Module 7 - notes Flashcards by Vicki schenk

Could you create an antibiotic that targets Archaea and Eukarya? What enzyme or process would you target?

Yes by:

Replication - target the replication machinery
Genome compacting by targeting the histone
Transcription by targeting the RNA polymerase

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How could you control the lac operon with regulatory RNA?

Small RNA that would bind the mRNA of the lac operon leading to stall translation or stall transcription
Small RNA that would bind the mRNA of the lac operon preventing the binding to RBS
Small RNA that would bind the mRNA of the lac operon affecting stability/degredation
Riboswitch that would bind glucose leading stall transcription or stall translation.

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Based on you knowledge of viruses, what could have gone wrong with Hershey-Chase experiments?

A. Use RNA virus
B. use of temperate phage
C. use a ‘tail-less’ phage
D. use a ‘fusogenic’ phage

A. Use RNA virus

If they would have infected the bacteria with an RNA virus, they would have completely changed how we saw things.

We now know that bacteria viruses will use DNA or RNA as their genetic material

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What is a virus?

Genetic element encapsulated in a protein shell (capsid)

Not living, does not carry independent metabolism

Needs a host for energy and protein synthesis

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When were viruses first identified?

1892

Tobacco mosaic disease

Infectious agent passed through a 0.1 micrometer pore size filter

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What do we know about the genetic element in a virus?

Either DNA or RNA (never both)

Double-stranded or single-stranded

Segmented (multiple fragments) or non-segmented (1 fragment)

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What is a naked virus?

A virus that is not surrounded by a membrane

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Are viruses alive?

A. No they lack cellular structure
B. No, they do not have independent metabolism
C. No, they do not replicate
D. No, they do not evolve
E. Yes

B. No, they do not have independent metabolism.

It is not a cell - a cell has independent metabolism

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What is the extracellular form of a virus called?

virion

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What types of life forms are affected by viruses?

As far as we know, viruses infect every single cellular life form.

There is a virus for every cell type.

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You have discovered a new type of microbe and you suspect it is a virus. What type of microscopy can be used to confirm the presence of the virus?

A. Transmission Electron Microscope
B. Light Microscope
C. Phase-Contrast Microscopy
D. Atomic Force Microscopy

A. Transmission Electron Microscope

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What are the structures of a virion?

Very small - not observable with a light microscope <1 micrometer

Genome: DNA or RNA, 1 or more fragment
1000 bases to 2.5 megabases
7 proteins to 1000 proteins

Capsid
protein subunit called capsomere
1 or more different protein

Symmetry
Rod - Helical symmetry
Spherical - icosahedral symmetry
Complex shape

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What is an example of helical symmetry?

Tobacco Mosaic Virus

Length of rod is dependent on the length of the nuclei acid strand

Width is dependent on size and packaging of capsomeres

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What is an example of icosahedral symmetry?

20 triangular faces
12 verticies

Simplest and most effective arrangement
fewest capsomeres required

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What is an example of a complex shape?

Variola Virus

Has a membrane

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What makes up a naked virus?

Capsid & Nucleic Acid

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What makes up an enveloped virus?

Membrane + Capsid + Nucleic Acid

Phospholipid bylayer derived from host (mostly animal viruses)

Host proteins + viral proteins

Fibrils - peptidoglycan-like polymer on amoeaba viruses

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What are spike proteins?

Proteins at the surface of the virus

Made of glycoproteins

Helps virus attach to host

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Spike proteins use proteins/enzymes to adhere and detach from the host cell. What does the influenza virus use?

Adhesion = Hemagglutinin

Detach = Neuraminidase (an nenzyme that cleaves the sugar and releases them from the host.)

H1N1

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We know that virion contain nucleic acid but do they carry anything else?

Some bacteria carry their own enzymes to help them during the infection process.

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You have discovered a new virus and it has lipids, knowing only this, what else can you now conclude about this virus?

A. It can be classified as an envelope virus
B. It is most likely a bacteriophage, or bacterial virus instead of one that infects human cells.
C. Its nucleic acid core will not contain RNA
D. It can be classified as a “naked” virus

A. It can be classified as an envelope virus

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How do we classify viruses?

Fast Evolution - Families and genera, species
-Species name in italic, viral name not in italics
- Differentiate name vs. disease

Nucleic Acid and how it replicates
- RNA/DNA, Single/Double, Segmented/Non-Segmented

Naked or Enveloped

Morphology

Baltimore Classification
(7 groups)

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What are the 7 groups of the Baltimore classification?

BCI = double-stranded (ds) DNA viruses
BCII = single-stranded (ss) DNA viruses
BCIII = dsRNA viruses
BCIV = Positive-sense (+)RNA viruses
BCV = negative-sense (-)RNA viruses
BCVI = reverse-transcribing RNA viruses
BCVII = reverse-transcribing dsDNA viruses

How would you determine the sequence of an RNA virus?

Step 1: Isolate the viral genome

Step 2: Reverse transcriptase to generate cDNA

Step 3: Sequence cDNA using nanopore or PacBio (or pyrosequencing, Illumina or Sanger)

What affects how viruses infect their hosts?

Depends on their Host Baltimore classficiation type (naked or enveloped)

How do Lytic Phages infect bacteria?

1 = Attachment 2 = Penetration 3 = Biosynthesis 4 = Maturation 5 = Lysis

What is the one-step growth curve of lytic phages?

Innoulation = You begin with lots of viruses outside the cell Eclipse = the virions penetrate the cell so the count of virions outside the cells starts to disappear Burst = Host cells start to release many viral particles. The burst size is the number of virions released per bacterium.

Why do lytic viruses exhibit a one-step growth curve? A. Lytic viruses are slowly but continuously released B. Lytic viruses only replicate during genome replication of their host C. Lytic viruses are only released all at once D. Lytic viruses do not require assembly for their release E. Lytic viruses combine genome replication and assembly in one step.

C. Lytic viruses are only released all at once. Lytic viruses burst the cell.

How do phages infect bacteria?

They need a receptor. Depending on the bacteria, if it is gram-negative or gram-positive, there will be different molecules at the surface All molecules can act as receptors. Sometimes the receptors are so specific that they are only able to infect specific strains.

You are creating a bacteriophage that will target gram-positive and gram-negative bacteria. Which receptor would be universal? The Capsule The s-layer The flagella The wall teichoic acids The lipopolysaccharide None of the above

None of the above Although they can be found in both, none are universal

What is a lysogen?

A bacterium that has a 'resident' [hage integrated in the bacterial genome or as a plasmid

What is lysogenic or phase conversion?

When the 'resident' phage changes the phenotype of the lysogen.

How do temperate phages infect bacteria?

A temperate bacteriophage has both lytic and lysogenic cycles. In the lysogenic cycle, phage DNA is incorporated into the host genome, forming a prophage, which is passed on to subsequent generations of cells. Environmental stressors such as starvation or exposure to toxic chemicals may cause the prophage to be excised and enter the lytic cycle.

True or false The lysogenic cycle is an example of horizontal gene transfer?

True

You find a phage that integrates its genome into a bacterial chromosome. What is the best explanation? It is a temperate phage It is a virulent phage It is a persistent phage It si an oncogenic phage

It is a temperate phage

How do viruses infect eukaryotes?

**Step 1: Attachment** binding to the receptor(s): spike protein, host and tissue specificity **Step 2: Penetration** englulfment - endocytoisis or membrane fusion **Step 3: Uncoating** viral content is released **Step 4: Biosynthesis** Production of genome, mRNA & Proteins Replication in nucleus **Step 5: Assembly** **Step 6: Release**

What are the possible outcomes of a viral infection?

Lytic - cell lysis to release viral particles Persistant - Latent = virus is dormant and reactivates - Chronic - Virus is not eliminated, continuous production of viral particle Cancer - Direct = viral oncogenes, activation of oncogenes of inactivation of 'safety' checks - Indirect = chronic infection

What is an example of a latent viral infection in humans?

Herpes virus or Varicella-zoster virus (Chicken Pox)

What is an example of a chronic viral infection in humans?

HIV

How do viruses chronically infect eukaryotes?

Step 1: Attachment Step 2: Penetration Step 3: Unocating - Step 3.2: Integration Step 4: Biosynthesis Step 5: Assembly Step 6: Release (Budding) - cell is not damaged

What is antigenic shift?

Point mutation over time Small mutations that changes the protein May cause epidemics

What is Antigenic shift?

Multiple fragments from 2 viruses will create a new type of virus Recombination of the genome May cause a pandemic

In which of the following stages of the viral infectious cycle do enveloped viruses acquire their envelope? Attachment Penetration Biosynthesis Assembly Release

Release

How do we grow viruses?

Needs living host cells Need the host cell type to support viral infection - permissive host - receptor Know the conditions to grow the host Quantification of virus -PFU = plaque for lytic viruses

Please explain why a lytic and a lysogenic (temperate) bacteriophage would not yield the same number of plaque forming units (PFU) despite infecting the cells with the same number of infectious viral particles

Plaques are formed during lysis and lysogenic infection do not always resulting lysis

How would you quantify the number of viral genomes in your cell culture without microscopy? RT-PCR qPCR Southern Blot Western Blot

qPCR The only one the give you quantitative measurements

What is the central dogma?

DNA to RNA to Protein

The central dogma does not work for viruses. How does the HIV virus go?

RNA to DNA to RNA the Protein

When RNA polymerase synthesizes mRNA, the copied strand is An exact copy of the template A complementary of the template A reverse and complementary copy of the template

A reverse and complementary copy of the template

What happens when you copy a positive Strand DNA?

You will get a negative strand DNA, but it won't give you an mRNA that can be translated

What happens when you copy a negative strand DNA?

You get a positive DNA and an mRNA that you can use as a template for translation.

What is the difference between positive strand RNA and negative strand RNA?

Positive strand RNA can be used as a template for translation, Negative strand cannot be used as a template for translation but it can be used as a template to create mRNA

What do you need to create mRNA

Positive strand DNA

What do you need to create a protein?

positive strand RNA