Midterm 1 Flashcards
How does the type of host influence the virus?
influences its viral replication and gene expression depending on whether its eukaryotic or prokaryotic
Where is eukaryotic genome located?
nucleus (nucleosomes chromatin, euchromatin)
eukaryotic genome encodes for proteins but a larger % does, what else does it code for?
RNA genes
regulatory regions
junk regions
where is the prokaryotic genome located?
cytoplasm
how does the prokaryotic and eukaryotic genome differ other than location?
pro lacks nucleosomes and is more compact
what does a virus need from its host?
1) replication of nucleic acids and viral particles (uses DNA rep. tools: DNA pol, primate, SSBPs ect.)
2) synthesis of viral proteins (transcription of viral genes to mRNA, translation of mRNA to proteins)
3) assembly and release of infectious viral particles
function of topoisomerase:
relaxes super-coiled DNA
function of DNA helicase:
unwinds double helix at replication fork
function of DNA primase:
provides starting point for DNA pol. to begin synthesis of new strand
function of DNA polymerase:
synthesizes new DNA strand; also proofreads and corrects some errors
DNA ligase:
re-joins two DNA strands into double helix and joins Okaski fragments of lagging strand
function of single-strand binding proteins (SSBP):
binds to separate DNA strands to keep them separated by holding them in place so each strand can be a template for new DNA synthesis
function of PCNA (proliferation cell nuclear antigen) sliding clamp:
protein complex that binds to DNA pol. and prevents the enzyme from dissociating from template DNA strand (processivity-promoting factor)
how does eukaryotic DNA replication get controlled, making it difficult from virus to get DNA replication done?
- genome of eukaryotic. is only ever ds DNA linear
- involves many enzymes and axhillary proteins (ability is affected by cell cycle)
- occurs in nucleus so virus must be able to get in
- DNA rep. is controlled by phase of cell cycle (only occurs in synthesis (S) phase)
- if PCNA isn’t available DNA rep. apparatus doesn’t assemble properly so rep. doesn’t occur
prokaryotic DNA rep.:
- ds circular or linear
- occurs just before binary fission
- diff. enzymes involved on rep. initiation than eukaryotic
what are the challenges viruses face when trying to replicate in host?
- euk and pro DNA rep. is under tight control
- DNA pol does replicate ssDNA
- Ori in euk. and pro. is diff and recognized by diff proteins (some proteins aren’t present until the cell is in DNA rep. mode)
- cellular forms can’t rep. RNA b/c they don’t have an enzyme that makes RNA for an RNA template, virus has to bring own RNA pol.)
what is needed to initiate DNA replication?
- proteins that recog. Ori
- DNA template
- DNA pol.
- material to build DNA (nucleotides)
in general, how can viruses replicate genome?
- manipulate host cell cycle (especially if virus needs cellular enzymes like DNA pol. that’s only present during cellular DNA rep.)
- have their own DNA pol and proteins to control viral DAN rep.
- mechanisms/designs to ensure good genome rep.
what does parvovirus do to rep. genome?
-uses host DNA rep. apparatus but infects young animals so cells are guaranteed to to be rep. therefore DNA rep. too
what do polyoma and papilloma virus do to rep. genome?
- uses host DNA pol. but encodes own Ori binding proteins
- has proteins that interfere with or manipulates the host cell cycle
what do HSV, poxvirus and adenovirus so too rep. genome?
-encode their own DNA pol. and Ori binding proteins
what are to features of the Ori?
- AT rich
- recognition sequences
how does linear viral DNA start rep.?
- some pack better as linear but become circular automatically before rep.
- other linear genomes have hairpin ends or terminal proteins at end that hold too strands together
DNA pol. and primase don’t start lying nucleotides at the very end of the viral linear genome making the new template strand shorter, how is this problem solved?
- some linear viral genomes become circular for rep. (ex. phage Lambda)
- some linear genomes have hairpin ends
- some have terminal proteins at their ends
how do eukaryotic linear chromosomes rep.?
- telomers (segments of junk DNA) are found at the end of each chr. segments
- telomers are produced by telomerase that synthesizes DNA from internal RNA template
how does Adenovirus rep. its linear DNA?
- viral DNA has no room for junk to protect ends
- uses terminal proteins that are covalently attached to 5” ends as primers
- terminal proteins already have the first nucleotide in place
how does Parvovirus rep. its linear DNA?
-hairpin ends produce temporary ds DNA that gets modified its two ss molecules later
how do viruses effect prokaryotic hosts DNA rep.?
- some degrade host DNA
- lysogeny: temperate phages integrate into the hosts chr. (pro-phage)
how do viruses effect eukaryotic host DNA rep.?
- apoptosis: incomplete degradation of host DNA
- tumour formation: de-repression of host DNA rep.
- pro-virus: integration of viral genome into host genome
how does gene expression of euk. and pro. differ?
- promoter structure and recognition features
- RNA pol.
- transcription termination
- mRNA features
- mRNA translation initiation features
- regulatory mechanisms for gene expression
- gene organization
features of euk. promoter?
- promoter has TATA box
- RNA pol II
- transcription factors
features of pro. promoter?
- prinow box, -35 and -10
- RNA pol holoenzyme made of two parts (sigma factor and core enzyme)
what are the three levels that regulation of gene expression is possible?
- transcriptional level (no mRNA)
- translational level (no protein)
- post-translational level (no protein activity)
how is the euk. transcription of heterochromatin regulated?
- DNA methylation
- nonacetylate histone
how is the euk. transcription of euchromatin regulated?
- acetylate histones
- genes can be transcribed
features of euk. transcription:
- occurs in nucleus
- mRNA must move to cytoplasm
- genes are split by axons (get expressed) and introns (removed during processing)
pre-mRNA to mRNA process:
modifications are made before exporting to cytoplasm:
- 5’ cap of 7-methylguanosine added
- removal of introns/ splicing together exons (by splicosomes: proteins and RNA molecule complex)
- addition of 3’ poly-A-tail
cap and tail protect and signal its ready for transport
how does alternative splicing allow one gene to code for more than one protein?
-exons are joined together in different ways
what are the three major types of euk. RNA pol?
RNA pol I: catalyzes rRNA synthesis
RNA pol II: catalyzes mRNA synthesis
RNA pol III: synthesizes tRNA molecules
how is transcription initiated in euk?
- RNA pol II needs to be aligned properly
- TFs bind to sequence motifs in DNA to help line up RNApol
- RNA pol II is recruited to a promoter (includes upstream regulatory enhancers, upstream elements, and TATA box)
how is euk. transcription regulated?
euk. gene expression is regulated by proteins that interact with elements associated with promoter region (enhancers can stimulate or decrease rate of transcription pf a gene)
what segments make up the euk. core promoter?
BRE: TFIIB-recognition element
TATA box: binding site for several transcription elements including RNA pol II
-Inr: initiator element
DPE: downstream promoter element
how do enhancers work?
transcription factors bind to them to stimulate or decrease rate of transcription of the gene
steps of euk. transcription:
- TFIID binds to TATA
- other TATA binding factors and pol II form pre-initiation complex
- TFIIE and TFIIH bind to complex to stabilize initiation complex
- pol II moves along template and new mRNA strand is made 5’ to 3’
components of the signal transduction cascade:
- JAK: sensor kinase located in membrane
- STAT: response regulator in cytoplasm
- alpha interferon: outside of cell (JAK is cell surface receptor)
steps of the signal transduction pathway:
- alpha IFN binds to JAK, JAK autophosphorylates
- JAK passes on phosphate group to STAT
- STAT migrates to nucleus and activates transcription of genes involved in interferon response
(helps cell defend itsself from virus)
features of bacterial RNA pol.:
- doesn’t edit
- doesn’t require a primer
- uses DNA as template
- made of two main components (core enzyme and sigma factor)
- diff. sigma factors designed for diff. promoters
- transcription termination signal is recognizer. on transcribed RNA
features of bacterial transcription:
- transcription and translation are simultaneous
- ribosomes start translating mRNA before its transcription is complete
- mRNA doesn’t need processing
- many mRNA encode for more than one protein (polycistronic/polygenomic)
what makes up bacterial RNA pol?
-tetrameric core and sigma factor= holoenzyme
how is the transcription of genes controlled in bacteria?
- only genes recognized by specific sigma factors are translated (broad scale)
- regulatory region on DNA (fine-tuning)
how does a repressor work?
binds to the operator and blocks RNA pol (ex. Lac operon repressor; a repressor of indictable genes)
what are the regulatory regions on bacterial DNA?
- promoter: recognizer. by sigma factors
- operator: located after promoter, controlled by repressors
- activator binding site: located before promoter, controlled by activators
- repressors: prevents transcription
- activators: stimulate transcription
how do euk. and bacterial translation initiation differ?
- euk. has a 5’ cap
- bacteria has ribosome binding site called shine-dalgarno sequence
what degrades ds RNA and what does it produce?
- dicer
- produces siRNA and miRNA