BIO 305 Exam 3 Chp 6-9 Flashcards
What are the general structural components of a virus?
Genome, capsid, possible spike proteins or extracellular proteins, possible envelope, and tegument (space between capsid and envelope) if an envelope is present.
What are viroids?
Viroids are the smallest infectious pathogens known. They are composed solely of a short strand of circular, single-stranded RNA that has no protein coating.
What are spike proteins?
Proteins made of glycoprotein that stick up from the virus. Can be used for identification. Can hold capsid and envelope together. Can be used for attachment.
What does icosahedral mean?
20 sided capsid.
What is a filamentous virus shape?
Helical. Longer than wide. Genome or capsid can be helical.
What are asymmetric viruses?
Asymmetrical viruses can have asymmetrical genomes with multiple “chromosomes” or an asymmetrical shape (ex: oval).
What do all viruses need to replicate?
A host.
What is the RNA world hypothesis?
That RNA did everything: storage, structural, and functional.
What is a virus?
Virus=noncellular dynamic particle that infects a host cell to reproduce.
What is a host range?
Host range=number of hosts that a virus can infect.
Can be broad or narrow.
What does promiscuous mean in relation to viruses?
Promiscuous=virus hopping around different hosts.
What is prophage?
Viral DNA integrated into bacteria.
What is a provirus?
Viral DNA integrated into a eukaryote.
What is an endogenous virus?
Endogenous viruses=viruses that get to the germ cells and are passed on to offspring.
What are some positive things that viruses do?
Contribute to nutrient cycling, get rid of microbial blooms, and mediate host population control.
What is a plaque?
Plaque=clear spot in a lawn of cells.
Due to lysing of the bacteria due to a phage.
What is the purpose of viruses having an envelope?
The envelope is usually from the host. Having the envelope means the cell can have an easier time getting into the cell.
How can integrated viral genomes be beneficial?
They can provide resistance to toxins and environmental factors.
For humans, some endogenous virus translates to essential proteins in the placenta.
What is the intracellular replication complex?
Inside the host cell, the virus recruits the cell’s proteins in the replication process to replicate the viral genome.
Where are giant viruses thought to originate from?
Thought to originate from cells, maybe obligate intracellular cells, that underwent reductive evolution.
What are tailed viruses?
The genome is connected to a helical neck that delivers the genome to the host cell.
Six jointed legs stabilize the virus on the host cell.
What are prions?
Prions=aberrant infectious proteins.
Unaffected by treatments that target RNA or DNA.
Includes nucleases and UV radiation.
Prions bind to normal proteins and then change their shape to the prion’s shape.
Describe dsDNA viruses.
Uses its own or hosts’ DNA polymerase for replication.
RNA polymerase can also come from the virus or the host cell.
Group 1.
Describe ssDNA viruses.
Uses hosts’ DNA polymerase to replicate the strand.
Double-stranded DNA can then be read by the hosts’ RNA polymerase.
Group 2.
Describe dsRNA viruses.
Require RNA-dependent RNA polymerase to make mRNA.
A virus may package an RNA polymerase before it leaves the host cell.
Ex: Reoviruses.
Includes rotavirus which causes diarrhea in children.
Group 3.
Describe + ssRNA viruses.
Single-stranded.
Contains + sense strand, the coding strand.
Still needs RNA polymerase to be replicated.
Cannot make more + strand without the - strand.
Can serve as mRNA to make proteins.
Includes coronaviruses.
Group 4.
Describe - ssRNA viruses.
Single stranded.
Contains the - strand which needs to be replicated before translation can occur.
Need to package viral RNA-dependent RNA polymerase.
Often segmented.
Ex: Influenza.
Group 5.
Describe retroviruses.
+ ssRNA.
Has reverse transcriptase which transcribes RNA into double-stranded DNA.
Integrated into the host genome.
Group 6.
Explain pararetroviruses.
Has double-stranded DNA.
Transcribes to RNA.
Then, uses reverse-transcriptase to turn RNA back to progeny DNA.
Reverse transcriptase is packaged into the virion.
Group 7.
Explain the lytic replication cycle.
The virus recognizes the host and attaches to it.
Genome must enter the host cell.
Viral phage progenies must be constructed.
Phage progenies must exit the cell to infect new hosts.
They lyse and break open the host cell as they do this.
Explain the pros and cons of the lytic replication cycle.
Pros: Fast, and can make a lot of virions.
Cons: Kills host cell.
Explain the lysogeny cycle.
The viral genome integrates with the host genome.
Usually site-specific.
The viral genome can cut itself out of the genome and turn back into the lytic cycle if environmental conditions or host health deteriorates.
Explain the pros and cons of the lysogeny cycle.
Pros: Can stay in the host genome a long time undetected so it can spread to daughter cells.
Cons: Cannot leave and go to new hosts. Not actively making virions while in the genome. Not getting genetic mutations as quickly.
Explain the slow release cycle.
Able to enter and exit the cell without killing it.
Single-stranded DNA is made into double-stranded DNA.
Double-stranded DNA slowly forms single-stranded viral progeny.
Uses negative supercoiling.
The virus, with the capsid, leaves the host cell alive.
The host cell is alive but grows and replicates more slowly than uninfected cells.
This is because the virus production took a lot of the host cell’s nutrients.
What type of phages does the lysogeny cycle?
Temperate phages.
What is specialized transduction?
Specialized transduction=transfer of certain genes from the host genome in a newly packaged virus to a new host.
What are the pros and cons of the slow release cycle?
Pro: Does not kill the host.
Cons: Slower and does not produce as many virions (smaller burst size).
List the great variety for viral genomes.
RNA or DNA.
For RNA, can be + or - based on whether it is the sense or antisense strand.
Can be single or double-stranded.
Can be linear or circular.
Whole or segmented.
Segmented=separated into separated “chromosomes”.
Why can’t viruses be related by gene-similarity of host type?
There is such a great variety in genomes that viruses with different genomes may be more closely related. Viruses of different hosts may be more similar than viruses with the same host.
So, to categorize viruses, they are categorized by the type of genome they have and relatedness is determined by the proteome.
What are orthologs?
Orthologs=different species, same function.
What are coliphages?
Coliophages=gut bacteripphages.
How can surface proteins change in relation to viruses?
The cell surface receptors that viruses bind to are very specific. A host can gain immunity by changing its cell-surface proteins.
What is a ghost?
An empty capsid one viral DNA has gone inside the cytoplasm.
What is burst size?
Burst size=size of virus progeny that leave a lysed host cell.
What is dsDNA?
Double-stranded DNA.
What is the difference between early genes and late genes?
Early genes are viral genes that are expressed soonest after translation. Closest to the beginning of translation point. Usually translates for polymerases and transcriptase to continue replication and translation.
Late genes are expressed at the end. They usually code for proteins that will lyse the host cell.
What is transduction?
When a virus takes some of the host’s cell DNA with it.
Explain how the CRISPR system acts as an immune system for bacteria.
When the cell can destroy phage DNA, some of it goes into the CRISPR system to be remembered.
CRISPR DNA becomes crRNA.
crRNA binds to the Cas protein complex.
This complex looks for analogous RNA that binds to genetic material from viruses.
What is the Arc system that viruses use to counteract CRISPR?
Phages have evolved anti-CRISPR proteins called Arc.
Can bind to the Cas system which prevents it to bind to viral genetic material. Therefore, the CRISPR system does not go off.
How do restriction endonucleases protect bacteria from viruses?
Bacteria put methyl groups on some of their bases.
Restriction endonucleases cut DNA without these methyl groups.
Viral DNA genomes do not have these methyl groups so they go off.
How do some viral genomes escape detection from restriction endonucleases?
Viruses with changed genomes such as RNA to DNA escape the restriction endonucleases because in the reverse transcription process methyl groups are added.
What are the 3 main ways that bacteria have resistance to viruses?
Genetic resistance (ex: mutations) Restriction endonucleases. CRISPR.
What is a virome?
Virome=community of viruses in a host.
What is transcytosis?
Transcytosis=human tissue taking up bacteriophages.
What is dysbiosis?
Dysbiosis=deterioration of health due to loss of health-promoting bacteria.
What are some hypotheses for why transcytosis occurs?
Because viruses are inert when not in a host, human cells may move bacteriophages around to help them find hosts.
Having phages inside human cells can provide defenses against bacteria that enter the human cell.
How can phages in the gut be useful?
Bring equilibrium in bacteria numbers to what the human gut can tolerate.
Can modulate the immune system.
Attack biofilms.
Can transfer use genetic material to hosts.
What is tropism?
Tropism=ability for viruses to affect different tissues in eukaryotic multicellular organisms.
Viruses can have a broad range (like Ebola) or a narrow range (like polio).
What is uncoating for viruses?
Uncoating=process by which the capsid comes apart.
Can happen in the cytoplasm or at a specific organelle.
What are ways that viruses can enter animal cells?
The viral membrane binds to receptor proteins and becomes part of the cell membrane.
The genome enters directly into the cytoplasm.
Viruses can be encoded in an endosome.
Endosomes can be broken up by a lysosome, and the genome enters the cytoplasm.
Or endosomes can bring the virus to a specific organelle, like the nucleus.
In the nucleus, viruses can take advantage of DNA polymerase, DNA binding proteins, and transcription factors.
What is an episome?
Episome=DNA that can live autonomously in the cell (like plasmids) or be integrated into the genome.
How can viruses cause cancer?
Oncogenes.
Can encode for abnormal oncogenes that deregulate growth.
Genome integration.
Viruses can encode for factors that stimulate host cell division.
Cell cycle control.
Express viral proteins that mess with host cell cycle controls.
What is an oncovirus?
Virus that causes cancer.
In animal cells, what are the two places where viral assembly most likely takes place?
At the ER and the nucleus for nuclear virions.
Why is it beneficial for viruses to make host cells cancerous?
This is beneficial because the more offspring the host has, the more cells now carry the virus. More viral progeny can be made.
How can low level chronic infections enhance the immune system?
The immune system has to be active and fight infections to gain a better memory and do better at its job.
How do viruses infect plant cells?
Viruses enter through damaged tissue.
Animals that eat plants cause damage and can transmit viruses that way.
Some enter the seed and can infect the next generation.
Enter through plasmodesmata (cell junctions that connect cells). Usually not the first mode of entry but how uninfected cells get infected.
Why can’t plant viruses just enter through the cell wall?
Too thick to penetrate.
What are animal and plant defenses against viruses?
Genetic resistance through mutations.
Harder for animals and crops in monoculture.
Immune system.
Interferons=immune system particles that recognize viral particles such as dsRNA.
The immune system has antibodies to recognize certain viral proteins.
RNA interference:
When translating mRNA, the host RNA complex can recognize the viral RNA and refuse to translate it.
Why must viruses be cultured in a host?
Because viruses cannot be cultured on their own.
What is batch culture?
Batch culture=liquid culture that allows the growth of a large number of viruses.
What is multiplicity of infection?
Multiplicity of infection=virus to host cell ratio.
Can manipulate it to make sure every host cell is infected.
In viral growth curves, what is the eclipse phase?
Eclipse phase=time when no virus progenies are made.
The viral genome is still being delivered.
In viral growth curves, what is the latent phase?
Latent phase=viral progeny have been made but have not yet burst out of the cell.
Easier to see in animal cells because virus progeny usually buds out of the cell.
What is the difference between latent phase and latent infection?
Latent phase=viral progeny have been made but have not yet burst out of the cell.
Latent infection=when a virus maintains its genome in the cell but does not produce any virions.
In viral growth curves, what is the rise phase?
Rise phase=increase in viral progeny from host cells.
What is a lysate?
Lysate=viral particles in suspension.
What is virulence?
Virulence=ability to cause disease.
Why is burst size bigger for animal cells than bacterial cells?
Animal cells are larger and have more resources to make more virions.
What are plaque-forming units (PFUs)?
Plaque forming units (PFUs)=by counting the number of plaques, we can estimate how many viruses there are.
How are viruses cultured in bacteria?
Seen by PFUs. Can generate a lysate for the virions in the burst size.
Why does the method for culturing animal viruses different than culturing viruses from bacteria?
Animal cells are cultured with liquid on top. You could not count the number of plaques because released virions would spread throughout the plate via the liquid.
What is a method for culturing animal viruses?
Infect monolayer.
Allow enough time for viruses to latch onto the host.
Remove liquid layer (aspirate it).
Add gelatin layer.
This will still allow host cells to grow but limit the dispersal of viral progeny.
What are focus methods for culturing animal viruses?
Focus methods are used for cells that are infected by a virus that does not kill them.
Can be visualized by fluorescence using an antibody.
Can be visualized by piles of transformed cells that have infected with oncogenic viruses that turn host cells into cancer cells.
What would happen if a virus did not uncoat inside of a host cell?
No replication would occur.
No viral progeny would be made.
The capsid could be digested and then the genetic material could be released.
What are LTR regions?
LTR regions=long-terminal repeats.
Can be on both ends of the viral genome.
What is a virophage?
A virus that infects a bigger virus.
What are cytopathic effects?
Cytopathic effects=changes in the structure of the cell due to infection by a virus.
What diversity do bacterial chromosomes have?
Circular or linear chromosome.
One or two chromosomes.
What is the assumption between the complexity of an organism and its genome?
More complex organism=more complex genome.
Not always true.
How does the genome compact in the cell?
Uses histones, radial loops, and supercoiling.
What is conjugation?
Conjugation=horizontal transfer of genetic material between two bacteria that takes place over a period of time.
What is site-specific recombination?
Inserting new DNA into a specific spot.
Compare the amount of non-coding DNA between prokaryotes and eukaryotes.
Prokaryotes have a lot less noncoding DNA than eukaryotes.
What is an operon?
Operon=genes operating in tandem.
Controlled by a single promoter.
What is a regulon?
Regulon=functional level of collection of genes and operons that may serve a unified process.
Less common than operons.
What is the nucleoid?
Nucleoid=protein bound domain that holds the genome.
What is positive supercoiling?
Positive supercoiling=overwinding.
Overwinding turns DNA in a clockwise direction and increases the number of twists.
What is negative supercoiling?
Negative supercoiling=underwinding.
Underwinding turns DNA in a counterclockwise direction and lowers the number of twists.
Explain the DNA compaction system in prokaryotes.
DNA is bound by histone-like proteins. The DNA is negatively supercoiled by topoisomerase.
What do topoisomerases and gyrases do?
Topoisomerases and gyrases help add or subtract supercoiling.
Change topology of DNA.
They cause a break in the end, pass DNA through the break and then reseal it.
When does positive supercoiling usually occur?
When DNA is open for replication or transcription. As the fork opens, the DNA will positively supercoil. The positive supercoils have to be removed to continue to open the DNA. Thus, a topoisomerase will be ahead of the fork removing the positive supercoils.
What does topoisomerase I do?
Cleaves one strand.
Thought to remove negative supercoiling.
What does topoisomerase II/gyrase do?
Cleaves both strands.
Uses ATP to generate negative supercoils.
Multisubunit protein.
2 GyrA and 2 GyraB.
What does the antibiotic quinoline target?
Quinoline=antibiotic that targets topoisomerase II.
How does DNA replication occur?
Semiconservative fashion and negatively supercoiled.
What is oriC?
Origin of replication.
What are ter sites?
Termination sites.
There are several and which ones are used depends on the speed of the strands and which one gets to the ter sites first.
What are catenanes?
Catenane=chromosomes are stuck together. Topoisomerase IV (activated by an increase in SeqA) breaks catenanes by a double-strand break and finishes off replicated chromosomes.
What inhibits DNA replication initiation and what promotes it?
SeqA protein inhibits DNA replication initiation.
DnaA promotes DNA replication initiation.
What does DNA adenine methylation (Dam) do?
Methylates the new strand.
