Exam Final
All of the following statements are true about the relationships between [S], Km and Vmax EXCEPT:
Km = Vmax/2.
As a result of mutarotation, D-glucose exists in all of the following forms EXCEPT
L-glucopyranose.
The enantiomer of D-mannose would be:
L-mannose.
Which of the following is not a conjugate acid-base pair?
B) H3O⁺/OH⁻
Which of the following statements about biological membranes is FALSE?
Lipids and proteins move laterally at approximately the same rate within the membrane.
Which of the following is CORRECT when considering the tertiary structure of globular proteins?
Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside.
The reaction A + B ⇒⇒ C has a ΔG°' of -20 kJ/mol at 25° C. Starting under standard conditions, one can predict that:
C) at equilibrium, the concentration of C will be much greater than the concentration of A or B.
In nucleotides and nucleic acids, syn and anti conformations relate to:
C) rotation around the sugar-‐base bond.
A biochemical reaction will proceed in the direction as written (forward) if:
C) △G < 0.
Which of the following are possible base compositions for single-stranded RNA?
%A %G %C %T %U A) 5 45 45 0 5 B) 25 25 25 0 25
Which of the following are possible base compositions for double-‐stranded DNA?
%A %G %C %T %U A) 5 45 45 5 0
11. Put the following steps of GroEL-GroES chaperonin function in order, starting with an unfolded polypeptide and ending with a polypeptide in its native conformation. (1) ADP and the folded polypeptide are released as ATP and Gro-ES binds to the other Gro-EL ring. (2) Gro-ES binds to Gro-EL, causing a conformational shift and displacing the polypeptide into the cavity. (3) A Gro-EL ring binds an unfolded polypeptide and 7 ATP (4) The Gro-ES "cap" dissociates from the Gro-EL ring. (5) ATP is hydrolyzed and the polypeptide, isolated from interfering contact, folds.
(a) (Unfolded) (1), (2), (3), (4), (5) (folded) (b) (Unfolded) (3), (4), (5), (2), (1) (folded) (c) (Unfolded) (3), (2), (5), (4), (1) (folded) (d) (Unfolded) (1), (5), (4), (3), (2) (folded)
Put the following steps of GroEL-GroES chaperonin function in order, starting with an unfolded polypeptide and ending with a polypeptide in its native conformation. (1) ADP and the folded polypeptide are released as ATP and Gro-ES binds to the other Gro-EL ring. (2) Gro-ES binds to Gro-EL, causing a conformational shift and displacing the polypeptide into the cavity. (3) A Gro-EL ring binds an unfolded polypeptide and 7 ATP (4) The Gro-ES "cap" dissociates from the Gro-EL ring. (5) ATP is hydrolyzed and the polypeptide, isolated from interfering contact, folds.
(d) (Unfolded) (3), (2), (5), (4), (1) (folded)
The standard free energy change of the glycolytic pathway to pyruvate is -79.9 kJ/mol, while the standard free energy change associated with gluconeogenesis from pyruvate is -42.7 kJ/mol. What would the standard free energy change be for a direct reversal of the glycolytic pathway.
+79.9 kJ/mol
Which of the following statements is FALSE?
- Oxygen is reduced to water at complex IV of the mitochondrial respiratory chain. - All of the protein complexes of the mitochondrial respiratory chain are bound in the inner mitochondrial membrane. - Cytochrome c and coenzyme Q are both soluble electron carriers that are loosely attached to the outside of the inner mitochondrial membrane.*** - The citric acid cycle is linked directly to the mitochondrial respiratory chain at the site of complex II.
Calculate the △Go' for the reaction fructose-6-phosphate → glucose-6-phosphate given the equilibrium constant is 1.97 and the physiological relevant temperature is 37oC.
-1.75 kJ/mol
The net charge on nucleotide monophosphates is:
-2
System does 435 kJ of work (w), and loses 312 kJ of heat (q) to the surroundings. What is the change in internal every of the system?
-747 kJ
Edman degradation will:
.d) determine the N-terminal amino acid.
Calculate the pH in a muscle cell from the HPO42-/H2PO4- ratio. If the internal pH of a muscle cell is 6.8, what is the [HPO42-]/[H2PO4-] ratio in this cell?
0.398
At which of the following pH values would histidine (pKa values of 1.8, 6.0 and 9.2) be found with a net negative charge?
11.0
In a sample of double-stranded DNA containing 32% cytosine, the percentage of adenine would be:
18%
Linolenic acid has cis double bonds with the formula CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH. Write out the abbreviated systematic numbering for this fatty acid.
18:3△c9,12,15
If an enzyme has a Vmax of 15 mM/min, what is the velocity if the substrate is present at 1/5 of the Km?
2.5 mM/min
Glutamic acid has pKa values of 2.2, 4.3 and 9.7. Calculate the isoelectric point for glutamic acid.
3.25
If a weak acid is 25% deprotonated at pH 4, what would the pKa be?
4.48
Calculate the pH of a 0.1 M phosphate buffer (pKa = 6.86) that contains equal amounts of acid and conjugate base.
6.86
Identify the step that is involved in oxidation-reduction reactions of glycolysis.
A
Which of the following statements about inhibitors of enzyme-catalyzed reactions is TRUE?
A competitive inhibitor does not affect Vmax.
Calculate the concentrations of acetic acid (pKa = 4.76) and sodium acetate necessary to prepare a 0.2M buffer solution at pH 5.0.
A) 0.13 M acetate and 0.07 M acetic acid
Calculate the equilibrium constant, Keq, for the following reactions at pH 7.0 and 25 °C. (Find out the standard gibbs free energy from the table given) Glucose 6-phosphate + H2O Glucose + Pi
A) 262
Formic acid is the active agent in an ant bite. What is the ratio of acid / conjugate base for formic acid (pKa = 3.9) in the blood stream at pH 7.4?
A) 3.16 x 10-4
A solution of DNA is heated slowly until the tm is reached. What is the likely structure of the DNA molecules at this temperature?
A) 50% double stranded and 50% single stranded.
The standard free energy change (ΔG'°) for ATP hydrolysis is -30.5 kJ/mol. ATP, ADP, and Pi are mixed together at initial concentrations of 1 M of each, then left alone until the reaction ADP + Pi à ATP has come to equilibrium. For each species (i.e., ATP, ADP, and Pi), indicate whether the concentration will be equal to 1 M, less than 1 M, or greater than 1 M.
A) ATP < 1 M, ADP > 1 M, Pi > 1 M
For the reaction A à B, the Keq is 104. If a reaction mixture originally contains 1 mmol of A and no B, which one of the following must be true?
A) At equilibrium, there will be far more B than A. B) The rate of the reaction is very slow. C) The reaction requires coupling to an exergonic reaction in order to proceed. D) The reaction will proceed toward A at a very high rate. E) DG'° for the reaction will be large and positive.
Which of the following statements is INCORRECT about the nature of the hydrogen bond.
A) The donor is a hydrogen atom bonded to an atom that is less electronegative than hydrogen.
Select the phrase that describes mixed inhibitor.
A) When present, Vmax of enzyme is unaffected B) Prevents substrate from binding enzyme C) When present, Km of enzyme will decrease D) Binds either Enzyme or Enzyme-Substrate complex
A true statement about hydrophobic interactions is that they:
A) are the driving force in the formation of micelles of amphipathic compounds in water.
For the helix in double-stranded B-form DNA, the majority of the stability can be attributed to:
A) base-pairing interactions via H-bonding. C) base-stacking interactions via van-der-Waals interactions. E) Both A) and C)
Which of the following properties describe both purines and pyrimidines?
A) they are aromatic C) they exhibit strong absorption of UV light E) both A and C are correct
The main energy-coupling compound in biochemical reactions that allows thermodynamically unfavorable processes to become favorable is ________.
ATP
Which of the below is not required for the oxidative decarboxylation of pyruvate to form acetyl-CoA?
ATP
Which of the following is not an intermediate of the citric acid cycle?
Acetyl-CoA
Which of the peptides would absorb light at 280 nm?
Ala-Ala-Trp
Which of the following types of reaction does NOT occur in glycolysis?
Aldol condensation
Which of the following statement is FALSE?
At a given temperature and time all molecules in a solution or a sample will have the same energy.
Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence (5')AGACTGGTC(3')?
B) (5')GACCAGTCT(3')
Calculate the acid dissociation constant Ka of a 0.2 M solution of weak acid that is 0.1% ionized.
B) 2 × 10-‐7
Calculate the pH of a 0.2 M acetate buffer (pKa = 4.77) that contains twice as much acid as conjugate base.
B) 4.47
Phosphoric acid is triprotic acid with pKa's of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is:
B) H2PO4-.
An enzymatic hydropysis of fructose-‐1-‐P is as follow. Frustose-‐1-‐P +H2O Frustose +Pi This reaction was allowed to proceed to equilibrium at 25°C. The original concentration of fructose-‐1-‐P was 0.2 M, but when the system had reached equilibrium the concentration of fructose-‐1-‐P was only 6.52 × 10-‐5 M. Calculate the equilibrium constant (Keq) for this reaction and the standard free energy (ΔG°') of hydrolysis of fructose-‐1-‐P.
B) Keq = 6.13 × 102 M, ΔG°' = -‐15.9 kJ/mol
In a highly basic solution, pH = 13, the dominant form of glycine is:
B) NH2—CH2—COO-.
Which statement pertaining to the three basic systems (open, closed, isolated systems) is true?
B) Open systems can exchange matter with other open systems.
Biological oxidation-reduction reactions never involve:
B) formation of free e-.
The DNA oligonucleotide abbreviated pATCGAC:
B) has a hydroxyl at its 3' end.
Many proteins interact with DNA at physiological pH because:
B) the negatively charged DNA is electrostatic ally attracted to positively charged regions on proteins.
Which of the following disaccharides indicates "α-glycosidic linkage" and "non-reducing sugar"?
C
For the reaction A ⇒⇒ B, ΔG'° = -60 kJ/mol. The reaction is started with 10 mmol of A; no B is initially present. After 24 hours, analysis reveals the presence of 2 mmol of B, 8 mmol of A. Which is the most likely explanation?
C) B formation is kinetically slow; equilibrium has not been reached by 24 hours.
Which of the following is not true of all naturally occurring DNA?
C) The ratio A+T/G+C is constant for all natural DNAs.
Glyceraldehyde has a chiral carbon so has two stereoisomers, which are called diastereomers.
False
The aqueous solution with the lowest pH:
D) 0.1M HCl.
Taking one mole of glucose through glycolysis and the citric acid cycle generates:
D) 6C02, 10 NADH/H+, 2FADH2 and 4 ATP.
If 0.2 moles of Na2HPO4 and 0.1 moles of NaH2PO4 are mixed in water, what is the resulting pH? The pKa values for phosphoric acid are provided in the pKa table.
D) 7.16
Which of the following is a palindromic sequence?
D) GGATCC CCTAGG
Nucleotide triphosphates and nucleotide diphosphates often form stable complexes with
D) Mg+2
Which of the following processes has a ΔS > 0?
D) Sodium chloride dissolves in pure water.
Triple-‐helical DNA structures can result from Hoogsteen (non Watson-‐Crick) interactions. These interactions are primarily:
D) hydrogen bonds involving the bases.
The double helix of DNA in the B-‐form is stabilized by:
D) nonspecific base-‐stacking interaction between two adjacent bases in the same strand.
For the oligoribonucleotide pACGUAC:
D) the nucleotide at the 5' end has a phosphate on its 5' hydroxyl. .
Buffers have all of the following characteristics EXCEPT:
D) they buffer best for polypro tic acids half-way between the two pKa values.
Biological oxidation-‐reduction reactions always involve:
D) transfer of electron(s).
Which of the following conditions is always true at equilibrium?
D) △G=0
Which of the following does NOT describe the secondary structure of DNA as proposed by Watson and Crick?
E) The base pairs are stacked on one other with their planes at 180o to the helix axis.
In micelles:
E) hydrocarbon tails are excluded from the water into hydrophobic domains.
In the Watson-‐Crick model of DNA structure (now called B-‐form DNA):
E) the bases occupy the interior of the helix.
Which of the following is FALSE when considering the standard genetic code?
Each of the three stop codons can also encode rare modified amino acids.
A thermodynamically unfavorable reaction can become favorable when coupled to a highly endergonic reaction.
False
All of the reactions of both glycolysis and gluconeogenesis occur in the cytosol.
False
Amphipathic molecules are not able to interact via van der Waals forces.
False
All amino acids have a chiral α-carbon EXCEPT ________.
Glycine
Which of the following statements BEST describes the Michaelis-Menton constant KM?
It is numerically equal to the substrate concentration required to reach half maximal velocity for an enzyme-catalyzed reaction.
Which of the following statements is FALSE?
Organisms are open systems as they can create energy from their environments.
Which of the following in biological compounds are sufficiently electronegative to serve as strong donors in a hydrogen bond?
Oxygen and nitrogen
Which of the following is unlikely to be a characteristic of a membrane protein?
Symmetric orientation across the membrane
Which of the following statements about nucleic acid secondary structure is FALSE?
The A-form of DNA exists at high humidity, whereas the B-form exists at low humidity.
Which of the following does NOT describe the secondary structure of DNA as proposed by Watson and Crick?
The base pairs are stacked on one other with their planes at 180 degree to the helix axis.
Which of the following statements is FALSE?
The difference in melting temperature between a saturated fatty acid and an unsaturated fatty acid with the same chain length is only a few degrees C.
Which of the following statements about insulin is INCORRECT?
The disulphide bonds form after the final proteolytic cleavage to yield mature insulin.
Which of the following statements is INCORRECT about the nature of the hydrogen bond
The donor is a hydrogen atom bonded to an atom that is less electronegative than hydrogen.
Where does the energy that drives ATP synthesis come from?
The proton gradient.
All of the following are properties of a coenzyme EXCEPT:
They are protein components.
How do catalysts work to accelerate a chemical reaction?
They lower the energy of activation.
Consider a reaction that has a positive ΔH and a positive ΔS. Which of the following statements is true?
This reaction will be spontaneous only at high temperatures.
A Lineweaver-Burk plot can be used to determine KM using initial-rate data for an enzyme-catalyzed reaction.
True
All of the enzymes of the citric acid cycle are located in the mitochondrion.
True
An important observation that assisted in the elucidation of the secondary structure of DNA was that the mole percent adenine was almost always the same as the mole percent of thymine.
True
Catabolic processes involve degradation of complex molecules into simpler molecules with the net release of chemical energy.
True
D-ribose can form a ring structure with either four or five carbons in the ring.
True
Integral membrane proteins can be inserted into the membrane and folded into the normal 3D structure during translation.
True
Much of the regulation of gluconeogenesis is a result of the inhibition of glycolysis.
True
NAD+, coenzyme A, thiamine pyrophosphate, lipoic acid and FAD are all cofactors used in the reaction catalyzed by pyruvate dehydrogenase.
True
Proteins have an asymmetrical tertiary structure, while multisubunit proteins can exhibit several types of symmetry.
True
The amino acid side chain residues in an α helix point outwards away from the center of the helix.
True
The average charge on an amino acid below its pI will be positive.
True
Membranes with unsaturated fatty acids in their components are more flexible and fluid because:
Unsaturated fatty acids bend at the double bond preventing close packing.
Properties of water that render it so suited to its role as a medium of life include all EXCEPT:
Unusually high dielectric constant of water explains water's ability to surround ions and increase the ions' attraction for one another.
A hydrophobic interaction might occur within a protein between which of the following amino acid pairs?
Val/Leu
The C-terminal residue of a polypeptide can be determined by first cleaving the polypeptide with:
a) chymotrypsin. b) CNBr. c) trypsin. d) carboxypeptidase.
The amino acid residue most likely to be found in a beta turn is:
a) glycine.
The difference between a nucleoside and a nucleotide is:
a phosphate group.
18. Among the following Ramachandran plots (I-III), select the plot for Gly residues.
a) (I) b) (II) c) (III) d) (I) and (III)
Predict the charge on the predominant species of the peptide E-D-K-R-A-S-T-H at pH 5.0
a) 0 b) 1 c) 2 d) 3
What is the V0/Vmax ratio when [S]=4 KM a
a) 0.8 b) 1.0 c) 1.2 d) 1.4
An enzyme catalyzes a reaction with a KM of 7.50 mM and a Vmax of 3.40 mMs-1. Calculate the reaction velocity, V0, for the substrate concentrations of 7.00 mM.
a) 2.26 mM/sec b) 1.20 mM/sec c) 1.64 mM/sec d) 4.52 mM/sec
Which of the peptides would absorb UV light at 280 nm?
a) Ala-Lys-Pro b) Gln-Gly-Asn c) Ala-Trp-Asn d) Leu-Pro-Leu
Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false?
a) As [S] increases, the initial velocity of reaction V0 also increases. b) At very high [S], the velocity curve becomes a horizontal line that intersects the y- axis at Km. c) Km is the [S] at which V0 = 1/2 Vmax. d) The shape of the curve is a hyperbola.
In uncompetitive inhibition:
a) I combines only with ES.
Given the partial sequence of a peptide: I L W A N R M S H V L F A V E A Which amino acid residues would you expect to be on the solvent-exposed surface once it folds into its native conformation (in vivo)?
a) I, L, W, A, M b) N, R, S, H, E c) M, V, F, W, M d) I, M, L, V, A
A hydrophobic interaction might occur within a protein between which of the following amino acid pairs?
a) Ser/Ile b) Tyr/Cys c) Lys/Asn d) Val/Leu
Which statement is False about amino acid?
a) The Ala side chain does not form hydrogen bonds with other amino acids. b) Asn and Gln are polar amino acids. c) Threonine has more than one stereo center (chiral center). d) The Gly have the most restricted phi and psi dihedral angles.
All of the following statements about assumptions made on Michaelis- Menten equation are true EXCEPT:
a) The reaction involves more than one substrate.
All of the following statements about assumptions made on Michaelis-Menten equation are true EXCEPT:
a) The reaction involves more than one substrate. b) The reaction ES à E + P is irreversible. c) [S]0 > [E]T and [E]T is held constant. d) All other variables that might influence the rate of the reaction are held constant.
All of the information necessary for folding the peptide chain into its "native" structure is contained in the of the peptide.
a) amino acid sequence
13. Michaelis and Menten assumed that the overall reaction for an enzyme-catalyzed reaction could be written as E+S K_1/K_(-1) ↔ES K_2/→E+P Using this reaction, the rate of breakdown of the enzyme-substrate complex ([ES]) can be described by the expression:
a) k1 ([Et] - [ES]). b) k1 ([Et] - [ES])[S]. c) k2 [ES]. d) k-1 [ES] + k2 [ES].
Flexible, disordered segments of proteins are commonly high in the amino acid:
a) lys b) ser c) pro d) asp
Which of the following would be a possible amino acid sequence for an oligopeptide given the experimental data below? I. The amino acid composition is found to be [ala, lys, phe, met, cys, trp]. II. Treatment with carboxypeptidase results in tryptophan and a peptide. III. CNBr treatment yields a tetrapeptide and a dipeptide. IV. Trypsin digestion produces an amino acid and a pentapeptide with met on the amino end. V. Chymotrypsin digestion yields a dipeptide and a tetrapeptide.
a) trp-lys-met-cys-met-ala b) trp-ala-phe-cys-met-lys c) lys-met-cys-phe-ala-trp d) lys-ala-cys-phe-met-trp
The formation of cyclic structures in sugars with creation of an additional asymmetric center results from an alcohol reacting with a(n):
aldehyde or ketone.
All of the information necessary for folding the peptide chain into its "native" structure is contained in the ____ of the peptide.
amino acid sequence
In an a helix, the R groups on the amino acid residues:
are found on the outside of the helix spiral.
Predict the charge on the predominant species of the peptide E-D-K-R-A-S-T- H at pH 5.0
b) 1
Which of the following is NOT a characteristic of a protein's overall conformation?
b) Achieved by breaking and reforming covalent bonds.
Given the partial sequence of a peptide: I L W A N R M S H V L F A V E A Which amino acid residues would you expect to be on the solvent-exposed surface once it folds into its native conformation (in vivo)?
b) N, R, S, H, E
An enzyme's specificity can be due to:
b) molecular recognition based on structural complementarity.
The formation of a disulfide bond would be an example of what level of protein structure?
b) tertiary c) quaternary d) both c and d are correct
Which of the peptides would absorb UV light at 280 nm?
c) Ala-Trp-Asn
Enzymes work by:
c) lowering the activation energy of the reaction
An enzymatic reaction has a Vmax of 30 mM/min and a Km of 50 mM. If the concentration of the substrate is 25 mM, which of the following is true?
c) the velocity will be 10 mM/min
14. In transforming the Michaelis-Menten equation into a straight line equation, y = mx + b, the Lineweaver-Burk double reciprocal plot, which of the following is NOT a true representation?
c) x-intercept is 1/Km
ATP has a high phosphoryl group transfer potential because:
cleavage of either of its two phosphoanhydride bonds proceeds with a large negative △G' of hydrolysis.
If an enzyme has a Vmax of 15 mM/min, what is the velocity if the substrate is present at 1/5 of the Km?
d) 2.5 mM/min
Which of the following best represents the backbone arrangement of two peptide bonds?
d) Ca—C—N—Ca—C—N
3. Arrange the steps involved in folding of globular proteins into a proper sequence. A."Molten globule" formation of assembled domains. B. Formation of domains through cooperative aggregation of folding nuclei. C. Adjustment in the conformation of domains. D. Rapid and reversible formation of local secondary structure. E. Final protein monomer formation.
d) D, B, A, C, E
An electrostatic interaction might occur within a protein between which of the following amino acid pairs at typical physiological pH?
d) Lys/ Asp
pH = pKa when:
d. [A-] = [HA]
The amino acid residue most likely to be found in a beta turn is:
glycine.
Saturated fatty acids are different to unsaturated fatty acids because they:
have no C=C double bonds.
RNA is ____ stable to alkaline hydrolysis than DNA because RNA's vicinal ____ group makes the 3'-phosphodiester bond susceptible to nucleophilic cleavage.
less; 2'-OH
For the following reaction, \Delta Δ G°' = 29.7 kJ/mol. L-Malate + NAD+ \longrightarrow ⟶ oxaloacetate + NADH + H+ The reaction as written:
may occur in cells at certain concentrations of substrate and product.
Protein folding is a thermodynamically favorable process under physiological conditions because:
of the large negative enthalpy change associated with many noncovalent interactions.
The nucleotide sequence of a polynucleotide chain is called the ________ structure.
primary
Acetyl CoA is a feed forward activator of the enzyme ________ ensuring sufficient oxaloacetate for the citric acid cycle to continue.
pyruvate carboxylase
The lock and key model of substrate binding and enzymatic catalysis explains:
substrate specificity
SDS gel electrophoresis can be used to determine:
the molecular mass of denatured protein subunits.
Because peptide bond formation is thermodynamically ____, biological systems must couple peptide bond formation to a thermodynamically ____ reaction.
unfavorable, favorable
The △Go of a reaction:
will not change if the temperature of the reaction is changed.
The intrinsic properties of the 20 amino acids include all EXCEPT:
α-Carbon is symmetric.
α-D-Glucose + ATP --> ____ + ____ + H+
α-D-glucose-6-phosphate; ADP