Biology 3020 Exam 1
A solution of 3.0 M H2SO4 has a pH of
-0.48
During DNA replication, which of the following events would occur and in what order (n/a = not applicable)?
1. Formation of a replication bubble. 2. Replication of the leading and lagging strand in 5' to 3' direction. 3. Ligation of the replicated strands on the lagging strand. n/a Ligation of the replicated strands on the leading strand. n/a Replication of the leading strand in 5' to 3' direction and lagging strand in the 3' to 5' direction.
What is the final pH if you have 700 mL of a sodium acetate buffer (50 mM, pH 5.0, Ka = 1.78×10-5) and you add 10 mL of 1 M NaOH?Final pH (3 significant figures)
1. Solve for the ratio of [conjugate base]/[acid] using the Henderson-Hasselbach equation. pH = pKa + log ([conjugate base]/[acid]) 5.0 = (-log(1.78×10-5)) + log([conjugate base]/[acid])log([conjugate base]/[acid]) = 0.25 [conjugate base]/[acid] = [A]/[HA] = 1.8 [A] = 1.8([HA]) 2. Substitute this expression into the mass balance equation for the buffer. 0.050 M = [HA]eq + [A]eq = [HA] + 1.8([HA]) 0.050 M = 2.8([HA]) [HA] = 0.0179 M [A] = 0.050 - 0.0179 = 0.0321 M 3. Calculate the moles of acid, conjugate base, and hydroxide used in the reaction. (0.0179 M)(0.700 L) = 0.0125 moles HA (0.0321 M)(0.700 L) = 0.0225 moles A (1.0 M)(0.010 L) = 0.010 moles OH-4. Calculate the change in moles for HA and A as a result of the reaction with hydroxide. 0.125 initial moles HA - 0.010 moles hydroxide = 0.0025 final moles HA0.225 initial moles A + 0.010 moles A produced = 0.0325 final moles A 5. Calculate the new pH using the new concentrations. pH = pKa + log ([(0.0325 moles/0.710 L)]/[(0.0025 moles/0.710 L])pH = 5.86
EcoRI recognizes the sequence 5'-G↓AATTC-3' (the 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 Blunt ends are also called non-cohesive ends
If the E. coli genome is 4.6 × 10^6 base pairs and is replicated in 30. minutes, what is the reaction rate of helicase in terms of nucleotides per minute?
15333 To find this answer you would take the size of the genome and divide it by the time it takes to replicate.
Nearly all known DNA polymerases can add a nucleotide only to the free _____ -OH of a base-paired polynucleotide.
3'
Pol I synthesizes new DNA with very high fidelity, due to its
3' → 5' exonuclease activity.
What would be the resulting pH if one drop (0.05 ml) of 1.0 M HCl was added to one liter of pure water (assume pH 7.0)?
4.3
The carbohydrate moiety in a ribonucleotide or deoxyribonucleotide are found in a _______ -membered rings, while the hydroxyl groups on carbons 2' and 3' point ______ the plane of the ring.
5' ; below
What percentage of a solution of acetic acid is ionized at pH 5.6 (Ka for acetic acid = 1.78×10-5)?% ionized
88.57 pH = pKa + log([conjugate base]/[acid]) 5.6 = (-log(1.78×10-5)) + log([conjugate base]/[acid]) log([conjugate base]/[acid]) = 0.85 [conjugate base]/[acid] = 7.1 assuming if [acid] = 1, then [conjugate base] = 7.1initial [acid] = [acid]i = [conjugate base] + [acid] = 7.1 + 1 = 8.1percent ionized = ([conjugate base]/[acid]i)*100percent ionized = (7.1/8.1)*100 = 88%
In prokaryotes, Mut proteins
A) recognize and bind to mismatches B) cleaves the newly synthesized strand at the site of a mismatch C) recognizes and binds to alkylated bases
The oriC sequence is rich in adenine and thymine. Why does this make sense chemically? Select all that apply. Could a sequence rich in guanine and cytosine work as well?
A-T base pairs have fewer hydrogen bonds. Less energy is required to expose the helix in A-T rich regions. Yes
In glycolysis, glucose is broken down to yield energy. As part of the glycolysis pathway, glucose-6-phosphate is isomerized to fructose-6-phosphate; this reaction has an equilibrium constant of 0.5 at 25 ˚C. A. The free energy of this reaction is _____ (use units of kJ/mol and 2 significant digits). B. If the initial concentration of glucose-6-phosphate is 1M and fructose-6-phosphate is absence, then the equilibrium concentration of glucose-6-phosphate would be ________ M, and the equilibrium concentration of fructose-6-phosphate would be ________ M. C. Which of the following statements best describes the free energy and outcome of this reaction?
A. 1.71KJ/mol ΔG° = -RT ln Keq ΔG° = -(8.314 J/K mol)(298 K) ln (0.5) ΔG° = +1.7 kJ/mol B. 0.67M; 0.33M K = 0.5 = [fructose-6-phosphate]final / [glucose-6-phosphate]final = (x /1.0-x) x = 0.33 C. The relatively low positive free energy indicates that the reaction will go forward but that the final product concentration will be less than the final substrate concentration, which is consistent with the equilibrium calculation.
Cisplatin is a chemotherapeutic drug used to treat several different cancers, including testicular cancer. It forms adducts to guanine residues that often result in cross-linking of two guanines, similar to a thymine dimer. How might this damage be repaired?
By nucleotide excision repair using the GG-NER pathway.
In this reaction, the ______ acts as a proton donor; also, the act as a conjugate base
Carboxylic acid; carboxylate
Which of the following statements about the fidelity of replication is FALSE?
Cells are not viable when DNA point mutations are incorporated. Cells maintaining an equal concentration of each dNTP helps maintain fidelity. DNA polymerase catalyzes synthesis in a two-stage reaction, ensuring the proper base is added. Pol I and Pol III are both involved in increasing fidelity. Specific repair systems repair and maintain DNA.
Mutations leading to changes that can be inherited by the next generation have to be introduced at the ______ level.
DNA
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
What reagents are required to perform PCR?
DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase
A prokaryotic replisome typically contains two molecules of DNA pol III, but only one molecule of DNA pol I. Why?
DNA pol I replaces the RNA primers with DNA, which really only needs to be done repetitively on one strand, while both strands are worked on by the DNA pol IIIs.
When considering O, N, and F, the shortest hydrogen bond with an -OH group would be formed with ________ since this atom is the most ________ in the group.
F; electronegative
The UvrABC endonuclease repair system is specific for the repair of pyrimidine dimers. Bacteria, which do not contain duplicate chromosomes, have no need for the mechanism of general recombination.
False
There are only 20 codons that code for a separate amino acid. The tRNA molecule contains the codon that binds to the anticodon on the mRNA strand. Proteins are produced in the C terminus → N terminus direction.
False
Transcription can only be regulated in prokaryotes. RNA interference (RNAi) is used to solely regulate translation.
False
Which of the following is found in high concentration in all telomeres?
G
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.
Bacteria have obtained the -lactamase gene which encodes a protein that renders all -lactam antibodies such as ampicillin and penicillin inactive. Which of the following would result in an increased number of bacteria with this ability? I. a transposon with the -lactamase gene II. a recombination event within the original strain that results in a point mutation inactivating β-lactamase III. an insertion in the original strain rendering transposase inactive IV. a deletion in the insertion sequence of the transposon
I
Which of the following statement(s) about DNA polymerase III (Pol III) is (are) TRUE? I. DNA polymerase III has greater accuracy than RNA polymerase. II. Pol III is the primary replicase of E. coli. III. Pol III does not contain 5 to 3 exonuclease activity.
I, II, III
In molecular biology labs researchers often use E.coli strains that are RecA minus (recA−) when transforming a cloned gene into a plasmid which explains why I. a Rec A-strain would have fewer replication errors. II. a Rec A-strain would have less opportunity forming DNA mutations. III. a Rec A-strain would increase error repair.
II
DNA gyrase is the target of several antibiotics, including nalidixic acid, novobiocin, and ciprofloxacin. How do these antibiotics function? Why are they not harmful to humans?
Inhibit DNA replication Human do not express DNA gyrase, therefore the target is missing
Why cannot O6-methylguanine-DNA methyltransferase be strictly classified as an enzyme?
It becomes inactivated after one reaction due to transfer of a methyl group to its active site Cys residue.
Why is it unlikely from a thermodynamic perspective that DNA synthesis would run 3′ to 5′?
It is unfavorable to form a sugar-phosphate linkage from monophosphates. The pyrophosphate group would no longer hydrolyze and release energy. The dNTP is sterically hindered at the 3' making addition more taxing to the cell.
What is the purpose of DNA polymerase?
It is used to replicate DNA in the 5' → 3' direction. It adds the correct nitrogenous base to the template strand. It facilitates annealing. It is required for transcription in order to generate more DNA.
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.
Phosphoglucomutase catalyzes the reaction in which a phosphate group is transferred from the C-1 of glucose to the C-6 of glucose (G1P ⇆ G6P). A student incubates a 0.2 M solution of glucose-1-phosphate overnight with a small amount of the enzyme. At equilibrium the concentration of glucose-1-phosphate is 9.0 × 10−3 M and the concentration of glucose-6-phosphate is 19.1 × 10−2 M.Calculate the equilibrium constant (Keq) and the standard state free energy (∆G°') for this reaction at 25°C. The equilibrium constant Keq = The standard state free energy ∆G°' =
Keq = [G6P]eq/[G1P]eq = 19.1 × 10−2 M/ 9.0 × 10−3 M = 21. ∆G°' = −RTlnKeq = −8.3145 × 298 J/mol × ln 21.2 = −7,600 J/mol.
Biochemically, would it make better sense for histones to be methylated or demethylated prior to replication? Why?
Methylated, addition of methyl groups decreases histone-DNA interactions Methylation of histones decreases the interaction of lysine in the histone with the anionic phosphate groups in the DNA backbone.
Uracil can be removed from DNA strands by the action of uracil N-________
N-glycosylase
Could a polymerase run in the 3′ to 5′ direction? Why or why not?
No, a polymerase has directionality due to the loss of the pyrophosphate group driving addition.
How might each of the types of damage caused by nitrosamine or formaldehyde be repaired by the cell? Select all that apply.
Nucleotide-excision repair;Base-excision repair
In vitro DNA replication (e.g., PCR) can occur with a template, primer, polymerase, and the four dNTPs. Where does the energy required for the formation of DNA come from?
Pyrophosphate hydrolysis of dNTP
The ketone body β-hydroxybutyrate is a small molecule found in some metabolic states. In organisms, β-hydroxybutyrate will spontaneously decarboxylate into acetone and carbon dioxide. Which of the rate laws best describes this overall reaction?
Rate=k [β-hydroxybutyrate] For this reaction, there is only 1 substrate needed to match the stoichiometry of the reaction, which supports expression of the rate law as Rate=k [β-hydroxybutyrate].
E. coli strains that are deficient in RecA are commonly used in molecular cloning experiments. Why might it be to a scientist's advantage to use these strains?
RecA assists in recombination and would lead to plasmid DNA being integrated into the bacterial chromosome.
Biological processes can be best understood in the context of water. a. What effect does water have on the noncovalent interactions between either charged or polar groups/molecules? Water_______ the strength of those interactions. b. Why is this effect important with respect to biochemical processes? Water ________ the strength of polar and ionic interactions. This makes those interactions _______ and life is based on _______ interaction between biomolecules.
Reduces Reduces; reversible; reversible
Which of the following statements about PCR is (are) true?
Small amounts of DNA can be easily amplified to millions of copies. PCR is often used in forensics laboratories. PCR reaction products can be used in molecular cloning. PCR is used in clinical laboratories.
Most cancer cells express elevated levels of telomerase. Why?
Telomerase helps to immortalize cell lines by maintaining telomere length, preventing chromosome degradation.
Phosphodiester bonds link DNA monomers to form a polymer by which mechanism?
The OH group on C-3 in the 2-deoxyribose carbohydrate forms a covalent bond to elongate the DNA chain.
Each of the five bases contains nitrogen. Why are these amines not drawn in the ionized state?
The amines are deprotonated because the pKa values are lower than the pH of the cell. The pKa value of these amines is well below the physiological pH, partially due to resonance stabilization. They do not protonate until a solution becomes quite acidic (purine and pyrimidine have pKa values of 2.4 and 2.8, respectively).
In the following plot, where is the melting temperature of DNA, and what does the melting temperature indicate?
The melting temperature is the final point on the curve; and the melting temperature indicates that 100% of the DNA has been melted. The melting temperature is the final point on the curve; and the melting temperature indicates that 50% of the DNA has been melted. The melting temperature is the midpoint on the vertical component of the curve; and the melting temperature indicates that 100% of the DNA has been melted. The melting temperature is the midpoint on the first horizontal component of the curve; and the melting temperature indicates that 50% of the DNA has been melted. The melting temperature is the midpoint on the vertical component of the curve; and the melting temperature indicates that 50% of the DNA has been melted.
Eukaryotic transcription differs from prokaryotic transcription in which manner?
The polyA tail is a component of all mRNA transcripts. AUG is the initiation codon. Spliceosomes are necessary to excise introns. The RNA is a continuous message.
How do the types of recombination that do not require ATP form the bonds needed in recombination?
The recombination events are transphophorlation reactions that have deltaG values close to 0
If these sequences are not found at these frequences, what does that say about them? Select all that apply.
The sequences are being selected for The sequences are being selected against
A PCR experiment was performed on a highly conserved gene from two species, one prokaryotic and one eukaryotic. Which of the following statements best describes the expected results?
The sequences of the PCR products would be different since eukaryotes have introns and exons.
Dideoxy analogs are used in Sanger sequencing for what reason?
They facilitate polymerization of the DNA. They facilitate fluorescent DNA sequencing. They facilitate elongation of the DNA fragments. They block further elongation of the DNA.
In addition to mediating their own insertion into host DNA, what else do transposons do?
They promote inversion, deletions, and rearrangements of the host DNA.
Which of the following is FALSE about transcription?
Transcription factors can either speed up or slow down the process. RNA polymerase binds to the promoter region. It converts DNA to RNA. It occurs on the ribosome.
Each amino acid has its own tRNA molecule. mRNA, rRNA, and tRNA are required for the process.
True
Riboswitches are used to regulate translation. RNA interference (RNAi) is used to regulate mRNA levels prior to translation.
True
E. coli DNA photolyase binds single or double-stranded DNA without regard to sequence, and has a cavity corresponding to a pyrimidine dimer. During general recombination, the crossover point can move in either direction in a process known as branch migration.
Ture
In the cell, ATP is also required for DNA replication. What steps of replication require ATP? Select all that apply.
Unwinding of double helix Release of supercoiling Joining DNA fragments
The active site of recombinase is similar to some other enzymes (such as some polymerases) that we have seen in that it uses two metal ions for binding and catalysis. What are the common divalent metal ions employed by enzymes that have a DNA substrate? Select all that apply.
Zn and Mg 2+
DNA sequencing by the chain-termination method uses DNA polymerase I to make a complementary copy of the target or template DNA molecule. A reaction with a 20 bp template and dideoxyadenosine nucleotides as terminators results in the production of a 5 bp fragment. Based on this result, we can conclude that the template contains _____.
a thymine at position 16
The most prevalent mode of DNA-protein interaction is achieved with a(n) _____ that binds to the _____ groove of DNA.
a-helix; major
If a phosphate buffer (pK = 6.82) was formulated such that its pH was 7.3, it would be best suited to buffer against _____. If instead, it was formulated such that its pH was 6.3, it would be best suited to buffer against _____.
acid; base
Dimethyl sulfate, nitrogen mustard, and ethylnitrosourea are ______ agents of nucleotides.
alkylating
Which of the following functional groups has two hydrogen bond donors and one hydrogen bond acceptor?
amine
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
Which type of DNA repair is used to remove and replace a single modified base that cannot be converted back to the normal base by a direct repair process?
base excision repair
During recombination in E. coli, the RuvB protein acts as a DNA-dependent ATPase that drives
brunch migration
Recombinant DNA technology is also called molecular ______ or genetic engineering.
cloning
Incorporation of which of the following would result in chain termination during sequencing of DNA?
ddTTP
The results of DNA sequencing are obtained by first separating different-sized pieces of DNA using _____ followed by detection of the particular dideoxynucleotide using _____.
electrophoresis; fluorescence spectroscopy
An _______ is an enzyme that cleaves a nucleic acid within the polynucleotide strand.
endonuclease
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 bond; pi-pi interaction; ionic interactions
The following image shows how DNA can be damaged by UV light. In this reaction, UV light promotes the formation of an _______ cross-link, through the formation of a ___________ group, which _________ impact DNA replication and transcription.
intrastrand; cyclobutane; would
DNA polymerase from Thermus aquaticus is used in PCR because
it is stable at high temperatures.
Of the different types of DNA damage we discussed, is UV damage more or less significant than ionizing radiation? Is an alkylation more or less significant than a double-strand break?
less significant
DNA _______ is an enzyme necessary for splicing together fragments of DNA with complementary ends.
ligase
Would you anticipate that telomerase levels are higher in short lived organisms like the shrew or long-lived organisms like the giant sequoia, or are they the same? Why?
long-lived The longer an organism lived the more cell divisions it undergos
Chaotropes will ______ the melting point of DNA due to the formation of _______ with the DNA.
lower; hydrogen bond
Use the following information to answer the next question: Suppose that an error in replication occurred at position 324 in the E. coli sequence below, and that a GATC motif used to regulate replication and restriction is located about 300 bp away. Note that the A on the bottom (shown by the underlining) strand is methylated. 5' GGACGGATCC...TAAGCTGGTGGTGGTGGGCGCCGGCGGTGT 3' CCTGCCTAGG...ATTCGACCACCACCACCCGCGGCAGCCACA What enzymes would be used to repair this error?
methyl-directed mismatch repair enzymes
mRNA tRNA rRNA
moves genetic information from the nucleus to the ribosomes in the cytoplasm. decodes the genetic message; it matches sequences of three nucleotides to amino acids. is involved in the catalysis of amide bond formation.
In the following reaction, the alkene is acting as a/n
nucleophile forms bonds with electrophiles by donating an electron pair
Normal blood pH is approximately 7.35 and the concentration of H2CO3 and HCO3- ions (total) is approximately 20 mM. What is the ratio of carbonate to bicarbonate ions in blood under these conditions (Ka for H2CO3 = 4.3×10-7)?
pH = pKa + log ([conjugate base]/[acid]) 7.35 = (-log(4.3×10-7)) + log([conjugate base]/[acid]) log([conjugate base]/[acid]) = 0.983 [conjugate base]/[acid] = 9.6
Besides the obvious role of keeping DNA in a single strand state, what do single-strand binding proteins do?
protect single strand DNA backbone from nucleases
Because of the high temperature _____ step during a PCR reaction, the DNA polymerase from _____ is used.
strand separation; Thermus aquaticus
Name these three types of RNA
t,m,rRNA
Organisms that harbor a foreign gene as a result of recombinant gene manipulation are termed as ________.
transgenic
Protein synthesis is the process known as _______________.
translation
Transposable elements, or ________ , are common in both prokaryotes and eukaryotes.
transposons
Oxidative deamination of cytosine leads to formation of
uracil
____________ - the free energy of the reaction under the actual reaction conditions. Select all that apply.
ΔG
When the reaction conditions match the biochemical standard states, the values of ________ and _______ will be equal.
ΔG; ΔG°'
____________ - the free energy under the standard states. Select all that apply.
ΔG°
____________ - the free energy under the biochemical standard states. Select all that apply.
ΔG°'
____________ is the free energy of the transition state.
ΔG‡
The ________ determines the rate constant, while ________ determines the favorability of a reaction under standard conditions.
ΔG‡; ΔG°
Which of the following would result in increased processivity in E.coli?
β (sliding) clamp