Microbial Metabolism, Enzymes, and Biogeochemical Cycles

Flashcards based on lecture notes about microbial metabolism, enzymes, and biogeochemical cycles.

What is microbial metabolism's role throughout Earth's history?

It has been a driving force behind the development and maintenance of the planet’s biosphere.

What is the term to describe all the chemical reactions inside a cell?

Metabolism

What is anabolism?

Endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy.

What is catabolism?

Exergonic pathways that break down complex molecules into simpler ones.

What are autotrophs?

Organisms that convert inorganic carbon dioxide (CO2) into organic carbon compounds.

What are heterotrophs?

Organisms that rely on more complex organic carbon compounds as nutrients.

What are phototrophs?

Organisms that get their energy for electron transfer from light.

What are chemotrophs?

Organisms that obtain energy for electron transfer by breaking chemical bonds.

What are organotrophs?

Chemotrophs that obtain energy from organic compounds.

What are lithotrophs?

Chemotrophs that get energy from inorganic compounds.

What is the importance of the transfer of electrons between molecules?

Most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons.

What are oxidation reactions?

Reactions that remove electrons from donor molecules, leaving them oxidized.

What are reduction reactions?

Reactions that add electrons to acceptor molecules, leaving them reduced.

What is the role of NAD+/NADH in metabolism?

It is a common mobile electron carrier used in catabolism.

What is the role of NADP+/NADPH in metabolism?

It plays an important role in anabolic reactions and photosynthesis.

What is the role of FAD/FADH2 in metabolism?

It is extensively used in energy extraction from sugars during catabolism in chemoheterotrophs.

What is the role of ATP in living cells?

It enables the cell to store energy safely and release it for use only as needed, it is called the energy currency of the cell.

What is phosphorylation?

The addition of a phosphate group to a molecule, which requires energy.

What is dephosphorylation?

The process of breaking high-energy bonds in ATP to release one or two phosphate groups, releasing energy.

What is a catalyst?

A substance that helps speed up a chemical reaction without being used or changed during the reaction.

What are enzymes?

Proteins that serve as catalysts for biochemical reactions inside cells.

What is the role of enzymes in the chemical reaction inside the cell?

Lowering the activation energy.

What are substrates?

The chemical reactants to which an enzyme binds.

What is the active site?

The location within the enzyme where the substrate binds.

What is induced fit?

The active-site modification in the presence of substrate, along with the simultaneous formation of the transition state.

How temperature influences enzyme activity?

Increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited to bind substrates.

How pH influences enzyme activity?

Extreme environmental pH values (acidic or basic) can cause enzymes to denature. Active-site amino-acid side chains have their own acidic or basic properties that are optimal for catalysis and, therefore, are sensitive to changes in pH.

How substrate concentration influences enzyme activity?

Enzyme activity is increased at higher concentrations of substrate until it reaches a saturation point at which the enzyme can bind no additional substrate.

What are cofactors?

Inorganic ions such as iron (Fe2+) and magnesium (Mg2+) that help stabilize enzyme conformation and function.

What are coenzymes?

Organic helper molecules that are required for enzyme action.

What is an apoenzyme?

An enzyme lacking a necessary cofactor or coenzyme and is inactive.

What is a holoenzyme?

An enzyme with the necessary associated cofactor or coenzyme and is active.

What is a competitive inhibitor?

A molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding.

What is a noncompetitive inhibitor?

A molecule that binds to the enzyme at an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate.

What is feedback inhibition?

Involves the use of a pathway product to regulate its own further production, slowing production during anabolic or catabolic reactions.

What is glycolysis?

The most common pathway for the catabolism of glucose that produces energy, reduced electron carriers, and precursor molecules for cellular metabolism.

Where does glycolysis take place?

In the cytoplasm of prokaryotic and eukaryotic cells.

What is the net gain from glycolysis?

Two ATP molecules, two NADH molecules, and two pyruvate molecules.

What is substrate-level phosphorylation?

A phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP.

What is the Entner-Doudoroff (ED) pathway?

An alternative glycolytic pathway used by some prokaryotes.

What is the pentose phosphate pathway (PPP)?

A glycolytic pathway that occurs in all cells, using intermediates for the biosynthesis of nucleotides and amino acids.

What happens to pyruvate after glycolysis?

It must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group in the transition reaction. Electrons are also transferred to NAD+ to form NADH.

What is coenzyme A (CoA)?

The carrier compound to which the two-carbon acetyl group must be attached to proceed to the next phase of the metabolic process.

What is the Krebs cycle?

A series of chemical reactions in a closed loop that captures the two-carbon acetyl group from the transition reaction; it produces two CO2 molecules, one ATP molecule, three molecules of NADH, and one of FADH2.

What is the role of oxidative phosphorylation?

Electrons are transferred from NADH and FADH2 through a series of chemical reactions to a final inorganic electron acceptor (either oxygen in aerobic respiration or non-oxygen inorganic molecules in anaerobic respiration) to generate ATP.

What is the electron transport system (ETS)?

The last component involved in the process of cellular respiration that comprises a series of membrane-associated protein complexes and associated mobile accessory electron carriers.

What are cytochromes?

The major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems.

What are flavoproteins?

The major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems.

What are iron-sulfur proteins?

The major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems.

What are quinones?

The major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems.

What is the final electron acceptor in aerobic respiration?

An oxygen molecule (O2) that becomes reduced to water (H2O) by the final ETS carrier.

What is anaerobic respiration?

Using an inorganic molecule other than oxygen as a final electron acceptor.

What are denitrifiers?

Important soil bacteria that use nitrate (NO3–) and nitrite (NO2–) as final electron acceptors, producing nitrogen gas (N2).

What is the proton motive force (PMF)?

The electrochemical gradient formed by the accumulation of H+ (also known as a proton) on one side of the membrane compared with the other.

What is chemiosmosis?

The flow of hydrogen ions across the membrane through a channel in the membrane via a membrane-bound enzyme complex called ATP synthase

What is ATP synthase?

A complex protein that acts as a tiny generator, turning by the force of the H+ diffusing through the enzyme.

What is fermentation?

A process which some living systems use an organic molecule (commonly pyruvate) as a final electron acceptor.

What happens during lactic acid fermentation?

Pyruvate accepts electrons from NADH and is reduced to lactic acid.

What is homolactic fermentation?

When lactic acid is the only fermentation product.

What is heterolactic fermentation?

Producing a mixture of lactic acid, ethanol and/or acetic acid, and CO2 as a result, because of their use of the branched pentose phosphate pathway instead of the EMP pathway for glycolysis.

What happens during alcohol fermentation?

The enzyme pyruvate decarboxylase removes a carboxyl group from pyruvate, releasing CO2 gas while producing the two-carbon molecule acetaldehyde. The enzyme alcohol dehydrogenase transfers an electron from NADH to acetaldehyde, producing ethanol and NAD+.

What is lipid catabolism?

The process of degrading lipids for use as carbon sources.

What are lipases?

The reactions breaking down triglycerides are catalyzed by lipases

What are phospholipases?

Breaking down phospholipids are catalyzed by phospholipases

What is β-oxidation?

The process of catabolizing released fatty acids, which sequentially removes two-carbon acetyl groups from the ends of fatty acid chains, reducing NAD+ and FAD to produce NADH and FADH2.

What is protein catabolism?

The process of degrading proteins for use as carbon sources

What are proteases?

Enzymes through the concerted action of a variety of microbial protease enzymes degrading protein.

What is photosynthesis?

The biochemical process by which phototrophic organisms convert solar energy (sunlight) into chemical energy.

What are the light-dependent reactions?

Energy from sunlight is absorbed by pigment molecules in photosynthetic membranes and converted into stored chemical energy.

What are the light-independent reactions?

The chemical energy produced by the light-dependent reactions is used to drive the assembly of sugar molecules using CO2.

What are photosynthetic pigments?

Molecules used to absorb solar energy such as bacteriochlorophylls, carotenoids, chlorophylls, phycocyanins, and phycoerythrins.

What is oxygenic photosynthesis?

H2O is split and supplies the electron to the reaction center, generating oxygen as a byproduct.

What is anoxygenic photosynthesis?

Other reduced compounds serve as the electron donor, and oxygen is not generated.

What is the Calvin-Benson cycle?

The biochemical pathway used for fixation of CO2.

What is a biogeochemical cycle?

The recycling of inorganic matter between living organisms and their nonliving environment.

What are methanotrophs?

Bacteria and archaea that use methane as their carbon source.

What are methanogens?

Archaea that use CO2 as a terminal electron acceptor in anaerobic respiration, producing methane.

What is nitrogen fixation?

Specialized biochemical pathways used to incorporate nitrogen into macromolecules.

What is ammonification?

The process in which certain bacteria and fungi convert nitrogenous waste from living animals or from the remains of dead organisms into ammonia.

What is nitrification?

Oxidation to nitrite (NO−2), then to nitrate (NO−3), by nitrifying soil bacteria.

What is denitrification?

Soil bacteria use nitrate as a terminal electron acceptor in anaerobic respiration, converting it into nitrogen gas that reenters the atmosphere.

What is microbial bioremediation?

Leverages microbial metabolism to remove xenobiotics or other pollutants.

What is in situ bioremediation?

Bioremediation conducted at the site of contamination and does not involve movement of contaminated material.

What is ex situ bioremediation?

Involves the removal of contaminated material from the original site so that it can be treated elsewhere.

How can protein catabolism help identify microbes?

Some clinically important pathogens can be identified by their ability to produce a specific type of extracellular protease. For example, the production of the extracellular protease gelatinase by members of the genera Proteus and Serratia.

How can lipases and phospholipases contribute to virulence in microbes?

These microbes use phospholipases to destroy lipids and phospholipids in host cells and then use the catabolic products for energy.

Which groups of microbes carry out the sulfur cycle?

Anoxygenic photosynthetic bacteria as well as chemoautotrophic archaea and bacteria use hydrogen sulfide as an electron donor, oxidizing it first to elemental sulfur (S0), then to sulfate (SO42−)

What are the four steps of the nitrogen cycle?

Ammonification, nitrification, and denitrification, nitrogen fixation

Describe the interaction between heterotrophs and autotrophs in the carbon cycle

Carbon Cycle Carbon is exchanged between heterotrophs and autotrophs within and between ecosystems primarily by way of atmospheric CO2, a fully oxidized version of carbon

the functions of the proton motive force

the PMF can also be used to drive other energetically unfavorable processes, including nutrient transport and flagella rotation for motility.

Name common Fermentation Pathways

Acetone- butanol-ethanol, Alcohol, Butanediol, Butyric acid, Lactic acid, Mixed acid, Propionic acid

Distinguish between noncompetitive inhibitor and competitive inhibitor

A competitive inhibitor is a molecule similar enough to a substrate that it can compete with the substrate for binding to the active site Noncompetitive (allosteric) inhibitors bind to allosteric sites inducing a conformational change

Explain the difference between autotrophs and heterotrophs

Organisms that convert inorganic carbon dioxide into organic carbon compounds are autotrophs Conversely, heterotrophs rely on more complex organic carbon compounds as nutrients

Explain the difference between catabolism and anabolism

anabolism refers to those endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules. conversely, the term catabolism refers to exergonic pathways that break down complex molecules

Summarize theoretical maximum yields of ATP from various processes during the complete aerobic respiration of one glucose molecule.

Overall, the theoretical maximum yield of ATP made during the complete aerobic respiration of glucose is 38 molecules, with four being made by substrate-level phosphorylation and 34 being made by oxidative phosphorylation

ATP synthase function

ATP Synthase Function Hydrogen ions flow back into the matrix through a channel protein called ATP synthase facilitate ATP

Enzyme are optimized to work best under

under an environment conditions in which the organisms that produce them live