Midterm 3 Flashcards
why do viruses want to go into a host?
it wants to replicate. thats it and in the case of humans the best way it can do that is by being passed on to more hosts.
its mindless
history of virus?
viral diseases have plagued humans since before we knew what they were – evidence for small pox in egypt
1800s we discovered viruses
walter reed
showed in 1901 that a human disease, yellow fever, was caused by a virus transmitted by a mosquito
viruses are defined as ______
intracellular obligate parasites
size of a virus
10 to 100 nm in size
can only see with electron microscope
viral genome has ____ nucleotides
a few thousand to 200,000 nucleotides in length
Sizes of viruses
HIV has 9200 bp for 9 genes
SARs-CoV-2 has 30000 bp which is large for a RNA virus
t or f viruses can be single or double stranded DNA or RNA
true
capsid
protein shell around genome composed of capsomere proteins
nucleocapsid
capsid and genome together
do all viruses have an envelope?
no! if they don’t they’re considered naked. an envelope is basically just a plasma membrane derived structure around capsid
shape of viruses
symmetry. tldr we have helical, polyhedral, and complex
capsids often exhibit either helical or polyhedral (iscosahedral = 20 triangular faces) shapes
can also have complex shapes. for example flu has 8 nucleocapsid structures
complex virus
bacteriophage head contains genome with elaborate tail structure
virion
viral particles that are infectious but they are metabolically inert
is a virus dead or alive?
depends on your definition of life!
replication cycle of a virus
attachment- stick on to host cell
entry (penetration/uncoating) - get into the cell and release genome
biosynthesis- replicate its genome and express its genes to make proteins
assembly- put everything together
exit- get the new virus particles out
coevolution
viruses orginated before the last universal common ancestor (LUCA), during the RNA world period and evolved along with their host cells.
descendents of the original RNA replicators in this view
no RNA viruses are known to infect any member of archaea AND some have proposed retroviruses as a case for transition from RNA world to DNA world BUT they only effect plants and animals so not really good enough
little evidence that this is true
regressive hypothesis
viruses are cells that lost some of the replicative and metabolic traits over time
doesnt adequately explain the origins of RNA viruses.
Giant DNA viruses are often cited as examples to support this hypothesis
example of regression is a tapeworm. used to be a real worm now he a creep
progressive hypothesis
most people prob think this is the way it happens
existing genetic elements gradually gained the ability to move from cell to cell
evidence in the form of transposons (for DNA viruses) and retrotransposons (for retroviruses)
how can we grow and quantify viruses?
bacteriophages –> add agar and then put on a nutrient agar base
animal viruses –> have to work with tissue culture of host cells to do viral cultivation.
what do we use for virus identifcation?
electron microscopy
nucleic acid analysis through pcr and reverse pcr
what is one thing that viruses always need the host cell for?
protein synthesis
bacteriophages
viruses that infect bacteria!
almost all have double stranded dna
almost always have complex morphology
most widely studied are viruses of e coli including t-even phages and phage lambda
bacteriophages have _____
double stranded dna most of the time
lytic cycle
a phage causes the lysis and death of its host bacterium as it replicates
example t even phages
lysogenic cycle
a phage incorporates its nucleic acid into thehost cell chromosme and remains dormant for a period of time
example temperate phages
stages of lytic cycle
attachment- sites on bacterophage tail fibers attach to receptor sites on bacterium
penetration- the tail sheath contracts to force the tail core through the cell wall, and phage DNA enters the cell
biosynthesis- transcription, translaton, and replication of viral DNA occurs
maturation- new phage DNA and capsids are assembled into virions
release - phage lysozyme destroys the cell wall, the cell bursts, and the new virions are released
stages of lysogenic
attachment/penetration - same as lytic cycle
viral dna recombines with the bacterial chromosome to form a prophage
the prophage replicates with the bacterial dna and will continue to do so until something triggers it to excise itself it then continues with the steps of the lytic cycle
t or f retroviruses never do the lysogenic cycle
true
how do viruses recognize appropriate cells?
each virus has a specific range/type of cells that it can infect
the possible range is dictated by the interaction between viral attachment proteins and host cell receptor molecules
host cell receptors are often molecules critical for the cellular function
can viruses get through the plant wall?
not really so plant viruses depend on damage to the plant tissues to find an open spot in the cell wall
damage can include: insects feeding on plants wind damage hail/rain damage fire damage human-induced damage
can cross kingdom viruses happen? like can plant viruses infect a human
NO
receptors arent the same
where are viral receptors in plant cells?
inside the cell
define uncoating
genome release
evens out animal viruses and bacteriophages
how are viruses grouped?
the way they get to the mRNA phase
DNA Viruses
usually carry their genome as dsDNA (exceptions exist)
example herpes virus.
Double stranded DNA viral life cycle
DNA travels to the nucleus
early genes are transcribed and subsequently translated creating viral enzymes necessary for later steps
late genes are trancsribed and viral dna is replicated
late translation synthesizes capsid proteins
capsid proteins migrate into the nucleus where maturation occurs
release of viral particles occurs through the endoplasmic reticulum via budding and does not need to kill the cell
herpesvirus is class _
I
Class I
basically makes mrna the way humans do
dsDNA –> mRNA
poxviruses
atypical dna virus
they do not use the host cell nucelus or the host cells dna or rna polymerase. brings its own rna polymerase to the party. difference between encoding and bringing! early genes has dna polymerase.
ex. smallpox
CHICKEN POX ISNT A POX VIRUS
in dna + strand is _____
coding “sense” strand; shares the same sequence as the mRNA
in dna the - strand is ____
template or “antisense” strand which is complementary to the mRNA
in rna the + sense strand _____
is the mrna or at least is able to function that way
in rna the - sense strand ______
complementary to the + strand ad usually only exists to act as a template to make + strands
rna viruses carry their genome as _______
+ or - RNA
do we need the whole virus to infect the cell?
No!
which “baltimore classes” are picornaviridae ?
Class IV which is single stranded RNA virus + used directly as the genome
which baltimore class are rhabdoviridae
Class V which is single stranded RNA virus - sense. transcribe the minus strand into + mrna
retroviral life cycle
+ single stranded RNA genome
they contain a reverse transcriptase which is RNA-dependent DNA polymerase
single strand + serves as a template to make dsDNA which migrates to the nucleus
The DNA integrates into a host cell chromosome and is now called a provirus
provirus
when viral dna integrates into the host cell chromosome
NEVER LEAVES THE DNA
t or f provirus never leaves the DNA
t
proviruses can be ____
transcribed and the + strands are translated into viral proteins including reverse transcriptase and the + strands also act as the genome to make new virions.
similarities and differences between retroviruses and bacteriophage
lambda leaves when cell dies and progeny go to the surrounding cell
provirus from retrovirus cannot do that^^^
unlike lambda retroviruses have a random insertion point
difference bw bacteria and human being
integrase
integrates dna into host cell
HIV is class ____
VI retrovirus reverse transcriptase takes single stranded positive sense RNA and turns it into double stranded DNA
coronavirus is class ___
IV single stranded positive sense RNA translated straight into protein
egress
exit from cell
mechanisms depends on virus type and host cell type
enveloped viruses plant viral proteins in the host cell plasma membrane, dock to them, and bud
t or f provirus can never leave dna
t
what happens to the provirus?
it can be transcribed and the + strand (mRNA) will be translated into viral proteins including reverse transcriptase and then the + strand can also act as the genome to make new virions so the virus can replicate without the provirus excising itself
T or F HIV is enveloped
t
HIV carries ____ copies of RNA, poliovirus only carries ______
2;1
T or F HIV can pass on its genes through vertical gene transfer
F
herpesvirus and poxvirus are class _
I
picornavirus is class
IV
rhabdovirus is class
V
coronavirus is class
IV
poliovirus is class
IV
viral self assembly
once proteins are translated the viral components translate themselves fast and cheaply
the capsid proteins may interact with packaging sequences on viral genome to coalesce around nucleic acid (tobacco mosaic virus)
empty capsids may partially form and then viral genomes insert into them (poliovirus)
with respect to the spike proteins where do they come from and where do they go?
any protein that is made from virus or you has to be made on rough ER/ribosome and then it follows secretory pathway to the host cell plasma membrane. they dock there and wait for the nucleocapsid to come to the surface and become enveloped
naked viruses exit by _______
lysing the cell
how do plant viruses move from cell to cell w/in one plant?
the plasmodesmata (cytoplasmic connections)
how do plant viruses move from one plant to another?
disruption of cell wall structure (often by insects)
SARS CoV 2
coronavirus hooks onto receptor, fuses, and then uncoats. single stranded + RNA, translated
creates new genomic RNA. the spike proteins are being exprssed on the insisde of the cell not outside and it is on the inside of the ER.
covid gets its membrane from the
ER
HIV gets its membrane from the
plasma membrane
covid is in group ____
IV
covid is different from polio bc
it has an envelope
conflict of interest
genome of virus has conflict of interest with the genome of the bacterial host
conflict is played out thorugh the vehicles that each genome creates – the virion and the bacterial cell
occurs when the replication of one genome occurs at he expense of the other genome
confluence of interest
when phage lambda inserts itself into its host cell genome. every time the host cell chromosome replicates, automatically, the viral dna also replicates
the virus in this case has no reason to harm the host cell
t or f infection with lambda confers immunity on the host cell from infection by other phages
t
where would a retrovirus have to integrate in order to establish a confluence of interest with human beings?
in the germline
evidence: junk dna endogenous retroviruses = 8%
professor says that bacteria ALWAYS produce ___
asexually
he doesnt classify horizontal gene transfer as sexual
fertilization
n + n –> 2n
recombination
how bacterial cells transfer DNA through the
incorporation of foreign DNA into the host cells chromosomes
Homologous recombination
occurs when two identical or nearly identical fragments of DNA line up and exchange pieces
(mediated by enzymes RecBCD and Rec A in ecoli)
enzyme necessary to homologous recombination
Rec A
single stranded dna binding protein
what can happen in homologous recombination?
type of molecule determines outcome:
single crossover of two circular molecules = integration
double crossover of two circular moleucles = DNA swap
double crossover of circular and linear molecule = DNA swap
what results in integration
single crossover of two circular molecules
what results in DNA swap
double crossover of two circular molecules
OR
double crossover of circular and linear molecules
Non homologous recombination
recombination of dna pieces with little to no simialrity
occurs in all forms of life but especially in viruses and transposable elements
temperate bacteriophages undergo lysogeny by site specific recombination, inserting their genome at particular points in the host cell DNA sequence. this requires integrase
what do we need for non homologous recombination
integrase
horizontal transfer
always donor and recipient
transformation
intro of extracellular dna directly into an org (uptake usually)
doesnt require cell to cell contact
some bacteria are naturally competent for transformation
others can be artifically induced with calcium cations
an electric pulse can also be used to create temporary holes in the plasma membrane (electroporation)
griffiths
strep experiments that proved that dna wasnt pathogenic
dna translocase
takes dna from outside cell and brings it inside during transformation
dna also goes from double stranded to single stranded and RecA will go at it
conjugation
transfer of dna from cell to cell via direct contact/sex filus formation
the f plasmid carries gene to form sex pilus bridge between two cells
the f plasmid can be copied using the rolling circle method and sent across the brdige into the recipient cell
this can turn an F- cell into an F+ cell capable of conjugating with another F- cell
F plasmids can be integrated into host dna by ____
HOMOLOGOUS RECOMBINATION
not what youd expect
Hfr
similar to F+ but doesnt result in the recipient cell turning from F- to F+
high freq recombination
Hfr strain dna transfer
incorporated F plasmid send the host cell DNA next to its incorporation site across the sex pilus over time
this can be used to map the location of genes in the host chromosome of multiple auxotrophic mutants monitored
for regain function
Hfr x F- —>
F-
F’
is like F+ but takes extra genes with it
F’ + F- —>
F’
Hfr cell has
F factor in the chromsome
F’ cell
has F factor but it excised itself from the main chromosome and is a separate plasmid
transduction
bacteriophage injects dna into bacteria
sometimes during phage replication a virus accidentally packages a fragment of host cell dna
when this odd virus infects the next cell it delivers that fragment instead of viral dna
- the odd virus usually unable to replicate because of lack of genome
homologous recombination must still occur
point of gene expression
avoid energy waste
how are gene expression and enzyme activity controlled?
cells dont require all gene products at all times
constitutive gnees do need to be constantly on
inducible genes are only required at particular times
basic control of gene expression dna take place during transcription, translation, or after translation
constitutive genes are ______
constantly on
inducible genes are _____
required only at particular times
why do bacteria need to have differential gene expression?
adjust to environment = natural selection/competition
efficiency of the bacteria will drive selection
housekeeping genes
genes that have to be constitutively on
ex glycolysis
regulation of enzymes
inhibition – may result from binding to inhibitor molecule. conformation altered and substrate no longer binds = allosteric inhibition
covalent modification may also alter enzyme conformations like phosphorylation
production of enzymes
while modifying enzyme activity can control a cells biochemistry, the energy input to make the enzyme is already expanded
a better means of energy conservation would be to only make enzymes as needed
operon
transcriptional unit with with a series of structural genes and their transcriptional regulatory elements
operator region is where regulatory proteins bind
which step might be the most energy efficient to regulate production of enzymes?
transcription
inducible system
normally the system is off – turned on when needed
negative control
some protein is acting to suppress transcription
positive control
some protein is acting to enhance transcription
negative control in lac operon
repressor binds to operator blocking RNA polymerase inhibiting transcription
positive control in lac operon
effector molecules inhibit binding of the repressor to the operator
repressible operon example
trp
repressible operon
under normal conditions it is on
positive control in operon
regulatory molecules bind and increase transcription rates
increases the affinity of RNA polymerase to the promoter region
effector molecule binds the activator and alters conformation which makes it more likelyto bind regulatory site on DNA
when are structural genes expressed in lac operon?
low glucose concentration
high lactose concentration
whenever there i slow glucose concentration there is _______
low cAMP concentration
crp camp complex
binds at the top of the operon in the activator binding site which allows it to work
diauxic growth in lac operon
lac operon isnt expressed until all glucose is consumed
how did we figure out that lacI is a transposable element
we used lac mutants that had it always on and noted that if the lacI was messed up in one plasmid but good in the other it could move there
this didnt work for a broken operator
repressor binds to ____
operator
activator binds to _____
activator binding site
effector
small molecule
size of a virus
10 to 100 nm
genome size of virus
typically a few thousand to 200,000 nucleotides in length
HIV 9200, 9 genes
E coli 5 million, 5000 genes
SARS-CoV-2 30000 nases, bc it is ss RNA
influenza virus contains ___ nucleocapsid structures in its envelope
8
picornavirus (polio)
host is humans, ssRNA, 30 nm diameter
TMV (tobacco mosiac virus)
host is tobacco and related plants, ssRNA, 300 x 18 nm diameter
T4 (bacteriophage)
host is e coli, dsDNA, 170,000 nm diameter
poxvirus (smallpox virus)
host is humans, dsDNA 300 x 250 nm diameters
mimivirus
host is amoeba, sDNA, 400 nm diameter
example of retroviridae and what kind of virus
HIV
RNA
example of picornavirdae and what kind of virus
polio
RNA
example of rhabdoviridae and what kind of virus
rabies
RNA
example of coronaviridae and what kind of virus
SARS-CoV-2
RNA
example of papovaviridae and what kind of virus
HPV
DNA
example of herpesviridae and what kind of virus
HSV (herpes simplex
DNA
walter reed (1901)
first guy to show that a human disease (yellow fever) was caused by a virus)
viruses do not have _____
a 16s ribosomal gene
viruses are ______ the host cell for gylcolysis
dependent on
t or f lambda phage integration is NOT a random event
t
it inserts in the same place in bacterial genome every time and doesnt disrupt bacterial host cells genome
lamB
phage lambda receptor also a maltodextrin transporter
what receptor does HIV recognize
CD4
what receptor does corona recognize
Bgp1a
what receptor does T2 recognize
OmpF
what receptor does phage lambda recognize
lamB
what receptor does the novel coronavirus recognize
H2
uncoating
genome being released from nucleocapsid
entry of enveloped viruses
hiv
spike hits the receptor and causes conformational change, envelope of virus becomes part of plasma membrane of host cell that is infecting and releases nucleocapsid (direct membrane fusion)
entry of noneveloped viruses
rhinovirus
when it binds with receptor it stimulates host to cause it to be endocytose, the endocytosis vesicle carries the virus in, the pH changes cause vesicle to release the whole nucleocapsid
entry of flu viruses
cell takes entire thing in, envelope and all, into endosome where pH changes occur, envelope does fuse with membrane of endocytic vesicle that what releases the RNA directly influenza has a nuclear capris that RNA wraps around uncoating is separation of nucleic acid
dna viruses are classes _ _ & _
I , II , and VII
herpes is class
I
double stranded dna
transcribes minus strand in mrna
+ RNA strand is the
coding strand. it is the mRNA without the u
- RNA strand is the
complementary strand. it acts as the template to make more + strands (u instead of t)
picornaviridae has ___- and ___ viruses
poliovirus and rhinovirus
ss + RNA
rhabdoviridae is _____
rabies virus
ss - RNA
retroviridae is _______
HIV
ss + RNA with reverse transcriptase
single stranded + RNA viruses are
RNA dependent RNA polymerase RdRp – they make this from their mRNA to produce more template strands
they can make RNA from RNA
single stranded - RNA viruses are not
RdRp so they have to bring it with it
herpes and pox are
class I
picornaviridae (polio) is
class IV
Rhabdoviridae (rabies) is class
V
coronaviridae (sars)
Class IV
retroviridae (HIV)
class VI
reverse transcriptase is _____
an RNA dependent dna polymerase
