Exam 2 Lecture 17

Question 1

Baltimore Classification System Group I

Answer 1

dsDNA either uses it’s own or the host DNA polymerase

Herpes

Question 2

Baltimore Classification System Group II?

Answer 2

ssDNA- needs to go through dsDNA intermediate to replicate the plus strand

Parvovirus in Euks

Phages- M13 or øX174

Question 3

Baltimore Classification System Group III?

Answer 3

dsRNA- Needs RNA dependant RNA polymerase to make mRNA and genomic RNA

Always RNA, never DNA!

Rotavirus

Question 4

Baltimore Classification System Group IV?

Answer 4

(+) ssRNA- the RNA can act as mRNA, needs RNA polymerase to make template stand for more mRNA or replication

Always RNA, never DNA!

Coronavirus, Polio, Hep C

Phage- MS2

Question 5

Baltimore Classification System Group V?

Answer 5

(-) ssRNA - Needs to be RNA polymerase to replicate and has to be transcribed to a complement strand/mRNA

Always RNA, never DNA!

Influenza, Measles, Rabies

Question 6

Baltimore Classification System Group VI?

Answer 6

Retrovirus, (+) RNA has its own reverse transcriptase to make dsDNA intermediate

HIV

Question 7

Baltimore Classification System Group VII?

Answer 7

dsDNA- pararetrovirus, requires host reverse transcriptase to make dsDNA

Hep B

Question 8

Plus strand DNA compared to mRNA code?

Answer 8

The same, mRNA always matches plus-strand!

Question 9

(-) strand DNA compared to mRNA?

Answer 9

Acts a template for mRNA

Question 10

(-) strand RNA?

Answer 10

Needs to be transcribed to make mRNA

Question 11

How easy is it to map viral evolution?

Why?

Answer 11

Difficult- there is not one conserved gene such as ribosomes to map it from.

They regularly exchange genomic data with hosts, tend to be mosiac

Are mapped using protein similarities sometimes

Question 12

Describe MS2 phage?

Answer 12

linear (+) ssRNA in an icosahedral capsid

binds to F pilus of E coli

Lytic phage ~25 mins to release 100s-1000s of progeny

Question 13

MS2 replication strategies?

Answer 13

+ strand used to make minus-strand with RNA replicase

+ strand translated to make viral capsid proteins and RNA replicate

(-) strand replicated with RNA replicase to make plus-strand

Self-assembly then lysis protein made and host is lysed releasing virions released

Question 14

Is there proofreading activity during MS2 replication?

Answer 14

No, so the mutation rate is high

Question 15

Do all MS2 genes replicate at the same time?

Answer 15

No, they exhibit temporal regulation. Ribosome binding site for capsid protein always available, once that is translated it opens up replicase gene binding site

Question 16

Where on F pilus do phages bind?

Answer 16

Icosohedral MS2 binds to side

M13 filamentous binds to tip of pilus

Question 17

Describe the M13 phage?

Answer 17

ssDNA 6400 base circular strand wound/encased in a long filament capsid w/ 90% coding sequences, No envelope

Asymmetric with distinct proteins at each end.

Some of the genes overlap

Question 18

M13 replication strategy?

Answer 18

1. ssDNA (+) uses host replicase to make dsDNA
2. The dsDNA neg strand uses host cell’s RNA polymerase to make more viral genomes and mRNA to make capsid proteins
3. Phages self assemble and exit host by budding

Notes- Host divides ore slowly while infected but can still divide and pass M13 on to each daughter cell, this is a common way to reproduce for filamentous phages

Question 19

What is the M13 assembly and export apparatus related to?

Answer 19

A Type II secretion system

Uses Proton Motive Force to secrete but still maintains PMF and cellular metabolism function

Question 20

dsDNA phage basic characteristics?

Answer 20

Large more complex genomes, heads and tails, defined order of gene expression, many are lytic but some interact differently

Question 21

Descride a T4 phage?

Answer 21

Linear dsDNA, 169 kb encoding 300 genes

Relies on E coli host core RNA poly for first transcription and translation

Binds to lipopolysaccharide and OmpC Porin

Clear temporal replication, DNA first and capsid proteins later

Question 22

Related viruses to T4?

Answer 22

T even phages, T2 and T6, closely related but have different binding sites