Viruses (#1) Flashcards
“virus” means _______ in latin
poison
genetic elements (DNA or RNA) that replicate independently of a cell’s chromosome, but require a living host in order to reproduce
viruses
viruses are ________ _________ parasites
obligate intracellular parasites
why are viruses called “obligate intracellular parasites?
they damage the cells they take over (parasite) + they are OBLIGATED to be inside the cells to take them over (obligate intracellular)
viruses infect _______ cell types
ALL (every living cell)
viruses are ______ infectious agents
accellular
what do viruses contain?
DNA or RNA
various shapes of DNA/RNA that viruses contain (5):
- single stranded
- double stranded
- linear
- circular
- segmented
shape of DNA/RNA: genome is one or more pieces; allows for reassortment of genome to increase their diversity
segmented
what kind of genome does influenza virus have?
segmented (can take pieces of human, swine, and bird flu to become a near virus – why we get a new vaccine every year)
we get a new flu shot every year because theres so much ___________ (due to segmented genome) that it changes our _________ reactions
reassortment; antibodies
extracellular form of viruses =
virion
the complete virus particle (nucleic acid surrounded by a protein coat, and possibly external layers); moves from host cell to host cell
virion
the protein coat that surrounds the nucleic acid in a virion is called the _______
capsid
most numerous microbe =
viruses!
size range of viruses:
10 - 2300 nm
size range of bacteria:
200 nm - 750,000 nm
virions contain a ________
nucleocapsid
what is a nucleocapsid composed of (3)?
- nucleic acid (DNA or RNA)
- protein coat (capsid)
- some have additional components
the polio virus is the size of a bacterial ________
ribosome
the most common size of viruses is up to ________ nm
400 nm
larger viruses tend to infect ________ and are _________
amoeba; aquatic
large viruses that infect amoeba have _______, which are hairs made of a similar material to peptidoglycan; make amoeba think they’re eating bacteria and then get infected by a virus
fibrils
virus structures can either be ________ or ______
enveloped or naked
what does a naked virus structure include?
- nucleic acid
- capsid (composed of capsomeres)
- can possibly have peplomers/spikes
what does an enveloped virus structure include?
- nucleic acid
- capsid
- glycoprotein (spikes/peplomers)
- envelope
what is the capsid composed of?
capsomeres
what is the envelope made of?
lipid bilayer
what are spikes made of?
glycoproteins
part of virus structure: protects nucleic acid and may have an attachment role as well
capsid
type of virus structure: only have nucleic acid + capsid (can possibly have protrusions)
naked virus
type of virus structure: has a LIPID bilayer and protein protrusions
enveloped virus
types of virus SYMMETRY (3):
- helical
- icosahedral
- complex (both)
virus symmetry refers to its _______ symmetry
capsid (does NOT include envelope)
type of virus/capsid symmetry: tube; if it has an envelope, it may look spherical
helical symmetry
type of virus/capsid symmetry: polyhedron – 12 equilateral triangles + 12 vertices; most efficient way to enclose a space; could also have an envelope
icosahedral symmetry
example of virus w/ helical symmetry =
tobacco mosaic virus
the structural subunits of capsids, called ________, is just long enough to cover the nucleic acid; all the same type of protein in helical symmetry
capsomeres
type of virus/capsid symmetry: no JUST helical or icosahedral; might have both or some other symmetry
complex symmetry
example of a virus w/ complex symmetry that has a STRANGE shape =
vaccinia (pox virus)
example of a virus w/ complex symmetry that has BOTH helical + icosahedral symmetry
T4 bacteriophage
complex symmetry that has BOTH helical + icosahedral symmetry
binal symmetry
T4 bacteriophage has complex symmetry that is term:
binal symmetry
the capsid head of T4 bacteriophage looks like _________ symmetry while the sheath looks like ________ symmetry
icosahedral; helical (tube)
theres ______-_______ general of viruses
200-300
of virus species:
1500 species
classification of viruses is based on (5):
1) what they infect (animals, amoeba, bacteria)
2) nature of virion (naked/enveloped)
3) nucleic acid (DNA, RNA, linear, circular, etc.)
4) strategies of infection + reproduction
5) nucleotide sequence
central dogma of biology:
DNA –> mRNA –> protein
T/F: all living cells are double-stranded DNA
true
the one strand of DNA used to make mRNA is called what?
antistrand
types of viral GENOMES for ssRNA viruses (2):
- positive sense
- negative sense
positive and negative sense genomes are only for what type of virus genome?
ssRNA (single-stranded RNA) viruses
type of ssRNA virus genome: genome and mRNA are the SAME sequence
positive sense (+, plus strand)
type of ssRNA virus genome: genome and mRNA are COMPLIMENTS to one another (ex: AUG –> UAC)
negative sense
example of virus with negative sense genome =
flu virus
mRNA is always in the ______ sense
positive
outer, flexible membranous layer
viral envelopes
lipids and carbohydrates in the viral envelope are usually _______ derived
host
viruses can acquire their envelope from their host through a process called _______
budding
process where virus exits the host cell and uses spikes to pull lipid bilayer with it
budding
very few ___________ have an envelope
bacteriophages
most bacteriophages have a ________ type of genome
dsDNA
envelope ______ may project form the envelope surface
proteins
protein projections on the envelope surgace
spikes or peplomers
spikes or peplomers are ________ encoded
viral (makes them inside the cell first)
functions of spikes (5)
- viral attachment to host cell (very specific)
- enzymatic activity
- role in nucleic acid replication
- identification of virus
- release of virus (nervinadose spikes)
the spikes viral attachment to host cells is very _______
specific
spike that the flu virus uses to attach to respiratory cells SPECIFICALLY; can attach to RBCs (blocking WBCs from attacking it)
Hemagglutinin spike
what spike is involved in the release of the virus?
nervinadose spikes
the ______ virus have nervinadose spikes
flu
Tamaflu inhibits the fomration of _______ spikes in order to decease the duration of the flu; prevents more viruses from spreading to other parts of the body through release
nervinadose spikes
most enveloped viruses are _______ viruses
animal
animal viruses don’t have a cell wall but they have a ________ _______
lipid bilayer
animal viruses are released via ________
budding
animal viruses type of genome:
dsDNA or ssRNA
specific polymerase that virus brings with it; reads NEGATIVE sense RNA virus genome and makes it into POSITIVE sense mRNA; host cells don’t have this
RNA-dependent RNA polymerase
spikes are _______
antigens
viral replication/reprod. steps (5):
- attachment (adsorption of phage virion)
- penetration of viral nucleic acid
- synthesis of viral nucleic acid + protein
- assembly and packaging of new viruses
- cell lysis and release of new virions
the viral replication mechanism used depends on viral ________ and ________
structure + genome
similar steps of viral replication for all viruses (6):
1) attachment
2) entry (of viral genome)
3) uncoating of genome
4) synthesis
5) assembly
6) release
attachment of viruses is specific (not random at all) and uses common ______ ________ for receptors
cell components (ex: LPS, peptidoglycan)
types of entry/penetration of viral nucelic acid into the host cell (3)
- injection
- endocytosis
- fusion of virion to cell membrane
which method of entry do most bacteriophages used to penetrate their genome into the host cell?
injection
which method of entry do most animal viruses/eukaryotes used to penetrate their genome into the host cell?
endocytosis + fusion
method of entry; cell is tricked into thinking the virus is food and brings it into the cell
endocytosis
step of viral replication: removes layer from nucleic acid (viral genome) so it can do its job; takes CAPSID off
uncoating of genome
T/F: if you INJECT DNA into the host cell; the nucleic acid is already uncoated from the capsid
true
step of viral replication: replicates its genome makes new nucleic acids + proteins; makes new virions and enzymes to take over the cell
synthesis
during fusion of the virion to the host cell membrane, the _______ is uncoated but you still have to uncoat the ________
envelope; capsid
if a virus uses fusion, uncoating of the capsid occurs in the __________
cytoplasm
in some ANIMAL cells (when using fusion), uncoating of the capsid from the nucleic acid may not occur until the ________
nucleus
methods of the release of new virions (3):
- lyse
- exocytosis
- budding
the genome of a negative sense RNA virus:
a) has the same sequence as the viral mRNA
b) has the complementary sequence of the viral mRNA
c) has the reversed sequence of the viral mRNA
d) is used as the viral mRNA
b) has the complementary sequence of the viral mRNA
viral replication phases (2):
- eclipse
- maturation
viral replication phase: making early viral enzymes to take over the host cell + to replicate its genome
eclipse
viral replication phase: assembling all new virions
maturation
once a virus is added to a host cell, there is a ______ period before its is released
latent period
period during viral replication; minutes to hours; nothing going on the OUTSIDE but a lot going inside
laten period
order of products created during viral replication:
- early enzymes
- nucleic acid
- protein coats (capsid)
of virions released from cell when infected
burst size
the burst size for most viruses is ________ virions
100
viruses that infect bacteria
bacteriophages
bacteriophages are also called _________
phages
bacteriophages are very ________ and structually ________
diverse; complex
most bacteriophages contain _________ genomes
dsDNA (contrast to animals which are dsDNA or ssRNA)
most bacteriophages have a ________ virus structure
naked
very few bacteriophages have __________; presence of peptidoglycan and other things makes it harder to steal lipid bilayer + there’s few that can bud
envelopes
which method of entry do bacteriophages use to get their genome inside the host cell?
inject (most)
viral infections of bacteria causes around ______ of ALL bacterial mortality; it’s very common
1/3
_____% of all marine prokaryotes are infected w/ viruses; ocean is chalk full of bacteriophages
70%
there are _________ - __________ viruses (bacteriophages) per mL of ocean water at the surface
1 mil - 100 million
viruses that lyse the host cell; deadly
virulent / lytic
virulent (lytic) bacteriophages begin _______ immediately after entering the host
multiplying
virulent bacteriophages ______ bacterial host cell for release
lyse
virulent (lytic) bacteriophages can ONLY go through which pathway?
lytic pathway
different types of phages:
- lytic (virulent)
- lysogenic (temperate)
example of lytic (virulent) virus =
T4
T4 infects which bacteria?
E. coli
burst size of T4 =
100
T/F: all viruses can go through the lytic (virulent) pathway
true!
T/F: animal viruses cannot lyse the cell
false (some can do it too in addition to phages)
T4’s receptor:
LPS
since T4’s receptor is LPS, they only infect what kind of bacteria?
gram-negative (E. coli)
T4 injects a _______ strand of DNA into the bacteria
linear
T4 has a __________ to break beta-1,4 of the peptidoglycan layer
lysozyme
T4 uses the enzyme ________ to put a hole in the cell membrane
polan (i think thats the name)
how long does it take for T4 to replicate and lyse the bacterial cell from the start of infection?
only 25 minutes!
order of T4 products after infection (6):
1) T4 nucleases, DNA polymerase, and new sigma factors
2) phage T4 DNA
3) phage head proteins
4) tail, collar, base plate, and tail fiber proteins
5) mature T4 virion
6) T4 lysozyme production
in T4, what are early mRNA used for?
T4 nucleases, DNA polymerase, and new sigma factors
changes specificity of host cell enzyme to make it work for the virus; makes sure RNA polymerase the cell has will ONLY bind to VIRAL protein; makes the cell make only viral mRNA
new sigma factors
in T4, what are late mRNA used for?
structural components of the virus — tail fiber proteins, capsid, collar, base plate, proteins (aka building VIRIONS)
break down host (bacterial) chromosomal DNA
T4 nucleases
used to replicate viruses DNA
DNA polymerase
T/F: viruses package their genome first and THEN add other stuff when replicating inside a host cell
true
why does T4 make lysozyme at the end?
to get out of the cell! (lyse)
type of phage: can go through the lytic pathway OR the lysogenic pathway
temperate (lysogenic) phages
pathway: reproduce as virulent phages
lytic pathway
pathway: remain within host cell without destroying it; integrate genome into host genome
lysogenic pathway
relationship when virus integrates its viral DNA/genome into the host’s genome (chromosome)
lysogeny
lysogeny is kinda like ______
dormancy (kinda)
example of lysogenic phage =
lambda
lambda has a ________ head and a __________ segment tail
icosahedral head; helical segment tail
lambda has a ______ tail that is very FLEXIBLE
flexis
lambda has ______ symmetry
binal (complex)
lysogenic process steps (4):
1) attachment of the virus to the host cell
2) injection of viral DNA
3) viral DNA is integrated into host DNA
4) viral DNA is replicated with host DNA at cell division (binary fission)
once viral DNA is incorporated onto bacterial chromosome, the virus is considered a ________
prophage
why is it advantageous to integrate the viral genome onto the hosts chromosome?
way to not kill host but still propagate
what is it called when the bacterial cell is triggered into the lytic cycle from the lysogenic cycle?
induction
what does “prophage” mean?
pro: incorporated onto the chromosome
phage: bacterial virus
nonlytic relationship between a phage and its host
lysogeny
cell has to be _________ for lysogeny to occur
permissive
integrated bacteriophage genome
prophage
lambda use _______ enzyme to integrate into host chromosome
integrase
lambda integrates its genome between ________ and ________ operons of the E. coli chromosome
galactose; biotin
the area between galactose and biotin where lambda integrates its genome is called the _________ _______
attachment site
lambas prophage replicates with its _____ genome
host
operon that allows bacteria to use galactose as a carbohydrate source
galactose operon
operon that allows bacteria to make biotin
biotin operon
essential growth factor
biotin
cluster of genes that are regulated together; under the SAME control
operon
infected bacterial host
lysogen
the lysogen appears and acts _______ during lysogeny
normal (
during lysogeny, the prophage may change the ________ of its host
phenotype
when the prophage changes the phenotype of its host (prophage in attic changes the shutters from red to orange; bacteria is the house)
lysogenic conversion
phage may switch from lysogenic to lytic cycle upon __________
induction
when prophage comes out of the hosts chromosome
induction
example of phenotypic change: Salmonella enterica mutates its ______ _________ on LPS so if you get infected with it again (and its mutated), your body has to create all NEW antibodies
O antigen
example of phenotypic change: diptherium toxin that makes ppl sick comes from a _________
prophage
diptherium toxin that makes ppl sick comes from a prophage makes it a __________
pathogen
prophage from diptherium toxin becomes a _______ virus; now PERMANENTLY part of its chromosome
cryptic
A lytic (virulent) bacteriophage:
a) can remain dormant in bacterial cell until induction
b) can incorporate into the bacterial chromosome
c) takes over the host cell immediately after infection and then releases the newly assembled virions via budding
d) takes over the host cell immediately after infection and then releases the newly assembled virions via lysis
d) takes over the host cell immediately after infection and then releases the newly assembled virions via lysis
Lambda genome has ___________ in __________ conformation with _______ _______
dsDNA; linear conformation; cohesive ends
sticky ends that if brought together will stick together
cohesive ends
Integration of lambda DNA into host steps (3):
1) lambda genome cyclizes at its cohesive ends
2) a site-specific endonuclease creates staggered ends of phage and host DNA (b/w galactose + biotin)
3) lambda genome integrates and gaps are closed by DNA ligase
in bacterial DNA; fights foreign DNA invaders
endonuclease
closes gaps in DNA/chromosomes
ligase
process by which temperate phage reproduction is initiated; results in switch to lytic cycle
induction
induction is triggered by drop in levels of _______ _______
lambda repressor
drops in levels of lambda repressor is usually caused by what?
DNA damage by UV light or chemical mutagens
cuts prophage out for induction by binding to INTEGRASE enzyme; enables integrase to reverse integration process
excisionase
T/F: when DNA damage occurs from UV light or chemical mutagens, it goes into a SOS response trying to salvage its DNA and one of its repair enzyme it makes breaks down the lambda repressor
true
for animal viruses, the _______ virion enters the animal cell
ENTIRE
what methods do animal viruses use to get inside the animal cell?
endocytosis or fusion to the membrane
many animal viruses replicate in the ________ of the animal cell
nucleus
many animal viruses are _________
enveloped
what kind of genome do animal viruses have?
dsDNA or ssRNA
Effects of Animal Viruses (4):
- virulent (lytic)
- latent
- persistent
- cancer
or doesn’t work
effect of animal virus: death of the cell and release of the virus
virulent (lytic)
effect of animal virus: slow release of virus without causing cell death (ex: HIV); doesn’t necessarily kill the cell, but compromises it in some way; sometimes viral genome goes on the chromosome
persistent infection
2 examples of PERSISTENT infection in animal cells =
HIV and hepatitis B
effect of animal virus: virus present but not replicating (until activation occurs + presents itself)
latent infection
2 examples of LATENT infection =
HSV (herpes) + varicella-zoster (chicken-pox then shingles)
effect of animal virus: formation of proviral state and transformation into tumor cell with tumor cell division; viruses that incorporate onto the chromosome – onto a tumor suppressor gene
cancer
mutated tumor suppressor genes =
proto-onco genes
T/F: cancer is always malignant
false ..
example of cancer virus =
strains of HPV
infection: virus stops reproducing and remains DORMANT for some time
latent viral infections
T/F: during latency of a viral infection, symptoms, antivirus-antibodies, and viruses are NOT detectable (hidden)
true
varicella-zoster (chicken-pox –> shingles) is there forever in your _____ cells
nerve
HSV (herpes) can be triggered by _______
stress
when stressed, ________ of bacteria change and can activate viruses
products
infection: virus almost always detectable
persistent viral infection
clinical symptoms of persistent viral infection are ______ or _______ for LONG periods
mild or absent
viruses associated with human cancers
oncoviruses
2 main ways viruses can cause cancer:
- integrates into DNA on proto-onco genes in host; mutates tumor suppressor gene tuning into an oncogene
- virus carries an oncogene (and incorporates it into ur DNA)
which of the following conditions could induce the lytic cycle of a prophage?
a) increased levels of a lambda repressor
b) decreased levels of a lambda repressor
d) exposure to UV light
d) B or C
d) B or C
RNA viruses that replicate through a DNA intermediate
retroviruses
retroviruses are _________-sense
positive
retroviruses have a ________ genome
segmented
T/F: retroviruses incorporate onto the host chromosome
true
retroviruses have an ________
envelope
what method do retroviruses use to insert there DNA?
fusion onto a membrane (uncoating occurs at membrane)
enzyme retroviruses bring with it to convert RNA —> DNA
reverse transcriptase
retroviruses have a ________ stage (HIV on chromosome)
provirus
retroviruses are released by ________
budding (steals lipid bilayer for envelope)
example of a retrovirus
HIV
retroviruses infection process (5 steps):
- entry and uncoating of the retrovirus
- reverse transcriptase activity (two steps)
- viral DNA enters nucleus and integrates into the host genome
- transcription by host RNA polymerase forms viral mRNA and genome copies
- translation of mRNA forms viral proteins; new nucelocapsids assembled and released by budding
severe acute respiratory syndrome virus
SARS-CoV-2
SARS-CoV-2 is _______ with ______-shaped spikes
enveloped; club-shaped
what kind of genome does SARS-CoV-2 have?
positive-sense, ssRNA
T/F: SARS-CoV-2 is negative-sense
false (its positive)
SARS-CoV-2 has ________ capsid symmetry
helical
SARS-CoV-2 infects host through its spike glycoprotein (S) attaching to a host receptor. what is the host receptor?
ACE2 on lung epithelial cells (can be on heart, kidney, and intestinal cells too)
ACE2 stands for:
angiotensin converting enzyme
SARS-CoV-2 enters host cell via which method?
fusion to host cell membrane
new virions of SARS-CoV-2 are released from the host cell by _________
exocytosis
SARS-CoV-2 transmission jumped from ______ to ______ to ________
bats to civets to humans
since SARS-CoV-2 came from bats and civets to humans, it is a _________ disease
zoonotic
SARS-CoV-2 is transmissed from person-to-person contact via ________ _____ or ______
direct contact or droplets (aerosal)
if you have SARS-CoV-2, you could be a _________ carrier
asymptomatic
each aerosal droplet from an infected person with SARS-CoV-2 can have up to _______ virions
10
T/F: the mask can’t stop the virions of SARS-CoV-2 from spreading since their so small, but it can stop the droplets
true
incubation period of SARS-CoV-2 =
5.2 days
common symptoms of SARS-CoV-2 infection (3):
fever, cough, fatigue
____% of colds are caused by coronaviruses
15%
vaccinated ppl with SARS-CoV-2 are more likely to ______
sneeze
build-up of fluid in lungs; looks like glass in lungs; caused by SARS-CoV-2
ground-glass opacities
as time goes by, SARS-CoV-2 is going to be less _______ but more ________
virulent; transmissable
the structure of SARS-CoV-2 looks like a _______
crown
coronaviruses make a ______- sense ____ to a _______-sense ______
negative-sense RNA –> positive-sense DNA
coronaviruses are assembled in the ________ of the host cell and then pick up the lipid portion in the ___________
cytoplasm; endoplasmic reticulum (ER)
coronaviruses are packed up in vesicles in the _________ for exocytosis (release)
golgi (apparatus)
