bioenergetics

Question 1

what is metabolism?

Answer 1

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)

Question 2

what are the laws of thermodynamics as they apply to living organisms?

Answer 2

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.

Question 3

what is the relationship between ∆G and Keq?

Answer 3

Keq>1 ∆G’ is -
Keq=1 ∆G’ is 0
Keq<1 ∆G’ is +
this can be explained by the equation ∆G’ = -RTlnKeq

Question 4

do you know how to couple reactions and see if they are spontaneous?

Answer 4

slide 5 and 6

Question 5

what does the ACTUAL free energy change of a reaction depend on?

Answer 5

the standard change in free energy ∆G’
actual concentrations of products and reactants Q
∆G = ∆G’ + RTln(products/reactants)

Question 6

most chemical reactions fall within a few categories (6)

Answer 6

1. Cleavage and formation of C-C bonds
2. cleavage and formation of polar bonds (Nu substitution, addition-elimination, hydrolysis, condensation)
3. Internal rearrangements
4. eliminations (without cleavage)
5. group transfers
6. oxidation-reductions (e- transfers)

Question 7

what are nucleophiles and electrophiles?

Answer 7

nucleophiles: electron donor, usually negatively charged
electrophiles: attacked by electrons, usually positively charged

Question 8

what are some examples of nucleophilic carbon-carbon bond reactions?

Answer 8

aldol condensation, claies ester condensation, decarboxylation of a beta-keto acid
slide 10 for mechanisms

Question 9

what are some group transfer reactions in biochemistry?

Answer 9

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)

Question 10

what reaction produces phosphate esters?

Answer 10

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

Question 11

why are phosphate linkage mechanisms important?

Answer 11

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!

Question 12

what does phosphatase do? draw mech

Answer 12

transfers phosphate group from phosphate monoester to H20. results in inorganic phosphate (Pi) and an alcohol. goes through pentavalent trigonal bipyramidal intermediate.
slide 19

Question 13

what is the role of Mg2+ in many reactions?

Answer 13

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

Question 14

what does kinase do? draw mech

Answer 14

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

Question 15

what is an example of phosphoryl transfer via kinase mechanism? think glycolysis

Answer 15

the first step in glycolysis is a phosphoryl transfer from ATP to glucose forming ADP and glucose-6-phosphate

Question 16

what does mutate do? don’t draw mech, but what is the important thing to remember about this mech?

Answer 16

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

Question 17

what does phosphodiesterase do? draw mech

Answer 17

hydrolysis of phosphodiester (eg DNA and RNA backbone). results in phosphate monoester and alcohol.
slide 26

Question 18

what does nucleotidyltransferase do? draw mech

Answer 18

transfers a phosphate monoester (nucleotides) to organic acceptors. common in adenylation (transfer of AMP from ATP to organic acceptor)
slide 28

Question 19

why is ATP hydrolysis highly favorable?

Answer 19

1. results in better charge separation in products, the neg charges on the O of each phosphate repel each other
2. better solvation of products, Pi allows more water to associate and increases enthalpy
3. more favorable resonance stabilization of products, Pi can spread neg charges across all 4 O atoms

Question 20

another very favorable molecule for hydrolysis is phosphoenol pyruvate (PEP), what makes it favorable? is it more favorable than ATP?

Answer 20

1. electrostatic repulsion within reaction is relieved (same as ATP)
2. products stabilized by resonance and favorable salvation (same as ATP)
3. product can undergo further tautomerization, keto-enol. (ATP does not do this)
   the tautomerization ability makes PEP even more favorable than ATP hydrolysis

Question 21

why are reduced organic compounds useful? can you calculate oxidation numbers of atoms to see which is most reduced?

Answer 21

reduced organic compounds serve as fuels from which electrons can be stripped off during oxidation.
slide 32 for oxidation numbers

Question 22

where do electrons move in oxidation reduction reactions? which molecule is oxidized/reduced?

Answer 22

LEO says GER
losing electrons is oxidation
gaining electrons is reduction
electrons move from the reducing agent to the oxidizing agent

Question 23

what is reduction potential (E)?

Answer 23

difference in electrical potential between anode and cathode. also measure of the affinity for electrons, higher E is higher affinity

Question 24

how to tell which agent is electron acceptor and donor from E?

Answer 24

acceptor has the higher E. electrons transfer from lower E to higher E

Question 25

what is the relationship between ∆E’ and ∆G’?

Answer 25

to get a negative ∆G’ (spontaneous) the ∆E’ must be positive.
∆G’ = -nF∆E’

Question 26

how to calculate ∆E’?

Answer 26

slide 34, 35
∆E’ = E’(acceptor) - E’(donor)
never change E when reversing reaction or doubling electrons or anything really.

Question 27

what is NAD and NADP commonly used for?

Answer 27

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

Question 28

what are flavin cofactors (FADH2)?

Answer 28

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