Section 2 Pt.1

Question 1

Uses of Bacteriophages as therapy include: (4 types)

Answer 1

1- phage therapy
2- phage enzyme
3- biofilm dispersal
4- drug sensitization

Question 2

Phages can effect bacteria in many ways that include: (8 types)

Answer 2

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

Question 3

Most abundant group of viruses on the planet is ______

Answer 3

Phages

Question 4

Despite viruses being in low abundance, they have ______ due to their size relative cellular counterparts

Answer 4

low biomass

Question 5

_____ ______ is taking a sample of something, removing the cells, concentrating the viruses into a small volume and extracting their nucleic acids for sequencing

Answer 5

Virus Metagenomics

Question 6

Virus metagenomics found that most genes in viruses ____ _____ _____ ____ Before

Answer 6

Have never been found before

Question 7

_____ ______ ______ 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

Answer 7

The Phage Grou[

Question 8

_____ _______ figured out how lysogen worked and combined the term “______” to describe the integrated form of the phage

Answer 8

Andrew Lwoff
Prophage

Question 9

Important terms found from early phage research

Answer 9

DNA ligases
DNA polymerases
Restriction Enzymes

Question 10

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

Answer 10

Restrictive
Permissive

Question 11

Restrictive, restorative and permissive phages found by noble prize winner _____ ______

Answer 11

Werner Arber

Question 12

“r” = ________ = resistance to foreign DNA, cells produce an enzyme that cuts up DNA

Answer 12

restriction

Question 13

Permissive cell

Answer 13

r-m-

Question 13

“m” = _______ = ability to confer resistance against “r” (cells modify DNA to make it resistant to cutting enzyme)

Answer 13

modification

Question 13

Restorative cell

Answer 13

r-m+

Question 14

Restrictive cell

Answer 14

r+m+

Question 14

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

Answer 14

MS2 and QB (leviviridae)

Question 15

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 ______

Answer 15

A maturation protein (required for attachment to the conjugation pilus)

Question 16

MS2 and QB (leviviridae) require ___ host proteins along with their virus encoded replicase (RdRp) to maximize genetic economy

Answer 16

four host proteins

Question 17

Hfq host factor QB in bacterial cells helps mediate RNA:RNA interactions to regulate gene expression, when a virus gets in, it _______

Answer 17

it is a cellular protein that helps unwind the 3’ end of the viral genome so that RdPd can get access there

Question 18

Two regulatory things happen in ssRNA phages

Answer 18

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

Question 19

How do head on collisions get avoided in ssRNA

Answer 19

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

Question 20

Protein synthesis of ssRNA phages is controlled by _______ ________ (_____) of RNA

Answer 20

Secondary Structure (folding)

Question 21

______ protein binding site (AUG) is available to bind ribosomes while lysis and RdRp are restricted

Answer 21

coat protein

Question 22

After coat protein translates, 2' structure is opened by ribosome and there is 5% chance of access to _____ gene

Answer 22

RdRp

Question 23

When ribosomes are done with the coat protein, they can readjust (go backwards) and that gives them access to ______ gene

Answer 23

lysis

Question 24

---- gene can only be obtained from RNA that was just synthesized and has not folded yet to the stable structure

Answer 24

A maturation gene

Question 25

The modes of regulation by RNA secondary structure lead to the following gradient of translated proteins

Answer 25

CP>>> RdRp = A = Lysis

Question 26

ssDNA: Microviridae has naked icosahedral capsids and is know for its ___ ___ projecting from the surface of the capsid

Answer 26

twelve (12) spikes

Question 27

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

Answer 27

Lipopolysaccharide (LPS) 12 Spikes

Question 28

ssDNA: Microviridae has circular genome and 7 out of 11 overlapped "nested" genes for _____ ______

Answer 28

genomic economy

Question 29

ssDNA: Microviridae controls its translation through :

Answer 29

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

Question 30

Inoviridae (M13) has ____ or ______ structure and circular ssDNA genome

Answer 30

rod or filamentous structure

Question 31

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 _____ _____

Answer 31

gene display

Question 32

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 ______

Answer 32

conjugation pilus Exits Lysed

Question 33

Cholera is caused by a bacterium (vibrio cholerae) that only infects humans if it has 2 genetic elements 1- 2-

Answer 33

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