test 1 Flashcards
Viruses are composed of _______
1) genome composed of ONE type of nucleic acid (DNA or RNA)
2) Protective protein or lipoprotein coat surrounding the genome
where do viruses replicate
ONLY inside living cells- viruses are completely dependent on cellular synthetic machinery for replication (no cellular organelles)… Also, viruses cannot capture and store energy
what do viruses use for replication
host cell synthetic machinery
can viruses survive and replicate in cell free media
NO (only bacteria can)
What is the purpose of the protective coat that surrounds the genome
made of proteins or lipoproteins, the coating allows the viruses to survive in the environment. Also, it GIVES THE VIRUS INFECTIVITY- without the glycoproteins attaching to cellular receptors, the virus will not be able to enter the cell
can a naked viral genome infect the cell?
NO- the naked viral genome by itself is not infectious
if the naked viral genome is artificially transfected (forced in), then it will be allowed to replicate the virus
what is a virion?
a mature virus particle
what makes up a virion?
nucleic acid genome (either DNA or RNA) and a capsid
what is a capsid?
protein coating that protects the genome, composed of capsomeres
what are capsomeres?
proteins that compose the capsid (polypeptides that are held together by non-covalent bonds)
Functions of the viral capsid
1) protects the genome from the environment
2) provides structural symmetry… creates stability
3) allows viruses to enter by recognizing and attaching to host cell receptors
4) Aids in virus replication- may contain enzymes necessary for virus replication (i.e. RNA transcriptase)
5) capsid proteins are very immunogenic
what is a nucleocapsid
aka the virion- capsid plus the nucleic acid genome
What distinguishes enveloped viruses and non-enveloped viruses
an extra outer coat to some viruses (enveloped viruses). Non-enveloped viruses are called NAKED VIRUSES
where is the envelope derived from
the host cell membrane (plasma or nuclear), acquired when the virus exits infected cells by budding
when does the virus acquire an envelope?
during a process called budding
what happens before budding
the virus inserts viral glycoproteins (PEPLOMERS) into the cellular lipid bilayer
where does the lipid bilayer envelope for viruses originate? Where do peplomers originate?
Lipid bilayer is of CELLULAR origin
the peplomers are of VIRAL origin
Functions of the viral envelope
1) provides structural symmetry
2) allows virus to enter cell (peplomers attach to host cell receptors)
3) may contain enzymes essential for viral replication
4) peplomers are very immunogenic (because they are virally produced)
4 important criteria for viral classification
size of the virion
symmetry of the nucleocapsid (icosahedral, helical, or complex)
presence of envelope?
type of nucleic acid
size of the virion
most important tool used to classify viruses
Viruses are expressed in NANOMETERS!!!!!!
what term describes the ability to distinguish one object from another?
Resolving power
normal eye ~250um
light microscope is 1000X better: ~.250um
electron microscope is 1000X better: ~0.250 nm (but the practical limit of EM is ~2.5 nm)
what is the smallest virus that light microscopy can see?
Poxvirus (350 nm)
what are the three types of nucleocapsid symmetries?
cubic/icosahedral
helical nucleocapsid
complex symmetry
Symmetry of nucleocapsid: Cubic symmetry
AKA Icosahedral
20-sided structure consisting of 20 equilateral triangles, 12 vertices
5:3:2 rotational symmetry
what makes up the triangles of the icosahedral symmetry
symmetrical clusters of capsomeres (Pentons and hexons)
What are pentons
term describing capsomeres situated at the 12 vertices of icosahedral symmetry nucleocapsids
What are hexons?
term describing capsomeres in icosahedral symmetry that are not at the vertices (surrounded by 6 neighboring capsomeres)
What is the significance of helical nucleocapsid?
ALL ANIMAL viruses with helical nucleocapsids are ENVELOPED
What is the only known animal virus with complex symmetry?
Poxvirus
types of nucleic acids in viruses
DNA or RNA
Single stranded or double stranded
linear or circular genome
segmented or non-segmented genome
what are the 2 classifications of RNA virus genomes that are single-stranded
positive polarity and negative polarity
if an RNA virus has a positive polarity, how is it translated?
it will be translated directly into protein by cellular ribosomes
if an RNA virus has a negative polarity, how is it translated?
negative polarity genomes must be transcribed into a COMPLEMENTARY positive strand before it is translated into protein
what enzyme converts strands from negative to positive polarity?
polymerase enzyme (ex: RNA dependent RNA polymerase)
for negative polarity RNA viruses, is cellular polymerase sufficient for transcription to its complementary positive strand?
NO
we need RNA dependent RNA polymerase (not made by cell)
the viruses bring the polymerase into the cell
Virus replication steps
1) attachment of virus to cells
2) entry of virus into cell
3) uncoating of virus
4) Early transcription of viral nucleic acid into viral mRNA
5) translation of early viral proteins (enzymes) from viral mRNA
6) Transcription of parental genomes into progeny genomes (DNA -> DNA; RNA -> RNA)
7) translation of late structural proteins
8) virus assembly within the cell
9) release of virus from the cell (lysis or budding)
Virus attachment or Adsorption into the cell
random
nonspecific
reversible
what initiates attachment/adsorption
electrostatic attraction
when does the attachment phase become specific?
when the capsid proteins (if naked virus) or peplomers (if enveloped virus) recognize complementary cell membrane receptors
what is viral tropism?
the affinity of viruses to only specific cells because of the presence of the specific receptors on certain cells
What 2 methods can a virus enter cell?
Viropexis: virus is engulfed by the cell membrane, enters the cytoplasm inside a phagocytic vacuole (primary way that most naked icosahedral viruses enter)
Fusion: viral envelope fuses with cell membrane (occurs with many enveloped viruses)
What initiates fusion of the virus envelope with the cell membrane?
the peplomers initiate fusion
What is viral uncoating?
the physical separation between viral nucleic acid and the viral capsid. Once a virus uncoats, the virus is no longer infectious
if an infected cell is broken up before the virus uncoats, will the virus still be infectious?
yes, the virus can still go infect other cells
if an infected cell is broken up after all virus particles have uncoated, is it still an infectious virus?
NO, you need a capsid to be infectious
when is viral uncoating complete?
when intracellular infectious virus particles cannot be detected in the infected cell, but a viral genome can be detected by PCR
what are the 2 mechanisms for uncoating
1) Digestion: digestion of viral protein coat by CELLULAR proteases
2) Conformational changes: changes in polypeptides that make up the capsomeres (due to changes in pH and ion concentration in the cytoplasm–> causes dissolution of the non-covalent bonds)
where do RNA viruses uncoat and replicate?
cytoplasm
where do DNA viruses uncoat and replicate?
uncoat in the vicinity of the nuclear pores, and uncoated genome will be immediately transported into nucleus for replication
what is the eclipse period?
the period where the infectious virus cannot be detected or demonstrated within the cell
begins when uncoating of tyhe virus is complete, ends with the formation of the first infectious virus progeny
what happens during the eclipse period
transcription of the viral genome and translation of the structural viral proteins (production of progeny viruses)
How do viruses usually produce the enzymes that are needed for viral replication?
the enzymes needed are produced from mRNA created during the early transcription phase of viral genomic nucleic acids into viral mRNA (mRNA is produced to go to the cytoplasm and be translated into these enzymes)
what is the major early protein/enzyme that is made with viruses
polymerase enzymes
where are the early proteins produced?
in the cytoplasm, using the host cell’s ribosomes
for RNA viruses with positive polarity genomes, does transcription need to occur?
NO!!
POSITIVE POLARITY RNA genomes serve as the mRNA, so it directly binds the cellular ribosomes and is translated into the proteins
NO need for transcription for ss(+)RNA viruses
for RNA viruses with negative polarity genomes, does transcription need to occur? How does it occur?
YES
the viral RNA must be transcribed into a POSITIVE complementary strand
to do this, the virus needs RNA-dependent RNA-polymerase
PROBLEM: there is no mRNA present yet to produce the polymerase
SOLUTION: negative polarity RNA viruses carry in the RNA dependent RNA polymerase
for DNA viruses, does transcription need to occur?
the DNA genome is directly transcribed by CELLULAR DNA dependent RNA polymerase to yield viral mRNA
AGAIN: DNA viruses use host cell polymerase to produce the viral mRNA
the viral mRNA then leaves the nucleus and travels to ribosomes in the cytoplasm for translation of early viral proteins
Where does translation of viral proteins occur?
cytoplasm
what early protein is translated in the case for RNA viruses?
RNA dependent RNA polymerase
negative polarity RNA strands bring in some of this, but it makes more for faster replication
positive polarity RNA strands do not bring this into the cell, so all of the polymerase for pos. strands is produced this way
What early protein is translated in the case for DNA viruses?
DNA dependent DNA polymerase
this is needed for DNA genome replication
other than just polymerases, what is the function of other proteins produced in translation of early viral proteins?
disrupt cellular protein translation so that cells focus on making viral proteins
regulate how the viral genome is transcribed
upregulate or down-regulate cellular proteins
Late transcription of the parental genome into progeny genomes: positive polarity RNA genomes
VIRAL RNA dependent RNA polymerase transcribes the parent strand (+ ss RNA) into a complementary (-)RNA strand, and then the negative strands are each transcribed into many (+)RNA progeny strands
Late transcription of the parental genome into progeny genomes: negative polarity RNA genomes
VIRAL RNA dependent RNA polymerase transcribes the (-)RNA parent strand into a complementary +RNA strand. The positive strand is then transcribed into many progeny (-) RNA strands (using RNA dependent RNA polymerase again)
How many times is RNA dependent RNA polymerase used to produce progeny RNA genomes?
twice
1) produces complementary strand
2) takes complementary strand and transcribes progeny strand
for DNA viruses, how is replication of the genome done?
the parental ds DNA genome is uncoiled and replicated into many progeny by VIRAL DNA dependent DNA polymerase
where are DNA virus genomes replicated?
nucleus
How do retroviruses work?
retroviruses carry into the cell a ss RNA molecule
the RNA is copied into a double stranded DNA molecule by reverse transcriptase (brought in by the virus)
what is reverse transcriptase?
RNA dependent DNA polymerase
What are the late viral proteins that are translated?
structural proteins: polypeptides that will produce capsomeres and peplomers, depending on whether the virus is enveloped or not
what is the mRNA used to translate the late viral proteins?
for +RNA viruses, proteins are translated directly from progeny RNA strands
for -RNA viruses, progeny strands are transcribed to a positive polarity strand, and this complementary strand is used to be translated to the proteins
for DNA viruses, late proteins are translated from viral mRNA derived from the progeny DNA genomes
What are the 2 stages of virion assembly?
Morphogenesis and encapsidation
What is morphogenesis?
process by which the viral capsid polypeptides come together and for assembled capsomeres and intact capsids (with no genome yet)
is morphogenesis spontaneous?
yes
what is encapsidation?
follows morphogenesis
process where the viral genome is inserted into the already formed capsid
does the capsid form around the genomes?
NO!!! the genome gets inserted into pre-formed capsids
What is released with many intact viruses?
many non-infectious, empty capsids
not all pre-formed capsids get encapsidated by genomes
where does assembly of the virion take place?
where the virus replicates
for RNA viruses, assembly takes place in the cytoplasm
for DNA viruses, assembly takes place in the nucleus
What are the 2 ways that a virus can be released from the host cell?
Lysis: physical bursting of the infected cell
Budding: opposite of phagocytosis
where does budding take place?
areas of the plasma or nuclear cell membrane that has been modified by the insertion of viral proteins
is budding destructive?
no
what is yield?
the number of infectious virus particles produced from each cell
replication of Picornavirus (foot and mouth disease)
non-enveloped (+) ssRNA virus with icosahedral capsid
1) attaches to specific cell receptors on the cell surface, enter via viropexis and uncoats in cytoplasm
2) +RNA virus, so no transcription needed
3) RNA dependent RNA polymerase translated form parental genome (parental genome serves as mRNA)
4) viral RNA dependent RNA polymerase binds to parent RNA strand and makes complementary negative strands, then does the same to the complementary strands to make progeny viral genomes
5) progeny strands are then translated by cell ribosomes into one long polypeptide strand tha tis then cleaved by viral proteases
6) morphogenesis of progeny occurs in cytoplasm, then encapsidation of progeny genome
7) virus is released via cell lysis
Replication of Herpesvirus
enveloped ds DNA virus with icosahedral capsid
1) peplomers bind and attach to cellular receptors, herpesvirus enters by fusion and uncoats in the vicinity of nuclear pores
2) uncoated DNA enters the nucleus before it is digested by cytoplasmic enzymes
3) DNA genome is transcribed into viral mRNA in the nucleus by host DNA dependent RNA polymerase, then the mRNA moves to cytoplasm to be translated into viral DNA dependent DNA polymerase and thymidine kinase… these then go back to the nucleus
4) polymerase and thymidine kinase initiate massive round of viral DNA replication in the nucleus to produce progeny viral DNA genomes
5) mRNA is transcribed from progeny DNA and goes to cytoplasm for translation into viral structural proteins (that move back to nucleus)–> capsomeres and peplomers
6) morphogenesis occurs in nucleus, followed by DNA genome insertion via encapsidation
7) virus leaves cell after viral peplomers are inserted into the nuclear membrane–> then virus leaves cell by budding, acquires envelope from nuclear cell membrane
Replication of retroviruses- what makes them special?
enveloped RNA viruses with helical nucleocapsid surrounded by icosahedral capsid
genome is single stranded and diploid
Replication of retroviruses
1) peplomers on envelope recognize and attach to CD4 receptors on Th lymphocytes, enter cell by fusion, uncoats in cytoplasm
2) Reverse transcriptase (RNA dependent DNA polymerase) is brought into cell by virus… it binds to uncoated viral RNA in cytoplasm and makes complementary double stranded DNA copy of the RNA genome (viral ds DNA moves to nucleus)
3) the viral ds DNA is then ligated into the cell DNA chromosomes
4) the viral DNA is transcribed into small viral mRNAs, move to cytoplasm, and are translated into viral proteins (peplomers, capsids, RT enzyme)
5) One long mRNA strand is transcribed form the entire DNA genome–> serves as the viral genome
6) morphogenesis occurs in cytoplasm
7) the viral nucleocapsid is encapsidated into the icosahedral capsid ALONG WITH reverse transcriptase
8) viral peplomers are inserted into the PLASMA membrane and virus is released by budding
What is a gene?
a nucleotide sequence that encodes for a specific polypeptide or protein
What is a mutation/
results from changes in nucleotide sequence within viral genes
what are the types of mutations?
substitution mutation: one (point) or several nucleotides are substituted
deletion mutation: one or several nucleotide bases are deleted from the genome
What are spontaneous mutations?
occur during normal virus replication
low rate of spontaneous mutations for DNA viruses (10^-8), but high rate of spontaneous mutations for RNA viruses (10^-3)
What are consequences of mutations?
- host range changes: virus adapts to unnatural host
- increase or decrease in virulence
- susceptibility to drugs can change (resistance)
- antigenic makeup of virus changes
What is phenotypic mixing/
occurs when 2 closely related viruses infect one cell and produce different progeny viruses
What is a pseudotype?
virus progeny that have acquired the genotype of one parent and phenotype of the other parent (A genotype, B phenotype)
What is a mixed phenotype?
virus progeny that have acquired the genotype of one parent and phenotype of both parents (A genotype, A and B peplomers/phenotype)
Are pseudotypes and mixed phenotype viruses genetically stable?
NO
if one of these infects a cell, they will only be able to produce the phenotype of the genome they have (A genotype can only produce A phenotype)
How does Genetic recombination occur?
2 genetically different but related viruses infect the same cell and replicate… And they exchange nucleic acid between parental viruses
progeny viruses are then formed whose nucleic acid is a combination of both parents
In essence, what is a recombinant?
part of one virus’ genome in the genome of another virus
When do recombinant viruses occur naturally?
when cellular genes are inserted into the viral genome during viral replication in animals
What is reassortment?
a type of genetic recombination specific to influenza virus
if a cell is infected with 2 different influenza viruses, progeny viruses have a genome that consists a mixture of segments derived from both viruses
How does influenza form now pathogenic strains?
genetic reassortment
Recombinant virus vaccines
Insertion of the GENE that encodes for an antigen (ex: G glycoprotein of rabies) into the genome of another virus (Ex: Pox virus). When the vaccine is inoculated into an animal, the rabies gG is translated along with the other pox proteins. The immune system sees the gG, resulting in humoral and cell mediated response to gG
Problems with Antiviral chemotherapy
> drugs can be toxic to cells and thus toxic to animals
by the time clinical disease is evident, virus replication has already peaked and the immune response is underway
Resistance to antiviral drugs occur quickly (RNA viruses mutate at high rates)
Strategy of antiviral drugs
kill the virus only, not normal cells
Idoxuridine and Trifluridine
analogue of thymidine which is incorporated into DNA in place of thymidine
good anti-herpesvirus drug
**Used only as ophthalmic drug to treat for herpes eye infections
converted into IdoxTP (analog of TTP and is inserted into the herpesvirus DNA genome by DNA dependent DNA polymerase–> blocks DNA replication)
Adenine arabinoside
nucleotide analog of dATP
inhibits DNA synthesis (inserted into genome by DNA dependent DNA polymerase–> blocks DNA replication)
Acyclovir
nucleoside analogue
transported into cells by guanine transporter and then phosphorylated by thymidine kinase into an active metabolite (thymidine kinase is only present in herpesvirus infected cells, so only active in infected cells)
once phosphorylated, it inhibits herpesviral DNA polymerase
ACV is also inserted into DNA terminating DNA synthesis
Amantadine
prevents influenza A infection
blocks the uncoating process of influenza by binding M2 protein (which is needed for uncoating)