Biol 409: Lecture 3 (1/26/16)

Front 1

What are the three hypotheses on the origin of viruses?

Back 1

1. Progressive (Escape): Viruses originally were in host cells but gained the ability to move between cells

2. Regressive (Reduction): Viruses are actually remnants of other cellular organisms and rely on host cells to reproduce

3. Virus First: Viruses predate or coevolved with current cellular hosts.

Front 2

Provide an example that supports the Progressive hypothesis of the origin of virus

Back 2

Viral-like transposons

Front 3

Provide an example that supports the Regressive hypothesis of the origin of viruses

Back 3

Mimivirus: putative genes associated with translation

Front 4

Provide an example that supoprts the Virus First hypothesis of the origin of viruses

Back 4

Complexity leads to cells

Front 5

Which of the following does NOT support the progressive hypothesis of the origin of viruses?

A. Self-replicating units

B. Genetic elements gained ability to move between cells

C. Viral-like transposons

D. Retrovirus mirrors retrotransposons

Back 5

A. Self-Replicating Units

Front 6

Which of the following does NOT support the Regressive hypothesis of the origin of viruses?

A. Remnants of cellular organisms

B. Originally symbiotic, then turned parasitic

C. Mimivirus

D. Complexity leads to cells

Back 6

D. Complexity leads to cells

Front 7

Which of the following does NOT suppot the regressive hypothesis of the origin of viruses?

A. Genetic elements gained ability to move between cells

B. Viruses predate or coevolved with current cellular hosts

C. Self-replicating unit

D. Complexity leads to cells

Back 7

A. Genetic elements gained ability to move between cells

Front 8

Why is a virus called the ultimate hitch hiker?

Back 8

1. It is an infectious obligate intracellular parasite. This means that it requires a host in order to survive

2. RNA or DNA genome. It can have either

3. Genome replication & protein production. All it does is replicate viruses and utilizes host machinery to do so

4. Virions-virus progeny. Its goal is viral reproduction

Front 9

A virion is composed of what two main components?

Back 9

1. Nucleic acids

2. Proteins

Front 10

Define a "Naked Virus"

Back 10

A virus surrounded only by viral proteins. It lacks an envelope

Front 11

Define an "Enveloped Virus"

Back 11

A virus surrounded by the host plasma membrane

Front 12

Which of the following is the "Naked Virus"

A. 1

B. 2

Back 12

A. 1

Front 13

Which of the following is the "Enveloped Virus"?

A. 1

B. 2

Back 13

B. 2

Front 14

Identify A

Back 14

Capsid

Front 15

Identify B

Back 15

Nucleic Acid

Front 16

Identify C

Back 16

Capsomere

Front 17

Identify D

Back 17

Nucleocapsid

Front 18

Identify E

Back 18

Capsid

Front 19

Identify F

Back 19

Nucleic Acid

Front 20

Identify G

Back 20

Envelope

Front 21

What three common functions do viruses share?

Back 21

1. Replication of viral genome

2. Packaging of viral genome into virions

3. Alter structure of the host cell making the host cell a virocell

Front 22

Deine "Virocell"

Back 22

A host cell that no longer does it's host function

Front 23

T/F: A virus requires cellular resource for replication

Back 23

True

Front 24

What type of organic molecules will a virus require for replication?

Back 24

1. Amino Acid

2. Sugar

3. Nucleoside

4. LIpids

Front 25

What type of naming conventions do viruses follow?

Back 25

There is no consistent naming system

Front 26

How have viruses been named in the past?

Back 26

1. Named after the type of disease caused

2. Origin of location

3. Discoverer

4. Associated diseases

5. Geographic location

6. How they are contracted

Front 27

Provide an example of a virus named after the specific type of disease it caused

Back 27

1. Poliovirus

2. Rabies virus

Front 28

Provide an example of a virus named after the origin of location

Back 28

1. Rhinovirus

2. Adenovirus

Front 29

Provide an example of a virus named after its discoverer

Back 29

1. Epstein-Barr

Front 30

Provide an example of a virus named after the associated disease

Back 30

1. Murine Leukemia Virus

2. Cricket Paralysis Virus

Front 31

Provide an example of a virus named after the geographic location

Back 31

1. Ebola

2. Coxsackievirus

Front 32

Provide an example of a virus named after they method of contraction

Back 32

1. Dengue

2. Influenza

Front 33

What criteria were used in the classical system of virus classification?

Back 33

1. Nature of nucleic acid in the virion

2. Symmetry of the protein shell

3. Presence of absence of lipid

4. Dimensions of the virion & capsid

Front 34

Baltimore Classification System classifies viruses based on the nature of..

Back 34

VIral Nucleic Acid

Front 35

How many groups are found in the Baltimore Classification System?

Back 35

7

Front 36

Describe Class I viruses in the Baltimore Classification System

Back 36

Class I virus genomes are double stranded DNA. They require DNA Dependent DNA polymerase to produce more double stranded DNA and DNA Dependent RNA polymerase to turn DNA to RNA

Front 37

What enzymes are used in Class I viruses?

Back 37

1. DNA Dependent DNA polymerase

2. DNA Dependent RNA polymerase

Front 38

Name all of the Baltimore Classes which use Double Stranded DNA

Back 38

1. Class 1

2. Class 7 (requires Reverse Transcriptase)

Front 39

Describe Class 2 viruses in the Baltimore Classification System

Back 39

Class 2 viruses have Single Stranded DNA. They require DNA dependent DNA polymerase to produce double stranded DNA intermediates. From these intermediates they can use DNA Dependent DNA polymerase again to produce more single stranded DNA or they can use DNA dependent RNA polymerase to produce single stranded viral mRNA

Front 40

What enzymes are used in Class 2 viruses?

Back 40

1. DNA dependent DNA polymerase

2. DNA dependent RNA polymerase

Front 41

Provide examples of Class I viruses

Back 41

1. Adenoviridae

2. Herpesviridae

3. Papillomaviridae

4. Polyomaviridae

5. Poxviridae

6. Siphoviridae

Front 42

Provide examples of Class II viruses

Back 42

1. Anelloviridae

2. Parvoviridae

Front 43

Name all classes which use single stranded DNA

Back 43

1. Class 2

Front 44

Describe Class 3 viruses in the Baltimore Classification System

Back 44

Class 3 viruses use double stranded RNA. They use RNA dependent RNA polymerase to both produce more double stranded RNA but also produce single-stranded viral mRNA

Front 45

What enzymes do Class 3 viruses use?

Back 45

1. RNA dependent RNA polymerase

Front 46

Provide examples of Class 3 viruses

Back 46

1. Birnaviridae

2. Picobirnaviridae

3. Reoviridae

Front 47

Name all classes which use double stranded RNA

Back 47

1. Class 3

Front 48

Describe Class 4 viruses in the Baltimore Classification System

Back 48

Class 4 viruses use single stranded (+) RNA. The single stranded (+) RNA itself can be used as a template for protein synthesis, however to produce more templates, the virus uses RNA dependent RNA polymerase to produce a single stranded (-) RNA intermediate which is then transformed to a single stranded (+) RNA using RNA dependent RNA polymerase

Front 49

Name the enzymes used by Class 4 viruses

Back 49

1. RNA Dependent RNA polymerase

Front 50

Name all of the Classes which use Single Stranded (+) RNA

Back 50

1. Class 4

2. Class 6 (With reverse transcriptase)

Front 51

Provide examples of Class 4 viruses

Back 51

1. Corona viridae

2. Flavivirdae

3. Herpeviridae

4. Picornaviridae

Front 52

Describe Class 5 viruses in the Baltimore Classification System

Back 52

Class 5 viruses have single stranded (-) RNA. (-) RNA can't be used to produce proteins and so RNA Dependent RNA Polymerase must first convert the single stranded (-) RNA to single stranded (+) RNA. Once it is single stranded (+) RNA it can be used as a template for protein synthesis or it can be used to produce more single stranded (-) RNA using RNA dependent RNA polymerase.

Front 53

What enzymes are used by Class 5 viruses?

Back 53

1. RNA dependent RNA polymerase

Front 54

T/F: Single Stranded (-) RNA can be used as a template for protein synthesis

Back 54

False. It must first be turned into single stranded (+) RNA by RNA Dependent RNA Polymerase

Front 55

What Classes use Single stranded (-) RNA?

Back 55

1. Class 5

Front 56

What viruses fall under Class 5?

Back 56

1. Filoviridae

2. Paramyxoviridae

3. Arenaviridae

4. Orthomyxoviridae

Front 57

Describe Class 6 viruses in the Baltimore Classification System

Back 57

Class 6 viruses use Single-stranded (+) RNA. They use RNA Dependent DNA Polymerase (Reverse transcriptase) to produce Double stranded DNA. Then it uses Integrase to incorporate the viral DNA into the host genome allowing the host to translate the viral DNA along with the host.

Front 58

What enzymes are used in class 6 viruses?

Back 58

1. RNA Dependent DNA polymerase (Reverse Transcriptase)

2. Integrase

Front 59

What is the main difference between Class 4 and Class 6 if both use Single Stranded (+) RNA

Back 59

Class 6 utilizes reverse transcriptase while Class 4 does not

Front 60

Provide examples of viruses that are Class 6

Back 60

1. Lentivirus

2. Spumavirus

Front 61

Describe Class 7 viruses in the Baltimore Classification System

Back 61

Class 7 Viruses are Double Stranded DNA and use Reverse transcriptase.

Front 62

Name viruses that would fall under Class 7

Back 62

1. Hepadnaviridae

Front 63

What ist he primary function of the capsid

Back 63

Protect

Front 64

Define "Metastable" and why must a virus be Metastable?

Back 64

A virus must be metastable meaning that it must both be strong enough to withstand harsh elements while being flexible enough to enter a host cell without rupturing it.

Front 65

Provide examples as to how a virus is strong

Back 65

1. The protective coat is capable of withstanding environmental assault

2. Protein-protein interactions in the coat provides resistance to many proteases

Front 66

T/F: Enveloped viruses have an additional layer of protection due to additional proteins and sugars provided by the host

Back 66

True

Front 67

How do enveloped and naked viruses differ in terms of exiting a cell?

Back 67

Enveloped viruses acquire the envelope by budding off of the host cell and taking with it a portion of the host's lipid membrane. Nake viruses do not have an envelope and so they leave the cell through lysis or secretory pathways

Front 68

T/F: The size of the virion is generally proportional to the size of the genome

Back 68

True

Front 69

T/F: There is a constraint on virus particle size

Back 69

True

Front 70

Rod-shaped virus type of symmetry

Back 70

Helical symmetry

Front 71

The length of a virus is determined by

Back 71

The length of nucleic acid

Front 72

The width of a virus is determined by

Back 72

Size and packaging units of protein subunits

Front 73

Spherical virus. Type of symmetry

Back 73

Icosahedral Symmetry

Front 74

How are viruses transmitted?

Back 74

1. Aerosal

2. Food & Water

3. Fomites

4. Body secretions

5. Sexual activity

6. Birth

7. Transfusion or transplant

7. Zoonoses (Animals, insects) -Rabies

Front 75

What are Pre-Infection precautions that can be taken?

Back 75

1. Vaccines

Front 76

What are the two types of vaccines?

Back 76

1. Live attenuated virus vaccines: Limited viral replication. progeny contained at site of infection. Infection induces mild or unapparent disease

2. Inactivated "killed" vaccines. Use chemical or physical means to eliminate infectivity but not antigenicity.

Front 77

What are some Post-Infection precautions that can be taken?

Back 77

Antivirals

Front 78

What are some targets of antivirals?

Back 78

1. Attachment

2. mRNA synthesis

3. Protein synthesis

4. DNA Replication

Front 79

HIV Antivirals target

A. Attachment

B. mRNA Synthesis

C. Protein Synthesis

D. DNA Replication

Back 79

A. Attachment

Front 80

Hepatitis A, B, and C Antivirals target

A. Attachment

B. mRNA Synthesis

C. Protein Synthesis

D. DNA Replication

Back 80

B. mRNA Synthesis

Front 81

HPV Antivirals target

A. Attachment

B. mRNA Synthesis

C. Protein Synthesis

D. DNA Replication

Back 81

C. Protein Synthesis

Front 82

Herpes Antivirals target

A. Attachment

B. mRNA Synthesis

C. Protein Synthesis

D. DNA Replication

Back 82

D. DNA Replication

Front 83

Provide some techniques used in identifying viral morphology

Back 83

1. X-Ray crystallography

2. Electron Microscope

3. Light Microscope (in rare cases)

Front 84

This technique is used to characterize virions by characterzing protein

Back 84

X-Ray crystallography.

Front 85

What alternative technique can be used if X-Ray crystallography can be done?

Back 85

1. Cryo-EM (Cryogenic Electro Microscopy)

Front 86

What is the difference between "Susceptible" and "Permissive" Cells?

Back 86

1. Susceptible cells mean that the host has the correct receptor which would allow the virus to enter.

2. Permissive cells mean that the host has the correct machinery which would allow the virus to synthesize more viruses

Front 87

T/F: A virus does not need to be Permissive in order to enter a Cell

Back 87

True

Front 88

T/F: A virus does not need to be Permissive to produce virus

Back 88

False.

Front 89

T/F: A virus must be both Permissive and Susceptible to enter a cell and produce viruses

Back 89

True

Front 90

What are the two types of cell lines

Back 90

1. Primary Cell Lines. These are obtained from tissues and subcultured. They have limited life span

2. Continuous cell lines. Often transformed and subcultured from cancer cells. They are immortal.