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MBB163 > Gilmour (Autumn) > Flashcards

Gilmour (Autumn) Flashcards

1
Q

What are the 3 high level divisions of eukarya?

A
  • fungi and animals
  • 1º endosymbiotic algae and plants
  • protists
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2
Q

Why are euk genomes harder to seq?

A
  • much larger

- lots of non coding DNA

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3
Q

What are the characteristics of opisthokonta?

A

= 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
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4
Q

What are choanoflagellates similar to and what does this suggest?

A
  • choanocytes inside sponges

- “missing link” between multicellular animals and microbial euks

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5
Q

Why were microsporidia moved classification groups?

A
  • protists to opisthokonta

- due to highly conserved peptide seq only found in fungi and animals

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6
Q

What has modern genetic analysis reclassified?

A
  • several groups of fungi as protists

- eg. slime and water moulds

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7
Q

What are the characteristics of 1º endosymbiotic algae? (how were they formed)

A
  • 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
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8
Q

What are the subdivisions of 1º endosymbiotic algae?

A

viridiplantae:

  • land plants
  • chlorophyta (green algae)
  • rhodophyta (red algae)
  • other algae
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9
Q

What are the characteristics of chlorophyta (green algae)?

A
  • 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
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10
Q

What are the characteristics of rhodophyta (red algae)?

A
  • many multicellular
  • some filamentous and unicellular
  • often found assoc w/ seaweeds, as source of several important gelling agents
  • coloured red by photopigment phycoerythrin
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11
Q

What are classified as part of the protists?

A
  • mixture of groups formerly divided into algae and protozoa
  • major reclassifications
  • inc alveolata, heterokonta, euglenozoa, metamonada, rhizaria, amoebozoa
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12
Q

What are the traits of 2º endosymbiotic algae separating them from 1º?

A
  • more than 2 membranes around chloro
  • mixotrophy or heterotrophy widespread and many organic compounds used
  • 1º can only catabolise simple substrates
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13
Q

What are the characteristics of diatoms?

A
  • 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
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14
Q

What are the characteristics of phaeophyceae (brown algae)?

A
  • 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
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15
Q

What are the characteristics of haptocytes?

A
  • 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
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16
Q

What are the characteristics of dinoflagellates?

A
  • 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
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17
Q

What are the characteristics of alveolates?

A
  • 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
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18
Q

What are the characteristics of apicomplexans?

A
  • 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
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19
Q

What are the characteristics of amoebas and slime moulds?

A
  • 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
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20
Q

What is the difference between slime moulds and amoeba?

A
  • slime moulds are amoeba that aggregate in 1000s into complex fruiting body
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21
Q

What are the characteristics of euglenozoa?

A
  • 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
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22
Q

What are acid tar lagoons?

A
  • liquid oil refinery waste in excavated clay pit
  • pH = 2.6
  • up to 9m deep
  • worldwide problem
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23
Q

What is the earliest form of life on Earth still existing today, and how old are they?

A
  • stromatolites (bacterial communities)

- fossils dated at 3.4 bil years old

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24
Q

What is the structure of stromatolites?

A
  • layers of MOs

- outermost photosynthetic and inner anaerobic, supporting sulphate red bacteria

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25
Q

What are the requirements for life?

A
  • 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
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26
Q

What is the evidence of life?

A
  • 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
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27
Q

What is the evidence for O2 in biosphere?

A
  • Fe2+ soluble, but Fe3+ insoluble and forms precipitates of Fe2O3
  • banded Fe formations suggests periods of alt rich and anoxic conditions
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28
Q

What do all models for the origin of life depend on?

A
  • formation of enclosed space = proto-cell
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29
Q

How are proto-cells formed?

A
  • FAs amphipathic so spontaneously form micelle w/ hydrophobic parts to inside
30
Q

Why was RNA proposed as 1st macromolecule?

A
  • 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
31
Q

What was a key breakthrough for the RNA world origin of life theory?

A
  • discovery that RNA molecules can act like enzymes
  • have catalytic properties
  • called ribozymes
32
Q

What roles of ribozymes have been discovered?

A
  • 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
33
Q

What evidence does peptide bond formation provide for the RNA world theory for the origin of life?

A
  • catalysed by peptidyl transferase activity found in rRNA, not in ribosomal proteins
34
Q

How does the age of ribosomes provide evidence for the RNA world theory for the origin of life?

A
  • v old part of cell machinery

- key ribosome activity may reflect ancient ubiquitous process

35
Q

How did proteins replace ribozymes in cells in the RNA world theory for the origin of life?

A
  • natural selection lead to them replacing catalytic function of ribozymes for most reactions
  • as much greater range of possibilities
36
Q

Why did DNA become genetic material in the RNA world theory for the origin of life?

A
  • greater stability
37
Q

What do we need macromolecules capable of doing for life?

A
  • storing info, eg. proteins
38
Q

What is a key feature of living cells?

A
  • rep (copying of info from 1 cell to daughter to allow daughter cell to carry out functions of mother cell)
39
Q

What is the problem w/ prebiotic soup/RNA world theories?

A
  • no obvious source of energy to drive RNA polymerisation

- UV light or lightning suggested, but more stable cont energy source req

40
Q

How do cells gain energy?

A
  • bacteria/archaea use H+ grad across cell membrane
  • euks use H+ grad across mito/chloro
  • gen of pmf fundamental for life
41
Q

What vent were 1st discovered at the bottom deep ocean, and could they be origin of life?

A
  • 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
42
Q

What was the 2nd type of vent discovered?

A
  • 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
43
Q

What element is all life based on?

A
  • carbon
44
Q

How do autotrophs acquire C?

A
  • fix CO2 and assemble into organic molecules
45
Q

What do all organisms req to acquire C?

A
  • energy source
46
Q

How do heterotrophs acquire C?

A
  • use preformed organic molecules
47
Q

How do phototrophs obtain energy?

A
  • from chem reactions triggered by light
48
Q

How do chemotrophs obtain energy?

A
  • from ox-red reactions
49
Q

How do organotrophs obtain energy?

A
  • use organic molecules as e- source
50
Q

How do lithotrophs obtain energy?

A
  • use inorganic molecules as e- source
51
Q

What is photoautotrophy?

A
  • harnessing of photo excited e-s to power cell growth
52
Q

What are the 3 major types of photoautotrophy, and in which organisms are they found?

A
  • bacteriorhodopsin
  • use of PSI and PSII (oxygenic ps) –> cyanobacteria, algae, plants
  • use of PSI or PSII (anoxygenic ps) –> phototrophic bacteria
53
Q

How is bacteriorhodopsin (BR) used as a form of photoautotrophy?

A
  • 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)
54
Q

What is a homologue of bacteriorhodopsin and where is it found?

A
  • proteorhodopsin

- in marine proteobacteria

55
Q

How do Halobacterium salinarum max their light absorption?

A
  • pack entire cell membrane w/ BR

- protein forms trimers that pack in hexagonal arrays, forming “purple membrane”

56
Q

How is use of PSI and PSII used as a form of photoautotrophy?

A
  • 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
57
Q

How is use of PSI or PSII used as a form of photoautotrophy?

A
  • 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
58
Q

How is PSI used alone as a form of photoautotrophy?

A
  • 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
59
Q

How is PSII used alone as a form of photoautotrophy?

A
  • 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
60
Q

What is lithotrophy?

A
  • acquisition of energy by ox of inorganic e- donors
61
Q

How does lithotrophy result in energy acquisition?

A
  • 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
62
Q

What is hydrogenotrophy and how is it used as a type of lithotrophy?

A
  • 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
63
Q

What is methanogenesis and how is it used as a type of lithotrophy?

A
  • 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)
64
Q

How does anaerobic resp result in energy acquisition?

A
  • 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
65
Q

What does the ETS consist of (aerobic resp)?

A
  • 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
66
Q

What does pmf drive? (aerobic resp)

A
  • chemiosmosis
  • flagella rotation
  • nutrient uptake
  • efflux of toxic drugs
67
Q

What happens during the Calvin Cycle?

A
  • 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
68
Q

Which organisms perform the Calvin Cycle?

A
  • oxygenic phototrophic bacteria
  • chloro of algae and plants
  • anaerobic purple bacteria
  • lithotrophic bacteria
69
Q

What happens during the Reverse TCA Cycle

A
  • 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)
70
Q

How is energy acquired through nitrogen fixation?

A
  • 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
71
Q

What are the 4 red cycles req for nitrogen fixation?

A
  • 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
72
Q

What is the general equation for nitrogen fixation?

A
  • N2 + 8H+ + 8e- +16ATP –> 2NH3 + H2 + 16ADP + 16PI

MBB163 (7 decks)

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