Section 2 Pt.1 Flashcards
Uses of Bacteriophages as therapy include: (4 types)
1- phage therapy
2- phage enzyme
3- biofilm dispersal
4- drug sensitization
Phages can effect bacteria in many ways that include: (8 types)
1- transformation - phages leave and take all of the cells DNA to give to another
2- generalized transduction - phages leave and package random host DNA with them
3- specialized transduction - phages leave after packaging specific flanks of DNA
4- PICIs - package genomic islands then transfer them
5-GTA -
6- Lysogenic conversion
7- chromosomal rearrangements
8- phage-related elements
Most abundant group of viruses on the planet is ______
Phages
Despite viruses being in low abundance, they have ______ due to their size relative cellular counterparts
low biomass
_____ ______ is taking a sample of something, removing the cells, concentrating the viruses into a small volume and extracting their nucleic acids for sequencing
Virus Metagenomics
Virus metagenomics found that most genes in viruses ____ _____ _____ ____ Before
Have never been found before
_____ ______ ______ a group of scientists with the initial interest to study viruses and cancer, began studying model Ecoli viruses to understand nature and replication of genes
The Phage Grou[
_____ _______ figured out how lysogen worked and combined the term “______” to describe the integrated form of the phage
Andrew Lwoff
Prophage
Important terms found from early phage research
DNA ligases
DNA polymerases
Restriction Enzymes
A phages host range changes depending on the host they came from
_______= can only replicate in same cells that they came from
_______= can replicate anything
Restrictive
Permissive
Restrictive, restorative and permissive phages found by noble prize winner _____ ______
Werner Arber
“r” = ________ = resistance to foreign DNA, cells produce an enzyme that cuts up DNA
restriction
Permissive cell
r-m-
“m” = _______ = ability to confer resistance against “r” (cells modify DNA to make it resistant to cutting enzyme)
modification
Restorative cell
r-m+
Restrictive cell
r+m+
RNA Phages = less common than DNA phages and discovered by accident (phage f2) but now the most studied RNA phages are _____ and ______ with +ve sense ssRNA
MS2 and QB (leviviridae)
MS2 and QB (leviviridae) have +ve sense ssRNA, icosahedral shape, and a very specific folding structure with 180 copy of coat proteins and 1 copy of ______
A maturation protein (required for attachment to the conjugation pilus)
MS2 and QB (leviviridae) require ___ host proteins along with their virus encoded replicase (RdRp) to maximize genetic economy
four host proteins
Hfq host factor QB in bacterial cells helps mediate RNA:RNA interactions to regulate gene expression, when a virus gets in, it _______
it is a cellular protein that helps unwind the 3’ end of the viral genome so that RdPd can get access there
Two regulatory things happen in ssRNA phages
1- Head on collisions by replicase and ribosome must be avoided so that simultaneous translation and replication don’t happen
2- expression of the 4 genes tightly controlled so that proper amounts of diff proteins and timing of their expression is right
How do head on collisions get avoided in ssRNA
RdRP must bind at 3’ to make a 5’-3’ -ve strand to be replicated
When RdRp binds, another protein “cellular S1” binds at the coat portion AUG site to block ribosomes from binding
** however gets there first stays there
Protein synthesis of ssRNA phages is controlled by _______ ________ (_____) of RNA
Secondary Structure (folding)
______ protein binding site (AUG) is available to bind ribosomes while lysis and RdRp are restricted
coat protein
After coat protein translates, 2’ structure is opened by ribosome and there is 5% chance of access to _____ gene
RdRp
When ribosomes are done with the coat protein, they can readjust (go backwards) and that gives them access to ______ gene
lysis
—- gene can only be obtained from RNA that was just synthesized and has not folded yet to the stable structure
A maturation gene
The modes of regulation by RNA secondary structure lead to the following gradient of translated proteins
CP»> RdRp = A = Lysis
ssDNA: Microviridae has naked icosahedral capsids and is know for its ___ ___ projecting from the surface of the capsid
twelve (12) spikes
ssDNA : When Microviridae goes to bind, first, _____ attaches to bring the virion into contact with target cells then 2’ receptor is one the _____ that has to bind for the DNA to go through into the cells cytoplasm
Lipopolysaccharide (LPS)
12 Spikes
ssDNA: Microviridae has circular genome and 7 out of 11 overlapped “nested” genes for _____ ______
genomic economy
ssDNA: Microviridae controls its translation through :
1- differences in promotor strengths
2- presence of terminator sites stopping genes from getting to the end
3-nested genes having weak ribosome binding sites
Inoviridae (M13) has ____ or ______ structure and circular ssDNA genome
rod or filamentous structure
Inoviridae (M13) is an important tool for molecular biology as it is used in the construction of cloning vector plasmids (preparing DNA for sequencing) as it packages whatever is added to its genome which is called _____ _____
gene display
Inoviridae (M13) uses ____ ______ from plasmids as a receptor (if u don’t have it you can’t get in)
they leave their sctructural proteins in cytoplasm so that DNA gets packaged as it ______
infected cells keep producing particles without being ______
conjugation pilus
Exits
Lysed
Cholera is caused by a bacterium (vibrio cholerae) that only infects humans if it has 2 genetic elements
1-
2-
1- CTX0 prophage: makes cholera toxin (CT) primary virulence factor
2- VPI: (vibrio pathogenicity island) : encoded a pilus required for the bacteria to attach to intestinal cells*
*VPI also receptor for CTX
