Viruses and Their Replication
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| the extracellular form of a virus that contains the genome, allows for intracellular travel, | virion
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| a virus infection is ______________ | the entry of a virus/virus genome into a suitable cell
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| a virus (can/cannot) respond to environment until entry into cell | a virus CANNOT respond until entry into a cell
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| the capsid of a virus contains _________________ | the virus genome
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| the capsid of a virus is composed of small proteins called | capsomeres
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| a naked capsid is | a capsid that does not have any layers and infects bacteria
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| describe the anatomy of a capsid with an envelope | the envelope is made of a phospholipid bilayer (similar to an animal cell plasma membrane) and a nucleocapsid which includes the nucleic acid and the capsid
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| what is the main purpose of the capsid | to protect the genome
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| (some/all) viruses contain virus-specific enzymes | SOME viruses contain virus-specific enzymes
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| name the two different "cycles" that a virus goes through after an infection | 1) virulent (lytic) and 2) lysogenic
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| the (Lytic/Lysogenic) cycle the virus replicates and destroys the host | LYTIC cycle the virus replicates and destroys the host
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| which virus cycle does the virus redirect the cell metabolism redirect to replicate and grow more virus genomes and virions | lytic cycle redirects the cell metabolism to replicate itself and grow more viruses
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| in what viral cycle does the virus cause the cell to lyse and releasing new viruses | lytic cycle the virus causes the cell to lyse and release new viruses
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| in the lysogenetic cycle the host cell (is/is not) destroyed | in the lysogenic cycle the host cell IS NOT destroyed
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| how does the lysogenic virus infection alter the cell | in lysogenetic viruses, the virus genome genetically alters the host cell
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| list the types of genomes that are found in capsids of viruses | single stranded RNA, single stranded DNA, double stranded RNA, double stranded DNA
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| in viruses, the genome is (linear, circular, both) | the virus genome can be BOTH linear and circular
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| a plus sense is | the viral mRNA that will be directly translated
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| a minus sense is | complementary base sequence to viral mRNA
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| viruses that only infect bacteria are called | bacteriophages
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| why are bacteriophages important, | they are used to study microbiology
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| in a virion, the nucleic acid is always surrounded by | the capsid
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| the capsid is composed of _____________________ arranged in precise pattern | capsomeres
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| Describe the structure of the Tobacco Mosaic Virus (TMV) | single stranded RNA, wound in a helix, capsomeres jutting out of the RNA
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| when virion assembly is spontaneous | self-assembly
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| name and describe the two types of virion structure | rod (symmetrical about an axis formed by a helix), spherical (radial symmetry created by icosohedral)
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| generally speaking, an icosohedral (spherical symmetrical) virus has _______________ triangles, __________________ verticies, and ____, ____, ______ axes | 20 triangles, 12 verticies, and 2, 3, 5 axes
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| why is the icosohedral the most common arrangement for virion because | it is the mores efficient arrangement with the smallest number of capsomeres per face
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| describe the shape of the T4 virion body shape | includes a head and a helical tail
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| describe the shape of enveloped viruses | a nucleocapsid surrounded by a lipoprotien membrane
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| envelope viruses primarily infect (animal/bacterial) cells | envelope viruses primarily infect ANIMAL cells
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| what is the mechanism for envelope virus infection | the envelope attaches to the plasma membrane and the nucleocapsid is let into the cell
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| the envelope (does/does not) assist with the virion exiting lysed cells | an envelope DOES assist with a virus leaving the lysed cell
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| in the case of an infection, the penetration of an envelope into a cell is determined by | the biochemistry of the envelope determines what type of cell the virus can penetrate
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| there (are/are not) virus-specific envelopes | there ARE virus-specific envelopes
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| viruses are metabolically inert meaning... | viruses do no carry out metabolic processes
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| how do viral enzymes play a role in infections | help to lyse the cell wall and aid in the release of the virus from the host
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| name the enzyme in the influenza virus that is known for releasing a flu virion from the host cell | neurominidase
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| retroviruses are only known to infect | retroviruses only infect ANIMAL cells
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| retroviruses only use __________________________________ enzymes to replicate DNA intermediates | RNA-Dependent DNA polymerase (reverse transcriptase)
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| how are virus infections in Bacteria/Archaea different from virus infections in eukaryotes | viruses inject their nucleic acid into the host cell and only the genome enters, while in Eukaryotes the entire Virion enters the cell
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| a _______________ cell is a cell that supports complete replication cycle | permissive
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| what are the five steps in virus - infection | 1) attachment (absorbtion) , 2) penetration (entry/injection), 3) synthesis, 4) assembly and packing, 5) release
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| _______________________ is the amount of time for a virion's number to increase in a culture medium | one-step growth curve
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| at what point is the virion number considered to have increased | when the cell bursts
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| name the two phases in the one-step growth curve | 1) eclipse phase and 2) maturation phase
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| what characteristics are part of the eclipse phase | the viral genome and proteins being replicated/transplanted and the virion is no longer available to infect another cell
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| in what phase of the growth cycle is characterized by new viruses being synthesized and packed into new capsids, while the number of new virions drastically increase. however, their number is not detected because they are inside the cell | maturation phase
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| what is burst size | the number of mature virions release after a cell lyses
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| in the attachment phase of a viral infection viruses can attack (any and every cell/only specific cells) | in the attachment phases, viruses can attack ONLY SPECIFIC CELLS
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| viruses can only attack specific cells during an infections, why | viruses will only infect the cells which carry specific receptors
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| if a mutation causes a change in a specific viral receptor on a cell, what will happen | the virus will be unable to infect that cell
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| what are cell receptors made out of | macromolecules (protiens, lipids, carbs)
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| what happens once a virus successfully attaches to a receptor on a cell | after binding to a receptor, changes will occur in the virion and the host cell
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| the virion attaches to the host cell, changes then occur in both virion and host cell, then what happens. | penetration
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| in Bacteria and Archaea, the penetration step is characterized by | the genome of the virus being injected into the cytoplasm eventually resulting in genome and protein replication
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| the genome for Bacteriophage T4 is | double stranded DNA (folded)
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| describe the virion shape of Bacteriophage T4 | series of tail fibers and tail pins attached to a icosohedral head
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| the point(s of attachment for a Bacteriophage T4 is/are) | tail fibers and tail pin
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| the DNA genome of the Bacteriophage T4 enters the cytoplasm via what structure on its virion | tail tube
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| what are two built-in mechanisms that cells have for destroying virus genomes | Toxin-Antitoxin modules and Antiviral system (CRISPR)
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| what is the function of restriction endonuclease | an enzymes that cleaves DNA at specific sites
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| what is the name of the mechanism in Bacteria and Archaea that uses restriction endonuclease to cleave virus DNA out of normal DNA | Restriction
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| how does host use viral DNA to make it into its own genome | modification
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| how is modification done | methylation of viral nucleotides by the host cell
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| what is a protective mechanism of T4 | substitutes base 5-hydroxymethycytosine in place of cytosine
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| name the two enzymes that are produced after T4 enters into a permissive cell | T4 primase and helicase
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| what is circular permutation | every copy of the virus consists the *exact same* set of genes
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| a viral genom of DNA that is duplicated on both ends of the DNA molecule | terminally redundant
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| what is a concatemer in DNA | several genomic unites that are recombined end-to-end
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| what is headfull packing | T4 DNA packed into a capsid....fills up the capsid
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| ________________________ begins the process of new virion formation | Transcription + Translation
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| _______________ begins almost immediately after a virus invades a cell | Transcription
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| name the three major sets of proteins (named in order of appearance) | - early proteins
- middle proteins
- late protiens
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| what is the function of early proteins in T4 | synthesis and glucosylation in 5-hydroxymethylcytosine, replisome, produce copies of phage-specific genome, modify host RNA polymerase
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| Middle and late proteins are responsible for | additional RNA polymerase and modifying proteins, producing structural + release proteins (head and tail proteins)
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| what do T4 modifications to host RNA do | hos RNA then only recognize phage promoters
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| what shuts down normal cell transcription during an infection | the phage encoded antisigma factor
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| what is the function of anti-sigma factors | binds to host RNA polymerase sigma factor, host then starts only transcribing only T4 genes
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| after anti-sigma factors are bound to RNA polymerase, what happens | viral assembly begins
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| During headful packing, ATP is provided by the | host cell
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| what are the three stages of the headful packing | 1) proheads, 2) packing motor, 3) proheads expand
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| the prohead stage of the headful packing is marked by.... | capsid assembly (but it's empty), scaffolding and structural protein building
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| during the packing morot stage of headful packing... | an opening to the prohead, and genome is pumped into the prohead using ATP, the prohead expands, while saffolding is discarded
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| during the motor discarding phase of the headful packing... | the capsid head is sealed
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| after the cell becomes full of virions the cell.... | breaks by osmotic lysing
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| T4 viruses (always/only sometimes/never) kills it's host | T4 viruses ALWAYS kill their hosts
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| what is a temperate virus | a virus that contains a double-stranded DNA, but establishes long-term relationships with their host via lysogeny
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| what happens to viral DNA when it enters the cell via lysogeny | the genome is not transcribed, rather it is replicated in synchrony with host DNA
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| a cell that harbors virulent DNA is called a | lysogen
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| lysogenic conversion is | the growth of a host cell that is controlled by the local environment and nutritional profile
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| name the two types of lysogeny | Lambda and P1
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| what the the Lambda form of lysogeny | the viral genome integrates into the chromosome
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| what is the P1 form or lysogeny | the viral genome exists inside the cell as a plasmid
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| what is a prophage | a viral genome that is living inside a lysogen
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| during normal replication of a lysogen, what happens to the prophage | the prophage will replicate along with the host cell and activation genes remain repressed
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| what organic structure in a cell is responsible for the maintenance of lysogenic state and inactivated when synthesis is prevented | repressive protein
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| when a stress occurs the host cell then enters into the lytic stage, this is known as | induction
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| what happens during inductions of a lysogen | the viral genome is excised from the host DNA (if it's not a plasmid already), then the transcriptions/translations process begins
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| describe the genome of bacteriophage Lambda | it is double stranded DNA which includes a head and a tail
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| what happens when the Bacteriophage Lambda enters a lytic pathway | the genome forms a cancatomeres by rolling circle replication, when attached to host DNA it will straighten out, cell lysis occurs after mature lambda virions are formed
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| the genome of the Bacteriophage Lambda is integrated to bacteria DNA with the help of ______________ | Lambda integrase
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| what determines which direction the type of cycle that the cell will take after it infects a bacterial cell | the accumulation on the type of repressor proteins
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| name the two main repressor proteins | Lambda Repressor (cI protein) and Cro
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| what happens when there is an accumulation of cI protien | represses transcription of Cro (lambda-encoded genes), the virus genome integrates into the host genome
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| under the (cI protein/Cro) accumulation, the host cell will continue a normal life cycle until triggered by a stressor | under the cI PROTEIN accumulation, the host cell will continue a normal life cycle until triggered by a stresser
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| what is the function of the Cro protien | represses the function of cII (which controls cI activation) and forces the Lambda to travel to the lytic pathway
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| in regards to the virus genome entering into the host cell, what are the differences between animals and bacteria | animal cells will engulf the entire virion, bacterial virion will "inject" their virion
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| what is the main difference between site of replication in animal cells and bacterial cells | in animal cells site of replication is in the nucleus
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| in (all/animal/bacterial) cells, viruses bind to receptors in order to initiate infection. | in ALL cells viruses bind to receptors in order to initiate an infection
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| explain why animals can get a virus in some areas of their body but not others. | animals have different systems, the cells in each system have different receptors. this is why you can only get a cold in your respiratory system
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| how does a virion enter an animal cell | endocytosis or the nuclear envelope fuses with the cytoplasmic membrane
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| if the viral genome is DNA, what happens after the virion enters into the host cell | the DNA genome passes through the nuclear envelope for replication
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| if the viral genome is composed of RNA, what happens after the virion enters host cytoplasm | the RNA genome is replicated/converted to DNA within the nucleocapsid
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| what are the four possible outcomes when a virus infects an animal | 1) virulent infection, 2) latent infection, 3) persistent infection, 4) transformation
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| what type of virus infects an animal cell includes a lytic cycle | virulent infection
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| of the four types of infections in animal cells, which one is the most common | virulent infections are the most common types
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| in animals cells, |
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