L2 Microbial diversity intro Flashcards by Ella Elston

What evidence is used to suggest bacteria diverged from a common ancestor of eukaryotes and archaea

RNA comparisons

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Did bacteria diverge from eukaryotes before or after Archaea
Where is the evidence for this

Before
Cell membrane. DNA, RNA and protein roles

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How can you use phylogenetics in defining bacteria and archaea

Relatedness of housekeeping genes

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How could you use the ecological niche to define bacteria and archaea

Related organisms are expected to occupy the same niche and share characteristics

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3 other ways of defining batceria and archaea

DNA hybridisation
SSU rRNA
Average nucleotide identity (ANI)

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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

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Give an example of bacteria ‘picking up’ genes from archaea

Bacteria picks up halophillic and thermophillic genes from archaea co-habitating extreme environments

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Is transfer faster or slower in closely related taxa

Faster

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Is gene transfer faster or slower in pathogenic species

Faster

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Give an example of a gene which only transfers vertically

RNA polymerase
Ribosomal RNA

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What is the main route of change and adaptation in bacterua

Mutation

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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

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How much of the genome of E.coli is made up of horizontal gene transfer

18%

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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

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What are the 2 types of genes

Informational (core)
Optional (accessory)

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Give an example of informational genes and operational genes

Informational - rRNA, elongation factors
Operational - virulence factors, N fixing

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Which gene type functions independendlty from other processes and which interacts with other cell components

Interact = informational
Indeoendent = operational

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Which of informational and operational genes are likely to undergo vertical and horizontal transfer

Informational = vertical transmission
Operational = horizontal

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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

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Where are chloroplasts likely to have evolved from

Cyanobacteria

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What do cyanobacteria cells contain

Chlorophyll a + b, accessory pigments, thylakoids, carboxysomes, gas vesicles

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What is the responsibility of gas vesicles in cyanobacteria

Maintain position in water column

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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

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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