Virology - Lecture 3 & 4

Front 1

Viral genome can contain genetic information in the form of both:

Back 1

RNA and DNA

Front 2

What are the 4 types of DNA genomes?

Back 2

1. ss linear (-) sense
2. ss linear (+) sense
3. ds linear
4. ds circular

Front 3

(+) sense is also considered?

Back 3

mRNA

Front 4

Why is (+) sense more pathogenic than (-) sense?

Back 4

(+) sense is readily able to be translated by host cells whereas as the (-) sense (antisense) is a compliment to the (+) sense and must be converted to (+) sense before translation

Front 5

What are the 5 types of RNA genomes?

Back 5

1. ss linear (-) sense
2. ss linear (+) sense
3. ss linear (-) sense; segmented
4. ds linear; segmented
5. ss circular (-) sense

Front 6

What are the two ways through which viruses maintain genetic diversity?

Back 6

1. mutation
2. recombination

Front 7

What are the 8 different types of mutations that can occur?

Back 7

1. point mutation (single change in nucleotide)
2. substitution mutation (nucleotide substituted from original at single pt)
3. inversion (b/w 2 adjacent molecules)
4. insertion (of one or more nt)
5. deletion (of one or more nt)
6. silent mutation (no change in phenotype)
7. missense mutation (effect on phenotype)
8. nonsense mutation (stop signal occurs which truncates gene product)

Front 8

Change in ________ leads to discovery of changes in __________.

Back 8

phenotype; genotype

Front 9

What are the 3 different types of mutant viruses?

Back 9

1. strain
2. type
3. variant

Front 10

Define strain mutant.
Ex from class.

Back 10

Same virus, but isolated from different patients or geographical locations.

ex. H5N1 - different levels of pathogenicity and infectivity for humans

Front 11

Define type mutation.

Also known as?

Ex from class.

Back 11

Same virus, but responds differently to antibody detection.

Serotypes

ex. adenovirus - over 100 serotypes which infect humans

Front 12

2 examples of adenovirus

Back 12

1. acute respiratory distress syndrome
2. conjunctivitis

Front 13

Define variant mutation.

ex. from class

Back 13

Virus that has phenotype different from wild-type (unknown genetic mutation)

ex. HIV - variants resistant to RT inhibitors

Front 14

_______ of viruses can have different _______.

Back 14

strains; variants

Front 15

Frequency of spontaneous mutations in 1. animals, 2. DNA and 3. RNA?

Back 15

1. animals - 1 nt/ every 10^9 (1 in a billion)
2. DNA - 1 nt/ every 10^9 (1 in a billion)
3. RNA - 1 nt/ every 10^3 (1 in a thousand)

Front 16

Reason for difference in mutation rate of RNA vs. DNA?

Back 16

RNA viruses have RNA-dependent RNA polymerase which is more error prone than DNA-dependent DNA polymerase

Front 17

1. All RNA viruses encode which polymerase?

2. What is the one exception of an RNA that encodes a different polymerase?

3. What polymerase does it encode?

Back 17

1. RNA dependent RNA polymerase
2. reverse transcriptase by retroviruses
3. RNA-dependent DNA polymerase

Front 18

What is recombination?

Back 18

Genetic information exchanged b/w 2 distinct genomes.

Front 19

What are the 2 mechanisms of recombination?

Back 19

1. intramolecular recombination through strand breakage and religation or strand switching occurring in all viruses that use DNA intermediate (some RNA viruses) during replication.

2. intramolecular recombination by copy-choice occurs only in RNA viruses; viral polymerase switches template strands during replication.

Front 20

What is homologous recombination?

Back 20

Similar strands of DNA cross-over and are incorporated into other virus genome during simultaneous replication of 2 proximal DNA genomes.

Front 21

What is reassortment?

Back 21

Exchange of genetic material b/w 2 segmented genomes.

Front 22

How does genetic diversity affect humans?

Back 22

Viruses become drug resistant, escape antibody recognition and/or recognize new host (swine -> human)

Front 23

7 steps of animal virus life cycle:

Back 23

1. recognition of host
2. attachment
3. penetration
4. uncoating
5. synthesis of nucleic acids/proteins: transcription, translation, replication
6. assembly
7. release from host

Front 24

The length of life cycle of a virus has clinical significance.

What is the discriminating factor that provides for a shorter window of treatment for polioviruses (8hrs) vs. herpesviruses (36 hrs)?

Back 24

polioviruses: (+) ssRNA
herpesviruses: dsDNA

since polioviruses are (+) ssRNA (aka mRNA), they are more readily translated, whereas herpesviruses needed to be transcribed first, then can be translated.

Front 25

Define attachment.

Back 25

Initial step involving specific binding of viral protein (attachment protein) to cellular protein (receptor protein).

Front 26

Type of viral attachment protein of enveloped vs. naked virus?

Back 26

Enveloped - glycoprotein

Naked - surface peptide

Front 27

Possible test question

What is tropism? ex?

Back 27

Interaction of viral attachment protein w/ cellular receptor protein.

hepatitis A has tropism for hepatocytes.

Front 28

Attachment of naked viruses?

How does this play a factor in difficulty of curing common cold?

Back 28

Naked viruses attach to host cell through direct interaction b/w viral capsid proteins (ligands) and host receptors.

In the interaction b/w rhinovirus and ICAM-1 receptor on host cell, ligand on virus is a group of aa's in a groove/canyon. Groove too small for antibody/virus recognition.

Front 29

Attachment of enveloped viruses?

Back 29

Envelope contains spikes (viral proteins), which protrude out from virion surface and interact with host receptor.

Front 30

3 types of penetration and are they seen in naked, enveloped or both?

Back 30

1. direct penetration - naked
2. fusion - enveloped
3. endocytosis - both

Front 31

Define direct penetration.

Back 31

Only genetic material enters hose cell while capsid remains extracellular

Front 32

Define fusion.

Back 32

Nucleocapsid (genome and capsid) enter the host cell

Front 33

Define endocytosis.

Back 33

Internalization of clathrin-coated or caveolin-coated pits at cell membrane. Endocytosed into intracellular vacuoles after attachment.

Front 34

What is uncoating?

Back 34

Describes the removal of the capsid to expose viral genome to the inside of the host cell.

Front 35

Once uncoated, what are the two possible next steps for genetic material?

Back 35

1. remain in cytosol for replication/gene expression (common w/ RNA viruses)

2. can be transported into nucleus (common w/ DNA viruses)

Front 36

What is the purpose of nuclear localization signals?

Back 36

Allow genomic material to "dock" at a nuclear pore and pass through nuclear membrane.

Front 37

Production of mRNA from DNA genomes:

1. (+) ssDNA - through intermediate
2. (+/-) dsDNA - direct

Back 37

1. (+) ssDNA -> synthesis of (-) strand -> (+/-) dsDNA intermediate -> transcription of (-) strand -> (+) mRNA

2. (+/-) dsDNA -> transcription of (-) strand -> (+) mRNA

Front 38

Production of mRNA from RNA genomes:

1. (+/-) dsRNA (direct)
2. (+) ssRNA (direct)
3. (+) ssRNA (RT) (dsDNA intermediate)
4. (-) ssRNA (direct)

Back 38

1. (+/-) dsRNA -> transcription of (-) strand -> mRNA
2. (+) ssRNA -> direct use as mRNA
3. (+) ssRNA -> RT makes DNA from RNA -> (-) ssDNA strand -> replicase copies the (-) strand -> (+/-) dsDNA intermediate -> transcription of (-) strand -> (+) mRNA
4. (-) ssRNA -> transcription of (-) strand -> (+) mRNA

Front 39

What occurs if genetic material enters nucleus for replication?

Back 39

The mRNA which is produced there must exit the nucleus for translation.

Front 40

1. How does replication of DNA genomes occur?

2. How do dsDNA viruses typically replicate?

3. How do ssDNA viruses typically replicate?

Back 40

1. Direct DNA -> DNA copying by either viral or cellular DNA polymerase enzyme

2. Typically replicate in nucleus using host factors.

3. In nucleus through dsDNA intermediate which functions as template for synthesis of ssDNA progeny.

Front 41

How are RNA genomes typically replicated?

Back 41

Usually replicated by direct RNA -> RNA copying requiring viral replicase enzyme

Front 42

Both DNA and RNA have exceptions to typical replication. What is the exception and how are they different from typical replication:

1. DNA
2. RNA

Back 42

1. Poxviridase - replication is in the cytosol

2. Retrovirus - RNA is copied indirectly through path of RNA -> DNA -> RNA

Front 43

What enzyme is required for retroviral replication (RNA -> DNA) step?

Back 43

Reverse transcriptase

Front 44

What 3 things does each virion contain before leaving the infected cell?

Back 44

1. viral nucleic acid
2. accessory proteins
3. viral enzymes required for infection

Front 45

What are inclusion bodies?

Back 45

Compact masses of viruses present in nucleus or cytoplasm of host

Front 46

_______ use packaging sequences for assembly, whereas ______ use pac sites.

Back 46

icosahedral virions; hilical virions

Front 47

How do icosahedral virions assemble?

Back 47

Spontaneous assembly occurs. The genome includes a packing sequence bound by a protein which stuffs genome into the empty capsid.

Front 48

How do helical virions assemble?

Back 48

Genomic material is used as a starting point. Capsomer subuints bind to pac sites in genomic material, and assembly begins. Continues spontaneously until genome is surrounded.

Front 49

What essential step is required during maturation for virion to be infection?

Back 49

Processing of protein precursors to final product through protease activity

Front 50

What are the 3 mechanisms of release of virions from infected cells?

Back 50

1. Budding
2. Cell lysis
3. Exocytosis

Front 51

What is budding? Examples of budding?

Back 51

Process by which assembled virions distend through membrane and become enveloped. Virions incorporate both host and viral proteins.

ex.
HIV - through plasma membrane
herpes - through nuclear membrane
Hep B - ER
Influenza virus - vesicles

Front 52

What is cell lysis?

Back 52

When cell becomes overwhelmed by viral load, cell breaks open and releases viral particles.

Front 53

What is exocytosis?

Back 53

Similar to budding, but does not acquire portion of host cell membrane. Budding occurs through internal membrane

Front 54

Naked, enveloped, both:

Exocytosis is done by ______
Budding is done by _____
Cell lysis is done by _____

Back 54

both
enveloped
naked