Gilmour - Metabolic Diversity of Microbes

Question 1

describe bacteriarhedopsin’s (BR) morphology and energy production system

Answer 1

simplest photosynthetic system
single protein light driven proton pump
found in halophilic archaea
a homologue proteorhodopsin found in marine proteobacteria
energy production system:
- 7 alpha helices span membrane
- surround retinal molecule linked to lysine
- photon absorbed by retinal => trans - cis
- relaxation to trans pumps H+ across mem
- uses F1F0 ATP synthase

Question 2

Which bacterium forms a purple membrane with BR?

Answer 2

Halobacterium salinarium

Question 3

Which wavelengths does BR absorb?

Answer 3

Green, reflects blue and red (appears purple)

Question 4

Which other method of metabolism does BR use to supplement organoheterotrophic mode of growth?

Answer 4

photoheterotrophy

Question 5

Which photosystems does oxygenic photosynthesis use

Answer 5

PS1, PS2

Question 6

Describe the steps of oxygenic photosynthesis

Answer 6

energy from photoexcitation of chlorophyll
- photolysis of H2O
- e- to ETS
- O2 = product
Light absorbed by PS2 (P680) & PS1 (P700)
Produce H+ grad and NADPH
Use of F1F0 ATP synthase

Question 7

Which photosystems are used in anoxygenic photosynthesis? Which general pigment is used?

Answer 7

Either PS1 or PS2

Bacteriochlorophyll

Question 8

Why does bacteriachlorophyll absorb red light more strongly?

Answer 8

There is less energy in the far red end of the spectrum which means no photolysis (anaerobic)
Infrared penetrates further in water

Question 9

Describe anaerobic PS1 photosynthesis

Answer 9

Found in chlorobia ‘green sulphur’ bacteria
use far red to separate e- from H2S/organic e- donor (succinate)/Fe2+
e- + NAD(P)+–>NADPH
bacteria also generate H+ grad => ATP synthesis

Question 10

describe anaerobic PS2 photosynthesis

Answer 10

found in alphaproteobacteria ‘purple nonsulphur’
uses low infrared energy which separates e- from bacteriochlorophyll
e- to ETS; e- returned to bacteriochlorophyll;ATP generated by cyclic photosythesis
PS2 has no direct way to make NADPH therefore must use ATP to drive reverse e- transport to make NADPH

Question 11

describe the principle of lithotrophy

Answer 11

energy required by oxidation of inorganic e- donors
reduced inorganics can be e- acceptors to and ETC with a terminal e- acceptor (TEA) that is a strong oxidant (O2/NO3-)
(inorganics are relatively poor donors

Question 12

give the equation for nitrogen oxidation

Answer 12

NH4{+}+0.5O2–>NH2OH+O2–>HNO2+0.5O2–>HNO3

Question 13

give the equation for sulphur and metal oxidation and the environmental issues this causes

Answer 13

H2S+0.5O2–>S+0.5O2–>0.5S2O3{2-}+O2+H2O–>H2SO4
causes environmental acidification
problem made worse by iron:
FeS2+14Fe3{+}+8H2O=15Fe{2+}+2SO4{2-}+10H{+}

Question 14

give the equation for dehalorespiration (a type of hydrogenotrophy) and state an application

Answer 14

C2Cl4+4H2–>C2H4+4H{+}+4Cl{-}
(form of anaerobic resp.)
can be used in bioremediation

Question 15

give the equation for methanogenesis and the domain that implements it

Answer 15

CO2 + 4H2 –> CH4 + 2H2O

Performed by archaea (methanogens) and provides niches for methanogens

Question 16

which two forms of lithotrophy can also be classed as anaerobic respiration?

Answer 16

dehalorespiration and methanogenesis

Question 17

what makes anaerobic respiration anaerobic?

Answer 17

not using O2 as the terminal electron acceptor

Question 18

which 3 common terminal electron acceptors can bacteria and archaea use instead of O2?

Answer 18

NO2-, NO3- and fumarate

Question 19

in a given environment the strongest electron donor and acceptor are chosen, what happens to the other potential donors/acceptors?

Answer 19

they are repressed

Question 20

what does a negative reduction potential indicate about the species?

Answer 20

that the reverse reaction ie the loss of electrons (oxidation) yields energy

Question 21

what does a positive reduction potential indicate about the species?

Answer 21

the forward reaction ie the gain of electrons (reduction) yields energy

Question 22

what does a positive change in reduction potential indicate about the Gibbs free energy?

Answer 22

its negative and therefore is a spontaneous reaction in the forward direction
(a negative reduction potential indicates the reaction is spontaneous in the reverse direction, however this can’t be used to produce electricity)

Question 23

describe the steps of aerobic respiration

Answer 23

electron from organic substrate donated to initial oxidoreductase (molecule which accepts one e- from one molecule and donates e- to another molecule)
e- transferred to quinone pool
quinol (QH2) e- transferred to terminal oxidase (Cyt bo)
during e- transport 8H+ moved across membrane (pmf)

Question 24

what can pmf power other than ATP synthesis?

Answer 24

flagella movement/uptake nutrients/efflux toxic drugs

Question 25

biosynthesis/anabolism is the building of complex molecules, what 3 things does it require?

Answer 25

essential elements/redox power (NADPH)/energy via coupling reaction (eg ATP synthesis/pmf)

Question 26

which 4 organisms perform the calvin cycle?

Answer 26

oxygenic phototrophic bacteria
chloroplasts in algae/plants
facultatively anaerobic purple bacteria
lithotropic bacteria

Question 27

describe the calvin cycle

Answer 27

3x Ribulose 1,5 bisphosphate + 3CO2 (and rubisco)
=> 6x 3-phosphoglycerate
=> 6x glyceraldehyde-3-phosphate (G3P)
=> 1G3P => glucose
=>5G3P => 3x ribulose-5-phosphate (via sugar phosphate intermediates)
=> 3x Ribulose 1,5 bisphosphate (start of cycle)

Question 28

what is the purpose of the calvin cycle?

Answer 28

CO2 fixation

Question 29

why is it important for CO2 to be concentrated around Rubisco? Why is this difficult?

Answer 29

rubisco has a low affinity for CO2 and its efficiency is further decreased by competition with O2 (photorespiration). difficult to manage as CO2 readily diffuses

Question 30

how is CO2 concentrated in cells to rubisco?

Answer 30

carbon concentrating mechanism

• CO2 HCO3{-} using carbonic anhydrase
• HCO3{-} can be stored in membranes

Question 31

which genes are expressed when CO2 conc is low and when it is high?

Answer 31

low conc CO2: ndhF4/ndhF3/sbtA/cmpA

high conc CO2: ndhF4 (constitutive expression)

Question 32

what is the purpose of the reverse TCA cycle?

Answer 32

assimilation of small quantities of CO2 via regenerating the intermediates of TCA cycle (anaplerotic reactions)

Question 33

what is the purpose of the reductive TCA cycle in some archaea and bacteria?

Answer 33

reduction of CO2 to regenerate acetyl-CoA and build sugars

Question 34

how many ATP and CO2 are used in the reductive TCA cycle? which moleclues are used for reduction?

Answer 34

The reductive TCA cycle uses 4–5 ATPs to fix 4 molecules of CO2 and generate one oxaloacetate. Reduction done by NADPH or NADH and by reduced ferredoxin (FDH2)

Question 35

state the steps of the reverse/reductive TCA cycle

Answer 35

oxaloacetate => malate => fumarate => succinate => succinyl-CoA + CO2 => 2-oxyglutarate + CO2 => isocitrate => citrate => oxaloacetate (cycle repeats)
acetyl-CoA + CO2 => pyruvate => phosphoenolpyruvate + CO2 => oxaloacetate

Question 36

what is the name of the specialised cell that aquatic cyanobacteria use to fix N2?

Answer 36

heterocysts

Question 37

which 2 domains can fix N2?

Answer 37

some archaea and bacteria

Question 38

how are anaerobic conditions maintained?

Answer 38

photosynthesis is ‘turned off’

Question 39

give the equation for nitrogen fixation and state how many ATP are consumed

Answer 39

N2 + 8H{+} +8e{-} + 16ATP => 2NH3 + H2 + 16ADP + 16Pi
(2e- require 3ATP equivalents)
requires 28 ATP

Question 40

which enzyme catalyses nitrogen fixation? how many reductive cycles are required to fix nitrogen?

Answer 40

nitrogenase

4 cycles

Question 41

state the 4 steps in nitrogen fixation

Answer 41

Fe protein accquires 2e{-} (from electron transport protein) and transfers them to FeMo centre
FeMo centre + 2H{+] => reduced H2 gas
N2 displaces H2
successive pairs of H+ and e- reduce:
N2 --> HN=NH --> H2N--NH2 -->2NH3
2NH3 + 2H+ --> 2NH4+