Gilmour (Autumn) Flashcards
What are the 3 high level divisions of eukarya?
- fungi and animals
- 1º endosymbiotic algae and plants
- protists
Why are euk genomes harder to seq?
- much larger
- lots of non coding DNA
What are the characteristics of opisthokonta?
= animals, true fungi, microsporidia, choanoflagellates
- name from backward pointing flagellum in spermatozoa of animals and zoospores of fungi
- many fungi prod non motile reproductive cells
What are choanoflagellates similar to and what does this suggest?
- choanocytes inside sponges
- “missing link” between multicellular animals and microbial euks
Why were microsporidia moved classification groups?
- protists to opisthokonta
- due to highly conserved peptide seq only found in fungi and animals
What has modern genetic analysis reclassified?
- several groups of fungi as protists
- eg. slime and water moulds
What are the characteristics of 1º endosymbiotic algae? (how were they formed)
- early euk cells that had already acquired mito
- used cyanobacterial cells as feedstocks
- v rare event as cyanobacterial cell not digested and became chloro
- indicated by double membrane around chloro, correspond to 2 membranes of bacteria, phagosomal membrane lost
What are the subdivisions of 1º endosymbiotic algae?
viridiplantae:
- land plants
- chlorophyta (green algae)
- rhodophyta (red algae)
- other algae
What are the characteristics of chlorophyta (green algae)?
- best studied eg is Chlamydomonas reinhardtii
- unicellular
- 2 anterior flagella that move cell forward by breast stroke action
- cell ultrastructure typical of algal cells –> made of cellulose and glycoproteins, pyrenoid concentrates CO2 for fixation and is surrounded by starch bodies for energy storage
- no. of newly discovered v small picoeuks (0.5-3μm) are green algae
What are the characteristics of rhodophyta (red algae)?
- many multicellular
- some filamentous and unicellular
- often found assoc w/ seaweeds, as source of several important gelling agents
- coloured red by photopigment phycoerythrin
What are classified as part of the protists?
- mixture of groups formerly divided into algae and protozoa
- major reclassifications
- inc alveolata, heterokonta, euglenozoa, metamonada, rhizaria, amoebozoa
What are the traits of 2º endosymbiotic algae separating them from 1º?
- more than 2 membranes around chloro
- mixotrophy or heterotrophy widespread and many organic compounds used
- 1º can only catabolise simple substrates
What are the characteristics of diatoms?
- responsible for 20% ps on Earth
- frustules (silica cell walls) prod diatomaceous earth, like petri dish and overlap
- normal asexual cell division leads to decrease in cell size, must be reversed in sexual reproduction
- 2 major types –> centric w/ radial symmetry and pennate w/ bilateral symmetry
What are the characteristics of phaeophyceae (brown algae)?
- some v large, up to 70m and form kelp forests
- others found on seashore, eg. Fucus
- have vacuoles of oily liquid (leucosin) used for energy storage
What are the characteristics of haptocytes?
- 1 group are coccolithophores, eg. Emiliana huxleyi
- pro exoskeleton of coccoliths, protects from predators
- E. huxleyi forms blooms over 1000s km ocean and important C sink when cells die and fall to ocean floor
What are the characteristics of dinoflagellates?
- SEA but grouped in alveolates due to alveoli presence
- swim w/ spinning motion, transverse and longitudinal flagella
- several species toxic, eg. Gonyaulax and can form red tides in coastal waters
What are the characteristics of alveolates?
- grouped based on flattened vacuole (alveoli) beneath outer membrane
- include ciliates
- contain 2 nuclei, diploid micronucleus gen macronucleus w/ many copies of DNA for gene expression, only micronucleus takes part in conjugation
What are the characteristics of apicomplexans?
- type of alveolates
- formerly sporozoa
- parasites w/ unique organelle, apicoplast, from endosymbiotic chloro
- no ps, essential for FA metabolism
- have apical complex that facilitates entry to host
What are the characteristics of amoebas and slime moulds?
- move using pseudopodia, which flow using gel-sol transition based on actin polymerisation
- most harmless, but Entamoeba histolytica can cause dysentery
- cAMP acts as aggregation molecule
- slime moulds important model system for multicellular organisms
- Dictyostelium is cellular slime mould, individual cells remain cellular
- others may be plasmodial, giant multinucleate structure
What is the difference between slime moulds and amoeba?
- slime moulds are amoeba that aggregate in 1000s into complex fruiting body
What are the characteristics of euglenozoa?
- include euglena (SEA) but lose flagella completely and grow heterotrophically
- some v acid tolerant and isolated from acid tar lagoon
- also contain group of obligate parasites, trypanosomes, prod major diseases, eg. African sleeping sickness
What are acid tar lagoons?
- liquid oil refinery waste in excavated clay pit
- pH = 2.6
- up to 9m deep
- worldwide problem
What is the earliest form of life on Earth still existing today, and how old are they?
- stromatolites (bacterial communities)
- fossils dated at 3.4 bil years old
What is the structure of stromatolites?
- layers of MOs
- outermost photosynthetic and inner anaerobic, supporting sulphate red bacteria
What are the requirements for life?
- essential elements = C, H, N, O, Mg, Ca, Na, K, Fe, all available on early Earth, but no free O2 in atmosphere
- temp = between boiling and freezing points of water
- source of energy = red minerals, sunlight
What is the evidence of life?
- stromatolites
- isotope ratios –> limestone depleted of 13CO2
- microfossils
- key event in planets history was evo of 1st photosynthetic cyanobacteria that split water to form O2
What is the evidence for O2 in biosphere?
- Fe2+ soluble, but Fe3+ insoluble and forms precipitates of Fe2O3
- banded Fe formations suggests periods of alt rich and anoxic conditions
What do all models for the origin of life depend on?
- formation of enclosed space = proto-cell
How are proto-cells formed?
- FAs amphipathic so spontaneously form micelle w/ hydrophobic parts to inside
Why was RNA proposed as 1st macromolecule?
- simplicity –> only 4 nucleotides, compared w/ 20 diff AAs in proteins
- req less energy than DNA to form and degrade
- unique U base formed early in biochem pathways
- used as genome of some viruses
What was a key breakthrough for the RNA world origin of life theory?
- discovery that RNA molecules can act like enzymes
- have catalytic properties
- called ribozymes
What roles of ribozymes have been discovered?
- 1st discovered catalysed simple reactions (cleave themselves or specific RNA molecules)
- synthesise complementary RNA strands –> model for early RNA rep
- most complex found in ribosome where protein synthesis takes place
What evidence does peptide bond formation provide for the RNA world theory for the origin of life?
- catalysed by peptidyl transferase activity found in rRNA, not in ribosomal proteins
How does the age of ribosomes provide evidence for the RNA world theory for the origin of life?
- v old part of cell machinery
- key ribosome activity may reflect ancient ubiquitous process
How did proteins replace ribozymes in cells in the RNA world theory for the origin of life?
- natural selection lead to them replacing catalytic function of ribozymes for most reactions
- as much greater range of possibilities
Why did DNA become genetic material in the RNA world theory for the origin of life?
- greater stability
What do we need macromolecules capable of doing for life?
- storing info, eg. proteins
What is a key feature of living cells?
- rep (copying of info from 1 cell to daughter to allow daughter cell to carry out functions of mother cell)
What is the problem w/ prebiotic soup/RNA world theories?
- no obvious source of energy to drive RNA polymerisation
- UV light or lightning suggested, but more stable cont energy source req
How do cells gain energy?
- bacteria/archaea use H+ grad across cell membrane
- euks use H+ grad across mito/chloro
- gen of pmf fundamental for life
What vent were 1st discovered at the bottom deep ocean, and could they be origin of life?
- volcanic origin, called “black smokers”
- superheated water (350ºC) and pH 1-2, percolates up through rock and emerges through cracks in ocean floor
- gen H+ grad between hydrothermal fluid w/in vent and seawater (pH6)
- temp too high and too unstable to be origin of life
What was the 2nd type of vent discovered?
- not volcanic, but prod thermodynamically
- 150-200ºC and pH 9-11 in mid Atlantic
- porous walls allow natural H+ grad to set up between fluid and seawater
- as fluids move past each other, H+ grad maintained
- suggested ATPase evolved in these alkaline vents and gradually cellular structure dev that allowed 1st organisms to escape from vents
- puts chemiosmosis as key process
What element is all life based on?
- carbon
How do autotrophs acquire C?
- fix CO2 and assemble into organic molecules
What do all organisms req to acquire C?
- energy source
How do heterotrophs acquire C?
- use preformed organic molecules
How do phototrophs obtain energy?
- from chem reactions triggered by light
How do chemotrophs obtain energy?
- from ox-red reactions
How do organotrophs obtain energy?
- use organic molecules as e- source
How do lithotrophs obtain energy?
- use inorganic molecules as e- source
What is photoautotrophy?
- harnessing of photo excited e-s to power cell growth
What are the 3 major types of photoautotrophy, and in which organisms are they found?
- bacteriorhodopsin
- use of PSI and PSII (oxygenic ps) –> cyanobacteria, algae, plants
- use of PSI or PSII (anoxygenic ps) –> phototrophic bacteria
How is bacteriorhodopsin (BR) used as a form of photoautotrophy?
- simplest photosynthetic system
- single protein, light driven H+ pump
- found in halophilic archaea
- contains 7α helices that span membrane in alt directions, surround molecule of retinal, linked to Lys residue
- photon absorbed by retinal, shifts config from trans to cis
- cycle of excitation and relaxation back to trans form, couple to pumping of 1 proton from cyto across membrane
- proton grad gen drives ATP synthesis by typical F1F0 ATP synthase
- BR absorbs light in green part of visible spectrum, reflects blue and red, appears purple
- ATP prod via BR supplements is main organoheterotrophic mode of growth of halobacteria (type of photoheterotrophy)
What is a homologue of bacteriorhodopsin and where is it found?
- proteorhodopsin
- in marine proteobacteria
How do Halobacterium salinarum max their light absorption?
- pack entire cell membrane w/ BR
- protein forms trimers that pack in hexagonal arrays, forming “purple membrane”
How is use of PSI and PSII used as a form of photoautotrophy?
- energy derived from photo-excitation of light absorbing chlorophyll
- photoexcitation leads to photolysis of water and e-s transferred to ETS
- O evolved as by product of water photolysis
- light absorbed by antenna chlorophyll molecules and channelled to reaction centres of PSII and PSI
- both PS work together to prod H+ grad and NADPH
- H+ pot drives synthesis of ATP through F1F0 synthase
How is use of PSI or PSII used as a form of photoautotrophy?
- use special type of chlorophyll = bacteriochlorophyll, absorbs more strongly in far red part of spectrum due to change in structure
- less energy in far red/infrared, so can’t split water = anaerobic
- IR radiation penetrates further down into water, where anaerobic conditions more likely to be found
How is PSI used alone as a form of photoautotrophy?
- found in chlorobia, “green sulphur” bacteria
- use for red light to separate e-s from H2S or organic e- donor
- e-s ultimately transferred to NAD+/NADP+ to prod NADH/NADPH
- gen net H+ grad to drive ATP synthesis
How is PSII used alone as a form of photoautotrophy?
- found in alphaproteobacteria, “purple sulphur” bacteria
- use low energy IR light and separate e- from bacteriochlorophyll
- e-s then transferred to ETS and e- returned to bacteriochlorophyll, and ATP gen by cyclic photophosphorylation
- provides no direct way to make NADPH for reductive biosynthesis
- must use ATP to drive reverse e- transport to prod NADPH
What is lithotrophy?
- acquisition of energy by ox of inorganic e- donors
How does lithotrophy result in energy acquisition?
- red inorganic compounds can serve as e- donors to ETS w/ terminal e- acceptor thats strong oxidant
- strong oxidant req as most inorganic substrates relatively poor e- donors, as shown by e- tower concept
What is hydrogenotrophy and how is it used as a type of lithotrophy?
- use of molecular hydrogen (H2) as e- donor
- H2 has sufficient red pot to donate e- to nearly all biological e- acceptors
- inc chlorinated organic molecules, via dehaloresp, has pot for aquifer bioremediation
- dehaloresp form of anaerobic resp
What is methanogenesis and how is it used as a type of lithotrophy?
- red of CO2 (and other single C compounds) to methane
- only performed by methanogens (archaea)
- simplest form involves H red of CO2
- provides niches for methanotrophs (= proks that oxidise methane w/ a TEA)
How does anaerobic resp result in energy acquisition?
- overlap between lithotrophy and aerobic resp
- using compound other than O2 as TEA and alt e- donors
- bacteria and archaea can use wide variety e- acceptors when O2 absent
- in any given env, strongest e- donor available is coupled w/ strongest e- acceptor available
- other pot reductases repressed
- any species can carry out 1/2 transformations in series of reductants
- as each successive TEA used up, red form appears, next best e- acceptor used, generally by diff MO species
What does the ETS consist of (aerobic resp)?
- e-s from organic substrate, donated to oxidoreductase
- e-s transferred to quinone pool
- quinol e-s transferred to terminal oxidase –> during e- transport up to 8H+ pumped across membrane, gen pmf
What does pmf drive? (aerobic resp)
- chemiosmosis
- flagella rotation
- nutrient uptake
- efflux of toxic drugs
What happens during the Calvin Cycle?
- rubisco has low affinity for CO2
- efficiency decreased by photoresp (= competing reaction w/ O2, prod 2-phosphoglycerate, not 3
- important to concentrate CO2 at site of rubisco activity, problem as CO2 easily diffuses through membrane
- cells use C concentrating mechanism, converting CO2 to HCO3 using carbonic anhydrase, as HCO3 can be retained w/ cell membranes
- rubisco often in carboxysome and CA converts HCO3 to CO2 w/in it
Which organisms perform the Calvin Cycle?
- oxygenic phototrophic bacteria
- chloro of algae and plants
- anaerobic purple bacteria
- lithotrophic bacteria
What happens during the Reverse TCA Cycle
- most reactions reversible, allowing assimilation of small amount of CO2
- all organisms can fix small amounts of CO2, regen TCA intermediates
- regen steps called anaplerobic reactions
- in some anaerobic bacteria and archaea, entire TCA cycle in reverse, allows red of CO2 to regen acetyl CoA and build sugars
- reverse uses 4-5 ATPs to fix 4CO2 and gen 1 oxalacetate
- red performed by NADPH/NADH and red ferredoxin (FDH2)
How is energy acquired through nitrogen fixation?
- N2 fixed into NH4+ by some species bacteria and archaea
- aquatic cyanobacteria dev special cells called heterocysts to fix NO2
- ps turned off to maintain anaerobic conditions
- v energy intensive process
- mechanism largely conserved across species
- ~28 ATPs consumed per N2 fixed, each 2e- req 3 ATP equivalents
- catalysed by nitrogenase
What are the 4 red cycles req for nitrogen fixation?
- Fe protein acquires 2e- from e- transport protein, eg. ferredoxin, and then transfers them to FeMo centre
- FeMo centre binds 2H+, red to H2 gas
- N2 can now bind to active site by displacing H2
- successive pairs of H+ and e- reduce: N2 –> HN=NH –> H2N-NH2 –> 2NH3
What is the general equation for nitrogen fixation?
- N2 + 8H+ + 8e- +16ATP –> 2NH3 + H2 + 16ADP + 16PI
