Genomes and Genetics Flashcards

1
Q

Universal functions of viral genomes are to produce proteins, and reproduce DNA/ RNA

Production of proteins uses host ribosomes. This requires mRNA.
All viruses have different methods to produce mRNA

What is unique about RNA viruses?

A

DNA viruses utilised human host cell machinery directly

+ssRNA mRNA used directly as mRNA

+ssRNA retroviruses need to convert to DNA. Virus must provide its own RT as humans do not have this enzyme

-ssRNA needs converted to +ssRNA. Virus must provide its own RNA-dependent RNA polymerase as humans do not have this enzyme

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2
Q

Viral genome encodes encodes all proteins for replication, expression of genome, assembly of virus, and modulation of host defences

What does it not encode?

A

• genes encoding a complete protein synthesis machinery (e.g., no ribosomal RNA and no ribosomal or translation proteins);
note: the genomes of some large DNA viruses contain genes for transfer RNAs (tRNAs), aminoacyl-tRNA synthetases, and
enzymes that participate in sugar and lipid metabolism

• genes encoding proteins of energy metabolism or membrane biosynthesis

• telomeres (to maintain genomes) or centromeres (to ensure
segregation of genomes)

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3
Q

mRNA is defined as the positive (+) strand, because it can be translated into a protein.

A strand of DNA of the equivalent polarity is also designated as a (+) strand; i.e., if it were mRNA, it would be translated into protein.

The RNA or DNA complement of the (+) strand is called the (-) strand.
The (-) strand cannot be translated; it must first be copied to make the (+) strand.

What polarity does ambisense RNA have?

A

Ambisense RNA contains both (+) and (-) sequences. e.g Arenavirida (Lassa) and Bunyaviridae

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4
Q

Ambisense RNA contains both (+) and (-) sequences. e.g Lassa

The ambisense RNA viruses and the minus-sense viruses are closely related. One family, the Bunyaviridae, even contains both types of viruses as members. The ambisense strategy is, in fact, a simple modification of the minus-sense strategy, and these viruses are generally lumped together as “negative-strand” or “minus-strand” RNA viruses

What are the benefits of an ambisense strategy?

A

(+) RNA can be directly translated to proteins, after virus enters cells
(-) RNA needs converted to (+) RNA

Thus, ambisense viruses modify the minus-sense strategy by synthesizing mRNA from both the genome and the antigenome. Neither the genome nor the antigenome serves as mRNA.

The benefit is to delay the synthesis of mRNAs that are made from the (-) RNA and thus to introduce a timing mechanism into the virus life cycle. Results in proteins being produced at most useful time for viral life cycle.

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5
Q

Gapped DNA genome is an incomplete template for transcription - e.g HBV

What must occur before transcription of gapped dsDNA?

A

HBV has gapped, circular, dsDNA

host RNA polymerase can only transcribe fully complete circular dsDNA

HBV reverse transcriptase coverts into complete circular dsDNA. Which then acts as template for transcription

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6
Q

ssDNA genome

How is RNA produced?

A

RNA can only be made from a dsDNA template, whatever the sense of ssDNA

therefore some DNA synthesis must occur, to produce dsDNA prior to mRNA production

cellular DNA polymerases are used for this

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7
Q

Human cells are unable to work with RNA as a template

Cells have no RNA-dependent RNA polymerases that can replicate genomes of RNA viruses, or make mRNA from RNA templates

How do RNA viruses overcome this?

A

1 - One solution to this problem is that RNA virus genomes encode RNA-dependent RNA polymerases that produce RNA from RNA templates.

2 - The other solution, exemplified by retrovirus genomes, is reverse transcription of the genome to dsDNA, which can be transcribed by host RNA polymerase.

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8
Q

dsRNA includes viruses such as Reoviridae

The (+) sense strand of dsRNA cannot be translated to viral proteins

What steps are required first?

A

While dsRNA contains a ( + ) strand, it cannot be translated as part of a duplex to synthesize viral proteins.

The ( - ) strand of the genomic dsRNA is first copied into mRNAs by a viral RNA-dependent RNA polymerase.

Newly synthesized mRNAs are encapsidated and then copied to produce dsRNAs.

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9
Q

+ssRNA are the most plentiful of viruses on planet

+ssRNA can be translated directly into protein by host ribosomes

How is the genome copied?

A

The genome is replicated in two steps.

1 - the ( + ) strand genome is first copied into a full-length ( - ) strand

2 - the ( - ) strand is then copied into full-length ( + ) strand genomes.

In some cases, a subgenomic mRNA is produced

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10
Q

+ssRNA with DNA intermedoate viruses (retroviruses) have a unique mechanism of replication

What are the steps?

A

In contrast to other ( + ) strand RNA viruses, the ( + ) strand RNA genome of retroviruses is converted to a dsDNA intermediate
by viral RNA-dependent DNA polymerase (reverse transcriptase).

This DNA then serves as the template for viral mRNA and genome RNA synthesis by cellular enzymes. T

here are three families of ( + ) strand RNA viruses with a DNA intermediate; members of the Retroviridae infect vertebrates.

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11
Q

-ssRNA viruses cannot be translated directly into protein

What steps occur for protein production?

A

-ssRNA acts as template for +mRNA, which can be used for translation

no enzymes in cell that can make RNA from -ssRNA

viruses encode RNA-dependent RNA polymerases to enable conversion

For -ssRNA replication, +ssRNA template produced, which acts as a template for creation of -ssRNA

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12
Q

What does 5’ and 3’ mean in relation to single strand of DNA or RNA

A

5’ - 3’ direction refers to the orientation of nucleotides of a single strand of DNA or RNA.

The 5’ and 3’ specifically refer to the 5th and 3rd carbon atoms in the deoxyribose/ribose sugar ring.

The phosphate group attached to the 5’ end of one nucleotide and the hydroxyl group at the 3’ end of another nucleotide have the potential to form phospodiester bonds, and hence link adjacent nucleotides.

This linkage provides the sugar-phosphate backbone that gives DNA its structural rigidity. Any single strand of DNA/RNA will always have an unbound 5’ phosphate at one end and an unbound 3’ hydroxyl group at the opposite end.

DNA is always read in the 5’ to 3’ direction, and hence you would start reading from the free phosphate and finish at the free hydroxyl group.

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13
Q

Previously thought that one gene, coded for one mRNA.

However compact viral genomes can produce many mRNAs, all encoding different proteins

What techniques to viruses use?

A

Extraordinary tactics for information retrieval, such as:

  • the production of multiple subgenomic mRNAs, mRNA splicing, RNA editing, and nested transcription
    units (Fig. 3.10), allow the production of multiple proteins from a single viral genome.
  • Further expansion of the coding capacity of the viral genome is achieved by posttranscriptional mechanisms, such as polyprotein synthesis, leaky scanning, suppression of termination, and ribosomal frameshifting. In general, the smaller the genome, the greater the compression of genetic information

Size of genome does not correlate to number of proteins that can be produced

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14
Q

RNA virus genomes are sometimes segmented

What does this mean?

A

RNA viruses can contain a single (unsegmented) or multiple (segmented) genomic molecules. However, the evolutionary connection between these two fundamentally different forms of genome organization is unclear.

Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle.

These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA

Arenaviridae, Birnaviridae, Bunyavirales, Orthomyxoviridae, Picobirnaviridae, and Reoviridae

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15
Q

RNA genomes are very susceptible to mutation

why is this?

A

RNA less stable - 1 mis-incorporation in 10 4 or 10 5 nucleotides polymerized. So for every copy produced, would expect 1 mutation

This therefore limits the length of RNA, as long RNA will invariably have a lethal mutation

Very few RNA exonucleases exist. Coronavirus has an exonuclease which can proof read and eliminate errors in RNA

DNA has proof reading to reduce errors

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16
Q

In virology, what does the term “wild type” mean?

A

Wild-type is defined as the original (usually lab) version of a virus, from which mutants may be selected

May not be identical to virus isolated in nature

We distinguish carefully between laboratory wild types and new virus isolates from the natural host. The latter are called field isolates or clinical isolates.

Wild-type polio virus in the lab, and in the field, may be different

17
Q

What does the term “transfection” mean?

A

term “transfection” is restricted to the introduction of viral DNA or RNA into cells with the goal of obtaining virus
reproduction. Virus should be able to be isolated afterwards

Adding polio virus to cell culture - will stimulate complete infection cycle
Adding polio RNA to cell culture - “transfection” will stimulate complete infection cycle

18
Q

What is a nonsense mutation?

A

Mutation gives rise to a stop codon, instead of an amino acid

19
Q

What are small interfering RNAs (siRNAs)?

What are they used for?

A

Short RNA molecules which are complementary to mRNA. In catergory of RNA interference molecules

They can bind to mRNA, and prevent specific protein production

New drugs for disease are in this class

20
Q

What does CRISPR-Cas9 technology stand for?

What is it used for?

A

CRISPR-Cas9 (clustered regularly interspersed short palindromic
repeat-CRISPR-associated nuclease 9)

Used to completely remove defective genes

21
Q

When should the terms mutation and deletion be used, when talking about nuclear material/ proteins

A

Accurate use is to describe changes in nuclear material

Erroneously used to describe changes in proteins. Truncation and amino acid substitution are better terms to describe the actual changes in the protein

22
Q

Why are viruses utilised for oncotherapy?

A

can enter tumour cells easily, as opposed to using specialised immune cells to target tumour

can cause lysis of tumour cells

can use non-human viruses, that cannot ordinarily infect human cells. They can infect cancer cells, limiting any collateral damage

23
Q

Why are retroviruses useful for gene therapy?

A

Life cycle means that dsDNA is inserted into host DNA

This is then present in all of the progeny cells - meaning that further treatment might not be required

24
Q

Which viruses are have segmented genomes?

All RNA viruses

A

orthomyxoviruses e.g. influenza
contains 8 segments that can undergo reassortment contributes to flu pandemics

bunyaviruses e.g. hantavirus

arenaviruses e.g. lassa fever virus

reoviruses e.g. rotavirus