Lecture 9

Question 1

What are some reasons why DNA take up can be beneficial to bacteria?

Answer 1

*nutrient source
*repair of damaged chromosomes
*drives genome evolution

Question 2

_________is the transfer of genes/genetic information from cell to cell

Answer 2

Horizontal gene transfer

Question 3

What is the rearrangement of genetic material, especially by crossing over in chromosomes or by the artificial joining of
segments of DNA from different organisms?

Answer 3

Recombination

Question 4

What are 3 mechanisms of horizontal gene transfer?

Answer 4

1.Conjugation
2.Transduction
3. Transformation

Question 5

Who discovered recombination
and conjugation in 1946?

Answer 5

Joshua Lederberg

Question 6

What did Joshua Lederberg mix to obtain recombinant prototroph?

Answer 6

Auxotrophs

Question 7

What is an auxotroph?

Answer 7

a mutant unable to synthesize an
essential nutrient, which has to be
supplemented externally for growth

Question 8

What is a phototroph?

Answer 8

a strain able to synthesizes all
necessary nutrients

Question 9

What is conjugation?

Answer 9

the transfer of DNA
from one bacterium to
another, requiring cell-to-cell
contact

Question 10

What is typically used to initiate conjugation from the donor cell?

Answer 10

sex pilius

Question 11

What does conjugation require?

Answer 11

Special transferable plasmids

Question 12

What do transferable plasmids contain?

Answer 12

all the genes needed for pilus formation and DNA export: tra genes, relaxase

Question 13

What are the two replication origins in the fertility factor (F factor) of E.coli?

Answer 13

• oriV: used in nonconjugating cells
• oriT: used during DNA transfer

Question 14

What is the donor cell called?

Answer 14

F+

Question 15

What is the recipient cell called?

Answer 15

F-

Question 16

Characteristics of the Relaxosome complex include:

Answer 16

• Nicks one strand at the
  nic site
• composed of Tra
  proteins encoded by the
  tra genes on the F
  plasmid

Question 17

Nicked strand of the F
plasmid is transferred to
the F- recipient by what?

Answer 17

A mechanism resembling
rolling-circle plasmid
replication

Question 18

What is the cell designated as when the F-factor plasmid is integrated into the chromosome?

Answer 18

Hfr (high frequency recombination) strain

Question 19

An Hfr cell is capable of
transferring parts of the
chromosome into a
recipient cell:

Answer 19

*Genes are transferred in
order
* The entire chromosome
takes about 100 minutes
to transfer

Question 20

True or False: Portions of the transferred
donor DNA can recombine
with the recipient chromosome

Answer 20

True

Question 21

What does aberrant excision result in?

Answer 21

F’ factor or F’ plasmid that carries genes

Question 22

True or False: An integrated F-factor can excise from the chromosome.

Answer 22

True

Question 23

What does Agrobacterium tumefacians contain that causes tumors in plants?

Answer 23

a Ti plasmid that can
be transferred via conjugation to plant cells

Question 24

True or False: Scientists also discovered that some genetic transfer also occurs from humans to bacteria

Answer 24

True

Question 25

What is the process in which bacteriophages carry host DNA from one cell to another.

Answer 25

Transduction

Question 26

True or False: Transduction occurs accidentally as a result of the phage packaging host genomic DNA into the capsid

Answer 26

True

Question 27

What type of transduction can transfer any gene from a donor to a recipient cell?

Answer 27

Generalized transduction

Question 28

What type of transduction can transfer only a few closely linked to the phage insertion site between cells?

Answer 28

Specialized transduction

Question 29

What is the process of importing free DNA into the bacterial or archaeal cell?

Answer 29

Transformation

Question 30

What are types of cells that can take up foreign DNA?

Answer 30

Competent cells

Question 31

What bacterium can extend a type IV pilus, which can actively take up free DNA in the environment?

Answer 31

Vibrio Cholerae

Question 32

Characteristics of the type IV pilus in vibrio cholerae include:

Answer 32

* The pilus spans the inner and outer membranes to access the environment. * Details of the homologous recombination event are not well understood and not shown

Question 33

Other gene transfer methods include:

Answer 33

* Membrane vesicles * Nanotubes * Gene transfer agents

Question 34

Bacteria evolved to have restriction and modification systems to prevent the free exchange of DNA. These systems include:

Answer 34

* Enzymatic cleavage (restriction) of alien DNA, by restriction endonucleases * Protective methylation (modification) of host DNA

Question 35

_________ is an adaptive phage immunity system found in bacteria and archaea.

Answer 35

CRISPR (clustered regularly interspaced short palindromic repeats)

Question 36

CRISPRs consist of _________that do not encode proteins, but near them lie CRISPR-associated gene families that do encode proteins

Answer 36

spacers and repeats

Question 37

The function of CRISPR can be divided into three stages:

Answer 37

1. Foreign DNA (spacer) acquisition 2. crRNA processing 3. RNA-guided targeting (effector)

Question 38

_________ move from one DNA molecule to another.

Answer 38

Transposons

Question 39

What can transposons do?

Answer 39

* Exist in virtually all life forms * Can move within and between chromosomes (transposition) * Carry genes (cargo) other than those required for transposition

Question 40

An ___________ contains simple transposable elements containing a transposase gene, flanked by short, inverted repeat sequences that are targets of the transposase enzyme.

Answer 40

Insertion sequence (IS)

Question 41

Antibiotic resistance gene serves as a __________.

Answer 41

selected marker

Question 42

True or False: A transposable element will randomly insert in the host genome.

Answer 42

True

Question 43

Random transposon insertions generate a collection of mutant bacteria referred to as a ___________.

Answer 43

Transposon mutant library.

Question 44

How do genomes evolve?

Answer 44

Through gain and loss of genes

Question 45

The fundamental processes that contribute to genome restructuring and evolution include:

Answer 45

1. Horizontal gene transfer 2. Duplication via homologous recombination followed by functional divergence through mutation 3. Genome reduction

Question 46

____________ are acquired by horizontal gene transfer.

Answer 46

Genome islands

Question 47

Examples of genome islands include:

Answer 47

* Pathogenicity islands * Symbiosis islands * Metabolic islands * Resistance island

Question 48

How can genomic islands be identified?

Answer 48

Guanine (G)/ Cytosine (C) content

Question 49

What is the most important mechanism for generating new genes?

Answer 49

Gene duplication

Question 50

What happens when a gene is duplicated?

Answer 50

frees a gene from its previous functional constraints and allows divergent evolution through mutation

Question 51

True or False: Superfamilies of proteins arising from divergent evolution share structural and functional features but may catalyze different reactions

Answer 51

True

Question 52

What are genes with shared ancestry have sequence similarity, or homology?

Answer 52

Homologs

Question 53

What are homologs found in different species that serve the same function?

Answer 53

Orthologs

Question 54

What are homologs found in single genome, related but have distinct functions?

Answer 54

Paralogs

Question 55

What is the large-scale loss of genes through evolution?

Answer 55

Genome Reduction

Question 56

Over half of the Mycobacterium leprae genome is composed of nonfunctional ________.

Answer 56

pseudogenes

Question 57

________ appear to encode an enzyme but are nonfunctional because a portion is missing as a result of mutation.

Answer 57

Pseudogenes