MCB Exam II

binary fission

DNA passed from mother cell to daughter cells

transformation

uptake of DNA from the environment, no contact required, stopped by DNase digestion; proved by Griffith (with mice) and Avery (by destroying DNA) and Hershey & Chase (radioactive DNA in viruses)

gene

promoter + operator + coding region + terminator

promoter

where RNA pol. binds to start transcription, but not transcribed itself

operator

where repressor protein binds to block RNA pol. (on regulated genes)

coding region

continuous stretch of bases (in bacteria), immediately translatable

terminator

signals RNA pol. to stop transcription

cistron

DNA/RNA structural unit that codes for a single protein

monocistronic

1 mRNA codes for 1 protein (in eukaryotes)

polycistronic

1 mRNA codes for several proteins (in bacteria)

multifork replication

in bacteria, multiple rounds of DNA replication start before the 1st round is complete, triggered by an increase in cell mass and triggers division

transcription

initiation via RNA pol. binding to promoter with the help of a sigma factor, elongation (unwinding helix and synthesizing mRNA), termination upon RNA pol. reaching a terminator seq.

regulation

requires repressor proteins to block enzyme at the operator

translation

70S (30S + 50S) ribosome binds to mRNA and reads, ribosomes attach as it’s being transcribed

operon

genes for one job are put together and transcribed together by the promoter, results in a single polycistronic mRNA

constitutive genes

genes that are always ON, includes essential housekeeping genes

inducible genes

genes that are always OFF until substrate appears (lac)

repressible genes

genes that are always ON until product accumulates (trp)

lac operon

• repressor attaches and blocks RNA pol

• lactose arrives

• inducer forms allolactose, binds to repressor

• repressor changes shape, falls off

• RNA pol transcribes lacZYA

  • lactose runs out, repressor returns to operator

lac Z

beta-galactosidase, which makes inducer allolactose

lac Y

lactose permease, which is a membrane transporter and imports lactose

lac A

transacetylase, which detoxifies odd sugars

cAMP

metabolic “alarm”, decreases when glucose is plentiful and increases when glucose runs out, responsible for 2-phase diauxic growth curve

trp operon

• trp repressor is inactive

• tryptophan acts as co-repressor, must bind to repressor to activate

• repressor + operator → RNA pol blocked, turns off

• tryptophan drops

  • repressor leaves, turned ON

regulon

several operons with their own promoters, all answer to 1 regulatory protein

why do bacteria adapt quickly?

• shorter generation time than eukaryotes

• acquire new genes from other microbes without waiting

• horizontal gene transfer

• positive selection

  • stress increases rate of HGT

spontaneous mutations

mutations that happen naturally with no outside agent; can be good/bad/neutral but ones with an advantage are kept; caused by replication errors, DNA damage, transposon insertions

induced mutations

mutations caused by mutagens like UV, DNA-modifying chemicals, anything else that damages DNA

positive selection

favorable mutations

antibiotics do not cause resistance…

they REWARD resistance by increasing selective pressure

persister state

not genetic characteristic, where bacteria become dormant (tolerant) in the presence of antibiotics (stress)

point mutation

mutation where 1 DNA base changes

silent mutation

type of point mutation that doesn’t result in change in amino acid

missense mutation

type of point mutation that results in a different, but still compatible, amino acid

nonsense mutation

type of point mutation that results in a noncompatible amino acid, ruining the protein

frameshift mutation

mutation where 1-2 bases are inserted or deleted

conditional mutation

mutation where the phenotype only appears in specific conditions like different temperatures

morphological mutation

mutation causing a change in cell or colony shape (EX: S. pneumoniae contains capsules when smooth, loses capsules when rough)

biochemical mutation

mutation causing a change in what a cell can metabolize (EX: E. coli can lose the ability to use lactose (lac-))

prototroph

wild type biosynthetic pathway, makes its own amino acids, grows on minimal medium (MM)

auxotroph

mutated biosynthetic pathway, needs nutrients from the environment (EX: arg- only grows if arginine is added)

Ames test

used his- Salmonella to measure if chemicals cause mutations, based on reversion rate back to his+, and more colonies grow if a mutagen is present

4 ways to repair DNA

1. excision repair

2. photoreactivation

3. recombination repair

4. SOS

excision repair

repair proteins sense a distortion in the helix, cut out damage, polymerase fixes it

photoreactivation

photolyase splits thymine dimer created by UV radiation, no cutting involved

recombination repair

damaged DNA is replaced with an undamaged copy

SOS

cell replicates entire genome, very fast but error-prone

vertical gene transfer

genes transferred from parent to offspring

horizontal gene transfer

genes transferred between unrelated organisms, done via transformation/transduction/conjugation

discriminating/selective cells

DNA is only accepted from the same/similar sp. for HGT

promiscuous/less selective cells

DNA is accepted from more distantly related sp. or genera, even across the Gram line

plasmids

dangerous, fast, have their own original copy of DNA, only helpful during selective pressure, costly and competes with chromosome for ATP, carries toxin gene + antitoxin gene with a shorter half life as a natural population cap

fertility (F) plasmid

contains sex pilus code, can turn into Hfr strain and drag the entire genome with it

resistance (R) plasmid

carries antibiotic resistance genes

virulence plasmid

carries genes for defensive capsules, lethal toxins, sticky adhesins

conjugation

cell-to-cell contact via pilus, episomes transfer, all cells survive, F+ donor and F- recipient that becomes F+

autolysis

some cells self-sacrifice to lyse and release DNA, neighbors that don’t lyse become competent (express binding proteins, build pores to pull DNA through)

transduction

accidental, virus-mediated, most influential method, can be general (any bacterial gene) or specialized (such as defense genes)

transposons

mobile DNA elements that copy themselves

non-replicative transposons

cut and paste

replicative transposons

copy and paste

restriction enzyme

protects cells from phage DNA by cutting it at target sites, shreds unmethylated (untagged) DNA

virus

nucleic acid with protein coating, must borrow from living cells to reproduce, only DNA OR RNA, no ribosomes, acellular, enveloped or non-enveloped

virion

complete virus particle, made up of at least 1 molecule of DNA or RNA in a protein coat

capsid

protein coat, protects the genome, aids in attaching to host cell, built from many copies of a few proteins, can be assembled without energy

nucleocapsid

nucleic acid + capsid

envelopes

derived from host cell membrane, required for attachment and entry into host, fragile, makes viruses easier to kill using soap/alcohol/drying, has spikes (functions like a key)

helical

hollow tube with protein walls

icosahedral

geometric, 20 faces and 12 corners, ID by counting pentamers and hexamers

complex morphology

layered, different kinds of morphology

binal symmetry

definitive mix of morphology (EX: icosahedral head + helical tail)

virus reproduction

1 step growth curve (eclipse period → rise/burst)

burst size

number of virions released per infected cell, PFU/mL

every virus must make _

host-readable mRNA

host polymerase can only read DNA so an RNA virus must have its own _

RNA polymerase

Class I dsDNA

• double-stranded DNA

• transcribed by DNA-dependent RNA pol

• EX: Poxviruses, Herpesviruses

Class II ssDNA

• single-stranded DNA

• host makes it double stranded, transcribed by DNA pol

• EX: parvovirus, AAV

AAV

adeno-associated virus, transgene + plasmid with rep and cap genes + plasmid helper virus genes + HEK 293

Class III dsRNA

• double stranded segments of RNA

• BYO RNA-dependent RNA pol

• EX: Reoviruses, Rotaviruses

Class IV (+)ssRNA

• virus genome acts as mRNA

• translated by host ribosomes, makes pol. first

• EX: Poliovirus, Hep A, COVID

Class V (-)ssRNA

• makes (+) strand first

• BYO RNA-dependent RNA pol

• 2 strains in 1 cell can reassort and make new strains

• EX: Measles, Influenza

Class VI Retroviruses

• (+)ssRNA with reverse transcriptase

• RT makes complementary strand, now double-stranded

• inserts strands into host chromosome

  • EX: HIV

Class VII gapped dsDNA

• also has RT

• partially double-stranded, circle with 1 incomplete strand

• host cell repairs gap and its RNA pol makes mRNA

• mRNA is put into capsids, RT converts RNA → DNA

• EX: Hep B

4 signs of viral activity

• plaques (localized tissue destruction)

• CPE (cytopathic effect, results in distorted cells)

• syncytia (giant multinucleated cells)

• inclusion bodies (build-up of viral nucleic acids and proteins)

plaque assay

shows how much of a virus there is BUT doesn’t indicate virulence or pathogenicity

viroids

circular RNA folded into a rod, no capsid, infects plants via RNA silencing or deactivation of dsRNA

prions

infectious proteins, no nucleic acids, misfolded protein becomes the template and kills neurons