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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
Q

Excision process (sites + enzymes used)

A

1) recombination sites AttB/P
2) integrase + excisase

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26
Q

Can phages uptake bacterial DNA that has antibiotic resistance genes?

A

Yes

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27
Q

What kind of phage is less restricted by DNA size? Why?

A

Filamentous phage given it shapes itself to fit DNA in capsid

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28
Q

How is DNA exchanged?

A

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)

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29
Q

What kind of DNA is exchanged? 2 types

A

Chromosomal DNA + mobile genetic elements

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30
Q

What are some examples of mobile genetic elements? 2 total

A

Lysogenic phage + plasmids

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31
Q

What are plasmids?

A

Small pieces of DNA that are separate from the chromo
Large plasmids - contain all genes required for DNA rep + more

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32
Q

What are transposons? What are the simplest transposons?

A

Jumping genes - move from 1 chromo to another

Insertion sequences (IS elements)

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33
Q

What is transposase genes used for? What about IR? What are the most active IS elements in E. Coli. ?

A

To move IS

Inverted repeats to help move + circularize and are recognized by transposaes

IS1 + IS5

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34
Q

What is a mediator

A

A virulent or temperate phage

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35
Q

what is antigenic shift? 3 points

A

-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

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36
Q

How fast do viruses evolve? what do they cross?

A

-quickly
-species barriers

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37
Q

what are bats considered? what are they also known as?

A

common reservoirs such that they are NOT actually infected, they are just carriers

also known as Asymptomatic carriers

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38
Q

Smaller organisms have shorter life spans. Bats however, live a lifespan of ……. longer compared to another organism of same size

***fill in the blank

A

3x

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39
Q

Are bats competing w/ parasites? Are they the only flying mammals that exists?

A

NO. They live in peace w/ parasites given LESS inflammation + oxidative stress + MORE energy to other properties

YES

40
Q

No inflammation results in…
3 points

A

less cellular death + longer lifespan + slower aging process

41
Q

What is disease X?

A

A new infection or existing pathogen with newly acquired potential to cause an epidemic

42
Q

Future epi/pandemics might occur as a result of…

A

Deforestation

43
Q

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?

A

SARS-COV 2
- Sever acute respiratory syndrome
- in china 2002
- Bats —> palm civet/raccoons —> human —> humans
- NO FDA approved vaccines

44
Q

Palm civet are carriers of coronavirus from dolphins. How is this possible?

A

Due to animal farming (black markets)

45
Q

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?

A

MERS-COV
-Middle eastern respiratory syndrome
-Bats —> camels 🐪—> humans
-NO FDA available vaccine
-less transmissible but more deadly

46
Q

What’s the 3rd coronavirus to exists? what were the animals that lead to this transmission? Are there are available vaccines?

A

SARS-COV 2
- Bats –> Raccoon dog —> humans
- mRNA vaccine develops

47
Q

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?

A

-ebola
-hemorrhagic fever virus
-YES
-transmission via consumption of bushmeat or direct contact

48
Q

Ebola is related to Marburg in what sense? what about its transmission? Is there a vaccine developed?

A

-Also one of the most deadly + hemorrhagic fever
-Bats –> nonhuman primates –> humans
-No vaccine yet but goal is to contain it

49
Q

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?

A
  • 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
Q

Pigs are…

A

viral mixing bowls, a massive location for viral recombination

51
Q

NHP are susceptible to human viruses and some viruses circulate between them. What are 2 examples of viruses that fit this scenario?

A

HIV and the Zika virus

52
Q

Carnivores and bats are central for…

transmission of what?

A

the transmission of RNA viruses in mammals

53
Q

Bats, primates and rodents have a higher proportion of…

A

zoonotic viruses

54
Q

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?

A
  • 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
Q

Kuru - How was it passed down? is it still an ongoing virus?

A

via people who practiced cannibalism

56
Q

What do BSE + kuru have in common?

A

they are prion diseases meaning a protein that folds the wrong way

57
Q

what are Integrons?

A

genetic elements that can capture and integrate gene cassettes encoding various functions, including antibiotic resistance.

58
Q

what is Genetic islands?

A

regions of DNA encoding specific functions

59
Q

what are examples of Proton transport proteins?

A

Carriers + channels + pumps + redox-coupled electron transfer proteins

60
Q

Bacterial rhodopsins are…

what kind of proteins

A

proton transport proteins

61
Q

Do ALL microbes have some form of rhodopsin?

A

YES

62
Q

why are Protons excluded from the membrane interior?

A

because of their charge

63
Q

Does bacteria rhodopsin show sequence similarity w/ mammalian rhodopsin thats found in eye?

A

NO

64
Q

Similarities of bacteria rhodopsin with mammalian rhodopsin? 2 total

A

-Same topology w/ 7 TMS
-Both are integral mem constitutes

65
Q

All viruses have how many channels to move protons, minimum?

A

at least one channel

66
Q

bacteria rhodopsin was first discovered in…

A

archaea

67
Q

Proton Transport proteins are important for…

A

facilitating cycle of events responsible for viral infection

68
Q

How are proton transport proteins able to enter the membrane?

A

w/ a specific protein that catalyzes transport in/out of cell

69
Q

Voltage gated proton channel look like…

A

voltage sensor in voltage gated ion channel proteins

70
Q

Voltage gated ion channels like Na+ K+ Ca+ commonly have how many TMS? how many inverted repeats?

A

6 TMS
1 inverted repeat

71
Q

what are 3 diff functions identified for protein transporting channels (in viruses)?

A

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
Q

Mote A/B functions as a proton channel used to…

A

power the movement of bacteria

73
Q

what are 2 examples of Mitochondrial Carriers?

A

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
Q

what are the 2 types of pumps responsible for pumping protons in/out of cell?

A

P-type ATPases + redox carriers

75
Q

function of P-type ATPases?

provide examples

A

pumps use ATP to transport protons across membranes
Ex. include enzymes in the stomach + those maintaining pH in plants and fungi.

76
Q

function of redox carriers?

A

use electron flow to pump protons out of the cell

77
Q

examples of redox carriers? 4 total

A
  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
Q

What is Bacteria R’s source of energy to pump protons out of cell?

A

light absorption

79
Q

what happens upon light absorption?

what is generated?

A

Generates a mem potential that’s (-) inside

80
Q

Bacteriorhodopsin contains a retinal chromophore. what is the chromophore linked to and on what residue?

A

linked to lysine residue of 7th TMS

81
Q

What protein is found in Fungal R? what is its function?

A

protein Foldase also known as chaperon proteins
function: to fold proteins after they have been made from ribosome via light energy

82
Q

Halorhodopsin’s function?

A

pump chloride INTO cell
Help create (-) mem potential INSIDE

83
Q

Anthorhodopsin function?

A

pump protons

84
Q

Proteal rhodopsin function?

A

bacterial proton pump
Pumps OUTward
Generate - mem potential inside

85
Q

Channelrhodopsin’s function?

A

Catalyze cation + ion + proton movement
When light is absorbed, channel opens. No light or not enough, channel closes

86
Q

what are some rhodopsin covalently linked to and why?

A

Covalently linked to histidine kinases for regulatory purposes

87
Q

Bacteriorhodopsin (Brho) uses what type of molecule? what is it a derivative of?

A

Retinal a chromophore - a derivative of vitamin A

88
Q

Retinal is parallel to what? what is it perpendicular to? what is it bound to?

A

-to the membrane
-Perpendicular to TMS that its attached to
-bound to the K216 residue in the middle of TMS #7

89
Q

how does bacteriorhodopsin use a light-sensitive retinal molecule linked to a lysine residue to act as a proton pump?

A

retinal forms an imine group by condensing amino/aldehydic/keto group resulting in a secondary imine known as Schiff Base

90
Q

what is Bacteriorhodopsin composed of?

in terms of structure

A

2 half channels
-internal cavity with a cytoplasmic
-external half close to outside

91
Q

Schiff Base: what is it? what is it attached to? what is it good at?

A
  • 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
Q

where does the proton bind to the Schiff Base?

A

external half channel

93
Q

is the external half hydrophobic or hydrophilic? what about the internal half? which region does a proton prefer?

A

external - hydrophilic
internal - hydrophobic

hydrophilic regions

94
Q

N terminus is…….and the C terminus is…….the membrane

A

outside; inside

95
Q

K216 is covalently linked to…via what?

A

retinal via the Schiff’s base

96
Q

process of light-activated proton pumping mechanism of brho

A

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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