Metabolism and Bioenergetics: Key Concepts and Pathways

What are the two main processes of metabolism?

Catabolism (breakdown) and anabolism (building).

What is the importance of microbial metabolism?

It plays a key role in energy cycling, element cycling, and symbiotic relationships.

What does the first law of thermodynamics state?

Energy cannot be created or destroyed, only transformed.

What is the second law of thermodynamics?

Entropy in a system tends to increase over time.

What does ΔG represent in metabolic reactions?

The change in free energy of a reaction.

What indicates an endergonic reaction?

A positive ΔG, meaning the reaction is energetically unfavorable.

What indicates an exergonic reaction?

A negative ΔG, meaning the reaction is energetically favorable.

What is ATP's role in metabolism?

ATP serves as the cellular energy currency, providing energy for various biological processes.

What are redox reactions?

Reactions that involve the transfer of electrons from a donor to an acceptor.

What are electron carriers in metabolic processes?

Molecules like NAD, FAD, and coenzyme Q that transfer electrons during redox reactions.

What is the function of enzymes in metabolism?

Enzymes act as biological catalysts that lower the activation energy of reactions.

What is the lock-and-key model?

A model describing how substrates fit into enzymes' active sites.

What is competitive inhibition?

A type of enzyme regulation where an inhibitor competes with the substrate for the active site.

What is noncompetitive inhibition?

An inhibitor binds to an enzyme at a site other than the active site, reducing its activity.

What is allosteric regulation?

Regulation of enzyme activity through binding at a site other than the active site, affecting enzyme function.

What is feedback inhibition?

A process where the end product of a metabolic pathway inhibits an earlier step in the pathway.

What are the three major mechanisms of metabolic regulation?

Control of enzyme activity, control of enzyme quantity, and compartmentation/metabolic channeling.

What is compartmentation in metabolism?

The differential distribution of enzymes and metabolites among cell structures or organelles.

What is the significance of metabolic channeling?

It allows for differential local concentrations of enzymes and metabolites within compartments.

What are the three types of cellular work in metabolism?

Chemical work, transport work, and mechanical work.

What is the role of free energy in metabolic reactions?

Free energy determines the favorability and direction of chemical reactions.

What is the significance of redox reactions in metabolism?

They are key energy sources that drive many metabolic processes, including respiration and photosynthesis.

What is the relationship between ATP and ADP?

ATP is converted to ADP and inorganic phosphate (Pi) during energy-releasing reactions.

What is the role of cofactors in enzyme function?

Cofactors are non-protein components that assist enzymes in catalyzing reactions.

What is the significance of the standard reduction potential (E0)?

It indicates the tendency of a reducing agent to lose electrons; more negative E0 means a better electron donor.

Metabolism

Sum of all chemical reactions occurring in a cell.

Catabolism

Larger, more complex molecules => smaller, simpler molecules; release of energy.

Anabolism

Synthesis of complex molecules from simpler ones; requires energy input.

Phototrophy

Energy source derived from sunlight.

Chemoorganotrophy

Oxidation of organic molecules for energy.

Chemolithotrophy

Oxidation of inorganic molecules for energy.

Fermentation

Energy source oxidized with endogenous electron acceptor; often occurs under anaerobic conditions; limited energy.

Aerobic respiration

Energy source oxidized with exogenous electron acceptor (O2); large amount of energy via electron transport activity.

Anaerobic respiration

Energy source oxidized with exogenous electron acceptors (not O2); e.g. NO3-, CO2; large amount of energy depending on reduction potential of E source/e- acceptor.

Glycolysis

A metabolic pathway that converts glucose into pyruvate; occurs in the cytoplasmic matrix.

Pentose phosphate pathway

Also known as hexose monophosphate pathway; can operate concurrently with glycolysis or Entner-Doudoroff pathway; aerobic or anaerobic.

Entner-Doudoroff pathway

A metabolic pathway that also converts glucose into pyruvate; operates alongside glycolysis.

TCA cycle

A series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins.

Oxidative phosphorylation

Process of ATP generation in which electrons are transferred through a series of protein complexes and ultimately to oxygen.

Amphibolic pathways

Pathways that function in both catabolic and anabolic processes; e.g. glycolysis, TCA cycle.

Exogenous electron acceptors

External molecules that accept electrons during oxidation processes.

Endogenous electron acceptor

Internal molecules that accept electrons during fermentation.

Energy release

The process of releasing energy from organic compounds through oxidation.

Carbon source

A source of carbon that provides building blocks for biosynthesis.

Nutritional classes of microorganisms

Categories of microorganisms based on their nutritional requirements, such as photoautotrophs and chemoheterotrophs.

Microorganisms

Organisms that are typically unicellular and microscopic, including bacteria, archaea, and some fungi.

Pentose phosphate pathway yield

Yield per glucose molecule: 1 ATP, 1 NADPH, 1 NADH.

Tricarboxylic acid (TCA) cycle

Also known as citric acid cycle or Krebs cycle; completes oxidation and degradation of glucose / other molecules; common in aerobic bacteria, free-living protozoa, most algae, and fungi; provides carbon skeletons for biosynthesis.

TCA cycle per acetyl-CoA oxidized

Produces: 2x CO2, 3x NADH, 1x FADH2, 1x GTP.

Electron transport chain (ETC)

Series of electron carriers that transfer electrons from NADH and FADH2 to terminal electron acceptor; electron flow: more negative E0 => more positive E0.

ATP yield from NADH

3 ATP / NADH; P/O ratio = 3.

ATP yield from FADH2

2 ATP / FADH2; P/O ratio = 2.

Chemiosmosis

Mechanism of ATP synthesis; energy released during electron transport establishes H+ gradient / charge difference across membrane; proton motive force (PMF) drives ATP synthesis.

ATP synthase

Catalyzes ATP synthesis via H+ flow; H+ active transport establishes PMF.

Inhibitors of ATP synthesis

Blockers: piericidin (CoQ); antimycin A (cyt b => c); cyanide / azide (cyt a => O2); uncouplers disconnect electron flow from oxidative phosphorylation.

ATP yield variation

Amount of ATP produced varies; depends on growth conditions; nature of ETC; prokaryotic P/O less than eukaryotes; e.g. E. coli bd branch: P/O = 0.67; bo branch: P/O = 1.3.

Prokaryotic ETCs

Located in plasma membrane; some resemble mitochondrial ETC; many differ: different electron carriers, branching, shorter, lower P/O ratio.

E. coli ETC

Has cyt bd branch for stationary phase / low aeration; cyt b558, b595, d with high O2 affinity; not a H+ pump.

Paracoccus denitrificans

Has aerobic and anaerobic ETC; examples of prokaryotic electron transport chains.

Ubiquinone-8

Part of E. coli ETC.

cyt bo branch

Active during log phase / high aeration; cyt b562, o with moderate O2 affinity; H+ pump.

MeOH dehydrogenase

Flavoprotein found in soil bacterium; Gm- facultative anaerobe; C source: MeOH, methylamine; e- donors: MeOH, NADH.

Chemiosmotic hypothesis

Mechanism of ATP synthesis; energy released during electron transport establishes H+ gradient / charge difference across membrane.

E0 of electron acceptor

Less positive than E0 of O2

Dissimilatory nitrate reduction

Nitrate as terminal electron acceptor; involves denitrification, which is the reduction of nitrate to nitrogen gas, causing loss of soil nitrogen and decreased fertility.

Substrate-level phosphorylation

ATP formed without the need for oxygen.

NADH oxidation

Occurs during fermentation to regenerate NAD+.

Lactic acid fermentation

Includes homolactic and heterolactic fermenters.

Alcoholic fermentation

A type of fermentation that produces ethanol.

Formic acid fermentation

Includes mixed acid fermentation and butanediol fermentation.

Stickland reaction

Amino acid fermentation where one amino acid is oxidized and another acts as an electron acceptor.

Hydrolases

Enzymes that cleave disaccharides and polysaccharides.

Phosphorylases

Enzymes that cleave glycogen and starch.

Poly-β-hydroxybutyrate (PHB)

A reserve polymer that can be converted to acetyl-CoA.

Triglycerides

Common energy sources that are hydrolyzed to glycerol and fatty acids.

β-oxidation pathway

The pathway for fatty acid oxidation.

Proteases

Enzymes secreted by certain bacteria and fungi to utilize protein as a carbon and energy source.

Deamination

The removal of an amino group from an amino acid.

Transamination

The transfer of an amino group to an α-keto acid.

Chemolithotrophs

Organisms that obtain energy from the oxidation of inorganic molecules.

Nitrification

The oxidation of ammonia to nitrate, requiring multiple genera of bacteria.

Nitrosomonas

A genus of bacteria that oxidizes ammonia to nitrite.

Nitrobacter

A genus of bacteria that oxidizes nitrite to nitrate.

What is the primary focus of anabolic processes in microorganisms?

The synthesis of complex molecules and structures.

What is meant by 'turnover' in the context of metabolism?

The continual degradation and resynthesis of cellular constituents.

How does the rate of biosynthesis compare to the rate of catabolism?

The rate of biosynthesis is approximately equal to the rate of catabolism.

What is the role of ATP in biosynthetic pathways?

ATP hydrolysis is coupled with reactions in biosynthetic pathways to provide energy.

What are precursor metabolites?

Carbon skeletons that serve as starting points for monomer synthesis.

What is gluconeogenesis?

The synthesis of glucose and fructose from non-carbohydrate precursors.

What are nucleoside diphosphate sugars used for?

They carry glucose in the cell and are involved in the synthesis of other sugars and polysaccharides.

What is the significance of peptidoglycan in microbial cells?

Peptidoglycan is essential for cell wall biosynthesis and provides structural integrity.

What are the two main types of nitrogen sources for amino acid synthesis?

Ammonia (NH4+) and nitrate (NO3-).

What is the function of anaplerotic reactions?

They replenish TCA cycle intermediates, allowing it to function during active biosynthesis.

How does the glyoxylate cycle differ from the TCA cycle?

The glyoxylate cycle bypasses decarboxylations of the TCA cycle and uses unique enzymes.

What are the two types of anaplerotic reactions mentioned?

Anaplerotic CO2 fixation and the glyoxylate cycle.

What is the role of NADPH in anabolic pathways?

NADPH serves as an electron donor for biosynthetic reactions.

What is the significance of having separate compartments for anabolic and catabolic reactions?

It allows for independent regulation and simultaneous operation of pathways.

What are the main components required for amino acid synthesis?

Carbon skeletons, an amino group, and sometimes sulfur.

What is the process of microbial starch and glycogen synthesis?

It involves the conversion of ATP and glucose 1-P into ADP-glucose, which is then polymerized.

What is the backbone composition of peptidoglycan?

Alternating sugars, specifically N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).