メタボリズム14

Question 1

Metabolic pathways have 3 key characteristics:

Answer 1

1. Irreversible 2. Have an exergonic step that serves as the first committed step and ensures irreversibility. 3. Catabolic and Anabolic pathways involving the interconversion of two metabolites differ in key exergonic reactions.

Question 2

Metabolite

Answer 2

Intermediate or product of metabolism

Question 3

Control of flux in the rate-determining step requires control of enzyme catalyzing it by:

Answer 3

(a) Allosteric control by feedback regulation. (short-term change)
(b) Covalent modification of enzyme, which may decrease or increase its ability to accelerate a reactin. (short-term change)
(c) Substrate cycles in which interconversion of two substrates utilizes different rate-determining enzymes. (short-term change)
(d) Genetic control, which regulates the steady-state levels of the enzyme. (long-term change)

Question 4

phosphoryl group-transfer potential

Answer 4

phosphoryl transfer potential is defined as the ability of a compound to transfer its phosphoryl group

Question 5

Transfer of acyl groups requires their “activation” by

Answer 5

by the formation of a thioester bond to a sulfer-containing compound such as coenzyme A. The hydrolysis of thioesters is about as exergonic as hydrolysis of ATP, thus thioester cleavage drives the otherwise endergonic transfer of the acyl group.

Question 6

ATP can be replenished from ADP by

Answer 6

by transfer of phosphoryl group to ADP from a compound with a higher phosphoryl group-transfer potential

Question 7

Oxidation-reduction reactions are important because:

Answer 7

Redox reactions are the principal source of free energy for life; energy released from catabolic reactions drive anabolic reactions, and the coupling requires free energy transmitters.
In oxidation-reduction reactions, the oxidation of organic compounds (catabolism) is coupled to the reduction of the nucleotide cofactors NAD+ (and NADP+) and FAD (essentially storing energy in the middle-man).

Question 8

The measure of the potential electrical energy in an electrochemical cell is described by the Nernst equation:

Answer 8

reduction potential = standard reduction potential - RT/nF ln(Q)
where Q = [A_red][B n+ _ox] / [A n+ _ox][B_red].
R= gas constant, F = Faraday constant, n=moles of electrons transferred per mole of reactants reduced

Question 9

The reduction potential is related to the free energy change in a redox reaction by:

Answer 9

Change in free energy = - nF * reduction potential

Question 10

Electrons flow spontaneously from a compound with ______ reduction potential to a compound with ______ reduction potential

Answer 10

lower, higher

Question 11

Methods of analyzing a metabolic pathway include:

Answer 11

1. Labeling metabolites with isotopes of certain atoms that can be detected by their radioactivity, or through NMR spectroscopy.
2. Use metabolic inhibitors which inhibit specific enzymes or Induce genetic mutations in enzymes
3. Use DNA microarrays, which are “DNA chips” that can be used to assess how transciptional activity of various genes differs between tissues or at different developmental stages
4. Proteomics, the identification and quantification of all of a cell’s proteins in a given tissue at a given time

Question 12

Nernst equation can be used to determine

Answer 12

whether or not a process involving reduction and oxidation is spontaneous or non-spontaneous under a given set of conditions

Question 13

General redox reaction has form:

Answer 13

A^{n+} (ox) + B (red) = A (red) + B^{n+} (ox)

Question 14

Nernst equation and deltaG equation both tell us:

Answer 14

how far from equilibrium (dG=0) a thermodynamic system is.

Question 15

Biochemical standrad state used in Nernst equation:

Answer 15

25 Celsius, 1 atm, pH = 7.0

Question 16

The delta E^{o’} term in the Nernst equation represents

Answer 16

the position of the reaction under the defined conditions of the system in relation to thermodynamic equilibrium, where dE=0. Convenient reference point.

Question 17

Positive values of the Nernst equation implies

Answer 17

the redox reaction is spontaneous

Question 18

Reduction Potential is defined as:

Answer 18

The more positive the reduction potential, the greater the species’ affinity for electrons and tendency to be reduced.

Question 19

A reaction rate being relatively insensitive to changes in the concentrations of reactant or product substrates, implies the enzyme is:

Answer 19

the enzyme is functioning far from equilbrium, and the enzyme likely catalyzes a rate-determining step of the metabolic pathway.

Question 20

Reactions that lie far from equilibrium in a metabolic pathway have enzymes that are:

Answer 20

enzymes whose activity is controlled by a variety of mechanisms such as allosteric regulation.

Question 21

Removal of divalent cations from ATP would affect dG of ATP hydrolysis by:

Answer 21

Without the shielding effects of the divalent cations, the phosphate groups in ATP would experience more repulsion, hence more unstable, thus more negative dG.

Question 22

What processes maintain the cellular concentration of ATP?

Answer 22

Oxidative phosphorylation, substrate-level phosphorylation, and reactions catalyzed by kinases

Question 23

Substrate-level phosphorylation is:

Answer 23

direct transfer of a phosphoryl group from a “high energy” compound such as phosphoenolpyruvate to ADP

Question 24

“High-energy” compounds such as phosphoenolpyruvate and phosphcreatie do not break down quickly under physiological conditions because:

Answer 24

Even though their breakdown is thermodynamically spontaneous, the kinetics of their breakdown depends on availability and activity of enzymes to catalyze such reactions. Thus, they are stable when enzymes are inactive.

Question 25

Explain how phosphocreatine acts as an “ATP buffer”:

Answer 25

ATP + creatine = phosphocreatine + ADP
The reaction catalyzed by creatine kinase is reversible in the cell.
When ATP is plentiful, phosphocreatine is formed by forward reaction. When ATP is lacking, reaction proceeds in reverse, so phosphocreatine transfers its phosphoryl group to ADP and replenish ATP. The extent of this reaction depends on the concentration of ATP, thus phosphocreatine acts as an “ATP buffer”; it keeps ATP concentration at a nearly constant value.

Question 26

At equilibrium, dG = ? dG^{o’]= ?

Answer 26

dG = 0,
dG^{o’} = -RT ln K_eq,
where Keq = [Product]eq/[Reactant]eq

Question 27

ATP hydrolysis has form _____________

Answer 27

ATP + H2O = ADP + Pi,

Question 28

In exponential form, K_eq =

Answer 28

K_eq = e^{-dG^{o’}/RT}

Question 29

In reduction of a substrate by NADH + H^+, the mechanism is:

Answer 29

Nitrogen in ring of NADH begins arrow pushing, results in nucleophic attack from H bond to the substrate carboxyl group. Then, carbonyl anion grabs H^+.

Question 30

Electrons move from _____ to ____ reduction potential

Answer 30

low to high. obviously since reduction potential is defined as tendency to get reduced(grab more electrons)

Question 31

Voltage between electrochemical cells =

Answer 31

E^o _high - E^o _low

Question 32

If a mutant requires two compounds for growth, then the pathway for synthesis of those two compounds is probably _________

Answer 32

probably branched; both are derived from a common precursor which is lacking in the mutant