bioenergetics Flashcards
what is metabolism?
the sum of all chemical reactions in the cell. a series of related pathways for metabolic pathways, energy producing reactions (catabolism) and energy using pathways (anabolism or biosynthesis)
what are the laws of thermodynamics as they apply to living organisms?
living organisms cannot create energy from nothing. They cannot desert energy into nothing. They may transform energy from one form to another.
the process of transforming energy must increase the entropy of the universe.
what is the relationship between ∆G and Keq?
Keq>1 ∆G’ is -
Keq=1 ∆G’ is 0
Keq<1 ∆G’ is +
this can be explained by the equation ∆G’ = -RTlnKeq
do you know how to couple reactions and see if they are spontaneous?
slide 5 and 6
what does the ACTUAL free energy change of a reaction depend on?
the standard change in free energy ∆G’
actual concentrations of products and reactants Q
∆G = ∆G’ + RTln(products/reactants)
most chemical reactions fall within a few categories (6)
- Cleavage and formation of C-C bonds
- cleavage and formation of polar bonds (Nu substitution, addition-elimination, hydrolysis, condensation)
- Internal rearrangements
- eliminations (without cleavage)
- group transfers
- oxidation-reductions (e- transfers)
what are nucleophiles and electrophiles?
nucleophiles: electron donor, usually negatively charged
electrophiles: attacked by electrons, usually positively charged
what are some examples of nucleophilic carbon-carbon bond reactions?
aldol condensation, claies ester condensation, decarboxylation of a beta-keto acid
slide 10 for mechanisms
what are some group transfer reactions in biochemistry?
proton transfer: very common
methyl transfer: various biosyntheses
acyl transfer: biosynthesis of fatty acids
glycosyl transfer: attachment of sugars
phosphorylation transfer: activate metabolites (and signal transduction)
what reaction produces phosphate esters?
a reaction of a phosphate and an alcohol (or a different nucleophile to get a different result) where the alcohol attacks the phosphate and replaces one of the oxygens. can happen twice to make phosphate diester. see slide 13 and 14
why are phosphate linkage mechanisms important?
convert poor leaving groups to good ones (OH)
stabilize structural elements (RNA and DNA)
increase solubility of hydrophobic molecule (phospholipids)
offer reactive handle to biological catalysis
signaling, enzyme regulation (on/off switch)
lots of energy!
what does phosphatase do? draw mech
transfers phosphate group from phosphate monoester to H20. results in inorganic phosphate (Pi) and an alcohol. goes through pentavalent trigonal bipyramidal intermediate.
slide 19
what is the role of Mg2+ in many reactions?
it is a cation that is essential for charge shielding, charge stabilization, and activation. It interacts with neg charged atoms (like O on phosphates) to allow nucleophilic attack
what does kinase do? draw mech
transfers phosphate group from phosphate monoester to an acceptor other than H2O, usually an oxygen nucleophile but could be nitrogen or sulfur etc.
slide 22
what is an example of phosphoryl transfer via kinase mechanism? think glycolysis
the first step in glycolysis is a phosphoryl transfer from ATP to glucose forming ADP and glucose-6-phosphate
what does mutate do? don’t draw mech, but what is the important thing to remember about this mech?
intramolecular transfer of phosphate group. Mechanism proceeds through a diphosphoenzyme intermediate, meaning that it is not the same phosphate group that is moving positions, but rather the original phosphate is leaving and a new one is being attached at a different position
what does phosphodiesterase do? draw mech
hydrolysis of phosphodiester (eg DNA and RNA backbone). results in phosphate monoester and alcohol.
slide 26
what does nucleotidyltransferase do? draw mech
transfers a phosphate monoester (nucleotides) to organic acceptors. common in adenylation (transfer of AMP from ATP to organic acceptor)
slide 28
why is ATP hydrolysis highly favorable?
- results in better charge separation in products, the neg charges on the O of each phosphate repel each other
- better solvation of products, Pi allows more water to associate and increases enthalpy
- more favorable resonance stabilization of products, Pi can spread neg charges across all 4 O atoms
another very favorable molecule for hydrolysis is phosphoenol pyruvate (PEP), what makes it favorable? is it more favorable than ATP?
- electrostatic repulsion within reaction is relieved (same as ATP)
- products stabilized by resonance and favorable salvation (same as ATP)
- product can undergo further tautomerization, keto-enol. (ATP does not do this)
the tautomerization ability makes PEP even more favorable than ATP hydrolysis
why are reduced organic compounds useful? can you calculate oxidation numbers of atoms to see which is most reduced?
reduced organic compounds serve as fuels from which electrons can be stripped off during oxidation.
slide 32 for oxidation numbers
where do electrons move in oxidation reduction reactions? which molecule is oxidized/reduced?
LEO says GER
losing electrons is oxidation
gaining electrons is reduction
electrons move from the reducing agent to the oxidizing agent
what is reduction potential (E)?
difference in electrical potential between anode and cathode. also measure of the affinity for electrons, higher E is higher affinity
how to tell which agent is electron acceptor and donor from E?
acceptor has the higher E. electrons transfer from lower E to higher E
what is the relationship between ∆E’ and ∆G’?
to get a negative ∆G’ (spontaneous) the ∆E’ must be positive.
∆G’ = -nF∆E’
how to calculate ∆E’?
slide 34, 35
∆E’ = E’(acceptor) - E’(donor)
never change E when reversing reaction or doubling electrons or anything really.
what is NAD and NADP commonly used for?
NAD and NADP are common redox cofactors. formation of NADH (from NAD+) can be monitored by UV spectroscopy at 340 nm. reduced NADH has a curve at 340 while oxidized NADH is flat
what are flavin cofactors (FADH2)?
Flavin cofactors allow single electron transfers (are reduced by a single electron instead of 2) and permit the use of molecular oxygen as an electron acceptor
