Ch 1 - 6 Flashcards
If a stretch of DNA on the parental strand of a replicating chromosome has the sequence 5′–AGCTCGATCGGCTA–3′, what will the sequence of the newly synthesized strand made from this stretch of template be?
3′–TCGAGCTAGCCGAT–5′
The parental strand will be used as a template for replication using complementary base-pairing rules. So, the new strand will be complementary and antiparallel to the other.
Meselson and Stahl performed a classic experiment to explore three models for the mechanism of DNA replication. Which of the models held that the two parental strands would remain associated after replication?
a) dispersive
b) liberal
c) conservative
d) semiconservative
c) conservative
The conservative model of replication posited that after replication of the parental strands, the original parental molecule remained intact. In this model, the two newly replicated strands would associate, forming their own new molecule.
Using the technique shown below, Meselson and Stahl did an experiment where they grew cells in a heavy medium for many generations, then after a single generation in a light-medium, they observed a single band of intermediate weight after centrifugation. This experiment ruled out which model of DNA replication?
a) dispersive
b) semiconservative
c) conservative
d) liberal

c) conservative
After one round of DNA replication in light-medium, the DNA molecules were of an intermediate weight, meaning that they had a mixture of light and heavy nitrogen isotopes. This could arise from either dispersive or semiconservative mechanisms but ruled out the conservative mechanism since it would produce molecules that are completely made up of light isotope as well as the parental molecules of all heavy isotope.
What is the name of the DNA sequence where replication begins?
a) replication origin
b) replication fork
c) DNA template
d) initiator
a) replication origin
DNA synthesis begins at replication origins, where local strand separation is promoted by initiator proteins.
The sequence at which DNA replication begins tends to have which characteristic?
a) AT-rich
b) GC-rich
c) A-rich
d) G-rich
a) AT-rich
Replication origins tend to be very rich in A-T base pairs to facilitate local strand separation by initiator proteins. A-T base pair is held together by fewer hydrogen bonds than is a G-C base pair. Therefore, A-T base pairs are easier to pull apart.
In which direction, and on which strands does DNA replication proceed from a replication origin on a chromosome?
a) only on one strand in the 5’ → 3’ direction
b) only on one strand in the 3’ → 5’ direction
c) in both directions, on both strands
d) from the left to the right, on both strands
c) in both directions, on both strands
The DNA replication machinery can only add nucleotides in the 5′ to 3′ direction, but both strands are replicated using a clever workaround by the cell. In addition, replication forks move in both directions from a replication origin.
The bonds that link two DNA strands together are
a) electrostatic interactions
b) phosphodiester bonds
c) phosphoanhydride bonds
d) hydrogen bonds
d) hydrogen bonds
Two DNA strands are held together by many weak noncovalent hydrogen bonds between complementary base pairs.
The energy for the polymerization reaction in DNA synthesis is powered by
a) the formation of phosphodiester bonds between nucleotides
b) the breaking of the hydrogen bonds between complementary base pairs
c) the breaking of high-energy phosphate bonds in the deoxynucleotides
d) the association/disassociation cycles of the DNA polymerase enzyme
c) the breaking of high-energy phosphate bonds in the deoxynucleotides
The formation of the phosphodiester bonds requires an input of energy. This is provided by the hydrolysis of the high-energy phosphoanhydride bonds in the incoming nucleotide triphosphates that are the building blocks for the DNA polymer. Pyrophosphate is further hydrolyzed to inorganic phosphate, which makes the polymerization reaction effectively irreversible.

Shown below is a replication bubble. At which location is the DNA polymerase adding nucleotides in a continuous manner?
a) C and D
b) A and B
c) B and C
D) A and D

d) A and D
DNA polymerase can only add nucleotides continuously in the 5′ to 3′ direction - when it is moving along the template strand in a 3′ to 5′ direction. This would be the locations marked A and D.
How does Polymerase help maintain the accuracy of DNA replication?
a) polymerase fixes its mistakes by adding the right base during the next round of replication
b) after DNA replication is complete, the polymerase re-scans the entire chromosome to check for errors
c) polymerase never makes mistakes; bases are added based on strict complementarity
d) DNA polymerase can cut out improperly base-paired nucleotides and add the correct one during synthesis
d) DNA polymerase can cut out improperly base-paired nucleotides and add the correct one during synthesis
Concurrent with the polymerization reaction, polymerase double-checks the base pair that it just formed and, if it is incorrect, it will snip it out. Then the right base will be added to form a correct base pair.
This proofreading mechanism is possible only for DNA polymerases that synthesize DNA exclusively in the 5’-to-3’ direction. This is because if this “backward” polymerase were to remove an incorrectly paired nucleotide from the 5’ end, it would create a chemical dead end – a strand that could no longer be elongated. Polymerization cannot proceed, as no high-energy bond is available to drive the reaction

How are the primers from which DNA synthesis starts different from the DNA itself?
a) The primers have three phosphates on each nucleotide
b) The primers are not properly based paired so they can be removed
c) The primers are made up of RNA not DNA
d) The primers do not have a 3’ –OH
c) the primers are made up of RNA not DNA
RNA primers are made by an enzyme called primase to provide a “seed” from which the DNA polymer can grow. The primer provides a base-paired 3′−OH for starting the reaction. DNA polymerase cannot start a new polynucleotide chain by joining together two triphosphates without the need for a base-paired 3’ end as a starting point.
What is the name of the enzyme that fills the sequence gaps after primers are removed from a newly synthesized DNA strand?
a) DNA ligase
b) primase
c) nuclease
d) repair polymerase
d) repair polymerase
After a nuclease removes the primers, there are gaps in the DNA molecule. A repair polymerase can come in and fill the gaps to produce a continuous strand.
What is the name of the protein that binds the two separated DNA strands to keep them from base pairing again before they can be replicated?
a) single-stranded binding protein
b) primase
c) sliding clamp
d) helicase
a) single-stranded binding protein
As a replication fork travels along the chromosome, the helicase pries apart the two strands of the double-helix. Single-strand binding protein holds these two strands apart and keeps them from reforming base pairs by binding to the single-stranded DNA.
What is the function of a topoisomerase in DNA replication?
a) it separates the DNA strands
b) it binds the template DNA to hold in place
c) it relieves the tension in DNA strands
d) it coils the DNA fro tighter packaging
c) it relieves the tension in DNA strands
The unwinding of the DNA by helicase produces tension in the DNA molecule because the DNA cannot freely rotate. Topoisomerases cut the DNA to allow the DNA to freely rotate and relieve this tension, avoiding supercoils and tangles, and then reseals the DNA.
Shown below is the end of a newly replicated chromosome. Which strand will telomerase elongate?
a) both strands
b) the template of the lagging strand
c) the incomplete newly synthesized lagging strand
d) neither of the strands, this is done by polymerase

b) the template of the lagging strand
Telomerase extends telomere repeat sequences at the end of chromosomes by extending the template of the lagging strand. The incomplete lagging strand will be extended by a polymerase, using the extended template.
The strand is incomplete because when the final RNA primer on the lagging strand is removed, there is no enzyme that can replace it with DNA. The template is extended beyond the DNA that is to be copied. The telomerase adds the telomere repeat sequences at the 3’ end of the template strand (carries its own RNA template). After the lagging strand replication is complete, a short stretch of single-stranded DNA remains at the ends of the chromosome, but the newly synthesized lagging strand contains all the information present in the original DNA

Which of the following is NOT a common source of DNA damage for cells in our bodies?
a) replication fork problems
b) UV light
c) soap
d) spontaneous loss of amino groups on cytosine
c) soap
DNA is continuously undergoing thermal collisions with other molecules.
Depurination (spontaneous reaction) removes a purine base from a nucleotide (does not break the backbone), giving rise to lesions that resemble missing teeth.
Deamination (spontaneous reaction) is the loss of an amino group from cytosine in DNA to produce the base uracil.
UV light promotes thymine dimers.
Mishaps at the replication fork can cause a double-strand break.
What is the name of the type of damage caused by an improperly paired base in the DNA?
a) thymine dimer
b) double-strand break
c) depurination
d) mismatch
d) mismatch
Sometimes mispaired bases escape the proofreading of DNA polymerase during replication. These are called mismatches and can be repaired after replication is complete.
What is the first step that must occur to repair damage on one strand of the double helix?
a) The DNA backbone on both strands must becut to make a double-strand break.
b) The damaged region must be removed
c) The gap caused by the damage must be filled
d) The DNA backbone must be sealed
b) the damaged region must be removed.
Repair of damaged bases occurs through three steps. The first step is to remove the damaged base and the neighboring bases. Then, the gap can be filled using the undamaged strand as a template and the backbone sealed by ligase.
In bacteria, how does the cell recognize which strand is the newly synthesized strand and thus contains the mismatch?
a) the newly synthesized strand is methylated
b) the newly synthesized strand is unmethylated
c) the sequences on both strands are cut
d) the sequence on the newly synthesized strand is made of RNA
b) the newly synthesized strand is unmethylated
In bacterial DNA, adenine bases are methylated. This occurs slowly, so newly synthesized strands remain unmethylated for a time after replication and give mismatch repair enzymes time to recognize the damaged strand.
Which double-strand break repair mechanism is a simple ligation mechanism?
a) DNA mismatch repair
b) nonhomologous end joining
c) DNA ligase
d) homologous recombination
b) nonhomologous end joining
Nonhomologous end-joining is a mechanism for sealing DNA double-strand breaks using DNA ligase. This “quick and dirty” mechanism rapidly seals the break, but it comes with a price: nucleotides are often lost at the site of repair. A nuclease chews back the broken ends to produce flush ends. The flush ends are then stitched together by a ligase.
Homologous recombination is more complicated, with end processing and copying of the damaged region from an intact copy of that sequence.
Homologous recombination
Flawlessly repair DNA double-strand breaks
Most often occurs shortly after a cell’s DNA has been replicated before cell division when the duplicated helices are sill physically close to each other.

Single nucleotide changes from unrepaired DNA damage that lead to uncontrolled cell division can lead to which of the following conditions?
a) sickle cell anemia
b) aging
c) cancer
d) cell death
c) cancer
DNA damage that is unrepaired can lead to mutations that alter the regularity of cell division. Uncontrolled cell division that occurs at the expense of the organ system or organism is called cancer.
Which of the following are critical components of the helicase mechanism of action necessary to unwind DNA?
a) dissociation of the helicase subunits
b) conformational changes of subunits
c) oscillating loops pulling the single-stranded DNA through a central hole
d) binding of four helicase subunits to the double-stranded DNA
e) ATP binding and hydrolysis
b) conformational changes of subunits
c) oscillating loops pulling the single-stranded DNA through a central hole
e) ATP binding and hydrolysis
Six helicase subunits go through cycles of ATP binding and hydrolysis to change conformation. The conformational changes lead to a pulling of the single-stranded DNA through the central hole.
Which of the following is a function of the protein component of chromosomes?
a) It helps to translate the genetic message
b) It contains the enzymes that replicate the DNA
c) It carries a portion of the genetic information
d) It packages the DNA strands
d) It packages the DNA strands
Chromosomes are made up of protein and DNA. The DNA carries the genetic information, and the protein component helps store the long DNA molecules in the cell, in addition to controlling access to the DNA molecules.













