L2 Microbial diversity intro Flashcards
What evidence is used to suggest bacteria diverged from a common ancestor of eukaryotes and archaea
RNA comparisons
Did bacteria diverge from eukaryotes before or after Archaea
Where is the evidence for this
Before
Cell membrane. DNA, RNA and protein roles
How can you use phylogenetics in defining bacteria and archaea
Relatedness of housekeeping genes
How could you use the ecological niche to define bacteria and archaea
Related organisms are expected to occupy the same niche and share characteristics
3 other ways of defining batceria and archaea
DNA hybridisation
SSU rRNA
Average nucleotide identity (ANI)
Why does horizontal gene transfer make it hard to define a species
Species are mostly defined by genetics
Bacteria can use horizontal gene transfer between species which are unrelated
This blurs the line between one species and the other if they share a significant proportion of their genome
Give an example of bacteria ‘picking up’ genes from archaea
Bacteria picks up halophillic and thermophillic genes from archaea co-habitating extreme environments
Is transfer faster or slower in closely related taxa
Faster
Is gene transfer faster or slower in pathogenic species
Faster
Give an example of a gene which only transfers vertically
RNA polymerase
Ribosomal RNA
What is the main route of change and adaptation in bacterua
Mutation
What is a downfall in using metagenomics to help measure bacteriak diversity
It is dependent on comparisons form known species
Not useful in highly divergent microbes or those that have acquired large portions of their DNA from elsewhere
How much of the genome of E.coli is made up of horizontal gene transfer
18%
What does pan-genome describe
Where a species is a community of differing individuals (having undergone mutation or horizontal gene transfer) as opposed to a clearly defined entity
What are the 2 types of genes
Informational (core)
Optional (accessory)
Give an example of informational genes and operational genes
Informational - rRNA, elongation factors
Operational - virulence factors, N fixing
Which gene type functions independendlty from other processes and which interacts with other cell components
Interact = informational
Indeoendent = operational
Which of informational and operational genes are likely to undergo vertical and horizontal transfer
Informational = vertical transmission
Operational = horizontal
When did deep branching thermophiles diverge
What environments are they associated with
What energy sources can they use
Diverged early. Earliest to diverge from bacterial lineage
High temperature environments - horizontal gene transfer with archaea
Hydrogen, sulfur, light - diverse
Where are chloroplasts likely to have evolved from
Cyanobacteria
What do cyanobacteria cells contain
Chlorophyll a + b, accessory pigments, thylakoids, carboxysomes, gas vesicles
What is the responsibility of gas vesicles in cyanobacteria
Maintain position in water column
What are the two ways thylakoids can be distributed in cyanobacteria and what do each of these mean
Notsoc = distributed throughout cell
Prochlorococcus = in concentric layers around cel
What forms can cyanobacteria take on
Single cells, long chains, colonies etc.
What kind of environments are gram positive bacteria found in
Harsh
What are 3 types of gram positive bacteria
Firmicutes
Actinobacteria
Tenericutes
Give an example of firmicutes
Bacillus
Ckostridium
Streptococcus
What specialised structure to firmicutes produce
Endospores
Where are actinomycetes likely to be found
Soil
What are the multiple peptidoglycan layers of gram positive bacteria joined by
Teichoid acids = chains of phosphodiester linked glycerol or ribitol with sugar or amino acid linked middle OH groups
What often surrounds gram positive bacteria
Polysaccharide capsule
What is the S-layer in gram positive bacteria
Crystalline protein or glycoprotein layer with large pores (uncertain function)
Are proteobacteria gram positive or negative
Gram negative
What makes proteobacteria gram negative
They only have a ingle peptidoglycan layer
What is the outer membrane of proteobacteria made of
Complex lipopolysaccharides
Give an example of proteobacteria
E. Coli
Salmonella
Pseudomonas
What is the periplasmic space of proteobacteria responsible for
Transporting specidic and protein folding proteins
Give an example of deep branching gram negative bacteria
Bacteriodetes
Where are bacteriodetes found
How do they gain energy
Gut
Obligate anaerobes
Ferment complex carbohydrates
What is chlorosis
Anaerobic photosynthesis using sulphides or hydrogen
Where is the cell membrane and cytoplasm of spirochetes
Contained in outer membrane = sheath
Where do spirochetes have flagella and what is their purpose
At each end to aid movement towards favourable conditions
Where are spirochetes found
Free living in awuatic and terrestrial environments
Give an example of pathogenic spirochetes
Syphilis
Lymes disease
Leptospirosis
What microbe carries out corkscrew movement and what is it useful for
Spirochetes
Useful for moving through viscous fluids such as mucus
What is missing in the cell walls of Chlamydiae, Planctomycetes and Verrucomicrobia
Peptidoglycan
What are chlamydiae
How do they transmit
Intracellular parasites
Create spore like elemental bodies which infect surrounding cells
Where to plactomycetes live
What structure do they produce
What is special about the nuceloid membrane
Free living, aquatic
Budding stalks
Extra double membrane around nuceloid similar to eukaryotic nucelar enveolpe
What is the life style of verrucomicrobia
What structures do they produce
Free licing
Wart-like structures
What dictates microbe cell shape
Cytoskeleton in cytoplasm, not peptidoglycan cell wall
What is the general structure of gram positive bacteria
Plasma membrane, periplasmic space, a layer of peptidoglycan (s-layer)
What is the general structure of gram negative bacteria
Plasma membrane, periplasmic space, peptidoglycan layer, periplasmic space, lipopolysaccharide outer membrane
How is the DNA nucleoid organised
Where is it attached
What is the role of DNA binding proteins
A circular chromosome looped in domains and attached to the membrane
Each domain is supercoiled and compacted by DNA binding proteins
How are related genes grouped
Into operons
When do transcription and translation occur (in respect of each other)
Simultaneously
What is a polysome
What does it enable
A single mRNA transcripy bound by several ribosomes
Lots of protein quickly made from single mRNA strand
How is bacterial cells being high in nucleic acids damaging to humans
Digested nucleotides form uric acid = toxic
What is the protein filament of the flagella
Flagellum monomers
What drives flagella movement
Proton transport and ATP synthase motor
