Chemistry 462 Biochemistry
First Hour Exam
General Questions:
1. (5 points) Calculate the standard free energy change ()Go’) for the reaction: (R = 8.3145 J/mol,
assume T = 25oC)
Dihydroxyacetone phosphate W glyceraldehyde 3-phosphate
given that the K’eq for this reaction is 0.0475
)G = -RtlnK
= -8.3145 j/mol@K x 298K x ln(.0475)
= +7550 j/mol or 7.55 kJ/mol
2
2. (10 points) In these chapters you have been introduced to several different electrons carriers,
NAD/NADH, FAD/FADH2, and Q/QH2. Give the proper names of these electron carriers, the
chemical structure of the part of the molecule that accepts electrons, and then compare and contrast the
role and function of these different groups
NAD Nicotinamide Adenine Dinucleotide - Water soluble electron carrier- enters and leaves enyzmes
as a co-substrate- Can only work in 2 electron reactions. Derived from vitamin Niacin
H
O
HH
NH2
N
+
+
2e-
+
O
NH2
2H+
+
H+
N
R
R
NAD+
NADH
FAD Flavin Adenine Dinucleotide - a less soluble electron carrier - usually appears tightly bound or
covalently bound to an enzyme so cannot leave enzyme to carry electrons. Can work in 1 electron or 2
electron steps.
H
O
H 3C
H 3C
+ e-
N
N
NH
N
+ H+
H 3C
N
H 3C
N
O
O
+
NH +
H+
+
O
e-
N
R
R
H
O
H3C
N
H3C
N
N
R
H
NH
O
Q - Ubiquinone or CoenzymeQ - Lipid soluble electron carrier readily enters and leaves enzymes in a
lipid soluble medium like a membrane - can add electrons in 1 or 2 electron steps.
CH3O
Hydrophobic tail
CH3 O
O
OH
O
O
CH3
+ e- + H+
CH3O
CH3O
OH
R
CH3O
R
CH3
CH3 O
CH3
+ e- + H+
OH
3
3. (17 points) . Below is an outline of the glycolytic pathway with many blanks. Fill in the blanks.
If you can’t think of the name of a compound I will accept its structure.
Reactant/Product
Glucose
RXN 1
9
Enzyme Name: _Hexosekinase__
Glucose-6-phosphate
RXN 2
9
Enzyme Name: phosphohexose isomerase
Fructose-6-phosphate
RXN 3
9
Enzyme Name: Phosphofructokinase-1
Fructose-1,6-bisphosphate
RXN 4
9
Enzyme Name: Aldose___________
Dihydroxyacetone phosphate + Glyceraldehyde-3-phosphate
RXN 5
9
Enzyme Name: Triose Phosphate isomerase
Glyceraldehyde 3-Phosphate
RXN 6
RXN 7
9
Enzyme Name:Glyceraldehyde-3-phosphate dehydrogenase
1,3-Bisphosphoglycerate
9
Enzyme Name: Phosphoglycerate kinase
3-Phosphoglycerate
RXN 8
9
Enzyme Name: Phosphoglycerate mutase
2-Phosphoglycerate
RXN 9
9
Enzyme Name: Enolase_______
Phosphoenolpyruvate (PEP)
RXN 10
9
Enzyme Name: Pyruvate kinase______
4
Pyruvate______
Other questions on the glycolytic pathway page.
4. (3 points) In what reactions does ATP appear as a reactant____1,3_________
5. (3 points) In what reactions does ATP appear as a product _____7, 10______
6. (3 points) In what reactions does NADH appear as a product ____6__________
7. (3 points) What reactions are under allosteric control _____1,3,10_______
8. (3 points) What is the structure of Phophoenolpyruvate
CH2
O
O P O
O
O
O
9. (5 points) When phosphoglycerate mutase catalyzes a single transformation of 3-phosphoglycerate
(reactant) to 2-phosphoglycerate (product), is the phosphate in the product the same phosphate that
was in the reactant? Why or why not?
No. The phosphate that is placed on the 2-phosphoglycerate is a phosphate that was already bond to
the enzyme on a phosphorylated histidine. The phosphate that was on the 3-phosphoglycerate is then
bound to the enzyme and will be placed on the next 2-phosphoglycerate that the enzyme reacts with
5
The Tricarboxylic Acid cycle
10. (10 points) Below are the names of all the intermediates in the Krebs Cycle.
Acetyl Co A
cis-Aconitate
Citrate
Fumarate
Isocitrate
"-ketoglutarate
Malate
Oxaloacetate
Succinate
Succinyl-CoA
On the page below make a diagram of the Kreb’s cycle, correctly placing each of the above
intermediates in the cycle.
Pyruvate
9 (control)
-1._Acetyl CoA___
9
(control)
9.__Oxaloacetate___
6
1._Citric Acid____
8.__Malate______
2.__[cis-Aconitate]___
NADH Synthesis
7.__Fumarate______
3.___Isocitrate_______
FADH2 synthesis
(Control) + NADH synthesis
6.__Succinate____
4. "-ketoglutarate
ATP or GTP synthesis
(Control) + NADH synthesis
5._Succinyl Co A__
6
Krebs cycle questions
11. (3 points) In the cycle on the previous page indicate all steps where NADH is generated.
12. (3 points) In the cycle on the previous page indicate all steps where FADH2 is generated.
13. (3 points) In the cycle on the previous page indicate all steps where ATP or GTP is generated.
14. (3 points) Which of the intermediates on the previous page is an enzyme bound intermediate that
usually never leaves the enzyme?
cis Aconitate
15. (3 points) In the cycle on the previous page indicate the reactions that are sites of metabolic control
16. (8 points) Many of the TCA cycle compounds are used as precursors for other biological
compounds. What compounds can be made from:
Citrate - Fatty acids - steroids
"-Ketoglutarate - Glutamic acid Purines, Arg, Pro, Gln
Succinyl-CoA - Heme
Oxaloacetate - Asp, asn, pyrimidines
17. (5 points) When we siphon off TCA intermediates to make other compounds, we need to replenish
the intermediates. Name at least one anaplerotic reaction that does this.
Puruvate can yield either malate or oxaloacetate
PEP can generate oxaloacetate
7
Oxidative Phosphorylation
18. (10 points) Describe the flow of electrons through the various electron carrier complexes in the
mitochondira. For each complex be sure to name the reactant, the product(s) and include a net
chemical reaction (including any vectorial H+ transport).
I was looking for an answer that contained a figure like 19-14 out of the text as well as the chemical
equations for each reaction.
I or NADH:ubiquinone oxidase
NADH + 5H+N + Q 6 NAD+ +QH2 + 4H+P
II or succinate dehydrogenase
Succinate + Q 6Fumarte + QH
III or cytochrome bc1 complex or ubiquinone:cytochrome c oxidoreductase
QH2 + 2cytcox + 2H+N 6 Q + 2 cytcred + 4H+P
IV or cytochrome oxidase
4cytcred + 8H+N + O2 6 4cytcox + 4H+P + 2 H2O
19.(10 points) Describe the structure of the ATPsynthase and tell how it works.
The synthase is composed to 2 major parts, the F1 ATPase that protrudes into the interior of the
mitochondrial matrix and the Fo which is membrane bound.
The F1 is a multi-subunit complex composed of "3$3(*, subunits this unit will hydrolyse ATP (hence
the name ATPase) when it is dissociated from the Fo unit, but makes ATP from ADP and Pi when
attached to Fo
The Fo is composed of a, b2, and c10-12 and acts as a gate to let H+ ions back into the mitochondrial
matrix.
At the interface between the " and $ sites of the F1 there is a binding site for either ATP or ADP and or
nothing. The conformation of this site changes depending on how these units interact with the ( protein.
The ( protein , in turn, extends all the way into the Fo unit, and it thought to physically move as H+ ions
mover through this protein on their way into the mitochondira. As the ( protein rotates, it toggles the
ATP bind site conformations in the F1 unit so it successively binds ADP and Pi, them joins them to
make ATP, then releases them into the matrix.
The generally accept value is that it takes 3 protons to synthesize a single ATP, and one
additional proton to transport Pi.ADP and ATP across the mitochondiral membrane.
Thus the oxidation of NADH that generates 10 protons could make a maximum of 2.5 ATP
and FADH2 that generates 6 protons can make a maximum of 1.5 ATP.