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MICR222 > Molecules, Origins Of Life And Evolution > Flashcards

Molecules, Origins Of Life And Evolution Flashcards

1
Q

What do we need to know to understand microorganisms

A

Need to undertstand physiology, ecology and how they evolved

Need to know what happened in the past to be able to predict their future

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2
Q

Human and microbe earth inhabitance

A

Humans only been here ~0.02% of the ~4.5 billion years
Microbes for ~88%
For 50% of time they were only living creatures so had heaps of time to evolve on their own

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3
Q

Key events in earth evolution

A

Diversification of aerobic prokaryotes
Oxygen-rich atmosphere= aerobic respiration= extinction of some anaerobes
Origin of photosynthetic bacteria

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4
Q

What assumption does the fact of LUCA lead to

A

All living things have similar characteristics= common architecture

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5
Q

What is the common architecture

A

Biochemistry between the 3 domains
Shared architecture organisation
Common basic mechanisms of biochemistry

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6
Q

Major components of a cell and what they are made from

A

Membranes, nucleic acid, proteins

Made from CHONSP molecules (carbon, hydrogen, oxygen, nitrogen, sulphur, phosphorus

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7
Q

Why are CHONSP molecules so important yet not most abundant on earth

A

Can all form covalent bonds= stability with more than one link possible except in H
All bonds can be broken for degradation= recycling

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8
Q

Main most essential component for life

A

Water

No evidence of life without water

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9
Q

Miller Urey experiment

A

Chemostat
Gave the things and conditions of early life and found that chemistry caused more organic molecules, most essential amino acids and most nucleic acid baases
Shows that if you have these things tighether and provide right conditions, chemistry will lead to the production of more molecules from these

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10
Q

Early earth and what each thing means for chemistry

A

Anoxic= no O2
High temp= heat to encourage certain reactions
High UV= allows diff reactions
Alternative energy forms eg radiant, geothermal, electric discharge= diff reactions

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11
Q

Molecules likely to form in early life had what tendencies

A

Aggregates (makes clumps) and has membrane-like interfaces

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12
Q

Membranes leading to evolution

A

Self assembled= coacervates, micelles and liposomes= semi permeable membrane= proto cell
Creates more environments for different things to happen (as in early life there was only the one environment so evolution would occur slowly)
Creates gradients for movement

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13
Q

Inside the proto cell

A

Coacervates + ribozymes (self catalytic RNA enzymes)= origin of life

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14
Q

Transition to the living state

A

RNA world= allows for reactions to happen to ensure that things happen the same way each time and can continue to happen (see slide 36)

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15
Q

Steps in RNA world hypothesis

A

RNA from inorganic sources
RNA self replicates via ribozymes
RNA catalyses protein synthesis
Membrane formation changes internal chemistry allowing new functionality
RNA codes DNA and protein- DNA becomes master template and proteins catalyse cellular activities

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16
Q

First organism

A

Lived at the bottom of the ocean, possibly in black smokers
Anaerobic and chemolithotrophic using FeS and H2S
Possibly used FeS +H2S-> FeS2 and H2 to use H to drive primative ATPase with S0 as potential e- acceptor

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17
Q

What is panspermia

A

Alternative explanation for life or living compounds
That a meteorite brought first life to earth
No evidence to support this

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18
Q

Why do we want to understand the evolution of microbes

A

Have big repercussions
Have caused the decrease of CO2 in the atmosphere and therefore, the increase in O2 in the atmosphere
However, burning of fossil fuels is causing CO2 levels to increase back to previous levels in ~200 years which has taken billions of years to decrease in the first place

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19
Q

What is diversity derived from

A

Gradients, niches and speciation

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20
Q

Gradients and diversity

A

As microbes grow they produce gradients (pH and chemical) and these create diversity of habitats which support more microbial diversity
Made with a biofilm. This allows for 2 gradients: substrate and O2= aerobic and anaerobic meaning 2 different environments created

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21
Q

An experimental example of evidence of evolution

A

Single E.coli chemostat was inoculated and grown in glucose limited media in a chemostat
3 clones emerged
Shows that can drive evolution in a population with no diversity by adding a sense of competition due to being glucose limited. 3 strains all used a different byproduct of glucose breakdown for their energy source

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22
Q

Bacteria and resistance to antibiotics as an example of evolutionary evidence

A

When the microbes have obtained resistance once (which is slow), it is quicker to become resistant to more harsh amounts of antibiotic in a shorter time period

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23
Q

How is diversity measured in microbial communities

A

Taxonomy
Function
Metabolism

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24
Q

Classifications of microbial diversity

A

Biological
Phenetic
Cladistic (phylogenetic)

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25
Q

Biological classification and link to microbial classification

A

Grouped based on ability to breed- can they breed and can their offspring reproduce itself and survive
Invalid for microbes as microbes are asexual

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26
Q

Phentic classification and link to microbial classification

A

Grouped based on overall physical similarity (analogues) with no account of evolutionary history- measures end product only Convergent evolution can lead to the same phenotypes with no shared recent ancestry= limitation
Not very valid for microbes as they dont have a lot of variability to allow for this

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27
Q

Cladistic classification and link to microbial classification

A

Grouping based on evolution from a shared ancestor (clade) as determined from a shared trait (phylogeny)
Longer organisms have had time apart, more likely they have obtained mutation between them
Closer= more similarity in genome

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28
Q

What are molecular clocks

A

Gene whos DNA sequence can be used as a comparative temporal measure of evolutionary divergence
Number of mutations is proportional to time taken to accumulate mutations= linear relationship
Any gene can be a molecular clock but 16S rRNA gene is most commonly used

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29
Q

Why is 16S rRNA commonly used as a molecular clock

A

Found in all living organisms (universally conserved)
Maintains function amongst all organisms- want it to be under the same selective pressure and do the same thing
Highly conserved with multiple hyper-variable regions (can be able to anchor it and want regions to be mutated faster to notice when species start to diverse)
Sufficient length- longer means more able to make a visualisation and comparisons

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30
Q

Life grouping

A

Into three domains (eubacteria, eukaryotes and archaelbacteria- base of the tree which everything else has derived from)
Instead of into 5 kingdoms as previously thought

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31
Q

Validation of 16S rRNA by other genes

A

Shows that other genes (eg RNA pol), aa sequences and enzyme structures are highly conserved across the three domains of life

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32
Q

Eocyte hypothesis and its evidence

A

Two domain hypothesis
Implies closest relative to eukaryotes is one or all of TACK archaea
TACK archaea and eukaryotes share genes not found in other archaea meaning the ancestor for eukaryotes was probably a member of a TACK archaea
Eukaryotes cluster within archaea and in TACK in phylogeny

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33
Q

Limitations to phylogeny

A

Horizontal gene transfer- can always trace where DNA has come from
Leads to trees not always being so straightforward

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34
Q

Three forms of fungi

A

Decomposers
Mutalists
Pathogens

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35
Q

Decomposing fungi

A

Saprophytic fungi
Convert dead organic material into fungal biomass, CO2 and small molecules eg organic acids
Absorptive nutrition- Obtain energy and nutrients in which digestive enzymes are secreted into a substrate, then smaller assimilated molecules are absorbed through the cell membrane

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36
Q

Mutualist fungi

A

Eg Mycorrhizal fungi- colonise plant roots, form little trees in the roots which enhance root network by helping with nutrient uptake
Can grow inside of or outside of plant

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37
Q

Fungi as pathogens

A

For pretty much every living species, they have a fungi that can act as a pathogen

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38
Q

What is the issue with defining a species

A

There is no true universal definition for a species. Species definitions are specific for prokaryotes, eukaryotes etc so what is applied to a species in microbiology is specific for prokaryotes

39
Q

What is a prokaryote species

A

There isnt a biological/ evolutionary definition
We use phenotypic assignment vs genotype similarity
Currently: “category that circumscribes a preferable genomic coherent group of individual isolates/ strains sharing high degree of similarity in many independent features and comparatively tested under highly standardised conditions”

40
Q

How to categorise species in prokaryotes- 4 things

A

“Genomically coherent group of organisms”= share close ancestor not too long ago
Must have a type strain that is live
ORGI should be within species cut off boundary eg using OrthoANI ~95% similar
If isolated new species by point 3, need to do more follow up experiments and compare with other species to describe it

41
Q

3 things for a definition of prokaryotic species

A

Phenotype consistency
70% of DNA-DNA binding
Over 97% of rRNA gene-sequencing identity

42
Q

History of the defining of prokaryotic species

A 
Historically based on growth characteristics (morphology, gram staining and growth medium) and disease caused
Is arbitrary (no real reason as to why), anthropocentric (based on classic microbiology) or rooted in practical necessity (cant come up with a better system, is imperfect and the best we can do)
43
Q

What is DNA-DNA hybridisation (DDH)

A

Measures degree of genetic similarity between two genomes
Dye goes between the two DNA strands and shows flourescence. This is melted and if one strand melts before the other then dye is released and flourescence is removed. Difference in melting temp= difference in genomes
Allows to see similarities and differences without the ability to read the DNA sequence

44
Q

Pros of DDH

A

> 70% DDH= same species, less than 70 suggests a new species

Good correspondence with phenotypically coherent clusters of strains in Enterobacteriaceae

45
Q

Issues with DDH

A

Unclear how it relates to whole-genome relatedness
Time consuming- grow, pure cultures, extract DNA, need to compare to something else
Carried our properly by few laboratories
Ill-suited for rapid identification
Only suited for pair-wise comparison
Previous classification must be present
Unavailable for non-culturable organisms- only 1-2% are cultivable

46
Q

Relationship between 16S rRNA and DDH

A

No organisms sharing <97% sequence similarity at 16S meet the DDH species criteria of >70%= 16S rRNA is a good tool
Rule only works to confirm differences, not similarities= one way

47
Q

Limitations to 16S rRNA

A

Good up to genus level, cant determine at species level
Cant discriminate between highly related species
Doesnt relate to metabolic capabilities
Relies on the single 16S gene
Can be slow evolving- recent evolutionary events not present and not enough positions to provide fine details

48
Q

What is average nucleotide identity (ANI)

A

Genomic version of DDH
Uses genomics to allow comparison of multiple genomes
Uses a 7 bp window to compare the genomes (like BLAST)

49
Q

DDH vs ANI

A

70% DDH = 95% ANI showing good correlation
Only defines species, therefore also rely on 16S rRNA for things such as genus and family
There is no biological definition or explanation as to why we use 95% ANI and 70% DDH

50
Q

DDH vs ANI vs 16S rRNA

A

> 70% DDH = >95% ANI = >98.5% 16S rRNA

Shows good correlation

51
Q

Another tool used for species level classification

A

Multilocus Sequence Typing (MLST)

52
Q

What is MLST and MLSA

A

MLST- genotypic characterisation of prokaryotes at infraspecific level using allelic mismatches of a small number (~7) of housekeeping genes
MLSA- multilocus sequence analysis- genomic characterisation of diverse group of prokaryotes, including entire genera, using sequences of multiple protein-coding genes

53
Q

What can MLSA show

A

Different species can be clearly separated

Ecotypes can be identified- populations which are genetically cohesive and ecologically distinct

54
Q

Pros of MLSA

A

Higher resolution
Uses multiple genes
Gives species classification or lower (whereas 16S rRNA only gives genus)
Good for recent evolutionary changes

55
Q

Cons of MLSA

A

Genes must be single copy
Must be present in all organisms being analysed
Dont know what constitutes a species

56
Q

What is metabolism, catabolism and anabolism

A 
Catabolism= breakdown of things to release energy
Anabolism= using energy for reactions
Metabolism= the balance of these two
57
Q

Why are noble gases not nutrients

A

Hard to breakdown and reuse

58
Q

Why is RNA content of a cell so high

A

Second highest, has a short lifespan

Needed to replenish and make more things

59
Q

Types of micronutrients and why they are needed

A

Many cofactors or part of catalytic sites of enzymes
Transition metals as they play a role in mediating redox reactions- readily able to change their charge and carry out redox reactions

60
Q

What is free energy (G)

A

Energy released that is available to do work

61
Q

Exergonic reaction

A

Releases energy eg cell respiration and catabolism

62
Q

Endergonic reaction

A

Requires energy eg active transport, cell movements, anabolism

63
Q

Two uses for flow of electrons

A

Tp be stored in bonds and used at a later time

To be used immediately as an energy source

64
Q

Parts of the redox tower

A

Top of the tower= better electron donors (reduced substances)
Bottom of the tower= better electron acceptors (oxidised substances)
Better the space between= more energy released

65
Q

Electron carriers

A

Intermediates

Two classes: prosthetic groups attached to enzymes and coenzymes which are diffusible eg NAD+ and NADP

66
Q

Chemical bonds and energy

A

Chemical energy is stored in bonds
Broken chemical bonds release energy that can be captured in new bonds (ATP)
Bonds can be later broken to release the energy- reduction and oxidation

67
Q

Different types of organisms based on energy source

A

Chemoorganotroph- from organic molecules
Chemolithotroph- from inorganic molecules
Phototroph- from light

68
Q

Different types of organisms based on carbon source

A

Autotroph- CO2

Heterotroph- organic molecules

69
Q

Different types of organisms based on electron source

A

Organotroph- organic molecules

Lithotroph- inorganic molecules

70
Q

What types of molecules can heterotrophs obtain from carbon breakdown

A

Energy- from energy harvesting
Intermediate compounds from the CAC- from carbon harvesting
Cells constantly deciding whether they want to build something from different carbon compounds or have too much energy so need to use carbon to make things or if they want to make energy

71
Q

What makes a good electron donor

A

Abundance of H, lack of O2

72
Q

What makes a good electron acceptor

A

Lack of H, abundance of O2

73
Q

Why do we get less energy from anaerobic respiration

A

Because microbes use 3 or more electron acceptors to reach the terminal electron acceptor (nitrate, ferric iron, sulfate, carbonate and organic compounds)

74
Q

What are microaerobes

A

Inbetween aerobe and anaerobe- use a bit of both

Make up most of microbes

75
Q

Three main technological advances in microbiology

A

Great plate count anomaly
Rare biosphere
Biological ‘dark matter’

76
Q

What is the great plate count analomy

A

Breaks into direct microscopy and culturing

Microscopic and culture enumerations differ by orders of magnitude and arent even across all ecosystems

77
Q

Reasons why Microscopic and culture enumerations differ by orders of magnitude and arent even across all ecosystems

A

Different nutritional requirements- all grow under specific conditions and culturing causes narrower conditions as to those in nature
Cells may be in a non-dividing state
Organisms may rely on other organisms/ cannot grow alone and we do not know what they require to grow

78
Q

Biggest limitation with the great plate count analomy

A

Uncultured microbial world is much greater than the cultured world

79
Q

Enrichment bias from culture dependent approaches

A

Each culture only selects for a few organisms as there is a narrow set of selective pressures
Microorganisms cultured in the lab are frequently only minor components of the microbial ecosystem
Dilution of inoculum is performed to eliminate rapidly growing, quantitatively insignificant weed species

80
Q

Reasons for enrichment bias in culture dependent approaches

A

Nutrients available in the lab cultures are typically much higher than in nature
Narrower set of conditions
Selects organisms that can grow fast and grow alone

81
Q

PCR methods of microbial community analysis

A

Anything requiring a PCR reaction
Need to know primer sequence= induces bias as we need to know this first about the organisms
rRNA sequences differ from those of all known laboratory classes
Molecular methods conclude <0.1% of bacteria have been cultured

82
Q

What is the rare biosphere and how was it found

A

Observation that a large proportion of taxa in microbial communities are uncommon
Missing a lot of whats in the ecosystem
Diversity we currently know/ have is in small abundance
Found through 16S sequencing

83
Q

Genomics definition

A

Mapping, sequencing, analyzing and comparing genomes

84
Q

What is comparative genomics

A

Compare the genomes of different species and identify trends/ conservations
Allows for predictions of metabolic pathways and transport systems
Comparative analysis

85
Q

What are hypothetical proteins

A

Uncharactierised ORFs- proteins that likely exist but whose function is unknown;
Likely encode non-essential genes
In E.coli, many predicted to encode regulatory or redundant proteins
Considered to be biological dark matter

86
Q

What is metagenomics and the metagenome

A 
Metagenomics= DNA from whole microbial community extracted and directly sequenced
Metagenome= total genetic content of all organisms present in an environment
87
Q

Pros of metagenomics

A

Non-biased
Yields picture of gene pool in environment
Can detect genes that are not amplified by current PCR primers
Powerful tool for assessing the phylogenetic and metabolic diversity of an environment

88
Q

Main difference between 16S surveys and metagenomics

A

16S targets single genes using PCR

Metagenomics targets all genes in a sample- whole genomes in a single cell are sequenced without needing to culture

89
Q

Transcriptome

A

Entire complement of RNA produced under a given set of conditions

90
Q

What can be learned from RNA experiments (transcriptome)

A

Expression of specific groups of genes under different conditions
Expression of genes with unknown function, can yield clues to possible roles
Comparison of gene content in closely related organisms
Identification of specific organisms

91
Q

Proteomics

A

Genome-wide study of the structure, function and regulation of an organism’s proteins

92
Q

Metabolomics

A

Complete set of metabolic intermediates and other small molecules produced in an organism
Broken into; glycomics, lipidomics, fluxomics

93
Q

Out of the omics, which gives the most information and why

A

Metabolomics
Because they are present at any given time in a sample. Shows the genes which are transcribed into functional products. Some transcripts are not expressed as a phenotype due to PTM or post-transcriptional modification or just might not be functional

MICR222 (8 decks)

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