MM&I Exam 1

What method of replication does Adenovirus useto ensure its ends are copied ? Describe it.

Unidirectional Strand displacement replication - Adenovirus had linear dsDNA - It has a preterminal protein that works with DNA Polymerase to form a preinitation complex at each terminal origin of replication - dCMP covalently links to a serine residue (DNA polymerase does this) - The serine residue binds a cytosine that is bound to the DNA sequence through hydrogen bonding at a guanine - This provides a free 3'OH group for the polymerase to work off of - viral encoded (E2) singe stranded binding protein binds to the strand that is being displaced - both strands have the inverted AAA sequence which means there is an origin at each end - then other parent strand with SSBP coating has its complementary ends reanneal forming a stem (this reforms origin and complex can once again bind and make new DNA strand based on displaced strand from before.

What is the virus that causes chicken pox?

Varicella zoster virus

What does Togavirus cause?

sindbis, Rubella

What are common challenges faced by RNA virues? (3)

1) They must replicate an RNA genome - This means they must bring their own viral encoded RNA dependent RNA polymerase) 2) Produce translation component of mRNA - This means they must be able to use their original RNA as a an mRNA or transcribe their original -RNA into +mRNA. 3) Switch from transcription to replication - often these two events are mutually exclusive

In general, do DNA viruses code for their own host transcription factors and RNA polymerase or use the host cell's machinery?

In general, DNA virues use the host transcription factors and RNA polymerase for transcription in the nucleus.

How does RNA dependent RNA polymerases accuracy affect RNA polymerase?

- RNA dependent RNA polymerases are very error prone and can help RNA viruses keep one step ahead of human immune systems. Every genome is a little different so there are many strains of these virus (like the flu)

What do the following viruses use to displace the DNA strand while replicating? - Adenoviruses - parvovurses - Poxviruses

- Adenoviruses (protein) - parvovurses (DNA hairpin) - Poxviruses (DNA hairpin)

How do small DNA viruses primarily regulate their gene expression? How do large DNA viruses primarily regulate their gene expression?

- Both small and large DNA viruses regulate gene expression primarily at the level of transcriptional initiation - Levels of transcription are regulated by virus-encoded transcriptional activators and repressors

Where does DNA synthesis occur for viruses? Where does packaging into capsids occur

- DNA synthesis occurs in replication centers which are formed by the virus within the nucleus of infected cells - DNA packaging occurs in nucleus close to replication center

Explain DNA virus regulation of cell cyle

- DNA viruses don't multiply in nondividing cells (quiescent cells) - DNA viruses force the infected cell into the cell cycle stage that is compatible with DNA synthesis (S phase) - In S phase, the cell produces enzymes (polymerases, helicases, topoisomerases) required for replication of its DNA. The viruses uses these too. - Usually, the virus encodes immediate early or early regulatory proteins that force the cell to begin DNA replication.

Describe large DNA viruses by definition

- DNA viruses with large (circular or linear) double stranded DNA genomes have more than 100kbp packaged into isometric or irregular capsids

How often is Gag-pol made vs just gag? Why is this ratio important? What causes GAG vis GAG-POl to be made?

- GAG-POL is made 10% of the time and GAG is made 90% of the time - This is important because the protease encoded by POL is a dimer. If there are low levels of the protease (RNase H), it does not form dimers. The proteases' main function is to cleave the GAG-POL complex to pacage reverse transcriptase and integrase inside the capsid (the maturation clevage). If this happened before the virion left the host, the virus would never leave. It would end up trying to reattack the same cell. This is avoided by low levels of protease. - The pseudoknot at the junction betwen GAG and POL causes the RNA polymerase to struggle. It sometimes slips back one nucleotide causing a -1 frameshift. Then it continues reading the POL.

Describe Sv40 (nine main features)

- It is a member of polyomavirdae - It is classified as a simple DNA tumor virus - It has a circular double stranded DNA genome which is about 5kp long - Its main virus-encoded regulator is Large T antigen (LT) (Large tumor antigen which can cause cancer) - It encodes six proteins: T-antigen (LT, sT), capsid proteins: VP1, 2, 3, and 4 - It uses host cell's transcription and DNA replication factors - Gene regulation divided into early and late phases - Controls cell cycle of the host through functions of the LT protein

Why must DNA viruses regulate early and late events in their multiplication cycles?

- It is needed for proper synthesis of genomic DNA and for proper production of viron components of virus assembly

Why don't large DNA viruses need to push host cell into S phase?

- Large DNA viruses carry their own DNA synthesis machinery. Small DNA viruses down't carry their own so they need to use the hosts. The host doesn't have these enzymes unless it is into s phase

What type of infection do most human DNA viruses cause?

- Latent infections They go dormant but can alternate between periods of active multiplication. Reactivation from latency can result in disease and shedding of infectious virus.

What do the basics of transcription look like?

- On DNA: 3' (Upstream) enhancers, transcription factors, promoter, area that gets transcribed, transcription termination 5' - On RNA: 5' primary transcript (pre mRNA) 3' - Remember: enhancers and transcription factors are what allow RNA polymerase two to work.

What different functions does Reverse Transcriptase Take on?Does Reverse Transcriptase have proofreading ability?

- RNA dependent DNA polymerase (it converts +RNA into ssDNA) - DNA dependent DNA polymerase (it coverts single stranded DNA into Double stranded DNA) - Helicase (it must unwind knots and such) - RNAse (destroys RNA after dsDNA is made) - It has no proofreading ability and is very error prone. There is about one mutation per genome.

How does SV40 make sure it gets the ends of its genome right during genome replication (draw a picture :) )

- SV40 is circular double stranded DNA - SV40 uses bidrectional replication with a replication fork around its ORI - It has symmetrical DNA palindromes at its ends that can base pair with eachother that allow it to become circular. - The palindromes are also the places large T binds to promote replication. - It also has AT rich regions around its origin that allow it to be more easily melted.

What regulates the timing and level of virus transcription for small DNA viruses?

- The DNA elements of promoters and enhancers that interact with RNA polymerase II

Describe the RNA dependent RNA polymerase

- The RNA dependent RNA polymerase catalyzes synthesis of RNA from an RNA template - They are needed because the host cell never does this - There are primer dependent and primer independent RNA polymerases depending on the virus - RNA polymerases have no proof reading ability and they are highly error-prone. They make a mistake every 1,000-100,000 nucleotides - RNA synthesis proceeds in the 5' to 3' direction meaning the product is produced building off the 3' end while the template is read from the 3' to 5'. - Function in replication (replicase) and transcription of mRNA (transcriptase)

Why are there technically two promoters in the dsDNA provirus? What does this cause?

- The promoter element is right downstream of the U3 element on the 3' end of the provirus. But there is the exact sequence downstream of the U3 element on the 5' end. - This can cause change in gene expression because the ghost mRNA could start to translate anything downstream if there is no host DNA stop codons early on.

What is the process of ss + RNA viruses concerning their genome?

- They start out with a positive sense genome and they translate their polymerase right after entry - The positive sense genome can be translated directly into proteins that make things like capsids - The + RNA can be transcribed into an -RNA intermediate then it is made into many +mRNAs to be packaged or make more proteins

What type of genome replication direction do these viruses use? - Adenoviruses - parvovurses - Poxviruses

- Unidrectional Strand displacement primer

What is the main way small DNA viruses produce a variety of proteins?

- alternative splicing of mRNA

Why is understanding genome replication important?

- antivirus drugs - cancer treatment

Inapparent hosts

- causing no noticeable signs or symptoms - These hosts are permissive hosts but the virus is only reproducing itself at low levels - Inapparent hosts fall somewhere on the spectrum between non-permissive and permissive hosts

Where type of genome does poxviridae have? Where does poxviridae replicate?

- dsDNA - cytoplasm (this is the exception for DNA virues)

What genome does herpes simplex virus-1 have? How many protein products does it encode? Does it have an envelope? What is the shape of its capsid? What is the importance of VP16?

- dsDNA genome - encodes 90 gene products - enveloped - icosahedral (T-16) capsid - proteins are packaged into the tegument. VP16 s a tegumnet transcription factor that is carried in the virion and gets into the nucleus with DNA

Describe a retrovirus particle

- enveloped - Contains 2 + RNA molecules - protease, integrase, and reverse transcriptase are packaged inside the capsid. - The RNA molecules are covered by nucleocapsids.

What does Picornavirus cause?

- polio, rhinovirus A, Foot and mouth disease

How is RNA dependent RNA polymerase like a hand in the C shape?

- the palm or where the thumb meets the 1st finger is the catalytic site - The fingers and end of thumb bring in and take out product.

Describe the steps in the retrovirus life cycle (16 steps)

1) Attachment 2) Viral core deposited into the cytoplasm following fusion of the virion and cell membranes 3) Viral RNA genome is reverse transcribed by the virion reverse transcriptase within a subviral particle. The product is a linear double-stranded viral DNA 4) Viral DNA and integrase protein go into nucleus 5) Integrative recobination catalyzed by integrase occurs 6) Transcription of integrated viral DNA (the provirus) by the host cell RNA polymerase II produces full-length RNA transcripts 7) Some full-length RNA molecules are exported from the nucleus and serve as mRNAs 8) These mRNAs are translated by cytoplasmic ribosomes to form Gag and Gag-Pol polyprotein precursors in a 10:1 ratio 9) Some full length RNA molcules are destined to become encapsidated as progeny viral genomes. A gag protein could help with this 10) Other full-length RNA molecules are spliced within the nucleus to form mRNA for the Env polyprotein 11) Env mRNA is translated by ribosomes bound to the endoplasmic rticulum 12) env proteins are transported through Golgi where they are glycosylated and vcleaved to form the mature SU-Tm complex 13) mature envelope proteins are delivered to the surface of the host cell 14) Virion components (2 copies of RNA, Gag and Gag-Pol precursor, and Su-TM) assemble at budding sites 15) particles bud 16) maturation (and infectivity) requires the action of the virus-encoded protease which is itself a compnent of the core precursor polyprotein. It cleaves Gag and Pol to produce mature viral proteins where the reverse transcriptase and integrase are packaged inside the other proteins.

Summarize all steps of adenovirus gene expression into three steps

1) First immediate early genes expressed by host RNA polymerase II. Alternitvely spliced mRNAs are synthesized, resulting in synthesis of proteins with different activities. - These regulate gene expression done by done by late early genes 2) First immediate early genes turn on transcription of late early genes. These mRNAs are alternatively spliced and end up making proteins needed for: - Viral DNA replication (pre-terminal protein, DNA polymerase, DNA binding protein) - Turn-on of major late promoter - Altering the splicing, polyadenylaiton - And transport of viral and cellular RNAs (VA RNA I) 3) Late genes are not expressed at high levels until after onset of viral DNA replication. - Important capsid proteins

Describe the three stages of expression of herpesvirus genes

1) Immediate early genes: they are major viral regulatory proteins. There expression is activated by VP16 which goes into nucleus with genome 2) Early genes: enzymes involved in DNA synthesis (replication). Expression of early genes is activated by immediate early genes 3) Late genes: structural genes that code for: - Capsid, tegument, envelope glycoproteins - Late genes are only expressed after DNA replication - The late gen expression is activated by early and immediate early genes

What three things should you know about integration of retrovirues?

1) Integration is carried out by integrase 2) Integration produces a small duplication of host DNA 3) Integration of the linear proviral DNA is random

Describe 5 important features of Adenovirus

1) Intermediate-sized DNA virus with a linear double stranded DNA genome (35kb) 2) Virion is non-enveloped with icosahedral symmetry 3) Causes acute respiratory infections 4) Oncogenic- generates tumors in newborn hamsters 5) model for virus gene regulation and DNA virus oncogenesis

What are the six reasons retroviruses are so famous?

1) Reverse transcription 2) Onccogenic potential (MANY cause cancer) 3) novel protein functions 4) prevalence in the human genome 5) Gene therapy vectors (can produce particular proteins) 6) Causative agent of AIDS and other human diseases

What two signals do the LTRs possess?

1) Signals for host RNA polymerase II mediated transcription of the genomic RNA (in the most upstream portion of the R region of the 5' end) 2) Sequences necessary to carry out reverse transcription of the genomic RNA (within virus particle) - the primer binding site is at the very downstream region of the 5' U5

Describe the 16 steps of infection of the SV40 virus

1) The virus attaches to a susceptible monkey cell through binding of a surface receptor to a glycolipid of the cell 2) The virus is endocytosed and transported to the endoplasmic reticulum 3) It enters the ER 4) It is transported to nucleus and uncoated 5) There, host factors package the viral genome into nucleosomes 6) Early transcription is started by the host RNA polymerase II 7) Alternative splicing and export to cytoplasm of mRNA 8) Early mRNAs are translated to produce the early protein LT and sT 9) LT is transported into the nucleus 10) LT binds to the origin of replication to initiate DNA synthesis. All other components needed for DNA synthesis are provided by host cell. 11) LT also stimulates transcription of the late gene from replicated viral DNA templates 12) Processed late mRNAs are exported to cytoplasm 13) late mRNAs prouce the four structural proteins 14) structural proteins imported into nucleus 15) assemble around viral DNA and form particles 16) release (VP4 drives)

What are the three exceptions to the clear cut +RNA vs -RNA?

1) There actually are two families of double stranded RNA virues 2) ambisense RNA viruses are positive sense and negative sense at same time 3) retroviruses have a positive sense RNA genome, but they need to bring in retrotranscriptase in order to finish their life cycle

What are the four main replication properties of Large DNA viruses?

1) Use host transcription machinery early, virus encoded later (poxvirus is exception) 2) encodes proteins required for DNA synthesis 3) RNA splicing does occur, but is usually rare (there are very few introns) 4) cause a variety disease in humans including late infections

Describe the steps in immediate early infection for Adenovirus (remember there is 9 steps and two parts to 9)

1) Virus attaches to human cell 2) virus enters through receptor-mediated endocytosis 3) the virus in an endosome has a protein on the virus particle that interacts with integrin 4) This causes partial disassmbly before the particles enter into the cytoplasm (it releases the protein needed to get into the cytoplasm) 5) viral genome is imported into nucleus 6) Host cell RNA polymerase II transcribes the immediate early genes 7) alternative splicing/ export into cytopaslm 8)early proteins are synthesized by the cellular translation machinery 9a) proteins imported back into nucleus 9b) proteins start to regulate transcription of cellular and viral genes

What two ways does adenovirus produce many proteins?

1) alternative splicing 2) differential poly (A) site usage

Describe steps of herpes simplex virus life cyle

1) attachment 2.3) particles enter via pH-independent fusion of viral envelope with plasma membrane through receptor interaction Or endocytosis 4) some tegument proteins in nucleocapsid released into cytoplasm 5a) viral nucleocapsid associate inner tegument proteins, microtubles transport to nucleus 5b) other tegument proteins transported in 6) virus Vhs remains in cytoplasm and shuts of cellular functions 7) viral nucleocapsids make a pore and instert DNA into nucleus 8) transcription by host cell RNA pol. II 9) mRNAs are spliced transported out of nucleus and translated 10) proteins transported back to nucleus and activate transcription/ regulate trancripton 11) Early gene transcripts (not spliced) undergo transcription, translation process 12) some stay outside, some transported back in 13) viral DNA synthesis from ORI 14) DNA replication and recombination produce long concatemetric DNA, templates for late gene expression 15) late proteins transcribed/ translated (no splicing) 16) some late proteins are glycosylated in ER membranes, etc. 17/18) assembly Rest of steps, budding then released through exocytosis

What are the three most important aspects of virus DNA genome replication?

1) faithful replication of a virus DNA genome requires unique mechanisms, especially for copying the ends of the genome. 2) DNA synthesis begins at an ORI and proceeds in the 5'-3' direction by semiconservative replication 3) Small DNA viruses use the host's DNA polymerase but larger more complex DNA viruses encode their own replication factors

What are the main replication factors? (6) What are their general functions?

1) origin binding protein: bind to ORI and regulate what viral origins will be used. (Herpes) 2) DNA polymerase (transcribes DNA) 3) Helicase (unwinds DNA) 4) exonucleases (helps cut out mistakes?) 5) single stranded DNA binding proteins (makes sure DNA strands don't reanneal) 6) primase (creates primers for DNA polymerase)

What are the four main properties to remember about small DNA virues?

1) they often use host transcription factors and DNA synthesis machinery because they replicate in the nucleus and have DNA 2) They use RNA splicing to generate multiple virus proteins 3) They often have the capacity to cause tumors 4) They usually cause mild diseases

What three main things do all DNA viruses do (small,simple DNA viruses and large, complex DNA viruses)

1. Genome expression 2. Genome synthesis 3. Host interaction (control of cell cycle and latent infections)

What are the five reasons we study DNA viruses?

1. They help us treat human and animal diseases 2. They are vectors for foreign gene expression 3. They are models for regulation of gene expression 4. They are models for oncogensis (cancer causation) 5. They are models for latency (life-long infection)

Describe the steps in early infection for Adenovirus (remember this is steps 10-13)

10a) E1a stimulates transcription of early viral genes by the host RNA polymerase II 10b) transcription of the VA genes by host RNA pol. III starts. 11, 12) alternative splicing/ processing occurs, transported out of nucleus, translated 13) early proteins imported back into nucleus

Describe the steps in late infection for Adenovirus (remember steps 14-21)

14) the viral replication proteins cooperate with some cellular proteins in viral DNA synthesis 15,16) Replicated viral DNA molecules serve as templates for further rounds of replication and transcription of late genes 17) processes late mRNAs are selectively exported from nucleus 18) VA is involved in efficient translation 19) VA also helps structural proteins get back into nucleus 20) capsids are assembled 21) virions mature when precursor proteins are cleaved by a viral protease 22) release (destroys host cell)

Does budding of retrovirueses kill the cell?

No

What is the layout of the provirus? (retrovirus) - Which direction will transcription occur? Describe Transcription - Draw a picture!

5'----U3,R,U5---------U3,R,U5---3' GPE - Note the provirus has U3 and U5 on both sides - Transcription of the double stranded DNA provirus starts downstream of the 5' U3 but upstream of the 5'R. It moves in the 3' direction. It terminates downstream of the 3' R, but upstream of the 3' U5. - Transcription is done by host DNA polymerase II

What is the layout of the +RNA when first entering the cell? (retrovirus) - Which direction will transcription occur? Describe Transcription - Draw a picture!

5'---R,U5-----------U3R---3' GPE - Directly downstream of the U5 there is the primer binding site with a tRNA bound to it. - Reverse transcription starts at the primer binding site. The primer is a tRNA. The reverse transcriptase transcribes towards the 5' end of the +RNA until it gets to the end of the R (repeat) sequence. Then it falls off. The piece anneals with the R on the 3' end of the +RNA. Then RT starts to work off the repeat and continues toward the 5' end transcribing the env, pol, gag, U5, then R

How much of human DNA is made up of retro-like sequences? What are they? What does this suggest?

5-8% - They are from ancient defective retroviruses (proviruses), which suggests that viruses have been around a long time and have co-evolved with animals

Chronic infection (give two examples)

A condition wherein virus is constantly present and multiplying. Thus, the host is a constant source of infectious virus. - HIV, Hepatitis C

What is the second most common cause of the common cold?

Adenovirus

What is the most common way for DNA viruses to control the variety of proteins they make?

Alternative RNA splicing. One RNA transcript can give rise to multiple proteins.

Non-permissive host

An organism or cells that do not allow completion of a virus' multiplication cycle. Infection is blocked, usually because the host lacks some required factor or uses a potent anti-virus mechanism. - Mice are a non-permissive host for HIV

Permissive host

An organism or cells thereof that permit completion of a virus' multiplication cycle - For example humans are a permissive host for HIV

How do retrotransposons effect evolution?

As they move throughout the host genome, they influence evolution through their capacity to cause mutations and alter gene expression

What are the two mechanisms of DNA synthesis common in small DNA viruses?

Bidirectional synthesis and strand displacement

what type of genome replication direction do these viruses use? - Herpesviruses - Retroviral proviruses - Polymaviures - Papillomavirues

Bidrectional - Replication fork

What does Flavivirus cause?

Dengue, yellow fever, west nile, HCV

What genome does SV40 have?

Double stranded DNA

What genome does adenovirus have?

Double stranded DNA

What genome does papilloma virus have?

Double stranded DNA

What genome does polyomavirus have?

Double stranded DNA

What are the four stages of large DNA virus infection?

During Early Infection: 1) Virus Entry 2) Immediate early genes: regulatory proteins 3) Delayed early genes: replication proteins During Late infection: - DNA Replication 4) Late Genes: Structural proteins, assembly proteins, and release proteins

What are the three stages of small DNA virus infection?

During early Infection: 1) Virus Entry 2) Early genes: regulatory proteins and DNA replication proteins During Late infection: - DNA replication 3) Late genes: structural proteins, assembly proteins, and release proteins

What does papillomaviurs use to force the host cell into S phase?

E7

What does adenovirus use to force the host cell into S phase?

EA1

What defines early and late infection of a virus?

Everything before DNA replication is early infection and DNA replication and afterword is late

What does Gag code for? What does Pol code for? What does Env code for?

GAG: capsid structural proteins POL: reverse transcriptase integrase proteins ENV: envelope glygoproteins GAG: MA-p10-CA-NC-PR: matrix, p10, capsid, nucleocapsid, protease POL: RT-IN: reverse transcriptase, integrase (and RNase H ENV: SU-TM: surface, transmembrane

What disease does retrovirus cause in humans, monkeys, cats?

HIV, SIV, FIV - retroviruses also cause disease in chickens, horses, fish, and flies

Human foamy virus is a retrovirus that does not cause any obvious symptoms. What type of infection is this?

Inapparent infection

What is a pseudoknot (draw a picture)

It is a stem loop structure where the end of the loop also is base pairing with a downstream area of sequence. They are difficult for RNA polymerase to work through.

What are the LTRs? What do they contain? How do they differ in the provirus and +RNA coming into the cell for retroviruses?

LTRs are Long Terminal Repeats. They surround the GAG-POL-ENV in retroviruses. - As a provirus, both LTRs contain U3, R, and U5. - As a +RNA coming into the cell the 3' end of the RNA has U3,R while the 5' end has RU5 U3= unique to 3' end (promoter found here) U4= repeated U5 = unique to 5' end

What does polyoma use to force the host cell into S phase?

Large T antigen

What cancer does hepatitis C cause?

Liver cancer

Inapparent infection

Low level infection wherein virus-specific multiplication is difficult to detect and symptoms are absent or inapparent, even to the host.

What genome do Orthomyxoviridae, Paramyxoviridae, and Rhabdoviridae have?

Negative sense RNA (ss-RNA)

What do the basics of RNA splicing look like?

Once the RNA polymerase II has made the primary transcript (pre-mRNA) from the 5' to 3' direction while reading the DNA from 3' to 5', the RNA is processed. A cap and tail are generally added and introns are excised. Exons are spliced together. Only then is the open reading frame with a stat codon and stop coding revealed between the 5' leader and the 3' end.

What are the parts of the glycoprotein on retrovirus? How is it used during assembly?

The glycoprotein is called Gp160. Gp120 and Gp41 are the two subunits. Gp120 is outside the membrane. Gp41 associates/interacts with the matrix of the forming virion and the psi sequence which "holds everything together" during assembly.

What was the original definition of a positive sense RNA virus vs a negative strand RNA virus? What are these definitions now?

Original +RNA: when purified RNA genome was put into cells, more viral particles were produced. Original -RNA: when purified RNA genome was put into cells, no production of viral particles occurred. New +RNA: Has a coding strand of RNA, the genome functions like mRNA once in the cell because it is translation-competent even if it has been purified New -RNA: non-coding or antisense strand, must be transcribed by virion polymerase to make mRNA. A purified genome will not cause infection because it usually brings in its own virally encoded RNA dependent RNA polymerase to transcribe itself right away .

What is a lethal virus in puppies?

Parvovirus

How does SV40 Regulate gene expression? Draw simple picture :)

Remember it has a circular double stranded DNA genome with a origin of replication with a control region on one side of it. Temporal control: - In early infection, enhancer region binds numerous cellular factors that activate transcription from the early promoter. This produces LT and sT proteins. The late promoter is repressed. Once LT builds up, it binds specifically to the intergenic control region. Upon binding, LT represses transcription of early promoter and initiates replication of the whole SV4 genome from ORI - In late infection, when LT concentrations are high, LT activates the late SV40 promoter by binding to the enhancers of the intergenic region on replicated DNA. This results in late gene expression. Remember that gene expression can "go either direction around the circle". Early gene direction without LT bound, with LT bound late gene direction.

Productive infection

Results in the production of infectious virus progeny

What are active retro-elements? How common are they in insects?

Retrotransposons - They are active retro-elements that have an internal intracellular life-cycle and do not transmit to other cells - Sometimes they could be packaged into another genome if another virus is infecting the host cell as the retrotransposon excises itself - They copy into RNA, then back to DNA and integrate somewhere else. - They make up 15-20% of the insect genome

What family are retroviruses part of? Describe the family

Retroviridae - Single stranded messenger sense (+) sense RNA viruses with host cell derived envelope - Have ability to copy themselves into dsDNa, integrate into the genome, create new mRNA and be translated

What method of replication does herpesvirus use? Describe it.

Rolling Circle Replication - HSV-1 has a linear DNA genome, but the genome has complementary ends that are about 50 base pairs long so the genome can circularize - A nick is formed in one of three specific sites of the outside half of the double stranded DNA which provides a free 3' OH group - The DNA polymerase synthesizes the DNA off of 3' end while helicase continually breaks the hydrogen bonds on the strand that started the 5' end. As the 5' end lengthens and "peels off" single stranded binding proteins bind to it so it won't reanneal. - Eventually the single stranded DNA that is peeling off is made into double stranded DNA through discontinuous DNA synthesis using RNA primers - Then the super long molecule (concatemers) are cut into genome length pieces by nucleases

What does Coronavirus cause?

SARS, MERS - Corona means crown and this virus can jump from animals to people

How do two copies of RNA get in every retrovirus capsid?

There is a packaging sequence, psi, that the nucleoside recognizes. There is a kissing structure that drives two copies of RNA in.

What genome do coronaviridae, Flaviviridae, and Picornaviridae have?

They have ss+RNA

What is the way larger DNA viruses use to copy their DNA?

They use rolling circle

Latent infection (give an example)

Virus goes dormant but can alternate between periods of active multiplication. Reactivation from latency can result in disease and shedding of infectious virus - herpes

Abortive infection

Virus infection is initiated but stalls or is terminated. Host usually survives.

What is the final product of +RNA being acted on by reverse transcriptase?

dsDNA with two LTR regions

What does orthomyxovirus cause?

influenza