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MBIO2020 > 3.1 - Bacterial Viruses pt1 > Flashcards

3.1 - Bacterial Viruses pt1 Flashcards

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1
Q

what are the characteristics of a virus?

A

-genetic element that can multiply only inside a host cell (obligate intracellular parasite)
-not a living entity (not included on the tree of life)
-can infect cells in all 3 domains

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2
Q

what does a virus rely on the host cell for?

A

-energy
-metabolic intermediates
-protein synthesis

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3
Q

what is odd about viruses not being considered cells?

A

-their genomes encode the functions needed to multiply
-they have a structurally intricate extracellular form (virion = complete virus particle) that protects the viral genome when it is outside the host cell

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4
Q

what must occur in order for the virion to reproduce?

A

-the virion itself or in some cases its genome only must gain entry into a suitable growing host cell
-process called infection
-needs to induce a living host cell to synthesize all the essential components needed to make new virions

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5
Q

what is the structure of the virion?

A

-composed of a protein shell/coat called the capsid and the virus genome enclosed in the capsid
-highly symmetric when rotated around an axis
-the structure of the nucleic acid genome and capsid proteins is called the nucleocapsid (minimum requirement for a virus aka naked virus)

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6
Q

what is the capsid composed of?

A

-individual protein molecules called capsomeres
-arranged in a precise and highly repetitive pattern around the nucleic acid

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7
Q

what is an extra layer that a virus can have?

A

-envelope
-phospholipid bilayer that gets taken from the host cell membrane
-has proteins on its surface to help attach it to its host cell
-becomes the outermost layer

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8
Q

are both viruses naked or enveloped?

A

-most bacterial and plant viruses are naked
-other types, specifically animal viruses are most often enveloped

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9
Q

what are the 2 kinds of symmetry recognized in viruses? what viral shapes do they correspond to?

A

-rod shaped viruses have helical symmetry (ex: Ebola)
-spherical shaped viruses have icosahedral symmetry (soccer ball) (ex: HPV)

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10
Q

what is the standard viral replication cycle?

A

-the virion attaches (adsorbs) to the host cell
-the viral genome enters the host cell
-synthesis of viral nucleic acid and protein occurs using the host cells machinary
-assembly and package of new virions takes place
-the host cell lyses and new virions are released

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11
Q

can dead host cells replicate viruses? why or why not?

A

-they cannot because of the biosynthetic and energy requirements for replication

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12
Q
A
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13
Q

what are the 2 forms of adsorption and which types of viruses can do each one?

A

-endocytosis (enveloped + naked)
-fusion (enveloped only)

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14
Q

how do virus infections upset regulatory mechanisms of the host?

A

-there is a noticeable (marked) overproduction of viral nucleic acid and protein in order to make new virions
-proteins are synthesized very soon after infection

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15
Q

what are the 2 groups of viral proteins?

A

-early proteins
-late proteins

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16
Q

what are early proteins?

A

-typically enzymes like nucleic acid polymerases and other factors used to shut down host cell transcription and translation
-need sooner to cause the infection

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17
Q

what are late proteins?

A

-typically structural components of the virion and other assembly components (protein coat)

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18
Q

what are the times it takes for viruses to replicate?

A

-bacterial viruses = 20-60 minutes
-animal viruses = 8-40 hours

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19
Q

what is burst size?

A

-average number of virions released

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20
Q

what is characteristic of the viral growth curve?

A

-occurs in one step (no growth until release)
-eclipse and maturation periods
-a latent period

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21
Q

how are viruses grouped?

A

-by genome structure (dsDNA, ssDNA, dsRNA, ssRNA)

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22
Q

how do viral genomes vary in size?

A

-vary almost a thousand-fold in size from the smallest to largest

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23
Q

what is the baltimore classification?

A

-classification of viral genomes
-developed by david baltimore
-based on the relationship of the viral genome to its RNA
-7 classes (3 with DNA genomes, 4 with RNA genomes)

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24
Q

what is the designated configuration of viral mRNA?

A

-(+) configuration which is 5’-3’
-this configuration is needed to go from transcription to translation

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25
how do DNA phages form the (+) mRNA strand?
-only a (-) strand can serve as a template for mRNA synthesis -the coding strand will be designated as the (+) strand since it has the same sequence as mRNA (except T's instead of U's)
26
what is the mechanism of mRNA production by Class I?
-dsDNA (+) virus genome -mechanism for mRNA production and genome replication is the same as used by cells -transcription of the (-) strand
27
what is the mechanism of mRNA production by Class VII?
-dsDNA (+) virus genome -highly unusual -transcription of the (-) strand -replicates through an RNA intermediate using reverse transcriptase (copies RNA into DNA)
28
what is the mechanism of mRNA production by Class II?
-ssDNA (+) virus genome -direct transcription would create mRNA (-) so a complementary DNA strand is generated first to get mRNA (+) -dsDNA intermediate replicative form used to do so as well as form new genome copies
29
what does replication of RNA viruses entail?
-depending on the virus it entails RNA-dependent RNA polymerase which is called RNA replicase -this is encoded in the genome
30
what is the mechanism of mRNA production by Class III?
-dsRNA (+) virus genome -transcription of the (-) strand to generate (+) mRNA
31
what is the mechanism of mRNA production by Class IV?
-ssRNA (+) virus genome -its genome is used as mRNA since it is already in the correct form
32
what is the mechanism of mRNA production by Class V?
-ssRNA (-) virus genome -RNA replicase synthesizes a (+) strand through transcription -genome = template
33
what is the mechanism of mRNA production by Class VI?
-ssRNA (+) retrovirus genome -the retrovirus term is specific to this class -replicates first through a dsDNA intermediate using reverse transcriptase -then transcribes the (-) strand
34
what are bacteriophages studied as?
-model systems for the molecular biology and genetics of virus replication
35
what are 2 examples of class II bacteriophages?
-PhageX174 -PhageM13
36
what are the structural characteristics of PhageX174?
-icosahedral -approximately 25nm in diameter with a circular genome of 5386 nucleotides (very small)
37
what does PhageX174 bind to?
-the LPS of E.coli (outer membrane)
38
what occurs to the PhageX174 upon infection?
-the viral DNA is separated from the protein coat -the viral genome is converted into a double stranded replicative form by host enzymes -the genome copies via rolling circle replication -the viral gene transcription for mRNA (+) occurs
39
what is special about the genome of PhageX174?
-there are overlapping genes within it (parts of the genome are transcribed in more than one reading frame) -genes reside within other genes but have different promoters and frame reads (translated seperately) -nucleotides are shared -this is done to conserve size
40
what is the reason for having overlapping genes?
-when there is insufficient DNA to encode all of the viral specific proteins
41
how is the PhageX174 converted into a replicative form by the E.coli host enzymes?
-gets initiated by secondary structure folding to recruit the primosome complex to lay down a primer -several copies are made by semiconservative replication before switching to rolling circle replication
42
how does rolling circle replication work?
-vital protein A nicks a specific site in the (+) strand of circular dsDNA (replicative form) -5' end is displaced and the 3' end serves as a primer for DNA synthesis to replicate the genome (+ strand synthesis) -dNTPs are added to the 3' end by using the exposed (-) strand as a template -the 5' end of the (+) strand peels away to expose more template -phage proteins (ssDNA binding proteins) coat the displaced 5' end (to prevent the (+) strand from being used as a template for transcription) -continued rotation of the circle results in a complete linear copy of the (+) strand -viral protein A cuts the (+) ssDNA and ligates the ends to make it circular for the genome -(+/-) dsDNA replicative form is ready for another round of asymmetric replication to accumulate genome copies
43
what occurs after enough replication of the PhageX174 genome has occured?
-virion assembly -SSBs are removed as the ssDNA is packaged into the capsid -host cell lysis is promoted by E protein (through inhibition of peptidoglycan synthesis)
44
what is the burst size of the PhageX174?
-500 virions
45
what is the purpose of the plaque assay?
-to quantify the number of infective virions -not a direct count because there may not be 100% effective infections and not all may have bursted (plating efficiency + growth conditions) -must be a lytic virus to use this technique
46
what are the structural characteristics of the Phage M13?
-filamentous virus with helical symmetry (virion is long and thin)
47
where does the Phage M13 attach?
-to the pilus of the host cell
48
how does the Phage M13 replicate?
-similarly to the PhageX174 -rolling circle replication
49
what is an unusual property of the Phage M13?
-is released from the host cell without the cell undergoing lysis (integrity of the host cell membrane is maintained) -infected cells can continue to grow (chronic/steady state infection) -infected cells continue to grow, divide, and shed virions -typical viral plaques are not observed -cannot perform the plaque assay because not a lytic virus
50
what is the lifecycle of the Phage M13?
-phage attaches to a new cell via the F pilus -phage DNA enters the host cell (capsid is left outside) -goes through rolling circle replication -PV (SSB protein) coats the ssDNA during replication -the capsid proteins then insert themselves into the cell membrane to form patches (aggregates of proteins) -major coat protein = PVIII which replaces PV as circular ssDNA enters through the cell membrane and becomes encapsulated in protein -PIII and PVI = minor coat proteins that do the closing and release the particle from the inner membrane (done by PIII) -PIII is the outer edge, PVI is the inner edge -PIV allows for the particle to be exported from the cell
51
what is the burst size of the Phage M13?
-no burst size since it does not lyse -1000 virions per generation
52
what are the structural characteristics of the T4 Phage?
-large -helical tail with an icosahedral head that holds the 170kbp linear genome that is folded inside -tail is surrounded by a contractile sheath that terminates in the base plate -tail has tail fibers (attached to the baseplate) and tail pins (part of the baseplate itself) -tail fibers and tail pins are used to penetrate the host cell -very complex structure
53
what type of phage is a T4 Phage?
-virulent phage (actively reproduces inside the host cell) -lytic phage (reproduction leads to the lysis of the host cell)
54
what are examples of class I phages?
-T4 Phage -T7 Phage -Lamda Phage
55
what is the basic process of a T4 Phage infection?
-adsorption: tail fibers contact LPS (phage receptor) of the E.coli cell -attachment: baseplate and tail pins contact the surface of the outer membrane -penetration: contraction of the tail sheath and injection of the genome
56
how is the T4 Phage able to penetrate the host cell?
-because of its tail enzyme (T4 lysozyme) which degrades the peptidoglycan layer -the products of degradation then signals the sheath proteins to contract -sheath consists of 24 protein rings with ATP bound to the sheath proteins -when ATP is hydrolyzed (after signalling) the 24 rings merge into 12 rings (contracted) -this drives the rigid tail through the baseplate and degraded cell wall (DNA enters the cell)
57
when does the T4 DNA initiate its transcription and translation?
-the synthesis of host DNA and RNA ceases within a minute of the viral genome entering the cytoplasm -transcription of specific phage genes begins
58
what does the T4 Phage genome encode for?
-3 major sets of genes (early, middle, and late) which refer to the order of their appearance
59
what is the process of the early genes transcription and translation for the T4 Phage?
-within the first 8 minutes -early phage gene promoters get recognized by the E.coli's sigma 70/RNA polymerase holoenzyme -T4 nuclease is transcribed and translated and it degrades the E.coli chromosome to stop gene expression and to provide nucleotides for synthesis of the phage genome -enzymes for synthesis and glucosylation of the unusual T4 base 5-hydroxymethylcytosine (HMC) are transcribed and translated -T4 replisome is transcribed and translated to allow for phage replication (about 5 minutes after infection and continues until halfway through late phase of gene expression) -proteins that modify RNA polymerase are transcribed and translated to recognize the phage promoters of middle genes
60
why does the sigma 70/RNA polymerase holoenzyme not recognized the middle and late genes?
-RNA polymerase needs to be modified first -middle genes have a -30 box sequence (not -35)
61
what is contained in the T4 replisome?
-T4 DNA polymerase, primase, helicase, clamp, clamp loader, topoisomerase, ligase -all encoded in the T4 genome
62
how does the linear T4 Phage DNA replicate?
-the linear genome has redundant ends (1-2kbp at each end of the genome that is identical to the other end) -helicase/primase complex is loaded on -primers get added by the T4 primase -replication is done by T4 DNA polymerase -primers are degraded by T4 exonuclease (results in a gap at the 5' end) -DNA polymerase cannot add onto the 5' end -since redundant ends are complementary they line up to base pair and get joined by T4 ligase -form concatemers (linear genomes linked end to end)
63
what is the purpose of the unusual T4 base 5-hydroxymethylcytosine (HMC) in the T4 Phage?
-protects from T4 nuclease activity -protects from host restriction endonucleases (enzymes that degrade foreign DNA)
64
what is the process of the middle and late genes transcription and translation for the T4 Phage?
-after 8 minutes of infection -additional RNA polymerase-modifying proteins are made for recognition of late gene promoters (including a T4 encoded sigma factor) -structural proteins are made (capsid, tail, sheath) -packaging motor proteins are made -T4 lysozyme is made
65
what is the purpose of the T4 lysozyme?
-degrades peptidoglycan -lysis of the host cell
66
how are the T4 virions genome packaged?
-concatemers are cut by T4 endonucleases at no specific seqeunce (simply sized to fit into the phage head) -the linear segment has a full T4 genome plus some extra (redundant ends) -have circularly permutated genomes
67
what is circular permutation?
-genomes with the same set of genes but arranged in a different order
68
what is the process of baseplate + tube assembly for the T4 virions?
-baseplate proteins are assembled first -tail pins are added onto the baseplate -helical tube is added onto the baseplate -sheath proteins are added around the tube to complete the tail
69
what is the process of capsid assembly for the T4 virions?
-capsid proteins aggregate to form a prohead (scaffold and capsid proteins) (packaging motor is then attached) -one end of the concatemer is cut and begins to fill the prohead by the ATP-driven packaging motor (ATP supplied by host cell metabolism) -scaffold proteins are discarded and the DNA is cut once it fits the head
70
what is the process of tail fiber assembly for the T4 virions?
-tail proteins are assembled to form tail fibers -tail fibers get added to the mature tail as the last step before maturation -forms the complete virion
71
what is the basic overview of the T4 lifecycle?
-adsorption to the host cell -genome is injected at time 0 -transcription of T4 early genes begins in less than 2 minutes -host chromosome is degraded at 3 minutes -T4 genome replication begins at 5 minutes -translation of the middle and late genes begins at 8 minutes -thousands of capsid proteins are made by 13 minutes -viral parts are assembled and the proheads are filled at 15 minutes -first complete virions are formed at 20 minutes -cell is filled with new virions at 25 minutes and T4 lysozyme has been produced cause the cell to lyse -virions are released
72
what is the burst size of the T4 Phage?
- 100-300
73
what are the structural characteristics of the T7 Phage?
-small -short tailed -icosahedral head with a 40kbp linear genome
74
what type of phage is the T7 Phage?
-virulent phage (actively reproduces inside the host cell) -lytic phage (reproduction leads to the lysis of the host cell)
75
what is difference in the T7 Phage from the T4 Phage concerning what they encode in their genome?
-T7 encodes its own specific RNA polymerase that recognizes only T7 gene promoters -T4 used the host RNA polymerase and had to modify it
76
what is difference in the T7 Phage from the T4 Phage concerning their genome replication and packaging?
-T7 replicates in a different manner than T4 (bidirectional replication) -packaging of the T7 genome is achieved by cutting at a specific site (T4 was cut anywhere)
77
what is similar regarding the T7 and T4 replication processes?
-T7 completed strands contain unreplicated terminal repeats (similar to redundant ends except redundant ends get replicated) -unreplicated terminal repeats are paired by DNA polymerase and ligase activity (joined to form a concatemer)
78
what is the process of cutting the concatemers for the T7 Phage?
-specific cutting sites -once cut the single strands get completed by DNA polymerase to form a mature T7 molecule with terminal repeats

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