Lecture 6 Flashcards
Bacteria are key players in
- energy flow
- nutrient cycling
- oxygen production
- human biotechnology.
Bacterial cumulative biomass likely equals
or exceed all Eukaryotes combined.
they cover every square mm of the environment including our gut and skin
Bacteria are classified as
Prokaryotes (before the nut) lacking a nucleus.
Prokaryotes include ___
and are the source of___
the ancestors of Eukaryotes
mitochondria & chloroplasts
phages are
Viruses that infect bacteria
(also known as bacteriophages)
phages often aid in __ making them ___
the regulation of bacterial populations
ecological key players
the single most common organismal interaction in nature is between
bacteria and their viral pathogens
Lysed bacteria return nutrients to
the ecosystem greatly impacting nutrient cycling
Bacterial genomes are
DNA based and circular (rather than linear)
Most bacteria have a single main chromosome, but a few have 2 or 3 chromosomes.
Bacteria can have (many) smaller circular self replicating genetic units, plasmids
plasmid (effect on) bacteria
are not essential but often beneficial to the bacteria.
Bacteria can have (many) smaller circular self replicating genetic units, plasmids.
____ bp genome of E. coli
4.6 million
parasitic bacteria have smaller genomes than
“free living” species.
operons
multiple genes transcribed together with a single promoter
Bacterial genomes may contain non-coding introns but at a ____ than typical Eukaryotes.
much lower percentage
Viral genomes vary greatly from
4kb to over 2000kb
(Eukaryotes vary in genome size from ~10mbp to 100,000mpb.)
bacteriophage “species” has ____ nucleotides and ____ genes
only 4200
4
Genetic material can be
- DNA or RNA (never both),
- single or double stranded,
- circular or linear
- a single piece or split into several pieces (segmented)
- have multiple copies of their genome (HIV), however most have a single copy
The reproductive straggles of Bacteria are likely the ____ of any group of organism.
most varied
bacteria can gain and loose genetic material by
1) taking up DNA from the environment (transformation)
2) directly too/from other bacteria (conjugation)
3) via a phage (transduction)
Sexual reproduction is
the equal (or semi equal) donation of genes between two individuals that result in an offspring.
the term horizontal transfer in bacteria is problematic because
it can be used to describe the movement of genes between unrelated species
termed horizontal transfer because the movement of genes does not require cell division (reproduction)
bacteria typically only need ___ to grow
water,
salts,
a carbon source (sugar),
some basic nutrients (combination termed minimal media)
Individual colonies of ____individuals become visible in ____ days.
10^7
1 to 2
auxotrophic
Bacterial mutants that require a particular nutrient not present in minimal media
Other mutations include those that are resistant (str^r), or sensitive (str^s) to particular conditions, usually antibiotics.
Resistant mutants are often used as
a genetic screen for individuals,
only those resistant to a particular antibiotic survive in the presence of that antibiotic.
“replica plating” is method to identify
colonies with a specific mutation
experiment (1946) by Lederberg and Tatum suggested
that bacteria could exchange genes.
used 2 diff strains of bacteria
each had three differing mutant loci that did not allow growth in minimal media
if they combined the two for several hours a few colonies (1 in 10,000,000 individuals) were able to grow
To test if bacteria needed physical contact to exchange genes B. Davis (1950) performed the following experiment
2strains were physically separated with a fine filter that would allow molecules to pass through but not whole bacteria.
no growth occurred of the separated bacteria even after many hours
need physical contact (pilus)
Bacterial conjugation typically occurs one-way between a donor and a recipient via a
‘pilus’ without the donor loosing genetic material.
different types of bacterial pili
- some attach to substrates to hold bacteria in place
- others can grab and pull
The ability to form a conjugation pilus and exchange plasmid genes is termed ___
The genes that produce the pilus and allow the transfer are located on ___
F+ (F for fertility).
the plasmid.
episome
special type of plasmid, which remains as a part of the eukaryotic genome without integration.
Conjugation is the transfer of
a single stranded copy of plasmid (or episome)
The single strand is complemented to form the circular double stranded plasmid after
it reaches the recipient.
This action can change a F- (non-donor) to a F+ capable of subsequent donation.
Hfr strain is a strain that
(high frequency recombinant)
produced many more recombinant individuals than the normal F+ strains
Hfr strain was produced by___
can cause__
(rare event) a F+ plasmid integrating into the larger non-plasmid genome of a F+ individual.
causing the chromosome to act like a plasmid (able to make a pilus and transfer portions of the main chromosome to another cell)
Hfr Transfer
Like F+ transfer,
a single strand of the donor main chromosome is produced and moves to the F- (or sometimes termed Hfr-) cell
via conjugation.
single strand —> double strand
double strand —> recombine with the recipient main chromosome
(takes two crossing over events)
Before recombination (in Hfr transfer) the recipient cell is termed a ___ and has ____several genes.
After the genes cross over this cell is a ____
exconjugant
two copies of
recombinant.
In Hfr transfer, the strand that is recombined out of the main chromosome ___ and is ___
This transfer is often termed a ___
degrades
“lost”.
“cross” of the two different genotypes.
If the donor has ____ from the receiver then the outcome of the “cross” (Hfr transfer) can be tracked using ____
different alleles
different media conditions.
the relative positions of the genes (in Hfr transfer) can be tracked using
interrupted mating in a time series
1) two strains are placed together in a flask with conditions suitable for conjugation
2) at time periods a sample is taken and shaken to stop conjugation (via breaking pillus bridges)
3) bacteria are placed on diagnostic media (recipient could not survive/donor could survive) and living colonies identified
able to grow on the diagnostic media must have taken up particular portions of the Hfr genome
higher frequency means
that the genes moved quickly
must be close to break site from donor and must be close to each other.
(relative distance map of the bacterial genes)
after interrupted mating in a time series how do we know that we screened out the donor?
str^r is used to screen out the donor
donor are str^s
the transfer from a Hfr+ cell to a Hfr- cell only very rarely makes the
Hfr- into a Hfr+
Because Hfr transfered last
When the Hfr moves genes to a new cell (Hfr-) the transfer begins at a specific location termed ___
and proceeds ____
the Origin (red arrow)
counter clockwise on the Hfr, (producing the segment on the right)
When is 1 transferred relative to the other genes?
last.
1 is Hfr ability
THUS, very unlikely tat Hfr transfer will turn a Hfr- cell into a Hfr+ cell.
genes from the Hfr cells can be transferred in different orders in general based on
where the initial Hfr was inserted.
However, the origin is always first and the transmission factor always last.
(in Hfr transfer) recombination into the circular genome occurs between
a fragment of the donor (exogenote)
and the full genome (endogenote) of the recipient.
Viability (in circular genome recombination) requires
a double crossing over (or an even number),
re-establishing the circular chromosome
A single recombination between the fragment and the recipient produces a non-viable linear piece of DNA.
F’ Plasmids
a plasmid has inserted into the main chromosome and then excised to once again form a plasmid.
abnormal excision may produce (in F’ Plasmids)
(abnormal out-looping)
a plasmid that includes some of the genetic material from the main chromosome.
IS (in F’ Plasmids) is ____
that ____
integration sequence on the chromosome
facilitates insertion/excision with the plasmid.
abnormal out-looping, uses ___ not ___
producing ___
IS2 not IS1
a novel plasmid that has gained the lac+ from the main chromosome.
R Plasmids are plasmids that contain ___ and may have ___
resistance genes
(e.g. antibiotic resistance)
may have genetic elements called transposons
transposons are ___
genetic elements that have the genetic machinery to excise themselves and splice into other sites
“jumping genes”
The movement between species is termed
horizontal transfer
R plasmids with transposons are a serious problem because
1) spread via conjugation (like normal F+ plasmids)
2) have the propensity to move via the action of the transposon
3) can occur both within the particular bacteria and between different species as well.
transposons facilitate
the snipping of genes in and out of locations and in between species
Results of Horizontal Transfer and transposons
Horizontal transfer can also occur via transposons moving genes from the main bacterial chromosome.
-For example, in E. coli 15 to 20 percent of the main genome originated from other species.
Bacteria can gain DNA directly from the environment from
dead and lysed cells or simply secreted DNA
competency
ability to undergo transformation
The ability to undergo transformation differs by ___
and is facilitated by ___
species and/or the individual cell (can be up or down regulated)
a surface DNA binding complex (left).
Bacteria can increase transformation when ____
and can secrete plasmids to ___
they experience stressful environmental conditions
saving energy, avoiding the cost of replication
Infection process by a phage
1) attachment to the bacteria
2) injecting their genetic material
3) material takes over the bacteria –> directing it to duplicate the viral genetic material and components
4) If the bacteria cannot mount a successful defense against the phage —> infection will result in bacterial lysis —->
surrounding area flooded with many more copies of the phage.
Studying bacteria is quite challenging because of
their small size
but viruses are much smaller
viruses cannot be visualized without
electron microscopy
thus, analysis is often performed through their effects on bacteria
(when phage and bacteria are together)
the clear areas of ____ in the petri dish are areas where the ___. These areas appear after___ hours because ___
plaques/lysed cells
the covering of bacteria has been disturbed
after ~15 hrs
because this is the necessary time for one phage to go through several rounds of infection and lysing to clear a observable area of the plate
plaques can take on different sizes and shapes depending on the ___.
phage “species” or type.
This can be used as a general (first round) diagnostic for a particular phage.
phage’s “host range”
can it infect or not
method of mapping phage genomes relies on ___
can be differentiated by ___
can produce a relative distance map by ___
on double infecting bacteria with two different phages (with different genotypes)
the two types of plagues they produce (b/c 2 strains, diff alleles)
counting the total recombinants (Recombination between the phage genomes produces a third and forth phenotype that are visible) (each genotype has own phenotype)
vs the total plaques
during transduction, when a bacterium has had its genome fragmented it reproduces _____
during this stage a phage can ___
parts of the phage
take in a portion of the bacterial genome (allele a+) and subsequently move it to another bacteria that was a-
how to screen for a+ movement (in transduction)
Selective media, or other indicators
Most phages are termed ___because ___
however there are also ___ pages
“virulent”
they quickly reproduce and lyse the infected cell
temperate
___ event that phages move from one bacteria to another without ___
rare
killing it
temperate phages are phages that ___
after infection, will enter a quiescent phase where they remain dormant for extended periods of time
(get into bacteria and do not cause lysis)
how do temperate phages can remain quiescent
they reproduce with the bacteria as the bacteria grows and divides
temperate phages can eventually become ___
can be caused by ___
lytic and lyse the cell.
cell stress
common method to turn a temperate phage lytic is
high doses of UV.
a resident temperate phage can cause resistance ____
mechanism for this is ___
one example is ____
to further infection from that same phage type
the resident phage produces a “repression” factor that restricts the action of a new phage
example- lambda phages
General vs. Specialized Transduction
Generalized phages typically pick up and move genes at random
specialized phages that only insert into particular locations in the bacterial genome
randomness of generalized phages can be used as a way to map bacterial genomes because
adjacent genes in the bacterial genome are more likely to be transferred together.
because specialized phages only insert into particular locations in the bacterial genome they are more likely to
transduce (move) genes that are adjacent to the specific insertion location
Each type of specialized phage uses a
specific (and differing) location in the bacterial genome for insertion
ex. For lambda it is between the gal and bio genes
The insertion of bacterial genomes in specialized phages occurs via a ____ event.
This is made possible through ___
“crossing over-like”
an enzyme produced by the phage.
if “abnormal” outlooping and excision occurs in Specialized Transduction
this is a mistake by the virus
the phage picks up genes from the bacteria and some of the viral genes are left behind.
This may cause the particular virus to be non-viable (if essential part of phage genome is left behind)
bacterial genes thst are most likely to be transduced (in abnormal outlooping in specialized transduction) are ____
those closest to the specific integration site.
CRISPR system of bacteria
protects them from invading phages
recognizes specific phage sequences and cuts them into fragments
causing the phage to be non-functional.
