M13: Introduction to Viruses: Viral Growth and Replication Flashcards Preview

Microbiology > M13: Introduction to Viruses: Viral Growth and Replication > Flashcards

Flashcards in M13: Introduction to Viruses: Viral Growth and Replication Deck (36)
1

Properties of viruses:

Viruses are (obligate / facultative) (intracellular / extracellular) parasites that use the machinery of the host to replicate.

The virus genome is composed either of _ or _ surrounded by a protein _: the capsid of some viruses is surrounded by an _

On its own, a virus may be considered as an inert biochemical complex since it cannot _ outside of a living cell.

Once it has invaded a cell it is able to direct the host cell machinery to _.

obligate
intracellular

DNA or RNA
capsid
envelope

replicate

synthesize new intact infectious virus particles (virions)

2

Properties of viruses:

Viruses attach to host cells by binding to receptors expressed on the host cell surface; the virus then enters host cells by _ or direct penetration of the host cell membrane.

Viruses lack the genetic information necessary for the generation of _ or for _.

Because viruses are _, they are entirely dependent on _ for chance movement and spread to infect other susceptible cells.

Can be acquired from other _ or from the _.

endocytosis

metabolic energy (ATP)
protein synthesis (ribosomes)

non-motile
external physical factors

humans
environment

3

Properties of viruses:

Infection within the host is controlled primarily by _. Some viruses can escape elimination by the _ (latent or persistent viral infections).

Can be diagnosed by inoculation of _, _ staining and identification of virus particles or antigens or by detection of viral nucleic acids (_).

Viruses are rapidly and constantly evolving – they have high _ and _ rates. This allows them to evade host defenses and to develop antiviral drug resistance.

There are relatively few effective treatments for viruses.

cell-mediated immunity
immune system

cell cultures
immunocytochemical
PCR

replication
mutation

4

Virus Structure:

The genome of a virus is either a _ molecule or one or more molecules of _

• The viral genome is always enclosed within a protein shell called a _. Most exhibit one of two kinds of symmetry (2)

• Capsids may or not be composed of _, which are defined as morphologic subunits of the capsid discernible by electron microscopy.

• Capsids are formed by the specific _ of capsid proteins.

• Virus particles come in two forms:
- _ – composed of a viral genome enclosed within a capsid (_).
- _ – composed of a nucleocapsid surrounded by a lipid-containing envelope.

DNA
RNA

capsid
- Helical or rod shaped capsids
- Spherical capsid with icosahedral symmetry

capsomeres

clustering

- Nonenveloped (nucleocapsid).
- Enveloped

5

Definitions:

Virion - The _

Viral Genome – the viral _

Capsid – The protein _ surrounding the viral _

Capsomere - a clustering of _ discernible by electron microscopy.

Nucleocapsid - The viral _ + the _

Nonenveloped viruses - have only the viral _ and _ (naked nucleocapsids, Adenovirus).

Enveloped viruses – have a _ external to the _

intact, infectious viral particle

nucleic acid (either DNA or RNA)

shell, nucleic acid

capsid proteins

genome, capsid

genome, capsid

lipoprotein membrane, protein capsid

6

Importance of viral surface proteins:

1. The proteins on the viral surface can determine viral _ (_)

2. Neutralizing antibodies can recognize and bind to proteins on the viral surface and interfere with the ability of a virus to _, thus neutralizing the infectivity of a virus.

a. For nonenveloped viruses, neutralizing antibodies recognize the _ proteins.

b. For enveloped viruses, neutralizing antibodies recognize the _ proteins, typically _ that stick out from the lipoprotein membrane.

3. The envelope is an essential part of the infectious virion for _ viruses.

a. Without its envelope, the virus is _.

b. Enveloped viruses are in general (easier / harder) to destroy than nonenveloped viruses.

1. tropism (what cell types the virus can infect)

2. enter a cell

a. capsid

b. outer envelope, glycoproteins

3. enveloped

a. noninfectious

b. easier

7

Symmetry:

Virus capsids demonstrate one of two types of symmetry. (2)

Helical
Icosahedral

8

Symmetry:
Helical:

_ proteins are arranged in a helical coil.

One can visualize a helix by forming a two-dimensional lattice and rolling it into a cylindrical structure of a diameter that accommodates the viral _.

Animal viruses with helical nucleocapsids also possess _.

Capsid

nucleic acid

envelopes

9

Symmetry:
Icosahedral:

Capsid proteins are arranged in an icosahedron or _ structure.

The most economical way to build a spherical shell of maximal internal volume is to arrange (symmetric / nonsymmetric) proteins with icosahedral symmetry.

An icosahedron comprises 20 triangular faces organized with characteristic _, _, and _-fold axis of rotational symmetry.

spherical

nonsymmetric

2-, 3-, and 5-fold

10

Classification of Viruses:

Baltimore Classification System – Six classes based on the nature of the viral genome.

DNA
- dsDNA
- ssDNA

RNA
- dsRNA
- ssRNA
--> plus strand --> retroviruses
--> minus strand

11

DNA Viruses:

• Two classes of DNA viruses – _ and _

• Seven families (7)

• The initials of DNA virus families spells (HHAPPPI)

• All DNA viruses except _ are dsDNA

• All are linear except _ and _ (circular).

• All have icosahedral capsid except _

• All replicate in the nucleus except _

• Enveloped (4)

• Naked (noneveloped) (3)

dsDNA and ssDNA

hepadna, herpes, adeno, pox, papova, parvo, irido

parvoviruses

papovaviruses and hepadnaviruses

pox

pox

hepadna, pox, herpes, irido

parvo, adeno, papova

12

DNA Viruses:

ssDNA

--> nonenveloped (1)

dsDNA

--> linear
--> --> icosahedral capsid, replicate in nucleus
--> --> --> enveloped (2)
--> --> --> nonenveloped (1)
--> --> nonicosahedral capsid, doesn't replicate in nucleus, enveloped (1)

--> circular
--> --> enveloped (1)
--> --> nonenveloped (1)

PARVOviridae

HERPESviridae
IRIDOviridae

ADENOviridae

POXviridae

HEPADNAviridae

PAPOVAviridae

13

RNA Viruses:

Four classes of RNA viruses containing thirteen medically relevant families.

1. ss(+)RNA - (#) families
2. ss(-)RNA - (#) families
3. segmented ss(-)RNA - (#) families
4. segmented dsRNA – _

six

three

three

reoviruses

14

RNA Viruses:

dsRNA
--> nonenveloped (1)

ssRNA(-)
--> enveloped (6)

ssRNA(+)
--> enveloped (4)
--> nonenveloped (2)

* segmented genomes

REOviridae*

ARENAviridae*
BUNYAviridae*
FILOviridae
ORTHOMYXOviridae*
PARAMYXOviridae
RHABDOviridae

TOGAviridae
CORONAviridae
FLAVIviridae
RETROviridae

PICORNAviridae
CALCIviridae

15

RNA Viruses:
Mnemonic

Courageous - corona
Bunyan - bunya*
Fighter - filo
Pilots - picorna
Can - calici
Fly - flavi
Over - orthomyxo*
Paraguay - paramyxo
And - arena*
Rhapidly - rhabdo*
Return - retro
To - toga
Reo - reo*

16

The Life cycle of Viruses:
Initiation Phase (3)

Attachment
Penetration
Uncoating

17

The Life cycle of Viruses:
Initiation Phase:

Attachment:

Attachment of the viral particle to the cell occurs via binding of a protein on the virion _ to a cell-surface protein that acts as the viral _.

The influenza virus _ protein binds to sialic acid, found as antennary sugars on most complex oligosaccharides found on cell surface proteins and lipids. Both _ and entry are mediated by this binding.

Penetration:

Movement of the complete _ or the _ through the cell plasma membrane

1. _ between the viral lipid envelope and the cell plasma membrane - this can occur for (enveloped / unenveloped) viruses only.
2. Receptor-mediated _ – enveloped or unenveloped viruses.
3. Some viruses enter cells by poorly understood mechanisms.

Uncoating:
_ of the viral genome from the viral capsid.

surface
receptor

Hemagglutinin (HA)
attachment

viral particle
nucleocapsid

1. Fusion, enveloped
2. endocytosis

Release

18

The Life cycle of Viruses:
Replication Phase (2)

Gene expression
Genome Replication

19

The Life cycle of Viruses:
Replication Phase:

Gene expression - synthesis of _.

Genome Replication - synthesis of _. Hundreds to thousands of copies of the viral genome are produced.

NOTE: Some viruses (e.g. _ viruses) have early and late gene expression phases

viral proteins

viral nucleic acid

DNA

20

The Life cycle of Viruses:
Release Phase (2)

Assembly
Release/Egress

21

The Life cycle of Viruses:
Release Phase:

Assembly - viral particles are assembled = the viral _ + the viral _ + other virion-associated _.

NOTE: _ are cellular structures or “factories” where viral replication and assembly takes place (can be nuclear or cytoplasmic, depending on the virus).

Release/Egress – movement to the _ and release of _.

1. _ of the infected cell may or may not occur.

2. Enveloped viruses exit from the infected cell either by
• _ through the plasma membrane
• _ of secretory vesicles containing virus particles with the plasma membrane.

3. All enveloped viruses derive their envelopes from the _ (e.g. _, or _).

4. Nonenveloped viruses usually exit by _ of the cell, but can also exit by unknown mechanisms that do not cause cell _.

Once the progeny virions have been released, they can initiate _. Hundreds to thousands of infectious virions are produced in each infected cell.

capsid
genome
proteins

Inclusion bodies

cell surface
infectious virus particles

1. Death

2. budding, fusion

3. cellular membrane, (plasma or nuclear membranes)

4. lysis, lysis

a new round of infection and virus replication in new cells

22

Replication Strategies of Viruses:

Although all viruses need _ in order to synthesize viral proteins, most viruses _ to replicate the viral genome (viral _).

EXCEPTION: _ (the only single-stranded DNA viruses) use the host-cell DNA polymerase to replicate their DNA.

host cell enzymes
encode their own enzymes
polymerases

parvoviruses

23

Replication Strategies of Viruses:
Sites of replication:

1. Most DNA viruses replicate their nucleic acid and assemble into nucleocapsid complexes in the _.

EXCEPTION: poxviruses are DNA viruses that replicate entirely in the _; they encode their own _, their own _ for transcription of mRNA, as well as enzymes for RNA _ and _.

2. Most RNA viruses replicate and assemble entirely in the _.

EXCEPTION: Influenza viruses are unusual segmented negative-sense RNA virus that replicate their RNA genomes and make mRNAs in the _.

1. nucleus

cytoplasm
DNA polymerase
RNA polymerase
capping
polyadenylation

2. cytoplasm

nucleus

24

Replication Strategies of Viruses:

Viral replication is associated with a (high / low) mutation rate. This is an important mechanism of _ and anti-viral _.

Viral polymerases are _ – especially the RNA-dependent RNA polymerases (RNA viruses) which lack _ ability.

high
immune evasion
drug resistance

error-prone
proofreading

25

Central Dogma of Molecular Biology:

Information flow in cells goes from:
DNA TO DNA (_)
DNA TO RNA (_)
RNA TO PROTEIN (_)

REPLICATION
TRANSCRIPTION
TRANSLATION

26

Replication Strategies of Viruses:
Central Dogma for virus infected cells:

Information flow during viral replication goes from:

DNA TO DNA - _ dependent _ polymerase - _ and _

RNA to RNA - _ dependent _ polymerase - _

RNA to DNA - _ dependent _ polymerase - _

DNA TO RNA - _ dependent _ polymerase - _

RNA TO PROTEIN (_)

DNA
DNA
(DdDp)
DNA Viruses and Cells

RNA
RNA
(RdRp)
RNA Viruses

RNA
DNA
(RdDp)
Retroviruses

DNA
RNA
(DdRp)
Cells

TRANSLATION

27

Replication Strategies of Viruses:

Once inside cells the viral genomes primary function is to _.

However, viral genomes do not encode the machinery to carry out protein synthesis so they must produce _ that can be read by host cells mRNA translation system.

make viral proteins

messenger RNAs (mRNAs)

28

Replication Strategies of Viruses:
Important conventions: plus (+) and minus (-) strands:

mRNA is defined as the (positive / negative) strand, because it contains _ information.

A strand of DNA of equivalent polarity is also designated as a (+ / -) strand: i.e., if it were RNA it would be translated into _.

The RNA and DNA complement of this strand is the (+ / -) stand.

This strand cannot be _; it must first be copied to the other strand.

The (+) strand has (5’-3’ / 3’-5’) polarity and the (-) stand (5’-3’ / 3’-5’) polarity.

positive (+)
immediately translatable

(+)
protein

(-)

translated

5’-3’
3’-5’

29

DNA Viral Genome Replication:

1. Encode their own viral _ (exception: _, the only single stranded DNA viruses).

2. The (host / viral) DNA polymerase is more efficient than (host / viral) DNA pol at replicating viral DNA.

3. Viral _ are important targets of antiviral therapy.

4. Only the viral DNA _ is “required” for infectivity. The cellular machinery can make all the necessary proteins from the DNA (including viral polymerase).

5. Early viral proteins are made (before / after) DNA replication and are important for altering the _ and for viral genome _ (e.g. viral polymerase).

6. Late viral proteins are made (before / after) DNA replication and are important for virus _ and _ (e.g. nucleocapsid structural proteins).

7. (Small / Large) DNA viruses like the herpesviruses, exhibit a more complex pattern of gene expression that is temporally divided into three classes (3)

Expression of the immediate early proteins is required for expression of _ and _ genes. The early genes encode proteins required for viral DNA _ and late genes encode _ proteins.

1. DNA polymerase, parvoviruses

2. viral, host

3. polymerases

4. genome

5. before, host cell, replication

6. after, structure, assembly

7. Large, immediate early, early, and late.

early and late
replication
structural

30

RNA Viruses:

The genomes of RNA viruses come in a number of conformations:
- _ stranded of _ or _ polarity
- _ stranded
- _ or _

These structurally diverse viral RNA genomes share a common requirement: they must make _ for assembly into virions and make _ for the synthesis of viral proteins. Require viral _.

The genomes of all RNA viruses except _ encode an RNA-dependent RNA polymerase to catalyze the synthesis of new genomes and mRNA.

- single, (+) or (–)
- double
- unimolecular, segmented

copies of themselves
mRNA
polymerase

retroviruses

31

Replication Strategy of Positive Sense RNA Viruses:

1. Viral RNA genome brought in with the virus can function as _ to encode viral proteins using host cell translation machinery.

2. Viral RNA polymerase made in step 1 used to make _ copies of the viral genome – some of the new genomes are used for _ of viral proteins (capsid, envelope, polymerase).

3. Some of the Viral (+) RNA is _.

1. mRNA

2. complementary, translation

3. packaged into new virus particles to generate new infectious virus

32

Replication Strategy of Negative Sense RNA Viruses:

1. Negative Strand Viruses Require a packaged _. (+ / -) RNA is converted to (+ / -) RNA using RNA polymerase brought into the cell as part of the virus particle.

2. Viral (+ / -)RNA are translated by the host cell machinery
- make (4)

3. RNA polymerase makes (+ / -) RNA which is packaged into virus particles along RNA polymerase to generate _.

RNA polymerase
(-)
(+)

(+)
capsid, envelope, RNA polymerase plus other viral proteins

(-)
new infectious virus

33

Segmented Negative Sense RNA Viruses:

1. _ like other negative sense RNA viruses

2. Can swap _ (reassortment)

3. Example: _

1. Replicate

2. RNA segments

3. Influenza viruses

34

Replication Strategy of Retroviruses:

1. +RNA is converted to dsDNA using _ brought into the cell as part of the virus particle

2. Integration of the viral dsDNA genome into host cell DNA to generate the _
- _ brought into the cell as part of the virus particle carries out this step.

3. Viral _ are made from the provirus genome using the host cell machinery.

4. Viral mRNAs are _ by the host cell machinery
- make (6)

5. Some of the viral RNA made in step 3 is packaged into new virus particles along with _, _, and _ to generate new infectious virus.

1. reverse transcriptase (RT)

2. provirus
- integrase

3. mRNAs

4. translated
- capsid, envelope, RT, protease and integrase plus other viral proteins

5. RT, integrase and protease

35

Hepatitis B Virus Replication (Hepadnavirus):

Hepadnavirus family

(Completely / Incompletely) (single / double) stranded DNA virus

Unique DNA virus that uses _ for replication

Gapped DNA repaired in the _ – covalently closed circle

Viral mRNA and Pregenomic RNA are made using _.

Pregenomic RNA is exported to the _ where it serves as template for RT to form _ within newly formed viral particles.

1.If enough envelope proteins available the particle is _.

2. If not enough envelope proteins, the particle is _.

Incompletely
double

reverse transcriptase

nucleus

host cell machinery

cytoplasm
dsDNA

1. released from the cell

2. directed back to the nucleus

36

Properties of viruses:

Direct contact routes (2)

Environmental routes (3)

sexual contact
vertical transmission

respiratory (aerosols)
gastrointestinal (fecal-oral contamination)
transcutaneous (inoculation)