12.1-12.3 - Viruses, prokaryotes, conjugation

Question 1

virus genetics

Answer 1

genes may overlap with each other, utilizing more than 1 ORF

Question 2

why injection into bacteria

Answer 2

bacteria have cell walls

animal cells don’t have cell walls

Question 3

virus is defined as a…

Answer 3

…obligate intracellular parasite – they must produce in cells
viruses are not cells, do not produce ATP

Question 4

virus genetics

Answer 4

DNA or RNA, single or double stranded, linear or circular

protein shell

a virus can have only one type of NA, and mature viruses do not contain nucleic acids outside of its genome

genes may overlap with each other (multiple reading frames), and host-encoded proteins are used for transcription/translation/replication

Question 5

capsid and envelope

Answer 5

protein coat surrounding the viral nucleic acid genome

the “capsid head” holds to genome

surrounded by an ENVELOPE - derived from the membrane of the host cell, made of phospholipids, proteins, and carbohydrates - acquired through BUDDING through the host cell membrane

enter a host through fusing envelope with the host’s plasma membrane = OPPOSITE OF BUDDING

The envelope is essential for entering a host.

no envelope = NAKED; all phages and plant viruses are naked (plants and bacteria have cell walls, which means the host membrane is ruptured during a lytic explosion)

Question 6

viral infection is extremely…

Answer 6

…specific

virus binds to a specific receptor on the cell surface, then internalized by fusion with plasma membrane or receptor-mediated endocytosis

the viral surface is important for recognition by immune system

the EPITOPE is capsid surface, which may be blocked by the envelope

Question 7

attachment and… before cycle

Answer 7

= adsorption (binding to exterior of bacterial cell)

penetration (eclipse) = removes infectious virus from the media

enters LYTIC or LYSOGENIC cycle

Question 8

lytic cycle

Answer 8

1. hydrolase is expressed, degrading the entire host genome
2. multiple copies of phage genome produced (using dNTPs) and capsid proteins
3. lysozyme (late gene) destroys the bacterial cell wall

Question 9

cell wall found in…

Answer 9

most bacteria/prokaryotes

algae, plants, fungi (but rarely other eukaryotes)

bacteriophage and plant viruses -> they don’t bud

Question 10

lysogenic cycle (define: lysogen, prophage)

Answer 10

phage genome incorporated into the bacterial genome, referred to as a PROPHAGE

the host is now a LYSOGEN

dormancy: phage-encoded repressor protein binds to specific DNA elements in phage promoter (operators)

the prophage may activate, removing itself from the host genome (EXCISION) and entering the lytic cycle

Question 11

transduction

Answer 11

when a virus excises with host DNA, and that new DNA becomes evident in the new host (e.g. the ability to metabolize galactose)

the dormancy, phage-encoded repressor protein may not repress the transduced genes

Question 12

detergent removes envelope

Answer 12

1. some of the protein released were encoded by the genome of the infected cell
2. Impacts infectivity (fusion with plasma membrane)

Question 13

viruses enter animal cells via…

Answer 13

…endocytosis

viral genome is uncoated - released from capsid

Question 14

animal virus life cycles

Answer 14

lytic (same as phages)
productive cycle - enveloped viruses exist the host cell by BUDDING and coating itself - the animal cell does not die

lysogenic cycle - provirus (like prophage)

Question 15

the role of RNA polymerase

Answer 15

the host cannot produce RNA from RNA, it must have DNA. but an RNA polymerase can produce RNA from RNA

Question 16

(+) RNA viruses

Answer 16

single-stranded RNA, immediately translated

one of its proteins must be RNA-dependent RNA polymerase (to replicate itself)

common cold, polio, rubella

Question 17

(-) RNA virus

Answer 17

the negative strand is a template for the (+) strand, which is the mRNA

the viral RNA-dependent RNA pol is brought in with the virus, which does the job of transcription and replication simultaneously without host enzymes

Question 18

retroviruses

Answer 18

a (+) viruses whose viral genome encodes for reverse transcriptase, which makes DNA from an RNA template

Question 19

dsDNA viruses

Answer 19

large genomes that encode enzymes require for dNTP synthesis and DNA replication

they carry genes for enzymes that synthesize dNTP (so that they don’t have to wait for the host to generate dNTP)

RNA viruses don’t have genes for enzymes that produce NTPs because transcription is always occurring in all cells

Question 20

prion diseases

Answer 20

prior is an abnormally folded protein that acts as a template and becomes infectious

Question 21

viroids

Answer 21

circulator single-stranded RNA (200-400 bps) with self-complementarity

non-coding

lack capsids

catalytic ribozymes

produce siRNA that can silence normal gene expression

usually infect plants

ex. Hep D - needs to co-infect with Hepatitis B

Question 22

prokaryotes

Answer 22

lack membrane-bounded organelles

bacteria, archea, blue-green algae

Question 23

proteins are made… C-N?

Answer 23

N->C

Question 24

three bacterial shapes

Answer 24

1. coccus (round)
2. bacillus (rod shaped)
3. spirillum (spiral-shaped)

Question 25

bacterial cell wall is made of… which is composed of…

Answer 25

peptidoglycan - cross-linked chains made of sugars and amino acids, including D-alanine, not found in animal cells

surrounds the lipid bilayer

Question 26

lysozyme

Answer 26

cracks open the bacterial cell wall (present in tears and saliva)

Question 27

gram positive

Answer 27

strongly stains, thick peptidoglycan layer outside the cell membrane

gram-negative have a thinner layer of PEP but an outer layer with LIPOPOLYSACCHARIDE, periplasmic space – increased resistance to abx

Question 28

capsule/glycocalyx

Answer 28

sticky layer of polysaccharide “goo” surrounding the bacterial cell and entire colony, strengthens bacteria and adherence to smooth surfaces

Question 29

flagella

Answer 29

found in bacteria

1. monotrichous
2. amphitrichous - both ends
3. peritrichous (multiple flagella)

encoded by over 35 genes

made of filament, hook, basal structure

Prokaryotic structure is DIFFERENT from eukaryotic

Question 30

fimbriae

Answer 30

smaller structure involved in adherence

Question 31

sex pilus

Answer 31

F+ and F-, formation of conjugation bridges

Question 32

chem/phototroph versus auto-heterotroph

Answer 32

chemo - energy from chemicals
photo - energy from light
auto - carbon from CO2
hetero - carbon from organic nutrients

chemoautotroph - CO2 loving, oxidize inorganic H2S
chemoheterotroph - humans
photoautotrophs - plants, CO2 loving
photoheterotroph - Sun-powered, but require organic molecules from other organisms

Question 33

auxotroph

Answer 33

auxiliary trophic

needs something in addition to minimal media (e.g. arginine)

results from a mutation

Question 34

lac-

Answer 34

bacterial incapable of growing with lactose as its only carbon source

lac+ -> only needs lactose

Question 35

types of anaerobes

Answer 35

= do not require oxygen

facultative - use oxygen when it’s around, don’t need it
tolerant - don’t care about oxygen
obligate - hate oxygen, cannot process free radicals -> typically the kind that infect wounds

Question 36

prokaryotic aerobic respiration

Answer 36

32 ATP per glucose, 2 ATP per glucose in fermentation

Question 37

how do you explain the lag period

Answer 37

a time when biosynthetic pathways are very actively producing new cellular components before division

NOT DORMANT

*transferring bacteria in log phase does not create a new lag phase

glycolytic pathways are very active during this phase

Question 38

endospores

Answer 38

tough, thick external shells composed of peptidoglycan, within are found genome/ribosomes/RNA that become active when conditions are favorable (germination)

heat-resistant

1 spore per cell

CANNOT INCREASE population through spore formation

occurs in stationary phase

Question 39

transformation

Answer 39

internalize DNA in bacterial culture, gaining genetic information in the DNA

Question 40

Hfr cell

Answer 40

when a cell with F factor integrates into the genome

Question 41

Archaea

Answer 41

has cell walls that lack peptidoglycan

share mRNA and presence of introns with eukaryotes

Question 42

parasitic bacteria

Answer 42

facultative - live and replicate inside or outside of host

obligate - must be inside a host cell to replicate