CC4 - Bacterial Metabolism

Question 1

Why do some bacteria form sulfur granules?

Answer 1

Bacteria such as Beggiatoa lack SoxCD and so can’t remove all 6 electrons from the sulfur compound. Instead, they use the Dsr system to oxidize sulfur. To regenerate SoxYZ for further sulfur transport, sulfur granules are formed which frees up SoxYZ.

The cells can then oxidize this sulfur granule to produce an electron transport chain.

Question 2

Describe secondary wastewater treatment methods.

Answer 2

Uses oxidative degradation under aerobic conditions to treat rich liquor. This is typically sufficient for domestic wastewater.

Industrial wastewater will usually also undergo anoxic digestion as well. This is a series of degradative and fermentative reactions under anaerobic conditions. It produces methane that can be captured and burned to power the sewage systems.

Question 3

What is the annamoxosome?

Answer 3

A membrane-bound organelle found in prokaryotes that carry out annamox reactions. It has a very dense membrane that protects the cell from the toxic intermediates of the annamox reaction, particularly hydrazine (N2H4).

Question 4

Why does nitrogenase need to use the Fe protein cycle?

Answer 4

The Fe protein cycle is necessary because the reduction of N2 to NH3 is a highly energy-intensive process that requires a large amount of reducing power in the form of electrons, which must be transferred from an electron donor to the MoFe protein via the Fe protein.

Question 5

Why do some hydrogen oxidizers have 2 hydrogenases?

Answer 5

One is membrane-bound and uses the electrons to generate a PMF.
The second is soluble and uses the redox potential to reduce NAD+.

Question 6

Why is methane monooxygenase of biotechnological interest?

Answer 6

It can potentially be used in bioremediation to capture methane and convert it into methanol.

Question 7

What is reverse electron transport?

Answer 7

RET is the consumption of PMF to generate energy that can then be used to drive electrons in a reverse direction i.e., up the redox tower. In chemolithotrophs, using an electron donor with a more positive redox potential than NAD+/NADH, such as nitrite or sulfur compounds, must use energy to reduce NAD+.

Question 8

What are flocs?

Answer 8

Slime-forming aerobic bacteria used in activated sludge that oxidize and break down materials within the sewage.

Question 9

Why is denitrification not the best for tertiary treatment?

Answer 9

You have to add carbon back into the water, and this produces nitrous oxide (a potent greenhouse gas) as waste. This is also very expensive.

Question 10

Why is NAD+/NADH so important, that cells will consume PMF to generate it?

Answer 10

Redox power is essential to life.

Question 11

What are the two major types of aerobic secondary treatment?

Answer 11

Activated sludge
Trickling filters

Question 12

Define methanotrophy.

Answer 12

The oxidation of methane as a fuel source.

Question 13

Define:
- methanogenesis
- methanotrophy
- methylatroph
- methanotroph

Answer 13

• methanogenesis: making methane
• methanotrophy: using methane
• methylatroph: species using organic compounds that lack C-C bonds
• methanotroph: type of methylatroph that only uses methane as both a fuel source and carbon source

Question 14

Why does aerobic oxidation of ferrous iron typically occur at low pH?

Answer 14

Ferrous iron isn’t stable at neutral pH and readily oxidizes to ferric iron. This reaction doesn’t occur as much at low pH. Thus, bacteria that oxidize ferrous iron are acidophiles to be able to utilize the energy from the oxidation, and must do this in large quantities.

Question 15

Why do only 2 electrons of the 4 produced make it to oxygen reduction in nitrosifying bacteria? How does this impact ATP production?

Answer 15

The electrons required originate from the oxidation of hydroxylamine to NO2- (produces 4 electrons). 2 of these electrons are required to make NADH (reverse electron transport). Thus for every 4 electrons generated from the oxidation of NH3 to NO2-, only 2 actually reach cytochrome aa3, the terminal oxidase that interacts with oxygen to form water.

Due to this, ATP production is limited due to the use of RET.

Question 16

What is assimilation?

Answer 16

Assimilation refers to the process by which living organisms take up nutrients, such as carbon, nitrogen, and sulfur. These nutrients are then converted into more complex organic compounds through metabolic processes such as photosynthesis or respiration.

Question 17

What are the 5 goals of sewage treatment?

Answer 17

1. Convert organic matter to inorganic parts.
2. Oxidize any reduced inorganic parts (reduce COD).
3. Remove microbial pathogens.
4. Remove toxic chemicals.
5. Remove macronutrients.

Question 18

How may short-circuiting occur in electron bifurcation?

Answer 18

Short-circuiting could occur if the normal flow of electrons is disrupted and redirected.

Question 19

How is reducing power generated in annamoxosomes for carbon fixation?

Answer 19

Reducing power for CO2 fixation by anammox bacteria is derived from reverse electron transport, but because electron transfer reactions are cyclic, the electrons needed for reverse electron transport derive from an independent set of reactions that oxidize nitrite to nitrate by a nitrite oxidoreductase, a reaction also present in Nitrobacter.
Interestingly, then, nitrite serves two different purposes for anammox bacteria: The reduction
of nitrite is required to generate ATP by chemiosmosis (annamox), and the oxidation of nitrite is required to generate reducing power for CO2 fixation.

Question 20

Define methanogenesis.

Answer 20

The biological production of methane (by strictly anaerobic archaea).

Question 21

Describe the electron flow during ferrous iron oxidation.

Answer 21

The periplasmic copper-containing protein rusticyanin receives electrons from Fe2+ oxidized by a c-type cytochrome located in the outer membrane. From here, the electrons travel a short ETC, resulting in the reduction of oxygen to water. Reducing power comes from RET.

Question 22

Where can reduced inorganic compounds come from?

Answer 22

1. Environment
2. Other species that use the compound as electron acceptors (ecosystems)
3. Organic compounds
4. Volcanic activity
5. Hydrothermal vents
6. Burning fossil fuels
7. Industrial waste

Question 23

Describe the process of hydrogen oxidation to produce PMF.

Answer 23

Electrons from hydrogen are initially transferred to a quinone acceptor. From there electrons travel through a series of cytochromes to generate a PMF and eventually reduce oxygen to water.

Question 24

Compare the microbiota of the skin, mouth, small intestine and large intestine.

Answer 24

Skin:
- low bacterial numbers on exposed areas
- concentrated around orifices, groin, etc.

Mouth:
- Far more species than skin
- contribute to a healthy oral cavity

Small intestine:
- low number of organisms
- bacteria can survive stomach acid

Large intestine:
- dense population with great variety
- mostly anaerobes

Question 25

Why does Hong Kong sewage smell particularly bad?

Answer 25

They use sea water to flush the toilets where acetate is mostly used in sulfur reactions, producing lots of H2S. The solution is to treat the sea water and remove the sulfate. This eliminates competition for the acetate to be used in methanogenesis.

Question 26

What are the main C1 carriers used in methanogenesis and what are their functions?

Answer 26

1. Methanofuran 2. Methanopterin 3. Coenzyme M These are used in the given order to carry the carbon in CO2 through a series of reductions.

Question 27

Define biological and chemical oxygen demands.

Answer 27

BOD: the ability of the microbial population in water to consume oxygen. COD: inorganic oxygen usage e.g., ammonia conversion.

Question 28

What are the pros and cons of methanogenesis to make fuel?

Answer 28

Pro: source of very clean and efficient fuel if we can capture the methane. Con: source of potent greenhouse gas if not captured.

Question 29

Where can methylatrophs be found?

Answer 29

These are found anywhere where there's lots of methane (typically in the anaerobic zone), but as they use oxygen as the final electron acceptor, they're often on the border of the aerobic and anaerobic zones.

Question 30

What is the acetyl CoA pathway for carbon fixation?

Answer 30

It is a metabolic pathway used by certain bacteria and archaea to fix carbon dioxide (CO2) into organic compounds, such as acetyl CoA, which can be used as a source of energy and building blocks for cellular processes. 1. CO2 condensed to a methyl group. 2. 2nd CO2 condensed to a carbonyl group. 3. Two molecules are joined to generate acetyl CoA.

Question 31

What happens in a sludge digester?

Answer 31

1. anaerobes use enzymes to digest solids and macromolecules. 2. the resulting soluble components are fermented. 3. the products of fermentation can be used by methanogenic archaea to make methane.

Question 32

What are the 2 reactions that occur in nitrosifying bacteria, and what enzymes catalyze these?

Answer 32

NH3 --> NH2OH (ammonia monooxygenase) NH2OH --> NO2- (hydroxylamine oxidoreductase)

Question 33

Why can't acidophilic bacteria make ATP for free?

Answer 33

There is a huge pH difference (thus, PMF) across the membrane that theoretically could be used to generate ATP. However, the organism can't make ATP from this PMF in the absence of an electron donor because the protons would acidify the cytoplasm if they weren't consumed.

Question 34

What are the 2 redox coenzymes used in methanogenesis?

Answer 34

F420 and coenzyme B.

Question 35

Why can mouthwash raise blood pressure?

Answer 35

Nitric oxide within the mouth acts as a vasodilator, reducing blood pressure. It's primarily produced by oral bacteria. Mouthwash kills these bacteria, raising the blood pressure.

Question 36

What are C1 carriers?

Answer 36

Coenzymes in methanogenesis that carry the C1 unit along its path of enzymatic reduction.

Question 37

Describe the Sox system.

Answer 37

The Sox system is composed of several proteins that work together to oxidize sulfur compounds. These proteins include SoxAX, which forms a complex with the membrane protein SoxYZ and helps to transport sulfur compounds across the cell membrane; SoxYZ, which binds to SoxAX and acts as a sulfur carrier; and SoxCD, which contains the active site for sulfur oxidation and transfers 6 electrons from sulfur to the electron transport chain. SoxB releases sulfate.

Question 38

Describe the process of nitrogen assimilation.

Answer 38

In plants, nitrogen assimilation begins with the uptake of inorganic nitrogen from the soil in the form of ammonium (NH4+) or nitrate (NO3-). This nitrogen is then transported to the leaves, where ammonia is incorporated into amino acids through a series of enzymatic reactions known as the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway. Nitrate is reduced to nitrite (NO2-) by the enzyme nitrate reductase, and then to ammonium by the enzyme nitrite reductase. The resulting ammonium is then combined with glutamate to form glutamine, which serves as a key precursor for the synthesis of other amino acids.

Question 39

What is the reaction for nitrification?

Answer 39

Ammonia --> Nitrite --> Nitrate Oxidation of ammonia to nitrate.

Question 40

Why might the Haber Process be classed as an ineffective method of fixing nitrogen?

Answer 40

It requires a huge amount of energy because nitrogen is thermodynamically inert, due to its triple bond.

Question 41

State the annamox reaction.

Answer 41

NH4+ + NO2 --> N2 + H2O

Question 42

Why doesn't methanogenesis occur in aquatic environments?

Answer 42

There's competition for use of acetate in both methanogenesis and sulfur production. As there's higher levels of sulfur in marine environments, it's the dominant user of acetate.

Question 43

How does nitrogen assimilation regulation differ between E. coli and K. pneumoniae?

Answer 43

K. pneumoniae controls other operons: - amt: controlled by NtrC (TF for GS), producing a transporter for more ammonia transport. - nif: controlled by NtrC, producing an EBP for sigma54 and an oxygen sensor.

Question 44

Describe primary wastewater treatment.

Answer 44

Uses only physical separation methods to separate solid and particulate organic and inorganic materials from wastewater.

Question 45

How are the nitrogen assimilation pathways controlled?

Answer 45

1. Each pathway has a different Km for ammonia 2. The pathways are controlled by cellular conditions such as ATP availability and ammonia presence. 3. Transcriptional control 4. Post-translational control

Question 46

Where are nitrifying bacteria found?

Answer 46

Aerobic environments (water, estuaries) Areas rich in organic matter (sewage)

Question 47

What are redox coenzymes in methanogenesis?

Answer 47

Coenzymes that donate electrons to the C1 unit.

Question 48

What is the mechanism of methanogenesis?

Answer 48

1. CO2 is activated by methanofuran and reduced by ferrodoxin. 2. It's transferred to methanopterin where it's dehydrated and reduced twice to methyl. 3. It's transferred to coenzyme M. 4. Methyl-CoM is reduced to methane, requiring other coenzymes, and released. 5. The coenzymes are regenerated through electron bifurcation. Reduction is achieved by the redox coenzymes, F420 and coenzyme B.

Question 49

What is chemolithotrophy?

Answer 49

Chemolithotrophy is a type of metabolism where organisms use inorganic compounds as electron donors to drive ATP synthesis. Unlike phototrophs (organisms that use light as their energy source) and heterotrophs (organisms that use organic compounds as their energy source), chemolithotrophs do not require organic matter to survive.

Question 50

What is phosphate scrubbing?

Answer 50

The removal of phosphate in wastewater by precipitating it out.

Question 51

Why are there multiple nitrogen assimilation pathways?

Answer 51

There are differences between the pathways that gives preferences for each under different conditions in the bacteria.

Question 52

What are the similarities between the annamoxosome and mitochondria?

Answer 52

- PMF generated across the membrane - Redox reactions are linked by an ETC

Question 53

What are the 4 things required for life?

Answer 53

- Source of carbon - Source of energy - Source of redox - Source of nitrogen