Chapter 9 - Bacterial & Viral Genetic Systems

Question 1

Pick the statement that is true regarding plasmids:
A. Certain types of plasmids called episomes can replicate independently of the main chromosome or insert themselves into the bacterial genome.
B. Plasmids are common in eukaryotes
C. Plasmids often carry genes for antibiotic resistance
D. Plasmids consist of single stranded DNA
E. More than one of the answers A-D are true.

Answer 1

E. More than one of the answers A-D are true (A and C)

Question 2

Bernard Davis’s U-shaped tube experiment indicated that bacterial genetic exchange requires:
A. the exchange of liquid medium between the two sides of the tube.
B. direct contact between the two bacteria.
C. mutations to be reverted to wild type.
D. None of the above.

Answer 2

B. direct contact between the two bacteria.

Question 3

Chromosomal DNA is transferred from \_\_\_\_\_ cells to \_\_\_\_\_\_\_ , where recombination occurs.
A. Hfr; F+ 
B. F− ; Hfr 
C. Hfr; F− 
D. F+;Hfr

Answer 3

C. Hfr; F−

Question 4

The following shows a partial chromosome map of an E. coli Hfr strain. Each mark equals 10 minutes. If transfer of genes begins at the arrow and goes in the direction of the arrow, what is one of the predicted results from this map?
ton-lac ➧ azi-gal
A. ton and lac will rarely be transferred together.
B. lac and azi will rarely be transferred together.
C. Ten minutes after transfer of ton, azi will be transferred.
D. It would take 30 minutes to transfer all of the genes that are shown.

Answer 4

B. lac and azi will rarely be transferred together.

Note: the 10 min thing and all the superfluous language in the question can be distracting - be careful when he asks these kinds of long-winded questions!

Question 5

The following shows the results of interrupted mating experiments with 3 different Hfr strains. What is the order of the genes, starting with C?
Order of transfer: (1) A, B, E, D, F; (2) D, F, C, G, A; (3) D, E, B, A, G

A. C, G, A, D, F, B, E
B. C, F, D, B, A, E, G
C. C, B, E, D, F, G, A
D. C, G, A, B, E, D, F
E. C, D, F, G, A, B, E

Answer 5

D. C, G, A, B, E, D, F

NOTE: starting with C or any other letter is not necessary. In this example, looking at the order of transfer for the first then finding its match is sufficient.

Question 6

Genetic exchange in bacteria follows one of three mechanisms (conjugation, transformation, and transduction). Which of the following is true regarding these three mechanisms?

a. Conjugation requires a special bacterial virus called a bacteriophage.
b. Transformation exchanges genetic material through direct interactions between two different bacteria.
c. Transduction involves a bacterium taking in genetic material found in the medium.
d. None of the above is a correct match.

Answer 6

d. None of the above is a correct match.

Question 7

_____ requires a special bacterial virus called a bacteriophage.

Answer 7

Transduction

Question 8

_____ exchanges genetic material through direct interactions between two different bacteria.

Answer 8

Conjugation

Question 9

____ involves a bacterium taking in genetic material found in the medium.

Answer 9

Transformation

Question 10

Prototroph v. auxotroph?

Answer 10

Prototroph is a prokaryote that can synthesize all of its own essential nutrients. Auxotroph lacks one or more enzymes to synthesize one or more essential nutrients (nutrient must be obtained exogenously).

Question 11

What is negative selection with regards to isolation of bacterial strains (serotypes)? How is that different from positive selection?

Answer 11

Bacterial colonies are ‘stamped’ onto nutrient media and minimal media; the colony missing from the minimal media is the serotype of interest.
In positive selection, you culture on media that will positively select for a serotype of interest (e.g. methicillin infused to grow MRSA).

Question 12

Prokaryotic cells evolved with circular chromosomes likely because…?

Answer 12

The terminal ends of chromosomes can be highly unstable; circle eliminates the issue.

Question 13

T or F: Bacteria have a high number of plasmid copies which is why losing some isn’t lethal.

Answer 13

Mostly false: usually there are 1 or maybe 2 copies of plasmids; a few have a high copy number. Whether they are all lost is of no consequence.

Question 14

Plasmids often have genes for ____ ____ and ____.

Answer 14

antibiotic resistance and mating.

Question 15

____ have been used extensively in ____ _____ (cloning).

Additionally, they replicate ____ of the main chromosome; and they are very rare in ___ cells (although some ___ have a plasmid called the ___ circle.

Answer 15

plasmids; genetic engineering

independently; eukaryotic; yeast; 2μm

Question 16

This subcategory of plasmids can exist independently of the chromosome, or they can integrate. Name one example that is required for mating and genetic exchange.

Answer 16

Episomes. One example is F factor in E. coli (F = fertility or fucking)

Question 17

The two ways that sexual reproduction differ in eukaryotes and prokaryotes is in prokaryotes genetic ____ (which is always ___-___) and cell ____ are not coupled; and the recipient remains _____.

Answer 17

exchange; one-way; reproduction

haploid

Question 18

The 3 mechanisms of genetic exchange for prokaryotes are ____ (sex-ish), ____ (exogenous); and ___ (phage).

Answer 18

conjugation; transformation; transduction

Question 19

What does it mean that some prokaryotes are “naturally competent”?

Answer 19

They more readily transform when they encounter genetic material.

Question 20

In a landmark experiment, Lederberg and Tatum mixed two different auxotrophic serotypes of E. coli (Y10 & Y24), they noted scant growth on minimal agar. What were they seeing? Why was growth scant?

Answer 20

The serotypes conjugated, and since genetic recombination was complimentary, some became prototrophic.

Few colonies were noted because one of two things had to happen: the origin of transfer (oriT) had to begin at the region of complementation; if the oriT was outside the complimentary area, conjugation had to last long enough for the complimentary region to be inserted.

Question 21

Lederberg and Tatum did not know what caused their auxotrophic serotypes to become prototrophic, so Barnard Davis grew the strains in a U-tube separated by a small micron filter; what did he see?

Answer 21

Davis did not recover any prototrophic E. coli, so he was able to conclude that the serotypes had to come into physical contact with each other.

Question 22

Conjugation between prokaryotes like E. coli is possible with __ ____; a special subtype of plasmid called an ____. When conjugation takes place, ___ project from the __+ cell, and once it connects with an ___= cell, it’s called a ___.

Answer 22

F factor; episome

fimbria; F+; F=; pilus

Question 23

T or F: the auxotrophic serotypes of E. coli that Lederberg and Tatum used in their experiment (conjugation) were F+. Explain.

Answer 23

False: they were Hfr+. F factor is an episome; when it is integrated into the bacterial genome, it can bring with it additional genetic material. In the case of their experiment, it brought with them the complimentary genes.

Question 24

F factor transfer starts when the plasmid is “____” at the ___. The break is at one of the ____ bonds between the ___ and the ___’ carbon of the sugar (which is a ___ bond), but the molecule doesn’t fall apart due to the stabilizing effects of the ___ bonds between the base pairs.

Answer 24

nicked; oriT.

phosphodiester; phosphorus; 5’; covalent; hydrogen

Question 25

The frequency of transfer for F factor is fairly ___; but the frequency of F- cells becoming F+ when conjugated with Hfr+ cells is fairly ___ because F factor is usually “___” in the ____.

Answer 25

high; low; “nicked”; middle

Question 26

Gene distance is mapped in ____ when mapping via conjugation.

Answer 26

minutes

Question 27

How can interrupted conjugation be used to map genes?

Answer 27

The genes successfully transferred in a given amount of time indicate their relative position on the chromosome (i.e. if conjugation is interrupted every 10 min and the chromosomes evaluated, every new gene is +10mu farther from the preceding gene.

Question 28

The F factor in Hfr+ cells is in a ____ position on the chromosome; but it is its ____ determines the ___ of transfer (either ___ or ____). Scientists have been able to exploit this to ___ genes with greater efficiency (it would be less efficient if the F factor were ____ because you would have to wait for ___ transfer and hope the ___ doesn’t break).

Answer 28

variable; orientation; direction; clockwise; counterclockwise.

map; fixed; complete; pilus

Question 29

The __ plasmid is easily transferred by ___ and ___ transfer which explains why so many bacterial species develop antibiotic resistance.

Answer 29

R plasmid; conjugation; horizontal

Question 30

____ requires two steps: (1) ___ source of DNA (DNA from the ___); and (2) ___ incorporation of DNA into the bacterial chromosome or ____. Naturally ___ cells are more capable of doing this.

Answer 30

Transformation; exogenous; environment; stable; plasmid.

competent

Question 31

A ___ cell can usually take up DNA from any ____ source; it doesn’t have to be bacterial.

Answer 31

competent; exogenous / extracellular

Question 32

E. coli can be made competent in one of two ways: (1) treatment with ____ followed by ___ ___; and ____, a procedure that uses a brief, ____-____ pulse which causes the ____ to become ____.

Answer 32

calcium chloride, heat shock

electroporation; high-voltage; membrane; porous

Question 33

Genetic mapping procedures: which is more detailed, transformation or conjugation?

But due to _____, ____ is used primarily in cloning experiments.

Answer 33

transformation

sequencing; transformation

Question 34

Complete sequencing of two bacterial sp. was completed in ____ and was a long and involved process. Now, ___-___, or ____ sequencing can perform the task in hours.

Answer 34

1995; Next-Generation; Nex-Gen

Question 35

What is horizontal gene transfer? How was it discovered? What types of genes are readily transferred via this process?

Answer 35

Gene transfer between different species. It was discovered as a result of gene sequencing. Genes for antibiotic resistance or increased infectiousness.

Question 36

This technology has been used to ID serotypes and trace sources of contamination.

Answer 36

gene sequencing

Question 37

NexGen sequencing overcame issues associated with ____ fastidious sp., and it enabled study of microbial _____ associated with specific environmental samples (also known as _____).

Answer 37

culturing; communities; metagenomics

Question 38

What is metagenomics? Give an example using the ocean. How might it be one day applied to humans?

Answer 38

The study of genetics derived from mixed populations of individuals isolated from the same environment. Sequence the filtrate of 1500L of seawater. Can be used for personalized medicine (hopefully).

Question 39

E. coli has about _._Mbp that encodes about ___ genes. It’s easier to isolate mutations due to the fact that they are ____. Although they remain the most studied prokaryote, we don’t know the function of about ___% of the genes.

Answer 39

4.6; 4,300

haploid

50%

Question 40

Viruses have DNA or RNA, can be ___-___ or __-___, the genome can be ___ or ____.

Answer 40

double-stranded; single-stranded; linear; circular

Question 41

There are 2 lifecycles for phages: ___ or ____. A ___ phage can go through either lifecycle. A virulent phage only goes through the ____ cycle.

Answer 41

lytic; lysogenic.
temperate
lytic

Question 42

In the ___ lifecycle of a phage, the genetic material is _____ into the host’s chromosome and is called a ____. It is replicated when the ____ genome replicates and is passed to ___ cells. Under certain conditions, the ___ excises and initiates a ___ ____.

Answer 42

lysogenic; integrated; prophage.

host; daughter; prophage; lytic infection

Question 43

During a lytic cycle, host DNA ____, phage DNA and proteins are ____ using the host’s ____, and the cell ____.

Answer 43

degrades; synthesized; systems; lyses

Question 44

In culture; ___ formations on bacterial “____” are indicative of a ____ infection (the ____ are dead areas where a high number of ____ can be found).

Answer 44

plaque; “lawns”; lytic; plaques; phages

Question 45

How does transduction enable genetic exchange?

Answer 45

The viral genome will also contain some host DNA.

Question 46

Many of the viruses responsible for major human diseases have ___ genomes.

Answer 46

RNA

Question 47

There are 3 major types of RNA viruses: ___-___ (self-sufficient); ___-___ (must bring some ____ polymerase); and ____ (uses ___ polymerase).

Answer 47

positive-strand; negative-strand; RNA; retrovirus; DNA.

Question 48

This type of RNA virus has a genome that is “ready to use” as mRNA for protein synthesis.

Answer 48

Positive-strand

Question 49

This type of RNA virus must make an RNA strand complimentary to its own to serve as mRNA, and it must bring RNA polymerase (QS) to initiate the process.

Answer 49

Negative-strand

Question 50

These RNA viruses both require RNA-dependent RNA polymerase.

Answer 50

Positive- and negative-strand

Question 51

____ use its genome to make a ___ copy of DNA that is then integrated into the host’s chromosome. It also must bring QS of a special DNA ____ called ___ ____. Once integrated, it sits in the host cell as a ____ until some event that causes excision.

Answer 51

Retroviruses; complimentary.

polymerase; reverse transcriptase.

provirus (NOT prophage - that’s for prokaryotes).

Question 52

This type of virus needs an RNA-dependent DNA polymerase.

Answer 52

retrovirus

Question 53

Re. retroviruses: Under appropriate conditions, ___ DNA produces ____ to serves as new genomes and ____ to direct the synthesis of viral ____. Note: this is not a ____ cycle; instead, the protein-coated RNA is ___ through the cell membrane which enables it to ____ the host’s _____.

Answer 53

proviral; RNA; mRNA; proteins

lytic; extruded; evade; immunity

Question 54

Some ____ have ____ that can lead to tumors.

Answer 54

retroviruses; oncogenes

Question 55

HIV’s host cell is?

Answer 55

Helper T-lymphs

Question 56

From what did HIV evolve?

Answer 56

From related simian viruses that double-infected a chimp and underwent recombination.