biochem study guide 3

evan406's version from 2016-04-18 03:42


Question Answer
ΔG° and ΔG°’

G°: Standard conditions; 298 K, 1 atm, 1 M concentration

ΔG’°: Biological conditions; when H2O, H+, and/or Mg2+ are reactants or products, their concentrations are not included in the equations, but are instead incorporated into the constants K’eq and ΔG’°.
High energy compounds and the phosphoryl transfer potentialThe transfer of a phosphoryl group to a compound effectively puts free energy into that compound, so that it has more free energy to give up during subsequent metabolic transformations
Why is ATP a “high-energy compound” under cellular conditions?1) The charge separation that results from hydrolysis relieves electrostatic repulsion among the four negative charges on ATP.

2) The Pi is stabilized by formation of a resonance hybrid

3) The product ADP2- immediately ionizes, releasing a proton thus increasing the entropy of the system.

4) The ΔG’° value is highly dependent on concentration of ATP, ADP, Pi, pH and Mg2+. Deviation from standard condition causes the value of ΔG’° to be more negative.

5) A greater degree of solvation of the products Pi and ADP relative to ATP, stabilizes the products relative to the reactants.
What are anabolic and catabolic pathways?Catabolism is the degradative phase of metabolism in which organic molecules are converted into smaller, simpler end products. Catabolic pathways release energy.

In anabolism small, simple precursors are built up into larger and more complex molecules. Anabolic reactions require an input of energy.


Question Answer
What is gluconeogenesis, and what useful purposes does it serve in people?Gluconeogenesis is the biosynthesis of glucose from simpler, noncarbohydrate precursors. During periods of fasting, when carbohydrate reserves have been exhausted, gluconeogenesis provides glucose for metabolism in tissues that derive their energy primarily from glucose metabolism.
How is gluconeogensis different from glycolysis and why?Three steps of the glycolytic pathway are different:
1) conversion of glucose into glucose 6-phosphate
2) conversion of fructose 6-phosphate into fructose 1,6-bisphosphate
3) conversion of phosphoenolpyruvate into pyruvate

Glycolysis is exergonic mainly due to these three irreversible steps.

In gluconeogenesis these three steps have to be catalyzed by other enzymes.

In glycolysis an ATP is consumed in step 1 and in step 2. To make the reverse process energetically favorable the reaction are uncouple from ATP synthesis and a single Pi is released instead.

In step 3 in glycolysis an ATP is produced. To make the reverse step possible an ATP and a GTP are hydrolysed to put in additional energy and make the step energetically favorable in the opposite direction.
Regulation of glycolysis/gluconeogenesisFructose-6-phosphate activates PFK-2 and inhibits F-2,6-BPase

The production of F-2,6-BP stimulates glycolysis by allosteric activation of PFK-1 and inhibits gluconeogenesis by allosteric inhibition of F-1,6-BPase

Phosphorylation by cAMP-dependent protein kinase inhibits PFK-2 activity and stimulates F-2,6-BPase activity
Function of the PFK-2/F-2,6-BPase enzymeSynthesis and degradation of fructose-2,6-bisphosphate are catalyzed by this enzyme


Question Answer
Synthesis of glycogenGlycogen synthesis start with the activation of glucose to UDP-glucose, a reaction catalyzed by UDP-glucose pyrophosphorylase.

Glycogen synthase uses UDP-glucose as a substrate and adds the glucose units to the growing glycogen chains.

Branches are introduced by the enzyme amylo(1,4→1,6)-transglycosylase (branching enzyme).

The enzyme transfers a six- or seven-residue segments of a growing glycogen chain to the C-6 hydroxyl group of a glucose residue on the same or a nearby chain.
breakdown of glycogenGlycogen breakdown start with the enzyme glycogen phosphorylase.

It cleaves glucose from the nonreducing ends of glycogen molecules and forms glucose-1- phosphate.

It can only do that with the long chain and leaves limit dextrans behind that have to be broken down by the debranching enzyme.

In the first step (oligo(α1,4→α1,4) glucanotransferase activity) a trisaccharide group from a limit branch is transferred to the end of a nearby branch.

The remaining single glucose unit from the branch is subsequently cut off (α(1→6) glucosidase activity).

The glucose-1-phosphate produced is converted into glucose-6-phosphate by phosphoglucomutase.
Regulation of glycogen synthesis and breakdown
Regulation of glycogen synthase
Regulation of glycogen phosphorylase

Pentose Phosphate Pathway

Question Answer
Regulation of the pathway (NADPH)/use of different pathways to address cellular needsWhen both ribose-5-phosphate and NADPH are needed by the cell, the first four reactions of the pentose phosphate pathway predominate. NADPH is produced and ribose-5-P is the principal product of carbon metabolism.

When more Ribose-5-phosphate is needed than NADPH, the oxidative reactions of the pentose phosphate pathway are bypassed. Withdrawal of fructose-6-phosphate and glyceraldehyde-3-phosphate from glycolysis and conversion into ribose-5-phosphate via a reversal of the transketolase and transaldolase reactions.
Role in redox homeostasis, role of glutathione, and of glutathione reductase.