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Virology test 1 lecture 4

front 1 Replication of DNA viruses I	back 1 what this class is about
front 2 steps in DNA replication	back 2 origins of replication - locations on DNA where replication always starts recognized by sequence DNA rep is semiconservative each strand in double helix acts as template for synth of new complimentary strand DNA polymerase enzyme that makes DNA once the RNA primer is in place require a template annd RNA primer (starter) synth DNA 5' to 3' direction (new strand complimentary to template) primase make primer RNA once on each leading strand template to initiate DNA synthesis make RNA primer repeatedly on lagging strand template to initiate okazaki fragment synthesis leading strand made continuously lagging strand made in small pieces (okazaki fragments) other enzymes required: DNA primase, DNA helicase, DNA ligase, topoisomerase
front 3 semiconservative DNA replication	back 3 In this model, the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand. This results in two DNA molecules with one original strand and one new strand. creates fork -> 1 leading and 1 lagging strand
front 4 topoisomerase	back 4 responsible for preventing DNA from tangling + relieves pressure of supercoiled DNA during replication DNA is supercoiled prevents supercoiling and tangling

front 5 DNA helicase	back 5 catalyze disruption of H bonds that hold 2 strands of DS DNA together
front 6 summary of DNA replication in proks	back 6 helicase opens DNA at replication fork single stranded binding proteins coat DNA around replication fork to prevent rewinding of DNA topoisomerase works at the region ahead of replication fork to prevent supercoiling primase synth RNA primers complementary to DNA strand (4-16 nucleotides long) DNA polymerase III extends the primers (add on 3' end to make bulk of new DNA) RNA primers removed + replaced with DNA by DNA polymerase I the gaps btw DNA fragments sealed by DNA ligase Proks: don’t have nucleus or chromosomes, their DNA floats in cytoplasm (bacteria) Euks: have nucleus and chromosomes
front 7 diff btw proks and euks DNA replication	back 7 origin of replication euks - multiple per chromosome proks - 1 per DNA molecule synth of DNA euks - DNA pol alpha, epsilon, etc. proks - DNA polymerase III removal of RNA primers euks - RNase H (5'-3' exonuclease) proks - DNA polymerase I replacement of RNA with DNA euks - DNA pol proks - DNA pol I rest same between them
front 8 helicase	back 8 opens DNA at replication fork single stranded binding proteins coat DNA around replication fork to prevent rewinding of DNA

front 9 topoisomerase	back 9 works at the region ahead of replication fork to prevent supercoiling
front 10 primase	back 10 synth RNA primers complementary to DNA strand (4-16 nucleotides long)
front 11 DNA polymerase III	back 11 extends the primers (add on 3' end to make bulk of new DNA)
front 12 RNA primers removed + replaced with DNA by	back 12 DNA polymerase I

front 13 The gaps btw DNA fragments sealed by	back 13 DNA ligase
front 14 steps involved in DNA replication	back 14 recognition of initiation point, origin unwinding of DNA template DNA RNA primer chain elongation replication forks proof reading error here during replication may lead to mutation DNA pol I and pol III = proof readers of new DNA remember RNA replication prone to more mutations bc of mistakes, and DNA mechanisms have proofreading/editing mechanisms that RNA mechanisms dont have removal of primer and completion of DNA strand joining of fragments
front 15 transcription	back 15 one strand - coding strand (sense strand) other strand - noncoding strand (antisense strand, template strand) contains anticodons coding strand is DNA strand whose base sequence is identical to base sequence of RNA transcript made (T replaced by U) this strand contains codons RNA pol II binds noncoding template strand, reads anticodons on it, and transcribes it to make mRNA with complementary bases coding strand = strand used when displaying DNA sequence. Presented in 5' to 3' direction Antisense strand – anticodons contained - template strand Sense strand = coding strand -> use to get RNA - codons contained mRNA = same as sense strand but T switch for U Anticodons complimentary to codons obviously
front 16 discovery of retroviruses and reversotranscriptase	back 16 david baltimore, nobel prize proposed the following classification of viruses based on relationship of viral genome to viral mRNA mRNA - identical to coding DNA strand (except T -> U) and complementary to template strand

front 17 mRNA configuration	back 17 plus (+) configuration
front 18 mRNA's complement configuration	back 18 minus (-) configuration
front 19 + strand RNA viruses	back 19 + strand RNA viruses = mRNA viruses, since they are mRNA, they can directly translate / make proteins. Do not need any machinery extra to translate
front 20 baltimore virus classification	back 20

front 21 3 groups of DNA viruses	back 21 ss DNA viruses (class I) genome = molecule of single DNA strand cannot transcribe unless get double strand of DNA, so it must have a ds DNA intermediate in order to do anything else ex: poxviruses ds DNA virus (class II) normal DNA molecule of genes ex: parvoviruses ds DNA viruses with retrovirus activity (that replicate through RNA intermediate by reverse transcriptase) - class VII separate classification/group ex: hepadnaviruses DNA viruses infect both proks and euks prominent DNA viruses - herpesvirus, papillomavirus, and poxvirus all replicated either by host or virally encoded DNA polymerases only some ds DNA and all retroviruses use reverse transcriptase
front 22 are DNA virus genomes larger or smaller than RNA genomes?	back 22 LARGER bc stability of DNA allows for genomes much larger
front 23 large DNA viruses have	back 23 ds DNA
front 24 small DNA viruses typically have	back 24 circular ss or ds DNA

front 25 families of DNA viruses	back 25 3 groups DNA viruses in humans - DS - SS - DS RNA with retrovirus intermediate step - today focus on SS DNA families
front 26 medically important DNA viruses	back 26 parvovirus no envelope - naked small DNA icosahedral ss linear hepadnavirus enveloped icosahedral DS herpesvirus icosahedral enveloped DS poxvirus complex capsid enveloped DS
front 27 poxes are very big viruses	back 27 Poxes – very big viruses Retroviruses – NOT a DNA virus, it is RNA - remember only 2 groups viruses in humans that are retroviral dependent We will focus on ssDNA parvovirus
front 28 DNA virus gallery	back 28

front 29 DNA viruses	back 29 I think may need to know these??? parvovirus - small, naked, ss virus
front 30 baltimore classification again	back 30 Again, Baltimore classification of viruses DNA viruses – green Again, 3 categories of DNA viruses - Ds DNA thru reverse transcriptase - Ds DNA - Ss DNA
front 31 overview of diff types of viruses to transcription	back 31 SS DNA must go through ds DNA stage (intermediate) step before doing anything else for RNA viruses transcription of (-) strand necessary to obtain mRNA (+ RNA) ds RNA ss RNA (-) if ss RNA (+) already, can just translate itself to make proteins
front 32 class II: ssDNA	back 32 ss DNA information flow DNA -> mRNA -> protein viral genome - either has same base sequence as mRNA (+ strand DNA) or be complementary to the mRNA (- strand DNA) + strand DNA -> DNA strand complementary to viral genome must be manufactured first -> form DS replicative form (RF) can be used to manufacture viral proteins + as template for viral genome copies - strand DNA viruses -> genome can be used directly to produce mRNA but complementary copy still needs to be made complementary copy to serve as template for viral genome copies ss DNA must be copied into mRNA before proteins can be produced RNA can only be made from ds DNA template, no matter what sense the single stranded DNA is -> DNA synthesis must precede mRNA production in replication cycles of these viruses single stranded genome is produced by cellular DNA polymerases flow of info follow normal pathway sort of viral genome - same base sequence after mRNA (+ strand DNA) OR complementary to mRNA (- strand DNA) complimentary DNA must be made first before making DS DNA ssDNA must be copied to mRNA before proteins produced

front 33 ssDNA viral genome	back 33 either has same base sequence as mRNA ( + strand DNA) or be complementary to the mRNA ( - strand DNA)
front 34 + strand DNA viruses	back 34 same sequence as mRNA must first create gene complementary to viral genome = form double stranded replicative form -> then use to make viral proteins + use as a template for viral genome copies (replication) DNA synthesis must occur before mRNA production, because must have double strand DNA in order to make mRNA
front 35 - strand DNA viruses	back 35 complementary sequence to mRNA genome can be used directly to make mRNA (bc genome is complementary to mRNA) still need to make complementary copy to serve as template for viral genome copies (replication) DNA synthesis must occur before mRNA production, because must have double strand DNA in order to make mRNA
front 36 complementary DNA must be made before making	back 36 double stranded DNA, as a SS DNA virus

front 37 single stranded genome is produced by	back 37 cellular DNA polymerases
front 38 ssDNA viruses	back 38 replication: euk ssDNA viruses replicate in nucleus most ssDNA viruses contain circular genomes replicated via rolling circle replication (RCR) parvoviruses - contain linear ssDNA genomes replicated via rolling hairpic replication (RHR), similar to RCR either positive or negative sense strand can be packed into capsisd almost all ssDNA viruses have + sense genomes, but a few exceptions + peculiarities exist parvoviruses may package either + or - sense strand into virions mRNA transcribed in nucleus - leave nucleus to cytoplasm where ribosomes translate to proteins -> proteins back to nucleus where assembly of virus occur -> Rolling hairpin replication – just know it’s the mechanism of linear ssDNA genomes ? <- not important
front 39 replication of ssDNA viruses	back 39 replicate in nucleus -> cytoplasm where ribosomes translate to proteins -> back to nucleus for virus assembly most ssDNA viruses have circular genome - replicated via rolling circle replication (RCR) process of unidirectional nucleic acid replication that can rapidly synth multiple copies of circular molecules parvovirus - linear use rolling hairpin replication (RHR) unidirectional, strand displacement form of DNA replication used by parvoviruses for us to know the diff, not very important
front 40 what is the replication mechanism of SS DNA genomes?	back 40 circular genome (usually) -> replicate via rolling circle replication (RCR) Linear ones (like parvovirus) - rolling hairpin replication (RHR)

front 41 (almost) all single stranded DNA viruses have what genome?	back 41 + sense circular
front 42 SS DNA viruses TRANSCRIPTION	back 42 transcription ssDNA viruses have same manner of transcription as DS DNA viruses BUT: single stranded -> must first make self into a double stranded form by host DNA polymerase upon entering host cell must be made into ds form (can only transcript from ds DNA) by host DNA pol in order to make mRNA mRNA is then synth from the double stranded form the double stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome = can either use to make more ss DNA (populate its genome) OR can use to make viral mRNA euk ssDNA viruses replicated in the nucleus
front 43 ssDNA virus replication cont.	back 43 ALL DNA VIRUSES USE CELLULAR DNA POLYMERASE FOR REPLICATION OF THE GENOME
front 44 human B19 parvovirus replication cycle	back 44 Right pic - virus enter thru receptor - go to nucleus -> to perform everything need to replicate DNA -> Transcription - mRNA out nucleus into cytoplasm to translate - back in nucleus to form viral particle - then leave cell Mistake in left pic – mRNA supposed to go outside gray box to do protein translation

front 45 parvovirus life cycle	back 45 GENOME. Interestingly enough, Parvoviridae is the only family of DNA viruses that infect humans that is single stranded. The DNA strand packaged in the virion can be either negative or positive sense, in approximately equal proportions. Replication takes place in the nucleus of dividing cells. The single-stranded DNA genome forms an intermediate double-stranded form, which replicates to form progeny-positive and -negative single-stranded DNA. Positive and negative strands are packaged separately in viral capsids in equal numbers. Internalization of both + and – DNA Genome – only family of DNA viruses infecting humans that is SS - replication in nucleus Leave, packaged separately in viral capsids Parvovirus must infect actively growing cells
front 46 what is the only ss DNA virus infecting humans?	back 46 parvovirus
front 47 second deadly dog disease	back 47 Canine parvovirus Vaccine important/mandatory for dogs Remember virus is naked – so is very resistant to environmental factors, temp, etc.
front 48 parvovirus B19 fifth disease: the human disease from parvovirus	back 48 Human disease from parvovirus There are 4 that we do not have today rash on face lace-like rash on extremities