Microbial Genetics I & II

Question 1

What genetic diversity of bacteria is composed of what two categories of genetic information?

Answer 1

1) core gene pool of chromosomal DNA

2) flexible gene pool

Question 2

What are some genes that the flexible gene pool may contain?

Answer 2

1) pathogenicity factors

2) abx resistance

Question 3

What does the core gene pool contain?

Answer 3

Genes that are essential to the bacteria such as those for ribosomes, cell envelope, DNA replication, etc.

Question 4

The DNA for bacteria has a noticeable lack of what element which is present in eukaryotic DNA?

Answer 4

1) non-coding DNA

2) introns

Question 5

Which gene pool is larger?

Answer 5

Flexible gene pool is considerably larger. Has ~16k genes which are distinct

Question 6

What is the approximate size of the different gene pools for an E. coli?

Answer 6

Core: 2k genes
Variable: 2-3.5k genes

Question 7

What are phages?

Answer 7

bacterial viruses

Question 8

What is a prophage?

Answer 8

A phage already integrated into a bacteria’s genome

Question 9

What are some flexible genetic elements?

Answer 9

1) plasmids
2) phages
3) integrons
4) transposons
5) genomic islands/islets

Question 10

What are genomic islands?

Answer 10

Long block of DNA which is from another organism and is associated with a particular function

Question 11

The integration of things like a phage, or a plasmid into the DNA of a commensal E. coli might do what?

Answer 11

-confer toxicity or pathogenicity to the bacteria

Question 12

What are the three mechanisms of horizontal gene transfer?

Answer 12

1) transformation
2) transduction
3) conjugation

Question 13

What is transformation?

Answer 13

transfer of free DNA

Question 14

What is transduction?

Answer 14

transfer by viral delivery

Question 15

What is conjugation?

Answer 15

plasmid transfer

Question 16

How do free fragments of DNA enter the cell in transformation?

Answer 16

through DNA binding proteins

Question 17

In what form does bacteria take up DNA?

Answer 17

single strand

Question 18

What proteins facilitate the recombination of free ssDNA?

Answer 18

recA, and rec proteins

Question 19

How does transformed DNA add into the genome?

Answer 19

true recombination, so alleles are traded for one another or the same one

Question 20

What is competence?

Answer 20

the preparation necessary to make a cell ready for taking up free DNA

Question 21

When does transformation and competence usually happen in the bacterial cell cycle?

Answer 21

stationary phase

Question 22

Which strains are constitutively competent?

Answer 22

Neisseria and H. influenzae

Question 23

What is one phenotypic change that bacteria undergo to become competent?

Answer 23

includes the expression of pore proteins

Question 24

How does a bacterium normally protect itself from foreign DNA?

Answer 24

restriction modification systems

Question 25

How do restriction enzymes work?

Answer 25

These enzymes make cuts at certain points in the DNA thus cutting it out of the genome

Question 26

How does a bacterium differentiate between its own DNA and foreign DNA?

Answer 26

methylation protects the bacterium's own DNA

Question 27

How do we induce E.coli to become competent in the lab?

Answer 27

- salt treatments | - electroporation

Question 28

What is the general shape of a bacteriophage?

Answer 28

- filamentous - icosahedral head - head and tail form together in "sputnik"-like shape

Question 29

What location on the bacteriophage does it recognize cell surface receptors?

Answer 29

at the base plate

Question 30

What limits host ranges for phages?

Answer 30

cell surface protein specificity

Question 31

What are the two types of phage?

Answer 31

1) virulent | 2) temperate`

Question 32

What are the two life cycles of the phage?

Answer 32

lytic and lysogenic

Question 33

Describe the lytic cycle.

Answer 33

The lytic cycle is when a phage will enter a bacterium, and use the cell's machinery to produce daughter phages. The cell is killed in the process.

Question 34

Describe the lysogenic cycle.

Answer 34

The lysogenic cycle is when a phage's DNA integrates with the bacterial genome and propagates itself in this fashion.

Question 35

What is a bacterial cell with a prophage called?

Answer 35

A lysogenic cell

Question 36

At what sites do phages combine their DNA in the lysogenic cycle?

Answer 36

ATT sites

Question 37

What types of infections, diseases, etc. are effectively treated with bacteriophages?

Answer 37

- wounds - suppurative infections - gut infections

Question 38

What is lysogenic conversion?

Answer 38

A new phenotypic property is conferred on a bacteria carrying that phage

Question 39

What usually causes the toxigenicity of bacteria?

Answer 39

incorporation of phage elements and viral dna

Question 40

What is transduction?

Answer 40

the transfer of DNA to another bacterium by viral delivery

Question 41

What are the two types of transduction?

Answer 41

1) generalized | 2) specialized

Question 42

Which type of transduction is more common?

Answer 42

generalized

Question 43

Describe generalized transduction.

Answer 43

Phage enters the cell and while assembling phage components a portion of bacterial DNA gets into a phage. The phage then propagates this DNA

Question 44

What cycle does generalized transduction depend upon?

Answer 44

lytic cycle

Question 45

Describe specialized transduction.

Answer 45

Phage DNA will integrate with the bacterial DNA and enter the lysogenic cycle. This segment can pop in and out and sometimes will take bacterial DNA with it

Question 46

What is CRISPR?

Answer 46

Clustered regularly interspaced short palindromic repeats

Question 47

What is thought to be the function of CRISPR in bacteria?

Answer 47

bacterial immunity

Question 48

How does CRISPR work in general?

Answer 48

In general, there is an array of repeated sequences which allow the integration of foreign DNA in between. These sequences then get transcribed and eventually act as primers for foreign DNA.

Question 49

How long are the non-repeating sections of the CRISPR array?

Answer 49

20-25 base pairs

Question 50

What chops up foreign DNA to put it into CRISPR DNA?

Answer 50

cas complex

Question 51

What is conjugation?

Answer 51

DNA transfer through plasmid DNA

Question 52

What is F factor?

Answer 52

fertility factor

Question 53

What does F factor confer to the bacterium?

Answer 53

Ability to transfer DNA via conjugation

Question 54

What is a bacterium with F factor called? one without F factor?

Answer 54

with F factor: F+; without: F-

Question 55

What are incompatibility groups?

Answer 55

groups which are defined by a set of genes that cannot coexist in bacteria to successfully reproduce, although they can exist in a bacterium at the same time

Question 56

What types of genes are on the F plasmid?

Answer 56

- transfer genes - insertional sequences - incompatibility group genes

Question 57

What is Hfr?

Answer 57

A bacterium which has had plasmid DNA inserted into its genome

Question 58

Can a HFr bacterium conjugate with a F- bacterium?

Answer 58

Yes.

Question 59

What are the two types of resistance?

Answer 59

1) intrinsic | 2) acquired

Question 60

What is intrinsic resistance?

Answer 60

intrinsic mechanisms of bacteria that might make them resistant to antibiotics

Question 61

To what types of antibiotics is mycoplasma resistant?

Answer 61

those that target the cell wall, as it has none

Question 62

What are the two types of acquired resistance?

Answer 62

1) vertical transfer | 2) horizontal transfer

Question 63

How is vertical transfer of antibiotic resistance conferred?

Answer 63

through mutations

Question 64

How is horizontal transfer of abx resistance conferred?

Answer 64

through plasmids

Question 65

Plasmids contain what kind of DNA?

Answer 65

circular dsDNA

Question 66

What is "selfish DNA"?

Answer 66

DNA that copies itself numerous times in the genome and confers no advantage to its host

Question 67

Why do some plasmids have selfish DNA?

Answer 67

if their DNA is gotten rid of it will kill the bacterium

Question 68

What the three types of transfer of plasmid DNA?

Answer 68

1) conjugative 2) non-conjugative but mobilizable 3) non-conjugative non-mobilizable

Question 69

What are the two most medically-important function of plasmids?

Answer 69

1) confer resistance to antibiotics | 2) confer resistance to heavy metals

Question 70

What are the three main ways that plasmids can specify resistance?

Answer 70

1) efflux pumps 2) modifying enzymes, modifying target of abx or the abx itself 3) degrading enzymes

Question 71

How is antibiotic resistance to tetracycline commonly conferred?

Answer 71

efflux pumps, but sometimes thru modification of the elongation element it identifies