ndicate whether each of the following statements are true of depurination, deamination or pyrimidine dimer formation and which repair process (base excision repair, nucleotide excision repair) is pertinent to the statement; and explain why. A given statement may be true of one, or more than one, of these processes. Be sure to include some molecular detail in your explanation. A. Repair involves an endonuclease B. Repair involves DNA ligase C. Repair involves a helicase

ndicate whether each of the following statements are true of depurination, deamination or pyrimidine dimer formation and which repair process (base excision repair, nucleotide excision repair) is pertinent to the statement; and explain why. A given statement may be true of one, or more than one, of these processes. Be sure to include some molecular detail in your explanation. A. Repair involves an endonuclease B. Repair involves DNA ligase C. Repair involves a helicase

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter28: Dna Metabolism: Replication, Recombination, And Repair

Section: Chapter Questions

Problem 10P: Homologous Recombination, Heteroduplex DNA, and Mismatch Repair Homologous recombination in E. coli...

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In the following sequence, a cytosine was deaminated and is now a uracil (underlined). 5’-GGTAUTAAGC-3’ a. Which repair pathway(s) could restore this uracil to cytosine? b. If the uracil is not removed before a DNA replication fork passes through, what will be the sequences of the two resulting double helices? Provide the sequences of both strands of both helices. Label the old and new strands and underline the mutation(s). c. Could the mismatch repair pathway fix the mutations you’ve indicated in part b? d. If the cell undergoes mitosis, and the replicated DNAs are distributed into the two daughter cells. Will 0, 1, or 2 daughter cells have a mutation in this sequence?
Cytosine can be deaminated to form Uracil What type of mutation is this classified as? Discuss what happens to the base-pairing properties from switching from C to U? When U is replicated in two rounds of synthesis, what substitution does this result in? Before Uracil alters the DNA during replication, what repair system can be used to correct this error? Describe how this type of DNA repair works?
DNA ligase has the ability to relax supercoiled circular DNA in the presence of AMP but not in its absence. (a) What is the mechanism of this reaction, and why does it depend on AMP? (b) How could you determine that supercoiled DNA had in fact been relaxed?
A temperature-sensitive mutation is one in which the defect is not presented functionally until the temperature is raised. In the case described below, the enzymes function normally in bacteria at 37 °C, but are non-functional at 40 °C. Predict the detailed molecular consequences of a loss of function in a temperature-sensitive mutant for each of the following enzymes: a) DNA gyrase, b) DNA polymerase III, c) DNA ligase, d) DNA polymerase I.
Homologous Recombination, Heteroduplex DNA, and Mismatch Repair Homologous recombination in E. coli leads to the formation of regions of heteroduplex DNA. By definition, such regions contain mismatched bases. Why doesnâ€™t the mismatch repair system of E. coli eliminate these mismatches?
The Enzymatic Activities of DNA Polymerase I (a) What are the respective roles of the 5 -exonudease and 3 -exonuclease activities of DNA polymerase I? (b) What might be a feature of an E. coli strain that lacked DNA polymerase I 3 -exonuclease activity?
Extrachromosomal DNA is critical to the antibiotic resistance found in microorganisms, how do these DNA elements account for this phenomena?
For each DNA repair process in column I, list all characteristics fromcolumn II that correctly describe that process.I(a) Nucleotide excision repair(b) Photoreactivation(c) Base excision repair(d) Recombinational repair(e) SOS-driven error-prone repair(f) Alkyltransferase repair(g) Mismatch repair(h) Double-strand break repairII1. RecA protein participates.2. Damaged nucleotides are removed by nick translation.3. A free radical mechanism is involved.4. The repair enzyme functions only once.5. The key enzyme contains a bound folate cofactor.6. No bases or nucleotides are removed from the DNA.7. Deficiency of this enzyme in humans greatly increases the risk of skincancer.8. This system is chiefly responsible for the mutagenic effect of ultravioletlight.9. This process begins with cleavage of two phosphodiester bonds.10. This process begins up to 1 kbp away from the site to be repaired.11. DNA ligase catalyzes the final reaction.12. This process also occurs in meiotic recombination.13.…
Deoxyadenylate residues in DNA undergo deamination fairly readily, as do deoxycytidylate residues. (a) What is the product of dAMP deamination? (b) The deamination product is known to base-pair with A, C, or T. What would be the genetic consequences if this deaminated site in DNA were not repaired and if it paired with C on the next round of replication?
DNA repair enzymes that correct deamination and depurination must preferentially recognize these defects on newly synthesized strands. Explain in 1-2 sentences.
There are two types of excision repair, base excision repair (BER) and nucleotide excision repair (NER). Which enzymes are used in Base excision repair in E. coli?And In nucleotide excision repair, what kind of damage is repaired by this mechanism and why are cutsmade on both sides of the damaged region of DNA?
Examination of the structure of DNA polymerases bound to nucleotide analogs reveals that conserved residues come within van der Waals contact of C-2' of the bound nucleotide. What is the potential significance of this interaction?