

Chemical Biology
Question Bank

Course Introduction
Chemical Biology explores the interface between chemistry and biology, emphasizing how chemical techniques and principles are applied to understand and manipulate biological systems at the molecular level. This course covers topics such as the chemical structure and reactivity of biomolecules, enzyme mechanisms, small molecule probes, and the design of drugs and therapeutic agents. Students will learn how chemical tools are used to study cellular processes, map biological pathways, and develop innovative treatments for diseases, preparing them for advanced research in the rapidly developing field of chemical biology.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 4th Edition by Donald Voet
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28 Chapters
1538 Verified Questions
1538 Flashcards
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Chapter 1: Introduction to the Chemistry of Life
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Sample Questions
Q1) Which three cellular components are present in both prokaryotes and eukaryotes?
A)ribosomes, chloroplasts, mitochondria
B)nucleus, ribosomes, RNA
C)RNA, DNA, ribosomes
D)endoplasmic reticulum, DNA, RNA
E)mitochondria, DNA, RNA
Answer: C
Q2) If gas molecules in an enclosed chamber are allowed to enter a second chamber, the resulting redistribution of gas molecules represents an increase in A)enthalpy.
B)entropy.
C)force.
D)chemical potential.
E)all of the above
Answer: B
Q3) Explain in one or two sentences why scientists believe that all living organisms are related (that they have all evolved from a common ancestor)?
Answer: Biochemically, all living organisms are very similar.
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3

Chapter 2: Water
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Sample Questions
Q1) Octane molecules dispersed in water tend to aggregate because that allows water molecules to be more ______.
A)hydrogen bond
B)rotational
C)H PO
D)H PO
E)HPO 2
F)disordered
G)positive entropy
H)negative entropy
I)higher electronegativity
J)insoluble
K)tetrahedral arrangement
L)acid
M)base
N)only partially ionized
Answer: F
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Chapter 3: Nucleotides, Nucleic Acids, and Genetic Information
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Sample Questions
Q1) A genomic library
A)is a collection of protein structures from a specific organism.
B)is a collection of cloned DNA fragments representing all of an organism's DNA.
C)contains only protein-coding DNA sequences.
D)is best constructed from very short DNA fragments.
E)is built from mRNA by reverse transcription.
Answer: B
Q2) A gene knockout is
A)a gene that has been inactivated or removed from an organism.
B)a dominant gene that knocks-out expression of other genes.
C)a gene inserted in place of another gene.
D)a gene present on a YAC.
E)none of the above
Answer: A
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Chapter 4: Amino Acids
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Sample Questions
Q1) Which of the following amino acids is the least abundant in proteins?
A)V
B)W
C)G
D)F
E)A
Q2) Which of the following amino acids has a sulfur atom in its side chain?
A)Asn
B)Ser
C)Phe
D)Met
E)Tyr
Q3) Residues 1 and 2 in the peptide shown above are connected through a A)hydrogen bond.
B)an isopeptide bond.
C)an ester linkage.
D)disulfide bond.
E)a glycosidic bond.
Q4) Glutamine is an amino acid (pK<sub>a</sub>s are 2.2, and 9.1).Draw the predominant structure of glutamine at pH 1.0.
Page 6
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Chapter 5: Proteins: Primary Structure
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Sample Questions
Q1) The pK<sub>1</sub>, pK<sub>2</sub>, and pK<sub>R</sub> of the amino acid lysine are 2.2, 9.1, and 10.5, respectively.The pK<sub>1</sub>, pK<sub>2</sub>, and pK<sub>R</sub> of the amino acid arginine are 1.8, 9.0, and 12.5, respectively.A student at SDSU wants to use ion exchange chromatography to separate lysine from arginine.What pH is likely to work best for this separation?
A)1.5
B)2.5
C)5.5
D)7.5
E)10.5
Q2) What can be done to increase the rate at which a protein of interest moves down an ion-exchange chromatography column?
A)reduce the ion concentration in the eluant
B)add a small amount of a non-ionic detergents to the eluant
C)change the pH of the eluant
D)add a protease inhibitor to the eluant
E)reduce the temperature of the eluant
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Chapter 6: Proteins: Three-Dimensional Structure
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Sample Questions
Q1) Based on what you know about fibrous protein structure and sequence, what type of fibrous protein is this sequence most likely to from (You can assume that the protein is longer than what is shown and is repeating as shown, also note the polarity of each amino acid.)?
Val - Cys - Lys - Val - Cys - Ala - Cys - Val - Cys - Lys - Val - Cys - Ala - Cys
A)(\(\alpha\) keratin)
B) keratin
C)collagen
D)pleated collagen
E)This sequence cannot be from any of the structural proteins.
Q2) Which of the following best describes the cause of Creutzfeld-Jakob Disease (a disease which human can develop with symptoms similar to those of mad cow disease)?
A)aggregation of a misfolded protein.
B)aggregation of random coil regions on a protein.
C)ingestion of ammonium salts.
D)the serious side effects of experimental treatment with Quinacrine
E)All are potential causes Creutzfeld-Jakob disease.
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Page 8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Sample Questions
Q1) The rearrangement of T state hemoglobin to the R state A)occurs in each protein subunit independently when its heme binds oxygen. B)requires the binding of at least three oxygen molecules. C)increases the ion pairing interactions of the C-terminal amino acids. D)involves the movement of the Fe(II)into the heme plane.
E)opens a central cavity for BPG binding.
Q2) The Hill plot shows that the fourth oxygen binds to hemoglobin with a ______-fold greater affinity than the first.
A)2
B)5
C)10
D)20
E)100
Q3) Hemoglobin's p<sub>50</sub> value is about ______ as great as myoglobin's p<sub>50</sub> value.
A)one-tenth
B)half
C)twice
D)ten times
E)twenty times

Page 9
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Chapter 8: Carbohydrates
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Sample Questions
Q1) Bulky ring substituents preferentially occupy ______ positions in the chair conformation.
A)eight
B)deoxy
C)peptidoglycan
D)axial
E)anomers
F)two
G)lactose
H)glyceraldehyde
I)amylopectin
J)epimers
K)sixteen
L)glycogen
M)equatorial
N)chitin
O)hyaluronic acid
P)amylose
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Page 10

Chapter 9: Lipids and Biological Membranes
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Sample Questions
Q1) Botox is used cosmetically to reduce wrinkles for a limited time interval.The function of Botox is described by which of the following?
A)Botox inhibits function of the hemagglutinin tag.
B)Botox relaxes small muscles by cleaving the leader peptide prior protein folding.
C)Botox functions by inhibiting function of the SNARE protein.
D)Botox functions by inhibiting the lysosomal protease cathepsin D.
E)None of the above describes the function of Botox.
Q2) Which of the following is (are)NOT found as covalently attached anchors in lipid-linked proteins?
A)isoprenoid groups
B)fatty acids
C)cholesterol and other sterols
D)glycosylphosphatidyl inositol groups
E)All of the above are found as covalently attached anchors in lipid-linked proteins.
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Chapter 10: Membrane Transport
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Sample Questions
Q1) D-Glucose and D-mannitol are similarly soluble, but D-glucose is transported through the erythrocyte membrane four times as rapidly as D-mannitol.What is the most likely explanation?
A)D-glucose undergoes simple diffusion more rapidly than mannitol because glucose is less polar.
B)D-glucose and D-mannitol enter the erythrocyte via an ion-gated channel.
C)D-glucose and D-mannitol are transported via a system that distinguishes the two sugars.
D)D-glucose flux through the membrane is linear whereas D-mannitol flux is described by a hyperbolic curve.
E)None of the above provides the explanation.
Q2) Which of the following channels open in response to an extracellular stimulus such as a neurotransmitter?
A)mechanoselective channels
B)ligand-gated channels
C)signal-gated channels
D)voltage-gated channels
E)All of these are sensitive to an extracellular stimulus..
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Page 12

Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) Enzymes that bind reaction transition states with greater affinity than substrates or products
A)have a lower free energy ES complex than E + S.
B)increase reaction rates by decreasing the concentration of the transition state .
C)progress slowly due to the stability of the transition state complex.
D)compensate for small differences in the energy of the free substrate and free product.
E)All of the above are correct.
Q2) Acid-base catalysis may be accomplished by:
A)active site specificity
B)charge delocalization
C)buffer effects
D)induced strain
E)conformational change
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Chapter 12: Enzyme Kinetics, Inhibition and Control
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Sample Questions
Q1) Enzyme activity in cells is controlled by which of the following?
I.covalent modifications
II.modulation of expression levels
III.feedback inhibition
IV.allosteric effectors
A)I
B)II
C)III
D)III, IV
E)I, II, III, IV
Q2) When [S] = K<sub>M</sub>, \(\upsilon\)<sub>0 </sub>= (_____)× (V<sub>max</sub>).
A)[S]
B)0.75
C)0.5
D)K<sub>M</sub>
E)k<sub>cat</sub>
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Page 14

Chapter 13: Biochemical Signaling
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Sample Questions
Q1) Oncogenes
I.function as cell cycle inhibitors.
II.encode a protein which block cell cycle inhibition.
III.are expressed by cells that have higher levels of human growth hormone.
IV.can function as transcription factors.
A)I, III, IV
B)II, III
C)III, IV
D)II, IV
E)II
Q2) The \(\beta\) cells of the islets of Langerhans secrete ______ in response to ______ glucose levels in the muscle and/or adipose tissue.
A)insulin; low
B)insulin; elevated
C)glucagon; low
D)glucagon; elevated
E)somatostatin; elevated
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Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) Which of the following are factors that contribute to the large negative standard free energy change for the reaction shown below?
ATP \(\rarr\) ADP + P<sub>i</sub>
A)the increase in resonance stabilization in the reactants compare to the products
B)the precipitation of the insoluble P<sub>i</sub>
C)the addition of a water molecule to the hydrophilic ATP molecule
D)the decrease in negative charge repulsion in the products compared to reactants
E)all of the above
Q2) The enzyme inorganic pyrophosphatase catalyzes the hydrolysis of bonds in ___.
A)ATP
B)ADP
C)AMP
D)PP<sub>i</sub>
E)phosphate
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Chapter 15: Glycogen Metabolism and Gluconeogenesis
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Sample Questions
Q1) Levels of glucose-6-phosphate (G6P)are affected by which of the following?
I.glycogen breakdown
II.activity of the pentose phosphate pathway
III.galactose preparation for entry into glycolysis
A)I, II
B)I, II, III
C)III
D)II, E)I, III
Q2) The glycogen debranching enzyme is required for
A)the transfer of 3-glucose units from one branch to another.
B)the transfer of phosphate from one position to another.
C)cleaving \(\alpha\)(1\(\rarr\)6)sugar linkages
D)A and C
E)A, B and C
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Chapter 16: Glucose Catabolism
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Sample Questions
Q1) Glycolysis forms ____ under either aerobic or anaerobic conditions.
A)fructose-1,6-bisphosphatase
B)pentose phosphate
C)pyruvate decarboxylase
D)hypoglycemia
E)phosphofructokinase
F)NADP+
G)thiamine pyrophosphate
H)ATP
I)galactosemia
J)NAD+
K)fluoride ion
L)pyruvate
M)glucogenic
N)FAD
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18

Chapter 17: Citric Acid Cycle
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Sample Questions
Q1) Which of the following enzymes of the citric acid cycle is inhibited by ATP?
A)citrate synthase
B)isocitrate dehydrogenase
C)(\(\alpha\)-ketoglutarate dehydrogenase)
D)succinyl-CoA synthetase
E)A and B
Q2) In eukaryotes, the citric acid cycle occurs in the _____ and therefore requires that reactants of the citric acid cycle be transported from the _____.
A)cytosol; mitochondrial matrix
B)mitochondrial matrix; cytosol
C)endoplasmic reticulum; mitochondrial matrix
D)inner mitochondrial membrane; mitochondrial matrix
E)outer mitochondrial membrane; cytosol
Q3) The reaction catalyzed by _____ requires an enzyme bound flavin coenzyme.
A)isocitrate dehydrogenase
B)(\(\alpha\)-ketoglutarate dehydrogenase)
C)succinyl-CoA synthetase
D)succinate dehydrogenase
E)malate dehydrogenase
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Page 19

Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Sample Questions
Q1) Based on the information in the chapter, which of the following is TRUE regarding Complex III?
I.A large portion of Complex III dissociates from the membrane bound portion of the complex.
II.Complex III contains three identical cytochrome redox centers.
III.The Q cycle allows stepwise reoxidation of the two electrons from CoQH<sub>2</sub>.
IV.A change in conformation of iron sulfur protein (ISP)ensures that the Reiske center is reduced preferentially by CoQ<sup>.-</sup>.
A)I only
B)I, II
C)III only
D)III, IV
E)I, III, IV
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Chapter 19: Photosynthesis
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Sample Questions
Q1) The redox centers PSII, PbRC, PbRC from Rps.viridis, and cytochrome b<sub>6</sub>f
A)have identical prosthetic groups that differ only in sequence of arrangement and spatial orientation.
B)have some degree of symmetry either based on their prosthetic groups or based on tertiary protein structure.
C)all become reduced due to activity of the OEC.
D)all of the above
E)none of the above
Q2) In photorespiration, reduction of hydroxypyruvate to glycerate requires ____ and occurs in the ____.
A)NADPH; mitochondrion
B)NADH; peroxisome
C)NADPH; chloroplast
D)NADH; chloroplast
E)none of the above
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Chapter 20: Lipid Metabolism
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Sample Questions
Q1) The molecules acetoacetate, acetone, and d-\(\beta\)-hydroxybutyrate are metabolic fuels termed ________.
A)HDL
B)propionyl-CoA
C)LDL
D)Dihydroxyacetone phosphate
E)malonyl-CoA
F)ACP
G)chylomicrons
H)phosphopantetheine
I)flavin
J)albumin
K)ketone bodies
L)cholesterol
Q2) Which of the following is the starting metabolite in ketone body biosynthesis?
A)acetyl CoA
B)malonyl CoA
C)propionlyl CoA
D)acetyl CoA and propionyl CoA
E)acetyl CoA and malonyl CoA
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Page 22
Chapter 21: Amino Acid Metabolism
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Sample Questions
Q1) Which of the following is TRUE regarding catabolism of leucine?
A)The pathway begins with aspartate.
B)The pathway requires \(\alpha\)-ketoglutarate.
C)The pathway requires TPP.
D)The pathway generates HMG-CoA.
E)none of the above
Q2) Individuals with an alanine to valine mutation in N<sup>5</sup>, N<sup>10</sup>methylenetetrahydrofolate reductase (MTHFR)
I.typically have higher levels of homocysteine.
II.have increased risk for cardiovascular disease.
III.typically have increased incidence of oxidative damage to the walls of blood vessels.
IV.are at increased risk, if female, of giving birth to a child with a neural tube defect.
A)I, II
B)II, III
C)I only
D)IV only
E)I, II, III, IV
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Page 23

Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Sample Questions
Q1) The glucose transporter in muscle cells is A)insulin.
B)glucagon.
C)GLUT2.
D)GLUT4.
E)none of the above
Q2) Phospholipase C cleaves PIP<sub>2</sub>, generating
A)IP<sub>3</sub> and DAG (inositol-1,4,5-trisphosphate and 1,2-diacylglycerol).
B)cAMP and PP<sub>i</sub>.
C)cAMP and DAG (1,2-diacylglycerol).
D)IP<sub>3</sub> and PP<sub>i</sub>.
E)IP<sub>3</sub> and P<sub>i</sub>.
Q3) The majority of glucose in the brain
A)is used to store adequate glycogen for extended periods of starvation.
B)is used to produce ATP for membrane Na<sup>+</sup>-K<sup>+</sup> ATPase required for nerve impulse transmission.
C)is synthesized from fatty acids due to the need for high ATP levels.
D)is synthesized in the adipose tissue and transported to the brain.
E)is synthesized from ketone bodies under conditions of prolonged fasting.
Page 24
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Chapter 23: Nucleotide Metabolism
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Q1) The synthesis of the dNTPs required for DNA production must be controlled by ________ in order to ensure minimal ________ activity from excess of one dNTP over the other dNTPs.
A)feedback inhibition; mutagenic
B)feed forward activation; synthesis
C)substrate availability; mutagenesis
D)secondary messenger systems; synthesis
E)feed forward; mutagenic
Q2) Atoms from which of the following amino acids are utilized in pyrimidine biosynthesis?
I.glutamine
II.glycine
III.asparagine
IV.aspartate
A)I, II
B)I.III
C)I, IV
D)II, III
E)II, IV
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Chapter 24: Nucleic Acid Structure
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Q1) Which of the following statements about the structure and conformation of DNA is FALSE?
A)DNA binding proteins distort DNA structure
B)Changes in ionic strength can alter DNA structure
C)Specific sequences can cause deviations in conformation.
D)Changes in DNA conformation result from energy minimizations and do not relate to in vivo conditions.
E)All of the above are true.
Q2) The sequence-specific binding of BamHI to DNA depends primarily on
A)hydrogen bonding and allows binding to less specific sequences as well.
B)hydrogen bonding and precludes binding to any other sequence.
C)stacking interactions and could be mimicked using an intercalation molecule.
D)hydrogen bonding and could be mimicked using an intercalation molecule.
E)none of the above
Q3) During which of the following processes are RNA DNA hybrids observed?
A)transcription, both eukaryotic and prokaryotic
B)translation, both eukaryotic and prokaryotic
C)replication, both eukaryotic and prokaryotic
D)transcription, prokaryotic only
E)replication, prokaryotic only
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Chapter 25: Dna Replication, Repair and Recombination
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Q1) DNA separated at the replication fork is stabilized by ______ .
A)SSB
B)Tus
C)primosome
D)ARS
E)ATS
F)primer
G)transposons
H)nick translation
I)photolyase
J)processive
K)G-loops
L)G-quartets
M)accurate
N)lagging strand synthesis
O)MCM
P)abortive
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Chapter 26: Transcription and Rna Processing
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Q1) CpG islands function analogously to prokaryotic ______.
A)Rho (Þ)
B)introns
C)sigma ( )
D)sense
E)operons
F)structural
G)Pribnow
H)promoters
I)antisense
J)exons
K)nucleolus
L)TATA
M)Sense
N)AAAA (poly A)
O)Ribosome
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28
Chapter 27: Translation
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Q1) Structural studies of the bacterial ribosome indicate which of the following important points regarding function?
A)The domains of the 30S subunit appear flexible during protein synthesis.
B)The large subunit of the ribosome appears to undergo domain motion during protein synthesis.
C)The small and large subunits of the ribosome appear static throughout protein synthesis.
D)all of the above
E)none of the above
Q2) The Shine-Dalgarno sequence is
A)used to align ribosome subunits and initiation translation.
B)functions as a stop codon.
C)is used to align RNA polymerase.
D)is used during transcription termination.
E)all of the above
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29

Chapter 28: Regulation of Gene Expression
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Q1) Progression through the cell cycle
I.is regulated by cyclins.
II.is controlled by Cdks.
III.is altered by CKIs.
A)I only
B)II only
C)III only
D)II , III
E)I, II, III
Q2) Which of the following is TRUE regarding eukaryotic mRNAs?
I.They uniformly stable.
II.The poly (A)tail appears to partially Moderate the rate of degradation.
III.The 5' cap appears to partially Moderate the rate of degradation.
IV.They have decay times ranging from 10-30 minutes.
A)I, II
B)II, III
C)II, IV
D)III, IV
E)II only
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