Gilmour (Autumn) Flashcards
1
Q
What are the 3 high level divisions of eukarya?
A
- fungi and animals
- 1º endosymbiotic algae and plants
- protists
2
Q
Why are euk genomes harder to seq?
A
- much larger
- lots of non coding DNA
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
4
Q
What are choanoflagellates similar to and what does this suggest?
A
- choanocytes inside sponges
- “missing link” between multicellular animals and microbial euks
5
Q
Why were microsporidia moved classification groups?
A
- protists to opisthokonta
- due to highly conserved peptide seq only found in fungi and animals
6
Q
What has modern genetic analysis reclassified?
A
- several groups of fungi as protists
- eg. slime and water moulds
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
8
Q
What are the subdivisions of 1º endosymbiotic algae?
A
viridiplantae:
- land plants
- chlorophyta (green algae)
- rhodophyta (red algae)
- other algae
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
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
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
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
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
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
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
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
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
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
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
20
Q
What is the difference between slime moulds and amoeba?
A
- slime moulds are amoeba that aggregate in 1000s into complex fruiting body
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
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
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
24
Q
What is the structure of stromatolites?
A
- layers of MOs
- outermost photosynthetic and inner anaerobic, supporting sulphate red bacteria
25
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
26
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
27
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
28
What do all models for the origin of life depend on?
- formation of enclosed space = proto-cell
29
How are proto-cells formed?
- FAs amphipathic so spontaneously form micelle w/ hydrophobic parts to inside
30
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
31
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
32
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
33
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
34
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
35
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
36
Why did DNA become genetic material in the RNA world theory for the origin of life?
- greater stability
37
What do we need macromolecules capable of doing for life?
- storing info, eg. proteins
38
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)
39
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
40
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
41
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
42
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
43
What element is all life based on?
- carbon
44
How do autotrophs acquire C?
- fix CO2 and assemble into organic molecules
45
What do all organisms req to acquire C?
- energy source
46
How do heterotrophs acquire C?
- use preformed organic molecules
47
How do phototrophs obtain energy?
- from chem reactions triggered by light
48
How do chemotrophs obtain energy?
- from ox-red reactions
49
How do organotrophs obtain energy?
- use organic molecules as e- source
50
How do lithotrophs obtain energy?
- use inorganic molecules as e- source
51
What is photoautotrophy?
- harnessing of photo excited e-s to power cell growth
52
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
53
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)
54
What is a homologue of bacteriorhodopsin and where is it found?
- proteorhodopsin
| - in marine proteobacteria
55
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"
56
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
57
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
58
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
59
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
60
What is lithotrophy?
- acquisition of energy by ox of inorganic e- donors
61
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
62
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
63
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)
64
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
65
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
66
What does pmf drive? (aerobic resp)
- chemiosmosis
- flagella rotation
- nutrient uptake
- efflux of toxic drugs
67
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
68
Which organisms perform the Calvin Cycle?
- oxygenic phototrophic bacteria
- chloro of algae and plants
- anaerobic purple bacteria
- lithotrophic bacteria
69
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)
70
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
71
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
72
What is the general equation for nitrogen fixation?
- N2 + 8H+ + 8e- +16ATP --> 2NH3 + H2 + 16ADP + 16PI
