Virology - general, replication Flashcards
Virus size range from
10 to 1000 nm in size
Genome size range
from 3000 nucleotides to >1,000,000 base pairs
viral Replication cycle time frame
from minutes to days
Explain Retrograde evolution theory
Intracellular parasites lost the ability for independent metabolism keeping only those genes necessary for replication
Explain this viral evolution theory: Origin from cellular DNA and RNA components
Some DNA genomes resemble plasmids or episomes.
Maybe this DNA acquired protein coats and the ability to be transferred from cell to cell efficiently
Explain viral evolution theory:
Descendants of primitive precellular life forms
Viruses originated and evolved along with primitive, self-replicating molecules
Name the 3 viral evolution theories.
retrograde evolution
origin from DNA/RNA components
descendents of primitive life forms
define variolation
obsolete method of immunizing patients against smallpox by infecting them with substance from the pustules of patients with a mild form of the disease
aka inoculation
Who was Edward Jenner?
was an English physician who observed that dairymaids who had had cowpox did not get small pox.
and pioneered the concept of vaccines
what is a Chamberland filter
also known as a Pasteur–Chamberland filter, is a porcelain water filter invented by Charles Chamberland in 1884.
Pasteur found that rabies passed through it
what is an eclipse period
The time between infection by (or induction of) a bacteriophage, or other virus, and the appearance of mature virus within the cell.
What is the baltimore system?
Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis.
By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group.
Virion
a complete virus with all the components needed for host cell infection
Virion is different from a virus. It is a virus in an extracellular phase.
Capsid
the protein shell of a virus particle surrounding its nucleic acid
Capsid + genome =
nucleocapsid
By definition, nucleocapsid is a viral protein coat that surrounds the genome (either DNA or RNA). N
Ø NB! Only as a substructure!
viral envelope
A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells.
surrounds the nucleocapsid
Protein spikes
a spike protein is a protein that forms a large structure known as a spike projecting from the surface of an enveloped virus. The proteins are usually glycoproteins.
helps to attach to the host cell
icosahedral definition
is a polyhedron with 20 faces
Icosahedron = polygon
with 20 faces, each an
equilateral triangle
how many types of viral genome?
7 types of viral genome
- ds DNA
- ss (+) sense DNA
- ds RNA
- ss (+) sense RNA
- ss (-) sense RNA
- ss (+) sense RNA with DNA intermediate in lifecycle
- ds DNA with RNA intermediate
define capsomere
is a subunit of the capsid, an outer covering of protein that protects the genetic material of a virus. Capsomeres self-assemble to form the capsid.
What is the difference between a viral envelope and a capsid?
Envelope and capsid are two structural parts in viruses. Capsid is the protein shell which surrounds the viral genome.
Envelope is the lipid membrane acquired by the viruses from the host cells. It covers the nucleocapsid.
not all viruses have envelopes but essentailly all have capsids
in which direction do positive sense strands code?
5’-3’
in which direction do negative sense strands code?
3’-5’
another name for sense strand
coding strand
carries the translatable code in the 5′ to 3′ direction
The main difference between sense and antisense strand is that sense strand is incapable of being transcribed into mRNA whereas antisense strand serves as the template for the transcription.
another name for antisense strand
template strand
is directed in the 5’ to 3’ direction.
The main difference between sense and antisense strand is that sense strand is incapable of being transcribed into mRNA whereas antisense strand serves as the template for the transcription.
describe the lytic viral lifecycle
In a lytic cycle, the virus introduces its genome into a host cell and initiates replication by hijacking the host’s cellular machinery to make new copies of the virus.
Once infection is complete, the newly replicated and assembled virus particles are released through lysis of the host cell into the surrounding waters.
is also commonly referred to as the “reproductive cycle” of the bacteriophage, is a six-stage cycle. The six stages are: attachment, penetration, transcription, biosynthesis, maturation, and lysis.
describe the lysogenic viral lifecycle
lysogenic cycle: The phage infects a bacterium and inserts its DNA into the bacterial chromosome, allowing the phage DNA (now called a prophage) to be copied and passed on along with the cell’s own DNA.
instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host.
Viral DNA multiplies as the host cell multiplies. Each new daughter cell created is infected with the virus’ DNA.
define non-covalent
a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule.
define Quasi-equivalence
quasiequivalent = Very similar, but different.
can be defined as the extent of similarity between these structurally unique environments occupied by the chemically identical subunits in the virus capsid.
Quasi-equivalent capsids should contain 60T subunits, however, there are exceptions.
The conceptual basis for viral quasi-equivalence is the interchangeable formation of hexamers and pentamers by the same protein molecule
define pentamer & hexamer
A pentamer is an entity composed of five sub-unit
hexamer is an oligomer having six subunits; A subunit of a viral capsid.
What are the 5 steps of the virus replication cycle?
- Attachment
- Penetration or viral entry
- Synthesis (replication)
- Assembly
- Release
cellualr receptors are needed for all viruses except for what 2 exceptions and why?
except for fungi and plant viruses because they enter the cells by mechanical damage so no receptors needed.
How many receptors does a virus need to bind in order to enter a cell?
2-3 receptors
but some require up to 5 like the polio virus
what was the first cell receptor to be discovered?
sialic acid receptor for the influenza virus
What are the 2 methods of viral entry?
- fusion with the membrane (only enveloped viruses)
- endocytosis of various kinds (both enveloped and non-enveloped)
what type of viruses use membrane fusion for cell entry
only enveloped viruses e.g. herpes virus
what type of viruses use endocytosis of various kinds for cell entry
both enveloped and non-enveloped
e.g. adeno virus
Name 3 types of viral entry endocytosis
clathrin-dependent
clathrin-and-claveolin-independent
caveolin-dependent
What is unique about calveolin-dependent viral entry?
The calveolin coated vesicle/endosome with virus is carried to the endoplasmic reticulum instead of the cell nucleus. The viral genome is then deposited into the endoplasmic reticulum instead of the cytosol or nucleus.
e.g. SV40 (simian virus 40)
What regulates viral fusion-entry?
location
pH
viral entry (fusion) at neutral pH at the plasma membrane requires what to complete entry?
needs second protein receptor interaction
viral entry (fusion) at low pH at the plasma membrane requires what to complete entry? (2)
▫ proteolytic cleavage for the fusion proteinactivation or
▫ Endosome fusion receptor
what are the 4 modes of nuclear entry?
- released segmented viral ribonucleoprotein (RNP) fit through the nuclear pores
- viral portal docks onto a nuclear pore
- Also involves portal docking to nuclear pore but in this case the virus is pulled apart on the outside of the nucleus
- Binding to nuclear pore causes disruption in the nuclear membrane through which virus passes
What does non-enveloped adeno virus require for entry via endocytosis? (2)
bind to cell surface receptor
and then also requires second binding to an integrin protein
so that it may be incorporated into an endosome
name 2 intracellular motor proteins
kinesin
dynein
genome type for class 3 of the baltimore system
Double stranded RNA (dsRNA) viruses
Have:
RdRp
& Naked RNA
genome type class 5 of the baltimore system
negative sense Single stranded RNA (ssRNA) viruses
meaning they must be transcribed by a viral polymerase to produce a readable strand of mRNA. The genomes of Class V viruses may be segmented or non-segmented.
Have:
RdRp
RNA coated with protein (nucleocapsid)
genome type class 4 of the baltimore system
positive sense Single stranded RNA (ssRNA) viruses
meaning they can be directly read by ribosomes to translate into proteins.
Have:
No RdRp
Naked RNA
Exceptons:
Retrovirus,
Coronavirus
explain RdRp
RNA dependent RNA polymerase
Viral enzymes that copy viral RNA from DNA.
catalyzes the replication of RNA from an RNA template.
note: diff sources claim either RNA or DNA as template
Builds new RNA strand in the 5’ to 3’ direction
what are The two modes of initiation of RNA synthesis
De novo initiation (de novo = anew)
&
Primer-dependent initiation
De novo initiation of RNA synthesis begins with?
the 3’ end of the template strand
Primer-dependent initiation of RNA synthesis begins with?
a terminal protein or a capped primer, and then goes from the 3’ end of the template strand
How many types of polymerase are there?
4 kinds:
RNA dependent RNA polymerase
RNA dependent DNA polymerase
DNA dependent DNA polymerase
DNA dependent RNA polymerase
the viral genome of polio virus is?
mRNA
this means it doesn’t need to visit the host cell’s nucleus at all, it just goes directly to the cell’s ribosomes
viral RNA synthesis always occurs on what type of “platform”?
on membranous vesicles induced by the virus
these don’t exist in cells not infected by viruses
what is the correct term for describing RNA virus replication?
mRNA synthesis
it is incorrect to call it transcription (only applies to dsDNA)
genome type for class 1 of the baltimore system
double-stranded DNA viruses
e.g. HSV, adeno- & papillomaviruses
It makes use of the host polymerases to replicate its genome, and is therefore highly dependent on the host cell cycle.
genome type for class 7 of the baltimore system
gapped double-stranded DNA viruses
e.g. hepatitis B virus
they replicate via a ssRNA intermediate. The dsDNA genome is gapped, and subsequently filled in to form a closed circle serving as a template for production of viral mRNA. To reproduce the genome, RNA is reverse transcribed back to DNA.
genome type for class 2 of the baltimore system
single-stranded DNA viruses
e.g. parvo virus
Most ssDNA viruses have circular genomes and replicate mostly within the nucleus by a rolling circle mechanism.
genome type for class 6 of the baltimore system
positive-strand RNA viruses with reverse trasnscriptase
e.g. retroviruses
they replicate through a DNA intermediate which is later incorporated into the cell genome.
What is the first biosynthetic event that must take place after viral DNA enters the cell?
The first biosynthetic event for viral dsDNA is mRNA synthesis (transcription).
what type of viral genome is the only type that you can make mRNA straight from
dsDNA is the only DNA that you can make mRNA straight from
DdRp
DNA-dependent RNA polymerase
Found in all Eukaryotic cells – we make them too in the nucleus!
◦ Three kinds of polymerase enzymes
All initiate RNA synthesis de novo (= no primer needed)
how many types of DdRp are there
RNA pol I
RNA pol II
RNA pol III
What type of viruses encode an RNA polymerase?
Only DNA viruses that replicate in cytoplasm
(e.g. Poxvirus, giant viruses) encode an RNA pol
Polyadenylation
is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA).
this happens to viral pre-mRNA just before it exits the nucleus on the road to becoming finished mRNA
tata sequence
also known as the TATA box
is a sequence of DNA found in the core promoter region of genes
The TATA box is considered a non-coding DNA sequence
it contains a consensus sequence characterized by repeating T and A base pairs.
is the site of preinitiation complex formation, which is the first step in transcription initiation in eukaryotes.
the core promoter region is
the DNA segment of 50–100 bp within which transcription initiates
what is Modular organization
DNA binding proteins have a modular organization
the proteins function is to control of transcription and translation, DNA repair, splicing etc.
modular organization means that these various proteins are organized together but in distinct modules of their own
“regions with specialized functions”
what is a promoter in relation to transcription
is a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene.
The resulting transcription produces an RNA molecule (such as mRNA).
Origin of transcriptional components for retroviruses with simple genomes?
Host only
Origin of transcriptional components for Bacteriophages T3, T7?
Host + 1 viral protein
Origin of transcriptional components for Hepadnaviruses, parvoviruses,
papillomaviruses, polyomaviruses, retroviruses with complex genomes?
Host + 1 viral protein
Origin of transcriptional components for Adenoviruses, herpesviruses?
Host + >1 viral protein that stimulate transcription
Origin of transcriptional components for Mimiviruses, Poxviruses?
Viral
what is Cascade regulation
a type of Regulation of transcription by viral proteins
a la You make one thing to will also effect something else downstream
what is Positive (or negative) autoregulatory loop
a type of Regulation of transcription by viral proteins
E.g. Protein X stimulates its own promoter, you make many more transcripts
Histone
A type of protein found in chromosomes. Histones bind to DNA, help give chromosomes their shape, and help control the activity of genes.
They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin.
what are the 2 types of splicing called?
what is the difference between them?
Constitutive splicing is the process of intron removal and exon ligation of the majority of the exons in the order in which they appear in a gene.
Alternative splicing is a deviation from this preferred sequence where certain exons are skipped resulting in various forms of mature mRNA.
Why is viral DNA replication always delayed after infection?
The transcription phase of replication is required first. Viral DNA replication always requires synthesis of at least one viral protein before replication can begin.
semi conservative and conservative replication
In semi-conservative replication each strand makes its own daughter strand.
In conservative replication only one daughter strand is produced. produces one helix made entirely of old DNA and one helix made entirely of new DNA.
which way is dna read and which way is it built
the template strand is read in the 3’ to 5’ direction
so
the new strand is synthesized in the 5’ to 3’ direction
exonuclease function
DNA replication enzyme that acts as a proofreaders during DNA polymerisation in DNA replication, to remove unusual DNA structures
What are the two main mechanisms of dsDNA synthesis called?
Replication fork-method & strand displacement method.
On what strand is DNA synthesis continuous?
on the leading strand
On what strand is DNA synthesis interrupted?
on the lagging strand
topoisomerase function
removes helical twists by cutting a DNA strand and then resealing the cut thus they unwind supercoiled molecules.
what is ori
is the origin of replication
They have binding sites for transcriptional regulators. Viruses have 1-3 Ori’s depending on the virus.
why do viruses not replicate well in quiescent(dormant/nonreplicating) cells?
Most of our cells do not divide or do so rarely.
Viruses do not replicate well in quiescent cells because they need the host’s replication machinery to replicate themselves.
So viruses must induce host replication proteins, done by the virus encoded early gene products.
