Unit 10

Question 1

Define bioenergetics.

Answer 1

The quantitative analysis of how organisms gain and expend energy as described by thermodynamics.

Question 2

Distinguish between catabolic and anabolic pathways.

Answer 2

Catabolism - break down, degrade molecules. Generally convergent (Ex: Many different molecules - glucose, fats, proteins - can be broken down to give acetyl CoA)
Anabolism - biosynthestic processes. Generally divergent (Ex: many biomolecules synthesized from single basic building block, Acetyl CoA)

Question 3

Define metabolism.

Answer 3

The sum of all transformative chemical processes taking place in an organism.

Question 4

Name and define each of the terms in: ΔG = ΔH - TΔS.

What units are used for each of these terms?

Answer 4

ΔG = change in Gibbs Free Energy or the amt. of energy available to do work in a system (joules/mole).
ΔH = change in Enthalpy or amt of energy stored in chemical bonds (joules/mole).
T = absolute temperature = measure of average heat in a system (Kelvin).
ΔS = change in Entropy or disorder of the system (joules/mole*K).

Question 5

Distinguish between ΔG, ΔG°, and ΔG’° .

Answer 5

ΔG = the ACTUAL change in free energy that, taking in to account the standard change and the given concentration of products and reactants, determines the free energy released (spontaneous) or sequestered (non spontaneous) in a reaction.
ΔG° = Standard Gibbs of rxn under 1 atm, 273 K, and 0 pH (standard conditions.)
ΔG'° = Standard Transformed Gibbs for a reaction occurring under biological standard conditions (1 atm, 273 K, and pH of 7).

Question 6

What is the sign of ΔG’° when the reaction proceeds in the written direction?

Answer 6

Forward driving force = negative ΔG’°.

Reverse driving force = positive ΔG’°.

Question 7

What is the relationship (both mathematical and conceptual) between ΔG and ΔG’°?

Answer 7

ΔG = ΔG’° + RT ln ([C][D] / [A][B]).
The actual change in free energy determines the driving force direction when the system does not start with 1M products to 1M reactants (as in the standard free change). Standard free change is a constant for that reaction based on the Keq that through the above equation, allows the actual free energy change to account for the equilibrium point that the system will be driven towards.

Question 8

Compare the free energy content of acid anhydride and ester bonds.

Answer 8

Ester bonds - relatively low free energy content in comparison to anyhydride (~ -15 kJ/mol vs. ~ -30 kJ/mol in ATP).

Question 9

Which term in the Gibbs equation can be used to predict whether a reaction will proceed?

Answer 9

ΔG.

Question 10

What does ΔG tell you about the rate of the reaction?

Answer 10

NOTHINNNNN

Question 11

What affect do enzymes have on ΔG?

Answer 11

No effect. ΔG purely depends on the ratio of products to reactants and the standard free energy constant for that specific reaction.

Question 12

Give at least two reasons why ΔG’° is such a large negative number (ca. -30.5 kJ/mol) for the reaction: ATP + H20 → ADP + Pi.

Answer 12

1) relief from strain of many close together negative charges.
2) released Pi group stabilized by resonance.

Question 13

Although the free-energy change for ATP hydrolysis is -30.5 kJ/mol, ATP is kinetically stable in water in the absence of enzymes. Suggest why.

Answer 13

The reaction may occur spontaneously thermodynamically, but there is a large energy barrier for the transition energy to initiate the reaction without the assistance of hydrolyzing enzymes to lower the reaction energy. The kinetics are limiting for this reaction.

Question 14

What is the relative amount of energy contained in thioester bonds (eg. acetyl CoA) and acid anhydride bonds (eg. 1,3-bisphosphoglycerate, ATP, etc.)?

Answer 14

Similar amounts of high energy. Rxns with these compounds has a free energy change more negative than -25 and are, by definition, high energy.

Question 15

Explain why thioester, but not oxygen ester, bonds are high energy.

Answer 15

The oxygen in the ester is resonance stabilized, but the sulfur in the thioester is not. Thus, thioesters are more destabilized to begin with and release greater energy upon hydrolysis to the same alcohol product.

Question 16

It is possible for a reaction with a positive ΔG’° to be driven by a coupled reaction which has a negative ΔG’°. Explain why this can occur.

Answer 16

Using the free energy of degrading a high energy phosphorylated compound to phosphorylate the lower energy compound of interest can make the phosphorylation of the reactant thermodynamically feasible. The free energies of the reactants are additive, and the phosphorylation gives the low energy molecule more free energy to react with in subsequent metabolic steps.

Question 17

Distinguish between a reducing agent (reductant) and an oxidizing agent (oxidant).

Answer 17

Reductant - donates electrons, is oxidized

Oxidant - accepts electrons, is reduced

Question 18

Define standard reduction potential, ΔE° and ΔE’°.

Answer 18

Property of a reaction combining two half cells (two conjugate redox pairs) to form a redox reaction where the reductant of one will act on the oxidant of the other. Difference is measured as ΔE’° = (E’° electron acceptor) - (E’° electron donor). Will give a more positive ΔE’° with a greater difference in reduction potentials = proportionate to the strength of the redox reaction.

Question 19

Which half reaction contains the strongest oxidant - one with a more positive ΔE’°, or one for which it is more negative?

Answer 19

More positive.

Question 20

Which half reaction contains the strongest reductant - one with a more positive ΔE’°, or one for which it is more negative?

Answer 20

More negative.

Question 21

What words do the letters of NAD+ stand for?

Answer 21

Nicotinamide Adenine Dinucleotide

Question 22

How are the components of NAD and NADP linked together?

Answer 22

Riboses linked through a phosphoanhydride bond. Each ribose has a “base” on it, with one containing adenine and the other with nicotinamide (the site of hydrogenation/reversible reduction). NADP has a phosphate group esterified to the 2’ C of the ribose ring.

Question 23

Distinguish between the physiological role of NADH and NADPH.

Answer 23

Enzymes typically use one or the other. NAD+/NADH has oxidizing roles (oxidant form (NAD+) present in higher concentrations in cell). NADP+/NADPH has reducing roles (reductant form (NADPH) present in higher concentrations).

Question 24

What words do the letters of FMN stand for?

Answer 24

Flavin Mononucleotide

Question 25

Using words, not structures, show how the component parts are arranged and linked together in FMN.

Answer 25

Isoalloxazine ring bound to open ring pentose at 1’ C and phosphate group is bound to 5’ C.

Question 26

Define monosaccharide in terms of functional groups and empirical formula.

Answer 26

A single unit of a polyhydroxyl aldehyde or ketone that has a usual empirical formula of (CH2O)n.

Question 27

Distinguish between aldose and ketose sugars.

Answer 27

Depends on whether the carbonyl group in the open chain form is at the end (aldose) or in the middle of the carbon chain (ketose).

Question 28

Using a structural formula of the type ROH, represent the reaction of an alcohol with an aldehyde to form a hemiacetal and with a ketone to form a hemiketal.

Answer 28

Attack of anomeric (carbonyl) carbon by deprotonated/activated alcohol = displacement of =O to form oxyanion. Negatively charged oxygen reacts with water to form two O-H’s and either an R and a H (hemiacetal) or two R groups (a hemiketal).

Question 29

For Amylose:

1) Identify the repeating monosaccharide.
2) Indicate the nature of the most prevalent glycosidic linkage (α, β, 1→X)
3) Point out the reducing and non-reducing ends.

Answer 29

1) D-glucose
2) α 1 –> 4 linkages (non branching)
3) 1 reducing end and 1 non reducing end (since there are no branches) at start and end of polysaccharide, respectively.

Question 30

For Amylopectin:

1) Identify the repeating monosaccharide.
2) Indicate the nature of the most prevalent glycosidic linkage (α, β, 1→X)
3) Point out the reducing and non-reducing ends.

Answer 30

1) D-glucose
2) α 1 –> 4 for straight chain segments, and then α 1 –> 6 branch point linkages every 24 - 30 units
3) 1 reducing end at start and n +1 non reducing end for a molecule with n branches.

Question 31

For glycogen:

1) Identify the repeating monosaccharide.
2) Indicate the nature of the most prevalent glycosidic linkage (α, β, 1→X)
3) Point out the reducing and non-reducing ends.

Answer 31

1) D-glucose
2) α 1 –> 4 for straight chain segments, and then α 1 –> 6 branch point linkages every 8 - 12 units
3) 1 reducing end at start and n +1 non reducing end for a molecule with n branches.

Question 32

What is meant by the “reducing end” of a polysaccharide?

Answer 32

The end of a molecule where the anomeric carbon is still free to mutarotate (aka, is not in a glycosidic linkage). This end can reduce (be oxidized) by a cupric (Cu2+) ion.

Question 33

What are the two phases of glycolysis?

Answer 33

1) Preparatory phase

2) Payoff phase

Question 34

What is invested in the preparatory phase?

Answer 34

2 ATP

Question 35

Name two molecules in which energy is conserved in the payoff phase of glycolysis.

Answer 35

ATP (x4) and NADH (x2)

Question 36

Explain the three catabolic fates of pyruvate.

Answer 36

1) aerobic metabolic pathway leading to complete oxidation of pyruvate into CO2. Pyruvate is decarboxylated to give CO2 and acetyl group. Acetyl used to form Acetyl CoA and enters the citric acid cycle. Completely oxidizes pyruvate and carries energy sequestered in electron carriers to ETC that will generate an abundance of ATP.
2) Lactic acid fermentation. Without O2 available to power ETC, carriers are not oxidized and available to continue glycolysis. Under these conditions, pyruvate is used to oxidize carriers and is reduced to lactic acid (that can then be excreted or recycled to glucose)
3) Ethanol fermentation - analogous to lactic acid, only pyruvate is reduced to ethanol.

Question 37

The pathway is more complex than would be needed chemically because the cell membrane must be impermeant to all the intermediates. How is this accomplished?

Answer 37

Phosphorylation of intermediates traps them in the cell until they are fully converted to pyruvate.

Question 38

What types of enzymes catalyze reactions that invest ATP during the preparatory phase?

Answer 38

Kinases which phosphorylate from ATPs

Question 39

Name the two compounds which donate phosphate to ADP in the payoff phase.

Answer 39

1) 1,3-biphosphoglycerate

2) phosphoenol pyruvate

Question 40

To what kind of energy rich group is the aldehyde of glyceraldehyde 3-phosphate converted in the oxidation step of glycolysis?

Answer 40

Converted to an acyl phosphate group.

Question 41

Name the type of linkage by which the other phosphate group is linked to 1,3- biphosphoglycerate.

Answer 41

Phosphate ester linkage.

Question 42

How does the free energy change of hydrolysis of the phosphate ester linkage in phosphoenolpyruvate compare to that of the combined free energy change of the hydrolysis of both phosphate linkages in 1,3-biphosphoglycerate?

Answer 42

SLightly larger for that single bond as compared to the two bonds in the 1,3-biphos.
1,3-biphos has -49.3 (phosphoanhydride) + -16 kJ/mol = about - 55 kJ/mol
Compare, phosphoenolpyruvate has -62 kJ/mol.
This makes the final conversion of phosphoenolpyruvate to pyruvate and ATP essentially irreversible.

Question 43

Indicate the general type of reaction catalyzed by:

1) kinases
2) isomerases
3) dehydrogenases
4) mutases
5) aldolase
6) enolase

Answer 43

1) Transfer of phosphoryl groups.
2) Alteration of stereochemistry.
3) Oxidation by removal of hydrogen.
4) Alteration of molecular structure.
5) Splitting/forming C-C bonds to generate carbonyl containing compounds or aldols (beta hydroxy keton or aldehyde)
6) Lysing reaction that unsaturates by removing a hydroxyl group

Question 44

Which of of the four kinase catalyzed reactions in glycolysis is reversible under cellular conditions?

Answer 44

ATP expenditure to phosphorylate fructose 6-phosphate to fructose 1,6-biphosphate. This has the smallest standard free energy change and is therefore, most likely to be reversible.

Question 45

Explain how glyceraldehyde 3-phosphate dehydrogenase uses a strategy involving a covalent enzyme-bound intermediate as a mechanism of energy coupling (i.e. the energy released during oxidation is used to make a high energy mixed anhydride bond). Note that the product of the oxidation is a thioester which is subsequently cleaved by HOPO3 2- (Pi).

Answer 45

Aldehyde on glyceraldehyde 3-phosphate nucleophilically attacked by S- on deprotonated Cys residue at active site (maintained with lower pKa). Forms covalently bound enzyme-substrate intermediate. NAD+ also in active site dehydrogenates thiohemiacetal. Nucleophilic attack by inorganic phosphate releases sulfur bond and produces 1,3-biphosphoglycerate product with NADH.

Question 46

How is NAD+ regenerated under aerobic conditions?

Answer 46

Fermentation, either to form lactic acid or ethanol from pyruvate.

Question 47

Write the reactions by which NADH is oxidized to NAD+ in :

1) anaerobic muscle.
2) anaerobic yeast.

Answer 47

1) Pyruvate (C3H3O3) + NADH + H+ → (lactate dehydrogenase) → Lactate (C3H5O3) + NAD+
2a) Pyruvate (C3H3O3) → Acetaldehyde (C2H4O) + CO2
2b) Acetaldehyde + NADH + H+ → Ethanol (C2H6O) + NAD+

Question 48

Phosphofructokinase 1 is the key regulatory enzyme in glycolysis. How is it regulated?

Answer 48

Allosteric modulation by an endproduct = negative feedback inhibition

Question 49

Name five substances which regulate the activity of phosphofructokinase 1 and explain why their action is logical.

Answer 49

Upregulated activity by:
AMP - makes sense because this is a product of ATP use.
ADP - also a product of ATP utilization, suggesting that more should be made.
Fructose 2,6-bisphosphate - production is catalyzed by signals relating to low blood glucose and stimulation of glycolysis by hormonal regulation systems.
Down regulated by:
ATP - end product of glycolysis - negative feedback inhibition.
Citrate - couples with inhibitory effect of ATP. sensible, because it is a major intermediate in the citric acid cycle. Abundance signals a lot of ATP production already happening = no need for more.