Chapter 6

Question 1

Definition of a virus?

Answer 1

A virus is an infectious obligate intracellular parasite compromising genetic material (DNA or RNA) that is surrounded by a protein coat called a capsid and sometimes a membrane

Question 2

What is the Baltimore classification?

Draw it out:

What is Ambisense?

Answer 2

• A way to classify viruses into 7 classes based on their genome type and replication mode.
• Ambisense= ss mix of negative and postive DNA or RNA (a mixture)

Question 3

1. What is the central Dogma?
2. Why doesn’t does it need modification for viruses?
   
   1. how information flow not always DNA > RNA > Protein
   2. RNA can be used as a template for for DNA synthesis
3. how do cells reverse transcribe?

Answer 3

1. The central dogma sates that genetic info is transmitted from DNA to RNA to protein. And also from DNA to DNA.
2. Modifications to the central dogma are done because of the various modes of virus transcription and genome replication.
   
   1. Can go from DNA → RNA (genome replication)
   2. RNA → DNA (reverse transcription)
   3. RNA→ RNA (genome replication
3. cells reverse transcribe via Telomerase

Question 4

1. What are the elements relating to control of transcription?
2. what is tropism

Answer 4

1. Promoters = binds transcription factors and RNA polymerase
   
   1. TATA box , is a consensus sequnece
2. Transcription Factors = binds to sequences with in promoter and enhancers. Capped at the 5’ and pollinated at the 3’ end
   
   1. can activate or suppress expression of genes
   2. some genes are active at different phases
3. Enhancers = bind transcription factors that significantly boost the rate of transcription factors.
   
   1. bind another transcription factor plus a promoter transcription factor
   2. increase the RNA polymerase 2 start rate
   3. Can be cell or tissue specific (liver) = Tropism
      
      1. tropism= ability of virus to infect a particular cell

Question 5

1. How do Transcription factors relate to gene expression?
2. Where do TF for viruses come from?

Answer 5

1. Transcription factors can activate or repress gene expression
   
   1. some genes can be activated at different phases
2. They can come from cells or the virus encodes its own
   
   1. Viruses use TF from Cells
      
      1. TFIID is an example of a cell TF. It is a complex of 13 proteins, including the TATA box binding protein. Once TFIID has bound to it, other TF and RNA polymerase II bind.
   2. Viruses encode their own TF
      
      1. herpes simple X virus VP16, a component of the vireo
      2. human t-lymphtropic virus 1 tax protein

Question 6

1. What is a transcriptase?
2. What viruses use cell derived transcriptase?
3. what viruses use encoded transcriptases?

Answer 6

1. An enzyme that carries out transcription (RNA pol)
2. Viruses that carry out transcription in the nucleus generally use cell RNA polymerase (retroviruses and DNA viruses)
3. DNA viruses that replicate in teh cytoplasm use a virus encode enzyme because there is no appropriate cell enzyme in the cytoplasm
   
   1. viruses in class 3, 4, 5 encode their own virus

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Question 7

1. What does it mean by mRNA’s are capped?
2. What are the features of the caps?
3. Function?
4. Where do the caps come from?

Answer 7

1. After RNA synthesis has started, transcripts are “capped” at the 5’ end.
2. The cap is GTP joined to the end nucleotide by a 5’-5’ linkage
   
   1. methyl group is added to the guanosine
   2. can be bound to one or both of the ribose residues on the firs and second nucleotides
3. Function
   
   1. transport of mRNA from the nucleus to cytoplasm
   2. proficient of the mRNA from degradation by exonuclease
   3. initiation of translation
4. Enzymes normally cap RNA
   
   1. capping enzymes are located in the nucleus
   2. influenza viruses are the exception, they snatch caps from cell mRNA
   3. viruses that replicate in the cytoplasm, many encode their own capping enzyme
   4. some transcripts are not capped

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Question 8

1. Function of mRNA polyAdenylation?
2. What is polyAdenylation?

Answer 8

1. polyAdneylation increases the stability of mRNAa and the
2. A series of adenosine residues added to the 3’ end of most primary transcripts of eukaryotes and their viruses

Question 9

1. What is mRNA splicing 2. Significance of alternative splicing