Chapter 10: Viral Genomics, Diversity, and Ecology

Question 1

Class I virus

Answer 1

dsDNA
- same as used by host (T4)
- primarily prokaryotic viruses, or animal hosts

Question 2

Class II virus

Answer 2

ss positive or plus-strand DNA
- needs DNA intermediate for replication
- more plant hosts than animals

Question 3

Class VII virus

Answer 3

dsDNA that replicates through RNA intermediate
- Hep B
- reverse transcriptase
- more common in plants than animals

Question 4

Class III virus

Answer 4

dsRNA, similar replication as class V
- infects fungi

Question 5

Class IV virus

Answer 5

ss(+)RNA, genome is RNA (can be translated, no transcription)
- primarily eukaryotic viruses, infects fungi

Question 6

Class V virus

Answer 6

ss(-)RNA
RNA replicase makes (+) strand used as mRNA and template for more (-) strand genomes
- only eukaryotic infection of animals

Question 7

Class VI virus

Answer 7

ss(+)RNA
-retroviruses
- via DNA intermediate and reverse transcriptase
- ie HIV
- infect only animals

Question 8

early proteins

Answer 8

synthesized soon after infection
- usually enzymes, in small amounts,
nucleic acid polymerases (shut down host translation/transcription)

Question 9

late proteins

Answer 9

synthesized later after infection
- structural and assembly proteins, in large amounts

Question 10

coronaviruses

Answer 10

largest of any RNA virus
respiratory infections (SARS)
glycoprotein spikes on surface
ss(+)RNA

Question 11

NSPS

Answer 11

NonStructural ProteinS
- single replicase gene has instructions for multiple NSPS in SARS-Cov-2

Question 12

Transreplicate RNA

Answer 12

RNA-dependent RNA Polymerase

Question 13

Protease Inhibitors

Answer 13

could prevent SARS-Cov-2 from processing NSPS proteases
- but didn’t really work in trials

Question 14

Spike

Answer 14

glycoprotein
homotrimer
2 subunits (S1 & S2)
can have different conformations (open/closed)

Question 15

S1 subunit

Answer 15

receptor binding
contains Receptor Binding Domain (RBD)
closed- all RBD down, hiding Receptor Binding Motifs (RBM)
open- at least one RBD is up, exposing its RBM for receptor binding

Question 16

S2 subunit

Answer 16

contains fusion machinery for merging viral membrane with host cell membrane (highly conserved - polypeptide)
- undergoes Transformer-level conformational change to bring about membrane fusion

Question 17

antibody-base drugs

Answer 17

could bind to and cover part of the spike protein to prevent virus from docking and getting in

Question 18

endosome

Answer 18

membrane-bound pouch enveloping the virus in the host cell

Question 19

RdRP inhibitors

Answer 19

could prevent RNA copies from being made in host cell
-remdesivir or favipiravir (Avigan)

Question 20

Estimated ______ viruses on earth

Answer 20

10^31

Question 21

approx. _____ prokaryotes/ml of seawater

Answer 21

10^6

Question 22

about ______ viruses/ml of seawater

Answer 22

10^7
Class I most common

Question 23

______% of seawater bacteria daily killed by phage

Answer 23

5-50

Question 24

Viral metagenome

Answer 24

all viral genes in an environment

Question 25

CRISPR

Answer 25

Clustered Regularly Interspaced Short Palindromic Repeats
- protect from bacteriophage infection

Question 26

Cas proteins

Answer 26

have endonuclease activity
destroy incoming DNA

Question 27

virome

Answer 27

entire population of viruses present in and on the human body
- dominated by DNA viruses

Question 28

Viroids

Answer 28

lack protein, infectious RNA
- small, circular, single-stranded
- plant diseases
- ie. coconut cadang-cadang viroid & potato spindle tuber viroid (PSTV)

Question 29

Prions

Answer 29

lack nucleic acid, infectious proteins
- animal diseases
- ie. scrapie, bovine spongiform, encephalopathy/mad cow, chronic wasting disease, kuru, and Creutzfeldt-Jakob disease

Question 30

nonpathogenic prions

Answer 30

in fungi, adapt to environmental conditions
- ie. URE3 - nitrogen metabolism genes
- ie MAVS - aggregation in humans triggers interferon production in response to viruses