MICR Chapter 9 Problem Set

Consider the reaction shown in the above illustration. This event is a potential source of mutations and results from exposure to

UV light.

Please correctly label the functions of the proteins that participate in the SOS response in E. coli.

c > b > e > a > d

Further analyses revealed that a region downstream of the seaweed-digesting genes in Bacteroides plebeius contained sequences homologous to conserved relaxase/mobilization proteins. These data provide additional evidence that the genes were acquired by

conjugation

Base excision repair is particularly useful for removing bases from DNA that have spontaneously

deaminated.

An E. coli strain with a mutation rate of about 10-10 per base pair replicated would be considered a ____________ strain.

normal

The phylogenetic tree of Prochlorococcus suggests that early lineages lived deeper in the euphotic zone below the limit of UV light penetration. What DNA repair adaptation currently allows Prochlorococcus cells to live in the upper photic zone?

photolyases

What are the basic parts of an insertion sequence?

transposase coding region, two flanking inverted repeats

The above illustration shows an example of a(n) ________________ mutation that results in a(n) _______________ mutation.

transversion, nonsense

Alison Buchan and her team used transposon mutagenesis to create a large pool of mutant Phaeobacter. Three of these mutants are shown in the figure. Why did culture II not have a zone of clearance around it?

A transposon in this culture interrupted a Phaeobacter gene required for indigoidine synthesis, thereby allowing the V. fischeri to grow close.

DNA mismatch repair is the primary mechanism for correcting misinserted base pairs caused by

DNA polymerase.

Upon successful completion of conjugation, the donor cell is ___ and the recipient cell is ____.

F+, F-

Sort the following events according to whether they occur in replicative transposition, nonreplicative transposition, or both:

- Replicative: Donor DNA retains a copy of insertion sequence., Recombination separates donor and target DNAs. - Nonreplicative: Hairpin structures form on each end of insertion sequence., Insertion sequence "jumps" into recipient DNA., Donor DNA loses insertion sequence. - Both: DNA polymerase fills in gaps, Transposase is required., Target sequence gets duplicated., DNA ligase seals nicks.

You have a strain of ampicillin-resistant Escherichia coli and a strain of ampicillin-sensitive Enterobacter. You mix the strains together and leave them overnight. In the morning, you discover that the Enterobacter is now resistant to ampicillin as well. Now you must decide what experiments you could do to determine the mechanism of genetic exchange (transformation, conjugation, or transduction). Assume there was no experimental error overnight (i.e., no contamination), and keep in mind that only small particles (like DNA and viruses) will remain suspended in cell-free extract. Consider the descriptions of genetic exchange methods below and match each description to the proper type of exchange.

- Transformation: This method would be affected by DNase, an enzyme that can degrade naked DNA that is unprotected. - Conjugation: This method of DNA exchange cannot occur using the recipient cells mixed with cell-free extract only. - Transduction: This method can occur with cell-free extract only and is not affected by DNase.

Consider the data from a hypothetical Ames test below. Then match the following chemicals to the best description of their mutagenicity: mutagenic to bacteria only, mutagenic to both humans and bacteria, or not mutagenic at all.

-Non Mutagenic: monosodium glutamate (MSG) -Bacteria only: caffeine -Humans and Bacteria: tobacco smoke, the fatty acid 4-hydroxyhexenal

Correctly order the following steps in bacterial conjugation from start to finish.

1. a sex pilus is formed that joins an F+ to an F- cell. 2. the sex pilus retracts, and a relaxosome forms 3. the F factor is nicked at oriT, and one strand starts to transfer into the recipient. 4. DNA polymerase III synthesizes a replacement strand in the donor 5. the transferred DNA strand circularizes and completes replication

Without base excision repair, the presence of unnatural bases may cause mutations or more serious effects. For example, the presence of _____________________ interferes with DNA synthesis, and is thus lethal to the cell.

3-methyladenine

For the mismatch repair system to work correctly, newly replicated DNA must

A.remain unmethylated long enough for mismatches to be repaired. B.become methylated before the subsequent round of replication.

What two conditions must be met to produce a heritable mutation?

A.There is a change in the DNA sequence. B.The mutation does not get repaired before the cell divides.

Examine and correctly label the following illustration of a bacterial restriction and modification system.

Counterclockwise: b > d > a > e > c

Please examine and correctly label the following model of horizontal gene transfer among the gut microbiota.

D > B > E > A > C

Label the diagram of naked DNA uptake by V. cholerae.

D > B, A, C

Why is it incorrect to refer to conjugation as bacterial sex?

It does not involve gametes., the recipient is haploid for the transferred genes, The transferred DNA is not required for normal cellular function.

How do Phaeobacter compete for limited resources in the coastal salt marshes?

Phaeobacter secrete the compound indigoidine that kills other bacteria.

How did Prochlorococcus now living in the upper euphotic zone acquire the ability to repair their UV-damaged DNA?

Prochlorococcus likely acquired the photolyase genes through horizontal gene transfer.

CRISPR-Cas9 may be used as a gene-editing tool to repair mutant genes (such as the gene that causes Huntington's disease in humans). This technique has been used in bacteria, mice, and even human embryos. First, CRISPR-Cas9 is used to target and remove the mutant gene. Second, naturally occurring repair enzymes will add the wild-type gene into the gap left from the site where the mutant gene was removed. Which of these bacterial repair mechanisms would most likely be responsible for repairing the DNA when used to edit bacterial genes?

RecA recombination repair

Select the true statement regarding the relationship between genotype and phenotype.

The phenotype reflects only the portion of the genotype that is expressed.

Listeria is a genus of Gram-positive Firmicutes closely related to Bacillus. There are six species, two of which are pathogenic and can cause listeriosis (L. monocytogenes and L. ivanovii) and four of which are non-pathogenic (L. innocua and others). The figure below shows a gene region alignment for the non-pathogenic species L. innocua compared to that of the pathogen L. monocytogenes. Based on this gene alignment, predict which of the following descriptions most likely apply to the genes in red.

They likely encode virulence factors, They were likely horizontally transferred.

Transposases are multifunctional enzymes. During nonreplicative transposition, the transposase does all of the following except

fill in single-stranded gaps that occur in the target region of the recipient DNA.

During base excision repair, a specific glycosylase catalyses

formation of an AP site.

The early stages of genome reduction in bacteria are normally characterized by the proliferation of pseudogenes. These most likely arise as a result of

frameshift and nonsense mutations.

Please examine and correctly label this image illustrating the two basic types of transposition.

going in counterclockwise: E > b > f > d > c > a

Genes that share a common ancestry are broadly referred to as ________________. They are further classified as ________________ if they exist within the same species but have distinct functions, while _________________ usually have similar functions but are found within different species.

homologs, paralogs, orthologs

Many Japanese people consume a diet rich in seaweed, including the edible red alga Porphyra, which is used for preparing sushi. Although humans cannot digest the seaweed polysaccharides (porphyran and agarose), certain marine Bacteroidetes do possess the necessary CAZymes. Curiously, Japanese individuals frequently harbor seaweed-digesting Bacteroides plebeius in their gut microbiomes, while individuals from North America do not. Bacteroides plebeius is not a marine bacterium, and its close relatives cannot digest seaweed. What is the mostly likely explanation for how B. plebeius acquired functional porphyranase and agarase genes?

horizontal transfer of genes from a marine bacterium

Consider the complex transposon in the above illustration. Suppose you discover a derivative of this element that replicatively inserts into target DNA but then becomes "stuck" as part of a cointegrate. Your graduate student sequences the respective gene products and finds no change in the primary amino acid sequences of the encoded enzymes. In which locus must the defect lie?

res

In bacteria, a partially diploid strain may result from

specialized transduction, acquisition of an F' factor

Association of RecA with an incoming piece of foreign DNA is required for a cell to do which of the following?

swap the incoming DNA with a homologous region on the chromosome

V. cholerae is capable of transformation, which means it can do what?

take up naked DNA