MIC105 Module A - Metabolic Diversity

Heterotroph

Utilizes organic carbon as energy source

Autotroph

Utilizes CO2 as energy source

Reduced

Requires oxygen

Oxidized

Requires electrons

Which carbon fixation pathway is used by the following:

chloroplasts, cyanobacteria, purple phototrophs, Not archaea

Calvin Cycle

What are the two essential enzymes of the Calvin Cycle

Rubisco & phosphoribulokinase

These are the key steps of which cycle:

1. CO2 fixation by Rubisco

2. Reduction of carbon

3. Regeneration of CO2 acceptor - phosphoribulokinase

Calvin Cycle

Name the Cycle:

6CO2 + 12NADPH + 18ATP -> C6H12O6 + 12NADP + 17 Pi

Calvin Cycle

Which carbon fixation pathway is used by the following:

green sulfur bacteria, non-phototrophic bacterial mesophiles & thermophiles

Reverse TCA Cycle

These are the key enzymes of which cycle:

fumarate reductase, a-ketogluterate synthase, citrate lyase

Reverse TCA Cycle

Which carbon fixation pathway is used by the following:

Green non-sulfur bacteria, anaerobic phototrophs

3-Hydroxypropionate bi-cycle

Name the cycle:

3CO2 -> Pyruvate + 5 ATP

3-Hydroxypropionate bi-cycle

These are the key enzymes of which cycle:

Acetyl-CoA & propionyl CoA carboxylases

3-Hydroxypropionate bi-cycle

The following are used by which domain of life:

Reductive Acetyl-CoA pathway

3-Hydroxypropionate/4-hydroxybutyrate cycle

dicarboxylate/4-hydroxybutyrate cycle

Archaea

Which carbon fixation pathway is used by the following:

thermoacidophilic Crenarchaeota

3-Hydroxypropionate/4-hydroxybutyrate cycle

Which cycle has multiple O2 sensitive enzymes, and can only operate in anaerobes and microaerophiles; no unique enzymes

dicarboxylate/4-hydroxybutyrate cycle

Which carbon fixation pathway is used by the following:

strict anaerobes; sulfate reducing bacteria, acetogens, fimicutes, planctomycetes, methanogens

Reductive Acetyl-CoA pathway

This the key enzyme of which pathway:

Acetyl-CoA synthase

Reductive Acetyl-CoA pathway

Phototrophy

harnessing photoexcited electrons to power cell growth

Who utilizes chlorophyll-based phototrophy

photoautotrophs & photoheterotrophs

Who utilizes retinal-based phototrophy

not autotrophs

What is the difference between Anoxygenic and Oxygenic phototrophy

Anoxygenic - does not produce oxygen

Oxygenic - produces oxygen

Which groups perform oxygenic phototrophy

cyanobacteria, chloroplasts

What is the electron source in oxygenic photosynthesis

H2O

Which group performs anoxygenic phototrophy

6 bacterial lineage

What are the following common features of:

1. photosynthetic pigments

2. photosystems

3. reaction center

4. production of reduced NADPH

photosynthetic apparatus

Where are cyanobacteria found

most environments, anywhere there's light; hot springs, oceans, microbial mats

What is the primary physiology of Cyanobacteria

Oxygenic photoautotrophs

What is the physiology of purple sulfur bacteria

photoautotrophic - utilize CO2 & H2S/H2

What is the physiology of purple non-sulfur bacteria

Anaerobic photoheterotrophic - utilize organic compounds

T/F: Purple phototrophs only have PSI

False: only have PSII

Where are purple sulfur bacteria found?

anaerobic environments with H2S and light; marine environments, freshwater muds, sulfur springs

Where are purple non-sulfur bacteria found?

widespread in soils are water

What is the physiology of green sulfur bacteria

anoxygenic photoautotroph, using H2S or H2 as electron donor

What is the physiology of green nonsulfur bacteria

photoheterotrophs

Which is aerobic/anaerobic, GS or GNS bacteria

GS - anaerobic

GNS - aerobic

Where are Green sulfur bacteria found

freshwater and marine sediments

Where are green nonsulfur bacteria found

alkaline hot springs (thermophilic), freshwater and marine environments

What does a chlorosome do and which bacteria do they reside in

absorbs light in low-light environments, present in GS and GNS bacteria; acidobacteria too

T/F: GS bacteria have both photosystems

F: only PSI

T/F GNS bacteria only have PSII

true

What is the physiology of Heliobacteria?

anoxygenic photoheterotrophs, strict anaerobes, cannot fix CO2

Where are heliobacteria found

anaerobic alkaline soils, rice paddies

Heliobacteria can fix: carbon/nitrogen

nitrogen

T/F: aerobic anoxygenic photogrophs can fix CO2

False, cannot fix CO2

-troph

one who nourishes

-gen

born of, produced by

What do acetogens use as e donor and acceptor?

e donor - H2

e acceptor - CO2

What do Acetogens produce?

acetate

What carbon fixation pathway do Acetogens use?

Reductive Acetyl-CoA pathway to generate acetate and fix CO2

The following are key enzymes of what pathway:

CO dehydrogenase

Acetyl-CoA Synthase

Electron bifurcating hydrogenase

Acetogenesis by the Reductive Acetyl-CoA pathway

Acetogens are strict anaerobes/aerobes

anaerobes

What do methanogens produce?

Methane

Who can perform methanogenesis

Archaea

What are the habitats of methanogens

anoxic soils, wetlands, digestive tracts, landfills, hydrothermal vents

T/F: Methanogens are very sensitive to O2, making them obligate aerobes

F: obligate anaerobes

What are the electron donor and acceptor for methanogenesis

e donor - H2

e acceptor - CO2

What are the three types of carbon substrates for methanogenesis

1. CO2 type substrates

2. methylated substrates

3. acetate

What is the initial energy inpuy for methanogenesis

Na+ or H+ potential on membrane

What carbon fixation pathway do methanogens use

reductive acetyl-coa pathway, but with methanogen-specific C1 carriers

Syntrophy

two different organisms cooperate in a metabolic process - both benefit

Define methylotrophy

use of one (C1) carbon compound as sole source of carbon (not CO2)

Where might you find aerobic methanotrophy taking place

oxic/anoxic interface in aquatic sediments and soil environments

What does Methan monooxygenase do (MMO)?

introduces oxygen into methane, producing methanol

What carbon fixation cycle do obligate type 1 methanotrophs use?

Ribulose monophosphate pathway

What carbon dixation cycle do type ii methanotrophs use?

serine pathway

Why does reverse methanogenesis need a partner and who is it?

the reverse process is not energetically favorable, partner is sulfate reducing bacteria

The following are major functions of which process?:

- degrade organic compounds to obtain energy

- convert carbon source into precursors for biosynthesis

- generate NADH & NADPH

Catabolism

What are the three main catabolic pathways for organic compounds?

1. Photoheterotrophy

2. Fermentation

3. Respiration

What is the most efficient way to produce ATP?

Proton motive force

What catabolism is the following: Oxidation of organic compounds to transfer of electrons to an external electron acceptor. Reoxidize NADH, coupled to energy conservation.

Respiration

What catabolism is the following:

internally balances redox reactions, excretion of products, substrate level phosphorylation

Fermentation

How does fermentation produce PMF?

ATPase - spend ATP to generate PMF

What is the difference between dissimulative and assimilatory nitrate reduction?

Dissimulative - energy conserving; using as e acceptor

Assimilatory - energy consuming, take it in

What is the key enzyme of nitrate reduction and what does it do?

Nitrate reductase, NO3 -> NO2

Rank the following as electron acceptors and in terms of energy yield:

- O2

- fumarate

- nitrate

O2 > nitrate > fumarate

What are the principle substrates for catabolism for most microbes?

Biopolymers - polymer of organic compounds

What are the two main strategies of aromatic ring cleavage?

1. Intradiol (ortho) cleavage - between the hydroxylated carbons

2. Extradiol (meta) cleavage - adjacent to one hydroxylated carbon

Which is faster: aerobic or anaerobic aromatic compound degredation?

Aerobic

What is the general reaction of Nitrogen Fixation?

N2 -> NH4

What is the key enzyme of nitrogen fixation, is it oxygen sensistive?

Nitrogenase, yes

N2 fixation evolved once/more than once?

Once and was spread

How do bacteria deal with O2 while fixing nitrogen?

quick diffusion

polysaccharide capsule

separate in time

separate in space

rhizobia - symbiont

What are the two forms of nitrification?

1. Ammonia to Nitrite ( NH3 -> NO2)

2. Nitrite to Nitrate (NO2 -> NO3)

Descrube Comammox

complete ammonia oxidation: NH3 -> NO3

How is comammox harmful?

agriculture - removes NH4 from soil

nitrate in rain water runoff

What makes planctomycetes unique?

the presence of internal compartments

Name the following Nitrogen Cycle reaction: N2 -> NH3

nitrogen fixation

Name the following Nitrogen Cycle reaction: NH3 -> NO2 -> NO3

nitrification

Name the following Nitrogen Cycle reaction: NH4 + NO2 -> N2 + 2 H2O

anammox

Name the following Nitrogen Cycle reactions: NO3 -> NO2 -> NO -> N2O -> N2

denitrification & nitrate respiration

Name the following Nitrogen Cycle reaction:

NH3 -> organic nitrogen compounds

NO3 -> NH3 -> organic nitrogen compounds

nitrogen assimilation