Deck 10: DNA Replication and Recombination

Question 1

Refer to the following diagram of a generalized tetranucleotide to answer questions
(a) through (e).
a() Is this a DNA or an RNA molecule? ________
b() Place an "X" (in one of the circles in the diagram) at the 3' end of this tetranucleotide.
c() Given that the DNA strand, which served as a template for the synthesis of this
tetranucleotide, was composed of the bases 5' - A C A G - 3', fill in the parentheses (in the diagram) with the expected bases.
d() Suppose that one of the precursors for this tetranucleotide was a 32P -labeled
guanine nucleoside triphosphate (the innermost phosphate containing the radioactive phosphorus). Circle the radioactive phosphorus atom as it exists in the tetranucleotide.
e() Given that spleen diesterase (breaks between the phosphate and the 5' carbon) digests the pictured tetranucleotide, which base(s) among the breakdown products would be expected to be attached to the 32P?

Answer 1

(a) DNA
a() place in bottom circle
b() 3' -TGTC -5'
c() phosphate on the 5' side of the guanine
d() thymine closer to the 5' end

Question 2

DNA polymerase I is thought to add nucleotides _.

A) on single -stranded templates without need for an RNA primer
B) to the 3' end of the primer
C) in a 5' to 5' direction
D) to the 5' end of the primer
E) in the place of the primer RNA after it is removed

Answer 2

E

Question 3

Which of the following terms accurately describes the replication of DNA in vivo?

A) semidiscontinuous
B) continuous
C) dispersive
D) nonlinear
E) conservative

Answer 3

A

Question 4

What three possible models were suggested to originally describe the nature of DNA replication?

Question 5

DNA polymerase III adds nucleotides _.

A) to both ends of the RNA primer
B) in the place of the primer RNA after it is removed
C) to the 3' end of the RNA primer
D) to the 5' end of the RNA primer
E) to internal sites in the DNA template

Question 6

Briefly describe what is meant by the term autoradiography and identify a classic
experiment that used autoradiography to determine the replicative nature of DNA in eukaryotes.

Question 7

The Meselson and Stahl experiment provided conclusive evidence for the
semiconservative replication of DNA in E. coli. What pattern of bands would occur in a CsCl gradient for conservative replication?

Question 8

What primary ingredients, coupled with DNA polymerase I, are needed for the in vitro
synthesis of DNA?

Question 9

Assume that you grew a culture of E. coli for many generations in medium containing 15N (from the ammonium ion), a heavy isotope of nitrogen. You extract DNA from a portion of the culture and determine its density to be 1.723 gm/cm3 (call this sample

A). You then wash the remaining E. coli cells, grow them for one generation in 14N,
and extract the DNA from a portion of the culture (call this sample
B). You let the
culture grow for one more generation in 14N and extract the DNA (call this sample
C) is then subjected to ultracentrifugation. Present the centrifugation profiles that you would expect under (a) semiconservative replication
and (b) conservative replication. (Note: Assume that unlabeled [14N] DNA has a density of 1.700 gm/cm3.)
C). Each sample of DNA (A, B, and

Question 10

Meselson and Stahl determined that DNA replication in E. coli is semiconservative. What additive did they initially supply to the medium in order to distinguish "new" from "old" DNA?

Question 11

The discontinuous aspect of replication of DNA in vivo is caused by

A) trinucleotide repeats
B) the 5' to 3' polarity restriction
C) topoisomerases cutting the DNA in a random fashion
D) sister -chromatid exchanges
E) polymerase slippage

Question 12

Assume that you are microscopically examining mitotic metaphase cells of an
organism with a 2n chromosome number of 4 (one pair metacentric and one pair
telocentric). Assume also that the cell passed through one S phase labeling (innermost phosphate of dTTP radioactive) just prior to the period of observation. Assuming that the circle below represents a cell, draw its chromosomes and the autoradiographic
pattern you would expect to see.

Question 13

Assume that you were growing cells in culture and had determined the cell -cycle time to be 24 hours. You introduce 3H thymidine and prepare autoradiographs of
metaphase chromosomes after 48 hours. Of the chromosomes that are labeled, you
expect two classes: one class that had completed one S phase in the label, and a second class that had completed a cellular division and an additional S phase in the label.
Draw the DNA (double -stranded) labeling pattern for each chromosome that you
would expect to find in these two types of metaphase chromosomes. (Use a broken line
{ - - -} for labeled single strands of DNA and a solid line for unlabeled single strands of DNA.)
a() metaphase chromosome having replicated once in label
b() metaphase chromosome having gone through two S phases in label

Question 14

Assume that you grew a culture of E. coli for many generations in medium containing 15N (from the ammonium ion), a heavy isotope of nitrogen. You extract DNA from a portion of the culture and determine its density to be 1.723 gm/cm3 (call this sample

A). You then wash the remaining E. coli cells and grow them for one generation in 14N, extract the DNA from a portion of the culture, and determine its density to be 1.715 gm/cm3 (call this sample
B). You let the culture grow for one more generation in 14N
and extract the DNA (call this sample
C) is then
heated to completely denature the double -stranded structures, cooled quickly (to keep the strands separate), and subjected to ultracentrifugation. Present the centrifugation
profiles for heat -denatured DNA (samples A, B, and
C) that you would expect. Use the graph below. (Note: Although not the case, assume that single -stranded DNA has the same density as double -stranded DNA.)
C). Each sample of DNA (A, B, and

Question 15

Which cluster of terms accurately reflects the nature of DNA replication in prokaryotes?

A) fixed point of initiation, bidirectional, conservative
B) fixed point of initiation, unidirectional, conservative
C) fixed point of initiation, bidirectional, semiconservative
D) random point of initiation, unidirectional, semiconservative
E) random point of initiation, bidirectional, semiconservative

Question 16

DNA replication in vivo requires a primer with a free 3' end. What molecular species provides this 3' end, and how is it provided?

Question 17

Structures located at the ends of eukaryotic chromosomes are called

A) recessive inversions
B) centromeres
C) telomerases
D) telomeres
E) permissive mutations

Question 18

Assume that a culture of E. coli was grown for approximately 50 generations in 15N (provided in the medium in the ammonium ion), which is a heavy isotope of nitrogen (14N). You extract the DNA from the culture, and it has a density of 1.723 gm/cm3
(water = 1.00 gm/cm3). From the literature, you determine that DNA containing only the common form of nitrogen, 14N, has a density of 1.700 gm/cm3. Bacteria from the
15N culture were washed in buffer and transferred to 14N medium for one generation immediately after which the DNA was extracted and its density determined.
a() What would be the expected density of the extracted DNA?
b() After you heat the extracted DNA until it completely denatures (95°C for 15
minutes), what would you expect the density of the DNA in the denatured extract to be? For the purposes of this question, assume that DNA has the same density
regardless of whether it is single - or double -stranded.
c() Assuming that the molar percentage of adenine in the extracted DNA was 20
percent, what would be the expected molar percentages of the other nitrogenous bases in this DNA?
d() Assume that a fraction of the extracted DNA was digested to completion with the enzyme snake venom diesterase. This enzyme cleaves between the phosphate and the 3' carbon. Present a "simplified" diagram that would illustrate the structure of the
predominant resulting molecule.

Question 19

Given the diagram below, assume that a G1 chromosome (left) underwent one round of replication in 3H -thymidine and the metaphase chromosome (right) had both
chromatids labeled. Which of the following replicative models (conservative, dispersive, semiconservative) could be eliminated by this observation?

Question 20

Which terms accurately reflect the nature of replication of the chromosome in E. coli?

A) multirepliconic and telomeric
B) bidirectional and multirepliconic
C) unidirectional and reciprocal
D) unidirectional and fixed point of initiation
E) bidirectional and fixed point of initiation

Question 21

Each of the following terms refers to the replication of chromosomes. Describe the role (relationship) of each in (to) chromosome replication.
a() Okazaki fragment
b() lagging strand
c() bidirectional

Question 22

During DNA replication, what is the function of RNA primase?

Question 23

Given that the origin of replication is fixed in E. coli, what signals the location of the origin?

Question 24

DNA replicates conservatively, which means that one of the two daughter double helices is "old" and the other is "new."

Question 25

What is the name of the replication unit in prokaryotes, and how does it differ in eukaryotes?

Question 26

The complex of proteins that is involved in the replication of DNA is called a(n)
________.

Question 27

Describe a somewhat extraordinary finding related to the Tetrahymena telomerase enzyme.

Question 28

During replication, primase adds a DNA primer to RNA.

Question 29

Below is a diagram of DNA replication as currently believed to occur in E. coli. Arrows start from numbers and end at specific points. Answer the questions relating to the
locations specified by the numbers.
1() Which end (5' or 3') of the molecule is here?
2() Which enzyme is probably functioning here to deal with supercoils in the DNA?
3() Which enzyme is probably functioning here to unwind the DNA?
4() Which nucleic acid is probably depicted here?
5() What are these short DNA fragments usually called?
6() Which enzyme probably functions here to couple these two newly synthesized fragments of DNA?
7() Is this strand the leading or lagging strand?
8() Which end (5' or 3') of the molecule is here?

Question 30

Which protein is responsible for the initial step in unwinding the DNA helix during replication of the bacterial chromosome?

Question 31

Given that the nature of DNA replication in eukaryotes is not as well understood as in prokaryotes, (a) present a description of DNA (chromosome) replication as presently viewed in eukaryotes and (b) state the differences known to exist between prokaryotic and eukaryotic DNA replication.

Question 32

DNA strand replication begins with an RNA primer.

Question 33

Compare the rate of DNA replication in prokaryotes and eukaryotes.

Question 34

In the Meselson and Stahl (1958) experiment, bean plants (Vicia faba) were radioactively labeled so that autoradiographs could be made of chromosomes.

Question 35

List four enzymes known to be involved in the replication of DNA in bacteria.

Question 36

DNA replication occurs in the 5' to 3' direction; that is, new nucleoside triphosphates are added to the 3' end.

Question 37

Describe the DNA base sequence arrangement at the end of the Tetrahymena
chromosome and the resolution of DNA replication at the end of a linear DNA strand.

Question 38

In general, DNA replicates semiconservatively and bidirectionally.

Question 39

Which structural circumstance in DNA sets up the requirement for the semidiscontinuous nature of its replication?

Question 40

As unwinding of the helix occurs during DNA replication, tension is created ahead of
the replication fork. Describe the nature of this tension and state the manner in which it is resolved.

Question 41

Chromatin assembly factors (CAFs) move along with the replication fork and assemble new nucleosomes.

Question 42

Telomerase is an RNA -containing enzyme that adds telomeric DNA sequences onto the ends of linear chromosomes.

Question 43

A nucleosome is a structure associated with the nuclear membrane. It helps maintain a stable relationship between the extracellular matrix and the membrane itself.

Question 44

In ligase -deficient strains of E. coli, DNA and chromosomal replication are unaltered because ligase is not involved in DNA replication.

Question 45

Bacteria are dependent on telomerase to complete synthesis of their chromosome ends.