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MICR220 > Module 2 - The World > Flashcards

Module 2 - The World Flashcards

(60 cards)

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1
Q

What is evolution?

A

Descent with modification.

A change in the frequency of alleles in a population over time

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2
Q

What 2 things are required for evolution to occur?

A
  1. A process that can create allele variants

2. A process that leads to change in allele frequencies

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3
Q

What are the sources of variation for evolution?

A

Mutation & recombination

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4
Q

What are mutations?

A

Random changes to DNA.
Substitutions, deletions, insertions & duplications
Can be neutral, deleterious, rarely can be beneficial
They accumulate over time

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5
Q

What is recombination?

A

Segments of DNA broken and rejoined to create new combinations.
Can be from horizontal gene transfer or DNA already present.

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6
Q

What drives the change in allele frequency?

A

Selection - in a given environment, mutations which advantage an organism to pass on its genetic material to future generations will increase over time

Genetic Drift - members of a population may have more offspring by chance leading to change over time.

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7
Q

How long ago did life first appear?

A

4.1 billion years

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8
Q

What is LUCA?

A

Last Universal Common Ancestor

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9
Q

What kind of metabolism did early cells have?

A

Anaerobic - no oxygen yet

Chemolithotrophy - metabolism of inorganic compounds, paving the way for production of organic compounds

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10
Q

What is the Great Oxidation Event and why is it significant?

A

Cyanobacteria producing oxygen for the first time, around 2.4 billion years ago.
Oxic atmosphere = oxygen metabolism = big energy advantage + ozone layer = UV protection

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11
Q

What is the endosymbiosis hypothesis?

A

That organelles in Eukaryotic cells (mitochondria & chloroplasts) descend from symbiotic relationship with bacteria

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12
Q

What are the 3 domains of life

A

Bacteria
Archaea
Eukaryota

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13
Q

What is systematics?

A

The study of diversity and relationships, links phylogeny and taxonomy

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14
Q

Why is phylogeny?

A

The evolutionary history of organisms, visualised as a tree (rooted with LUCA)

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15
Q

How are phylogenetic trees made?

A

Differences in nucleotide sequences between organisms.
More differences = distantly related
Less differences = closely related

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16
Q

What are orthologs and paralogs?

A

Orthologs = homologous genes with same function as ancestor

Paralog = homologous genes that have evolved a different function

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17
Q

What kind of DNA is most commonly used for phylogenetic analysis and why?

A

Small subunit rRNA

Because it is highly conserved and easily sequenced/analysed

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18
Q

What is sequence alignment and why is it important?

A

Lining up homologous genes. Mutations can be insertions or deletions which can change the length genes, so they can get misaligned. Need to be aligned so they can be correctly compared.

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19
Q

What is monophyletic, paraphyletic and polyphyletic?

A

Monophyletic = includes all descendants of an ancestor (whole family)

Paraphyletic = Includes a common ancestor but NOT ALL of its descendants (some kids missing)

Polyphyletic = A group that lacks a common ancestor (bunch of kids w no parents)

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20
Q

What can complicate phylogenetic analyses?

A

Convergent evolution, horizontal gene transfer

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21
Q

What is a species in phylogeny?

A

Genetically and phenotypically cohesive

Distinct from other species

Monophyletic

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22
Q

WHat is a traditional approach to separate species of bacteria and archaea?

A

DNA-DNA hybridisation less that 70%

Greater than 3% difference in SSU rRNA genes

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23
Q

What is DNA-DNA hybridisation

A

Cutting up 2 different samples of DNA and seeing how easily it creates hybridised DNA (DNA with a strand from each)

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24
Q

What is a core genome and pan genome?

A

Core genome is genes common to all strains of a species

Pan genome is core genome + all other genes across all strains

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25
Why can microbial strains within a species have genetic variation?
Microbial genomes grow/shrink quickly HGT Mutations/Deletions Non essential genes often deleted over time
26
What is taxonomy?
Identification, classification, nomenclature. Relies on phylogenetic, genotype and phenotype analyses
27
What methods are used in taxonomy for differentiating organisms?
- ssu rRNA not as useful, so recA highly conserved gene - multilocus sequence typing (housekeeping genes) - genome fingerprinting (ribotyping)
28
What are some things that could be observed phenotypically?
- fatty acids - morphology - motility - metabolism - cell wall
29
What is the order of classification?
``` Domain Kingdom Phylum Class Order Family Genus Species Strain ```
30
What are the 2 main energy sources for microbes?
Chemicals & Light
31
What is a habitat?
A part of the ecosystem that is suitable for just a few populations
32
What is a Community?
2+ populations sharing a place and time
33
What is a population?
A group of organisms of the same species, same place and same time
34
What is a guild?
Populations which a metabolically similar and use the same resources
35
What are important factors of micro environments?
Diffusion is a factor in resource availability Can be quickly disrupted (wind, rain, stepped on) Nutrient changes can be fast (leaf falling onto soil) Extended exponential growth unlikely - spurts and plateaus with nutrient availability
36
What is competition and cooperation?
Competition - organisms competing for resources Cooperation - some microbes work together to complete a task they can’t do on their own. Can be limiting if 1 depends on output of another
37
How is species diversity measured?
Species richness (# distinct species present) Species abundance (proportion of each species)
38
WHy are surfaces like rocks, skin, catheters good habitats?
Access to nutrients Physical protection from disturbance Some surfaces have nutrients themselves
39
What is a microbial mat?
A thick, complex, stable mix of autotrophs and heterotrophs
40
What is a biofilm?
Microbial cells attached to a surface together using an adhesive matrix made of cells (alive or dead)
41
What are the benefits of a biofilm?
Cells stay attached Catch food Penetration more difficult (chemical and mechanical) Proximity (cell to cell communication & exchange)
42
WHat are soil layers
O horizon - not yet decomposed plant matter A horizon - surface soil, microbial activity high B horizon - subsoil, some microbial activity but lower than A C horizon - soil base, very low microbial activity
43
How can microbes contribute to soil formation
Exposed rock -> mosses, lichen -> support bacteria/fungi -> colonies of bacteria, archaea, eukarya = respiration -> CO2, in water -> carbonic acid which dissolves limestone, cracks appear -> particles + organic matter = substrate for pioneering plants etc
44
What are limiting factors in soil?
Phosphorus Nitrogen Water
45
What do I use to test which bacteria are in soil?
16S ribosomal RNA
46
What is notable about arid soil?
Most microbial fertile soil. Can have extreme environments. Microbes stabilise soil near surface
47
What is notable about terrestrial subsurface?
Presence of groundwater = microbes >3km deep
48
What is notable about freshwater?
can become stratified with different chemical conditions. Ie aerobic on top, anaerobic on bottom. Periods of mixing can effect community structures
49
What is notable about saltwater?
Largest microbial biomass on earth. Largest organic C pools, marine microbes return organic C to the food web. Nearer to shore = more nutrients, can have local community changes. Contain oxygen minimum zones - 100-1000m, source on N2O, increasing with global warming
50
What makes pelagibacter successful in the ocean?
Very small - high surface-to-volume ratio = better nutrient uptake in low nutrient environment Has lots of proteins for catching nutrients Small genome = low cost of replication Can make ATP from light when organic carbon is low
51
What are the major microbial groups in the ocean?
Bacteria - alphaproteabacteria, gammaproteobacteria, cyanobacteria Archaea Viruses - more viruses in the ocean than cellular microbes (mostly bacteria/archaea viruses)
52
What is notable about the deep sea?
Below 1000m (so no light = no photosynthesis) Cold - so microbes are psychrophilic or psychrotolerant High pressure - so peizophilic or piezotolerant Unsaturated fatty acids in membranes (help at low temp & high pressure)
53
What is notable about hydrothermal vents?
High levels of inorganic chemicals, dissolved gas and warmth = chemolithotrophic bacteria Dominated by proteobacteria Some thermophiles where it gets really hot
54
What are some nutrient cycles microbes play a role in?
- carbon - nitrogen - Sulfur - iron - manganese - phosphorus - calcium - silica
55
Where is most of the earth’s carbon?
In earth crust, forest, crops, grassland
56
What is the most important source of CO2 in the atmosphere?
Microbial decomposition of dead matter
57
What is the carbon cycle?
Autotrophic phototrophs remove CO2 from the air It gets returned through biological processes ie microbial decomposition & aquatic microbes
58
What is the nitrogen cycle and why is it important?
Abundant N2 but only some organisms can access it in this form: nitrogen fixers. Nitrification - ammonia to nitrate Denitrification - nitrate as e acceptor in anaerobic respiration Ammonification/DNRA - ammonia released Annamox - ammonia to N2
59
What is an example of how carbon and nitrogen cycles interact?
CO2 fixation controlled by photosynthetic organisms with N the limiting factor (depends on N cycle)
60
What is the Sulfur cycle?
Microbes cycle Sulfur through different forms: elemental, sulphides & sulphate

MICR220 (3 decks)

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