VIRUS I

Question 1

What is a virus?

Answer 1

-Contains nucleic acid surrounded by a protein coat
-Viral replication takes place inside the host cells
-CAPSID: generally composed of only a few protein subunits (capable of self-assembly)

Question 2

What are the basic types of viruses?

Answer 2

-DNA virus: ss or ds
-RNA -> DNA: ssRNA (retrovirus) or dsDNA (hepadravirus)

Question 3

What is the life cycle of a bacteriophage

Answer 3

1) attachment
2)penetration (coat protein left outside)
3) virus enzymes synthesized
5) nucleic acid replication
5) synthesis of protein coat
6) assembly + packaging
7) release (lysis) -> host cell dies

Question 4

Where do the virus usually attach

Answer 4

viruses attach to structure like pili, flagella, or receptors

Question 5

How do viruses penetrate through bacteria cell wall

Answer 5

-packaged material that can drill holes in bacteria cell wall (lysozyme-like proteins
-only necleic acid injected

Question 6

What does replication look like for lytic cycle

Answer 6

make more phage and break host cell and release new phage

Question 7

What does a typical growth curve for bacteriophage look like

Answer 7

-two phases
-latent period
assembly and release
time varies depending on type of virus

Question 8

What is the experimental set up of plaque assay

Answer 8

-phage dilution and bacterial cells mix together on top of agar

Question 9

What are phage plaques

Answer 9

-indicate where cell was killed and phage were released to attach to another cell
-each plaque represent 1 viral particle
-size of plaque depends on the virus and host
-not all viruses will infect cells
-viral titer= # of plaque forming units

Question 10

What type of bacteriophage is Lambda

Answer 10

ds DNA bacteriophage

Question 11

What is temperate phage

Answer 11

have the option of settin gup a state of coexistence with host cell (lysogeny)

Question 12

What is lysogeny

Answer 12

-genes that would harm the hose are prevented from being expressed, while a small set of genes that provide benefit to the hose are expressed
-integrates into the bacterial genome

Question 13

What is the genetic switch

Answer 13

-competition between CI and Cro determine lifestyle
-rightward transcription: induction of the lytic genes (Cro)
-Leftward transcription (leads to lysogeny)
-CI: lambda repressor inhibits lytic cycle

Question 14

What is a switch box

Answer 14

-competetion for binding to OR3, OR2, and OR1
-Pr: rightward promoter
-Prm: leftward promoter

Question 15

What is CI (lambda Repressor) structure

Answer 15

-dimer
-N-term bind to DNA
-high affinity for the operator sites on lambda genome

Question 16

What is Cro structure

Answer 16

-dimer
-can also bind to all three operator sites on lambda genome

Question 17

What is negative control look like for lambda

Answer 17

-the repressor @ Or2 prevents transcription of Pr transcription through Pr
-No RNA pol binding= no transcription

Question 18

What does positive control look like for lambda

Answer 18

-repressor @ Or2 helps RNAP bind + increases transcription of Prm approximately 10X
-binds to RNA pol alpha c+d to promote leftward transcription

Question 19

What does cooperative binding look like for lambda

Answer 19

-repressor can bind to both sites while interacting w/ each other (more stable)
-binding to Or1: repressor has greatest affinity + stimulates repressor bind to Or2 via protein- protein interactions between dimers
-during lysogeny, repressor is constantly bound to Or2 + Or1 blocking expression of Cro
-Cro preferentially binds to Or3 so it doesn’t block RNAPol binding
-Cro has no cooperative binding
-binding to Or1 + shuts off own transcription (auto regulation)
-high [Cro] = binding to OR1

Question 20

Explain SOS repair

Answer 20

-damaged DNA binds to recA
-leads to cleavage of lexA repressor
-therefore expression of genes involved with DNA repair

Question 21

Explain induction by DNA damage

Answer 21

-active RecA cleaves repressor rendering it unable to bind cooperatively
-leads to Cro binding + induction of the lytic genes
-need to run out of the burning house
-DNA damage = cell is under stress

Question 22

What does CRISPR/CAS systems target

Answer 22

Target DNA or RNA to interfere w/ replication of viruses or plasmid DNA

Question 23

What is the Cas complex

Answer 23

detect foreign DNA or RNA + saves a bit (CRSIPR locus)

Question 24

What is the CRISPR locus

Answer 24

repeat-spacer unit
-folds into a hair pin structure at one end of the guide RNA

Question 25

How does Cas used Guide RNA

Answer 25

uses it to target foreign DNA and cleave it

Question 26

What is PAM

Answer 26

is a short recognition site that stabilizes CAS during cleavage
-spacers= immune memory

Question 27

What transcribes guide RNA

Answer 27

CRISPR locus transcribed guide RNA on 2nd exposure