Flashcards in Viruses and Phage Deck (43):
How are viruses different than cells?
Require host for replication, energy metabolism, and protein synthesis.
What are the five steps in viral lifecycle?
What are the three types of viral symmetry?
What is the difference between lytic and lysogenic lifestyles?
Lytic kills the host.
Lysogenic is dormant.
What are examples of subviral entities?
Defective viruses, viroids, and prions.
How can viruses be sorted?
They are classified based on the host(s) they infect such as animal, plant, bacteria (called bacteriophages), archaea (called archaeaphages), and other eukaryotes.
What do viruses require a host cell for?
Replication, energy, metabolic intermediates, protein synthesis.
Which is more abundant, living cells or viruses?
Viruses, by 10-fold
How are viruses classified?
There are two types of classification: Baltimore Classification and ICTV Classification.
What is the Baltimore Classification based on and what are its 7 classes?
It is based on genome and mRNA production methods.
1. Double-stranded DNA genome
2. Single-stranded DNA genome
3. Double-stranded DNA genome
4. Single-stranded RNA genome of plus configuration
5. Single-stranded RNA genome of minus configuration
6. Single-stranded RNA genome that replicates with DNA intermediate
7. Double-stranded DNA genome that replicates with RNA intermediates
What is the ICTV Classification based on and how is it broken down?
It is based on phenotypes such as morphology, nucleic acid, mode of replication, host organisms, and type of disease. Over 3000 types are unclassified, however there are 7 orders with 111 families with >22 subfamilies with >420 genera and >2681 species included.
What is the difference between a capsid, a capsomere, and the nucleocapsid in a virion, or the external virus?
DNA/RNA is stored inside a "capsid" which si enclosed in proteins called "capsomeres" in a regular pattern. A "nucleocapsid" is DNA/RNA with protein and is located inside the virion.
Note: the virion can be naked or enveloped.
What is an enveloped virus?
Membrane surrounding the nucleocapsid that primarily infects animal cells. The matric between nucleocapsid and envelope filled with proteins and is jelly-like. The lipid bilayer with proteins is embedded. Shape of the envelope is determined by capsomeres. They contribute to host-specificity and attachment to host cells.
What is a naked virus?
Pertain to those that only have nucleocapsid, which is a protein capsid that covers the genome of the virus. It lacks an envelope.
What are the symmetries found in viruses and do all viruses conform to these shapes?
Nucleocapsids are symmetrical because of the arrangement of capsomeres.
1. Rods which have helical symmetry and the length is based on length of the nucleic acid.
2. Spherical which have icosahedral symmetry (20 triangle faces) and the 60, 180, 240, 420 capsomeres determine the size. Proteins on each face dictate the size. More proteins, the larger it is.
What are complex viruses?
Have both icosahedral and helical features. Mostly bacteriophage. These are not human viruses and generally infect bacteria. They have a head, collar, tail, tail pins, endplate, and tail fibers.
What are examples of enzymes in virions and what do they do?
Adhesion proteins - help find appropriate host cells
Lysozyme - puncture holes in cell walls for infection. Helps break up Beta 1,4 linkages in peptidoglycan
Polymerases - to replicate nucleic acids and to reverse transcriptases turning RNA into DNA
Neuraminidases - break glycoproteins and glycolipids in cell walls to free virions.
What occurs during viral attachment of the initial steps of viral entry?
It is mediated by the viral attachment protein (VAP) - in other words they are always proteins. VAPs are host specific via receptors which can be proteins, carbs, glycolproteins, lipids, lipoproteins, or mixtures. These VAPs can evolve and be tissue specific. Multiple receptors can be used.
What occurs during viral penetration of the initial steps of viral entry?
The goals is to get the viral genome +and- viral proteins into the host. This is done through either fusion or injection. The virus knows how to manipulate a host cell and can even force themselves inside. Compare it to rape. After it injects its DNA, the speak will stay attached/stuck to the membrane. It doesn't leave because eventually the cell will lyse.
What occurs during fusion, a step of viral penetration?
Enveloped viruses either fuse with host cells or they are endocytosed. It requires the uncoating of a nucleocapsid.
What occurs during injection, a step of viral penetration?
Occurs for hosts with cell walls. Most complex are bacteriophage T4
What needs to be replicated for packaging in viruses?
Nucleic Acids and Proteins
What is the inherent problem for RNA viruses?
Their genomes are not recognized by host machinery.
How do RNA viruses replicate?
Host DNA polymerases and Host RNA polymerases require a dsDNA template. There are two options: one of two different enzymes.
1) Convert genomes to dsDNA - retrovirus
2) Bring your own RNA-dependent RNA polymerase (RdRp)
In RNA virus replication synthesis, what happens when genomes are converted to dsDNA?
These are generally retroviruses such as HIV and lentivirus. Reverse transcriptase (RT) - RNA-dependent DNA polymerase
RNA=template, DNA = the copies
In RNA virus replication synthesis, what happens when you bring your own RNA-dependent RNA polymerase (RdRp) to the mix?
It recognizes RNA templates, makes copies of RNA. Its for transcription and genome replication. Found with RNA viruses like rotovirus, ebola, measles, rabies, hantavirus, influenza, west nile, yellow fever, polio, and rubella.
What are the classes of genome replication for DNA viruses and for RNA viruses?
-Class 1: Classical semiconservative
-Class 2: Classical semiconservative, discard (-) strand
-Class VII: Transcription followed by reverse transcription
-Class III: Make ssRNA (+) and transcribe from this to give ssRNA (-) partner
-Class IV: Make ssRNA (-) and transcribe from this to give ssRNA (+) genome
-Class V: Make ssRNA (+) and transcribe from this to give ssRNA (-) genome
-Class VI: Make ssRNA (+) genome by transcription of (-) strand of dsDNA
During synthesis, how do viruses make proteins?
Host ribosomes only recognize mRNA in the + configuration.
(+) strand RNA = sense; coding strand; has RBS and AUG codon
(-) strand RNA = antisense; template strand; reverse complement of coding strand. On hypothetical 'other' strand.
IT has to get the RNA in correct orientation if not already. mRNA must be encoded with a start codon and ribosomal binding site (Shine Delgarno site). Output is positive sense mRNA. Class 3 will transcribe the (-) strand.
What do early genes of viral synthesis do?
Encode enzymes and regulatory proteins needed to start viral replication processes.
-Shutting down host processes
-Transcription factors for late genes
What do late genes of viral synthesis do?
Encode structural proteins, proteins needed for assembly.
Ducks must be in a row because it will begin assembling on its own.
What are the two lifestyles of viruses during synthesis phase?
What is the lytic lifestyle?
Part of viruses during the synthesis phase. IT is the rapid progression through viral synthesis phase. No viral DNA incorporation into host genome.
What is the lysogenic lifestyle?
Incorporates viral DNA into host DNA but it is not expressed. Virus wants to lay dormant for a while until conditions get better. Activation (by external stimuli/signals) switches to lytic cycle. Only becomes lytic every so often.
What occurs during the assembly and release final stages of viral infection?
Self assembly of nucleocapsid, proteins into intact virions inside the cytoplasm of the host cell.
-Budding: induced extrusion carrying host membranes with it.
-Lysis: Late viral genes encode proteins that break down membranes/wall and allow release.
Infection of neighboring cells.
What is burst size?
Bursting occurs when the infected cell finally lyse. The true burst size varies considerably. For every 1 host cell, 500 viruses burst out. The larger the burst size, the faster the spread.
What is host restriction in Eukaryotes and Bacteria?
Immune systems try to halt viral entry/synthesis .
-RNA interference recognizes viral DNA and leads to degradation
-Innate and adaptive memory of previous pathogens and antibody production.
-CRISPRs: memory based short DNA fragment interference and degradation
-Restriction endonucleases - to protect from foreign DNA
What can counter host restrictions for viruses?
The molecular arms race. Think of the red queen hypothesis.
What are bacteriophage?
Most contain dsDNA genomes, naked, are complex with heads and tails, and engage in both the lytic and lysogenic lifestyle.
1)Virulent phages - lytic lifestyle (get-in-get-out)
2)Temperate phages - lysogenic lifestyle (When the going gets tough - the tough get going)
what are virulent phages?
These kill their host cells rapidly? An example is T4. Has an unusual genome with 250 protein coding genes, encodes some of its own tRNAs, and T4 DNA contains 5-hydroxymethylcytosine instead of cytosine = resistant to restriction modification by hosts.
What is the lifecycle of virulent phage T4?
Early, Middle mRNAs code for DNA replication and transcription.
-Inhibits host transcription by inactivating essential host co-factors
-Modifies host transcription machinery so it recognizes viral promoters
Late mRNAs encode structural proteins
-Head and tail
-T4 lysozyme for degrading host peptidoglycan
What are temperate phages?
-Capable of non-killing via lysogeny.
-Exists as a prophage in the genome
-It just sits quietly and doesn't express proteins
-During stressful times, virus can become lytic
-Most well studied example-bacteriophage lambda.
What is temperate phage, phage lambda?
-Infects E. coli
-Both lytic and lysogenic. Decision is based on a genetic switch between 2 proteins
-Genome incorporates at specific sites in the genome (attachment sites)
-Rolling circle DNA replication during lytic cycle