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Name: _______________________
Chem 351 Exam 4
1
Multiple Choice – For Problems 1-15, pick the BEST answer. Write the letter corresponding
to your choice in the box.
1) Which of the following statements about insulin release and the processes involved in
signaling the fed state is false?
A) Insulin granules are vesicles containing fully formed insulin hormone.
B) Increased blood glucose concentration leads to increased glucose breakdown in
pancreatic B cells.
C) The closure of a voltage-gated calcium channel is correlated to insulin release.
D) Calcium moves passively into the pancreatic B cell when the membrane is
depolarized.
E) Different cells in the pancreas are responsible for secreting different peptide
hormones.
2) Which of the following is not true of fatty acid synthesis and its regulation?
A) Citrate serves as an allosteric activator of fatty-acyl synthase.
B) Carboxylation of the acetyl unit makes it much more nucleophilic.
C) During the condensation step, the acyl carrier protein always carries a longer chain.
D) The first acetyl-CoA unit to be incorporated into a fatty acid is not initially positioned
on the acyl carrier protein arm.
E) None of the above is untrue.
3) Which of the following statements about topoisomerases and supercoiling is false?
A) Topoisomerases change the Lk for a section of DNA.
B) The extent and nature of supercoiling in DNA leads to varying amounts of
compaction.
C) On average cellular DNA might have a superhelical density of -0.05.
D) All topoisomerases break both phosphoribose backbones during catalysis.
E) None of the above is false.
4) Which of the following “stages” is not observed in the normal development of
atherosclerosis?
A) Adhesion of monocytes to areas of the arterial wall that are rich in lipoproteins.
B) Uncontrolled absorption of cholesterol turns macrophages into foam cells.
C) Foam cells are extravasated (extruded) from the arteries into the surrounding tissue.
D) Apoptosis of foam cells.
E) Differentiation of monocytes into macrophages.
F) All of the above are observed.
5) Cancer development is generally caused by all of the following, except:
A) Uncontrolled tyrosine kinase activity in receptors like ErbB.
B) Mutations in genes that code for tumor suppressors.
C) Increased p53 production leading to faster cell division in the p21-mediated response.
D) Hypermethylation and inactivation of genes devoted to DNA repair.
E) All of the above situations have been correlated to cancer development.
Name: _______________________
Chem 351 Exam 4
2
6) Which of the following statements about cyclins and regulation of the cell cycle is true?
A) CDKs phosphorylate cyclins in order to regulate their production and destruction
during the cell cycle.
B) Phosphorylation of a specific T residue in the T loop of CDK leads to enhancement of
CDK activity.
C) The p53/p21 effect increases the activity of p21’s target complex: cyclinE/CDK2.
D) Fully active cyclin-CDK complexes dephosphorylate and activate proteins like DBRP,
leading to ubiquitinylation of the cylin.
E) more than one of the above is true.
F) none of the above is true.
7) Which of the following is not required for DNA polymerase activity?
A) RNA primer with a nucleophilic -OH terminus.
B) ssDNA.
C) A template strand of DNA.
D) two Mg2+ ions in the active site.
E) 3’-dNTPs as a source of incoming nucleotides.
F) all of the following are required.
8) Which of the following statements about the genetic regulation of cholesterol biosynthesis
is true?
A) Cholesterol levels within the cell impact the level of transcription of the LDL receptor.
B) SCAP is released from the endoplasmic reticulum when cholesterol is low within the
cell.
C) SREBP is a sequence of DNA that codes for a variety of proteins involved in
cholesterol synthesis.
D) Proteolysis plays an important role in the production of nuclear effectors of
transcription.
E) more than one of the above is true.
F) none of the above is true.
9) Aminoacyl-tRNA synthetases
A) catalyze the addition of a 7-methyl guanosine is attached to the 5’triphosphate group
at the end of the tRNA polymer.
B) hold most of the responsibility for translational sequence fidelity.
C) facilitate the nucleophilic attack by the phosphate group on the tRNA to the activated
amino acid.
D) utilize amino acids adenylated at their α-amino groups as activated substrates.
E) none of the above are true.
10) Pick the false statement about the regulation of the tryptophan operon of E. coli.
A) The trp operon codes for many enzymes required for trp biosynthesis.
B) Attenuation is caused by the formation of a hairpin loop that disrupts transcription.
C) When [trp] is low in the cell, transcription levels are at their highest.
D) Tryptophan down-regulates a negatively regulated operon.
E) The trpL (leader sequence) is only transcribed when attenuation is prevented.
Name: _______________________
Chem 351 Exam 4
3
11) RNAi (RNA interference) is an incredibly important topic right now in biochemistry.
Which of the following statements about RNAi is false?
A) miRNAs are single-stranded polymers when fully mature and active.
B) Drosha and other nuclear proteins serve as endoribonucleases cutting RNA
substrates in the processing of miRNA.
C) The RISC protein carries miRNA to target mRNA transcripts.
D) RNAi always reduces protein production at the level of translation.
E) None of the above is false.
12) Which of the following is a false statement about DNA/RNA metabolism and its
regulation?
A) RNA dependent DNA synthesis may be seen in the production of telomeres.
B) Acetylation of histones is a regulatory mechanism in DNA replication.
C) Retroviruses turn their RNA genome into a viral DNA in the host cell.
D) Nitrogen mustards are used to specifically damage DNA in cancer treatments.
E) All of the above are true statements.
13) Which of the following is a true statement about the regulation of cholesterol
biosynthesis?
A) HMG-CoA reductase activity is significantly increased with AMPK activity.
B) Oxysterol and other sterol derivatives directly block the production of mevalonate.
C) Statins like Atorvastatin directly inhibit the production of HMG.
D) Intracellular cholesterol stimulates cholesterol esterification catalyzed by LCAT.
E) All of the above are true.
14) When cell death is initiated by extracellular signals that target specific receptors like Fas
and TNF
A) G proteins are generally used to send the extracellular “death signal” to various
cellular proteins.
B) death domains refer to areas in the receptors that are susceptible to protease activity.
C) caspase activity targets destruction of cytochrome c, an essential protein for cell
survival.
D) procaspases present in the cytosol become activated when the receptor binds the
signal.
E) More than one of the above.
F) None of the above.
15) Transcription is a process that:
A) produces RNA by bringing in ribonucleotides that hydrogen bond to the coding DNA
strand.
B) is virtually identical in eukaryotic and prokaryotic cells.
C) creates RNA (of many types) that require no further modification in order to be
functional in the cells of both prokaryotic and eukaryotic organisms
D) can be inhibited by antibiotics and other agents that block DNA polymerase activity.
E) is not accurately described by any of the above.
Name: _______________________
Short Answer - fill-ins
1) Consider the following
reaction scheme that is
occurring in cells that are
undergoing rapid fatty
acid synthesis.
A) Draw in all missing
intermediates (2 pts each).
Chem 351 Exam 4
inner
mitochondrial
membrane
Cytosol
1
A
acetyl-CoA
2
acetyl-CoA carboxylase
oxaloacetate
Vm
= -46 mV
3
B) Name the enzyme:
Reaction 1:
COO
B O
Reaction 4:
4
solute B
C) Name the protein:
A:
B:
D) Considering reactions 1-4 (write “NA” if none apply):
1) Which require(s) ATP as a substrate in the direction shown?
2) Which require(s) NADPH as a substrate in the direction shown?
3) Which require(s) or release(s) CO2?
E) Given the information provided in the figure, what must be the difference
in concentration of solute B in the cytosol vs. in the matrix in order to insure
favorable movement of the solute? Show your work.
R = 8.3 J/molK
T = 298K
F =96,500 J/Vmol
F) T/F
a)
PPARs are receptors that dimerize to genetically regulate fat oxidation and storage.
b)
LCAT is a lipid essential for the proper development of HDLs.
2) Fill in the information on the figure below, using the boxes provided for your answers.
Lactose is (circle one):
High Low
Effector:
Protein:
Transcription is (circle one): On Off
Glucose is (circle
one):
High Low
Protein:
4
Name: _______________________
Chem 351 Exam 4
3) Various points on the figure shown are labeled and
5
A
indicated with arrows. For A-E, name the protein (as
specifically as possible). Then answer questions 1-4.
A)
B)
B
1
C)
D)
E)
1) What cell is indicated by 1?
2) What cell is indicated by 2?
3) What is the effect that is being shown by 3?
C
3
2
D
4) Circle the terms that are associated with the effective
use of this process?
Orexigenic
Anorexigenic
E
α-MSH Neuropeptide Y
4) Matching
For each of the terms listed below, pick the best description(s) from each column of the
table that best applies. Each of these terms represent something that participates in some
part of information processing. Choose that process and the phase(s) of that process that
apply. Also state what class of biomolecule (composition) it is made of.
Process
A: Replication
B: Transcription
C: Translation
i) σ factor:
ii) f-Met:
iii) Tu-Ts:
iv) Shine-Dalgarno:
v) HRE:
vi) Primase:
vii) ρ factor:
viii) TATA box:
Phase
Composition
D: Initiation
G: DNA
E: Elongation H: RNA
F: Termination I: Amino acid/protein
Name: _______________________
Chem 351 Exam 4
5) Each of the following figures represents a key regulatory mechanism for the enzyme/protein
listed. Briefly describe how the regulation works and whether the active or inactive form of the
enzyme is represented.
PII as a transcription factor
Glutamine synthetase
CyclinE-CDK2 cascade
Trp repressor
6) Labeling experiments: Pay attention to the labeled atoms and the conditions for each
experiment.
Experiment 1) only one equivalent of NADPH is available, but all other fatty acid synthesis
ingredients are present. After a short time, a mixture of two products, equal in carbon content,
nearly equal in concentration, and each linked to ACP, was obtained: one radiolabeled and one
unlabeled. Draw these products, and be sure to indicate the position of the label.
1)
18O
draw the unlabeled fat-ACP product
draw the fat-ACP carrying radiolabel
ACP
O
+
+
1 NADPH only
SCoA
Experiment 2) Follow the production of HMG-CoA by drawing the intermediates that form. Be sure
to indicate any atoms that carry a radiolabel.
2)
18O
SCoA
+
HMG-CoA
acetoacetyl-CoA
O
O
SCoA
SCoA
6
Name: _______________________
7) Short Answer.
This picture shows a section of
the thylakoid membrane
containing some of the machinery
for the electron transport chain.
Chem 351 Exam 4
1
7
2
A) Draw directly in the figure
Reaction B
(showing position clearly, or
describing it clearly): (8 pts)
Reaction A
C
1) The solute being moved
AND THE DIRECTION of
movement indicated by C in
the figure
2) N and P sides
3) Plastoquinone (PQ)
4) Plastocyanin (PC)
5) CF1 and CF0 (label each protein carefully) and provide the reaction catalyzed in the
appropriate space.
B) Name the proteins that catalyze the two main chemical reactions in this process, and give the
reactions that they catalyze. Be sure to specify the number of electrons moving in your
balanced reaction. (2 pts each)
1) Protein 1:
Reaction A (initial reaction delivering electrons):
2) Protein 2:
Reaction B (terminal reaction delivering electrons to final acceptor):
8) Provide the curved arrow mechanism for the carboxylation step (only the direct addition of the
CO2) that occurs in Rubisco’s catalysis. This is the key step in which carbon dioxide is fixed into a
sugar carbon skeleton. Draw the resulting product.
H
N
PO 3-2
His 294
N
O
H
O
O
C
O
H
O
O
H
O
PO 3-2
Name: _______________________
Chem 351 Exam 4
8
9) Synthesis!
A) Arginine is a very important amino acid because it plays diverse roles in nitrogen
metabolism. Provide the missing information in the two syntheses shown below, each of
which starts with arginine. (10 points).
Draw substrate
H 2N
NH 2
name carrier:
NH 2
NH
NH 3
H 2N
O
NH
O
enzyme:
O
O
enzyme:
Draw creatine
1
other substrate(s) for
both reactions:
+ NO
hydroxyarginine
2
B) T/F Syntheses
a)
α-ketoglutarate is the main N donor in the synthesis of Gly from 3-phosphoglycerate.
b)
Phosphocreatine contains a higher energy bond than ATP does.
c)
Glutathione is produced by the chemical fusion of Gln, Cys, and Gly.
d)
Bilirubin is a byproduct of heme breakdown and a strong oxidizing agent in blood.
e)
Ribonucleotides are produced from deoxyribonucleotides via hydroxylation.
f)
The ammonia channel is a protein transporter specifically used to move N across a
membrane barrier.
10) Quick Calculations
i) Considering only proton-motive force, calculate the membrane potential required to generate
enough energy to form a high energy phosphate bond (~31 kJ/mol) if the difference in pH is
~2.9 units.
ii) Calculate the ΔE˚ and ΔG˚ for the
reaction most likely to occur if these
electron carriers transfer electrons
successfully.
Oxidized Form
ZQ
Fd (ox)
iii) WHICH ACTS AS THE REDUCING AGENT (circle one)?
Reduced Form
ZQH2
Fd (red)
ZQ
Electrons
2
1
E’˚ (V)
+0.12
-0.43
ZQH2 Fd(ox) Fd(red))
Name: _______________________
Chem 351 Exam 4
9
11) Apply the information - read ALL the details (13 points total)
The genetic makeup of this cat was modified to include a gene called “stitious”, mainly
expressed in muscle tissue. This regulated gene codes for a protein called Furase.
Transcription of the gene requires the release of a DNA-binding protein (cat). In the
absence of a metabolite (black), however, cat is not able to be released from the DNA.
Black is produced after prolonged fasting (glucagon hormonal signal) and the initiation of an
epinephrine signal in the muscles. Once expressed, this protein is known to be activated by
calmodulin (Ca2+) binding, which is enhanced by the opening of a ligand-gated calcium channel in
muscle cells.
When Furase activity is high in muscle cells, extremely furtive behaviors and aggression are
observed in the animal.
A) For each of the following treatments, circle the effect that is expected to occur on the
molecules/activities listed, compared to having no treatment at all. Circle all that apply or NA.
i) An epinephrine agonist would increase
kcat of furase
Vmax of furase
[stitious transcript]
[furase]
NA
ii) A calcium channel antagonist would decrease which of the following (circle all that apply, or NA)?
kcat of furase
Vmax of furase
[stitious transcript]
[furase]
NA
iii) A miRNA sequence that is highly complementary to the stitious transcript would be unlikely to
affect:
kcat of furase
Vmax of furase
[stitious transcript]
[furase]
NA
iv) Enhancing the turnover rate of the protein using a ubiquitinylation process would impact:
kcat of furase
Vmax of furase
[stitious transcript]
[furase]
NA
B) T/F Regulation
a)
This system provides an example of positive genetic regulation.
b)
c)
An insulin hormonal signal would be likely to influence the genetic regulation of this
system.
Black would be considered an up-regulator of the gene stitious.
d)
Black would fall under the category of co-repressor in this system.
e)
When Furase activity is high, cat muscle cells are likely to have high concentrations of
phosphocreatine.
An agonist of the calcium channel would lower Furase activity.
f)
C) The stitious gene is 6500 bp in length, including its strong promoter sequence. If it has a
superhelical density of -0.0484, what can you say about its Lk (be specific)?
Name: _______________________
Chem 351 Exam 4
10
12) Some very interesting chemistry involving aldol reactions has been done to study
RNA production in DNA templates.
1) First, the starting material shown below (modified nucleotides 1 and 2 of a
disconnected DNA polymer) react in a one-step aldol condensation to yield an
unbranched 5-carbon sugar that reconnects the DNA chain.
2) In the next step, the sugar cyclizes into a hemi-acetal form.
Show the curved arrows that are required for each step of the transformation and show the
intermediate formed. You may abbreviate any part of the nucleotides, but you should
clearly show the sugar that is formed, and you should NUMBER the carbons of that sugar to
keep track of the aldol fusion step. You may use bases (:B) and proton donors (H+ or HB+)
as needed; they are provided for the first step. (12 points)
Nucleotide 1
Base 1
Chain
O
H
H O
H
O P O
C
C
C
O
H H O
O
BH
H B
H
H
C
O
O
C H
Base 2
O P O
O
O
O
Nucleotide 2
O P
O
O
Chain
Chain
O
Base 1
Nucleotide 1
O
O P O
O
HO
O
OH
O
O P O
O
O
Base 2
O
O P O
Chain
O
Nucleotide 2
Multiple Choice
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