Prokaryotic Gene Structure 3

Question 1

how do bacteria replicate?

Answer 1

through process of asexual reproduction process called binary fission

Question 2

what is DNase I ? (2)

+ what it acts on

Answer 2

• an endonuclease that nonspecifically cleaves DNA,
• acts on single & double stranded DNA, chromatin & RNA:DNA hybrids

Question 3

what are the 3 types of horizontal gene transfer (lateral gene transfer)?

Answer 3

1. conjugation
2. transduction
3. transformation

Question 4

how does HGT occur?

Answer 4

through mobile genetic elements (MGEs) (plasmids, transposons, viruses) that enter bacterial cell

Question 5

what makes up the total genome?

Answer 5

bacterial genome + MGEs

Question 6

what is the supergenome?

Answer 6

total number of genes available to bacterial community (large number of cells) via MGEs within same environment

Question 7

what is metagenome?

Answer 7

the collection of supergenomes within the wider environment

Question 8

what is conjugation?

Answer 8

donor bacterial cells transfers plasmid DNA to a recipient bacterial cell only when both cells are in physical contact through a specialised pilus (sex pilus)

Question 9

what is transformation?

Answer 9

recipient bacterial cell takes up cell-free/naked DNA from the environment

Question 10

what is transduction?

Answer 10

transfer of DNA from donor bacterial cell to recipient that is mediated by a bacteriophage

Question 10

what are de novo mutations? (3)

Answer 10

• single nucleotide polymorphisms (SNPs)
• insertions
• deletions (indels result in frameshift)

Question 11

how do plasmids vary in size?

Answer 11

< 2000 bp to > 100 000 bp

Question 12

what are the 2 forms of plasmids?

Answer 12

circular dsDNA (common)
linear dsDNA (rare)

Question 13

what are the 6 types of plasmids? (12)

Answer 13

1. fertility (F) plasmids (direct conjugation)
2. resistance (R) plasmids (resistance to antibacterial agents)
3. col plasmids **(for colicins, bacteriocins in pneumococcal defense)
4. metabolic (degradative) plasmids (for metabolism of unusual molecules)
5. virulence plasmids (pathogenicity to host bacterium)
6. cryptic (no obvious phenotype)

Question 14

what was the conclusion of lederberg & tatum’s experiment?

Answer 14

auxotrophic bacteria can be converted to prototrophs through gene transfer & recombination

Question 15

what was the conclusion of davis’ experiment?

Answer 15

physical contact between 2 bacterial cells is required for conjugation

Question 16

what did william hayes discover about genetic transfer? (2)

Answer 16

was polar (occurred in one direction), thus not reciprocal (one is a definite donor and definite recipient)

Question 17

what is F+?

Answer 17

donors that donate fertility factor (F)

Question 18

what is F- ?

Answer 18

recipient cells of the fertility factor

Question 19

what is mating pair formation?

Answer 19

conjugation bridge/pore forms between F+ and F- cells, membranes fuse to allow DNA to pass through

Question 20

what are the steps of conjugation (F+ x F- mating) (4)

Answer 20

1. F+ produces sex pilus to contact F- → contact made → pilus contracts to bring F- cell closer
2. mating pair formation
3. one DNA strand on F plasmid is nicked at oriT & separates → intact F plasmid replicated in F+ cell. 5’ end of nicked DNA passes into F- via pore. as ssDNA of F plasmid enters F- = replicated to become dsDNA producing F plasmid copy (F- becomes F+)
4. F+ plasmids produce surface exclusion proteins (prevent host cells from conjugating w other F+ cells)

Question 21

what are the two surface exclusion proteins ?

and what do they do

Answer 21

• TraT blocks mating pair formation
• TraS blocks DNA transfer at pore

traS: Stops (after connection)
traT: Terminate (before connect)

Question 22

what are Hfr strains?

Answer 22

bacteria with integrated plasmid that can transfer their chromosome & transfers chromosomal genes with high efficiency

Question 23

what are the two methods through which plasmids can integrate into chromosomes?

Answer 23

1. recombination between shared sequences on plasmid & chromosome
2. recombination via insertion elements shared between chromosome & plasmid

Question 24

what are the **3 steps of episomal insertion**?

Answer 24

1. association of plasmid & bacterial **insertion sequences** 2. **integration** of F plasmid in bacterial chromo 3. F plasmid intact (with O **origin of transfer** sequence → **directs transfer of genetic material** between bacterial cells) ## Footnote **integration is reversible** (F plasmid can be excised & exist independently again)

Question 25

what happens when **Hfr** cells mate with **F+** cells?

Answer 25

Hfr cells **revert to F+ cells** if F plasmid is excised from chromosome

Question 26

# how is it formed what is the F' plasmid

Answer 26

when the F episome excises itself from chromosome and an error occurs, where it picks up a portion of the chromosome, making it distinct from the F plasmid

Question 27

what is a potential result from the mating of **F' x F-**?

Answer 27

can transfer bacterial genes acquired during excision, recipients **becomes F' and is a partial diploid** **(merozygote)**

Question 28

explain the general concepts of transformation

Answer 28

1. bacterial uptake mechanisms allow them to take up DNA 2. DNA fragment in medium binds to cell-surface receptor 3. extracellular endonuclease cuts dsDNA into smaller fragments 4. one DNA strand degraded = remaining strand transported into cell 5. single strand aligns itself with homologous region on bacterial chromosome (recombination)

Question 29

what was the conclusion of **hershey & chase's** study

Answer 29

**only DNA of virus** needs to enter a bacterium **to infect** it

Question 30

what was the conclusion of avery, mcleod & mccarthy experiment

Answer 30

DNA carries info responsible for transformation

Question 31

what are the **two types** of **transformation**?

Answer 31

**natural & artificial**

Question 32

what are **competent** cells?

Answer 32

cells that **can take up DNA**

Question 33

how can bacteria be artificially induced tp become competent

Answer 33

1. chemical treatment (Ca ions makes bacteria competent - increase permeability of membrane) 2. electroporation (wash w cold, non ionic solution to prevent arcing = high potential diff is applied across washed bacterial cells mixed with naked DNA = strong electric field creates hydrophilic pores

Question 34

what was the conclusion of ledeberg & zinder's experiment?

Answer 34

genetic exchange didn't take place by conjugation (bacteriophage was agent of transfer)

Question 35

why can bacterial genes incorporate into a phage capsid

Answer 35

because of errors made during virus life cycle

Question 36

what are the 2 types of transduction?

Answer 36

1. generalised transduction 2. specialised transduction

Question 37

describe the **steps of the bacteriophage lytic cycle** (4)

Answer 37

1. **adsoprtion & penetration** (phage attaches to specific receptor on cell & injects phage dsDNA) 2. phage forces bacteria to **make virus DNA & proteins** 3. **daughter phages assembled** (virus DNA is packaged into virus protein coat) 4. **mature viruses released by cell lysis**

Question 38

what are **virulent phages** ?

Answer 38

phages that reproduce using a lytic cycle

Question 39

explain **generalised transduction**

Answer 39

1.phage DNA **enters host**, bacterial **chromosome is degraded** 2. packaging of viral chromosomes into capsid = some fragments of degraded bacterial DNA can be packaged → **generalised transducing particle** 3. **bacterial DNA is injected** by transducing particle **into another** bacterial cell (no initiation of lytic cycle because no phage DNA) 4. **3 possible outcomes** for injected bacterial dsDNA | occurs during **lytic cycle**

Question 40

what are the **3 possible outcomes** for injected bacterial dsDNA?

Answer 40

* integration into host genome (**stable**) * non-integration but genes expressed (**abortive** transduction -- bacterial cell is a partial diploid) * **degradation** of DNA

Question 41

explain **specialised transduction** (3)

Answer 41

* carried out only by **temperate phages** that have **established lysogeny** * only **specific portion of genome** transferred * when **prophage is incorrectly excised**