microbiology final exam

3 characteristics of Transformation

1 characteristics of Direct uptake of free DNA

translocasome takes up DNA and is located in the nuclear envelope

3 characters in how competence is induced in different species

bacterial sex

types of secretion system in conjugation

how conjugation works

conjugations requires the presence of special transferable plasmids

F factor

2 sites of replication origins of F factor

When is the replication site used
oriV
oriT

conjugation begins with contact between the donor cell and recipient cell

plasmid transfer in conjugations requires specific genetic elements such as these 3

when the F factor plasmid can integrate into the X, the cell is now a

this cell is capable of transferring X parts into a recipient cell

3 characters of Hfr cell transfer

3 characteristics of X mobilization

in Hfr, F factor integrates on bacterial X and tries to transfer entire X

2 characteristics of F' factor

how transduction works

process in which bacteriophages carry host DNA from one cell to another

2 types of transduction

this kind of transduction can transfer any genes from one donor to a recipient cell

this kind of transduction can transfer only a few closely linked genes between cells

4 characters of defense against transferred DNA

bacteria cut entering DNA to pieces at specific restriction sites

2 reasons bac add methyl groups to DNA

in transferred DNA the entering DNA is destroyed unless these 2 occur

entering DNA replaces X DNA

recombination occurs if

3 ways DNA can enter the cell

3 specific recombination proteins

2 reasons for recombo to occur besides DNA transfers

Two different DNA molecules in a cell can recombine by these 2

this kind of recombo requires that the 2 recombining molecules have a considerable stretch of homologous DNA sequences

this kind of recombo requires very little sequence homology between the recombining DNA molecules

how site specific recombo is diff from generalized

heritable changes in DNA sequence

this mutation is due to a change in one base pair

point mutation
transition ex
transversion ex

3 examples of larger mutations

4 ways in which there is no effect of a mutation

change in genotype

effect of a mutation on an organism

4 different causes of mutations

single base change

5 types of mutations

insertions and deletion mutations are known as

4 types of mutations on a molecular basis

suppressor mutations are known as

2 examples of electromagnetic radiation

3 characters to chemicals causing mutations

chemical intercalators insert between bases causes what kind of mutations

2 types of DNA repair

this kind of repair pathways prevents mutations

this kind of repair pathways risk introducing mutations

this repair operates only when damage is so severe that the cell undergoes apoptosis

examples of error proof repair

all microbial genomes have a mosaic nature

transfer free DNA from environment

DNA transfer after cell contact

DNA transfer via bacteriophages

restriction modification systems are used to

transposable elements include these 2

genomes evolve primarily by horizontal gene transfer and by duplications follow by functional divergence through mutation

5 ways DNA repair occurs

how does mismatch repair work

nucleotide excision repair that is induced by UV

what cuts out the nucleotide in the excision repair

this DNA repair is excised by specific enzymes in damaged bases

damaged bases are replaced by

this kind of repair occurs after strand has replicated

when the strand is repaired in recombo it is copied and its catalyzed by RecA recombinase

3 characters of SOS repair

the rapid polymerization of DNA is error prone but better than no repair

this mobile genetic element moves from one DNA molecule to another

this element can move within and between X

these are simple transposable elements containing transposase gene which is flanked by short inverted repeat sequences

these are targets for the transposase enzyme

IS elements can transfer by 1 of 2 mechanisms

are complex transposable elements that carry additional genes

small changes in gene sequence

large changes in X occurs these 3

large changes in X insertions of new material in genome evolution via

duplications if genes causes

movement of genes between cells

transposons carry genes to X

plasmid carries genes between cells
without having to become part of X

effects of gene transfer

3 ways the effects of gene transfer spreads useful genes among bacteria

archaea share many genes with bacteria

genes in one cell may not have been inherited from parents
obtained instead from other bacteria
bacterial species are related through lateral transfer as well as through parentage

most cancer results from multiple mutations

ames test uses bacterial strain auxotrophic for histidine

mutagen causes reversion

more colonies on measurement of mutagens means

transposable elements can do these 3

when transposable elements
jump from one side to another its known as
can copy itself to a new site is known as

4 characters of regulating gene expression

2 ways microbes respond to the changing environment

how microbes sense their environment

the altering of gene expression in microbes leads to these 2

5 ways microbes control gene expression at several levels

Cells use different mechanisms to sense and respond to conditions within or outside the cell.

help a cell sense internal changes and alter its gene expression to match.

lacZ gene encodes

lacY gene encodes

the product of lacZ and Y genes both need proteins to digest lactose

2 characters of E.coli lac operon

3 things that sigma factors are controlled by

Small regulatory RNAs can bind to mRNA and help stabilize it or make it susceptible to degradation.

bacteria can communicate with each other

In quorum sensing, bacteria can communicate with each other at high cell densities via

DNA microarrays (RNA) and two-dimensional gels (protein) provide global snapshots of expression

The lacZYA operon is regulated as follows:
 

The tryptophan operon is regulated by

Induction of a quorum-sensing gene system requires the accumulation of a secreted small molecule called

At a certain extracellular concentration, the secreted autoinducer reenters cells.

autoinducer reenters cells.
  - It binds to a regulatory molecule. Once bound

2 characters if quorum sensing

Cells work together at high cell density causes these 2

Autoinducer chemical for V. fishcheri

when microbes send signal chemicals to other cells these 2 occur

Chemical accumulation

the binding to sensor in a cell in cell signaling does what

this alloq bac to switch type of flagellum made

In phase variation, the section of a X undergoes inversion in 2 orientations

trp operon in a cell must make

trp operon requires many proteins made from one operon

trp repressor must bind tryptophan to bind DNA

sensor kinase protein in PM function

sensor kinases activates itself via phosphorylation

2 component signal transduction 2

3 functions of cytoplasmic response regulator

since lactose cannot pass through PM what2 ways does it undergo to enter the cell

lactose must be converted to glucose to be digested, what enzyme converts lactose

this repressor protein blocks transcription

how LacI blocks transcription

how the repressor responds to presence of lactose

inducer of lac operon

sigma factor guides RNA pol to initiate transcription at promoter

2 functions of sigma factors when it comes to proteins

3 characters when proteins can help guide sigma factor to promoter

3 characters when protein block sigma factor from binding

this acts as repressor to block transcription

2 characters of ara operon

2 occurances to when an addition of arabinose changes conformation on ara operon

is the easiest sugar to digest

sugars converting to glucose require syn of proteins beta gala

if glucose is present, lac operon is not transcribed

how the presence of glucose affects signals inside cell 2

high glucose = low cAMP

CRP protein is what kind of protein

3 function of CRP protein

CRP responses to presence of cAMP

what happens when CRP responds to presence of cAMP

high glucose>low cAMP levels>CRP inactive

When CRP is inactive, this happens

trp operon weakening 3 steps

thiamine prevents translation of thiamine biosynthesis enzyme

translational control riboswitches function

small regulatory RNAs

Antisense RNA base-pairs to mRNA
Usually prevents translation
Until removed via endonuclease
Targets the mRNA for degradation
Universal method of gene control—found
in all creatures

sigma factors regulate transcription of all genes

sigma factor 70 function

Bs sigma 28 function

sigma 38

sigma 32 function

sigma 28

this structure allows translation of sigma 32 only at high temperatures

this rapidly removes sigma factors
the rapid turnover allows more exact control

anti-sigma factors block sigma activity until needed and respond to the environment

what are the 3 mechanisms that set the levels of a particular protein in the cell

researchers won a nobel prize for discovering that genes can be induced

what happens during phase variation

the protein product of the lacI gene is a

one advantage to using sRNAs to control protein expression is that

lac operon will be maximally transcribed when this occurs

an inducer causes gene expression by

cAMP receptor protein has binding sites for

cell function is regulated at what level

AraC is one of a large family of AraC-like proteins. what do all of the proteins have in common

this occurs in response to low energy stores

what is composed of DNA

when weakening occurs at the trp operon, when will the ribosome pause at the leader sequence

lac operon includes which 3 proteins

what technique can analyze proteome patterns

accumulation of the heat shock factor, sigma H, increases at high temps because

to get maximal expression of the lac operon, low glucose is

enzyme activity can be most rapidly changed at what level

ppGpp serves as a signal to the cell that

similar to trp operon, genes encoding proteins for histidine synthesis are in a his operon that is under weakened control. The his operon leader seq probably

trp operon are regulated by these 2

when glucose if present, enzyme IIA glc is not phosphor and LacY is inhibited

these factors bind anti sigma factors, releasing sigma factors to activate transcription

what may indicate a DNA site that binds a regulatory protein

proteome refers to

some sRNA are responsible for

what functional group do kinases transfer to other molecules

a DNA microchip, scanned with cDNAs, can give info about

Acyl homoserine lactone produced by LuxI of vibrio is an example of

AraC-like regulator differ from the LacI repressor in that

bacteria may dontate DNA to

during DNA synthesis, if DNA polymerase incorporates a wrong nucleotide

pathogenicity islands (PAIs) are often found intergrated near

DNA encoding for which capability is part of the flexible gene pool

the enzyme photolyase repairs DNA damage caused by

if a bacterial cell is missing AP endonuclease genes, what could not occur

if a bacterial cell is competent, it means

a mutation always results in

a bacterial strain lacking the RecA protein will be

what type of DNA uptake is dependent on viruses

uptake of foreign DNA into a bacterium

the relaxase enzyme, used during conjugation, has what enzymatic activity

in the basic ames test for mutagenesis, a mutagen is tested to see if it can

an insertion sequence contains a gene for which enzyme

one sign of horizontal gene transfer is

which of the following is a laboratory technique for inducing transformation

if a cytosine deaminates and becomes uracil, which enzyme will cleave the uracil from the DNA backbone in the first step of a repair process

transduction is an example of

which type of DNA uptake is dependent on transferable plasmids

which of the following enzyme is used in methyl mismatch repair, nucleotide excision repair and base excision repair

in generalized recombination, which protein complex is responsible for homology searching

overtime, the genome of a species

which of the following DNA repair mechanisms is error prone

based on gel electrophoresis, a nonfunctional pro is found to have a smaller molecular weight than its wild type counterpart. A likely explanation for this observation is a

what function do bacterial pheromones promote

horizontal gene transfer can occur via these 3 ways

the process of importing free DNA from the environment into cells is called

the mutation rate in a wild type E. coli cell is on the order of

this kind of recombination needs very little sequence homology between the donor and the recipient DNA

transposable elements differ from plasmids in that

how did so many different types of bacteria acquire such genomic blending? 3

reason for bac gene transfer

how to artificially manipulate the drive DNA into the cell like transformation?2

3 reasons why species undergo natural transformation

vertical gene transfer is the same as cell division

natural transformation in gram+ typically involves the growth phase depend assembly of a translocasome complex across the cell membrane

this is composed of a binding protein that captures extracellular DNA floating in the environment

once a translocasome is assembled, the cell can import free DNA fragments and incorporate them into its genome

gram- are capable of natural transformation and do not make competence factors, why?

gram- organisms import DNA through type IV pilus assembly

type IV pili assemble and disassemble at the cell surface expanding and contracting as a result. what does this do? 2

specificity is due to particular sequences in DNA that are recognized by part of the uptake apparatus, but not all gram- competence systems display such specifics

grams positives use nonpilis attachment proteins

bacterial conju requires the presence of special transferable plasmids that contain all the genes needed for pilus formation and DNA export

F factor contains 2 rep origins

plasmid
oriV function
oriT function

plasmid can exist in extra chromosomal and integrated forms, this is called

refers to the fact that there are more cells capable of transferring chromosomal DNA in a Hfr pop

why a F- never becomes an Hfr when an Hfr undergoes conjugation with it

Hfr was used to determine map genes based on how long it took the genes to transfer

the mapping process require mating an Hfr strain with a F- recipient that contained a mutation in the gene to be mapped. it is important in any genetic cross that the mutation create an observable phenotype

an aliquot of the mating mix is removed and the conjugation bridges are broken by blending

The F factor derived from the plasmid that was inside of the chromosome (host DNA)

F' plasmids do not have to recomb into the recipient X to be maintained, extra genes can be expressed a part of the F' plasmid

extra genes can be expressed as part of the F' plasmid, this established merodiploid situation

conjugal recipient of the F' factor contains 2 copies of those few genes, on the set of X and other on the F' factor

the conjugal recipient's 2 copies of those few genes could be used to

1 group of plasmids that cannot transfer themselves can be mobilized if a transferable plasmid is also present in the same cell

mobilizable plasmids usually contain this

antibiotic resistance genes on plasmids

mobilizable plasmids along with transferable plasmids is one way in which antibiotic resistance genes can spread throughout a microbe pop

conjugation can be promoted by chem communication between cells

plasmid pAD1 produces a prot called aggregation substance in which it

when pheromone molecules are release by bac, they are these and how do they work?

Ti plasmid in the plant cell genome triggers the release of plant hormones that stimulate tumor growth of the plant. Plant cells within the tumor release this and do this

bacteriophages can accidently move bac genes between cells as an offshoot of the phage life cycle

bac phages capable of gen transduc have trouble distinguishing their own DNA from that of the host when attempting to package DNA into their capsids. Host DNA gets packed in the phage capsid as well

this defines the ends of the phage genome, marking where packaging system cuts the P22 DNA and starts packing DNA into next empty phage head

specialized or restricted transduction is a phage mediated gene transfer mech that resembles the formation of the F' factors

how is specialized transduc diff from general

specialized transduction will establish another merodiploid situation how

safe sex approach to gene exchange

the enzymatic cleavage of alien DNA and then protective methylation of self DNA

Bac produce restriction enzymes that recognize short DNA seq and cleave DNA at or near those seq

how do bac avoid committing suicide

only one strand of a seq needs to be methylated in order to be protected from cleavage from restriction enzyme

this type of restriction enzymes are used most for cloning and only possess endonuclease activity

this type of restriction enzyme generally recognize palandromic

these 2 types of restriction enzymes have their restrict and mod activities in one multifunctional pro and cleave DNA from recog site

if DNA is capable of autonomous replication
if DNA is not

kind of recomb requires two recomb molecules have a considerable stretch of homo DNA seq

this recomb occurs via mech that requires very little sequence homology between the recomb DNA molecules

this recomb requires a short seq recognized by recomb enzyme

a second CO that is some distance away from the first will lead to

3 ways recomb is advantageous

RecA aka

Before recA can find homology between 2 DNA molecules, the donor double stranded DNA molecule must

the lacz+ gene product is normally used to

if lactose is the only carbo available the lacz mutant fails to grow

radiation resistant radiodurans is thought to use RcA protein to patch together homologous ends of fragmented DNA in a way that reconstructs the X after extreme radiation damage

phase variations are freq employed by pathogens to evade the host immune system by

a short 15bp seq known as the att site is present on these 2

this phage encoded protein engages the 2 att sites and through strand breakage and rejoining combines the molecule into 1

a mutation that eliminates function

spontaneous mutations are rare, and have a freq occurrence ranging from 10^-6 to 10^-8 per gen

this is a change in bonding properties of amino and keto groups

a spon mutation can arise from tautomeric shifts in the chem structure of the bases

purine are particularly susceptible to spon loss from DNA by breakage of glycosidic bond connecting the base to sugar backbone. the result of this loss is formation of an apurinic site

apurinic

DNA damage can occur as result of metabolic activities of the cell that produce intermediates such as H2O2, etc

naturally occurring intracellular methylation agents can spontaneously methylate DNA to produce a variety of altered bases

mutagens tend to increase the mutation rate by increasing the # of mistakes in a DNA molecule as well as by inducing repair pathways tat themselves introduce mutations

mutation rate for a given gene

tells you how many mutant cells are present in a pop

ratio of mutants per total cells in a pop

when a yeast cell rep to form a colony, a spon mutant yeast is unable to metabolize a compound which then accumulates and turns red

microbial survival depends on

types of repair mech depends on 2 things

some repair mech exise whole fragment og DNA or precisely excise the damaged bases or reverse them

if there has been extensive damage of DNA,

how can a cell repair a mutation after it has been introduced during rep

Dam methylates the palindromic seq GATC to produce GAmeTC

the pyrimidine dimers that form as a result of ultraviolet irradiation can be repaired by light activating mech

photoreactivation function

this operates in the dark and is used to excise other kinds of damaged DNA as well as pyrimidine dimers

this 3 subunit exonuclease excises a patch of 12-13 nucleotides that includes the dimer

An RNA polymerase that encounters a UV dimer orother unrecognizable base on a template DNA strand willstall during transcription. The stalled RNA polymeraseis then recognized by a protein that mediates a processcalled transcription-coupled repair. The transcriptioncoupledrepair protein then snares a nearby UvrAB tobegin nucleotide excision repair.

examples of error proof pathways