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BIMM 120 - Microbio > Week 3 material > Flashcards

Week 3 material Flashcards

1
Q

what is Antigenic drift? 3 points NOT 4

4 points

A

-slow accumulation of point mutations over time leading to antigen variation + adaptation

-Antibodies will NO longer work

-There is conservation of useful mutations

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2
Q

Steps of lytic life cycle (6 total)

A

1) Attach to cell
2) Inject linear DNA
3) Replicate DNA
4) Capsids + tails
5) Newly replicated viral DNA packaged inside capsid
6) Lysis - kill host

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3
Q

What is capsid? Tail?

A

Capsid: a protein shell that encases viral DNA
Tails: structure that helps virus attach + inject DNA into host cell

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4
Q

Lysogenic life cycle (5 total)

A

1) Attach to cell
2) Inject linear DNA
3) Integrate OR replicate DNA
4) Propagate for many gens
5) Goes into lytic cycle if stressed

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5
Q

What happens to the host cell in a lytic life cycle? In a lysogenic life cycle?

A

Lytic: Host cell is killed during replication process

Lysogenic: Host cell lives alongside viral DNA give its integration into host DNA

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6
Q

When will a virus go from a lysogenic life cycle to a lytic life cycle?

A

Under stress aka UV given it kills phages

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7
Q

What is the speed of viral replication in a lytic cycle? Lysogenic cycle?

A

Lytic = quick
Lysogenic = slow given integration w/ host

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8
Q

Do viral genes spread slowly or quickly in a lytic cycle? Lysogenic cycle?

A

Lytic = quicker
Lysogenic = slower but MORE persistent

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9
Q

Phage P1 lifestyle

Lysogenic or lytic?
Relationship to host genome?
How many copies on chromo?
What proteins are used and why?

A

Lysogenic
Becomes part of host genome - replicates independently + not integrated but attached
1 - 2 copies on chromo
Uses ParAB to segregate

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10
Q

Phage lambda Lifestyle

What is its relationship to host genome?

A

Integrates into host genome/chromo

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11
Q

What are lysogens? Give 2 examples

A

Lysogens = bacterial cells that harbor viruses w/o killing
Ex. Phage P1 and Phage lambda

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12
Q

What are lysogens resistant to?

A

Phages of same kind that enter bacterial genome

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13
Q

What is transduction?

A

The process of moving chromosomal DNA from 1 cell to another by a phage

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14
Q

General transduction process

A

1) phage infects donor cell by taking bacteria DNA after lysis
2) phage infects recipient cell
3) recipient can incorporate NEW foreign bacterial DNA

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15
Q

Does transduction always happen?

A

No. Only when there is a mistake during packaging stage

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16
Q

In general transduction, what is the success rate of the process happening w/ the correct DNA?

A

1/10 or 1/1,000,000

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17
Q

In transduction by lytic phage, what happens if there is too much phage?

A

Then there is LOW multiplicity of infection

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18
Q

In transduction by lytic phage, what rate do we want in terms of phages and cells?

A

1 phage/cell

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19
Q

In transduction by lysogenic phage, what happens if there are too many phages/cell

A

Too much phages leads to lysis instead of lysogeny

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20
Q

Most phages interface…

A

At specific locations given attachment site proteins

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21
Q

What is prophage?

A

DNA segment of phage

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22
Q

What genes can be transferred?

genes have to be near what?

A

Only genes near prophage could be transferred

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23
Q

What’s the integration process? (Sites + enzymes used)

A

1) recombination sites AttB + Attp
2) integrase enzyme

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24
Q

What is specific transduction?

A

Phage DNA incorporation at specific location into bacterial chromosome

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25
Excision process (sites + enzymes used)
1) recombination sites AttB/P 2) integrase + excisase
26
Can phages uptake bacterial DNA that has antibiotic resistance genes?
Yes
27
What kind of phage is less restricted by DNA size? Why?
Filamentous phage given it shapes itself to fit DNA in capsid
28
How is DNA exchanged?
1) Transformation: takes up exogenous DNA from the environment 2) Conjugation: Direct transfer between cells 2) Phage transduction 3)Gene transfer agent (similar to a phage)
29
What kind of DNA is exchanged? 2 types
Chromosomal DNA + mobile genetic elements
30
What are some examples of mobile genetic elements? 2 total
Lysogenic phage + plasmids
31
What are plasmids?
Small pieces of DNA that are separate from the chromo Large plasmids - contain all genes required for DNA rep + more
32
What are transposons? What are the simplest transposons?
Jumping genes - move from 1 chromo to another Insertion sequences (IS elements)
33
What is transposase genes used for? What about IR? What are the most active IS elements in E. Coli. ?
To move IS Inverted repeats to help move + circularize and are recognized by transposaes IS1 + IS5
34
What is a mediator
A virulent or temperate phage
35
what is antigenic shift? 3 points
-when cells get 2 or more viral strains -Reassortment of genes -Recombination of genes resulting in a novel virus w/ virulent genes from 2 diff strains
36
How fast do viruses evolve? what do they cross?
-quickly -species barriers
37
what are bats considered? what are they also known as?
common reservoirs such that they are NOT actually infected, they are just carriers also known as Asymptomatic carriers
38
Smaller organisms have shorter life spans. Bats however, live a lifespan of ....... longer compared to another organism of same size ***fill in the blank
3x
39
Are bats competing w/ parasites? Are they the only flying mammals that exists?
NO. They live in peace w/ parasites given LESS inflammation + oxidative stress + MORE energy to other properties YES
40
No inflammation results in... 3 points
less cellular death + longer lifespan + slower aging process
41
What is disease X?
A new infection or existing pathogen with newly acquired potential to cause an epidemic
42
Future epi/pandemics might occur as a result of...
Deforestation
43
What's the 1st coronavirus to exists? where did it originate and in what year? what were the animals that lead to this transmission? Are there are available vaccines?
SARS-COV 2 - Sever acute respiratory syndrome - in china 2002 - Bats —> palm civet/raccoons —> human —> humans - NO FDA approved vaccines
44
Palm civet are carriers of coronavirus from dolphins. How is this possible?
Due to animal farming (black markets)
45
What's the 2nd coronavirus to exists? what were the animals that lead to this transmission? Are there are available vaccines? is it more or less transmissible than SARS?
MERS-COV -Middle eastern respiratory syndrome -Bats —> camels 🐪—> humans -NO FDA available vaccine -less transmissible but more deadly
46
What's the 3rd coronavirus to exists? what were the animals that lead to this transmission? Are there are available vaccines?
SARS-COV 2 - Bats --> Raccoon dog —> humans - mRNA vaccine develops
47
Marburg virus is related to what other virus? what are they symptoms of the RELATED virus? is this the deadliest virus yet? what about its transmission to humans?
-ebola -hemorrhagic fever virus -YES -transmission via consumption of bushmeat or direct contact
48
Ebola is related to Marburg in what sense? what about its transmission? Is there a vaccine developed?
-Also one of the most deadly + hemorrhagic fever -Bats --> nonhuman primates --> humans -No vaccine yet but goal is to contain it
49
Influenza's origin is...? In 1918, the flu was known as.... but in present day, it's known as....? What's the biggest transmission for this virus? what virus are we still NOT immune to?
- avian/bird origin - H1N1 = Spanish Flu back then, but today it is the swine flu - pigs-->birds-->humans crossover -H5N1 is the strain we are not immune to, from cattle (cows)
50
Pigs are...
viral mixing bowls, a massive location for viral recombination
51
NHP are susceptible to human viruses and some viruses circulate between them. What are 2 examples of viruses that fit this scenario?
HIV and the Zika virus
52
Carnivores and bats are central for... | transmission of what?
the transmission of RNA viruses in mammals
53
Bats, primates and rodents have a higher proportion of...
zoonotic viruses
54
BSE (Bovine Spongiform Encephalopathy). How did this viral epidemic came to be? What's its the origin? How was the spread stopped? BSE transformed into what? Symptoms of this disease?
- via recycling sheep and cattle waste parts - scrape-like agent in sheep/cattle infected with the scrape-like agent - banned certain animal parts from entering the food chain - Mad Cow Disease - spongy degeneration of the brain and spinal cord
55
Kuru - How was it passed down? is it still an ongoing virus?
via people who practiced cannibalism
56
What do BSE + kuru have in common?
they are prion diseases meaning a protein that folds the wrong way
57
what are Integrons?
genetic elements that can capture and integrate gene cassettes encoding various functions, including antibiotic resistance.
58
what is Genetic islands?
regions of DNA encoding specific functions
59
what are examples of Proton transport proteins?
Carriers + channels + pumps + redox-coupled electron transfer proteins
60
Bacterial rhodopsins are... | what kind of proteins
proton transport proteins
61
Do ALL microbes have some form of rhodopsin?
YES
62
why are Protons excluded from the membrane interior?
because of their charge
63
Does bacteria rhodopsin show sequence similarity w/ mammalian rhodopsin thats found in eye?
NO
64
Similarities of bacteria rhodopsin with mammalian rhodopsin? 2 total
-Same topology w/ 7 TMS -Both are integral mem constitutes
65
All viruses have how many channels to move protons, minimum?
at least one channel
66
bacteria rhodopsin was first discovered in...
archaea
67
Proton Transport proteins are important for...
facilitating cycle of events responsible for viral infection
68
How are proton transport proteins able to enter the membrane?
w/ a specific protein that catalyzes transport in/out of cell
69
Voltage gated proton channel look like...
voltage sensor in voltage gated ion channel proteins
70
Voltage gated ion channels like Na+ K+ Ca+ commonly have how many TMS? how many inverted repeats?
6 TMS 1 inverted repeat
71
what are 3 diff functions identified for protein transporting channels (in viruses)?
Mech 1: protons dissociating from proteins that depend on RNA/DNA viruses BFEORE injection of NA into host cell Mech 2: facilitate packaging + excision of cell back into viral particle Mech 3: facilitate uptake of viral nucleic acids from viral particle
72
Mote A/B functions as a proton channel used to...
power the movement of bacteria
73
what are 2 examples of Mitochondrial Carriers?
Uncoupling proteins - Transports protons down chemical gradient to generate heat to maintain body temperature Secondary Carriers - electrochemical gradient of protons (or sodium) drives the movement of solutes into/out of cell
74
what are the 2 types of pumps responsible for pumping protons in/out of cell?
P-type ATPases + redox carriers
75
function of P-type ATPases? | provide examples
pumps use ATP to transport protons across membranes Ex. include enzymes in the stomach + those maintaining pH in plants and fungi.
76
function of redox carriers?
use electron flow to pump protons out of the cell
77
examples of redox carriers? 4 total
1. complex 1 - NADH dehydrogenase - Pump protons out in response to electron flow + 14 TMS subuntis 2. complex 2 - succinate dehydrogenase 3. complex 3 - Quinone Cytochrome C electron transfer system 4. Cytochromoxidases
78
What is Bacteria R's source of energy to pump protons out of cell?
light absorption
79
what happens upon light absorption? | what is generated?
Generates a mem potential that’s (-) inside
80
Bacteriorhodopsin contains a retinal chromophore. what is the chromophore linked to and on what residue?
linked to lysine residue of 7th TMS
81
What protein is found in Fungal R? what is its function?
protein Foldase also known as chaperon proteins function: to fold proteins after they have been made from ribosome via light energy
82
Halorhodopsin's function?
pump chloride INTO cell Help create (-) mem potential INSIDE
83
Anthorhodopsin function?
pump protons
84
Proteal rhodopsin function?
bacterial proton pump Pumps OUTward Generate - mem potential inside
85
Channelrhodopsin's function?
Catalyze cation + ion + proton movement When light is absorbed, channel opens. No light or not enough, channel closes
86
what are some rhodopsin covalently linked to and why?
Covalently linked to histidine kinases for regulatory purposes
87
Bacteriorhodopsin (Brho) uses what type of molecule? what is it a derivative of?
Retinal a chromophore - a derivative of vitamin A
88
Retinal is parallel to what? what is it perpendicular to? what is it bound to?
-to the membrane -Perpendicular to TMS that its attached to -bound to the K216 residue in the middle of TMS #7
89
how does bacteriorhodopsin use a light-sensitive retinal molecule linked to a lysine residue to act as a proton pump?
retinal forms an imine group by condensing amino/aldehydic/keto group resulting in a secondary imine known as Schiff Base
90
what is Bacteriorhodopsin composed of? | in terms of structure
2 half channels -internal cavity with a cytoplasmic -external half close to outside
91
Schiff Base: what is it? what is it attached to? what is it good at?
- a secondary imine attached to Lysine (K) - at being protonated at the N group which can then quickly protonate something else and have itself be deprotonated
92
where does the proton bind to the Schiff Base?
external half channel
93
is the external half hydrophobic or hydrophilic? what about the internal half? which region does a proton prefer?
external - hydrophilic internal - hydrophobic hydrophilic regions
94
N terminus is.......and the C terminus is.......the membrane
outside; inside
95
K216 is covalently linked to...via what?
retinal via the Schiff’s base
96
process of light-activated proton pumping mechanism of brho
1) Brho absorbs light energy via its retinal molecule 2) Absorption triggers all-trans to 13-cis conformational changes in retinal 3) Conformational changes alters the pKa of aa + SB. Changes in pKa influence the access of protons to the SB from different sides of the membrane 4) SB can either a) be protonated from the cytoplasm b) deprotonate outside 5) reset - retinal molecule goes back to all-trans

BIMM 120 - Microbio (6 decks)

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