Module 2 (EU)
*gapped dna* -viral family: h____dnav_____ -starts as partially ds... has to be repaired before it is made into mRNA
hepadnaviridae
Animal cells cannot copy viral RNAs and make mRNA from them, so the RNA virus must encode NUCLEIC ACID_________
polymerase
dsDNA uses the host DNA _____ to copy their dsDNA
polymerase
Gapped circular dsDNA must be ______ before translation
repaired
Which types of viruses use reverse transcriptase (RT) in their replication cycle? Check all that apply. retroviruses ssDNA viruses ss(-) RNA viruses gapped, circular dsDNA viruses
retroviruses gapped, circular dsDNA viruses
Norovirus is an example of ss + ____
rna
*replication of RNA viruses* -only RNA viruses have rna d_____ rna p___
rna dependent rna polymerase
Rna viruses encode _ _ _ _
rna dependent rna polymerase
cells have NO rna-dependent RNA pol that can replicate rna viruses or make mRNA from RNA templates. 1. solution is to have RNA virus genomes encode ______ ______ . 2. solution is to have r____- t______- of the genome to ds DNA which can then be transcribed
rna dependent rna polymerases (rdrp) reverse transcription
how many viruses encode to MODULATEhost immune response
some
how many viruses encode to regulate the replication timing
some
these are proteins encoded by (all/some/none) viruses 1. reg of rep timing 2. virual release and spread 3. modulate host immune response
some
which rna virus is most efficiend and can be directly translated
ss + rna
*ss ___ RNA can be directly translated* -ex: n____________ -most e__________ -it is rna so it ENCODES for _____ -*retrovirus encodes rna dependent rna polymerase BUT it also packages ______
ss + rna norovirus efficient rna dependent rna polymerase reverse transvriptase
From ____ came the principle that the nucleic acid-based repository of the information needed to build, reproduce, and transmit a virus
viral genome
The ____ ____ is the nucelic acid-based repository of the information needed to build, reproduce, and transmit a virus
viral genome
What information is not contained in viral genome?
• 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)
What are some gene products and regulatory signals required for viral genome?
• replication of the genome • efficient expression of the genome • assembly and packaging of the genome • regulation and timing of the reproduction cycle • modulation of host defenses • spread to other cells and hosts
Identify which group(viral genome) is being described: i. The DNA must be converted into double stranded DNA ii. then cellular enzymes can do their normal thing and convert that into mRNA
(+)ssDNA
Which of the viral genomes have to go through some intervening step before the nucleic acid can be converted into messenger RNA
(+)ssDNA, (+)ssRNA(retroviruses), (+/-)dd/ssDNA
Identify which group(viral genome) is being described: i. Their genomes can actually be used as messenger RNA ii. Can be immediately translated once it is inside the cell
(+)ssRNA
Identify which group(viral genome) is being described: i. Don't use their nucleic acid as messenger RNA ii. Go through the process of reverse transcription, convert their RNA into DNA, and then that DNA gets converted back into messenger RNA
(+)ssRNA (retroviruses)
Which statement about viral RNA genomes is correct? Copying of (+)ssRNA during virus replication does not require a (-) strand intermediate (+)ssRNA genomes may be translated to make viral protein RNA genomes can be copied by host cell RdRp dsRNA genomes can be directly translated to make viral protein
(+)ssRNA genomes may be translated to make viral protein
mRNA is always + or -
+
Terms -mRNA is always the ___ strand -The DNA strand that is of equivalent polarity to mRNA is the ___ strand -mRNA can be translated by ____ into protein without any alteration
+ + ribosome
Complements of the (+) strand is the (__) strand
-
What kind of drift is being described here? i. Influenza viruses 1. Have 8 segments 2. With very replication there will be small changes in the nucleic acid 3. If these proteins change that means that the antibodies in my body won't recognize this new mutation that well
Antigenic shift
What kind of drift is being described here? i. More dramatic change ii. Two different strains infecting the same cell 1. Human and pig influenza affecting same cell 2. Union packing you can get mix of viral genome in one new viral genome iii. Cause widespread disease, cause large pandemic
Antigenic shift
Which type of viral evolution results in large changes to the viral genome? Lytic evolution Antigenic shift Progressive evolution Antigenic drift
Antigenic shift
T/F: Viruses do not encode proteins for assembly or packaging of that genome. Capsid proteins that are responsible for making that virus shell are encoded by all the host
False Protein encoded: Assembly packaging of genome a. All viruses encode proteins for assembly or packaging of that genome i. Capsid proteins that are responsible for making that virus shell are encoded by all viruses
T/F: Proteins are responsible for complete protein synthesis machinery
False Proteins NOT encoded: Complete protein synthesis machinery 1. Some viruses can encode a part of the protein synthesis machinery but they cannot encode all of it
T/F: Viruses encode proteins that are responsible for membrane synthesis
False Proteins NOT encoded: Membrane synthesis 1. Virus don't encode proteins that are responsible for membrane synthesis 2. Specially don't encode proteins that generate lipids 3. Which is why virus gets membrane from its host
T/F: Gapped circular dsDNA can be immediately converted into messenger RNA
False a. Even though they have dsDNA, they cant be immediately converted into messenger RNA
T/F: Viruses and host cells do not share genetic information with each other
False i. Supported by genetic similarity 1. Between study of viruses and host cell (they share a lot of genetic information) a. Would make sense that they probably originated from the cells in which they share these genetic similarities
T/F: Viruses do not encode for proteins that are needed for releasing and spreading of those viruses after they've gone through the cycle of replication
False Protein encoded: Viral release and spread a. Genes responsible for releasing and spreading of those viruses after they've gone through the cycle of replication
The cellular origins hypothesis of viral evolution can be supported by which of the following. Check all that apply. Genetic similarity between viruses and host cells. The presence of prions. The presence of plasmid
Genetic similarity between viruses and host cells. The presence of plasmid
Gapped circular DNA uses _______ to convert RNA to DNA. ______ is not an enzyme that is encoded by any host proteins, this is strictly a virtually-encoded enzyme.
Reverse transcriptase
T.F: Gapped circular dsDNA has a portion that is dsDNA and portion that is ssDNA and also have an RNA molecule woven in there
True First, the single portion of DNA needs to be repaired and converted into ds DNA i. This virus uses the host cellular enzymes to repair its genome ii. Once the genome is repaired, it can then go through the normal process of transcription and translation
T/F: (-)ssRNA viruses must package their own RdRp
True
T/F: A. The coevolution hypothesis assumes viruses came first
True
T/F: Gapped circular dsDNA uses the mRNA that was made using host transcriptional factors to copy its genome ( not the original one it came with)
True
T/F: Not all (+) RNA is mRNA
True
A temperate bacteriophage has both lytic and lysogenic cycles. In the _____ cycle, the phage replicates and lyses the host cell. In the ______ cycle, phage DNA is incorporated into the host genome, where it is passed on to subsequent generations.
A temperate bacteriophage has both lytic and lysogenic cycles. In the lytic cycle, the phage replicates and lyses the host cell. In the lysogenic cycle, phage DNA is incorporated into the host genome, where it is passed on to subsequent generations.
Which of the following is a protein encoded by the virus?
A)Viral release and spread B)Complete protein synthesis machinery C)Energy production D) Membrane synthesis
These are proteins encoded by (all/some/none) viruses 1. rep of genome 2. assembly package 3. amplify immune response
ALL
how many viruses encode to assemble/package the genome
ALL
Cells have no RNA-dependent RNA polymerases that can replicate the genomes of RNA viruses or make mRNA from RNA templates. One solution to this problem is that RNA virus genomes encode _______ RNA from RNA templates. The other solution, exemplified by retrovirus genomes, is ______ of the genome to dsDNA, which can be transcribed by host RNA polymerase.
Cells have no RNA-dependent RNA polymerases that can replicate the genomes of RNA viruses or make mRNA from RNA templates. One solution to this problem is that RNA virus genomes encode RNA-dependent RNA polymerases that produce RNA from RNA templates. The other solution, exemplified by retrovirus genomes, is reverse transcription of the genome to dsDNA, which can be transcribed by host RNA polymerase.
This theory of evolution is described here? i. Cells came first and then viruses ii. Viruses are deprived from bits of nucleic acids that somehow "escaped" 1. Slipped out of cellular homes from the cellular organism they were housed in 2. Nucleic acid are free and stayed intact and from there you get viruses that evolved 3. Plasmid a. Circular DNA found in prokaryotes 4. Explains why viruses are so specific a. because they come directly form the cells that they possibly are going to infect
Cellular Origin hypothesis (progressive hypothesis )
This theory of evolution is described here? i. Starting cells and viruses may have evolved together ii. Viruses defiantly must have appeared early in the history of life, before the 3 domains that cells diverge 1. Bacteria, vs arches vs eukaryotes
Co evolution hypothesis
______ lead has lead to the formation of only seven major times of viral genome
Evolution
T/F dsRNA genomes can be DIRECTLY translated to make viral protein
F
ssDNA a. First step: ssDNA has to be converted to _____ before it can be replicated and converted into messenger RNA (This uses cellular host ____ to do this process) b. Replication then happens the same way dsDNA replicates c. DNA ____ is used for copying the DNA genetic material (Get both negative and positive strand and either one of these can be incorporated into the new viral particle)
I a. First step: ssDNA has to be converted to dsDNA before it can be replicated and converted into messenger RNA(This uses cellular host proteins to do this process) b. Replication then happens the same way dsDNA replicates c. DNA polymerase is used for copying the DNA genetic material (Get both negative and positive strand and either one of these can be incorporated into the new viral particle_
In a ______ cycle, once the DNA gets incorporated into the bacterial chromosome, it can sit _____ in the DNA of the bacterium until the bacterial decided to replicate. This lead to the theory of _____.
In a lysogenic cycle, once the DNA gets incorporated into the bacterial chromosome, it can sit silently in the DNA of the bacterium until the bacterial decided to replicate. This lead to the theory of evolution.
Which of the following is not a protein encoded by the virus? A)Replication of genome B) Assembly/packaging of genome C) Regulation of replication timing D)Viral release and spread E)Modulation of host defences F)Membrane synthesis
Membrane synthesis
_____viruses are an example of viral +ssRNA, which can be directly ____. They have the most _____replication strategy. Although it does need ____, it does not package it into its capsid.
Noraviruses are an example of viral +ssRNA, which can be directly translated. They have the most efficient replication strategy. Although it does need RdRp, it does not package it into its capsid.
A virus that is integrated into the host genome is called a ________.
Provirus
Which enzyme is used by RNA viruses to synthesize mRNA? DNA-dependent RNA polymerase Ribonuclease Reverse Transcriptase RNA-dependent RNA polymerase
RNA-dependent RNA polymerase
Which enzyme is used by RNA viruses to => mRNA?
RNA-dependent RNA polymerase (RdRp)
What is the difference between RdRp and RT?
RdRp: makes mRNA from RNA template RT: Make dsDNA from RNA template
This theory of evolution is described here? i. Suggests viruses were once free-living organism that lost genetic information 1. some types of bacteria are also obligate intracellular parasites that have to be inside of a cell to replicate 2. They devolved into what we know now as mitochondria
Regressive hypothesis
Replication of viral dsDNA mimics host DNA replication a. Once dsDNA gets into the nucleus it _____ can be converted to mRNA b. Virus will use ____ cellular proteins (Host RNA polymerase II) c. Once mRNA is made, it can make ____ d. Some of those proteins can be used for the formation of a ____ viral particle e. Other proteins are going to go off and impact cellular process of some sort (things that will ____ viral infection) f. Others will go on and be involved in the replication of copying of the genetic martial
Replication of viral dsDNA mimics host DNA replication a. Once dsDNA gets into the nucleus it immediately can be converted to mRNA b. Virus will use host cellular proteins (Host RNA polymerase II) c. Once mRNA is made, it can make proteins d. Some of those proteins can be used for the formation of a new viral particle e. Other proteins are going to go off and impact cellular process of some sort (things that will increase viral infection) f. Others will go on and be involved in the replication of copying of the genetic martial
Retroviruses packages its own ____. Once it gets converted to ssDNA it used _____ enzymes to convert that into dsDNA. The DNA then goes into the nucleus and gets integrated into the host _____ (unique). Once this integration happens it is called a ____.
Retroviruses packages its own RT. Once it gets converted to ssDNA it used cellular enzymes to convert that into dsDNA. The DNA then goes into the nucleus and gets integrated into the host chromosomes (unique). Once this integration happens it is called a provirus.
This enzyme only encoded by the virus, they need this for replication of their genetic material
RpRp
T/F + ss RNA genomes may be DIRECTLY translated to make viral protein
T
T/F There are some viruses that only encode 1 viral protein
T
The cellular origin hypothesis is also called the ______ hypothesis. This theory is based on the idea that these mobile genetic elements or _____, progressed overtime to gain the ability to exit and enter cells on their own
The cellular origin hypothesis is also called the progressive hypothesis. This theory is based on the idea that these mobile genetic elements or plasmids, progressed over time to gain the ability to exit and enter cells on their own
There are no known host cell enzymes that can copy the genomes of RNA viruses. However, at least one enzyme, ________ , can copy an RNA template.
There are no known host cell enzymes that can copy the genomes of RNA viruses. However, at least one enzyme, RNA polymerase II, can copy an RNA template.
Replication of viral dsDNA mimics host DNA replication ______ and ____ of the proteins must happen first because all copying of genetic material uses some sort of viral protein
Transcription, translation
T/F: Viruses have proteins that are responsible for regulating replication
True Protein encoded: Regulation of replication timing i. Herpes that can go latent inside of a cell ii. The genes that are responsible for latency cant be turned on as soon as the virus infects iii. The timing and expression of those genes is very important to whether or not the virus is causing an acute infection or whether the virus or causing a latent infection
T/F: All of the energy that a virus gets, it gets from a host cell
True Proteins NOT encoded: Energy production 1. Viruses don't produce enzymes can that generate ATP
T/F: Viruses are responsible for encoding proteins that will modulate host defenses
True Protein encoded: Modulation of host defenses i. All viruses have proteins on their surface which 1. amplify the immune response 2. Cause the generation of antibodies 3. Recruitment of cytokines and T cells ii. Some viruses encode for proteins that dampen the immune response 1. Allow them to go into latency or hide from the immune system so they can cause more widespread disease
T/F: Every virus must encode some sort of its own genome replication machinery
True Protein encoded: Replication of genome
Identify which group(viral genome) is being described: i. The viral DNA gets converted into RNA ii. Goes through the process of RT to make ds DNA, which then can be converted into messenger RNA
a. (+/-)ds/ssDNA
Hoe does (-)ssRNA work?
a. RdRp is what is used for the conversion of the viral genome into messenger RNA, which will then get translated into proteins, and those can get used for the formation of the viral capsid or for copying of the genetic material b. They make more of the RdRp which not only copies from the (-)RNA to make (+)RNA, but it is also used in the conversion of that (+) into (-) strand c. -RNA is what
how many viruses encode for replication of genome
all
how many viruses encode to amplify immune reponse
all
*viral genomes vary widely in size* -____________________= smallest virus
circovirus
hepatitis are what shape of viral genome
circular gapped
Identify which group(viral genome) is being described: use host enzymes to convert its double-stranded DNA into messenger RNA using the cellular process of transcription
dsDNA
Which DNA genome, on entry into the cell, can be immediately copied into mRNA?
dsDNA
Which DNA genome, upon entry into the cell, can be immediately copied into mRNA? Linear ssDNA all types of DNA can be immediately copied to mRNA Circular ssDNA Gapped dsDNA dsDNA
dsDNA
ssDNA(can be - or +) must become ______ before it can be replicated in the cell
dsDNA
What are the three groups in the Baltimore system that can be immediately converted into mRNA using either host or cellular enzymes
dsDNA, ssRNA, (-)ssRNA, (+)ssRNA
dsRNA viruses must package an _____ Can be made up of (-/+) RNA needs to be converted into mRNA, in order to do that they need ____ , which comes from inside the viral particle. Package genetic material and ____
dsRNA viruses must package an RdRp Can be made up of both -/+ RNA needs to be converted into mRNA, in order to do that they need RdRp, which comes from inside the viral particle. Package genetic material and RdRP
Identify which groups(viral genome) are being described: genomes use viral enzymes that are packaged within the virus and come in with the virus to immediately convert their type of genome into messenger RNA
dsRNA, (-)ssRNA
*Viral Genomes* -___________________: (flaviviridae) one long strand of nucleic acid... can be one long or divided into segments -____________________(reoviridae).. -_____________________(circoviridae)... can be ds or ss -___________________(ds circular genome) ONLY VIRUS WITH BROKEN CIRCULAR GENOME : hepadnaviridae.. ds and ss portions of circles -_________________: both + and - rna in one long strand
linear segmented circular gapped ambisense
The Baltimore Scheme - all viruses must make ____ before proteins are made -Once they make ____, they can translate proteins, and then replicate
mRNA
The use of which nucleic acid is common to all viral replication?
mRNA
DS DNAand DS RNA can immediately be made into _______. However, SS __ RNA's genome already acts as mRNA and can be immediately __________-
mRNA translated
*Two important principles of viral genomes* 1. all viral genomes must be copied to produce ______ _______that can be read by the host ribosomes. 2. there is unity in diversity: evolution has led to the formation of only ____ major types of viral genome
mRNA (messenger RNAs) 7
Composition and structure of viral genomes are (more/less) varied than archea, bacteria, and eukaryotes.
more
there are (less/more) ds dna viral families than ss dna
more
The + strand RNA viruses are the (most/least) abundant
most
Does the genome of most viruses follow the "one gene, one mRNA" rule? -there (is single/ are multiple) proteins from a single viral genome *** CAN BE
no are multiple
how many viruses encode for complete protein synthesis
non
how many viruses encode for energy production and metabolism
non
these are proteins encoded by (all/some/none) viruses 1. COMPLETE PROTEIN SYNTHESIS MACHIENERY 2. energy pdtn 3. metabolism
none
DS RNA (packages/encodes) rna dep rna pol, while ss RNA + (packages/encodes) ir
packages encodes