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Bis 2c > microbes > Flashcards

microbes Flashcards

midterm 1

1
Q

what is the tree of life?

A
  • refers to descendant-ancestor connections across all living things
  • represents the common ancestry of all life
  • the simile of tree came from Darwin
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2
Q

What is meant by universal homology?

A
  • characters found in all living things

- all life is related therefor some features will be the same due to common ancestor

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3
Q

provide examples of universal homology

A

DNA and RNA and Lipoprotein Cell Membrane
Ribosome
Mitochondria is not UH

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4
Q

Ribosomes

A

RNA is translated into protein using ribosomes

Ribosome’s structure and function is conserved throughout life

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5
Q

DNA to RNA

A

DNA (ACTG) -> transcription -> RNA (ACUG)

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6
Q

history of three domains tree

A

carl woose examined the rRNA (ribosomes) and divided it from bacteria, archaea bacteria, and eukaryotes
-Arcahe nd eukarya are sister taxa

history:

  • Aristotle had the great chain of being, where it suggested that all organisms tries to climb the great chain of being, which ultimately leads up to God
  • Charles Darwin proposed that all organisms had a single common ancestor
  • Ernst Hackel divided organisms into 3 kingdoms: plantate, protista, animalia
  • Whittaker: 5 kingdom tree - plantae, fungi, animalia, protista, monera
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7
Q

prokaryote

A

Archaea and bacteria are prokaryotes
they lack a nucleus
pro= before
karyon = nucleus

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8
Q

two domain vs three domain tree of life

A

in three domain archaea and eukarya are sisters… in two domain eukaryotes is only sisters to SOME of archaea

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9
Q

two domain tree (Asgard)

A

sample study from Loki’s castle = Asgard group of archaea

suggests eukarya is part of archaea

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10
Q

LUCA

A

Last Universal Common Ancestor

lived near deep sea hypothermal vents

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11
Q

why is microbial morphology and biology problematic for phylogeny reconstruction?

A

most microbes have the same morphology

many are capable of movemnet

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12
Q

nitrogen fixation

A

microbes run nitrogen and carbon cycling

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13
Q

virus does not = bacteria

A

virus does not = bacteria

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14
Q

extremophile

A

mostly archaea but bacteria and some eukarya are extremophiles as well.
live in extreme environments pH, temperature, and salinity wise

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15
Q

microbiome

A

“cloud of microbes”

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16
Q

aerobes vs anaerobes
facultative anaerobe
obligate anaerobes
aerotolerant anaerobes

A 
aerobes = needs oxygen
anaerobe = does not need oxygen
facultative = doesn't need oxygen but will use it when available
obligate = oxygen is toxic
aerotolerant = can't use oxygen but isn't harmed by it
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17
Q

bacteria and archaea don’t have a chloroplast but.

A

they can photosynthesize

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18
Q

eukaryote vs. prokaryote (5differences)

A

Eukaryote ———- Prokaryote

nucleus ------------ no nucleus
strand DNA-------  circular DNA
membrane bound organelles -----none
mitosis------binary fusion
haploid diploid more ----- haploid
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19
Q

what does mitosis and binary fission result in

A

aesexual processes that result in identical duplicates

-mutations can occur

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20
Q

eukaryotic cells are able to go through meiosis why can’t prokaryotes?

A

prokaryotes are haploids

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21
Q

how do bacteria and archaea make new genetic recombinants… (eukaryotes =sex)

A

lateral gene transfer

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22
Q

lateral gene transfer

A
  • exchange of DNA across lineages (regardless of genetic history)
  • vertical transmission of DNA
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23
Q

what are the three mechanisms of LGT in prokaryotes

A

1) conjugation : bacteria and archaea can directly exchange their genome by transfer of plasmid
2) Transformation : bacteria and archaea pick up chromosomes from environment (usually from dead bacteria or archaea
3) transduction : viruses can transmit DNA from host to host

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24
Q

plasmid

A

a small circular chromosome not intact with main chromosome… used in conjugation

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25
Q

how is LGT limited

A
  • large/complex sets of genes are less likely to be transferred
  • only portions of genome are transferred
26
Q

how does LGT complicate making of phylogenies

A

bacteria and archaea can exchange genes even though they are not the same species
-it erases phylogenetic history

27
Q

can LGT happen in eukaryotes?

A

Yes ex: snake and cow

28
Q

if LGT is common how can we reconstruct the phylogeny

A

1) sample many taxa
2) use multiple genes and compare their results
3) use multiple independent types of data
4) check for congruence or conflict from other trees

29
Q

the great plate count anomaly

A

many more cells are present in the environment than can be grown in the lab

30
Q

What are culture independent DNA studies ?

A

instead of growing pure lab cultures, go to the environment and sequence environmental sequences

31
Q

the two types of culture independent DNA studies and the people associated with them

A

1) pace : DNA

2) Hug et al : genome

32
Q

peptidoglycan

A

in cell walls of bacteria
gram positive = thick layer (penicillin will work)
gram negative = thin layer
cross linkages with peptidoglycan make stronger cell walls

33
Q

how does penicillin work with structure of cell

A

penecillin will work on gram positive cells (thick layer of peptidoglycan)

34
Q

multicellularity

A

bacteria congregate

  • division of labor
  • some cells give up reproduction
35
Q

nitrogen fixation

A

some cyanobacteria are able to fix nitrogen and photosynthesize using folded membranes

36
Q

biofilms

A
  • communities of organisms that are irreversibly bound to a substrate ; they secrete extracellular polymers (slime)
  • a means of way of communicating between prokaryotes that enables them to function multicellularly
37
Q

quorum sensing

A

expression of group behavior genes as a result of density dependent interactions
- seen in biofilms

Group Behavior Genes:

  • Virulence
  • Antibiotics Production
  • Sporulation
  • Conjugation
38
Q

cyanobacteria

A
  • photolithoautotrophic
  • fix nitrogen
  • chloroplast from endosymbiotic cyanobacteria
39
Q

importance of microbes on human

A
  • digestive microbes
  • infant microbe
  • psychology
40
Q

alphaprotobacteria

A

gram negative bacteria that have common ancestors with mitochondria
gram negative

41
Q

peptidoglycan in bacteria vs. archaea

A

peptidoglycan is only present in bacteria not archaea

42
Q

biofilm key features

A

Key features:

  1. Extracellular polysaccharide matrix
  2. Surface attachment
    - solid surface OR
    - soft tissues in living organisms
  3. Structural heterogeneity AND diversity (bacteria, archaea, protists, fungi, algae, etc.)
43
Q

chloroplast and origin

A

endosymbiotic cyanobacteria

44
Q

endosymbiosis

A

explains origin of mitochondria and chloplasts
evidence :
1. mitochondrial/chloroplast size
2. mitochondrial/chloroplast structure and presence of DNA; their DNA is similar in structure, size and shape to bacterial DNA

45
Q

halophile (extremophile)

A

live in salty environment

46
Q

methanogens (extremophile)

A

produce methane gas as a waste product

47
Q

thermophiles (extremophile)

A

live in extreme cold / hot

48
Q

Gram Stain (q: which cell are antibiotics most likely to be effective?)

A

Peptidoglycan is sensitive to staining agents. Some antibiotics work by affecting the peptidoglycan layer, and thus cell wall synthesis
- bacteria are characterized by the peptidoglycan layer

  • Gram+ bacteria: peptidoglycan layer is thick and outside of the cell wall
  • Gram- bacteria: peptidoglycan layer is thing and lies between the plasma membrane and the outer membrane of cell wall
    a: antibiotics are most likely to be effective on gram+

**Antibiotics are prescribed to someone by determining if the bacteria is gram+ or gram-

49
Q

Lateral Gene Transfer

3 different ways & similarities + differences w/ genetic recombination

A

Similarities:

  • both create new genetic combinations
  • both may involve recombination

Differences (LGT):

  • only involves small part of genome
  • not reproduction
  • multiple mechanisms
  • can occur across large phylogenetic differences
50
Q

mutualism

A

symbiosis where both benefit

51
Q

organelles

A

An organized or specialized structure within a living cell

52
Q

gram + vs gram -

A

A special polymer of amino sugars

  • gram+: peptidoglycan is outside of cell wall
  • gram-: peptidoglycan is between plasma membrane and outer membrane of cell wall

only bacteria have peptidoglycan

53
Q

phagocytosis

A

The ingestion of bacteria or other material by phagocytes and amoeboid protozoans.

54
Q

photoautotroph

A

organisms that carryout photsynthesis

55
Q

photoheterotroph

A

Organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source

56
Q

stigmatella

A

a multicellular organism that is made of many proteobacteria (gram- bacteria)

57
Q

symbiosis

3 types & why eukaryotes form symbioses

A

Symbiosis is an association between at least two different organisms in which at least one of them benefits

  1. Mutualism: both benefit
  2. Commensalism: one benefits, one does not gain or lose
  3. Parasitism: one benefits, one suffers

Eukaryotes

  • metabolically limited in their capabilities relative to archaea and bacteria
  • less able to “acquire” metabolic processes from other species via lateral gene transfer
  • eukaryotes can “acquire” more capabilities by engaging in symbiosis with archaea and bacteria
58
Q

spirochetes

A
  • gram- bacteria
  • Motile
  • Axial filaments (modified flagella)
  • Many are pathogens
59
Q

stigmatella

A

a multicellular organism that is made of many proteobacteria (gram- bacteria)

60
Q

vertical transmission

A

transmission from parent to child

Bis 2c (7 decks)

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