Quiz 10

Besides CRISPR and restriction enzymes, give one example of another defense mechanism used by bacteria against foreign DNA.

A. Removal of certain surface proteins

What is a HFR cell?

An HFR cells refers to a "High Frequency of Recombination" bacterial cell. These cells are created when an F+ plasmid, received upon conjugation is integrated into the bacterial chromosome itself. From there, when conjugation occurs (because the cell is now F+) the F+ content is excised from the genome, but now parts of the genome adjacent to the F+ content are now excised as well, this leads to a high frequency of recombination in the cell, and subsequent cells.

Fill in the blank. The enzyme encoded by some viruses that allows them to become incorporated into the host genome is called ______.

Integrase

What is the main function of proteins encoded by the genes on the F plasmid?

It expresses genes that enable conjugation, such as constructing the conjunctive pilus which connects the two cells undergoing conjugation. Many of the genes on an F+ plasmid are referred to as tra genes.

List and define three mechanisms of lateral gene transfer between bacterial cells.

Transformation: The aquiring of foreign DNA from the enviromentTransduction: The aquiring of genes from a virusConjugation: The interaction wherein an F+ bacteria inserts DNA into another bacteria.

What is the name of the enzyme that catalyzes the excision of DNA elements?

Transposase (endonucleases also excise DNA, however the use of " DNA elements" here indicates Transposons to me)

True or false? "A functional transposable element is a discrete piece of DNA that can catalyze its own movement between genomes." Explain your answer.

False Transposable elements catalyze their own movement to another location within the same genome. Transposons are not transferred between genomes unless they happen to be transferred by another process.

Fill in the blank. Most transposable elements have become mutated and have lost the capacity to move on their own. Elements that are capable of moving on their own are termed ___ elements.Fill in the blank. Most transposable elements have become mutated and have lost the capacity to move on their own. Elements that are capable of moving on their own are termed ___ elements.

Autonomous

Streptococcus pneumoniae can cause pneumonia, meningitis, and blood infections. S. pneumoniae can change rapidly and evade the immune system. Which characteristics of S. pneumoniae facilitate this rapid evolution? Please select all that apply. A. S. pneumoniae has a linear genome B. S. pneumoniae is naturally competent C. Capsule genes can be acquired by horizontal transfer D. Host immune systems cannot recognize the carbohydrate capsule that surrounds the bacterial cell

B. S. pneumoniae is naturally competent C. Capsule genes can be acquired by horizontal transfer

Plasmids can be transferred between bacteria via a pilus. What structure do plasmids adopt during transfer? Please select all that apply. A. Single-stranded RNA B. Single-stranded DNA C. Double-stranded DNA D. Linear DNA E. Circular DNA

B. Single-stranded DNA D. Linear DNA

Provide an explanation of the following terms:(a) Lytic phage(b)Generalized transduction(c) Lysogenic phage(d) Prophage(e) Specialized transduction(f) Temperate phage

(a) The Lytic Phage is a bacterial virus that infects bacterial cells, inserts its genome into the cells, and then the bacterial machinery transcribes and assembles the viral proteins, and once a sufficient quantity of viruses are produced, they lyse the bacterial cells and spread out to infect more cells.(b) Generalized transduction occurs when a virus infects a bacteria integrates bacterial DNA into the capsid, afterwards the resulting phage can transduce this bacterial DNA into another bacteria. As opposed to viruses that insert in a specific or consistent area in the genome such as attb, these viruses do not and so the DNA that they bring with them is random, and not site specific, hence the name "general transduction."(c) A lysogenic phage is a phage that integrates itself into the host genome, and as a result its genome is replicated and passed along with the hosts, and by the host cell. However if certain conditions are met the phage may elect to lyse the cell. However, the process for understanding this is complex.(d) prophage is a term used to describe viral DNA that has been integrated into the bacterial genome.(e) Specialized transduction occurs when viruses that insert into a specific site in the bacterial genome, and bring adjacent DNA with them when they leave the bacertia. For example, viruses inserting at the attb site, bring bacterial DNA adjacent to that site along with them in the capsid and thus infect other bacteria with this DNA mix. This is specialized because since it always inserts at the attb sequence, and it is always DNA adjacent to this site that is brought along with the viral DNA.(f) A temperate phage such as M13 , is a phage that infects a bacteria and replicates, but then extrudes itself without causing Lysis of the bacterial cell.

How do bacteria avoid destroying their own DNA with their restriction endonucleases?

Bacteria methylate the restriction endonuclease recognition sites in their own genome that match their own restriction endonucleases. This prevents the enzyme from cleaving the DNA at the recognition site. Invading DNA often does not have these methylations and is destroyed.

Building phylogenetic trees can be challenging when horizontal transfer has occurred in bacteria. Why?

Because the inserted foreign DNA, evolves alongside the organism, gaining mutation, and it makes it difficult to track its history.

The CRISPR mechanism helps bacterial cells defend themselves against foreign DNA. Please provide a description of how this mechanism works.

CRISPR, starts with a phage infection. Most of the bacteria infected by the phage die. However, in the few that survive, a Cas protein (typically Cas9) retrieves a sequence of DNA adjacent to the PAM motif known as the protospacer.This protospacer is then incorporated into the genome, between sequences of DNA known as repeats, this incorporated sequence is now called a spacer. The bacterial sequence containing these spacers is like a record of past viral infections.Upon the next infection from a phage the bacterial repeats form loops, allowing for the excision of the spacer sequence. From there the spacer is paired with the invading foreign viral genome, and a cas protein arrives at the location to cleave the invading DNA that is matched to the Spacer, thus disarming the infection.

How can CRISPR be exploited in molecular biology laboratory experiments?

Since the CRISPR + Cas9 complex will cleave whatever sequence is on the spacer, a spacer can be introduced to the complex that is from an organisms genome.From there the CRISPR Cas9, can cut this gene in the organism. This will cause the gene to try and fix itself, and can be mutated. This allows for knock out studies. Where scientists disable a gene and see what the resulting phenotype is.Or a stretch of DNA intended to be incorporated can accompany the CRISPR + Cas9 complex and then when the previous genome is clipped, this new stretch of DNA will be integrated into the genome, allowing the addition of this gene into the genome. Quite an exciting method!

List two characteristics that scientists use to identify genomic islands in bacteria.

genomic islands tend to be integrated near tRNA genes. Similarly areas with lower concentrations of G-C are indicators of foreign DNA. Another clue is if there is present Transposon DNA such as inverted terminal repeats are present.