week 5 Flashcards
most bacterial cells double by
binary fission
binary fission results in 2 mostly……products
identical
the next generation following binary fission shares the same….. and……
semi-conservative replicated DNA
aged cytoplasmic contents
no true …… cells, essentially two……cells
mother
daughter
two general categories of cell division
equal
unequal
true or false: binary fission is a type of unequal cell division
false, it’s the equal cell division process
3 different unequal cell division methods
- simple budding
- hyphal budding
- stalked cell division
budding cell division
unequal cell growth
forms 2 different products
clear “mother” and “daughter”
hyphal cell division
growth in long, thin filaments
gram + filamentous bacteria
stalked cell division
cell differentiates into non-motile
releases motile daughter cell
senescence
loss of a cell’s power of division and growth
caulobacter reproduction
stalked
gram - a-proteobacteria exhibit great…… in cell division forms
diversity
lateral elongation
grows from inside out
polar elongation
grows from ends
bacillus division
binary fission
streptomyces division
hyphal
how does binary fission work
proteins localize to poles + septum to guide elongation
how does hyphal growth work
proteins localize to the tip to guide elongation
how does stalked growth work
proteins localize to flagellar pole (old division site) which turns into a stalk n grows
divisome complex
consists of >20 proteins + FtsZ
constricts inner/outer membranes
synthesizes peptidoglycan @ division site
MinCDE complex
forms pole-to-pole oscillating system that pushes Z-ring formation to midcell
(inhibits FtsZ at poles)
Nucleoid Occulusion
works w/MinCDE complex to ensure good spatial + temporal regulation of chromosome segregation
prevents chromosome from being cut in half by division septum
elongasome
complex regulating + coordinating cell elongation
MreB
homolog of eukaryotic actin
forms linear filaments to help traffic protein complexes throughout the cell
MreB filaments run…… around the cell
latitudinally
RodZ
connects MreB to the rest of the elongasome
helps guide PBP around the cell to break/reform peptide crosslinks to make peptidoglycan
PBP
penicillin binding proteins
MreB and RodZ are found in……shaped cells
bacilli
deletion of MreB/RodZ genes results in……..
cocci
MreB and RodZ contribute to the…….shape
bacilli (rod)
true or false: in rods, elongation is occurring at one site probs at a pole
FALSE, is occurring at multiple sites within a cell
cocci cells lack…… which means elongation only happens in one location
MreB and RodZ
in cocci cells, elongation occurs at one site next to the……
FtsZ ring
caulobacter shape
kinda like crescents
caulobacter shape is due to…….
the localization of cresentin (protein) that is concentrated on one side of the cell
cresentin forms a rigid filament which limits growth on that side of the cell
features that allow prokaryotes to constantly replicate genes
no membrane-bound organelles
no nucleus
smaller, circular genomes
no mitosis/meiosis
main chromosomes vs. plasmids
main: where all essential genomic info is
plasmids: accessory info/extrachromosomal
bacteria and arches generally have……. shaped chromosomes
circular
microbial chromosomes are “streamlined,” meaning
less intergenic space, smaller regulatory regions than larger counterparts
in viruses and prokaryotes, the number of protein coding genes increases……. with genome size
linearly
in eukaryotes, genome size increases……of the number of protein coding genes
independent
prokaryotic genes are clustered in……
operons
operons
transcriptional unit of multiple genes that will be transcribed on a single mRNA
microbes can maintain……
plasmids
plasmids
extrachromosomal DNA that can be shared between bacteria sexually
annotation
the description of genomic features
4 main features described by annotation
origin/ terminus or replication
location of genes/ ORF
identification of gene products
location of mobile elements
ORF
open reading frames
circular bacterial genomes are replicated……
bidirectionally
how many origins/termini of replication
1 and 1
bacteria can maintain multiple……, allowing cell division to accur faster than genome replication
replication forks
in high nutrient environments, bacterial genomes are replicating more……. and are functionally……
frequently; polyploid
genes closer to oriC will be in……copy numbers than genes closer to ter
higher
3 distinct phases during Slow Growth
cell Birth = B
Chromosome replication = C
cell Division = D
cell birth phase
between end of cell division and beginning of replication
DNA replication phase
“prokaryotic S-Phase”
cell division
chromosomes are partitioned and prokaryotic cell divides
during fast growth, cell cycle phases……
overlap
3 Main Parts of DNA replication (in slow and fast growth)
Initiation
Elongation
Termination
read depth
number of sequencing reads you have that map to a specific section of the genome
replication can be visualized with…….
in situ hybridization
fluorescent marker to the ori is the color…..
green
fluorescent marker to the ter is the color…..
purple
how is replication initiated?
binding of DnaA-ATP to DnaA boxes within oriC
GATC motifs
contained in DnaA box
targets of adenine methylation
immediately after replication, GATC motifs are……
hemi-mylated
GATC are then semi-mylated until….
the enzyme dam methylase is able to methylate the new DNA strand
methylation of the new DNA strand (by dam methylase) activates……
transcription of dnaA
once the replication moves past oriC, DNA is again……
hemi-methylated
when DNA is semi-methylated, dnaA expression is……and replication is……
repressed
paused
SeqA
ori sequestration protein
with ongoing replication and multiple ori’s, it takes…… for a critical number of DnaA-ATP to bind to dnaA boxes
longer
prokaryotic primase
DnaG
prokaryotic helices
DnaB
prokaryotic polymerase for both strands
Pol III
prokaryotic dimerization subunit
Tau (DnaX)
…….. antibiotics interfere with DNA replication
quinolone
quinolones get their name from their…..
quinolone-like backbone
quinolones interfere with……topoisomerases like
DNA gyrase
DNA gyrase
runs ahead of replication machinary
cuts into DNA double strands,
unwinding strands to relieve supercoil
re-ligating the double strands back together
how do quinolone’s interfere w/replication
bind to DNA gyrase after the cut is made,
preventing DNA gyrase from repairing the cut
replication machinery then collides with stalled gyrase, results in cell death
MIC
Minimum Inhibitory Concentration
minimum concentration needed of drug to inhibit bacterial growth
E. coli has how many DNA polymerases?
5
e.coli dna polymerases vary based on….and….
number of subunits
exonuclease function
the main replicative polymerase
dna Pol III
DNA pol I
single subunit
gap fills Okazaki fragments
DNA pol II
single subunit
backs up Pol III subunit a
restarts replication at stalled forks
DNA Pol III
elongates DNA
DNA Pol IV and V
error prone polymerases
help bypass lesions from DNA damage
SOS response
job is to lay down nucleotides and prevent cell death
ter
= terminus of replication
location where replication forks converge
replication fork traps
terA-terJ
allow replication fork to enter but not leave
prevent collision and regulate termination
replication forks are trapped by….
binding of Tus proteins to the multiple ter loci
the shape of Tus allows the fork to…..
pass in one direction but not the other
replication forks meet in middle of Tus proteins and are decatenated in order to…..
segregate into daughter cells during cell division
chromosome segregation
required so daughter cell gets copy of genome
required for septum formation
Par system
partitioning system
in many bacteria,
distributes decatenated chromosomes and plasmids equally
nucleotide content is…… between the leading strand and lagging strand
asymmetric
leading strand biased toward…….and…….
guanine
thymine
lagging strand biased toward……and…..
adenine
cytosine
location of oriC and terC can be estimated by…..
GC skew
oriC: skew changes from…to..
C to G
up to down
terC: skew changes from…to…
G to C
down to up
Mutational Theory
cytosine is not preferred in leading strain because of spontaneous deamination of C—> T
coding strand is single stranded more often than template strand = thus vulnerable to C—>T mutation
Codon Bias Theory
in prokaryotes, G is more common in the +3 (wobble) position of codons than C
this results in more G’s on the leading strand
