Viral Structure and Genome Replication

Question 1

What are the three main functions of the capsid and other virion proteins?

Answer 1

PPD

1) Protection of Genome
2) Packaging Genome properly
3) Delivery of Genome into new Host

Question 2

What is a protein subunit?

Answer 2

single folded polypeptide chain

Question 3

What is the structural unit of the virus?

Answer 3

A protomer, a unit from which capsids are built

Question 4

What is the capsid?

Answer 4

Protein shell surrounding the nucleic acid genome of the virus

Question 5

What is the nucleocapsid?

Answer 5

Nucleic Acid and Protein assembly that is packaged within the virion

Question 6

What is the envelope?

Answer 6

Host-cell derived lipid bilayer carrying glycoproteins

Question 7

What is the virion?

Answer 7

infectious virus particle

Question 8

Each type of virus has a specific type of capsid. What are the types?

Answer 8

1. Icosahedral - 20 sided “soccer ball”
   
   • Made up of multiple repeating virus proteins
2. Helical - rolled up like newspaper
   
   • Flat planar net of protein subunits

Question 9

What is significant about the “spikes” found on the membranous envelopes surrounding the capsids of some viruses?

Answer 9

These glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell

Question 10

What is the viral genome?

Answer 10

Nucleic acid storage of information that’s needed to BUILD, REPLICATE, and TRANSMIT a virus

Question 11

What are the types of Viral Genomes?

Answer 11

Either DNA or RNA Virus

• ssDNA or dsDNA
• ssRNA or dsRNA

Question 12

What are the two types of RNA genome strand polarities?

Answer 12

Strand Type determines what the virus has to do in order to initiate replication and express viral genome

Positive (+) (5’ to 3’)

• first step is translation = produce viral proteins
• already 5’ to 3’ so it can go directly to ribosome

Negative (-) (3’ to 5’)

• first step is transcription = make mRNA
• makes positive sense mRNA which can now be used for translation

Question 13

What must all viruses do early on in infection to ensure replication?

Answer 13

express their genes as functional mRNAs to direct the cell’s ribosomes to make viral proteins

Question 14

How do dsDNA viruses create viral proteins?

Answer 14

1) Have to get into host cell nucleus
2) Host cell RNA Polymerase II binds to viral DNA genome and transcribes viral DNA genes into mRNA
3) mRNA is then read by host cell ribosomes which translates it into viral proteins

Question 15

How do (+) RNA viruses produce viral proteins?

Answer 15

1. Virus enters host cell
2. Capsid disassembles (uncoats)
3. Viral genome is (+) RNA so it acts as mRNA for translation

Question 16

Cells don’t have the machinery to recognize an RNA template and make an RNA transcript. How do RNA Viruses get around this?

Answer 16

RNA-dependent RNA Polymerase (RDRP)

• (-)RNA viruses have to physically carry the RDRP enzyme with them into the cell
• (+)RNA code for RDRP but don’t have to carry an RDRP enzyme with them into the cell

Question 17

What kind of viruses have a high mutation rate? Why?

Answer 17

RNA viruses because RNA Polymerase has no proofreading ability

• also have a higher error rate than DNA viruses
• mutations occur frequently

Question 18

Walk through the process of Positive strand (+) RNA virus replication.

Answer 18

1. Infection
2. Virus uncoating
3. Immediate production of viral proteins (including RDRP)
4. RDRP binds to positive sense (+) genome and produces a complimentary negative sense (-) antigenome
5. RDRP binds to antigenome and Positive (+) strand genomes generated
6. These new genomes are packaged into pre-assembled capsids

Question 19

Walk through the process of Negative strand (-) RNA virus replication.

Answer 19

1. Infection
2. Uncoating
3. RDRP (brought in with virus) binds to negative sense (-) genome and produces mRNA and complimentary positive (+) strand antigenome
4. Production of viral proteins using mRNA produced by RDRP
5. RDRP binds to antigenome and Negative (-) strand genomes generated
6. Genomes packaged into pre-assembled capsids

Question 20

Walk through the process of dsDNA virus replication.

Answer 20

1. Infection
2. Uncoating
3. Transcription to produce mRNAs and Replication to produce viral genomes
   
   • Most DNA viruses use host RNA polymerase for transcription
   • Some DNA viruses use host DNA polymerase for replication
   • Some DNA viruses encode their own DNA polymerase
4. Viral Proteins made
5. Generation of dsDNA genomes
6. Genome packaged into pre-assembled capsids

Question 21

Walk through the process of RNA Genome Retrovirus replication.

Answer 21

1. Infection w/ ssRNA genome
2. Make ssDNA copy from RNA genome using Reverse Transcriptase (RT physically brought into host cell w/ virus)
   
   • RT also can be called RNA Dependent DNA Polymerase
3. DNA replicated to make dsDNA
4. DNA is integrated into the host genome
5. Host polymerase generates mRNAs and viral genomes
6. Genomes packaged into pre-assembled capsids