Question 1

Metabolic Principles:

Accepted Answer

All microbes follow core rules: they conserve energy (make ATP), use reducing power (electrons for redox reactions), and maintain redox balance by passing electrons to external acceptors.

Question 2

Metabolic Diversity:

Accepted Answer

Microbial diversity comes from mixing and modifying metabolic reactions—horizontal gene transfer and enzyme variations create many pathways (e.g., different electron donors/acceptors).

Question 3

Conservation of Energy (in Cells):

Accepted Answer

The principle that cells conserve energy by linking the movement of electrons to the production of ATP.

Question 4

Redox Reactions:

Accepted Answer

Chemical reactions where electrons are transferred from an electron donor to an electron acceptor; these reactions drive electron flow in cells.

Question 5

Reduction Potential (E₀′):

Accepted Answer

A measure of a molecule’s tendency to donate or accept electrons; higher (more positive) values indicate a stronger tendency to accept electrons.

Question 6

Energy Yield and E₀′ Difference:

Accepted Answer

The greater the difference in reduction potential between paired half-reactions, the more energy is released and available for cellular work.

Question 7

Electron Donors and Acceptors:

Accepted Answer

Cells can use many organic or inorganic substances as electron donors, pairing them with a wide range of possible electron acceptors.

Question 8

ATP Synthesis Pathways:

Accepted Answer

Electron flow powers ATP production through three mechanisms — substrate-level phosphorylation, oxidative phosphorylation, or photophosphorylation.

Question 9

Fermentation:

Accepted Answer

A chemotrophic metabolism that requires no external electron acceptor. ATP is produced by substrate-level phosphorylation, and electron balance is maintained by reducing intermediates that are excreted as fermentation products.

Question 10

Phototrophs:

Accepted Answer

Organisms that obtain their energy from light.

Question 11

Chemotrophs:

Accepted Answer

Organisms that obtain their energy from chemical compounds.

Question 12

Organotrophs:

Accepted Answer

Organisms that use organic molecules as their electron source.

Question 13

Lithotrophs:

Accepted Answer

Organisms that use inorganic molecules as their electron source.

Question 14

Heterotrophs:

Accepted Answer

Organisms that use organic carbon as their carbon source.

Question 15

Autotrophs:

Accepted Answer

Organisms that use CO₂ as their carbon source.

Question 16

Aerobic Respiration:

Accepted Answer

Metabolism using O₂ as the electron acceptor; ATP is produced via oxidative phosphorylation driven by a proton motive force; electron donors can be organic (chemoorganotrophs) or inorganic (chemolithotrophs).

Question 17

Chemolithotrophs:

Accepted Answer

Organisms that generate energy by oxidizing inorganic compounds (e.g., H₂, NH₃, Fe²⁺) as electron donors, often using O₂ as the electron acceptor; energy yield varies by compound.

Question 18

Anaerobic Respiration:

Accepted Answer

Metabolism using electron acceptors other than O₂; yields less energy than aerobic respiration; dominates in oxygen-poor environments.

Question 19

Reducing Power:

Accepted Answer

Low-potential electron carriers (e.g., NAD(P)H, reduced ferredoxin) used for biosynthesis; generated by oxidizing organic compounds in chemoorganotrophs. Chemolithotrophs/phototrophs often need energy-coupled reactions to reduce NAD(P)⁺ or ferredoxin.

Question 20

Redox Balance:

Accepted Answer

Maintenance of electron flow in cells by transferring electrons to external acceptors (respiration) or intermediates (fermentation); ensures proper metabolism and availability of reducing power.

Question 21

Three methods of energy coupling to increase reducing power or achieve redox balance:

Accepted Answer

ATP hydrolysis coupling, reverse electron transport, electron bifurcation.

Question 22

ATP Hydrolysis Coupling:

Accepted Answer

Uses energy from ATP breakdown to drive otherwise difficult reactions and increase reducing power.

Question 23

Reverse Electron Transport:

Accepted Answer

Uses proton motive force to push electrons uphill and reduce NAD(P)⁺ when electron donors are weak.

Question 24

Electron Bifurcation:

Accepted Answer

Splits electrons from one donor to reduce both high- and low-potential acceptors at once, powered by flavin enzymes.

Question 25

Bifurcating Enzyme Mechanism:

Accepted Answer

Flavin-containing enzymes split electrons, sending one to a high-potential acceptor and one to a low-potential acceptor. This generates strong reducing intermediates and boosts fermentative energy yield by oxidizing NADH to NAD⁺, often producing H₂.

Question 26

Assimilative Processes:

Accepted Answer

incorporate inorganic nutrients into cells. Consume energy (ATP and reducing power), only done to acquire nutrients for biosynthesis, variety of assimilative reduction reactions.

Question 27

What’s the most important Assimilative Process?

Accepted Answer

CO2 fixation.

Question 28

Dissimilative Processes:

Accepted Answer

conserve energy, electron acceptors must be reduced and excreted, dissimilative reductions are part of anaerobic respiration.

Question 29

Autotrophs & CO2:

Accepted Answer

autotrophs can assimilate CO2 into cell material. Include many microbes, including almost all phototrophs and chemolitotrophs. CO2 supplies carbon for biosynthesis. In phototrophs, CO2 is the ultimate photosynthetic electron acceptor.

Question 30

Mixotrophs:

Accepted Answer

Organisms that can use both inorganic and organic sources of energy or carbon, switching depending on availability.

Question 31

The Calvin Cycle:

Accepted Answer

most widespread, globally important pathway for CO2 fixation, used by all oxygenic phototrophs. The key enzyme is RubisCO (reduces O2 to G3P), requires NADPH and ATP to synthesize 1 fructose-6-phosphate from CO2).

Question 32

Carboxysomes & The Calvin Cycle:

Accepted Answer

carboxysomes are proteinaceous microcompartments containing RubisCO. Carboxysome also protects RubisCO from O2, which competes with CO2. Cycle originated before the Great Oxidation Event.

Question 33

Photosynthesis:

Accepted Answer

use of light energy to drive biosynthesis, like sunlight and infrared radiation in the dark sea floor.

Question 34

What kind of organisms do photosynthesis?

Accepted Answer

Photosynthetic organisms are autotrophs (reduce CO2 to organic compounds → photoautotrophy), not all phototrophs are autotrophs, photoheterotrophs are phototrophs that use organic carbon as a carbon source.

Question 35

Light Reactions:

Accepted Answer

Convert light energy into ATP and proton motive force.

Question 36

Light-Independent Reactions (Calvin Cycle):

Accepted Answer

Fix CO₂ into organic compounds using ATP and reducing power from light reactions.

Question 37

Oxygenic Photosynthesis:

Accepted Answer

Uses H₂O as an electron donor, produces O₂, performed by cyanobacteria, algae, and plants.

Question 38

Anoxygenic Photosynthesis:

Accepted Answer

Uses donors other than H₂O (e.g., H₂S), does not produce O₂; light drives CO₂ reduction and ATP production.

Question 39

Respiratory Processes Defined by Electron Donor:

Accepted Answer

Electron donor (oxidized; energy source):
Organic compounds, H₂, sulfur compounds, nitrogen compounds (nitrification, anammox), Fe²⁺

Question 40

Respiratory Processes Defined by Electron Acceptor:

Accepted Answer

O₂ (aerobic respiration), NO₃⁻/NO₂⁻ (denitrification), SO₄²⁻ (sulfate reduction), CO₂ (methanogenesis), Fe³⁺ (iron reduction)

Question 41

Nitrification:

Accepted Answer

Aerobic, two-step bacterial process that oxidizes ammonia (NH₃) to nitrite (NO₂⁻), then nitrite to nitrate (NO₃⁻). Performed by specialized chemolithotrophic bacteria.

Question 42

Nitrifying Bacteria:

Accepted Answer

Chemolithotrophic microorganisms that catalyze nitrification. Most are specialists (Nitrosomonas, Nitrobacter) performing only one oxidation step; some Nitrospira can perform both steps completely.

Question 43

Nitrification Carbon Metabolism:

Accepted Answer

Aerobic nitrifying bacteria fix CO₂ via the Calvin cycle, generating NAD(P)H through reverse electron flow.

Question 44

Metabolic Flexibility of Nitrifiers:

Accepted Answer

Nitrite oxidizers can grow chemoorganotrophically on organics. Ammonia oxidizers range from obligate chemolithotrophs to autotrophs/mixotrophs; archaeal ammonia oxidizers use a modified 3-hydroxypropionate/4-hydroxybutyrate cycle.

Question 45

Denitrification:

Accepted Answer

Anaerobic respiration using nitrate (NO₃⁻) as the electron acceptor, reduced to N₂. Some microbes fully reduce to N₂, others stop at nitrite. Releases N₂O and causes soil nitrogen loss.

Question 46

Denitrifying Microorganisms:

Accepted Answer

Mostly Proteobacteria (e.g., Pseudomonas) that are facultative aerobes; some Archaea and one eukaryote (Globobulimina pseudospinescens) also denitrify. Many can use alternative electron acceptors (Fe³⁺, organics) anaerobically or ferment.

Question 47

Ecological Impact of Denitrification:

Accepted Answer

Detrimental to agriculture (removes fertilizer nitrate), produces N₂O greenhouse gas and NO (consumes ozone), NO₂⁻ contributes to acid rain. Beneficial in sewage treatment by removing fixed nitrogen that would otherwise trigger algal blooms.

Question 48

Methanogenesis:

Accepted Answer

Anaerobic respiration where CO₂ (or small C compounds) is the terminal electron acceptor, producing methane (CH₄)

Question 49

Washington-Paine Experiment

Accepted Answer

The first U.S. scientific experiment showed that “magical mud” containing microbes could produce methane from organic matter, demonstrating that microbial activity, not just chemistry, drives methane production in anaerobic environments.

Question 50

Methane Hydrate-Flammable Ice:

Accepted Answer

A crystalline solid where methane is trapped in a water-ice lattice. It forms under high pressure and low temperature (deep ocean sediments or permafrost) and releases flammable methane when heated or depressurized.

Question 51

Comparison Between Methane and CO2:

Accepted Answer

methane is 84x more potent than CO2 in the short term.

Question 52

Methanogenesis from CO2 + H2:

Accepted Answer

H2 is the major electron donor for methanogenesis. Uses reductive acetyl-CoA pathway to assimilate CO2. Has two types with/without cytochromes.

Question 53

Methanogenesis Without Cytochromes:

Accepted Answer

relies heavily on electron bifurcation to generate reducing power. These organisms use H₂ to reduce CO₂ step-by-step, producing methane while recycling CoM and CoB.

Question 54

Methanogenesis With Cytochromes:

Accepted Answer

Some methanogens use cytochromes in their electron transport chain, creating a stronger H⁺ or Na⁺ gradient across the membrane and producing more ATP than methanogens without cytochromes.

Question 55

Methanogenesis with Methanol and Acetate:

Accepted Answer

methanol or acetate replaces H₂ + CO₂. Methanol provides electrons while methyl groups are reduced to CH₄. Strong H⁺/Na⁺ gradients increase ATP yield and allow reverse steps for extra energy.

Question 56

Limitations with Fermentation:

Accepted Answer

defined by lack of an external electron acceptor. Two major challenges are that it conserves much less energy than respiratory organisms, difficult to achieve redox balance.

Question 57

Diversity of Fermentation:

Accepted Answer

there’s tremendous reaction diversity. Many only ferment when lacking external electron acceptors anoxically. Many are more exclusively fermentative.

Question 58

Achieving Redox Balance:

Accepted Answer

Total atoms and electrons in reactants/substrates must equal products. Achieved by excreting fermentation products (acids, alcohols) and through H₂ production mechanisms.

Question 59

Fermentations of Obligate Anaerobes:

Accepted Answer

Many fermenters are obligate anaerobes, growing in highly reducing conditions and unable to tolerate O₂, often producing H₂. Ex: Clostridium species

Question 60

Secondary Fermentation:

Accepted Answer

Fermentation where products of one organism's fermentation serve as substrates for another organism. Common in microbial communities living in close association. Important in food production and environmental nutrient cycling.

Question 61

Propionic Acid Fermentation:

Accepted Answer

Used by Propionibacterium, converting lactate into propionate, acetate, and CO₂, generating ATP via substrate-level phosphorylation. Responsible for Swiss cheese holes and part of the human skin microbiome.

Question 62

Syntrophy:

Accepted Answer

Obligate cooperation between two different microbes to perform a thermodynamically unfavorable reaction that neither can do alone. Most syntrophic reactions are secondary fermentations involving interspecies electron transfer.

Question 63

Interspecies Electron Transfer (IET):

Accepted Answer

One species donates electrons and another accepts them. Types: Direct (DIET) via cell-to-cell contact or nanowires, and Mediated (MIET) via diffusing products like H₂.

Question 64

Direct Interspecies Electron Transfer (DIET):

Accepted Answer

A syntrophic process in which microbes pass electrons directly between cells through physical contact or conductive structures like nanowires/pili, allowing electron exchange without diffusible intermediates.

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