HELP!!!! 1. Calculate the DNA length of T2 bacteriophage (1.8x105 bp), E. coli g
ID: 195521 • Letter: H
Question
HELP!!!!
1. Calculate the DNA length of T2 bacteriophage (1.8x105 bp), E. coli genome (4.6x106 bp), and human genome (3.0x109 bp). Assuming their particle and cell sizes of 0.21, 1, and 20 um, calculate the respective compaction ratio in the particle and cells. Further assuming human cell nucleus size of 6 um, calculate the genome compaction ratio.
2. The base composition of phage M13 DNA is A, 23%; T, 36%; G, 21%; C, 20%. What does this tell you about the DNA of phage M13?
3. An enzyme isolated from rat liver has 192 amino acid residues and is coded for by a gene with 1,440 bp. Explain the relationship between the number of amino acid residues in the enzyme and the number of nucleotide pairs in its gene?
4. A closed-circular DNA molecule in its relaxed form has an Lk of 500. Approximately how many base pairs are in this DNA? How is the linking number altered (increases, decreases, doesn’t change, becomes undefined) when (a) a protein complex is bound to form a nucleosome, (b) one DNA strand is broken, (c) DNA gyrase and ATP are added to the DNA solution, or (d) the double helix is denatured by heat?
5. Bacteriophage infects E. coli by integrating its DNA into the bacterial chromosome. The success of this recombination depends on the topology of the E. coli DNA. When the superhelical density () of the E. coli DNA is greater than -0.045, the probability of integration is <20%; when is less than -0.06, the probability is >70%. Plasmid DNA isolated from an E. coli culture is found to have a length of 13,800 bp and an Lk of 1,222. Calculate for this DNA and predict the likelihood that bacteriophage will be able to infect this culture?
6. (a) Describe two structural features required for a DNA molecule to maintain a negatively supercoiled state. (b) List three structural changes that become more favorable when a DNA molecule is negatively supercoiled. (c) What enzyme, with the aid of ATP, can generate negative superhelicity in DNA? (d) Describe the physical mechanism by which this enzyme acts.
7. Yeast Artificial Chromosomes (YACs) are used to clone large pieces of DNA in yeast cells. What three types of DNA sequences are required to ensure proper replication and propagation of a YAC in a yeast cell?
8. Early evidence that helped researchers define nucleosome structure is illustrated by the agarose gel below, in which the thick bands represent DNA. It was generated by briefly treating chromatin with an enzyme that degrades DNA, then removing all protein and subjecting the purified DNA to electrophoresis. Numbers at the side of the gel denote the position to which a linear DNA of the indicated size would migrate. What does this gel tell you about chromatin structure? Why are the DNA bands thick and spread out rather than sharply defined?
9. The Meselson-Stahl experiment proved that DNA undergoes semiconservative replication in E. coli. In the “dispersive” model of DNA replication, the parent DNA strands are cleaved into pieces of random size, then joined with pieces of newly replicated DNA to yield daughter duplexes. Explain how the results of Meselson and Stahl’s experiment ruled out such a model.
10. The E. coli chromosome contains 4,639,221 bp.
(a) How many turns of the double helix must be unwound during replication of the E. coli chromosome?
(b) From the data in this chapter, how long would it take to replicate the E. coli chromosome at 37 °C if two replication forks proceeded from the origin? Assume replication occurs at a rate of 1,000 bp/s. Under some conditions E. coli cells can divide every 20 min. How might this be possible?
(c) In the replication of the E. coli chromosome, about how many Okazaki fragments would be formed? What factors guarantee that the numerous Okazaki fragments are assembled in the correct order in the new DNA?
11. Predict the base composition of the total DNA synthesized by DNA polymerase on templates provided by an equimolar mixture of the two complementary strands of bacteriophage X174 DNA (a circular DNA molecule). The base composition of one strand is A, 24.7%; G, 24.1%; C, 18.5%; and T, 32.7%. What assumption is necessary to answer this problem?
12. Kornberg and his colleagues incubated soluble extracts of E. coli with a mixture of dATP, dTTP, dGTP, and dCTP, all labeled with 32P in the a-phosphate group. After a time, the incubation mixture was treated with trichloroacetic acid, which precipitates the DNA but not the nucleotide precursors. The precipitate was collected, and the extent of precursor incorporation into DNA was determined from the amount of radioactivity present in the precipitate.
(a) If any one of the four nucleotide precursors were omitted from the incubation mixture, would radioactivity be found in the precipitate? Explain.
(b) Would 32P be incorporated into the DNA if only dTTP were labeled? Explain. (c) Would radioactivity be found in the precipitate if 32P labeled the b or g phosphate rather than the a phosphate of the deoxyribonucleotides? Explain.
13. All DNA polymerases synthesize new DNA strands in the 5’3’ direction. In some respects, replication of the antiparallel strands of duplex DNA would be simpler
if there were also a second type of polymerase, one that synthesized DNA in the 3’5’ direction. The two types of polymerase could, in principle, coordinate DNA synthesis without the complicated mechanics required for lagging strand replication. However, no such 3’5’ synthesizing enzyme has been found. Suggest two possible mechanisms for 3’5’ DNA synthesis. Pyrophosphate should be one product of both proposed reactions. Could one or both mechanisms be supported in a cell? Why or why not? (Hint: You may suggest the use of DNA precursors not actually present in extant cells.)
14. Prepare a table that lists the names and compares the functions of
the precursors, enzymes, and other proteins needed to make the leading strand versus the lagging strand during DNA replication in E. coli.
15. Some E. coli mutants contain defective DNA ligase. When these mutants
are exposed to 3H-labeled thymine and the DNA produced is sedimented on an alkaline sucrose density gradient, two radioactive bands appear. One corresponds to a high molecular weight fraction, the other to a low molecular weight fraction. Explain.
16. What factors promote the fidelity of replication during the synthesis of the leading strand of DNA? Would you expect the lagging strand to be made with the same fidelity? Give reasons for your answers.
17. Vertebrate and plant cells often methylate cytosine in DNA to form 5-methylcytosine. In these same cells, a specialized repair system recognizes G–T mismatches and repairs them to G-C base pairs. How might this repair system be advantageous to the cell? (Explain in terms of the presence of 5-methylcytosine in the DNA.)
18. Write the chemical reaction for DNA replication.
19. Draw structures of tautomers of C and T. Explain how it can happen with misincorporation of C in place of T, and T in place of C. When that happens, how can DNA pol make the correction?
20. Compare and contrast DNA pol I, II, and III – the number of subunits, associated properties and functions.
Explanation / Answer
2. The base composition of phage M13 DNA is A, 23%; T, 36%; G, 21%; C, 20%. What does this tell you about the DNA of phage M13?
The complementarity between A and T and between G and C, in the two strands of duplex DNA underlies Chargaff's rule that the sum of pyrimidine nucleotides equal to that of purine nucleotides in DNA from all species that is A-T, G-C and A,G,C,T for duplex DNA. In M13 DNA, the percentage of A (23%) does not equal that of T (35%) nor does that of G (21%) equal to that of C (20%) and A-G 44% whereas CT 58%. This lack of equality between purine and pyrimidine nucleotide shows that M13 DNA is single stranded not double stranded. The relationships expected from complementarity between two strands of a duplex DNA are not seen. The M13 DNA is double stranded only when replicating in the host cell.
Related Questions
Navigate
Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.