Exam 3 BIO 326R

how does a bacteria cell respond to amino acid starvation

decrease tRNA & rRNA & increase in specific amino acid biosynthetic enzymes

stringent response is activated in the transition from [ ] to [ ] phase

exponential to stationary; response to environmental changes that reduce nutrient availability

When starved of amino acids, uncharged tRNAs enter ribosomal A site, and triggers an enzyme called

RelA

RelA catalyzes synthesis of what 2 alarmones in amino acid starvation

ppGpp and pppGpp

a structurally related molecule to GTP and competative inhibitor of translation initiation factors; also disrupts transcription by destabilizing RNA polymerase promotor open complexes

(p)ppGpp

under good growth conditions the concentration of (p)ppGpp is [ ] but nutrient limitation [ ] synthesis of (p)ppGpp

low; increases

second messenger that is a cyclic dinucleotide and well studies

cyclic dimeric guanosine monophosphate or c-di-GMP

catalyzes synthesis of c-di-GMP

DGC (diguanylate cyclase)

catalyzes degradation of c-di-GMP

PDE (phosphodiesterases)

when a cell attaches to a substrate by adhesion c-di-GMP concentration

increases (by DGC activity)

c-di-GMP initiates a cascade of gene expression to shut down [ ] rapidly and activate the synthesis of

motility; adhesion proteins that promote surface attachment

when a cell returns to free living by breaking adhesion, what increases in concentratio nto eliminate c-di-GMP

PDE

regulates movement and measures the attractant concentration in its environment in e coli

chemotaxis

smooth swimming motion, flagella rotates in CCW (counterclockwise) - default mode

RUN

change of direction, flagella rotates CW (clockwise)

TUMBLE

when an attractant is present, signal transduction system control flagella rotation for more [ ] movement

run; less tumble

Signal transduction sytem controlling flagella rotation receptors are [ ], sensor kinase is [ ] and response regulator is [ ]

MCPs, Che A, Che Y

if CheA is activated by autophosphorylation which direction are flagella roating

CW (tumble); if inactive CCW (run)

when any of the MCPs bind an attractant, CheA autophosphorylation is [ ] the flagellum continues rotating CCW, and the cell continues its run

inhibited

if the attractan levels decrease because the cell is moving in the wrong direction, the level of attractan bound to the MCPs decrease and CheA is [

stimulated to autophosphorylate; Che Y gets phosphate and tumble begins

E. coli measures concentration of attractants every few seconds & remembers the previous ocncentratio nthat involves [ ] of MCPs

methylation; MCP methylation level is high if number of mCPs bound to attractan is high

Vibrio uses quorum sensing to regulate light production within the organ of its squid host; cells produce light only at a [ ] density

high density

vibrio and many gram (-) bacteria use a [ ] signal to communicate

N-acyl homeoserine lactone

controls intitation of sporulation

Spo0A

during sporulation in bacillus, [ ] sense nutrient depletion and starts to phosphorelay - multiple phosphorylations

KinA

microbes methylate the nitrogenous bases in short stretches o DNA throughout the chromosome using restriction endonucleases to hydrolyze phosphodiester bonds only if DNA has NOT been methylated → ways bacteria protect from viral infection

restriction modification (innate immunity)

uses part of invading virus’s genome to document an attack and prep for possible future attack

CRISPR/Cas system (adaptive immunity)

heritable permanent changes in DNA sequence

mutations

alterations of single nucleotides, addition/deletion of 1, etc

point mutations

2 types of mutations

spontaneous or induced

a type of spontaneous mutation where nucleotides shift so A can bond wit hC and G can bond with T

tautomerization

2 tautomeric forms

keto & enol; amino & Imino

The shift between forms due to tautomerization changes purine for purine or pyrimidine for pyrimidine is a spontaneous mutation called a

transition mutation

mutations that result from the substitution of a purine base for a normal pyrimidine or vice versa are

transversion mutations

occur where there is a short stretch of repeated nucleotides; slippage in a new strand causes addition; slippage in parent strand causes a deletion

insertion/deletion mutations

purine nucleotides can lose their base (depurinated) while the phosphate sugar backbone remains intact; this forms an apurinic site which cannot base pair and can cause a mutation in the next round of replication

lesions in dna (spontaneous)

5-bromouracil; an analogue of thymine that undergoes a tautomeric shift frequently is an example of an induced mutation by what type of chemical mutagen

base analog

methyl-nitrosoguanidine is an induced mutagen that adds methyl groups to guanine - it is what type of chemical mutagen

DNA-modifying agent

ethidium bromide which inserts itself into the helix of dna is what type of chemical mutagen

Intercalating agent

UV radiation at 260 nm max can cause

thymine dimers

wild type to mutant form

forward mutation

mutant form to wild type form

reverse mutation

wild type phenotype is restored by second mutation at dif. site than OG mutation

suppressor mutation

substitution point mutation that changes amino acid to same amino thereby not affecting the protein

silent

substitution point mutation that changes codon to another amino acid

missense mutation

substitution point mutation that changes codon to a stop codon

nonsense mutation

point mutation that is caused by insertion or deletion of nt that alters reading frame

frameshift mutations

correction of errors in base pairing made during DNA rep. is done by

DNA polymerase

excision repair that removes thymine dimers or damaged bases is performed by what enzymes

DNA polymerase I and DNA Ligase

direct repair that involves light to separate thymines with photolyase

photoreactivation

corrects DNA when both strands are damaged using another undamaged molecule (another copy of chromosomes)

recombinational repair

a global control network that activates over 50 genes to repair

SOS Response

transfer of genes from parents to progeny via meiosis

vertical gene transfer (eukaryotes; sexual reproduction)

genes transferred to the same or different species (bacteria and archaea; asexual rep.)

horizontal gene transfer

HGT mechanism: a donor cell dies, releases dna to the environment, it is picked up by recipient

Transformation

HGT mechanism: pili is used between donor cell and recipient cell to transfer DNA

Conjugation

HGT mechanism: DNA is transported from donor cell to recipient cell with a bacteriophage

Transduction

after DNA is transferred in HGT it can pair with recipient DNA and recombine known as

integration

crossing over btwn non-homologous chromosomes, requires long regions of DNA with similar nucleotide sequences

homologous recombination

protein that carries out homologous recombination

RecA

doesn’t require long sequence homology; recombination occurs at specific target sites in DNA

site specific recombination

the catalyst used in site specific recombination

recombinase

small segments of DNA that move around genme to random locations; can alter gene function

mobile genetic elements (jumping genes)

enzyme involved in mobile genetic elements

transposase

more complex jumping genes that carry additional genes besides the ones for transposase

transposons

the simplest transposable elements; short sequences of DNA which only have genes for transposase with inverted sequences at either end

insertion sequences

transposase catalyzes the excision of the mobile genetic element (MGE), followed by cleavage of a new insertion site and ligation into a new site

simple transposition (cut-and-paste)

MGE remain at OG site in DNA and copy is inserted in the new DNA site

replicative transposition (copy & paste)

conjugation (transfer of genes) requires what 3 things

1. cell-to-cell physical contact 2. conjugative plasmids (f-factor) 3. sex pili

which of the following is (are) correct regarding plasmids

small, double stranded dna molecules that can exist independently of host chromosomes

have their own replication origins so can replicate independently of the chromosome

are stably inherited but not required for the host cells growth and reproduction

some plasmids carry genes that code for enzymes that destroy or modify drugs

all of these

all of these

genes responsible for cell attachment; genes for formation of sex pilus, contains genes for type IV secretion system

F-factor (conjugative plasmids_

these plasmids can stay outside chromosome in the cytosol OR be integrated

episomes

incubated 2 auxotroph bacteria together and notice they were able to undergo recombination to wild type

Lederberg & Tatum

used U-tube experiment that kept cells separate and showed no gene transfer; cell-to-cell contact required

Davis

showed transfer of genes is unidirectional in bacteria

Hayes

F+ x F- mating results in

F+; recipient cell has F-factor

donor with a conjugative plasmid integrated into its chromosome

High Frequency Recombination (Hfr)

Hfr x F- results in

F- recipient

F factor can leave bacterial chromosome and resume status as autonomous plasmid

F’ conjugation

F’ x F- results in

F’ recipient cell

F. griffith discovered another HGT mechanism in which DNA from environment (from unknown donor) is taken up into the recipient cell

transformation

type of transformation observed in some archaea and several bacteria; occurs in soil, aquatic ecosystem, in biofilm, and other microbial communities

natural

this bacteria that does natural transformation & becomes competent during the exponential phase of bacterial growth

streptococcus pneumoniae

this bacteria that does natural transformation becomes competent during the stationary phase of bacterial growth

bacillus substilis

this bacteria that does natural transformation takes up DNA only from closely related species

haemophilus influenzae

other type of transformation that is a lab technique which induces cells to take up DNA (compentence)

artificial transformation

transfer of bacterial genes by viruses (bacteriophage)

transduction

any part of bacterial genome transferred through a virus; occurs during lytic cycle; incorporated into chromosome

generalized transduction

inserts into specific site of bacterial genome is transfered through a virus bc of an error in the lysogenic cycle

specialized transduction

carries the antibiotic genes in bacteria; is able to transfer

R plasmid

genus of bacteria that are hyperthermophile bacteria that is a chemolithoautotroph which captures energy by oxidizing hydrogen, thiosulfate, and sulfur with oxygen as the terminal electron acceptor

Aquifex

genus that are hyperthermophiles that are chemoorganotrophs, shaped like rods with an outer sheathelike envelope, have outer membranes that lack LPS

Thermotoga

sherical or rod shaped gram negative bacteria that stain gram (+) and are extraordinarily resistant; more resistant than endopsore formers bc not affected by reactive oxidative species

Deinococci

which types of bacteria carry out oxygenic photosynthesis? which carry out anoxygenic photosynthesis?

cyanobacteria carry out oxygenic photosynthesis

purple bacteria, green bacteria carry out anoxygenic

the oxygenic photosynthetic bacteria that is the major nitrogen fixer; converting atmospheric N2 gas to ammonia with the enzyme nitrogenase

cyanobacteria

difference between green sulfur and green nonsulfur bacteria (both non-proteo gram negative anoxygenic bacteria)

green sulfur - photolithoautotrophs, and are found in sulfide-rich zones of lakes

green nonsulfur - are photoheterotrophic (use pyruvate, acetate, glycerol, glucose) and are found in alkaline hot springs

small bacteria that have own ribosomes, make own nucleic acids & lipids, have outer membranes (gram negative), and ARE susceptible to antibiotics

chlamydia

the enzyme nitrogenase is located inside of what cell of cyanobacteria

heterocysts

which bacteria are obligate intracellular parasites meaning they MUST have a host to survive

chlamydia are obligate intracellular parasites