Exam 3 Flashcards
- regulates the expression of a structural gene
- does not encode RNA or protein
- includes promoters and binding sites for regulatory proteins
DNA control sequence
- all the genetic information that defines an organism
- consists of one (usually) or more DNA chromosomes
genome
made up of contiguous packets of information called genes
chromosomes
produces a functional RNA, which usually encodes a protein
structural gene
- identifies conserved sequences
- the consensus sequence for sigma-70 promoters is called
the -10/-35 box
- subunit that directs RNA pol to different genes as needed to initiate transcription
- dissociates
sigma factors
always transcribing (s70 in E. coli)
housekeeping sigmas
recognize different promoters
specialized sigma factors
recognize promoters for genes that encode nitrogen metabolism and other functions
sigma 54
recognize promoters for genes that are heat shock-induced
sigma 32
recognize promoters for genes that encode motility and chemotaxis
sigma 28
recognize promoters for genes that encode stationary-phase and stress responses
sigma 38
what is the function of the omega subunit of the RNA polymerase holoenzyme
helps to protect the integriity of the complex in stressful situations
act as scaffolding proteins in the RNA polymerase holoenzyme
alpha 1 and alpha 2
what is the function of the Beta (and Beta prime) subunits of the RNA polymerase holoenzyme
catalyzes the synthesis of RNA
when the sigma factor is bound to the core enzyme, the six-subunit complex is termed
the RNA polymerase holoenzyme
RNA polymerase DNA and lays down a complementary and antiparallel strand of RNA
transcription
stages of transcription
- initiation
- elongation
- termination
RNA transciption begins at which nucleotide
+1
in bacteria, a gene can operate independently or in tandem with other genes in
an operon
1 gene under control of a single promoter
monocistronic RNA
more than one gene under control of a single promoter
polycistronic RNA
occurs when a bacteriophage accidentally packages a fragment of host cell DNA
transduction
steps to transduction
- P22 phage DNA infects a host cell and makes subunit components for more phage
- DNA is packaged into capsid heads, some capsids package host DNA
- new phage assembly is completed
- cell lyses; phage is released
- transducing phage particle injects host DNA into new cell, where it may recombine into the chromosome; recombination crossover events exchange host DNA for donor DNA
what genome characteristics would be useful for computationally identifying genes acquired by HGT
- guanine-cytosine content
- codon usage
benefits of fast replication of bacteria
- competitive advantage
- rapid evolution
- rapid colonization
- biofilm formation
- survival under stress and changing conditions
what features enable prokaryotes to replicate rather quickly
- small genomes that contain only essential genes
- genes lack introns
- only short control sequences between genes (high gene density)
- form when an integrated F plasmid is inaccurately excised from the genome
- some host cell DNA is excised and ends up on the plasmid
F’ plasmid
what happens when the F’ plasmid conjugates
sends host cell DNA to recipient
- the F factor loops out of the chromosome with thr and leu genes in the loop
- a crossover excises the F factor carrying the thr and leu genes, producing an F’ thr leu
can transfer chromosomal genes between cells
integration of the F- plasmid
which type of genome has a lot less non-coding DNA
bacterial genomes
methods of gene transfer
- vertical gene transfer
- horizontal gene transfer
- allows the introduction of new genes into an organism that may be of selective advantage
- segments of DNA can move between bacteria
horizontal gene transfer
the introduction of extracellular DNA directly into an organism
transformation
cells express machinery for DNA uptake (proteins are encoded in the genome)
natural competence
researchers make cells competent through electrical or chemical manipulation
induced/artifical competence
the transfer of DNA from cell to cell via direct contact/sex pilus formation
conjugation
steps to conjugation
- the F+ plasmid donor extends the sex pilus component of its T4SS, making contact with the F- recipient cell
- contraction of the pilus draws the two cells together. Relaxase unwinds the DNA at oriT; a second relaxase is recruited to this bubble
- one strand of the F factor is nicked at the nic site in oriT. one relaxase attaches to the 5’ end of the nicked strand and trasnfers it through teh T4SSS. the other relaxase remains in the donor and unwinds the DNA
- the strand remaining in the donor replicates by DNA pol III
- once in the recipient, the transferred strand circularizes and replicates by DNA pol III
- the recipient has been converted to a donor
the sequential addition of ribonucleotides
elongation
relies on a protein called rho and a strong pause site at the 3’ end of the gene
Rho-dependent transcription termination
requires a GC-rich region of RNA, as well as 4-8 consecutive U residues (terminator haripin loop and RNA being built)
Rho-independent transcription termination
functions as ATPase and RNA-DNA helicase activity
Rho
steps to rho-dependent termination
- Rho binds to C-rich regions
- Rho is threaded through Rho hexamer, pulling Rho toward RNA polymerase
- contact between Rho and RNA polymerase causes termination
contact between hairpin, NusA protein, and RNA polymerase cause termination
Rho-independent termination
70S
prokaryotic ribosome
80S
eukaryotic ribosome
happens at ribosomes
translation
match amino acids to mRNA
tRNAs
amino acids are linked to this region of tRNA through charging
acceptor end
when is translation initiated in bacteria
when the 16S rRNA recognizes the Shine-Dalgarno sequence
AGGAGG at the 5’ end of bacterial mRNA; positions the start codoon into catalytic site for translation
Shine-Dalgarno sequence
how do eukaryotes initiate translation
through recognition of the 5’ cap and start codon
what happens in eukaryotes vs prokaryotes if there is a start codon mutation
- eukaryotes: keeps scanning
- prokaryotes: ribosome gets stuck and translation does not begin
after inititation, the ribosome moves along the RNA until
it reaches a stop codon
what prevents the degradation of mRNA in prokaryotes
coupling of transcription and translation
have multiple Shine-Dalgarno sequences
polycistronic mRNAs
accepts the incoming aminoacyl-tRNA
A site of ribosome
holds the tRNA with the peptide attached, which is to be transferred to the new amino acid residue in the course of the peptidyltransferase reaction
P site of ribosome
which type of control system is most efficient in resource usse
transcriptional control
which type of genomic control is fastest
post-translational
bind DNA near the promoter, affects transcription
regulatory proteins
DNA sequences recognized by regulatory proteins
sequence motifs
what is the effect of an activator on transcription
increases transcription (positive regulation)
what is the effect of a repressor on transcription
decreases transcription (negative regulation)
protein binds to DNA, assisting binding of RNAP
activator
protein binds to DNA, blocking RNAP
repressor
effects on transcription when the activator binding site is occupied
increases transcription
effects on transcription when the operator is occupied
decreases transcription
DNA sequence bound by activator
activator binding site
DNA sequence bound by repressor
operator
small molecules that bind to regulator proteins to modify their activity; help regulatory proteins to modify their activity
effectors
enable activators or disable repressors
inducers/coactivators
enable repressors or disable activators
corepressors
what type of operon utilzes corepressors
repressible operons
decreases transcription when present
what type of operon utilizes inducers/coactivators
inducible operons
increase transcription when present
true or false:
gene transcription is all or nothing: off is zero
false
located in E. coli genome, encodes the proteins needed to catabolize lactose
Lac operon
- plays as an inducer
- breaks lactose into monosaccharides
- encoded by LacZ
B-Galactosidase
- brings lactose into cell, transport protein
- encoded by LacY
lactose permease
- moves acetyl group
- not really understood
- encoded by LacA
thiogalactoside transacetylase
encodes Lac repressor
LacI
compared to the eukaryal genome, the bacterial genome
contains a larger percent of DNA that encodes for functional proteins
characteristics of HGT
- transduction, conjugation, transformation
- genes from one independent mature organsim transferred to another mature organism
Suppose a microbe has died and lysed, exposing its DNA to the environment. Some of this DNA was taken up by another unrelated microbe and incorporated into its genome. This is an example of which process(es)?
transformation (HGT)
carries genes responsible for formation of sex pili, has several insertion elements to assist plasmid integration into host cell’s chromosome
F plasmid
following an F+ x F- mating, the donor is … and the recipient is …
F+, F+
the order of gene transfer in a completed Hfr x F- mating is best represented by
part of the plasmid followed by the chromosome followed by the rest of the plasmid
suppose a strain of E. coli is identified as an Hfr strain. In a conjugal experiment between the donor Hfr strain and a recipient E. coli strain that is F-, what would you expect to result
the recipient to remain F-
an Hfr cell and an F- cell result from conjugation between a donor cell and a recipient cell. which statements are true regarding this event
- donor could have been Hfr
- recipient could have been F-
if a segment of RNA reads 5’ GCCUUAA 3’, then the corresponding DNA template strand reads
5’ TTAAGGC 3’
in the language of nucleic acids, sequences that are complementary…
have matching nucleotides, A with T or U and G with C
when compared to a template strand of DNA, the corresponding RNA strand is
complementary
the mRNA of bacterial cells is often polycistronic. what does this term mean?
it contains the code for multiple peptides
which statement best describes the process of prokaryotic transcription initiation
sigma factor directs RNA polymerase to the promote by binding the -10 and -35 regions
the sigma factor is directly required for
transcription initiation
in E. coli, why is sigma-70 considered the “housekeeping” sigma factor
it keeps essential gnes and pathways operating
a Rho-independent terminator
is a hairpin loop structure that forms in RNA
the termination of transcription can be caused by which of the following
- stem-loop structure and NusA
- Rho factor
what is common to both rho-dependent and rho-independent transcription termination
both types of termination occur following a pause by the polymerase
the 30S and 50S ribosomal subunits are so designated to indicate
their sedimentation rate in a centrifuge
three bases on the mRNA that is read by the ribosome in the 5’ to 3’ direction
codon
a mutation occurs upstream of gene A in the region encoding the ribosome binding site. predict how this mutation will impact the levels of mRNA and protein preduced for gene A
mRNA levels will remain constant, proteins will decrease
the ability of Vibrio fischeri to produce bioluminescence chemicals only when a certain population density has been reached relies on control of the lux operon, which is regulated by
positive control by an activator protein
upon reorienting after a tumble, an E. coli cell
points in a random direction
an E. coli strain is mutated such that it can only rotate its flagellum in the counterclockwise direction. therefore, this strain moves in what manner
runs only
motile bacteria have been placed in an environment with a gradient of a chemical attractant. which of the following behaviors would you predict
the bacteria will both reduce tumbling frequency and increase run duration in the direction of the chemical
In E. coli, chemotaxis signaling relies on Che proteins. In response to an attractant, which of the following ultimately results in a run
decreased phosphorylation of CheA
what is the role of CheR in the E. coli positive chemotaxis pathway
adaptation; methylates and desensitizes the chemoreceptor to the attractant
what parts of a virus are always found in every virus
- nucleic acid
- capsid
what is the viral capsid composed of
protein
how big are most viruses compared to the cells they infect
much smaller–between 10-100nm
steps to viral replication
- bind receptor on host cell
- viral particle enters host cell
- uncoating viral particle to make genetic material accessible
- replication of viral genetic material
- assembly of mature viral particles
- exit out of host cell
the range of cell types that can serve as host for viral infection
host range
a specific animal virus always infects
the number of species depends on the virus
what determines host range?
receptor on cell surface
compared with cellular genomes, viral genomes
are smaller, with fewer base pairs
viral genomes may comprise
ds/ssDNA or ds/ssRNA
compared with cells that are surrounded by a lipid membrane, viruses
may be surrounded by a membrane derived from the host cell
a non-enveloped virus will have its attachment proteins present in its
capsid
how can the seven Baltimore classes of viruses be distinguished from one another
- nucleic acid usage (DNA vs RNA)
- ss or ds
- utilization of reverse transcriptase
- positive or negative sense
which viral genome can be immediately translated upon entry into the host cell
positive-sense RNA
which enzyme is utilized by a human host for genome replication
DNA dependent DNA polymerase
which enzyme is utilized by a human host for transcription
DNA dependent RNA polymerase
in which subcellular compartment would you expect to find human polymerases
nucleus
adenoviruses are a family of Baltimore Group I viruses that cause the common cold in humans. based on this, which description best fits the Adenovirus family
double stranded DNA virus using DNA polymerase to replicate
what enzyme do “typical” group 1 viruses that enter the host nucleus use to replicate their genome
host encoded DNA dependent DNA polymerase
members of the poxviridae family are atypical Group I viruses that replicate and transcribe their genome through the use of
- virus encoded DNA-dependent RNA polymerase
- virus encoded DNA-dependent DNA polymerase
reoviruses are a family of Baltimore Group III viruses that cause diarrheal disease in infants. based on this, which description best fits the reovirus family
dsRNA viruses using an RNA polymerases to replicate
a viral genome contains 5% adenine, 25% thymine, 29% guanine, and 41% cytosine. thus, this virus belongs to Baltimore Group …
2
when a group IV virus infects a human cell, many copies of its genome are produced and packaged into new virions. what type of molecule is used as a template for the production of many genome copies
dsDNA
what type of enzyme is carried in the capsid of Group V
RNA dependent RNA polymerase
HIV uses a viral enzyme called reverse transcriptase to synthesize DNA for integration into the host genome. what is another name for HIV viral reverse transcriptase
RNA dependent DNA polymerase
which enzyme transcribes the integrated HIV genome to make mRNA
host RNA polymerase
there are fewer antivirals currently available in most pharmacies than there are antibacterials because
selective toxicity is much easier to achieve for bacteria
true or false:
unlike bacteria, viruses do not develop resistance to antiviral drugs
false
the Lac operon is regulated by a negative inducible system that responds to …
allolactose
the lac operon is regulated by a positive inducible that responds to
glucose
what is the relationship between cAMP and glucose concentration
inversely proportional
less glucose = more cAMP
what happens to the phosphotransferase system when glucose is present
PTS blocks lactose uptake
inducer exclusion
what happens in the PTS in the absence of glucose
phosphorylated IIA accumulates and LacY is free to transport lactose
what happens in the presence of glucose in the PTS (steps)
- glucose moves from protein IIC to IIB, wich transfers a phosphate from IIA to glucose
- unphosphorylated IIA(Glc) inhibits lacY
inducer exclusion
what happens during the first log phase of the dilauxic growth curve
- glucose is utilized – intracellular cAMP low
- intracellular allolactose low
- lac repressor bound to operator
what happens in the second log phase of the dilauxic growth curve
- lac repressor bound to inducer
- crp activator bound to coactivator and activator bound to ABS
- transcription of lac operon occurring at high levels
codes for enzymes needed to synthesize tryptophan
Trp operon
which stem loop terminates transcription
3:4
transcription is regulated at which levels
intitiation (repressor) and elongation (attenuation)
steps to what occurs in the trp operon in high tryptophan environments
- ribosome translates through trp operons and encounters translation stop codon
- ribosome stops covering mRNA regions 1 and 2. polymerase continues to transcribe regions 3 and 4. the 3:4 termination loop forms
- the 3:4 loop binds RNA polymerase and causes its release before reaching trpE
what happens in the trp operon when there are low levels of tryptophan
- ribosome initiates leader
- scarce trp tRNA makes ribosome stall at trp codons. polymerase continues through attenuator
- stalled ribosome covers region 1, allowing 2:3 stem loop to form. the less energetically favorable 3:4 transcription terminator loop cannot form
- polymerase transcribes trpE
coordinates gene expression within a dense population
quorum sensing
percent of population that needs to have immunity to prevent the spread of disease
herd immunity
factors that play a role in herd immunity
- how easily the disease is spread
- population density
- vaccine efficiency
- provide your body with instructions for making pathogen proteins
- a vaccine that uses a viral vector to deliver genetic material that can be transcribed by the recipient’s host cells as mRNA coding for a desired protein, or antigen, to elicit an immune response
viral vector vaccines
a type of vaccine that uses a copy of a molecule called messenger RNA to produce an immune response
mRNA vaccines
vaccines derived from one or more components, such as capsid subunit proteins produced by engineered industrial bacteria
subunit vaccines
ex: HPV, Shingles
how are inactivated vaccines typically produced
virulent microbe is inactivated by chemicals or irradiation
how are attenuated vaccines produced
virulent microbe grown under adverse conditions or passed through differenjt hosts until avirulent
are inactivated or attenuated vaccines more stable
inactivated vaccines are more stable
is the immune response stronger in an attenuated or inactivated vaccine
attenuated vaccine
reverts to a virulent form; common in attenuated vaccines
reversion tendency
a live virus was weakened by procedures such as heat treatment or by mutation
attenuated vaccine
memory cell formation steps
- apcs engulf pathogens at sites of infection
- apcs present antigens on their surface on their surface and more into regional lymph nodes
- in the lymph node, free antigens interact with B cells, APCss engage T cells; activated B cells differentiated into plasma cells and memory cells; CTL cells. are activated
- plasma cells, memory cells, and CTLs leave the lymph node and enter the circulation
- plasma cells and memory cells enter bone marrow, CTLs migrate to infection site
a virus coated with what cannot attach to host cells
neutralizing antibodies
activates lux transcription
luxR
steps to autoinducer Acyl-homoserine synthesis
- the LuxI protein synthesizes an acyl homoserine lactone autoinducer (AI)
- AI diffuses into medium and accumulates
- at threshold concentration, AI diffuses into cell and binds LuxR, which activates lux transcription
chemotaxis is regulated by
post translational protein modification
alternating runs and tumbles result in
no directed movement
when flagella rotate in one direction, what occurs
straight line movement occurs
counterclockwise movement =
run
clockwise movement =
tumble
what happens when flagella change their direction of rotation
cell tumbles and randomly changes direction
prolonged runs can move a bacterium
toward or away from a chemical
initiated by chemoreceptor membrane proteins that detect chemicals in the environment
chemotaxis
chemotaxis signaling relies on
PT regulation of Che proteins
what type of movement is favored in the presence of an attractant
runs
how can chemorecptors be desensitized?
via methylation
methylates MCP
CheR
sensor kinase, autophosphorylates itself and phosphorylates both CheY and CheB
CheA
response regulator; controls direction of flagellar rotation
CheY
response regulator; demethylates MCP
CheB
dephosphorylates CheY-P
CheZ
involved in transduction of signal from MCP to CheA
CheW
- small infectious agents that use host cell machinery to replicate
- no organelles, no cytoplasm, no ribosomes
viruses
complete infective form of a virus
virion
a virion always contains which components
- covering (capsid)
- central core (nucleic acid)
cannot reproduce outside their host cell, meaning that the parasite’s reproduction is entirely reliant on intracellular resources
intracellular obligate parasites
how are viruses classified
via their genomes
characteristics of viral genomes
- 1K to 200K+ bases
- can be linear or circular
- can be a single molecule or segmented
the ability of a virus to infect a particular cell, tissue, or host species
viral tropism
recognizes viruses based on genome structure and replication strategy
Baltimore Classification System
dsDNA viruses
group I viruses
ssDNA viruses
group II viruses
dsRNA viruses
group III viruses
+ssRNA viruses
group IV viruses
-ssRNA viruses
group V viruses
RNA reverse transcribing viruses (retroviruses)
group VI viruses
DNA reverse-transcribing viruses (pararetroviruses)
group VII viruses
give virions their shape
capsid
steps to foreign invaders triggering an adaptive immune response
- APCs engulf microbes at the site of infection, digest them, and present antigens on the AP surface
- free-floating antigens form the microbe bind to B cell receptors
- T cell-independent antigens trigger B cell differentiation into plasma cells
- plasma cells secrete antibodies
- APCs present antigens to helper T cells and cytotoxic T cells
- Tc cell becomes an activated cytotoxic lymphocyte (CTL)
- CTL circulates, finds, and destroys infected host cells
- some helper T cells help B cells respond to T cell-dependent antigens OR other helper T cells help Tc cells become CTLs
methods of viral evolution
- mutation
- recombination
- reassortment
through reassortment of gene segments from very different strains
antigenic shift
- when multiple viruses with segmented genomes infect the same cell, they can swap segments in newly formed viruses
reassortment
fusion of pieces of two separate viral genomes to create a new hybrid genome
recombination
the gradual accumulation of mutations
antigenic drift
viral polymerases lack
proofreading capability
mutation rate is particularly high for
RNA dependent RNA polymerase
why are antiviral drugs difficult to develop
- antibiotics work b/c they target bacterial structures viruses don’t have
- viruses use host cell machinery
- few targets are unique to the virus
- typically narrow spectrum
- lack or reliable animal models
- resistance develops very quickly
why is the principle of selective toxicity complicated when targeting viruses
viruses use host cell machinery, and if you inhibit a host cell process, toxicity will be high
make DNA from their RNA genome; use reverse transcriptase
group VI retroviruses
HIV
carry viral polymerase in with their antisense genome
group 5 -ssRNA viruses
ebola, influenza, measles, mumps, rabies
carry mRNA into the cell
group 4 +ssRNA viruses
Coronaviruses, Flaviviruses, Poliovirus
types of viral capsids
- filamentous/helical
- tailed
- icosahedral
- asymmetrical
if a plasma membrane surrounds the capsid, the virus is
enveloped
how are viral envelopes acquired
from host cell membranes with viral proteins
steps to the viral replication cycle
- attachment (to host cell)
- entry and uncoating of genome
- genome expression and protein production
- genome replication
- assembly of new viral particles
- exits host cell
what does a successful virus need to be able to intitate infection
adhere to a host cell
true or false:
host cell receptors vary between species
true
what is the most important determinant of tropism
interaction between surface proteins and host cell receptors
how do viruses enter the cell and release its genome
- envelope fusion with the cell membrane
- receptor-mediated endocytosis
enzymes that are used for genome replication and transcription
- DNA dependent DNA polymerase (I)
- DNA dependent RNA polymerase (IV)
- RNA dependent RNA polymerase (V)
- RNA dependent DNA polymerase (VI)
usually access the host nucleus and use host polymerases
typical group I viruses
Epstein Barr, Herpes Simplex, Varicella Zoster, HPV
