MRM 301 - ch 8 (bacterial genetics)

what is bacterial transformation?

"naked" DNA is taken up from the environment by a bacterial cell

chromosome transfer involves... how is the F plasmid implicated in this?

- Higher Frequency of Recombination cells - f plasmid has been integrated into the chromosome by homologous recombination (reversible)

base substitutions are more common when bacteria are growing in (aerobic/anaerobic) conditions. this is because...

- aerobic - reactive oxygen species such as superoxides are produced from O2

what are intercalating agents?

- agents that insert between base pairs in a DNA double helix - increase the frequency of frameshift mutations

what are F' donors?

- an error occurs during excision and a piece of bacterial chromosome is removed along with the F plasmid DNA - this brings a chromosomal garment into the F plasmid

define prototroph and provide an example

- an organism that can generate all the organic products it needs - E. coli

plasmids are found in...

- bacteria - archaea - some eukaryotes (yeast)

what are restriction modification systems?

- bacterial system that uses restriction enzymes to defend against invading foreign DNA - modification enzymes that methylate the host DNA to protect it

what are the 3 different mechanisms by which genes can be transferred from a donor to a recipient?

- bacterial transformation - transduction - conjugation

what are the 3 sets of genes in a pan genome?

- core genome - accessory genome - unique genes

what are the 2 kinds of transduction?

- generalized - specialized

what is a missense mutation?

- including an incorrect nucleotide creates a codon that codes for a different amino acid - effects depend on the position and nature of the change within the protein

what is a synonymous (silent) mutation?

- including an incorrect nucleotide creates a codon that encodes the same amino acid as the original - due to the redundancy of the genetic code

what is a nonsense mutation?

- including the wring nucleotide creates a stop codon - often results in a non-functional protein

what are genomic islands? how can we tell that something is a genomic island?

- large DNA segments in a cell's genome that originated in other species - their nucleotide sequence composition is different from the rest of the cell's genome (different G-C ratio)

genetic change in bacteria occurs by 2 mechanisms. name them

- mutation - horizontal gene transfer

is the entire chromosome transferred in conjugation?

- no, it would take too long - only a portion of the f plasmid is transferred - chromosomal DNA is not a replicon and will only maintains if it integrates into the recipient's chromosome through homologous recombination

mobilizable plasmids encode and ___ __ _____ but lack...

- origin of transfer - other genetic information required for transfer

what is a replicon? give 2 examples

- piece of DNA that contains an origin of replication and therefore can potentially be replicated by a cell - plasmids and chromosomes

MBEs include...

- plasmids - transposons - genomic islands - phage DNA

what is penicillin enrichment?

method for increasing relative proportion of auxotrophic mutants in a population by using penicillin to kill growing prototrophic cells

an agent that induces a genetic change is called a...

mutagen

do transducing particles contain phage RNA/DNA?

no, they only contain the bacterial DNA

what is homologous recombination? what are the limitations to which it can occur?

- process by which a cell replaces a stretch of DNA with a segment that has a similar nucleotide sequence - can only happen if the donor DNA is similar in nucleotide sequence to a region in the recipient cell's genome

What is a virion composed of?

- protein - either RNA or DNA - possibly lipid.

what are mobile genetic elements (MGEs)?

- segments of DNA that can move from one DNA molecule to another - total set of MBEs is called a mobliome

conjugative plasmids are ___-_____, meaning they...

- self-transmissible - carry all of the genetic information needed for transfer, including origin of transfer

base substitutions in a protein-encoding gene can lead to 3 possible mutation outcomes. what are they?

- synonymous mutation - missense mutation - nonsense mutation

In insertion sequences, the ___ gene (the only gene) is flanked by ___ repeats

- transposase - inverted

In insertion sequences, the ___ gene (the only gene) is flanked by ___ repeats.

- transposase - inverted

Which of the following are components of the simplest transposon, an insertion sequence?

- transposase gene - inverted repeats

what is a prophage?

the structure following the time when phage DNA has been inserted into the host's chromosome

while plasmids do not encode information essential to the life of a cell, why are they important?

they provide cells with the ability to survive in a particular environment

what is the significance of nitrosoguanidine?

this alkylating agent adds a methyl group to guanine, which then pairs with thymine instead of cytocine

what is the consequence of exposure to UV light?

thymine dimers

what is generalized transduction?

transfers any genes of the donor cell

what is specialized transduction?

transfers only a few specific genes

what is the consequence of exposure to X rays?

x rays cause single and double strand breaks in DNA and changes to the nucleobases

What is a defective phage?

A virus that has lost some of its genetic material, and therefore cannot replicate within a new target cell

what is conjugation?

DNA is transferred during cell to cell contact

what is transduction?

DNA is transferred from one bacterial cell to another by bacteriophage

base substitutions are due to an error by which enzyme?

DNA polymerase

(T/F) phages consist of RNA and DNA surrounded by a protein coat

F; they only consist of one or the other, surrounded by a protein coat

(T/F) a point mutation is when only one base pair is changed

T

(T/F) both gram positive and gram negative bacteria can do conjugation

T

(T/F) most plasmids have a narrow host range; they can only replicate in one species

T

what are recombiants?

a cell that carries DNA molecules derived from 2 different DNA molecules

define auxotroph

a microorganism that requires an organic growth factor

what is a bacteriophage?

a virus that infects bacteria, aka a phage

what is indirect selection?

allows parent cells and mutants to grow (replica plating)

what is DNase?

an enzyme that degrades DNA

what is a transducing particle?

bacteriophage progeny that contains part of a bacterial genome instead of phage DNA due to an error during packaging

what is the most common type of mutation?

base substitution

naked DNA often originated form cells that have...

burst

what is an R plasmid?

carries genetic information for resistance to one or more anti-microbial medications and heavy metals

define mutation

changes in the existing nucleotide sequence of a cell's DNA (passed on through vertical gene transfer)

what are base analogs?

compounds that structurally resemble nucleobases closely enough to be incorporated into a nucleotide in place of the natural nucleobase

Which of the following plasmids encodes all the necessary genetic information for transfer from one bacterial cell to another: conjugative/mobilizable/both

conjugative

mutants that can grow under conditions in which the parent cells cannot are usually easy to isolate by ___ ____

direct selection

what is insertional inactivation?

disruption of the function of a gene due to a DNA segment inserted into the gene (usually from transposons)

In the replication of phage containing positive-sense DNA the host's enzymes are used to make ___

dsDNA

The viral envelope closely resembles the...

eukaryotic cytoplasmic membrane

When an excision errors produces a plasmid containing both chromosomal and F plasmid DNA, the resulting plasmid is called a(n) ___ plasmid

f'

what are unique genes?

found in only one strain of the species

____ transduction results from a packaging error during the virus replication cycle, when a piece of bacterial DNA is included in the new virus particle.

generalized

what is the core genome?

genes common to all strains of a species

penicillin only kills...

growing cells

what does it mean for a cell to be competent?

in HGT, physiological condition in which a bacterial cell is capable of taking up DNA

which is more common, plasmid or chromosome transfer?

plasmid

what are conjugative plasmids

plasmid that carries the genes for a sex pilus and can transfer copies of itself to other bacteria during conjugation

what is the accessory genome?

present in more than one but not all strains of the species

what is the role of modification enzymes?

protects the cell's own DNA from the action of restriction enzymes by adding methyl groups to certain nucleobases recognized by the restriction enzyme

what is the role of restriction enzymes?

recognizes a specific short nucleotide sequence within the cell and then cuts the DNA molecule at that sequence

what is a frameshift mutation?

resulting from the addition or deletion of a number of nucleotides not divisible by 3, shifting the reading frame of the mRNA molecule

what are transposons?

segments of DNA that can move from one region of DNA to another

what is a pan-genome?

sum of total genes encoded by the various strains of a given species

what is direct selection?

technique of electing mutants by plating organisms on a medium on which the desired mutants but not the parent will grow