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Biology & Life Science
Q:
Although mutations have been observed in many different genes, they have not been isolated in histones. Why does this seem reasonable? If one wanted to produce antibodies to histones, would it be an easy task? Explain your answer.
Q:
How does a polytene chromosome differ from a typical eukaryotic chromosome?
Q:
Describe the chromosomal conformations of X†X174 and polyomaviruses.
Q:
List several configurations that characterize different viral chromosomes.
Q:
A particular variant of the lambda bacteriophage has a DNA double-stranded genome of 51,365 base pairs. How long would this DNA be?
Q:
In addition to highly repetitive and unique DNA sequences, a third category of DNA sequences exists. What is it called, and what types of elements are involved in it?
A) composite DNA; telomeres and heterochromatin
B) dominant DNA; euchromatin and heterochromatin
C) multiple gene family DNA; hemoglobin and 5.0S RNA
D) moderately repetitive DNA; SINEs, LINEs, and VNTRs
E) permissive DNA; centromeres and heterochromatin
Q:
In human chromosomes, satellite DNA sequences of about 170 base pairs in length are present in tandem arrays of up to 1 million base pairs. Found mainly in centromere regions, these DNA sequences are called ________.
A) telomeres
B) primers
C) alphoid families
D) euchromatic regions
E) telomere-associated sequences
Q:
That some organisms contain much larger amounts of DNA than are apparently "needed" and that some relatively closely related organisms may have vastly different amounts of DNA is more typical in ________.
A) viruses than in bacteria
B) RNA viruses than in DNA viruses
C) eukaryotes than in prokaryotes
D) the alphoid rather than the diploid family
E) prokaryotes than in eukaryotes
Q:
Chromatin of eukaryotes is organized into repeating interactions with protein octamers called nucleosomes. Nucleosomes are composed of which class of molecules?
A) histones
B) glycoproteins
C) lipids
D) H1 histones
E) nonhistone chromosomal proteins
Q:
Eukaryotic chromosomes contain two general domains that relate to the degree of condensation. These two regions are ________.
A) called heterochromatin and euchromatin
B) uniform in the genetic information they contain
C) separated by large stretches of repetitive DNA
D) each void of typical protein-coding sequences of DNA
E) void of introns
Q:
In E. coli, the genetic material is composed of ________.
A) circular, double-stranded DNA
B) linear, double-stranded DNA
C) RNA and protein
D) circular, double-stranded RNA
E) polypeptide chains
Q:
Viral chromosomes exist in a variety of conformations and can be made up of ________.
A) protein- or lipid-coding sequences
B) DNA only
C) DNA or RNA
D) RNA only
E) DNA, RNA, or protein
Q:
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.
Q:
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 (95C 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%, 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"² carbon. Present a "simplified" diagram that would illustrate the structure of the predominant resulting molecule.
Q:
Structures located at the ends of eukaryotic chromosomes are called ________.
A) centromeres
B) telomerases
C) recessive mutations
D) telomeres
E) permissive mutations
Q:
The discontinuous aspect of replication of DNA in vivo is caused by ________.A) polymerase slippageB) trinucleotide repeatsC) the 5-² to 3-² polarity restrictionD) topoisomerases cutting the DNA in a random fashionE) sister-chromatid exchanges
Q:
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) random point of initiation, bidirectional, semiconservative
D) fixed point of initiation, bidirectional, semiconservative
E) random point of initiation, unidirectional, semiconservative
Q:
Which terms accurately reflect the nature of replication of the chromosome in E. coli?
A) bidirectional and fixed point of initiation
B) unidirectional and reciprocal
C) unidirectional and fixed point of initiation
D) multirepliconic and telomeric
E) bidirectional and multirepliconic
Q:
DNA polymerase I is thought to add nucleotides ________.
A) to the 5"² end of the primer
B) to the 3"² end of the primer
C) in the place of the primer RNA after it is removed
D) on single-stranded templates without need for an RNA primer
E) in a 5"² to 5"² direction
Q:
DNA polymerase III adds nucleotides ________.
A) to the 3"² end of the RNA primer
B) to the 5"² end of the RNA primer
C) in the place of the primer RNA after it is removed
D) to both ends of the RNA primer
E) to internal sites in the DNA template
Q:
Which of the following terms accurately describes the replication of DNA in vivo?
A) conservative
B) dispersive
C) semidiscontinuous
D) nonlinear
E) nonreciprocal
Q:
G-quartets are G-rich single-stranded tails that loop back on themselves forming G-G double stranded sections. Such looping is involved in aligning chromosomes for homologous recombination.
Q:
Bacteria are dependent on telomerase to complete synthesis of their chromosome ends.
Q:
Telomerase is an RNA-containing enzyme that adds telomeric DNA sequences onto the ends of linear chromosomes.
Q:
A characteristic of aging cells is that their telomeres become shorter.
Q:
A nucleosome is a structure associated with the nuclear membrane. It helps maintain a stable relationship between the extracellular matrix and the membrane itself.
Q:
Chromatin assembly factors (CAFs) move along with the replication fork and assemble new nucleosomes.
Q:
In ligase-deficient strains of E. coli, DNA and chromosomal replication are unaltered because ligase is not involved in DNA replication.
Q:
An endonuclease is involved in removing bases sequentially from one end of DNA or the other.
Q:
During replication, primase adds a DNA primer to RNA.
Q:
DNA strand replication begins with an RNA primer.
Q:
DNA replication occurs in the 5-² to 3-² direction; that is, new nucleoside triphosphates are added to the 3-² end.
Q:
DNA replicates conservatively, which means that one of the two daughter double helices is "old" and the other is "new."
Q:
In the Meselson and Stahl (1958) experiment, bean plants (Vicia faba) were radioactively labeled so that autoradiographs could be made of chromosomes.
Q:
In general, DNA replicates semiconservatively and bidirectionally.
Q:
Describe the function of the RecA protein.
Q:
What term is used to describe genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology?
Q:
Describe a somewhat extraordinary finding related to the Tetrahymena telomerase enzyme.
Q:
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.
Q:
What is the name of the replication unit in prokaryotes, and how does it differ in eukaryotes?
Q:
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.
Q:
Compare the rate of DNA replication in prokaryotes and eukaryotes.
Q:
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 this tension is resolved.
Q:
Which structural circumstance in DNA sets up the requirement for its semidiscontinuous nature of replication?
Q:
List four enzymes known to be involved in the replication of DNA in bacteria.
Q:
The accompanying figure diagrams DNA replication as currently believed to occur in E. coli. From specific points, arrows lead to numbers. Answer the questions relating to the locations specified by the numbers.(1) Which end (5-² or 3-²) 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 (5-² or 3-²) of the molecule is here?
Q:
During DNA replication, what is the function of RNA primase?
Q:
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
Q:
Given the accompanying diagram, 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?
Q:
DNA replication in vivo requires a primer with a free 3-² end. What molecular species provides this 3-² end, and how is it provided?
Q:
Which protein is responsible for the initial step in unwinding the DNA helix during replication of the bacterial chromosome?
Q:
Given that the origin of replication is fixed in E. coli, what signals the location of the origin?
Q:
The complex of proteins that is involved in the replication of DNA is called a(n) ________.
Q:
Refer to the accompanying 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 3-² 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 5-² A C A G 3-², 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 5-² carbon) digests the pictured tetranucleotide, which base(s) among the breakdown products would be expected to be attached to the 32P?
Q:
What primary ingredients, coupled with DNA polymerase I, are needed for the in vitro synthesis of DNA?
Q:
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.
Q:
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?
Q:
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, 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). Each sample of DNA (A, B, and 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.)
Q:
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). Each sample of DNA (A, B, and 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.)
Q:
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
Q:
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?
Q:
What three possible models were suggested to originally describe the nature of DNA replication?
Q:
In 1953, Watson and Crick published a paper that described the structure of DNA.
Q:
When considering the structure of DNA, we would say that complementary strands are antiparallel.
Q:
G and C are present in both DNA and RNA.
Q:
DNA has no sulfur, and proteins have no phosphorus.
Q:
In RNA, uracil is present instead of the thymine in DNA.
Q:
In ribose, the 2"² C has an OH attached to it.
Q:
Deoxyribonuclease is an enzyme that adds 3"²-hydroxyl groups to RNA.
Q:
Avery et al. (1944) determined that DNA is the genetic material in T2 bacteriophage.
Q:
Hershey and Chase used labeled DNA and protein to determine that DNA is the genetic material in bacteria.
Q:
The transforming principle discovered by Griffith is RNA.
Q:
Explain how and why the following circumstances influence characteristics of temperature-induced DNA melting.
a) Percentage of GC base pairs
b) Urea (forms hydrogen bonds with bases)
c) Sodium chloride (neutralizes negatively charged phosphates)
Q:
Consider the structure of double-stranded DNA. When DNA is placed into distilled water, it denatures; however, by adding NaCl, the DNA renatures. Why?
Q:
All other factors being equal, the renaturation of the three classes of complementary nucleic acid sequences occurs in what order, from fastest to slowest?
Q:
At what approximate wavelengths do DNA, RNA, and proteins maximally absorb light?
Q:
When and in which journal did Watson and Crick publish their now-famous paper entitled "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid."
Q:
What is meant by the term antiparallel?
Q:
Suppose that the dinucleotide in the accompanying figure was cleaved with the enzyme spleen diesterase, which breaks the covalent bond connecting the phosphate to C-5"². After such cleavage, to which nucleoside is the phosphate now attached?
Q:
Is the accompanying figure DNA or RNA? Is the circle closer to the 5"² or 3"² end?