Genetics Chapter 9: Bacterial and Viral Genetic Systems

reproduction is rapid and many progeny can be produced

regarding reproduction, what is beneficial about using bacteria and viruses for genetic studies?

the haploid genome allows all mutations to be expressed directly, genomes are small

regarding their genome, what is beneficial about using bacteria and viruses for genetic studies?

it simplifies the isolation of genetically pure strains

why does asexual reproduction give bacteria and viruses advantages for genetic studies?

can be done in a laboratory and is easy, requires little space

regarding their growth, what is beneficial about using bacteria and viruses for genetic studies?

10,000

how many species of bacteria have been characterized?

after they have been cultivated and studied in a lab

when can species of bacteria be characterized?

archaea and eubacteria

what two groups make up prokaryotes?

viruses

what are the most common biological entity on Earth?

a group of diverse prokaryotes that are found in almost all environments, including extreme environments such as hot springs and the bottom of oceans

what are archaea?

bacteria

eubacteria are usually referred to as ___

distinct

bacteria and archaea are ___ in their genetic makeup

eukaryotes

are archaea more closely related to bacteria or eukaryotes?

their haploid genome and small size

what makes observations of bacterial phenotypes difficult?

wild-type, bacteria that can grow on minimal medium

what are phototrophic bacteria?

medium that contains the nutrients required by only prototrophic bacteria—typically a carbon source, nitrogen and phosphorus, certain vitamins, and other required ions and nutrients

what is minimal medium?

mutant bacteria, can't grow on minimal medium, must be provided biological molecules it cannot synthesize

what are auxotrophs?

a medium that contains all the substances required by bacteria for growth and reproduction

what is complete medium?

complete medium

what medium can auxotrophs grow on?

test tubes contain broth, a few bacteria are added, grow and divide until all nutrients are used up/toxins accumulate

how can bacteria be grown in test tubes?

solidified agar is suspended, bacteria are spread on the surface (plating), colonies form

how can bacteria be grown on Petri plates?

clump of genetically identical bacteria derived from a single bacterial cell that undergoes repeated rounds of division

what is a colony?

by collecting bacteria from a single colony and transferring them to a new broth tube or agar plate

how can genetically pure strains of bacteria be isolated?

it allows one to isolate and count bacteria, which individually are too small to see without a microscope

what is the chief advantage of plating bacteria?

transfer of colonies to plates that can distinguish genetic mutants, like auxotrophs

what does replica plating allow for?

one that lacks an essential nutrient

what is a selective medium?

a single circular chromosome that contained a single double-stranded DNA molecule

describe the bacterial genome

several million base pairs

what is the length of the typical bacterial chromosome?

about 4.6 million

how many base pairs does E. Coli have?

yes, some have more than one, a few have linear

is it possible for a bacterium to not have a single circular chromosome?

small, usually circular DNA molecule that is distinct from the bacterial chromosome; capable of replicating independently of the bacterial chromosome.

what are plasmids?

carry genes that are not essential to bacterial function but may play important roles in the life cycle and growth of their bacterial hosts (often antibiotic resistance genes!)

in general, what do plasmids do?

several thousand base pairs in length

what is the length of most plasmids?

allows a plasmid to replicate independently of the bacterial chromosome

what does the origin of replication on a plasmid do?

plasmids that are capable of replicating freely and are able to integrate into bacterial chromosomes

what are episomes?

fertility factor of E. coli, controls conjugation and gene exchange between E. coli cells (contains genes for conjugation)

what is the F factor?

antibiotic resistance, origin of replication, multiple cloning site (MCS)

what are the 3 features of plasmids used in DNA technology?

conjugation, transformation, transduction

what are the 3 mechanisms bacteria use to exchange genetic material?

when two bacterium lie close to another, a connection forms, and genetic material passes from one (donor) to the other (recipient)

what is conjugation?

cytoplasmic bridge (sex pilus)

what is the connection formed during conjugation called?

when a bacterium takes up DNA from the medium in which it is growing

what is transformation?

when bacterial viruses (bacteriophages) carry DNA from one bacteria to another

what is transduction?

transformation

which type of gene exchange takes place to a limited extent in many bacteria?

normally between bacteria of same or closely related species only

when does transduction take place?

not linked

in bacteria, DNA exchange and reproduction are ___ ___

reproduction occurs by asexual binary fission

why does gene exchange not accompany reproduction in bacteria?

1. DNA exchange and reproduction are not coupled in bacteria

2. in bacteria, donated genetic material that is not recombined into the host DNA is usually degraded, so the recipient remains haploid

how does genetic exchange in bacteria differ from diploid eukaryotic sexual reproduction?

bacteria can transfer and recombine genetic information, able to occur when they can physically interact = conjugation

what did Lederberg and Tatum show?

auxotrophic strains of E. coli, when cultured together produced a wild type strain

what did Lederberg and Tatum study?

sex pilus

conjugation occurs through the formation of a ___

when one of the DNA strands on the F factor is nicked at an origin of transfer (oriT)

how is transfer initiated in conjugation between F+/F-?

the oriT site, followed by the rest of the plasmid

during F+/F-conjugation, what enters the cell first?

single strand F factor replicates, producing a circular, double-stranded copy of the F plasmid, F- cell becomes F+

what happens once the F factor enters the recipient cell in F+/F_ conjugation?

F+ cells

Hfr cells behave like ___

it's integrated into the bacterial chromosome

what is significant about the F factor in Hfr cells?

the chromosome follows the F factor into the recipient cell

what is different conjugation in Hfr cells?

crossover happens, remainder of transfer DNA degrades (how auxotrophs became prototrophs in Lederberg and Tatum experiment)

what happens to transferred DNA in Hfr/F- conjugation?

F- cell almost never becomes F+ or Hfr, entire donor chromosome would have to be transferred

what happens in mating between an Hfr and F- cell? why?

cells containing an F plasmid with some bacterial genes

what are F' cells?

when an Hfr cells excises the F factor and removes a small amount of the bacterial chromosome with it

how are F' cells made?

F-

F' cells can conjugate with ___ cells

donor

what is the role of an F+ cell?

recipient

what is the role of an F- cell?

high-frequency donor

what is the role of an Hfr cell?

donor

what is the role of an F' cell?

the F plasmid is transferred to the F- cell, any genes on F plasmid (including those from the bacterial chromosome) may be transferred to the F- recipient cell

what happens during conjugation between an F' cell and F- cell?

merozygotes (partial diploids)

what is produced from conjugation between an F' cell and F- cell?

partial diploids, cells with two copies of some genes, one on the bacterial chromosome and one on the newly introduced F plasmid

what are merozygotes?

two F+ cells (F- becomes F+)

what is the outcome of F+ x F-?

one Hfr cells and one F- cell (no change)

what is the outcome of Hfr x F-?

two F' cells (F- becomes F')

what is the outcome of F' x F-?

using conjugation of Hfr and F- cells

how was mapping of bacterial genes performed?

no, it is simpler to sequence the genome of new strains

is mapping of bacterial genes using conjugation of Hfr and F- cells done today?

competent

what are cells that can be transformed called?

growth stage, the concentration of available DNA in the environment, and other environmental factors

what si competency influenced by?

by double crossover events

how does integration of DNA occur in transformation?

transformants

what are cells that receive DNA in transformation called?

residual- degraded

involved in double crossover- incorporated and replicated with the bacterial chromosome

in transformation, what happens to DNA involved in double crossovers and residual DNA?

horizontal gene transfer

gene exchange in nature results in ___

transfer of genes from one organism to another by a mechanism other than reproduction

what is horizontal gene transfer?

from other bacteria by horizontal gene transfer

how has E. coli acquired about 17% of its genome?

DNA replication and binary fission

how do genes in bacteria acquire their genome?

by horizontal gene transfer

how do genes in bacteria acquire DNA?

restriction enzymes, modification enzymes, CRISPR-Cas systems

what are some methods bacteria use to block foreign DNA introduction?

a type of bacterial defense that uses restriction enzymes to cleave foreign DNA; the bacteria protects its own DNA from cleavage by modifying the sequences recognized by the restriction enzymes.

what is restriction-modification system?

a system used by bacteria and archaea as a defense against foreign DNA, has been adapted for use as a molecular tool for precisely cutting DNA, providing a powerful way of editing the genome (act like immune ystem)

what is the CRISPR-Cas system?

clustered regularly interspaced short palindromic repeats

what does CRISPR stand for?

CRISPR associated proteins

what does Cas stand for?

a series of repeated DNA sequences (palindromic repeats), part of immune system

what are CRISPR arrays?

1. adaptation (memory formation)

2. expression (preparation)

3. interference (defense)

what are the steps in CRISPR?

virus injects DNA into bacterium, Cas proteins cut viral DNA into pieces called photospacers, piece of DNA is added as new spacer at the 5' end of array where it enhances immunity against recent invaders

what happens during adaptation in CRISPR?

CRISPR array is transcribed into long piece of RNA which is chopped into smaller pieces called crRNAs, crRNAs bind with Cas proteins, forming an effector complex

what happens during expression in CRISPR?

if the same virus/plasmid enters cell again, crRNA matches its DNA, Cas protein cuts and destroys foreign DNA, the virus is stopped

what happens during interference in CRISPR?

recognition sequence stored in bacterial genome

what is a photospacer used as?

adjacent DNA sequences required for binding by a CRISPR-Cas effector complex; the complex associates with the PAM and unwinds the DNA nearby

what are PAM sequences?

simple replicating structures made of nucleic acid (DNA or RNA) and a protein coat

what are viruses?

recognizes receptors on the cells, allowing it to inject its genetic material into the cell

what does a virus' protein coat do?

bacteriophages that reproduce strictly through the lytic cycle and kill the host cell

what are virulent phages?

lytic and lysogenic cycles

what are the two alternative life cycles of a bacteriophage?

a phage attaches to a receptor on the bacterial cell wall and injects its DNA into the cell, host DNA is degraded while phage DNA is replicated, transcribed, and translated

what happens during the lytic cycle?

bacteriophage that can undergo the lysogenic cycle or lytic cycle

what are temperate phages?