viruses

Question 1

virus

Answer 1

a small infectious particle that consists of nucleic acids ( either ssRNA or dsDNA) packaged in a capsid protein (protein coat)

Question 2

capsids

Answer 2

composed of one or more protein subunits called capsomeres

Question 3

what do viruses have that help them bind to a host cell

Answer 3

protein fibers with a knob or a spike glycoprotein

Question 4

viral envelope

Answer 4

viruses take some of the plasma membrane from the host to make up a lipid bilayer

Question 5

bacteriophages

Answer 5

phages
viruses that infect bacteria

Question 6

host cell

Answer 6

cell infected by virus

Question 7

host range

Answer 7

number of species and cell types that viruses can infect

Question 8

phage t4

Answer 8

host = ecoli
causes lysis

Question 9

tobacco mosaic virus

Answer 9

host = many plants
causes necrosis of leaves

Question 10

life cycle of a virus

Answer 10

1. virus attaches to host cell plasma membrane via spikes/knobs
2. virus enters cell ; viral envelope fuses with plasma membrane and releases the genetic material (RNA and capsid protein)
3. viral genome replicates inside the cell; host enzyme replicates
4. transcription occurs; host enzymes transcribe viral genome to make mRNA and this is translated to make capsid proteins
5. viral stealth assembly; viral genomes and capsid proteins self assemble to make more viruses
   6; exit/release

Question 11

life cycle of an animal virus: HIV

Answer 11

leads to AIDS
1.attachment; spike glycoproteins binds to specific host cell receptors on host cells plasma membrane
2. entry; the viral envelope fuses with the host cell membrane —> some capsid proteins are removed by host cellular enzymes
3. integration; replication and transcription and translation occurs; integrase
4. pro-virus; directs synthesis of more viruses —> self-assembly process

Question 12

integrase

Answer 12

integrating viral double stranded DNA that is made from reverse transcriptase into the host chromosome

virus is now called pro-virus

Question 13

reverse transcriptase

Answer 13

how an rna virus integrates its viral genomes into the host cell’s DNA

viral enzyme carried within capsi protein and released into the host cell along with genetic information (ssRNA)

able to use this ssRNA to make a complementary copy of DNA that is used as a template to make double stranded DNA

Question 14

life cycle of a virus = host = bacteria/e.coli

Answer 14

attachment of phage ; phage dna is binding to cell membrane of bacteria

entry : injecting its DNA into the cytoplasm

integration: either integrate into bacterial chromosome —> prophage (virus + bacterial chromosome) or go through process of lysis and spill virus into environment

Question 15

lytic cycle

Answer 15

lysis
breaking virus out of host cell

after gene expression processes the phage DNA make mRNA and then translates to make proteins

this makes new phages through viral assembly

then lysis can occur where the cell is broken up via lysosome enzymes

death of host cell

Question 16

two alternative versions of replication for phages

Answer 16

lysogenic cycle
lytic cycle

Question 17

virulent phage

Answer 17

virus that only replicates via lytic cycle

not capable of integrating viral genome into bacterial host chromosome

Question 18

lysogenic cycle

Answer 18

viral genome becomes integrated into bacterial host chromosome

doesn’t kill host cell nor produce new phage particles

Question 19

temperate phages

Answer 19

viruses that can replicate through either cycle

Question 20

why do viruses need protein receptors on cell’s surface to attach to and infect host cell?

Answer 20

lipid bilayer of the plasma membrane of the eukaryotic host cell is not permeable to all molecules, especially hydrophobic proteins, so viruses can’t just fuse through

host cells have protein receptors for normal cell functions, like responding to chemical stimuli or cell signaling

viruses take advantage of this system by having glycoproteins that recognize those receptors, then attach to the host cell

Question 21

bacteriophages also recognize and bind to specific molecules on the surface of the host cell

how

Answer 21

bacteriophages have more complex protein coats with accessory structures used for anchoring the virus to the host cell and injecting nucleic acid into it

Question 22

what happens to the capsid proteins after entry into host cell?

Answer 22

entry: some capsids are removed by host cellular enzymes (un coating)

synthesis of viral components: more capsids are made

viral assembly: capsids combine with RNA, reverse transcriptase, integrate , etc

Question 23

where in host DNA genome does viral genome integration occur?

Answer 23

any gene region, but there are viral integration sites specific to various viruses

Question 24

what is major reason why bacteria have been spared from extinction

Answer 24

lysogenic cycle
virus is able to propagate without killing host cell

Question 25

bacterial defense system against phages

Answer 25

CRISPR - Cas system
provides bacteria with defense against phages

Question 26

CRISPR gene

Answer 26

chromosome is made up of CRISPR gene that is a group of clustered, regularly interspaced, short, palindromic repeats
DNA sequence with spacers, repeats, spacers, repeats, etc.

Question 27

repeats

Answer 27

short segments of DNA and they are palindromes(reads the same forwards and backwards)

Question 28

spacers

Answer 28

DNA from previous infections by other phages

Question 29

CAS

Answer 29

CRISPR-associated genes) (Cas9,Cas1,Cas2) will make Cas proteins

Question 30

CRISPR-Cas system

Answer 30

bacterial immune system

when a phage infects a bacterial cell, it injects its viral genome into the cytoplasm of the host cell
go through lytic or lysogenic cycle or the CRISPR-cas system

Question 31

infection by a phage triggers:

Answer 31

transcription of repeats from Crispr gene region of DNA to make RNA transcript/RNA guide

transcription and translation of Cas gene
region of DNA to make Cas protein

RNA guide binds to Cas proteins to form a complex

Complementary guide RNA binds to DNA from invading phage

Cas proteins cut phage DNA
phage DNA degrades (virus no longer replicates)

Question 32

scientists use CAS9 for

Answer 32

gene therapy or gene editing

Question 33

gene editing

Answer 33

altering DNA sequences of a gene for a specific predictable way

Question 34

gene therapy

Answer 34

used to treat genetic diseases by repairing a gene that may have a harmful mutation

Question 35

how is CRISPR-CAS9 used for gene editing

Answer 35

cas9 protein and guide rna come together to form a complex

the complex is introduced into a cell

guide rna is engineered to guide the cas9
protein to a target gene

cas9 protein has active sites that can cut DNA so once the complex is introduced into cell, the guide RNA will bind to a complementary sequence —> part of target gene —> then the protein cuts

Question 36

where on the target DNA sequence does Cas9 protein cut?

Answer 36

protospacer-adjacent motif (PAM)
short conserved 2-6 base pair sequence that ends in NGG

Question 37

after cutting of gene using CRISPR-Cas9

Answer 37

the broken strands of DNA are repaired by the cell in one of two ways

could be inserting or deleting random nucleotides and altering the nucleotide sequence enough that it is no longer functional
repair a gene that has a harmful mutation —> you could put in a repair enzyme to help the DNA sequence becomes functional again —> editing gene

Question 38

PCR amplification

Answer 38

make many many copies of DNA

Question 39

gel electrophoresis

Answer 39

figuring out which segment of DNA you have and how long/heavy it is

DNA negatively charged
go towards positive electrode