Lecture 7 (2) - viral genetics 1

Question 1

How many phage particles are in sea water?

Answer 1

10^7 phage particles/ml

Question 2

How many virus species have been described in detail?

Answer 2

4958

Question 3

What are viruses?

Answer 3

• genetic elements that can’t replicate independently of a living host cell
• they can exist as virus particles outside the host

Question 4

How small are viruses?

Answer 4

• smallpox - 200nm, poliovirus - 28nm
• this places great restrictions on the sizes of viral genomes - ranging from 0.5-1000kb
• some viruses have fewer than 5 genes

Question 5

What are the general properties of viruses?

Answer 5

• the virion is the extracellular form - nucleic acid surrounded by protein (as well as other molecules)
• the intracellular form is the replicative state

Question 6

How do tail fibres attach to S-layer?

Answer 6

1. unbound + extended
2. bound + extended + full capsid
3. bound + contracted + full capsid
4. bound + contracted + partially full capsid
5. bound + contracted + empty capsid

Question 7

Describe the characteristics of viral genomes

Answer 7

• very small & reliant on the host replication & metabolic machinery
• DNA or RNA genomes
• single stranded or double stranded
• linear or circular

These characteristics bring challenges to assembly & replication

Question 8

What is a solution to being small as a virus?

Answer 8

• one solution is to have just a small number of protein species making up the capsid
• capsid proteins are often capable of self-assembly without the need for additional machinery
• an example is TMV (tobacco mosaic virus)

Question 9

Describe the typical lifecycle of a virus?

Answer 9

1. attachment (adsorption)
2. penetration (injection)
3. synthesis of nucleic acid and protein
4. assembly and packaging
5. release (lysis)

Question 10

What 2 types of proteins do viruses need, as they only have a few genes and proteins?

Answer 10

• early proteins
• late proteins

Question 11

What is the function of early proteins?

Answer 11

for replication of viral nucleic acid etc…, such as enzyme

Question 12

What is the function of late proteins?

Answer 12

include coat proteins

Question 13

What are bacterial viruses called?

Answer 13

phages

Question 14

How does T4 use various mechanisms to ensure that its genes, rather than the host, are transcribed?

Answer 14

• infection
• nuclease, DNA polymerase, new sigma factors
• phage DNA
• phage head proteins
• phage tail, collar, base plate, and tail fiber proteins
• mature phage particle
• T4 lysozyme production

Question 15

How is viral transcription assured?

Answer 15

• T4 doesn’t encode its own RNA polymerase - it uses that of the host
• this is modified to specifically recognise PROMOTERS on the PHAGE DNA
• for early proteins, host sigma factors are used

Question 16

How is the switch to middle proteins achieved?

Answer 16

• some early phage proteins modify the host RNA polymerase a subunits
• other early proteins bind to the host RNA polymerase
• these modifications alter the polymerase specificity so as to recognise MIDDLE PROMOTERS
• one of the early proteins, MotA - recognises a sequence in the middle promoters, and guides RNA polymerase to the correct sites

Question 17

How does transcription occur from late promoters?

Answer 17

• this requires a new T4-encoded sigma factor
  most of the late genes encode structural proteins