Module 7 - notes Flashcards
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
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.
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
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
When were viruses first identified?
1892
Tobacco mosaic disease
Infectious agent passed through a 0.1 micrometer pore size filter
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)
What is a naked virus?
A virus that is not surrounded by a membrane
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
What is the extracellular form of a virus called?
virion
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.
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
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
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
What is an example of icosahedral symmetry?
20 triangular faces
12 verticies
Simplest and most effective arrangement
fewest capsomeres required
What is an example of a complex shape?
Variola Virus
Has a membrane
What makes up a naked virus?
Capsid & Nucleic Acid
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
What are spike proteins?
Proteins at the surface of the virus
Made of glycoproteins
Helps virus attach to host
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
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.
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
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)
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
