Exam 1 Flashcards
If a reaction has a negative delta G, is it spontaneous?
The reaction is spontaneous because the delta G is negative.
______ is the free energy of the reaction under the actual reaction conditons
Delta G
______ is the free energy under the standard states.
Delta G degree
______ is the free energy under the biochemical standard states.
Delta G degree prime
______ is the free energy of the transition state.
Delta G transition symbol
When the reaction conditions match the biochemical standard states, the values of _____ and _____ will be equal.
Delta G and Delta G degree prime
The _____ determines the rate constant, while _____ determines the favorability of a reaction under standard conditons.
Delta G transition and Delta G degree
An endergonic reaction with a ______ Delta H and a ______ Delta S can be changed into an exergonic reaction by decreasing the temperature.
negative; negative
For the reaction phosphoenolpyruvate + ADP + H+ –> pyruvate + ATP, if Keq>1, which of the following conditions is TRUE?
-[pyruvate][ATP] > [phosphoenolpyruvate][ADP][H+}
-[pyruvate][ATP] < [phosphoenolpyruvate][ADP][H+}
-[pyruvate][ATP] = [phosphoenolpyruvate][ADP][H+}
-none of the above
[pyruvate][ATP] > [phosphoenolpyruvate][ADP][H+}
Change in enthalpy (Delta H) is best defined as _____.
-the sum of heat absorbed and work done
-the heat transferred at constant pressure
-the pressure change at constant temperature
-the measure of disorder in a system
-none of the above
The heat transferred at constant pressure
For a reaction with Delta H=23 kJ/mol and Delta S=22 J/L mol, at 2 degrees Celsius, the reaction is ____.
-spontaneous
-nonspontaneous
-at equilibrium
-impossible to determine reactivity
-none of the above
Nonspontaneous
A spontanous process always has ____.
-Delta G < 0
-Delta G > 0
-Delta H < 0
-Delta H > 0
-none of the above
Delta G < 0
Is adenine a purine or pyrimidine?
Purine
What is the name of the molecule that is composed of adenine linked to the C-1’ of ribose?
Adenosine
In the structure of DNA, the bases in complementary strands interact through _______, while the bases within one strand interact through _________. Lastly, phosphodiester groups interact with magnesium ions through _________.
-hydrogen bonds
-pi-pi interactions
-ionic interactions
In order to perform PCR, which of the following describes the reagents that must be included in the reaction mixture?
-DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase
-DNA fragment, primers flanking the region of interest, dNTPs, ddNTPs, DNA polymerase
-DNA fragment, one primer, dNTPs, DNA polymerase, DNA ligase
-DNA fragment, primers flanking the region of interest, dNTPs, DNA ligase
-None of the above
DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase
EcoRI recognizes the sequence 5’G arrow AATTC-3’ (arrow indicates the point of cleavage). Treatment of the following oligonucleotide with EcoRI would produce two oligonucleotides with sizes of _____ nucleotides containing _____ ends.
5’- AAGTCGATACAGAATTCGTACCTAG-3’
-12 and 13; sticky
-11 and 8; sticky
-12 and 8; blunt
-9 and 13; sticky
-12 and 13; blunt
12 and 13; sticky
Which component is not necessary for transformation?
-foreign DNA
-growth media
-plasmid
-gene gun
Gene gun
Which of the following statements is TRUE regarding phosphodiester bonds that link adjacent nucleotides in both RNA and DNA?
-Phosphodiester bonds join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next
-Phosphodiester bonds are uncharged at pH 7.0
-Phosphodiester bonds always link G with C and A with either T or U
-Phosphodiester bonds are positively charged.
Phosphodiester bonds join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next
Phosphodiester bonds link DNA monomers to form a polymer by which mechanism?
-The OH group on the C-2 in the 2-deoxyribose monosaccharide forms a covalent to elongate the DNA polymer
-The OH group on the C-3 in the ribose carbohydrate forms a covalent to elongate the DNA chain
-The OH group on the C-3 in the 2-deoxyribose carbohydrate forms a covalent to elongate the DNA chain
-The OH group on the C-2 in the ribose carbohydrate forms a covalent to elongate the DNA polymer
The OH group on the C-3 in the 2-deoxyribose carbohydrate forms a covalent to elongate the DNA chain
Which of the following statements is most correct?
-DNA polymerase can only add a nucleotide to the free 5’-OH group of a base-paired polynucleotide
-DNA polymerase can only add a nucleotide to the free 3’-OH group of a base-paired polynucleotide
-DNA polymerase can only add a nucleotide to the free 3’-OH group of a polynucleotide that is not base-paired
-DNA polymerase can only add pyrophosphate to the free 3’-OH group of a base-paired polynucleotide
DNA polymerase can only add a nucleotide to the free 3’-OH group of a base-paired polynucleotide
DNA polymerase from Thermus aquaticus is used in PCR because
-the enzyme is readily deactivated by heat, effectively halting the reaction
-the genes from Thermus aquaticus are readily distinguished from those of ‘normal’ organisms
-it is stable at high temperatures
-it is not infectious
-it is a soluble protein
It is stable at high temperatures
DNA ______ is an enzyme necessary for splicing together fragments of DNA with complementary ends.
ligase
Which of the following is a function of the ribosome?
-binds mRNA and allows codon recognition
-mediates the binding of proteins necessary for initiation, elongation, and termination
-catalyzes the synthesis of peptide bonds
-translocate such that multiple codons can be read
All of the above
Which level of protein architecture is composed of multiple subunits in a protein?
-tertiary
-quarternary
-primary
-secondary
Quareternary
RNA occurs primarily as single-stranded molecules that can give rise to ____ structures.
-tautomeric
-parallel
-haploid
-stem-loop
-diploid
Stem-loop
The pyrimidine found in both DNA and RNA is ______.
cytosine
The pyrimidine found only in DNA is _______.
thymine
The pyrimidine found only in RNA is ______.
uracil
Which one of the following statements about peptide bonds is FALSE. Peptide bonds are:
-rigid and planar, with partial double-bond character
-charged
-amides
-covalent
-involved in forming the primary structure of proteins
Charged
Which of the following statements BEST describes a prosthetic group?
-They are the active part of an enzyme
-They are nonpeptide molecules or ions critical to a protein’s structure
-They are short peptide chains attached to a larger protein
-They are nonfunctional components of a protein
They are nonpeptide molecules or ions critical to a protein’s structure
The _____ character of most standard amino acids causes solutions of amino acids to rotate the plane of polarized light.
-chiral
-zwitterionic
-polar
-hydrophobic
-none of the above
Chiral
For the reaction H+ (aq) + HCO3- (aq) <–> H2CO3 (aq), if the reaction is at equilibrium, which conditions must be maintained?
-[H2CO3] > [H+][HCO3-]
-[H2CO3] < [H+][HCO3-]
-[H2CO3] = [H+][HCO3-]
-none of the above
[H2CO3] > [H+][HCO3-]
Please rank the following acids in order of increasing pKa.
-CH3COOH, HF, HCl, H2O
-HF, HCl, H2O, CH3COOH
-H2O, CH3COOH, HF, HCl
-HCl, HF, CH3COOH, H2O
HCl, HF, CH3COOH, H2O
Guanine, a DNA base, tightly bonds to cytosine through which intermolecular forces?
-covalent bonding
-dipole-dipole interactions
-hydrogen bonding
-London dispersion forces
Hydrogen bonding
The second law of thermodynamics states ____.
-that spontaneous processes are characterized by the overall conversion of order to disorder
-that spontaneous processes are characterized by the conversion of work to force
-that nonspontaneous processes are characterized by the conversion of order to disorder
-that spontaneous processes are characterized by the conversion of heat to pressure
-none of the above
That spontaneous processes are characterized by the overall conversion of order to disorder
Change in enthalpy (Delta H) is best defined as ____.
-the sum of heat absorbed and work done
-the heat transferred at constant pressure
-the pressure change at constant temperature
-the measure of disorder in a system
-none of the above
The heat transferred at constant pressure
A spontaneous process _____.
-occurs without the addition of free energy
-has a Delta G < 0
-is exergonic
-is all of the above
-is none of the above
Is all of the above
The term used to indicate the degree of randomness within a system is _____.
entropy
Spontaneous processes are characterized by a change in Gibbs free energy that is ______.
negative
The symbol for free energy under standard biochemical conditions is ______.
-Delta H degree prime
-Delta G degree prime
-Delta T
-Delta H
-is none of the above
Delta G degree prime
For a reaction with Delta H = 23 kJ/mol and Delta S = 22 J/K mol, at 2 degrees Celsius, the reaction is _____.
-spontaneous
-nonspontaneous
-at equilibrium
-impossible to determine reactivity
-none of the above
nonspontaneous
An increase in disorder in the system _____.
-is required for a process to be spontaneous
-results in a decrease in entropy
-is characteristic of a system increasing in enthalpy
-results in the factor T Delta S being positive
-is found in every exergonic process
Results in the factor T Delta S being positive
The ketone body Beta-hydroxybutyrate is a small molecule found in some metabolic states. In organisms, Beta-hydroxybutyrate will spontaneously decarboxylate into acetone and carbon dioxide. Which of the rate laws best describes this overall reaction?
-Rate = k[Beta-hydroxybutyrate]
-Rate = k[Beta-hydroxybutyrate]^2
-Rate = k[acetone][CO2]
-Rate = k[Beta-hydroxybutyrate][acetone][CO2]
-Rate = k([acetone][CO2])/[Beta-hydroxybutyrate])
Rate = k[Beta-hydroxybutyrate]
Read the following 3 statements and determine which are true and false.
i.) Nucleic acids are synthesized in the 3’-5’ direction.
ii.) The sugar-phosphate groups which form the “backbone” of the DNA double-helix are located on the outside of the helix because they are polar.
iii.) RNA polymerase “reads” a template strand by running along it in a 5’-3’ direction.
ii is true
i and iii are false
Which of the following does NOT apply to the reaction catalyzed by a DNA polymerase?
-It is a phosphoryl group transfer reaction.
-It involves a nucleophilic attack by an -OH group.
-It is a biosynthetic (anabolic) reaction and so has a positive free energy change (Delta G).
-It is facilitated by the hydrolysis of a pyrophosphate group.
-It requires an abundant supply of deoxynucleoside triphosphates.
It is a biosynthetic (anabolic) reaction and so has a positive free energy change (Delta G).
(While the reaction catalyzed by DNA polymerases is biosynthetic, reactions in biological systems cannot proceed unless they have an overall negative free energy change.)
What is the function of a restriction enzyme?
-It seals breaks in the sugar-phosphate backbone.
-It cuts DNA.
-It adds a nucleotide base to the template strand of DNA.
-It unwinds DNA.
It cuts DNA.
Why does the polymerase chain reaction require a heat-stable DNA polymerase?
-High temperatures are necessary to cause strand separation after each cycle of synthesis.
-High temperatures are necessary for annealing primers.
-High temperatures are necessary for initiating DNA synthesis.
-High temperatures are necessary for high-fidelity in DNA synthesis.
High temperatures are necessary to cause strand separation after each cycle of synthesis.
Nucleotides play a central role in living organisms because ____.
-they mediate transport of energy within the cell
-they are involved in oxidation-reduction reactions
-they are involved in intracellular signaling
-they function as building blocks for nucleic acids
-all of the above
All of the above
Inside our cells, free nucleotides are almost always associated with ____.
-proteins
-cholesterol
-Cl- counterions
-fatty acids
-Mg2+ counterions
Mg2+ counterions
Nucleoside triphosphates are useful for energy transfer because the phosphoanhydride bonds are relatively _____.
-stable
-high energy
-biocampatible
-large
-low energy
High energy
Which of the following nucleotides contain energy rich bonds?
-ATP
-TTP
-CTP
-GTP
-all of the above
All of the above
Which of the following molecules does not contain an energy-rich phosphoanhydride bond?
-ADP
-GDP
-AMP
-CDP
-all of the above
AMP
DNA forms a double _____.
helix
The two strands run _____.
antiparallel
The sugar is ______.
deoxyribose
The sugar-phosphate groups are _______.
on the outside of the helix
The bases are _______.
in the center of the helix
The bases are planar, and their plane is oriented ______ to the axis of the helix.
perpendicular
The helix has a minor and major _____ on its surface.
groove
The link between a purine and ribose is made from the _____ of the purine ring to the _____ of the ribose.
N-9 and C-1’
In DNA, the ribose derivative lacks an _____ on C-_____.
-alcohol; 2
-alcohol; 3
-amine; 2
-amine;3
-none of the above
Alcohol; 2
What type of bond is made between nucleotides?
-ester
-phosphoester
-phosphodiester
-glycosidic
-none of the above
Phosphodiester
The most common base pairs in DNA are ____ and ____.
C-G and T-A
An A-T base pair consists of _____ H-bonds and a G-C base pair consists of ____ H-bonds.
2 and 3
Which of the following correctly describes the B-DNA double helix?
-antiparallel strands
-right-handed helix
-base pairs are located in the center of the helix
-one helical rotation has a rise of 3.4 nm
-all of the above
All of the above
