Respiration

Question 1

What is respiration?

Answer 1

Respiration is a type of catabolism that encompasses a range of catabolic processes that yield a chemiosmotic gradient.

Question 2

What are the three functions of catabolism?

Answer 2

Energy conservation, providing reductant (to anabolism), providing building blocks.

Question 3

What are essential elements of aerobic respiration?

Answer 3

Physically separate half reactions, half reactions connected via ETC, proton translocation, energy transduction (chemical energy to osmostic energy).

Question 4

What’s the relationship between TEAs and energy yield?

Answer 4

Better TEA provides more energy.

Question 5

Where do anaerobic environments usually occur?

Answer 5

Where oxygen consumption exceed oxygen supply.

Question 6

A fundamental difference between aerobic and anaerobic respiration?

Answer 6

Anaerobic respiration often has limiting e- acceptors.

Question 7

What is respiratory diversification?

Answer 7

Since TEAs are a source of competition, many organisms can use multiple TEAs.

Question 8

What are oxygen relationships based on?

Answer 8

Ability to respire oxygen and tolerant ROS (reactive oxygen species).

Question 9

What do TEAs have to do with competition and regulation?

Answer 9

Presence of TEAs regulate what organisms use as a TEA. More energetically favourable TEA gets used first. Better TEA also supports higher growth rate, meaning nitrate respiring organism will outgrow sulfate respiring organism.

Question 10

Describe sediment profile redox gradients.

Answer 10

Best TEAs get used first, redox potential goes down.

Question 11

Why is soil a heterogenous and dynamic environment?

Answer 11

It forms crumbs and aggregates that make different microenvironments. The environments can also change radically.

Question 12

How does water impact soil microenvironments?

Answer 12

Water is essential for activity, is the main control on aeration of soil, and is essential for movement of nutrients and solutes.

Question 13

What is denitrification?

Answer 13

It is the dissimilatory reduction of nitrate or nitrite to nitric oxide, nitrous oxide, or dinitrogen. Substrates are soluble ions and the products are gasses.

Question 14

What are some weird aspects of denitrification?

Answer 14

The complete process of denitrification involves four steps, each a separate half-reaction. But, denitrification may involve fewer steps and some denitrifiers can use NO or N2O as a respiratory TEA. In this case, the organism is still a denitrifier, but the process does not fit the definition of denitrification (ie, only part of the pathway is used).

Question 15

Define dissimilation.

Answer 15

All respiration is dissimilatory, meaning a substance is metabolized and excreted. Catabolism. Electron donors and TEAs are taken up, transformed and their products are excreted. This is in contrast to assimilatory processes, which involve incorporation of a substance into biomass (i.e., anabolism). The assimilatory and dissimilatory processes involving nitrogen are independent and can occur simultaneously.

Question 16

Describe the diversity of denitrifiers.

Answer 16

Broadly but thinly distributed. Many groups, but onlya few members of the group may actually use it.

Question 17

Explain denitirification vs nitrate respiration.

Answer 17

Nitrate respiration is the dissimilatory reduction of nitrate to nitrite or ammonium (note that neither product is a gas). Organisms do not seem to be capable of both dentirification and dissimilatory reduction of nitrate to ammonium.

Question 18

What e- donors do denitrifiers use?

Answer 18

Can be heterotrophic or lithotrophic.

Question 19

Explain the mechanisms of denitrification.

Answer 19

The 4 steps of denitrification are carried out by 4 reductases in the membrane. A total of 10 e- are required to reduce 2 NO3- to N2. Each half reaction uses 2 e-.

Question 20

What are some results of denitrification?

Answer 20

Loss of fixed N from the biosphere, loss of N from soil, removes N from sewage (prevents eutrophication), greenhouse gas production (N2O), ozone depletion (NO), NO and N2O removal, anaerobic organic decomposition (C cycle), bioremediation.

Question 21

Describe anammox.

Answer 21

Anaerobic ammonium oxidation, is another mechanism for loss of fixed N. NH4+ + NO2− → N2 + 2H2O.

Question 22

Describe iron respiration.

Answer 22

Reducation of ferric to ferrous iron. 1 e-. Reduction potential is pH dependent. Diverse.

Question 23

What are the 5 proposed mechanisms for extracellular e- transfer?

Answer 23

Microbial nanowires (biofilm with pili), multistep e- hopping (redox cofactors in biofilm), direct cell-mineral contact, release of chelating agents (chemicals that can bind to ferric iron), microbial or environmental e- shuttles. All probably require cytochromes except for chelators.

Question 24

What is the significance of iron respiration?

Answer 24

Subsurface environment and ore formation, water quality (ferric iron isn’t soluble, ferrous iron is).

Question 25

Describe electromicrobiology.

Answer 25

The use of microorganisms to transfer e- to an electrode. Example: The metal reducing bacterium Geobacter colonizes a graphite anode in an anaerobic chamber, oxidizing acetate and transferring electrons to the anode. Those electrons move to the cathode in an aerobic chamber where they abiologically reduce oxygen to water. This process creates a current of electrons. The two chambers are separated by a membrane permeable to small ions.

Question 26

Describe dehalorespiration.

Answer 26

Catalysis of the reductive removal of a halogen substituent (F,I,Br,Cl) from an organic compound (reductive dehalogenation). The displacement of the halogen involves addition of electrons (and often protons). Important because it breaks down compounds that are recalcitrant.

Question 27

Describe Perchloroethene (PCE).

Answer 27

PCE is the most common contaminant of groundwater aquifers. This toxic, xenobiotic, anthropogenic compound was widely used as a solvent for dry cleaning, degreasing machinery and other applications. PCE is sufficiently water soluble to travel through soil and reach groundwater where it can exist at harmful concentrations. Reductive dechlorination is the only known mechanism for biodegradation of PCE, and this appears to be possible only under anaerobic conditions. The first intermediate in PCE biodegradation is trichloroethene (TCE), which was also a widely used solvent and is also a common contaminant. TCE can be anaerobically biodegraded via reductive dechlorination or aerobically biodegraded via another process. Each step consumes 2 e- and 2 H+.

Question 28

Describe Dehalococcoides ethenogenes.

Answer 28

A bacterium capable of respiration with PCE, an obligate lithotrophic dehalorespirer.

Question 29

Describe Polychlorinated biphenyls (PCBs).

Answer 29

Pollutants from things like paint additives and electricial transformers. Hydrophobic, tend to bioaccumulate. PCBs actually occur in complex mixtures of congeners. Each congener is a molecule with a unique pattern of chlorine substitution. There are 209 possible PCB congeners. All PCBs are recalcitrant. Some PCB congeners with few chlorine substituents (less than four) can be aerobically biodegraded. More highly chlorinated PCBs appear to be biodegraded only anaerobically via reductive dehalogenation.