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Molecular Virology > Genetics and replication > Flashcards

Genetics and replication Flashcards

1
Q

Principles of viral genetics:

A

2 Major principles:
A universal function of the viral genome: encode for specific proteins
All viral genomes must be copied to produce mRNA that can be read by the host ribosomes

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2
Q

The Baltimore system integrates these 2 principles:

A

There are 7 major types of viral genomes within this system

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3
Q

All viruses with RNA genomes must either…

A

encode an RNA-dependent RNA polymerase (to synthesize mRNA) or reverse transcriptase (RNA-DNA)

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4
Q

Rule:

A

Viral genomes must make mRNA that can be read by host ribosomes

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5
Q

What info is encoded in a viral genome:

A

Gene products and regulatory signals required for:
Replication
Efficient expression of the genome
Assembly and packaging of the genome
Regulation and timing of the replication cycle
Modulation of host responses
Spread to other cells and hosts

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6
Q

What information is encoded in a viral genome?

A

Information not contained in viral genomes
Genes encoding a complete protein synthesis machinery (e.g. ribosomal RNA and translational proteins)
Genes encoding proteins of energy metabolism

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7
Q

Terminology:

A

mRNA: positive (+) strand because it can be translated ( RNA is ready!)
Negative (-) strand cannot be translated and must first be copied to make the + strand
Ambisense RNA contains both (+) and (-) sequences
A strand of DNA is considered as a (+) strand

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8
Q

DNA VS RNA Genomes:

A 
DNA genomes
The host genetic system is based on DNA
Many DNA viruses emulate host
Use host polymerases to replicate genome
Evolved mechanisms

RNA genomes
Cells have no RNA-dependent RNA polymerase (RdRp)
RNA virus genomes encode RdRp
RdRp produce RNA genomes and mRNA from RNA templates

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9
Q

The seven classes of viral genome:

A 
dsDNA
Gapped dsDNA
ssDNA
dsRNA
ss(+)RNA
ss(-)RNA
ss(+)RNA with DNA intermediate
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10
Q

What is dsDNA transcribed by?

A

dsDNA is transcribed by either host DNA polymerase( generally smaller viruses because of limited space) eg. Polyoma and papilloma

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11
Q

What do other larger DNA genomes encode?

A

Other larger DNA genomes encode their own DNA polymerase- genome is larger- herpesvirus

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12
Q

Gapped dsDNA ( 7th) Hepadnavirus ( hepatitis B).

A

Gapped dsDNA ( 7th) Hepadnavirus ( hepatitis B). Partially dbl strand.This genome cannot be transcribed- fill the gap – has an attached RNA – RT – RNA- DNA

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13
Q

Parvovirus linear ssDNA:

A

small genome genome first made double stranded by cellular enzymes – dbl stranded and transcribed into mRNA

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14
Q

dsRNA (Reoviridae) + and - strand:

A

Ds RNA( Reovirirdae) + and – strand ds RNA cant be translated directly into MRNA therefore have package their own RdRp.

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15
Q

Structure and complexity of viral genomes:

A 
Linear
Circular
Segmented
Gapped DNA ( 7th Baltimore class)
Single-stranded (+) strand
Single-stranded (-) strand
Single stranded, ambisense ( ambisense RNA contains both (+) and (–) sequences) 
Double-stranded
DNA with short RNA segment
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16
Q

Sources of diversity in viral genomes: Mutations

A

Mutations: A change in the genotype of an organism not resulting from recombination. In short it is a substitution of one nucleotide for another.
There are different types of mutations

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17
Q

Sources of diversity in viral genomes: Effect of a mutation

A

Effect of a mutation: may lead to a change in the structure of the protein coded for by a nucleotide sequence or modify gene regulation.

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18
Q

Types of mutations:

A
  • Normal
  • Substitution[Silent mutation, Missense mutation, Nonsense mutation]
  • Insertion [Frameshift mutation]
  • Deletion
  • Inversion
  • Wild - type mRNA
  • Wild - type polypeptide
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19
Q

Types of mutations:

A

. a. Single nucleotide polymorphism aka point mutation
- when a single nucleotide in a genome differs between members of a species

  b. Indels (insertions, deletions)  Frameshift mutations - involves single nts or small blocks of nts
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20
Q

Single-nucleotide polymorphism

A

Transition:
- a mutation changing a purine to another purine, or a pyrimidine to
another pyrimidine

  • A ↔ G C ↔T(U)

Transversion:

A mutation changing a purine to a pyrimidine or a pyrimidine to a purine

  • A ↔ C A ↔ T(U)
    G ↔ C G ↔ T(U
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21
Q

INDELS:

A

Changes the reading frame of the genetic code- misreading of all downstream nucleotides

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22
Q

Effects of Mutations:

A
  1. Synonymous or silent mutation
    - does not give rise to an amino acid substitution –
    point mutation in 3rd nt of codon often silent – encodes same AA
    5’ AUG UUU ACA AAA CUG UAA 3’
    met- phe- thr- lys- leu- COOH

5’ AUG UUU ACC AAA CUG UAA 3’
met- phe- thr- lys- leu- COOH

  1. Non-synonymous or missense mutation
    - gives rise to an amino acid substitution - may be lethal because non-functional gene product may be produced
    5’ AUG UUU ACA AAA UAA 3’
    met- phe- thr- lys- COOH

5’ AUG UUU AUA AAA UAA 3’
met- phe- Ile- lys- COOH

  1. Neutral mutation (neutral not always = silent)
    - does not affect the fitness in the environment under consideration
  2. Nonsense mutation
    - point mutation that results in a premature stop codon

5’ AUG UUU AUA AAA CUC UAA 3’
met- phe- Ile- lys- leu- COOH

5’ AUG UUU AUA UAA CUC UAA 3’
met- phe – Ile - COOH

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23
Q

Interaction between viruses:

A

Genetic recombination between viruses
Recombination

Reassortment

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24
Q

Reassortment: A consequence of segmented genomes

A
  • a type of recombination which occurs in viruses that have segmented genomes, whether ssRNA or dsRNA
  • single cell infected with 2 segmented (related) viruses
  • exchange of segments
  • production of various stable reassortants
    {Influenza, Rotavirus}
25
Q

Recombination:

A

Formation of new covalently linked combinations of genetic material from 2 different parental genomes or between different sites of the same genome

26
Q

What does recombination occur with?

A

Recombination occurs with both DNA and RNA viruses, with participation of the host or viral replication machinery

27
Q

Two methods of recombination:

A

Strand breakage and re-ligation (– less common)

Recombination by ‘copy-choice’

28
Q

Reactivation:

A

Non-infectious parents  infectious progeny

Reactivation is the generation of infectious (recombinant) progeny from non-infectious parental virus genomes.

29
Q

Reactivation (example):

A

Example: the rescue of defective, long-dormant HIV proviruses during the long clinical course of acquired immune deficiency syndrome (AIDS) may result in increased antigenic diversity and contribute to the pathogenesis of the disease

30
Q

Reversion:

A

A mutant organism sometimes regains its WT characteristics (process of regaining the original phenotype)

– occurs by means of an additional mutation in the mutant which restores function

31
Q

Phenotypic expression of a mutation in a gene may be reversed by

A
  1. a back mutation in the substituted nucleotide
  2. a suppressor mutation occurring elsewhere in the same gene or even in a different gene → negates the biological effect of the original mutation
32
Q

Quasispecies:

A
  • Certain viruses e.g. HIV exists as quasispecies
  • A complex mixture of rapidly evolving and competing molecular variants of RNA virus genomes that occurs in most populations of RNA viruses
  • The population of virus consists of a fleeting majority type that dominates the dynamic equilibrium
33
Q

What is the purpose of viral replication?

A

The purpose of viral replication is to generate new viral genomes and proteins in order to continue their infectious cycle and spread to a new host

34
Q

The replication strategy of viruses is dependent on the coding capacity of the genome:

A
  • Small viruses e.g. parvovirus - heavy reliance on host cell
  • Large virus e.g. poxviruses – encode most of the information required for replication. Only needs the cells for its machinery e.g. ribosomes
35
Q

Where do most genomes replicate?

A

Most RNA viruses replicate in the cytoplasm
(except Influenza and HIV)
Most DNA viruses replicate in the nucleus
(except Poxvirus)

36
Q

Overview of viral replication:

A

Viruses attach to the host cell, enter, release the genome (uncoating), replicate the genome, express whatever structural or non-structural proteins are required, self assemble and then exit

37
Q

Virus attachment:

A

Virus particles bind to host cell receptors to initiate entry
Viruses may use more than one receptor – i.e. infect different types of cell
Viruses may use a receptor and a co-receptor
Note: The first cell surface molecule essential for viral attachment is called its RECEPTOR

38
Q

Virus attachment (Example):

A

Example: HIV binds to the CD4 cell receptor and then requires an additional co-receptor such as CXCR4 for entry

39
Q

What does the cell receptor determine?

A

The cell receptor may determine the tropism of viruses (i.e. the type of cell its able to replicate in) and the host range

40
Q

What does the binding of virions to cell receptors activate?

A

Binding of virions to cell receptors may activate signalling pathways and facilitate viral entry or stimulate cellular responses that enhance pathogenesis

41
Q

Entry into the cell:

A

Is an energy-dependent process that occurs shortly after attachment: 2 mechanisms

42
Q

Two mechanisms of the entry into the cell:

A

Receptor mediated endocytosis into intracellular vacuoles via coated pits at the cell membrane
After endocytosis, vacuole fuses with lysosome
Inner environment becomes more acidic, and degradative enzymes accumulate
Fusion – only enveloped viruses. Either at the cell surface, or after internalization

43
Q

Entry into the cell:

A
  • Membranes of enveloped viruses fuse with each other, membrane fusion takes place during other cellular processes such a cell division and exocytosis.
  • Membrane fusion is mediated by binding of receptors eg with HIV hairpin movement of the heptad repeats that place the two membranes in close proximity with each other.
  • Virus and cell membrane brought together- the precise mechanisms by which the bilipid layers fuse together is not completely understood but the fusion protein – makes an opening called a fusion pore allowing exchange of material across the membrane. – specific process to ensure viral material goes to the correct compartment of the cell.
44
Q

Uncoating

A
  • Exposing the viral genome via partial or complete removal of the capsid
  • May be triggered by acidification of endosome e.g. influenza
  • Some virus genomes are released through a pore which forms by interaction of the capsid proteins with the endosomal membrane – penetration and uncoating are coupled e.g. polio
  • Some capsids are involved with trafficking the genome toward the nucleus e.g. herpesviruses
45
Q

Central dogma of molecular biology:

A

The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein. Transcription is the synthesis of an RNA copy of a segment of DNA

46
Q

What does the genomes of RNA viruses encode?

A

The genomes of all RNA viruses encode RNA dep RNA polymerase, except HIV to start the synthesis of new genomes and mRNA.

47
Q

Group 1:

A
  • dsDNA E.g. herpesviruses, adenovirus
  • Most replicate in the nucleus (exception: poxvirus)
  • Produce factors which act on host cellular machinery, and control further transcription, regulating the phases of replication (i.e. early – non-structural proteins, late – structural proteins)
48
Q

Group 2:

A
  • ssDNA e.g. Parvovirus
  • Highly reliant on host cell machinery because they possess small genomes
  • Replicate in the nucleus
  • ds DNA intermediate – forms a template to make progeny ss DNA nucleic acids
49
Q

Group 3:

A

*ds RNA with segmented genomes e.g. Reovirus
*Each segment is transcribed separately to produce monocistronic mRNAs
*Each segment is transcribed post cleavage of the polyprotein into small functional proteins
*Partial uncoating – transcription mediated by core associated RdRp
*

50
Q

Group 4:

A

*+ve sense ssRNA
2 subgroups –
*Polycistronic mRNA (i.e. polyproteins) e.g. poliovirus
*More complex with two rounds of transcription e.g. rubella
*Regulate expression in terms of ratios of the different proteins and stage of replication cycle in which they’re produced
*Successful class, with multiple members and various hosts

51
Q

Group 5:

A
  • –ve sense ss RNA
  • Two subgroups – segmented (e.g. influenza) and non-segmented (e.g. rabies)
  • The genomes is first transcribed by vRdRp to produce monocistronic mRNAs
  • This is the template for genome replication
52
Q

Group 6:

A

*+ve sense ss RNA with a DNA intermediate
E.g. HIV
*The RNA genome is a template for reverse transcription to dsDNA
*Integrates into the host cell genome

53
Q

Group 7:

A

*ds DNA with RNA intermediate
E.g. Hepatitis B virus
*Complex poorly understood replication
*Contain overlapping reading frames – compact genome

54
Q

Assembly:

A
  • Collection of all the components necessary for the formation of a mature virion
  • Viral components may accumulate within compartments in the cell – seen as inclusion bodies
55
Q

Interactions during encapsidation:

A
  • Between nucleic acid core, capsid, other cargo

* Depends on physical size, electrostatics, sequence-specific interactions

56
Q

Lipid rafts:

A
  • Membrane microdomains, usually at the cell membrane
  • Enriched with glycolipids, tightly packed cholesterol, proteins
  • Limited lateral diffusion of lipids in the membrane
57
Q

Maturation:

A

Maturation is when the virus becomes infectious

  • Involves structural changes of the viral particle
  • Frequently requires cleavage of larger proteins into smaller ones – usually requires proteases
  • Some viruses mature within the cell. Some mature after release from the cell.
58
Q

Release - Lytic:

A
  • Infected cell breaks open and releases the virus

* Usually non-enveloped viruses

59
Q

Release - Budding:

A
  • Virus buds through cell membrane or an intracellular vesicle to acquire envelope
  • May (e.g. paramyxoviruses) or may not (e.g. hepadnaviruses) be damaging to the cell

Molecular Virology (26 decks)

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