Properties of Viruses: Structure and Fundamentals of Viral Replication Flashcards
Define Peptide
two or more amino acids linked together by a peptide bond
Define oligopeptide
a short peptide, 5-20 amino acids
Define polypeptide
extended peptide of undefined length 20+ amino acids
What is polymerase
proteins involved in replication by creating a complementary strand of DNA or RNA from a template molecule
What is mRNA
the template for protein translation with positive sense polarity and a 5’ cap and 3’ poly-A tail
Define Positive Sense
A positive sense DNA or RNA molecule is one where the genes are encoded in a form that is directly translated to the protein.
Define negative sense
Negative sense DNA or RNA molecule is one where the genes are encoded in the reverse complement of the protein coding version
Viral genomes can be encoded on a single molecule and known as
non-segmented
Viral genomes can be encoded on several different molecules and are known as
segmented
What is a virus/virion mainly comprised of
- Nucleic acid
- A protein shell/capsid
- Lipid envelope derived from host membrane (some viruses)
List of structural proteins in viruses
- Surface proteins: Hemagglutinin envelope of influenza A (IAV), VP7 of rotaviruses, gp120 of HIV
- Ion channels: M2 of IAV
- Capsid and matrix proteins : VP1-VP4 of rhinoviruses
List of non-structural proteins in viruses
- Enzymatic Functions
- Cellular Pathway disruptors
- Immunomodulators
Three examples of Enzymatic functions in virions
- for copying viral genome reverse transcriptase enzyme (e.g HIV)
- Proteases are used to cleave viral proteins (e.g FMDV 2a protein, NS3/4A of hepatitis C)
- Modifying enzymes (e.g heparinase enzyme of herpes simplex virus 2
Group 1 viruses are _______ stranded _NA viruses which replicate in the ___________ using cellular proteins or in the __________ and make their own enzymes for _________ ________ ___________.
double
DNA
nucleus
cytoplasm
nucleic acid replication
Give four examples of group 1 viruses
- Adenovirus from adenoviridae
- Herpesvirus from Herpesviridae
- Papillomavirus from papovaviridae
- Molluscum contagiosum from Poxviridae
Group 2 viruses are ___________ stranded _NA viruses. Their replication takes place in the ___________ and involves the formation of a ________ sense strand which serves as a template for the __________ strand RNA and DNA synthesis
single
DNA
nucleus
negative
positive
Give an example of a group 2 virus
Parvoviridae which causes the parvovirus B19
Group 3 viruses are _______________ stranded _NA viruses. Their genomes can be both ____________ and ___________________ as well as _____________ or ____________. There replication does not include a ______ phase
double
RNA
non-segmented
segmented
linear
circular
DNA
Give an example of a group 3 virus
Reoviridae responsible for the human rotavirus
Group 4 viruses are _____________ sense ___________ stranded _NA viruses. Their genomes can be both ____________ and _________________. Genomes act as a _____________ template for translation meaning the genome is equivalent to mRNA. Their protein generates a _____________ and all the proteins are translated simultaneously.
The genome of group 3 viruses must encode RNA dependent ___________ polymerase enzyme (_____) and its replication does not include a ___________ phase
positive
single
non-segmented
segmented
direct
polyprotein
RNA
RdRp
DNA
What are two examples of group 4 viruses
Coronaviridae responsible for corona virus
Picornaviridae reponsible for Hep A
Group five viruses are ___________ sense ___________ stranded _NA viruses. Their first step in replication is the production of ________ and the _______ act as a template for mRNA synthesis. Their replication cycle does not include a ______ phase.
negative
single
RNA
mRNA
genome
DNA
Give two examples of a group 5 viruses
Paramyxoviridae which is responsible for measles
Filoviridae which is responsible for the ebola virus
Group 6 viruses are ____________-transcribing ___________ sense, ________ stranded _NA viruses. Their genomes are ______________ but the virion may contain multiple copies. The genome must encode for _______ dependent DNA polymerase ( ) enzyme also known as reverse transcriptase. The first step in replication is production of _______ stranded _NA
reverse
positive
single
RNA
non-segmented
RNA
RdDp
double
DNA
Give an example of a group 6 virus
Retroviridae which causes HIV
What is an example of group 7 virus
Hepadnaviridae which causes Hepatitis B virus
Define taxonomy
the hierarchy of virus classification
Which committee is responsible for classifying viruses?
International Committee on the taxonomy of viruses (ICTV)
The primary criteria for classification of viruses is
pairwise sequence identity comparisons
Other than pairwise sequence identity what other criteria is used to classify bacteria?
Genome composition
Virus capsid structure
Whether the virus is enveloped or not
The mechanism of gene expression
Tropism
Pathogenicity
Define tropism
The point of entry via interactions between virus surface proteins and host cell molecules
The three types of tropism
host
cellular
tissue
What are the steps taken in virus replication
- Attachment
2 Entry - Uncoating
- Genome Replication and production mRNA (transcription)
- Production of protein (translation)
- Particle assembly
- Virion release (egress) and virion maturation in some viruses
Describe the attachment step in virus replication
- a protein on the surface of the virus binds to a receptor on the surface of host cell in accordance with its tropism
Describe the entry step in virus replication
-As the cell membrane is impermeable the virus cannot diffuse across the cell and uses types of facilitated entry like plasma membrane membrane fusion and endocytosis
Describe the uncoating process in virus replication
-This is when the virus genome is exposed to the intracellular environment of he host cell in the nucleus or cytoplasm depending on the virus
- During this stage there ma be a small change to the genome or a complete disintegration of the virion.
- Uncoating may occur at the same time as entry where the genome and other associated proteins are deposited inside
Describe the protein production process of virus replication (translation)
-some viruses synthesis their protien as a single continuous chain from a single mRNA with one start codon
-these are cleaved post translation by protease and release the individual mature proteins (Flaviviruses)
- post translational modifications like glycosylation, myristylation and the addition of a gpi anchor is common
An example of a virus that regulates the timing of translation to control their cellular environment when replicating
Herpesviruses
Describe the particle assembly process of viral replication
-New virions are assembled with all structural proteins and their genome
- Occurs in various locations depending on the virus
Describe the egress and maturation process in viral replication
-new virions are released from the host cell in a manner that is specific to the virus
-there is then complete cellular breakdown of the host cell
-there is then budding of the cell before it fully dies
-the bud then exits through exocytosis and moves on to infect the rest of the body
