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Question	Answer
How long have microbes been around for?	at least 4 billion years
What is essential to sustain life?	Water SPONCH (not most abundant but most suited under earths conditions)
What can all SPONCH do?	Form stable bonds
What did the Miller-Urey experiment show?	That we could synthesise most essential amino acids and most nucleic bases under a probable stimulation of early earth
What was early earth like?	Anoxic, high temp, high UV and alternative forms of energy, radiation and electric discharge
Molecules most likely to form where?	Aggregates and membrane like interfaces
Explain coacervate growth and division	Coolection of aggregated polymers, grow by addition of new polymers forms a semi permeable membrane when joins to the other end of its polymer When they get too big they divide
What two things formed the origin of life?	Self catalytic RNA enzymes - Ribozymes Spontaneously forming micropheres that replicate by pinching
What was the first cell likely to have been like?	Chemolithotrophic and anaerobic
What is a possible metabolism of the first cell?	H2S + FeS = FeS2 +H2 H2 could have been used to drive an early ATPase
What changed the earths atmosphere	Microbes
How do gradients and niches evolve organisms?	One organism fills a niche and creates a gradient, say an aerobic bacteria, it consumes O2 and creates a gradient of O2 that has many niches that can be filled, drive outcompeted organism to fit these niches
How was gradient and niches used with E.coli to demonstrate evolution?	A single E.coli strain inoculated into glucose limited media and grown in a chemostat. Three clones emerged First wild type used Glucose, Second used Acetate the product of glucose metabolism and third used glycerol product of acetate metabolism
What is biological classification of diversity?	Grouped based on ability to breed
Phenetic	Grouped based on overall similarity with no account of evolutionary history. Liable to error due to convergent evolution
Cladistic	grouping based on evolution from shared ancestors as determined from shared trait liable to make ignore useful descriptive trait by focusing on just on trait.
Molecular clock	A gene whose DNA can be used as a comparative measure of evolutionary divergance Often linked to information, translation and transcription Highly conserved
16srRNA why do we use it	Gene that encodes small subunit of ribosomes found in all living organisms same function in all organisms highly conserved sufficient length
How did mitochondria and chloroplasts become incorporated into eukaryotic cells?	endosymbiosis Once has a mutualistic relationship.
What are bacteria and fungi responsible for in soil?	Most functions Gas exchange, nutrient exchangee, decomposition of organic matter
How many fungal species are described and how many are estimated to exsist	70,000 1.5 million
Decomposer	Converts dead organic matter to fungal biomass, orangic acids and CO2
Absorptive nutrition	Secretion of enzymes and smaller particles absorbed
Mutualist fungi	Give plants nutrients and phosphorus and take carbon from the plant
What are the three types of fungal groups?	decomposers mutualists absorptive
Fungal pathogens	cause death or destruction to plant roots or other organisms
How much bacteria is in a teaspoon of soil?	Between 100 million and a billion bacteria
Photoautotroph	Energy from sunlight Carbon source from inorganic carbon
Chemoheterotroph	Energy from inorganic oxidation organic carbon source
Heterotrophs	Most common group breakdown carbon substrates convert energy in soil organic matter into forms useful for soil organisms
Lithotroph	Use H2S as electron souce
Species	A taxonomic rank A group of organisms capable of interbreeding A strain of organism with separately evolving lineage that forms a single gene pool
What defines a prokaryotic species?	>70% DNA-DNA hyridisation >97% 16s rRNA gene sequence identity
How are pathogens put into species	By disease No evolutionary or ecological significance
DDH	DNA-DNA Hybridisation similarity between complete genomes is measured by the amount of heat required to melt the hydrogen bonds between the base pairs in DNA
DDH limitations	Time consuming carried out by only few labs ill suited for rapid identification Unavailable for unculturable organisms
Modern versions of DDH	Average nucleotide identity
<50% binding value	different species
Downsides of 16s rRNA comparison	Can't discriminate between closely related species DNA can be too well conserved doesn't show recent evolution Relies on single gene
MLST	multi locus sequencing typing genotypic characterisation by using mismatches in alleles Uses a small number (7) of house keeping genes
MLSA	Multi locus sequencing analysis Sequencing of the genes befoe MLST
Pros and Cons MLSA	Pro - high resolution, uses multiple genes, MLSA give species where 16s rRNA only give genus Con- genes must be single copy, genes must be present in all organisms
Ecotype	Populations that are genetically cohesive but ecologically distinct e.g. E.coli evolution experiment
Metabolism	Sum total of alll chemical reactions in the cell
Anabolism	Energy requiring metabolic reactions. Biosynthesis
Catabolism	Energy producing biochemical reactions
Macronutrient	A nutrient needed in large quantities SPONCH
micronutrient	Trace elements usually found in centre of enzymes
Prosthetic groups	side chains attached to enzymes
Coenzymes	diffusible facilitate redox reactions without being consumed
Where is chemical energy stored?	In phosphorylated compounds ATP, Glucose-6- phosphate, phosphenolpyruvate
Where does energy originally come from?	The breakdown of glucose from glycolysis and krebs cycle.
How much energy yields from one glucose molecule?	38ATP
Anaerobic respiration	Use electron receptors other than oxygen
Aerobic respiration	use O2 as electron acceptor
Photophosphorylation	Uses light- mediated ATP synthesis
Chemolithotrophy	Use inorganic chemicals as electron donors H2S, H2, Fe2+, NH3 oxidation of inorganic electron donor Uses electron transport chain
How are amino acids and nucleotides synthesised?	Carbon backbone from intermediate of glycolysis and krebs Addition of ammonia by glutamine dehydrogenase or glutamine synthease Amino group added by transaminase and synthase
Great plate count anomaly	Leap to being able to culture organisms Prior to this used microscope estimated 99% of microbes under microscope were unculturable Not true because plates were selective
The more diverse an environment is the more the microscope and the cultures differ	2 fold in human gut 6 fold in marine 100 fold in soil
What do we know from the great plate count anomaly?	The uncultured world is far greater than the cultured world
Enrichment bias	Nutrient components in media are generally much higher than in nature and as such the organisms that prodominant are actually minor in the environment. Dilution of inoculation to get rid of rapid growing but qualitatively insignificant weed species
PCR methods	Found DNA different from all known lab cultures it was concluded that less than 0.1% of bacteria has been cultured
The rare biosphere	Only 0.1% of bacteria has been cultured The rare biosphere is enormous and highly diverse
Number of genes that have a role that can be clearly identified is...	70% of total ORF
Biological dark matter	Hypothetical proteins. Likely encode nonessential genes
Metagenomic	Entire complement of DNA in a community
Metagenomic	Entire complement of DNA in a community
Transcriptome	Entire complement of RNA produced under a given set of conditions
Proteomics	Genome wide study of structure function and regulation of an organisms proteins
Metabolomics	complete set of metabolic intermediates and other small molecules produced in an organism

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	Created by ruby.white94 over 10 years ago