Coronavirus

Question 1

Genome structure

Answer 1

(+) ssRNA, enveloped, 26-32 kb

Question 2

N protein

Answer 2

Helical nucleocapsid, transcription, immunogenic epitopes

Question 3

M protein

Answer 3

Matrix, maturation and release

Question 4

E protein

Answer 4

Envelope, maturation and release

Question 5

S glycoprotein

Answer 5

Spike, binds to ACE2 receptor, species-specific, neutralizing epitopes

Question 6

Order of genes on basic genome (6)

Answer 6

Orf 1a, Orf 1b, S, E, M, N

Question 7

SARS structural proteins (3)

Answer 7

Orf 3a, 7a, 7b

Question 8

SARS nonstructural proteins (5)

Answer 8

Orf 3b, 6, 8a, 8b, 9b

Question 9

What are TRSs and what is their role?

Answer 9

Transcriptional regulatory sequences, produces nested mRNAs from 3’ end. Transcription gets stuck at each TRS (produces nested sets)

Question 10

Which nsps do Orf 1a and 1b produce?

Answer 10

Orf 1a = nsp 1-11 (70% more than Orf1b)

Orf 1b = nsp 12-16

Question 11

What liberates nsp 1-3?

Answer 11

Protease PLP

Question 12

What cleaves nsp 4-16?

Answer 12

Protease 3CL

Question 13

How do coronaviruses produce 2 Orfs?

Answer 13

RNA pseudoknots and frameshifting; Complex RNA structure causes ribosome to “slip” within a UUUAAA region

Question 14

Nsp1

Answer 14

degrades RNA, blocks IFN induction

Question 15

Nsp2

Answer 15

nonessential

Question 16

Nsp3

Answer 16

PLP protease, IFN antagonist of IRF3 nuclear import

Question 17

Nsp4 and nsp6

Answer 17

scaffold (build replication complexes on membranes)

Question 18

Nsp5

Answer 18

3CL (also called M protease)

Question 19

Nsp7 and nsp8

Answer 19

processivity factor (increase replication rates); primase activity

Question 20

Nsp9

Answer 20

interacts with nsp8 to bind ssRNA

Question 21

Nsp10

Answer 21

negative strand synthesis, binds ssRNA

Question 22

Nsp12

Answer 22

RdRp

Question 23

Nsp13

Answer 23

helicase (unwinds nucleic acid in 5’ to 3’ direction)

Question 24

Nsp14

Answer 24

ExoN (degrades RNA in 3’ to 5’ direction, implicated in proofreading); 7 methyl transferase (5’ cap)

Question 25

Nsp15

Answer 25

Endoribonuclease

Question 26

Nsp16

Answer 26

2’-O-methyltransferase (helps with caps)

Question 27

Does replication produce more (+) or (-) strands?

Answer 27

10:1 ratio of (+):(-) strands

Question 28

How are subgenomic mRNAs synthesized?

Answer 28

RNA splicing (genome length mRNAs spliced into subgenomic); internal starts and post-transcriptional modification

Question 29

How are leader sequences joined to each mRNA?

Answer 29

Leader-primed transcription; discontinuous transcription, where pol jumps to end during (-) strand synthesis