Download Module 10: Catabolism of Amino Acids

Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Bioc 3321 Study guide
Module 6: Bioenergetics and channels
1. The hydrolysis of ATP has a standard Gibbs free energy of -30.5 kJ/mol
ATP4- + H2O  ADP3- + P- + H+
a. Explain if the Gibbs free energy will increase, decrease or remain the
same if we increase the pH of the medium.
b. Will the equilibrium constant be larger, smaller or the same at this
larger pH?
2. The reaction of combustion
a. Sort in decreasing order of Gibbs free energy
i. CH3CH2COOH
ii. CH3CH2CH3
iii. CH3CH2CH2OH
iv. CH3CH2CHO
b. Since a combustion reaction is a redox reaction. Do the same with
redox potentials
3. The E′° values for the NAD+/NADH and pyruvate/lactate conjugate redox
pairs are −0.32 V and −0.19 V, respectively.
a. Which pair is likely to oxidize and which to reduce in standard
conditions? Why?
b. Suggest conditions of concentrations in which the reaction may be
reversed
4. The plasma membrane Na+-glucose symporter of an epithelial cell uses the
electrochemical gradient of sodium cations to create a gradient of glucose
molecules.
+
[glucose]out
+
[glucose]in
[Na ]out
[Na ]in
a. If [Na+]out > [Na+]in. This means that (circle one)
i. [glucose]out > [glucose]in
ii. [glucose]out < [glucose]in
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
b. If the sodium gradient is substituted by a calcium gradient Ca2+ of the
same amount. Will the ratio of glucose glucose(one side) / glucose
(other side): (circle one, ignore the cell potential)
i. Increase by double
ii. Increase by less than double
iii. Increase by more than double
iv. Why?
Module 7: Catabolism of Carbohydrates
5. The third step of glycolysis is a retroaldol reaction in which aldolase
catalyses the conversion of fructose 1,6-biphosphate into glyceraldehyde
phosphate and dihydroxiacetone phosphate:
6.
7.
8.
9.
Draw the structures of glyceraldehyde phosphate and dihydroxiacetone
phosphate indicating how the numbers indicated in the fructose above.
At the end of this test there is a scheme of the glycolysis pathway. Just by the
molecules involved in the pathway:
a. Which step of the glycolysis pathway will yield a molecule of reduced
NADH?
b. Why does the overall glycolysis pathway yields two and not one
molecule of NADH?
Breaking down glycogen yields glucose-6-phosphate without spending one
molecule of ATP. How many molecules of ATP will yield each molecule of
glucose coming from glycogen when its converted into pyruvate?
In some bacteria glucose is transformed anaerobically into ethanol. If [114C]glucose (glucose labeled at C-1 with 14C) is used as a substrate, what is
the location of 14C in the product ethanol? Explain.
The transformation of fumarate into succinate has the following potential:
Fumarate + 2H+ + 2e– → succinate E'° = +0.031 V
Explain with this information, which one will appear first in the Citric Acid
Cycle.
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Module 8: Regulation of Metabolism
10. Phosphofructokinase is one of the enzyme in the glycolysis pathway
subjected to more regulation. Concentrations of ATP and ADP can change the
activity of the enzyme.
a. From what you know about glycolysis. Will [ADP] will be an activator
or an inhibitor of the enzyme. Why?
b. The graph shown below shows the activity of the enzyme (velocity) as
a function of [ATP]. The different lines show the activity of the enzyme
at different concentrations of the activator F-2,6-P
i. 1M F-2,6-P
ii. 0.1 M F-2,6-P
iii. No F-2,6-P
Identify what concentration of F-2,6-P each curve represents.
11. The free energy for converting malate to oxaloacetate is highly endergonic
(∆G’o = 30 kJ/mol). This reaction is the last step of the citric acid cycle and it
is driven forward by maintaining low concentrations of oxaloacetate.
a. Explain why a low concentration of oxaloacetate may drive forward
this endergonic reaction.
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
b. What is the maximum concentration of oxaloacetate that allows the
reaction to go forward. Assume [malate] = 1mM, pH=7, [NADH] = 1μM
and [NAD+] = 1μM, and all are in steady state.
Module 9: Catabolism of Lipids
12. What is the structure of the partially oxidized fatty acyl group that is formed
when oleic acid, 18:1(Δ9), has undergone three cycles of β oxidation?
13. Below is list of events that occur during fatty acid oxidation. For each fatty
acid drawn below, fill in the blank with the letter corresponding to any event
required for 1 cycle of -oxidation of the acyl chain. (Note:  -oxidation
produces acetyl-CoA and/or propionyl-CoA.)
The steps do NOT have to be given in the order they occur. A letter may be
used in more than one blank. Some letters may not be used.
Each blank will have more than one letter. If a step is used more than once
per blank, put it down only once per blank.
a. A dehydrogenase transfers a hydride ion to NAD+.
b. A dehydrogenase transfers a proton to NAD+.
c. A dehydrogenase transfers two hydrogens to FAD.
d. A dehydrogenase transfers two protons to FAD.
e. A reductase reduces the fatty acyl chain.
f. Propionyl CoA is formed.
g. ATP is hydrolyzed to AMP + PPi.
h. NADH is oxidized.
i. An isomerase converts a 3=4 double bond to a 2=3 double bond.
j. NADPH is oxidized.
Module 10: Catabolism of Amino Acids
14. Write the hydrolysis of a peptide bond by water indicating the motion of
electrons and the overall balanced reaction.
15. Explain why the skeletal muscle converts the product of transamination
glutamate into alanine and not into glutamine like the rest of the tissues?
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Additional information
Useful equations
DG 0 = DH 0 -TDS 0
RT
lnK
nF
RT
o
Ecell = Ecell
lnQ
nF
𝑝𝐻 = −log⁡[𝐻3 𝑂+ ]
o
E cell
=
DG = DG 0 + RT lnQ
𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔
[𝑏𝑎𝑠𝑒]
[𝑎𝑐𝑖𝑑]
Metabolic pathways
Glycolysis:
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Citric Acid cycle
Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2 H2O 
2CO2 +3NADH + FADH2 + GTP + CoA + 3H+
Beta-oxidation of fatty acids:
From C-16 to C-14
Palmitoyl-CoA + CoA + FAD + NAD+ + H2O
→
myristoyl-CoA + acetyl-CoA + FADH2 + NADH + H+
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Amino acid catabolism and urea cycle
2 NH3 + CO2 + 3 ATP + H2O → urea + 2 ADP + 4 Pi + AMP
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester