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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
Biological classification and link to microbial classification
Grouped based on ability to breed- can they breed and can their offspring reproduce itself and survive Invalid for microbes as microbes are asexual
26
Phentic classification and link to microbial classification
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
27
Cladistic classification and link to microbial classification
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
28
What are molecular clocks
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
29
Why is 16S rRNA commonly used as a molecular clock
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
30
Life grouping
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
31
Validation of 16S rRNA by other genes
Shows that other genes (eg RNA pol), aa sequences and enzyme structures are highly conserved across the three domains of life
32
Eocyte hypothesis and its evidence
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
33
Limitations to phylogeny
Horizontal gene transfer- can always trace where DNA has come from Leads to trees not always being so straightforward
34
Three forms of fungi
Decomposers Mutalists Pathogens
35
Decomposing fungi
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
36
Mutualist fungi
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
37
Fungi as pathogens
For pretty much every living species, they have a fungi that can act as a pathogen
38
What is the issue with defining a species
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
What is a prokaryote species
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
How to categorise species in prokaryotes- 4 things
“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
3 things for a definition of prokaryotic species
Phenotype consistency 70% of DNA-DNA binding Over 97% of rRNA gene-sequencing identity
42
History of the defining of prokaryotic species
``` 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
What is DNA-DNA hybridisation (DDH)
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
Pros of DDH
>70% DDH= same species, less than 70 suggests a new species | Good correspondence with phenotypically coherent clusters of strains in Enterobacteriaceae
45
Issues with DDH
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
Relationship between 16S rRNA and DDH
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
Limitations to 16S rRNA
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
What is average nucleotide identity (ANI)
Genomic version of DDH Uses genomics to allow comparison of multiple genomes Uses a 7 bp window to compare the genomes (like BLAST)
49
DDH vs ANI
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
DDH vs ANI vs 16S rRNA
>70% DDH = >95% ANI = >98.5% 16S rRNA | Shows good correlation
51
Another tool used for species level classification
Multilocus Sequence Typing (MLST)
52
What is MLST and MLSA
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
What can MLSA show
Different species can be clearly separated | Ecotypes can be identified- populations which are genetically cohesive and ecologically distinct
54
Pros of MLSA
Higher resolution Uses multiple genes Gives species classification or lower (whereas 16S rRNA only gives genus) Good for recent evolutionary changes
55
Cons of MLSA
Genes must be single copy Must be present in all organisms being analysed Dont know what constitutes a species
56
What is metabolism, catabolism and anabolism
``` Catabolism= breakdown of things to release energy Anabolism= using energy for reactions Metabolism= the balance of these two ```
57
Why are noble gases not nutrients
Hard to breakdown and reuse
58
Why is RNA content of a cell so high
Second highest, has a short lifespan | Needed to replenish and make more things
59
Types of micronutrients and why they are needed
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
What is free energy (G)
Energy released that is available to do work
61
Exergonic reaction
Releases energy eg cell respiration and catabolism
62
Endergonic reaction
Requires energy eg active transport, cell movements, anabolism
63
Two uses for flow of electrons
Tp be stored in bonds and used at a later time | To be used immediately as an energy source
64
Parts of the redox tower
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
Electron carriers
Intermediates | Two classes: prosthetic groups attached to enzymes and coenzymes which are diffusible eg NAD+ and NADP
66
Chemical bonds and energy
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
Different types of organisms based on energy source
Chemoorganotroph- from organic molecules Chemolithotroph- from inorganic molecules Phototroph- from light
68
Different types of organisms based on carbon source
Autotroph- CO2 | Heterotroph- organic molecules
69
Different types of organisms based on electron source
Organotroph- organic molecules | Lithotroph- inorganic molecules
70
What types of molecules can heterotrophs obtain from carbon breakdown
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
What makes a good electron donor
Abundance of H, lack of O2
72
What makes a good electron acceptor
Lack of H, abundance of O2
73
Why do we get less energy from anaerobic respiration
Because microbes use 3 or more electron acceptors to reach the terminal electron acceptor (nitrate, ferric iron, sulfate, carbonate and organic compounds)
74
What are microaerobes
Inbetween aerobe and anaerobe- use a bit of both | Make up most of microbes
75
Three main technological advances in microbiology
Great plate count anomaly Rare biosphere Biological ‘dark matter’
76
What is the great plate count analomy
Breaks into direct microscopy and culturing | Microscopic and culture enumerations differ by orders of magnitude and arent even across all ecosystems
77
Reasons why Microscopic and culture enumerations differ by orders of magnitude and arent even across all ecosystems
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
Biggest limitation with the great plate count analomy
Uncultured microbial world is much greater than the cultured world
79
Enrichment bias from culture dependent approaches
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
Reasons for enrichment bias in culture dependent approaches
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
PCR methods of microbial community analysis
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
What is the rare biosphere and how was it found
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
Genomics definition
Mapping, sequencing, analyzing and comparing genomes
84
What is comparative genomics
Compare the genomes of different species and identify trends/ conservations Allows for predictions of metabolic pathways and transport systems Comparative analysis
85
What are hypothetical proteins
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
What is metagenomics and the metagenome
``` Metagenomics= DNA from whole microbial community extracted and directly sequenced Metagenome= total genetic content of all organisms present in an environment ```
87
Pros of metagenomics
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
Main difference between 16S surveys and metagenomics
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
Transcriptome
Entire complement of RNA produced under a given set of conditions
90
What can be learned from RNA experiments (transcriptome)
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
Proteomics
Genome-wide study of the structure, function and regulation of an organism’s proteins
92
Metabolomics
Complete set of metabolic intermediates and other small molecules produced in an organism Broken into; glycomics, lipidomics, fluxomics
93
Out of the omics, which gives the most information and why
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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