Ch 19 review

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Terms in this set (...)

where does replication starts? (location)
origin of replication
what happens at the origin of replication?
The DNA opens up there to form a small bubble.
after forming the bubble of replication, what binds to DNA and what does?
Molecules of an enzyme called helicase attach to the DNA at the ends of the bubble and continue the unwinding of the double helix.
what is the name of the location at end of the bubble?
on one end of the bubble, on the Y-shaped region called a replication fork.
The two strands would naturally tend to rewind but are held apart by molecules of a_
single-strand binding protein.
the synthesis of a new strand begins when an enzyme called_attaches. what does? how is called what is added?
-primase
-it attaches and synthesizes a short RNA strand that is complementary to one of the DNA strands.
-This piece of RNA is a primer.
what happens after the primer is added?
DNA polymerase then adds DNA nucleotides to the 3' end of the primer. It continues to lengthen the new DNA strand by adding nucleotides complementary to the template strand.
what is the direction of DNA syntehsis?
DNA synthesis always proceeds in a 5' to 3' direction.
strand made in 5'-3'direction continuously is called_
leading strand
what is the name of the other strand made beside the leading strand?
lagging strand
how lagging strand is different from leading strand?
Unlike the leading strand, the lagging strand cannot be made continuously because DNA polymerase can only add nucleotides at the 3 prime end. Instead, the lagging strand must be made of fragments that are linked together.
in what direction with respect to the fork of replication the following strands are being made:
a. leading strand
b. lagging strand
a. leading strand is being synthesized 5'->3' direction toward the fork of replicaiton
b. lagging strand is being synthesized 5'->3' direction away from the fork of replication
what is the name given to the fragments formed in the lagging strand?
okizaki fragments
explain the steps of making the lagging strand
an RNA primer, shown here in red, forms the beginning of each fragment. The rest of each fragment is then synthesized from DNA nucleotides in a 5 prime to 3 prime direction. The resulting segments are called Okazaki fragments. Next, each RNA primer is replaced with DNA. Then the gaps are closed to form the lagging strand.
Explain how enzymes are involved in synthesizing the lagging strand
the enzyme primase removes the single-strand binding proteins, shown here in blue, and makes an RNA primer to begin an Okazaki fragment. The enzyme DNA polymerase then adds the complementary DNA nucleotides to synthesize the rest of the fragment. The assembly process continues, as primase makes new RNA primers and DNA polymerase adds DNA nucleotides to create more Okazaki fragments.

After the fragments are made, another kind of DNA polymerase replaces each RNA primer with DNA. Next, the enzyme DNA ligase links the Okazaki fragments to form the lagging strand.
what enzyme is needed to assemble:
a. leading strand
b. lagging strand (3)
a. DNA polymerase assembles a continuous leading strand
b. primase, other DNA polymerases, and ligase all work together to make the lagging strand.
what enzyme unwinds DNA?
The enzyme helicase continues to untwist the double helix, exposing more template strand DNA for replication.
In a DNA double helix an adenine of one strand always pairs with a(n) _____ of the complementary strand, and a guanine of one strand always pairs with a(n) _____ of the complementary strand. how this is referred to?
guanine ... adenine
cytosine ... uracil
uracil ... cytosine
thymine ... cytosine
cytosine ... thymine
thymine ... cytosine
This is referred to as specific base pairing
After DNA replication is completed, _____. (include name of model)
each new DNA double helix consists of one old DNA strand and one new DNA strand
each new DNA double helix consists of two new strands
one DNA double helix consists of two old strands and one DNA double helix consists of two new strands
there are four double helices
each of the four DNA strands consists of some old strand parts and some new strand parts
-each new DNA double helix consists of one old DNA strand and one new DNA strand
-DNA replication is semiconservative.
The first step in the replication of DNA is catalyzed by _____.
primase
DNA polymerase
helicase
ligase
single-strand binding protein
helicase
what is the first step of DNA replication?
The first step of DNA replication is unwinding the DNA double helix by helicase.
The action of helicase creates _____.
DNA fragments and replication forks
DNA fragments and replication bubbles
primers and replication bubbles
primers and DNA fragments
replication forks and replication bubbles
replication forks and replication bubbles
what is replication fork
A replication fork is the transition region between paired and unpaired DNA strands.
Why is the new DNA strand complementary to the 3' to 5' strands assembled in short segments? (include name of enzyme that binds the fragments)
it is more efficient than assembling complete new strands
DNA polymerase can assemble DNA only in the 5' to 3' direction
only short DNA sequences can extend off the RNA primers
DNA polymerase can assemble DNA only in the 3' to 5' direction
the replication forks block the formation of longer strands
DNA polymerase can assemble DNA only in the 5' to 3' direction
Since DNA polymerase can assemble DNA only in the 5' to 3' direction, the new strand complementary to the 3' to 5' strand must be assembled in short 5' to 3' segments, which are later joined together by ligase.
The synthesis of a new strand begins with the synthesis of a(n) _____.
poly(A) tail
single-strand binding protein
Okazaki fragment
short pieces of DNA
RNA primer complementary to a preexisting DNA strand
RNA primer complementary to a preexisting DNA strand
The synthesis of a DNA strand begins with the formation of an_
RNA primer.
An old DNA strand is used as a _____ for the assembly of a new DNA strand.
primer
model
source of nucleotides
complement
template
template
An old DNA strand is used as a _for the synthesis of a _ new strand
-template
-complementary
DNA synthesis reaction requires a_(what use to copy?); the enzyme_; and _(monomers)
-DNA template strand
-enzyme DNA polymerase
-deoxynucleoside triphosphates, or dNTPs
what are dNTPs?
building blocks for making a new strand
why DNA polymerase requires primase? what is the role of primase?
-DNA polymerase cannot start the synthesis on its own. An enzyme called primase begins the task by creating a short sequence of RNA that is complementary to the DNA
how is named the segment made primase?
RNA primer
RNA primer provides a_group on its_end. DNA polymerase can add _(monomer) only to a preexisting _
-hydroxyl group on its 3' end
-dNTPs
-3' hydroxyl group
dNTPs enter the reaction site. this base is_to the base in the opposite strand, and the two form_bonds
-complementary
-hydrogen bonds
what bond DNA polymerase forms? between what two structures?
-covalent bond between the 3' hydroxyl group at the end of the strand and the 5' alpha phosphate group of the new arrival dNTP
each added nucleotide provides a _group for the next reaction to occur
3' hydroxyl group
DNA polymerase add nucleotides in what direction?
5'-to-3' direction
DNA synthesis begins at a particular on the_, where proteins open and the double-stranded DNA into a_of single stranded DNA
-chromosome
-bubble
what is meant by saying that strands of DNA are antiparallel?
-they are parallel to one another but oriented in opposite directions: the 3' end of one strand points at the same direction as the 5' end of the other
enzymes called _enter the bubble and continue to unwind the DNA. the open DNA provides the replication machinery with access tot eh nucleotides in the strands
-helicases
after the action of helicase,_bind to the open DNA and prevent the strands from_
-single strand DNA-binding proteins
-closing back together
what the unwinding process creates in the helix? who solves it?
-the unwinding process creates tension farther down the helix.
-an enzyme called topoisomerase nicks the DNA and then untwists and reseals it to relives this tension
after the formation of the bubble of replication, what enzyme enters? what does? what direction are the added nucleotides?
-primase enter the replication bubble and add short segments of complementary RNA to the single-stranded regions of template DNA. these RNA primers are antiparallel to the template strands they are attached to
_continues to open the double helix, and _follows behind
-helicase
-primase
the RNA primers provide _groups at their _ends. These groups allow _(enzyme) to add additional nucleotides to the chain.
-hydroxyl groups
-3' ends
-DNA polymerase
what is the name of the DNA polymerase used by E coli?
DNA polymerase III (DNA gyrase)
As DNA polymerase _(type in prokaryotes) elongates each strand in _direction, helicase continues to_. One strand, called leading strand, elongates _(how elongates?)
-III
-unwind the double helix
-elongates continuously in the direction of the widening replication bubble
the DNA polymerase on the opposite strand travels in_direction. Therefore, the _(enzyme) must make additional RNA primers for this strand as the replication bubble widens. what happens after that?
-opposite direction (3'-->5')
-primase
-DNA polymerase III adds nucleotides to the new primer. Primase continues to add new RNA primers as the bubble widens
the fragments of DNA produced on the opposite strand are called_
okizaki fragments
all okizaki fragments make up the_strand
lagging
a leading and lagging stand are associated with each of the two _in a replication bubble
-replication forks
DNA synthesis is still not complete because the new strands have segments of RNA in them. what enzyme solves this?
DNA polymerase I removes the RNA nucleotides, one by one, and adds DNA nucleotides in their place
after substituting the RNA nucleotides by DNA polymerase I, what happens? what enzyme involved in this? Include types of bonds
-Notice that small nicks are left in the new strands of DNA
-An enzyme called DNA ligase seals the nicks by catalyzing the formation of phosphodiester bonds
What catalyzes DNA synthesis?
Primer
dNTPs
DNA polymerase
Replication fork
DNA polymerase
Which of the following statements about DNA synthesis is true?
DNA polymerase adds dNTP monomers in the 3' to 5' direction.
Primers are short sequences that allow the initiation of DNA synthesis.
As DNA polymerase moves along the template strand, each new nucleotide provides a 5' hydroxyl group for the next reaction to occur.
Nucleotides are added in a random fashion to single-stranded DNA.
Primers are short sequences that allow the initiation of DNA synthesis
When a primer is added to a single strand of DNA, _can start adding nucleotides to synthesize a complementary strand.
-DNA polymerase
Which part of a deoxynucleoside triphosphate (dNTP) molecule provides the energy for DNA synthesis?
Free 3' hydroxyl (-OH) group
Phosphate groups
Base
Sugar
-Phosphate groups
The potential energy stored in the bonds of the phosphates provides the energy for DNA synthesis.
Which of the following enzymes creates a primer for DNA polymerase?
Topoisomerase
Ligase
Helicase
Primase
Primase
This RNA polymerase synthesizes an RNA primer _(direction) to the template DNA strand.
antiparallel
Which of the following statements about Okazaki fragments in E. coli is true?
They are synthesized in the 3' to 5' direction.
They are formed on the lagging strand of DNA.
They are usually 50 to 500 bases long.
They are sealed together by the action of helicase.
They are formed on the lagging strand of DNA.
While DNA is synthesized continuously on the leading strand, Okazaki fragments are formed on the _strand because DNA synthesis always proceeds in the _direction.
-lagging
-5' to 3'
Which of the following enzymes is important for relieving the tension in a helix as it unwinds during DNA synthesis?`
Helicase
Topoisomerase
Single-stranded binding proteins
Ligase
Topoisomerase
what toposiomerase does?
This enzyme untwists the coils that occur in the DNA as it is being unwound into a single-stranded template
True or false? Single-stranded DNA molecules are said to be antiparallel when they are lined up next to each other but oriented in opposite directions.
True
what is said to be antiparallel?
When the 3' end of one DNA strand points in the same direction as the 5' end of the other DNA strand, the strands are said to be antiparallel.
Which of these answers accurately describes the sequence of protein involvement in the initiation of prokaryotic DNA replication from beginning to end?
DNA ligase, DNA polymerase I, DNA polymerase III, primase, DNA helicase and gyrase, initiator protein
Initiator protein, DNA helicase and gyrase, primase, DNA polymerase I, DNA polymerase III, DNA ligase
initiator protein, primase, DNA polymerase III, DNA helicase and gyrase, DNA ligase, DNA polymerase I
initiator protein, DNA helicase and gyrase, primase, DNA polymerase III, DNA polymerase I, DNA ligase
initiator protein, DNA helicase and gyrase, primase, DNA polymerase III, DNA polymerase I, DNA ligase
Which of the following would NOT be a potential signal the cell would need in order to progress through the G1 checkpoint?
sufficient nucleotides and nutrients for DNA synthesis
an active p53 protein
The necessary extracellular cues should be present (growth factors, etc...).
lack of DNA damage
an active p53 protein
The amount of nuclear DNA in the cell doubles
G1
S
G2
M
none of the phases
S
The nuclear envelope breaks into fragments
G1
S
G2
M
none of the phases
M
Sister chromatids separate from each other.
G1
S
G2
M
none of the phases
M
Cells that will never divide again are likely to be arrested in this phase.
G1
S
G2
M
none of the phases
G1
The primary cell wall of a plant cell forms.
G1
S
G2
M
none of the phases
M
Chromosomes are present as diffuse, extended chromatin.
Select all that apply
G1
S
G2
M
none of the phases
G1
S
G2
This phase is part of interphase.
Select all that apply.
G1
S
G2
M
none of the phases
G1
S
G2
Mitotic cyclin is at its lowest level.
G1
S
G2
M
none of the phases
M
A Cdk protein is present in the cell.
G1
S
G2
M
none of the phases
G1
S
G2
M
A cell cycle checkpoint has been identified in this phase.
G1
S
G2
M
none of the phases
G1
S
G2
M
The phase of the cell cycle associated with the doubling of the amount of DNA in the cell is
G1.
M.
G2.
S.
G0.
S.
The phase of the cell cycle associated with the replication of DNA is
prophase.
telophase.
interphase.
anaphase.
metaphase.
interphase.
DNA replication is
conservative.
dispersive.
irregular.
semiconservative.
none of the above
semiconservative.
DNA replication
is not edited once polymerization has occurred.
proceeds by making two continuous strands.
is conservative.
requires a type of RNA polymerase.
is partially regulated by promoter/terminator sites.
requires a type of RNA polymerase
All of the following are associated with replicons except
initiator proteins.
helicase loaders.
origin of replication.
minichromosome maintenance proteins.
single-strand binding proteins.
single-strand binding proteins.
A NASA probe returned samples of rocks from the surface of Mars. From these rocks, a prokaryotic organism was isolated and remained viable under conditions similar to that of Mars. The organisms are capable of dividing to replicate themselves. In order to determine whether the DNA replication of these organisms was semiconservative, an experiment using N15/N14 (similar to that of Mendelson and Stahl) was performed. If the method of DNA replication were conservative, after one generation one would expect to see
half of the DNA in the light band, the other half in the heavy band.
all of the DNA at a point midway between the heavy and light bands.
all of the DNA in the light (N14) band.
all of the DNA in the heavy (N15) band.
none of the above
half of the DNA in the light band, the other half in the heavy band.
An isolate of a mutant bacterium appears to grow more slowly than the population (wild type) from which it was isolated. Further studies showed that the slower growth was due to a markedly reduced DNA polymerase I activity. From this information, one would expect that this organism would also be deficient in the activity of DNA
unwinding.
excision repair.
recombination.
translation.
transcription.
excision repair.
For each of the following pairs of phases from the cell cycle, indicate how you could tell in which of the two phases a specific cell is located.
G1 and G2
G1 has the haploid set of DNA; G2 has the diploid set.
DNA is being synthesized during G1; little or no synthesis occurs during G2.
G1 has the 2C amount of DNA; G2 has the 4C amount.
Chromosomes are in an extended form during G2; in a condensed form during G1.
G1 has the 2C amount of DNA; G2 has the 4C amount.
For each of the following pairs of phases from the cell cycle, indicate how you could tell in which of the two phases a specific cell is located.
G1 and S
During S phase chromosomes are invisible; in G1 they are visualized.
DNA is being synthesized during S; little or no synthesis occurs during G1.
G1 has the 2n amount of DNA; S has the 4n amount.
Chromosomes are in an extended form during S; in a condensed form during G1.
DNA is being synthesized during S; little or no synthesis occurs during G1.
For each of the following pairs of phases from the cell cycle, indicate how you could tell in which of the two phases a specific cell is located.
G2 and M
Chromosomes are in an extended form during G2, but in a condensed form during most of M phase.
M has the 2C amount of DNA; G2 has the 4C amount.
Chromosomes are in an condensed form during G2, but in an extended form during most of M phase.
During M phase chromosomes are invisible, and in G2 they are visualized.
Chromosomes are in an extended form during G2, but in a condensed form during most of M phase.
For each of the following pairs of phases from the cell cycle, indicate how you could tell in which of the two phases a specific cell is located.
G1 and M
DNA is being synthesized during M; little or no synthesis occurs during G1.
G1 has the 2C amount of DNA; M has the 4C amount.
Chromosomes are in an extended form during G1, but in a condensed form during most of M phase.
During M phase chromosomes are invisible; in G1 they are visualized.
Chromosomes are in an extended form during G1, but in a condensed form during most of M phase.
Which of the following statements regarding DNA replication is true?
The rate of DNA replication is constant at all stages of development in eukaryotes.
Bacterial replication is faster than eukaryotic replication.
Cyclin-dependent kinases (Cdk) are not involved in the DNA replication process.
Early-replicating genes are those that are not actively transcribed.
DNA replication during embryonic development occurs at a slower rate than in the early stages of neonatal life.
Bacterial replication is faster than eukaryotic replication.
Ultraviolet (UV) light-treated bacteria would most likely have DNA damage in the form of
intercalation of the bases.
direct transition of the bases.
pyrimidine dimer formation.
analog incorporation.
deamination.
pyrimidine dimer formation.
A mutant strain of yeast possesses a mutation in the nda2 gene, resulting in no production of α1 tubulin. As a result, these cells would most likely
keep the nuclear membrane intact.
not enter M phase.
not duplicate their chromosomes.
have little or no spindle formation.
not enter S phase.
have little or no spindle formation.
Cyclins modulate the progression of cells through the cell cycle by
directly activating G proteins.
increasing the production of DNA polymerases.
activating protein kinases that are critical regulators of cell division.
inducing synthesis of constitutively active forms of growth cell receptors.
degrading histones.
activating protein kinases that are critical regulators of cell division.
During the G2 checkpoint in eukaryotic cells, the cell is assessed with regard to
chromosome attachment to the spindle.
DNA damage.
presence of growth factors.
nutrients.
DNA replication.
DNA replication.
Which of the following proteins is observed exclusively in association with prokaryotic DNA replication?
DNA polymerase I
telomerase
single-strand binding proteins
primase
helicase
DNA polymerase I
Which of the following proteins is observed exclusively in association with eukaryotic DNA replication?
DNA polymerase I
single-strand binding proteins
DNA gyrase
telomerase
DNA ligase
telomerase
The longest phase of the cell cycle is
anaphase.
prophase.
metaphase.
interphase.
telophase.
interphase.
The phase of the cell cycle that varies most in duration in various cell types is
G1.
M.
S.
G2.
M and G1.
G1.
The proteins most actively synthesized during the S phase of the cell cycle are
rRNA proteins.
cyclins.
histones.
single-strand binding proteins.
DNA polymerases.
histones.
Which enzyme is involved in proofreading during DNA replication?
3' to 5' exonuclease
5' to 3' exonuclease
DNA polymerase
5' to 3' endonuclease
3' to 5' endonuclease
3' to 5' exonuclease
The multiple sites of DNA replication along eukaryotic chromosomes are known as
ARS elements.
multireplication forks.
helicase loaders.
replicons.
none of the above
replicons.
The protein(s) that facilitate the unfolding of chromatin fibers ahead of the replication fork is (are)
chromatin remodeling proteins.
replisomal proteins.
helicase.
scaffold proteins.
helicase and scaffold proteins.
chromatin remodeling proteins.
Mice lacking the ability to make caspase-9 die as the result of numerous defects. During the necropsy (animal autopsy) of the animal you note that the brains of these mice are
overproduction of the Etr1 receptor protein.
overstimulation of G-protein-mediated transduction.
unregulated growth of the nerve cells.
lack of apoptosis of some cells.
all of the above
lack of apoptosis of some cells.
the model of mitotic chromosome movement based on three roles played by _
-motor proteins
what are the three types of motor proteins microtubules?
-kinetochore MTs
-polar MTs
-astral MTs
kinetochore MTs have a motor proteins associated with both their_ (2 and location)
-plus ends (embedded in the chromosomal kinetochore) and their minus ends (located in the centrosome of the spindle pole)
what the motor proteins found at the kinetochore do? what is the result of this interaction?
-the motor proteins located at the kinetochore depolymerize the plus ends of the kinetochore MTs, while the motor proteins depolymerize the minus ends of the kinetochore MTs
-In this way, the chromosome is pulled toward the spindle pole as the kinetochore MTs are shortened and reeled in
what polar microtubules do?
-motor proteins crosslink the polar MTs and cause them to slide apart, thereby forcing the spindle poles away from each other
-As the polar MTs slide apart, they are lengthened by the addition of tubulin subunits to the plus ends where they overlap near the spindle center
what astral microtubules do?
-astral microtubules link the plus ends of astral MTs to the cell cortex and exert a pull on the spindle poles by inducing astral MT depolarization at their plus ends
Which type of microtubule is responsible for the elongation of the cell in Anaphase B?
astral
polar
kinetochore
motor proteins
polar
Based on the direction of movement, the kinetochore molecular motor is most likely _____-based.
tubulin
dynein
myosin
kinesin
kinesin
The molecular motors that are most active in Prophase are the ones attached to __________.
polar microtubules
kinetochore microtubules
astral microtubules
axonemal microtubules
astral microtubules
Which microtubules shrink during mitosis?
kinetochore microtubules
astral microtubules
polar microtubules
astral and kinetochore microtubules
astral and kinetochore microtubules
What would be the effect of adding colchicine to cells that were at the metaphase-anaphase transition?
The chromosomes would segregate but the cell would not elongate.
The cell would not elongate and the asters would be released from the cell membrane.
The cell would elongate but the chromosomes would not segregate.
The asters would be released from the cell membrane and the chromosomes would not segregate.
The chromosomes would segregate but the cell would not elongate.