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. Calculate the pH of a dilute solution that contains a molar ratio of potassium acetate to acetic acid
(pKa = 4.76) of 2:1. The answer is:
Hydrophobic interactions account for
why biomolecules are amphipathic.
why the nonpolar regions of molecules cluster together in water.
the tendency of lipids to disperse in water.
why the polar regions of molecules are associated with water.
A weak acid has a pKa of 7.4. To 100 mL of a 1.0 M solution of this compound at pH 8.0 is added 30 mL of 1.0 M hydrochloric acid. The resulting solution is pH:
pH = 6.5
pH = 6.8
pH = 7.1
pH = 7.4
pH = 7.8
Phosphoric acid, H3PO4, is tribasic with pKa values of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is:
2.14 6.86 12.4
H3PO4 + H2O ⇌ H3O+ + H2PO4-
None of the above
Ammonia is a weak base: NH3 + H2O ⇌ NH4+ + OH ̄ At what pH is the ratio of [NH4+]/[NH3] = 2.0?
100 mL of 0.1 M NaOH is added to 55 mL of 0.2 M lactic acid. The pKa of lactic acid is 4.1. The resulting mixture has a pH close to:
A. pH = 2
B. pH = 3
C. pH = 4
D. pH = 5
E. pH = 6
Consider a buffer made from acetic acid (CH3COOH) and sodium acetate (CH3COONa), initially at the same pH as the pKa of acetic acid, 4.76. When sodium hydroxide (NaOH) is mixed with this buffer, the:
pH remains constant.
pH rises more than if an equal amount of NaOH is added to an acetate buffer
initially at pH 6.76.
pH rises more than if an equal amount of NaOH is added to unbuffered water at
ratio of acetic acid to sodium acetate in the buffer falls.
ratio of acetic acid to sodium acetate in the buffer increases.
The weak acid, hippuric acid, is 5.0% ionized (dissociated) at pH 2.3. What is the pKa of the hippuric acid?
A. pKa = 2.3
B. pKa = 3.6
C. pKa = 4.9
D. pKa = 6.5
E. pKa = 8.3
What is the isoelectric point of Asp, its three pKa values are:
pKCOOH = 2.09, pKNH3 = 9.82, and pKR-group = 3.86. What is the isoelectric point for Asp?
What is the isoelectric point for the tripeptide, Gly-Arg-Val, given the data in the table below?
Which group or groups on a protein contribute most to its overall acid-base properties?
The α-amino groups of all nonterminal amino acids.
The N-terminal α-amino group on the protein.
The R groups on the protein.
The C-terminal α-carboxyl group on the protein.
The amide bonds in the chain
A peptide has the sequence Glu–His–Trp–Ser–Gly–Leu–Arg–Pro–Gly
What is the net charge of the molecule at pH 3, 8, and 11?
at pH 3, +3; at pH 8, +2; at pH 11, +1
at pH 3, +1; at pH 8, 0; at pH 11, −1
at pH 3, +2; at pH 8, +1; at pH 11, −0
at pH 3, +1; at pH 8, 0; at pH 11, −2
at pH 3, +2; at pH 8, 0; at pH 11, −1
In the a-helix, the hydrogen bonds:
are roughly perpendicular to the axis of the helix.
are roughly parallel to the axis of the helix.
occur mainly between electronegative atoms of the R
occur only between some of the amino acids of the helix.
Quaternary structure describes the:
linear sequence of amino acids from the N-terminus to the C-terminus.
the sum of a-helices, b-sheets, and b-turns in a functional protein
relative orientation of one protein to another in a multi-protein functional unit
the planar peptide bond
the formation of salt bridges in a protein
A protein binds to a ligand with a Kd of 1.0 10-5 M. At what concentration does equal 0.5?
three-dimensional structure of a protein is determined primarily by:
A d-amino acid would interrupt an α-helix made of l-amino acids. Another naturally occurring hindrance to the formation of an α-helix is the presence of:
a nonpolar residue near the carboxyl terminus.
a negatively charged Arg residue.
two Ala residues side by side.
a Pro residue.
Describe the Bohr effect, with regard to the binding of O2 to hemoglobin?
A. In the presence of H+ and CO2, the O2 binding capacity of hemoglobin decreases.
B. In the presence of H+ and Cl-, hemoglobin dissociates in monomers.
C. In the presence of CO2 and 2,3-bisphosphoglycerate, the O2 binding capacity of hemoglobin increases.
D. In the presence of 2,3-bisphosphoglycerate and H+, the Hill number for the binding of O2 to hemoglobin decreases from 3.2 to 2.0.
E. In the presence of H+ and CO2, the Hill number for the binding of O2 to hemoglobin increases from 2.0 to 3.2.
What is effect of 2,3-bisphosphoglycerate (BPG) on the binding of O2 to hemoglobin?
A. BPG decreases the Hill number and decreases the affinity of hemoglobin for O2.
B. BPG decreases the Hill number and increases the affinity of hemoglobin for O2.
C. BPG increases the Hill number and decreases the affinity of hemoglobin for O2.
D. BPG increases the Hill number and increases the affinity of hemoglobin for O2.
E. BPG has no effect on the Hill number and increases the affinity of hemoglobin for O2.
Which of the following statements regarding hydrogen bonding in secondary structures is true?
Both α-helices and β-sheets only use intrachain hydrogen bonds.
Both α-helices and β-sheets only use interchain hydrogen bonds.
α-helices only use intrachain hydrogen bonds and β-sheets can use either
intrachain or interchain hydrogen bonds.
α-helices can use either intrachain or interchain hydrogen bonds and β-sheets only use interchain hydrogen bonds.
None of the above
intrachain or interchain hydrogen bonds.
What happens when a protein is denatured?
Its secondary structure is disrupted but its primary structure remains intact.
Its primary structure is disrupted but its secondary structure remains intact.
It is broken apart into its constituent amino acids.
It becomes all α-helix.
Covalent bonds break.
Thermolysin, a protease isolated from Bacillus thermoproteolyticus, only cleaves peptide bonds found on the N-side of isoleucine, leucine, methionine, and valine. Thermolysin treatment of peptide T1 (shown below) generates which products.
T1 = LGADMKSCTV
A. No reaction, so the product is LGADMKSCTV
B. There are 3 products: L, GADM, and KSCTV.
C. There are 3 products: LGAD, MKSCT, and V.
D. There are 2 products: LGADM and KSCTV.
E. There are 2 products: LGADMK and SCTV.
A mixture of Asp, His, Ser, and Lys applied to an anion-exchange column and the amino acids were eluted from the using an elution gradient of increasing NaCl concentration in pH 6.2 buffer. What would be the correct elution sequence?
A. Asp, His, Ser, and lastly Lys
B. His, Ser, Lys, and lastly Asp
C. Ser, Lys, Asp, and lastly His
D. Lys, His, Ser, and lastly Asp
E. Lys, Asp, His, and lasty Ser
A protein retained on an affinity chromatography column is usually eluted off the column by:
A. gradually increasing the salt concentration of the elution buffer.
B. adding excess of the protein's ligand
C. changing the pH of the elution buffer.
D. allowing the retained protein to naturally come off the column after the non- specifically bound proteins have first passed through the resin.
E. none of the above
B. adding excess of the protein's ligand
Which of the following is true concerning how enzymes work in the cell?
Enzymes are consumed in the process of converting one molecule to another.
Enzymes are needed to carry out only endergonic reactions.
Enzymes are needed in the cell to increase the rate of a chemical reaction.
Enzymes eliminate the activation barrier.
Enzymes increase the activation barrier
To calculate the turnover number of an enzyme, you need to know:
A. the enzyme concentration.
B. the initial velocity of the catalyzed reaction at [S] >> KM.
C. the initial velocity of the catalyzed reaction at low [S].
D. the KM for the substrate.
E. both A and B.
For an enzyme that obeys standard Michealis-Menten kinetics, what does θ equal? Hint, remember the concept of θ from our discussion of O2 binding to myogoblin or O2 binding to hemoglobin.
D. KM × VMAX
E. KM /VMAX
You do an enzyme kinetic experiment and calculate the VMAX of 200 μmol of product per minute. If each assay used 50 μL of enzyme solution that had a concentration of 0.25 mg/mL, what would be the turnover number if the enzyme had a molecular weight of 100,000 g/mol?
A. 200 sec-1
B. 1000 sec-1
C. 2.7 × 104 sec-1
D. 1.0 × 105 sec-1
E. 1.6 × 106 sec-1
At what substrate concentration would an enzyme with a Km of 0.0050 M operate at one-eighth of its maximum rate?
A. 7.1 X10-4 M
B. 6.1X 10-3 M
C. 7.9X10 -3 M
Which of the following is true about the free-energy changes involved in reactions that favor the formation of product?
The ground state free energy of the product must be lower than the ground state free energy of the substrate.
The activation energy is the difference between the substrate and product ground state free energies.
Enzymes lower the overall free standard free-energy change (ΔG′°) of a reaction.
The difference between the energy levels of the ground state and transition state is
Enzymes increase the activation energy.
An allosteric interaction between a ligand and a protein is one in which:
A. binding of a molecule to a binding site affects binding of additional molecules
to the same site.
B. binding of a molecule to a binding site affects binding properties of another site on the protein.
C. binding of the ligand to the protein is covalent.
D. multiple molecules of the same ligand can bind to the same binding site. E. two different ligands can bind to the same binding site.
Enzyme X exhibits maximum activity at pH = 6.3. X shows a fairly sharp decrease in its activity when the pH goes much lower than 5.8. One likely interpretation of this pH activity is that:
A. a Glu residue on the enzyme is involved in the reaction.
B. a His residue on the enzyme is involved in the reaction.
C. a Tyr residue on the enzyme is involved in the reaction.
D. the enzyme uses NADH has a cofactor.
E. the enzyme uses coenzyme A has a cofactor.
Considering enzyme mechanisms, what group is often attacked by a nucleophile?
A. The R-group of leucine.
B. The carbon atom of a carbonyl group.
C. The 3’-hydroxyl group of nucleosides and nucleotides.
D. The oxygen atom of an alcohol group.
E. The nitrogen atom of the imidazole group.
Which of the following is true about general acid-base catalysis?
It requires the ions of water.
Amino acid side chains on enzymes can act as proton donors or acceptors.
It often involves covalent bonds formed between a metal ion and the substrate.
It involves a transient covalent bond between the enzyme and the substrate.
It involves an expenditure of energy supplied by ATP
Which of the following is true about the phosphorylation of proteins?
Proteins are usually phosphorylated at amino acids that have hydroxyl group- containing side chains.
Phosphorylation of proteins is catalyzed by phosphatases.
Phosphoryation always activates enzymes.
Proteins are usually phosphorylated at the N terminus of the chain.
Phosphorylation always decreases the activity of the enzyme.
Facilitated diffusion occurs:
in either direction depending on the temperature
in either direction depending on the concentration gradient of the molecule
in either direction depending on the size of the molecule
into the cell only
out of the cell only
Facilitated diffusion in membranes is a process wherein:
molecules move up the concentration gradient in the membrane without the need
to supply energy.
molecules move against the concentration gradient assisted by energy from ATP.
molecules move down the concentration gradient assisted by a carrier.
molecules move up the concentration gradient assisted by a carrier.
molecules move up a concentration gradient via energy supplied by secondary
Which of these is a general feature of the lipid bilayer in all biological membranes?
Individual lipid molecules in one face (monolayer) of the bilayer readily diffuse
(flip-flop) to the other monolayer
Na+ and K+ ions readily diffuse across the bilayer
Individual lipid molecules are free to diffuse laterally in the surface of the bilayer
The bilayer is stabilized by covalent bonds between neighboring phospholipid
The polar head groups face inward toward the inside of the bilayer.
Which of the following lipids is used for energy storage?
Which of the following statements is true about active transport?
The transported species always moves against its electrochemical gradient.
It is needed only for the transport of polar molecules.
It is exergonic.
It must be linked to ATP hydrolysis.
It must be regulated by phosphorylation
The compound that consists of ribose linked by an N-glycosidic bond to the N-9 of adenine is:
a purine nucleotide.
a pyrimidine nucleotide.
What is the nucleotide sequence of the DNA strand that is complementary to 5'- ATCGCAACTGTCACTA-3'?
Which of the following statement is incorrect when double stranded bacterial DNA is denatured by heat?
The higher the G+C content, the higher the melting temperature.
The transition from double-stranded DNA to single-stranded DNA is cooperative.
The fraction of DNA that is single-stranded is 0.5 at its Tm.
The absorbance at 260 nm decreases about 40%.
The viscosity of the DNA solution decreases.
The glycosidic linkage (-N-Glycosidic Bond) in RNA and DNA nucleotides:
always links A with T and G with C
is susceptible to proteolysis
links the base to the sugar moiety
is a special form of hydrogen bonding found in nucleic acids
links the base to the phosphate moiety
What is the complete base composition (in %) of a double-stranded eukaryotic DNA that contains 22% guanine?
52 A, 8 C, 22 G, 18 T
28 A, 22 C, 22 G, 28 T
16 A, 16 C, 22G, 46 T
46 A, 16 C, 22G, 16 T
18 A, 8 C, 22 G, 52 T
Which of the following is true about the denaturation of double-helical DNA?
Denaturation increases with decreasing temperature.
Denaturation is accompanied by an increase in the absorption of UV light by
G-C rich DNA melts at lower temperature than A-T rich DNA.
Once denatured, DNA strands cannot anneal.
After denaturation DNA retains its secondary structure.
Which of the following is true about the structure of nucleotides?
Purine nucleotides contain a base and a phosphate while pyrimidine nucleotides
contain only a base.
Pyrimidine bases are larger than purine bases.
Purine and pyrimidine bases are found in DNA and RNA.
Thymine bases are found in DNA and RNA.
DNA contains uracil
The role of the Dam methylase is to:
add a methyl group to uracil, converting it to thymine.
modify the template strand for recognition by repair systems.
remove a methyl group from thymine.
remove a mismatched nucleotide from the template strand.
replace a mismatched nucleotide with the correct one.
In our discussions about replication, we talked about processivity? What is processivity?
The number of nucleotides joined to the growing nucleotide chain before DNA polymerase dissociates from the DNA template.
The kcat for DNA polymerase.
The v/VMAX ratio for DNA polymerase.
The ratio of the kcat for DNA polymerase to the kcat for primase.
The average KM value for the four deoxynucleoside triphosphates as
substrates for DNA polymerase.
During DNA replication the lagging strand is complemented with Okazaki fragments that still contain the RNA primer. Which pair of enzymes removes the RNA primer and seals the DNA nicks?
DNA polymerase III and helicase
DNA polymerase III and primase
DNA polymerase I and ligase
the DNA polymerases II and III
All of the following are characteristic of replication of the E. coli circular chromosome EXCEPT:
replication is bi-directional.
replication forks move in opposite directions.
the unwinding of the duplex DNA is driven by the translocation of the DNA
torsional stress introduced in the duplex DNA is relieved by DNA gyrase.
it initiates at a unique position called oriC.
In DNA replication Okazaki fragments
are synthesized in the 3′ to 5′ direction.
are found on the leading strand.
are synthesized discontinuously.
are synthesized without the need for a prime.
are synthesized in the same direction as fork movement.
Which of the following proteins unwinds the two parental DNA strands in E. coli? A. DNA gyrase
D. SSB protein
The sigma factor () of E. coli RNA polymerase:
associates with the promoter before binding core enzyme.
combines with the core enzyme to confer specific binding to a promoter.
is inseparable from the core enzyme.
is required for termination of an RNA chain.
will catalyze synthesis of RNA from both DNA template strands in the
absence of the core enzyme.
What is the role of the catabolite activator protein (CAP)?
CAP stimulates the transcription of the lac operon structural genes when the intracellular concentration of cAMP is high.
CAP stimulates the transcription of the lac operon structural genes when the intracellular concentration of cAMP is low.
CAP stimulates the transcription of the lac operon structural genes by catalyzing the conversion of lactose to allolactose.
CAP stimulates the transcription of the lac operon structural genes by inhibiting the conversion of lactose to allolactose.
CAP is facilates promoter clearance by RNA polymerase by binding to holoenzyme and causing the subunit to dissociate.
A branched (“lariat”) structure is formed during:
attachment of a 5' cap to mRNA.
attachment of poly(A) tails to mRNA.
processing of preribosomal RNA.
splicing of group I introns.
splicing of group II introns.
Processing of a primary mRNA transcript in a eukaryotic cell does not normally involve:
A. attachment of a long poly(A) sequence at the 3' end.
B. conversion of normal bases to modified bases, such as inosine and pseudouridine.
C. excision of intervening sequences (introns).
D. joining of exons.
E. methylation of one or more guanine nucleotides at the 5' end.
If E. coli encounter an environment that is high in the concentration of glucose and the concentration of lactose, which of the following scenarios would result?
lac repressor bound to the promoter, CAP bound to promoter, and no transcription of the lac operon
lac repressor bound to the inducer, CAP bound to promoter, and no transcription of the lac operon
lac repressor bound to the inducer, CAP bound to promoter, and the lac operon is transcribed
Lac repressor bound to the inducer, CAP not bound to promoter, and no transcription of the lac operon
lac repressor bound to the inducer, CAP not bound to promoter, and the lac operon is transcribed
Properties common to the reactions catalyzed by DNA polymerase and RNA polymerase are:
Use of a template strand of nucleic acid
Synthesis in the 5′→3′ direction
Use of nucleoside triphosphate substrates
Formation of phosphodiester bonds
All of the above
In transcription, promoters
are required for elongation of transcription.
B.are recognized by topoisomerases
are described as the sequence on the DNA template strand.
tend to be G-C rich.
are proteins that bind to RNA
Aminoacyl-tRNA synthetases exhibit selectivity which functions to verify that:
the correct amino acid and tRNA are attached to the enzyme
the N-formyl-met-tRNA synthesis is complete
the first aminoacid incorporated into the chain is formylated methionine.
the amino acids are attatched to both the 2’ and 3’position on the ribose ring.
all class I Aminoacyl-tRNA synthetases transesterify the 2’-O aminoacyl-tRNAs
formed in the reaction.
Which of the following is true about aminoacyl-tRNA synthetases?
They generate charged tRNAs.
They add an amino acid to the 5′ end of a tRNA.
They recognize only the anticodon arm of tRNAs.
They cannot proofread.
Three of the above are correct.
Chain termination in translation requires:
rho hexamer, 30 rhibosome and IFfactors
release of the initiation factor, stop codons and ATP
70 S ribosome, stop codons and EF-Tu units
rho hexamer, release factors and ATP
stop codons, release factors and GTP
Which of the following is true for the Shine-Dalgarno sequences:
Which of the following are features of the Wobble hypothesis?
A naturally occurring tRNA exists in yeast that can read both arginine and lysine
A tRNA can recognize only one codon.
Some tRNAs can recognize codons that specify two different amino acids, if both
The “wobble” occurs only in the first base of the anticodon.
The third base in a codon always forms a normal Watson-Crick base
What would be the effect of adding 2',3'-dideoxyadenosine triphosphate (ddATP) to an in vitro DNA replication reaction in large excess over of the normal DNA polymerase substrate, 2'-deoxyadenosine triphosphate? This is not a trick question and ddATP will serve as a DNA polymerase substrate.
fluorescent dye method for sequencing DNA:
Sticky ends are single stranded DNA overhangs that:
are recognized by the RNA polymerase during transcription
are recognized by the DNA polymerase during replication
form primers during transcription
provide complementary hydrogen bonding for ligation
stabilize DNA from nucleases
DNA can be sequenced by the Sanger dideoxy method in which
radioactively labeled DNA is subjected to four sets of base-specific cleavage
automated sequencing can be done using different fluorescent-labeled 2′
a primer is not needed.
the sequence can be read by a laser beam.
radioactive labelling must be used with the dideoxy method.
In the Sanger (dideoxy) method for DNA sequencing, a small amount of a dideoxynucleotide triphosphate—say, ddCTP—is added to the sequencing reaction along with a larger amount of the corresponding dCTP along with the corresponding dATP, dTTP, dGTP nucleotides. What result would be observed if the dCTP were omitted?
No reaction takes place.
When the first G residue is encountered in the template, ddCTP will be added, and polymerization will halt.
If there are 7 G residues in the template there will be 7 fragments ending in a C residue.
The strand produced will only contain A,T, and C residues
When the first C residue is encountered in the template, ddCTP will be added, and
polymerization will halt.
Consider the following reaction: Succinate +FAD Fumarate + FADH2 How many of the following statements are true?
Succinate is the reducing agent
FAD is the oxidizing agent
Fumarate is reduced
FAD is reduced
Succinate is reduced
What is ΔS°′ for the reaction below at 298 K if ΔG°′ = -28.3 kJ/mol and ΔH°′ = +3.9 kJ/mol
+108 J/mol K
+0.108 J/mol K
-32.2 kJ/mol K
The standard free energy change of hydrolysis (at 298 K) for acetyl phosphate (shown below) is ΔG°′ = - 42.3 kJ/mol.
Acetyl-P + H2O → acetate + Pi
The free energy change for acetyl phosphate hydrolysis in a solution of 2 mM acetate, 2 mM phosphate and 3 nM acetyl phosphate is:
At 300 K, the standard free energy for the hydrolysis of ATP to ADP (ATP + H2O ↔ ADP + Pi) is ΔG°′ = -31.0 kJ/mol. If the concentration of ATP, ADP and Pi are 1 nM, 0.4 mM and 0.9M, the reaction:
go to the left
go to the right
is in equilibrium
will never reach equilibrium
all the above
Consider this rxn at 298 K which has a ΔG° = +0.4 kJ/mol.
succinate + FAD <—> fumarate + FADH2
1 mM of each compound are mixed & the reaction is allowed to come to equilibrium. Which statement is correct about the resulting concentration of FAD at equilibrium?
[FAD] > [FADH2]
Cannot be determined from the information provided.
Which best describes the ΔG for hydrolysis of creatine phosphate under cellular conditions in which the concentration of creatine phosphate, creatine, and phosphate all equal 1 mM at 25°C. The ΔGo for the hydrolysis of creatine phosphate at 25°C is –43 kJ/mol.
ΔG < -43 kJ/mol
ΔG = -43 kJ/mol
-43 kJ/mol < ΔG ≤ 0 kJ/mol
ΔG > 0 kJ/mol
None of the above
The standard free energy change for ATP hydrolysis is -30.5 kJ/mol. Therefore the free energy change for this reaction in a cell in which the concentration of ATP, ADP, and Pi are 3.4 mM, 1.3 mM and 4.8 mM, respectively, and assuming a physiologically relevant temperature (37 oC), is:
Substrate-level phosphorylation requires that:
oxidative phosphorylation occurs
ATP is converted to ADP + Pi
the free energy of the hydrolysis reaction is more negative than the free energy of
hydrolysis of the new phosphate compound formed
the free energy of the ATP hydrolysis is more negative than the free energy of hydrolysis of the molecule donating the phosphate to ADP
NADH is coupled to the phosphorylation to yield an overall negative free energy for the reaction
hydrolysis of the new phosphate compound formed
When pyruvate is formed in glycolysis what are the possible reactions that it can undergo?
anaerobic alcohol fermentation
production of fructose-1,6-bisphosphate
production of fructose-6-phosphate
1, 3 and 4
1, 2, 3, 4 and 5
1, 2, and 3
2, 3 and 4
3 and 4
During glycolysis, seven of the ten reactions that convert glucose to pyruvate exhibit free energy changes close to zero (either very small negative or very small positive). This suggests that:
a) these reactions are near equilibrium
b) they are not control points for glycolysis
c) they are reversible
d) none of the above
e) a,b and c
Pyruvate kinase is allosterically inhibited by:
high concentrations of AMP
high concentrations of ATP
high concentrations of citrate
low concentrations of acetyl-CoA
none of the above
In glycolysis 3-phosphoglycerate to is converted to 2-Phosphoglycerate. The enzyme that catalyzes this reaction is: is:
In glycolysis, ATP is synthesized by
both substrate-level and oxidative phosphorylation.
all three of the above methods.
Which of the following steps occurs during the payoff phase of glycolysis?
the conversion of phosphoenolpyruvate to pyruvate
the conversion of fructose 6-phosphate to fructose 1,6-biphosphate
the conversion of glucose 6-phosphate to fructose 6-phosphate
the conversion of glucose to glucose 6-phosphate
The conversion of fructose-6-phosphate to fructose1,6-bisphosphate
What types of reactions do phosphorylases catalyze?
Displacement reactions in which an attacking phosphate becomes covalently attached at the point of bond breakage.
The removal of a phosphoryl group from a phosphate ester.
The transfer of a phosphoryl group from a nucleoside triphosphate to an acceptor
Ligation reactions in which phosphate esters join molecules.
All of the above.
High concentrations of fructose-2,6-bisphopshate
stimulate glycolysis and inhibit gluconeogenesis.
inhibit glycolysis and stimulate gluconeogenesis
stimulate both glycolysis and gluconeogenesis.
inhibit both glycolysis and gluconeogenesis
have no effect on either glycolysis or gluconeogenesis
Which of the following statements concerning the initial phase of the pentose phosphate pathway is false?
A CO2 molecule is released from glucose.
Two molecules of NADPH are produced per glucose.
Ribulose-5-phosphate is produced by an oxidative decarboxylation of 6-
The process reduces glucose-6-phosphate.
All of the above are true.
When glycogen synthase is phosphorylated:
its activity decreases.
its activity increases.
its activity is unaffected.
it is not allosterically controlled
it never gets phosphorylated
is inhibited by glucose-6-phosphate
responds differently to ATP levels in its phosphorylated and unphosphorylated
exists in two forms, phosphorylase a and phosphorylase b
is activated by AMP
all of the above
Which of the following statements concerning biotin and gluconeogenesis is false?
Biotin is used to add CO2 to certain intermediates in gluconeogenesis.
CO2 is incorporated into the glucose product.
Biotin is capable of binding covalently to CO2.
Biotin helps synthesize an important precursor of phosphoenolpyruvate.
ATP hydrolysis is required to attach CO2 to biotin.
UDP-glucose pyrophosphorylase works by this mechanism:
It adds a phosphate group to glucose from UTP, leaving behind UDP.
It adds a UMP molecule to glucose-1-phosphate by splitting out pyrophosphate.
It adds a pyrophosphate group to glucose, using UTP.
It adds a UDP molecule to glucose by splitting out phosphate.
It transfers a phosphate from ATP to ADP.
Which of the following is not a control mechanism for glycogen phosphorylase?
Inhibition by glucose.
Subunit association and dissociation.
Allosteric stimulation by AMP.
All of these mechanisms regulate the activity of glycogen synthase.
During the pentose phosphate pathway (glucose-6-P –> ribose-5-P):
There is a net oxidation of the substrate carbon atoms.
There is no net oxidation of the substrate carbon atoms.
NADP+ is generated.
NAD+ is generated.
None of the above.
What role does coenzyme A play in the citric acid cycle?
It is an electron carrier.
It carries hydride ions.
It is an acyl group carrier.
It is an oxidizing agent.
It initiates an isomerization reaction.
Citrate is converted to isocitrate because:
tertiary alcohols are easier to oxidize
secondary alcohols are easier to oxidize
citrate is a good substrate for oxidation
the C-C bonds are easy to break
isocitrate is achiral.
Which of the following is true about TCA cycle.
The TCA cycle in activated by ATP
The TCA cycle in activated by NADH
The TCA cycle inactivated by ADP
The TCA cycle in activated by citrate
The TCA cycle in inactivated by ATP and NADH
All are enzymes of the pyruvate dehydrogenase complex but:
pyruvate dehydrogenase kinase
What is/are the chemical change(s) involved in the conversion of citrate into isocitrate?
hydration followed by dehydration
oxidation followed by reduction
dehydration followed by hydration
What properties of RNA lead scientist to believe that RNA, rather than DNA, is the original coding material of life?
List the three types of van der Waals forces in decreasing order of strength.
Calculate the hydroxide ion concentration [OH-] for human urine (pH = 6.2).
Which amino acid is achiral?
Why is protein folding thermodynamically favored?
Which of the following is true regarding the levels of protein structure?
Under physiological pH conditions (~7.4) cysteines are important for:
50 mL of 0.5 M HCl is added to 200 mL of 0.2 M ammonia (pKa = 9.25). The resulting mixture has a pH close to:
Which of the following is FALSE?
If you were conducting an experiment with pepsin, which has optimal enzymatic activity at pH 2.3, what buffer would be the best choice?
Which of the following is FALSE regarding secondary structures?
How many of the following properties, amino acid composition, molecular weight, secondary structure, primary sequence and isoelectric point, do the following peptides share in common: AVVSTHPMALEKA, AVVSTHAMALEKP
Assume that a protein exists either in a native state or in a denatured (unfolded) state. If ΔH and ΔS of denaturation are 512 kJ/mol and 1.6 kJ/K•mol, respectively, the temperature at which the denaturation becomes spontaneous is: (°C = K – 273)
Denaturation can be brought about by all of the following EXCEPT
Which of the following tripeptides has a net charge of +1 at pH 8?
Calculate the pH of a buffer solution prepared by mixing 80 mL of 1.0 M acetic acid (pKa = 4.76) and 20 mL of 1.0 M sodium acetate.
Hyperventilation results in decreased blood pCO2. This will lead to:
What is the isoelectric point of tyrosine? Its three pKa values are:
pKCOOH = 2.20, pKNH3 = 9.11, and pKR-group = 10.07
Which of the following is true regarding fibrous and globular proteins?
What is the [CH3COO-]/[CH3COOH] ratio in an acetate buffer (pKa = 4.76) at pH 3?
2,3-Bisphosphoglycerate (BPG) decreases the affinity of hemoglobin for O2 by
Protein Y has a Hill coefficient of 0.87. We can therefore say that protein Y
What kind of kinetics is observed in an enzymatic reaction, under conditions where the substrate concentration is low compared to the Km? Assume that a non-allosteric enzyme is studied.
a) zero order
b) first order
a) catalytic antibodies
b) different enzymes that catalyze the same reaction
c) inactive enzymes which can be activated by cleavage of covalent bonds
d) inactive enzymes which can be activated by phosphorylation
e) active enzymes which can be deactivated by phosphorylation
According to the concerted model for allosteric regulation, binding of an activator will:
a) lower the value of L
b) shift the equilibrium towards the R state
c) make substrate binding less cooperative
e) all the above
Which of the following is NOT a characteristic of most fatty acids?
a) presence of trans double bonds.
b) even number of carbon atoms.
c) only one carboxyl group.
d) absence of conjugated double bonds.
e) all of these characterize fatty acids.
Which of the following statements is true about active transport?
a) the transported species always moves against its concentration gradient
b) it is required only for the transport of polar molecules c) it is regulated by proteolysis of the transporter
d) it occurs only at animal membranes
e) it occurs only at plant membranes
Which of the following lipid molecules possess a fundamentally different structure from the others?
c) phosphoacylglycerols d) sphingolipids
The general structure of the DNA backbone is:
In two-dimensional SDS-PAGE protein analysis, proteins in a mixture are separated by their:
a) PI and molecular weight
b) molecular weight and overall hydrophobicity
c) overall hydrophobicity and PI
d) affinity for polyacrylamide and overall hydrophobicity e) affinity for polyacrylamide and molecular weight
In the DNA double helical structure, the stabilizing van der Waals interactions are referred
What is the nucleotide sequence of the DNA strand that is complementary to 5'-ATCGCAACTGTCACTA-3'?
If the Km of an enzyme is altered in the presence of an inhibitor, then this is: a) a competitive inhibitor
b) an uncompetitive inhibitor
c) a noncompetitive inhibitor
d) a or b
e) b or c
An enzyme-catalysed reaction has a Michaelis constant of 0.042 mol L-1. If Vinit for this reaction is 2.45 × 10-4 mol L-1s-1 when the concentration of the substrate is 0.890 mol L-1, what is the Vmax?
a) 1.55 10-3 mol L-1 s-1
b) 2.09 10-4 mol L-1 s-1
c) 2.57 10-4 mol L-1 s-1
d) 3.59 10-4 mol L-1 s-1
e) 4.04 10-4 mol L-1 s-1
A DNA binding protein exhibits high specificity for adenine-rich stretches of DNA (poly-A) while it interacts non-specifically with the phosphate backbone. The best suited chromatographic technique to purify this protein would be:
a) cation exchange
b) anion exchange
c) affinity, using a poly-A modified resin
d) affinity, using a poly-T modified resin
e) either a or c
Two proteins are of similar size, but one has a more negative net surface charge than the other. Which technique would you use to separate the two proteins without denaturing them?
A) Gel filtration
B) SDS electrophoresis
C) Cation exchange chromatography
D) Anion exchange chromtography
E) Ammoniumsulphate precipitation
What distinguishes nucleotides and nucleosides? a) nucleosides lack the sugar group
b) nucleosides lack the phosphate group
c) nucleotides lack the sugar group
d) nucleotides lack the phosphate group
e) nucleosides contain deoxyribose
What effect is seen on a Lineweaver-Burk graph when a competitive inhibitor is added to an enzymatic reaction?
a) the y-intercepts changes
b) the slope of the line changes
c) both the y-intercept and the slope change
d) neither the y-intercept nor the slope change
e) the line is inversed
Homotropic effects for allosteric enzymes involve
a) the same molecule binding to different enzymes
b) the same molecule binding to different sites in an enzyme
c) different molecules binding to the same site in an enzyme
d) different molecules binding to different sites in the same enzyme
e) all of these are homotropic effects
Enzymatic activity has an optimum temperature because
a) the component amino acids have varying melting points
b) the rate of reaction is thermodynamically controlled
c) the side chains of active site residues are chemically degraded at high temperatures
d) raising the temperature speeds up the reaction until protein denaturing
e) the organism dies beyond a certain temperature
In lipid bilayers, there is an order-disorder transition similar to the melting of a crystal, that occurs at a characteristic temperature, termed Tm. Which of the following is true for the Tm value of the fatty acids (i) n-Octadecanoic, (ii) cis-9-Octadecenoic and (iii) cis,cis-9,12- Octadecenoic
a) (i) > (ii) > (iii)
b) (iii) < (i) < (ii)
c) (iii) > (ii) > (i)
d) (i) < (ii) = (iii)
e) (i) = (ii) = (iii)
Which of the following classes of lipids is the principal lipid component of biological membranes:
How do ATP and CTP affect the function of ATCase?
a) ATP decreases K0.5, while CTP increases K0.5
b) both ATP and CTP affect the Vmax of ATCase
c) neither ATP nor CTP are ATCase effectors
d) ATP affects K0.5, while CTP affects Vmax
e) ATP is not an ATCase effector, while CTP increases the K0.5
Which of the following properties enables histone proteins to effectively wrap DNA? a) they bind DNA with negative cooperativity
b) they are fibrous
c) they are basic
d) b and c
e) a and b
Which of the following statements is NOT correct about double-stranded (ds) DNA:
a) Supercoiling assists in vivo packing
b) The Tm of a given dsDNA increases with increasing NaCl concentration
c) The % content in adenine is equal to the % content in thymine
d) The two strands of DNA run parallel from their 5’ to their 3’ end
e) Base pairing occurs between a purine and a pyrimidine
Which of the following best describes the process of DNA replication in a prokaryote?
How many of the following are required for RNA polymerase to catalyze transcription? a primer, Mg2+, a template, ribonucleoside triphosphates, ribonucleoside monophosphates
What is the function of the sigma (σ) subunit of RNA polymerase in E. coli?
Which of the following is the best description of an operon?
The genetic code is said to be degenerate. This means that
Formation of the initiation complex during translation requires which of the following?
At which position on tRNA is the wobble base of the anticodon triplet?
A Shine-Dalgarno Sequence is a
What happens when a stop codon is reached by a ribosome (in the A site)?
Which is most likely to have a high processivity?
If E. coli encounter an environment that is LOW in the concentration of glucose and the concentration of lactose, which of the following scenarios would result?
Which of the following best describes the order of events at the promoter during transcription?
The following general reaction scheme corresponds to:
NTP(NMP)n + NTP → NTP(NMP)n+1 + PPi
Double-stranded regions of RNA
Which of the following is NOT true for both DNA and RNA polymerases:
Primases are enzymes that facilitate replication by:
Replication on the lagging strand
Chain termination during translation requires:
Transcription in prokaryotes is regulated by all but:
a) alternative σ factors
d) rho hexamer
e) transcription attenuation
The function of EF-Ts during protein synthesis is:
a) to guide the aminoacyl-tRNA to the E site
b) to guide the fmet-tRNAfmet to the P site
c) to assist GDP release from EF-Tu
d) to assist ATP binding to EF-G
e) to guide the Shine-Dalgarno sequence of the transcript to 16S rRNA
The mRNA produced when the following sense strand DNA sequence is transcribed is:
5’- ATGGATGATTGGGAAATT -3’
a) 5’- AUGGAUGAUUGGGAAAUU -3’
b) 5’- UUAAAGGGUUAGUAGGUA -3’
c) 5’- AATTTCCCAATCATCCAT -3’
d) 5’- TACCTACTAACCCTTTAA -3’
e) 5’- UACCUACUAACCCUUUAA -3’
Meselson and Stahl demonstrated that the mode of DNA replication is semiconservative by growing bacteria originally in 15N enriched media and following 15N incorporation into DNA of subsequent generations upon changing media to 14N. The ratio of 14N over 15N single stranded DNA of the second generation after changing media is:
Which of the following is true about the mismatch repair mechanism mediated by the Mut complex (MutH, MutL and MutS)?
a) The repair machinery corrects the error on the methylated, template DNA
b) The repair machinery corrects the error by excising a single base
c) The process of DNA repair by the Mut complex does not require a polymerase
d) A DNA ligase is required to link the repaired DNA to the rest of the newly synthesized
e) all the above are correct
Which of the following proteins separates the template double-stranded DNA in E. coli?
The standard free-energy changes for the reactions below are given. Phosphocreatine → creatine + Pi ∆ G'° = –43.0 kJ/mol ATP → ADP + Pi ∆ G'° = –30.5 kJ/mol What is the overall ∆ G'° for the following reaction? Phosphocreatine + ADP → creatine + ATP
What is the net ATP yield per glucose during glycolysis?
The order of compounds in the conversion of glucose to pyruvic acid is as follows: (PEP = phosphoenolpyruvate)
An enzyme not involved in the control of glycolysis is
The compound uridine diphosphate glucose (UDPG) plays a role in
Which of the following mechanisms can be used to regulate metabolic pathways?
The citric acid cycle is amphibolic, meaning
Which of the reactions of the citric acid cycle requires FAD as a coenzyme?
When acetyl-CoA reacts with oxaloacetate to form citrate
Which of the following is true about the role of lipoic acid during the conversion of pyruvate to acetyl-CoA:
Fructose-1-P is hydrolyzed according to: Fructose-1-P + H2O → Fructose + Pi
If a 0.2 M aqueous solution of Froctose-1-P is allowed to reach equilibrium, its final concentration is 6.52 × 10-5 M. What is the standard free energy of Froctose-1-P hydrolysis?
The following set of enzymes is utilized during gluconeogenesis to bypass the irreversible steps of glycolysis:
What is not true about hexokinases (isozymes I-III)
Which of the following reactions produce NADH?
Which of the following reactions is considered anapletotic
The transition of phosphorylase-a -R state, to phosphorylase-a -T state is promoted by:
The polymerase chain reaction is achieved by cycling 3 steps, referred to as
What type of restriction endonucleases are most often used in creating recombinant DNA molecules?
In the Sanger method of DNA sequencing, what causes the termination of chain elongation?
Use the half reactions and reduction potential provided below to calculate the ΔGo’ of :
isocitrate + NAD+ → α-ketogluterate + CO2 + NADH + H+
NAD+ + H+ + 2e- → NADH (Eo’=-0.32V)
α-ketogluterate + CO2 + 2H+ + 2e- → isocitrate (Eo’=-0.38V)
Consider the phosphorylation of glucose at 37 oC: glucose + ATP → glucose-6-phosphate + ADP, with ΔGo’= -16.5 kJ/mol. If glucose and glucose-6-phosphate (G6P) reach equilibrium and assuming that the ratio of [ATP]/[ADP] is constant at 12, what is the ratio of [G6P]/[glucose]?
Which of the following best describes the function of debranching enzyme?
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