
*ATP -> AMP + PPi (pyrophosphate) + (-10 kcal)
*ATP -> ADP + Pi + (-7.3 kcal of energy)
*ADP -> AMP + Pi + (-7.3 kcal of energy)
*AMP + H20 -> Adenosine + Pi + (-3.4 kcal of energy)