"class" directed review Flashcards
provide and overview on the 4 main structural components of a virus
• Viruses are non-living particles outside a host cell called virions.
• Virions house the genetic material and functions as a gene transfer system.
• Viruses are made up
of 2 key components:
- Capsid: A layer of protein covering the genetic material.
- Genetic material: Either a DNA or RNA, but never both.
Other components varies between viruses: - Envelop: May have an extra outer covering of the capsid called an envelop.
- Nucleocapsid: Made up of capsid + envelop.
Note: Viruses without capsid are referred to as naked
Provide an overview on the functions on the capsid of a virus
Functions of the capsid
• A capsid protects the genetic component of a virus from inactivation.
• Another function is to recognize, attach and gain entry into host cells
for genetic replication.
• Capsid ensures that the virus is transported to the right host cell
where the genome can be transcribed and replicated.
• A capsid can alters its conformation and ensures the release of the
genetic material into host cells
Provide an overview on the components that constitute a viral capsid, and their symmetry
• Capsids are made up of many molecules of the same or two or more
proteins.
• Molecules making up a capsid are asymmetrical but are arranged to
form symmetrical structures.
• Symmetrical capsids entails that the appearance looks unchanged if
rotated at several angles.
• Virus capsid are Polyhedrons (exist in many forms and shapes like rod,
spiral, spike, helical).
what are the main types of capsid symmetry
- Helical shape
- Icosahedral shape
- Rod shaped
- Complex shape
Provide an example of a virus with helical symmetry
• Helical shape: ssRNA spiral or coiled shaped viruses. E.g. Tobacco Mosaic virus (TMV), influenza viruses, measles, some bacteriophages.
Provide an example of a virus with rod-shaped symmetry
• Rod-shaped viruses: Tobacco rattle virus (2 unequal RNAs).
Provide an example of a virus with filamentous symmetry
• Filamentous: some bacteriophages have either ssDNA or dsDNA.
Provide an example of a virus with icosahedral symmetry
• Icosahedral shape: Polyhedron shape. E.g. herpes simplex virus,
poliovirus, parvovirus.
Provide an example of a virus with complex symmetry
• Complex shaped viruses: smallpox and bacteriophages.
Provide an overview of helical symmetry
• Helical shaped capsids are found in many ssRNA viruses.
• The RNA is coiled in the shape of an helix and many copies of the
same protein are arranged around the coil
provide an overview of icosahedral symmetry
• Viruses with icosahedral symmetry consist of a shell made from protein molecules and arranged in the form of a scaffold to form a polyhedron.
• The virus genome have
less contact with the
capsid proteins compared
to helical-shaped viruses.
A virus icosahedron has five-, three, and two-fold axis of rotational
symmetry
What are virus capsomeres and provide an example
• Are the building blocks of a virus capsid arranged from discrete structures.
• Each capsomere is usually made up of many identical protein molecules.
• For example, the capsids
of the papiloviruses are
built from 72 identical
capsomeres.
• Note that the capsids of
some viruses can also be
constructed from more
than one type of capsomere;
E.g. Herpes viruses and
AdenovirusesProvide an overview on what a virion envelope is
(Membranes)
• Viruses may have an extra layer of protection of the capsid called an Envelop.
• Envelop is a lipid-protein structure which surrounds the capsid and the genetic material (nucleic acid) inside known as a Nucleocapsid.
• Although, the envelop may be positioned in the capsid for some viruses.
• Majority of the enveloped viruses are mostly spherical or nearly spherical
Provie a few examples of viruses wiht envelopes
Many viruses infecting animals possess envelops with helical
configuration such a the influenza virus, while a good number have
icosahedral shape (E.g. Herpes viruses).
• Fewer enveloped viruses infect plants (potato yellow dwarf virus),
while infection is rear among prokaryotes [Pseudomonas phage
φ(Phi) 6]
Provide an overview of complex viruses
- Have both the helical and icosahedral symmetry.
- Most have a icosahedral head and a helical tail attached at one of the vertices.
- The tail is attached to the head through a protein structure referred to as a Connector or Portal.
- The connector has a powerful motor that drives the virus DNA into the young virus head during assembly.
- The tail may be long (Phage λ) or short (Phage T7).
- Some specialized structures may be attached to the tail (fibres and/or base plate).
- The head houses the genome of the virus made up of dsDNA.
- Examples are the bacteriophages with complex architecture are T7 and Phage λ.
Overview of viral classification and nomenclature
• Defined viral characteristics are required prior to placing them in
specific orders, family, subfamily and genus while species grouping is
based on a number of similar characteristics.
• Thus, member of a virus species may vary in;
- Strain
- Serotypes: differences in virus antigen reaction to antibodies
- Genotype: differences in a virus gene sequence
Virus classification based on taxonomy hierarchy
- Order (ending in virales)
- Family (ending in viridae)
- Subfamily (ending in virinae)
- Genus (ending in virus)
- Species (ending in virus)
- Subspecies (may end in a number)
- strain
Modern virus taxonomy and nomenclature
aming of some virus taxonomic groups incorporated the old
name together with the taxonomic suffix. E.g. the generic and
family name for picornaviruses (small viruses) were derived by
placing the suffix (virales) and (viridae) respectively, in place of
the word virus
look at table 4 (purple) in the review slide set
Genetic classification of viruses
• A virus is made up of genetic material which is either DNA or RNA.
• This differentiates viruses from cellular organisms whose genetic unit is a DNA.
• Viruses can be divided into four groups of based on the number of strand in its genome.
1. double-stranded DNA (dsDNA)
2. single-stranded DNA (ssDNA)
3. single-stranded RNA (ssRNA)
4. double-stranded RNA (dsRNA
The genetic approach as suggested byDavid Baltimore
- DNA virus
- RNA virus
- Reverse-Transcribing Viruses
• seven classes of viruses exist based on: - type of genome
- the way in which the genome is transcribed and replicate
What is Baltimore classification based on?
Viral genome replication
• Due to the unique mode of virus transcription among
dsDNA and ssRNA gene groups, the four groups of
viruses can be subdivided into seven.
• This discovery was made by David Baltimore and now
named after him.
• He developed the system for classifying viruses based
on genome type and was named Baltimore method
for virus classification.
• This classification places virus into classes I - VII
What is the role of a capsid
• Capsid protects the nucleic acid when the virus is outside the host
cell.
• Helps bind to a suitable host cell surface receptors using spike
proteins on an envelop (if present) or transfer it’s genetic material
into host cell through endocytosis if it’s a naked virus (that is no
envelop).
• E.g. Poxvirus (complex virus) lacks a typical capsid and are covered by
a dense layer of lipoprotein
What is the role of genetic material in viruses
• Carries gene necessary to invade host cells.
• Note that the number of genes varies for each virus (few to hundreds).
• Redirect or manipulate host cell machinery into producing viral cells.
• Viruses lack protein synthesizing machinery. However, they contain
parts needed to evade host cells and manipulate the cell replicating
machinery into producing more copies of the virus rather than normal
cellular proteins
What are the basic steps of virus genome replication
- Attachment of virion to suitable host cell.
- Entry of virus into the cell
- Transcription of virus genes into mRNA (messenger RNA) molecules.
- Translation of virus mRNA into virus proteins.
- Genome replication
- Assembly of virus proteins and genomes into new virions.
- Exit of virions from host infected cells.
Note: not all viruses undergo all seven steps above, some viruses may need extra steps while some steps may occur concurrently in some viruses in which case steps 3-7 may occur at the same time
What are the important host compontents utalized by virions to attach to host cells
• Viruses that infect animals and bacteria must first attach themselves to host cell
surface barriers (cell wall for bacteria or cell membrane for animals)
• Cell membrane: Animal cells possess a cell membrane which the virus must
attach itself to via specific cell surface receptors in order to invade the cell.
• Cell wall: Likewise, bacteria cells possess a cell wall which the virus must attach
itself to via specific cell surface receptors in order to invade the cell.
• Note that virus attachment and entry in plants cell are mostly mediated by
vectors
Attachment of Animal viruses via cell receptors
- Host cell surface receptors are proteins which a virus can bind using its attachment structures prior to cell entry.
- Binding of cell surface receptors and virus attachment structures are specific like a ‘’Lock and key’’.
- Sometimes a virus may need to bind to a second host cell receptor known as a co-receptor prior to binding.
- Cell receptors and co-receptors function to mediate cell-to-cell contact and binding as well as receptors for chemokines and growth factors.
- Binding of cell surface receptors and virus attachment structures result in a conformational change in virus proteins which initiates the binding.
- Most host cell surface receptors used by viruses contain sugar molecules (glycoproteins) composed of folded domains similar to immunoglobulin.
Virus attachment sites
• Viruses possess multiple binding sites on their surfaces which is largely dependent on the absence (naked viruses) or presence of an envelop.
Virus attachment sites
naked viruses
- Naked viruses: The attachment sites for naked viruses are on the capsid which differ in topology and may be in the form of ridges (foot and mouth disease virus), or within depressions (poliovirus). Both belong to the picornavirus group of viruses.
- Also, attachment sites for some naked viruses could be on specialized structures such as spikes of rotaviruses, or on fibers and knobs of adenoviruses.
- Binding of picornaviruses to host cell receptors result in major structural changes in the virion.
Virus attachment sites
enveloped viruses
• Enveloped viruses: Host cell attachment structures for enveloped viruses are on glycoproteins present on the envelope.
Virus attachment sites
haemagglutinins
- Haemagglutinins: Some virions possess proteins which binds to immunoglobulin causing them to clump (haemagglutination). E.g. are measles virus and influenza virus.
- Forces involved in virus-host cell binding are weak forces involving hydrogen bonding, van der Waals forces and ionic forces.
- Sugar molecules on host cell receptors and /or on the virion are involved in the binding forces
- Initial binding of viruses to host cells involves weak forces which are reversible, which become irreversible with binding of more receptor.
Provide an overview on entry of viruses into animal cells
Entry: a virus must gain entry into host cells either
through the cell surface or through the an endosome
membrane (tiny vesicle forming part of a plasma
membrane which break offs into the cytoplasm) in a
process called endocytosis.
• Endocytosis: A process which serve several roles for
cells including nutrients uptake and defense against
pathogens is hijacked by viruses to gain entry into
cells.
Provide an overview of endocytosis
Entry of viruses into animal cells (Endocytosis)
• Animal viruses gain entry into host cells through two main endocytic
mechanisms:
1. Clathrin-mediated endocytosis: Clathrin is a cell protein found around
the inner side of cell membrane. Clathrin forms a coat around viruses
resulting in pit and invagination of the cell membrane which is budded
off and shed allowing the virus entry into cell. Virus examples are the
adenoviruses and vesicular stomatitis virus.
- Caveolin-mediated endocytosis: Similarly viruses such as simian virus
40 coat themselves with cell membrane protein (caveolin) allowing
them entry into cells through endocytosis
what are the two main mechanisms of viral entry into host cells
• Host cell entry may occur either by
1. Endocytosis or fusion of virus envelop containing glycoprotein with plasma membrane
2. Fusion of virus envelop with the cell endosome membrane.
Virus fusion proteins are hidden in the envelop and are released upon the binding of a virus to a
host cell receptor resulting in a series of conformational changes.
The changes fuse the virus envelop and cell membrane first from the outer layers in a process called
hemifusion, followed by fusion of the inner layers, completing the fusion process
Intracellular transport of cell-invading virus
• Microtubules: One of the cell transport systems exploited by viruses to arrive at
the nucleus.
• Most RNA viruses replicate in the cytoplasm.
• Exceptions are:
1. Retroviruses: They copy their RNA genome into DNA in the cytoplasm which
is then transported to the nucleus during cell division (mitosis) for
replication.
2. Influenza viruses: require the cell splicing machinery in the nucleus to get rid
of intervening sequences (introns).
Note that the lentiviruses, e.g. HIV can transport its DNA from the cytoplasm into
the intact nucleus with cell division in progress.
• Most DNA viruses can only replicate their genome in the nucleus and so utilize
the microtubule as a transport to the nucleus before entry through the nuclear
pores (parvoviruses, herpesviruses, retroviruses and adenoviruses).
• Exemptions are poxviruses and iridoviruses: replicate their DNA in the
cytoplasm.
provide an overview of uncoating
- Viruses shed their capsid on entry into a host cell releasing its genome.
- For animal viruses, uncoating can occur either in the cytoplasm, nuclear pore or in the nucleus.
- Virus gene replication may not occur immediately upon successful virus-cell entry.
- Host intracellular defenses such as lysosomal enzymes may neutralize infectivity before or after virus uncoating.
- In certain cases, invading viruses may initiate a latent infection rather than begin a complete replication cycle.
- Also, under favourable cell conditions (that is virus survives and in right cell), gene replication involving transcription can commence.
Provide an overview of host cell entry via bacteriophages
lysozymes to aid genome injection through the cell wall.
• Mycoplasma: Are exemptions as they lack a cell wall.
Provide an overview on the different types of viral genome replication
Virus genome replication is the fifth step in replication cycle in which
an invading virus makes copies of its genes for progeny offspring.
• Most DNA viruses copy their genes directly to DNA
• Most RNA viruses copy their genes directly to RNA
• A few DNA virus replicate their genes through RNA intermediate
• A few RNA virus replicate their genome through DNA intermediate
Replication of viruses in eukaryotic cells
• Eukaryotic viruses upon cell entry either replicate
their genome in the cytoplasm or transported into the
nucleus. Destination is dependent on the type of
genome
The genome of most DNA viruses are replicated in the nucleus; but those of some dsDNA are replicated in the cytoplasm. Most RNA viruses replicate their genome in the cytoplasm with exemption of some minus-strand RNA viruses. The reverse transcriptase viruses (retroviruses and pararetroviruses) each replicates RNA to DNA in the cytoplasm and DNA to RNA in the nucleus
Check out figure 11 in the review slide set
provides an overview of the enzymes for genome replication in viruses
Provide an overview of replication of DNA viruses
• Class I (dsDNA) and class II (ssDNA) viruses replicate their genome via dsDNA
• ssDNA synthesizes its complimentary strand to become dsDNA.
• Each viral DNA has at least one specific sequence where replication is initiated
(replication origin).
• Proteins involved in DNA replication binds to this site and they include:
1. A helicase (unwinds the double helix at that site)
2. A ssDNA binding protein (keeps the two strands apart)
3. A DNA polymerase
Provide an overview of replication of ds RNA viruses
• dsRNA replication is similar to dsDNA in that the double strand must
be unwound by helicase before replication can occur.
• Some dsRNA viruses replicate their genome by two mechanisms:
1. Semi-conservative mechanism: Some dsRNA viruses replicate their
genome similar to dsDNA whereby each double stranded progeny
molecule is made up of the parent strand and a daughter strand
(Pseudomonas phage phi 6).
2. Conserved mechanism: Some dsRNA viruses replicate their genome
in a process whereby the double stranded molecule of the infecting
virus genome is conserved
Provide and overview of replication in ss RNA viruses
• Viruses with ssRNA in class IV (+ssRNA) and class V (-SSRNA) replicate
their genome by synthesizing their complimentary strands.
• Synthesis of each RNA molecule requires the RNA-dependent RNA
polymerase at the 3’ end of the template.
• Plus-strand RNA viruses of eukaryotes replicate their RNA in
association with membranes derived from the cytoplasmic
membranous structures.
• Minus-strand RNA replicate by coating their RNA template with viral
protein and not host membrane.
Provide an overview of replication of rt viruses
• Some RNA viruses replicate their genes through DNA
intermediates.
• Some DNA viruses replicate their genome through RNA
intermediate.
• Both virus groups utilize the reverse transcriptase enzymes.
• Reverse transcription occurs within the viral structure in the
cytoplasm of host cell
list some viral culture techniques
- Virus culture techniques:
• Virus cultivation or culture: techniques involving the use of specific characteristics of a virus for multiplication.
• Virus isolation: use for obtaining identical strains of a virus.
• Virus purification: E.g. centrifugation
list some virus id techniques
- Virus identification techniques:
• Microscopy: the use of highly sensitive microscopes for the analysis of virus architecture for identification.
• Electrophoresis: separation of viral DNA and proteins by differential movement of charged particles through a membrane for identification.
• Gene analysis techniques: PCR, RT-PCR, Real-time PCR, Microarrays
Provide an overview of virus cultivation
• This refers to the propagation or growing of a virus for research
purposes.
2 major techniques:
1. Cell free culture (absence of living cells): Made from extraction of
internal components of different organisms for the cultivation of
viruses.
2. Cell culture: Majority of viruses requires supply of appropriate cells
to enable growth and multiplication
