metabolism, catabolism, & anabolism

Metabolism

The total of all chemical reactions in a cell, including both energy-releasing (catabolic) and energy-requiring (anabolic) processes.

Catabolism

Breakdown of large molecules into smaller ones; releases energy (exergonic); produces reducing power and precursor metabolites for anabolism.

Anabolism

Synthesis of large molecules from smaller ones; requires energy (endergonic); reductive; enzyme-catalyzed.

Exergonic Reaction

Reaction that releases free energy; ΔG°′ is negative.

Endergonic Reaction

Reaction that requires energy input; ΔG°′ is positive.

Free Energy Change Formula

ΔG = ΔH - TΔS; relates enthalpy, entropy, and free energy.

Chemical Work

Synthesis of complex molecules.

Transport Work

Uptake of nutrients, elimination of wastes, and ion balance maintenance.

Mechanical Work

Motility of the cell and movement of internal structures.

ATP

Adenosine triphosphate; the energy currency of the cell; transfers energy between reactions.

ATP Hydrolysis

ATP + H₂O → ADP + Pi + H⁺; releases -7.3 kcal/mol of energy.

Other Triphosphates

GTP, CTP, and UTP; used in specialized energy roles similar to ATP.

Oxidation

Loss of electrons or hydrogen; exergonic.

Reduction

Gain of electrons or hydrogen; endergonic.

Redox Tower

Chart of standard reduction potentials (E₀′); greater electron fall = more energy released.

Electron Carriers

Molecules like NAD⁺, NADP⁺, and FAD that transfer electrons and energy.

Reduced Form

Energy-rich forms such as NADH or FADH₂ that carry electrons to the electron transport chain.

Enzyme

Biological catalyst that speeds up reactions by lowering activation energy.

Enzyme-Substrate Complex

Temporary complex where substrate binds enzyme active site, enabling reaction.

Factors Affecting Enzymes

pH, temperature, and substrate concentration.

Competitive Inhibition

Inhibitor binds to enzyme's active site, preventing substrate binding.

Noncompetitive Inhibition

Inhibitor binds to allosteric site, changing enzyme shape and reducing activity.

Allosteric Regulation

Binding of an effector molecule changes enzyme shape, altering activity.

Covalent Modification

Addition/removal of chemical groups (like phosphate) to activate or deactivate enzymes.

Feedback Inhibition

End-product of a pathway inhibits the first enzyme, regulating metabolic flow.

Metabolic Channeling

Separation of enzymes/metabolites into compartments to control reaction location and rate.

Chemoorganoheterotrophs

Use organic compounds for energy, electrons, and carbon; most pathogens fall here.

Photolithoautotrophs

Use light for energy, inorganic electron donors, and CO₂ for carbon.

Fueling Reactions

Reactions that generate ATP, reducing power, and precursor metabolites for biosynthesis.

Aerobic Respiration

Complete oxidation of glucose to CO₂ and H₂O using oxygen as final electron acceptor.

Aerobic Respiration Phases

1. Glycolysis 2. Formation of Acetyl-CoA 3. Citric Acid Cycle 4. Electron Transport & Oxidative Phosphorylation.

Glycolysis

Glucose → 2 Pyruvate + 2 ATP (net) + 2 NADH.

glucose in glycolysis

-step 1

-starting substrate of glycolysis

-providing the carbon backbone and energy that drive ATP and NADH production

-it is enzymatically converted into pyruvate through a series of ten steps

fructose 6-P in glycolysis

-step 4

-rearranged intermediate in glycolysis that prepares glucose for further phosphorylation and eventual cleavage

-a critical transition step that enables efficient energy extraction in later reactions

glyceraldehyde 3-P

-step 5

-G3P

-the key three-carbon intermediate in glycolysis

-oxidized to harvest energy

-forms: NADH and high-energy phosphate compounds

1, 3 biphosphoglycerate in glycolysis

-step 6

-1,3-bisphosphoglycerate donates a phosphate group to ADP via phosphoglycerate kinase

-forms: ATP and 3-phosphoglycerate

-the first ATP-producing reaction of the pathway

aldolase in glycolysis

-step 4

-catalyzes the splitting of fructose-1,6-bisphosphate into G3P and DHAP

glyceraldehyde 3-P dehydrogenase in glycolysis

-step 6

-catalyzes the oxidation and phosphorylation of G3P

-forms: 1,3-bisphosphoglycerate and NADH

results of glycolysis

2 ATP, 2 NADH, 2 pyruvate

Formation of Acetyl-CoA

Pyruvate → Acetyl-CoA + CO₂ + NADH.

Citric Acid Cycle

Acetyl-CoA → 2 CO₂; generates 2 ATP (GTP), 6 NADH, and 2 FADH₂.

oxaloacetate and citrate in citric acid cycle

-begins by acetyl-CoA combining with oxaloacetate to form citrate (aka citric acid)

-over 7 steps citrate is converted back to oxaloacetate

-oxaloacetate is the one permanent member of the cycle

result of citric acid cycle

2 ATP, 6 NADH, 2 FADH2

Electron Transport Chain

series of redox carriers transferring electrons to oxygen; creates proton motive force for ATP synthase

oxidative phosphorylation

the production of ATP using energy derived from the redox reactions of an electron transport chain

ATP Synthase

Enzyme that uses proton gradient energy to synthesize ATP (oxidative phosphorylation).

ATP Yield

Eukaryotes ~30 ATP; Prokaryotes up to 38 ATP (actual 16-28).

Anaerobic Respiration

Uses electron acceptors other than O₂ (e.g., NO₃⁻, SO₄²⁻, CO₂); yields less energy.

Denitrification

Reduction of nitrate (NO₃⁻) to nitrogen gas (N₂).

Sulfate Reduction

Reduction of sulfate (SO₄²⁻) to hydrogen sulfide (H₂S).

Dissimilative sulfate reduction

sulfate acts as a final electron acceptor

Assimilative sulfate reduction

part of molecules that make up mass of our body (amino acids)

Methanogenesis

Reduction of CO₂ to methane (CH₄) in archaea.

Fermentation

Incomplete oxidation of substrates without O₂ or ETC; ATP produced only via substrate-level phosphorylation.

Fermentation Products

Acids, alcohols, gases (e.g., lactic acid, ethanol, CO₂).

Fermentation Examples

Yogurt, bread, sauerkraut, beer, wine.

Catabolism of Carbohydrates

Other sugars and polysaccharides are funneled into glycolytic pathways.

Lipid Catabolism

Lipases hydrolyze lipids → glycerol (glycolysis) and fatty acids (β-oxidation → acetyl-CoA).

Protein Catabolism

Proteases degrade proteins → amino acids → deaminated to pyruvate or TCA intermediates.

Chemolithoautotrophy

Energy and electrons from oxidation of inorganic compounds; CO₂ fixed via Calvin cycle.

Hydrogen Oxidizers

Use H₂ → H⁺ + e⁻ for energy.

Sulfur Oxidizers

Oxidize H₂S or S⁰ to SO₄²⁻.

Nitrifying Bacteria

Oxidize NH₃ → NO₂⁻ → NO₃⁻.

Reverse Electron Flow

Process to generate NAD(P)H from inorganic electron donors for biosynthesis.

Phototrophy

Light used as energy source for ATP and reducing power generation.

Oxygenic Photosynthesis

Light energy converts CO₂ and H₂O to glucose and O₂ (plants, algae, cyanobacteria).

Anoxygenic Photosynthesis

Uses H₂S or Fe²⁺ as electron donor; produces sulfur instead of oxygen.

Z-Scheme

Two linked photosystems (PSI & PSII) that drive ATP and NADPH formation in oxygenic photosynthesis.

Anabolism Overview

Energy-requiring, reductive synthesis of complex molecules from simple precursors.

Assimilatory Use

Element is incorporated into cell material (e.g., nitrogen into amino acids).

Dissimilatory Use

Element used in metabolism but not retained in biomass (e.g., as terminal electron acceptor).

Biosynthetic Principles

Macromolecules built from few precursors to save energy and genetic material.

Precursor Metabolites

Carbon skeletons from glycolysis and TCA cycle used in biosynthesis.

Gluconeogenesis

Synthesis of glucose from non-carbohydrate precursors (e.g., PEP, OAA); shares 7 enzymes with glycolysis, 4 unique.

Calvin Cycle

Pathway for CO₂ fixation; requires 18 ATP and 12 NADPH to form 1 glucose.

Polysaccharide Synthesis

ATP + glucose-1-phosphate → ADP-glucose → glycogen/starch/peptidoglycan.

Amino Acid Biosynthesis

Uses TCA and glycolysis intermediates as carbon skeletons; nitrogen added via ammonia assimilation.

Ammonia Assimilation

NH₃ incorporated by glutamate dehydrogenase or GS-GOGAT pathways.

Transaminases

Transfer amino groups between molecules during amino acid synthesis.

Assimilatory Nitrate Reduction

NO₃⁻ → NO₂⁻ → NH₃ for biosynthetic use.

Nitrogen Fixation

N₂ → NH₃ via nitrogenase enzyme in certain bacteria and archaea.

Sulfur Assimilation

SO₄²⁻ reduced to H₂S → used to form cysteine and other sulfur compounds.

Phosphorus Assimilation

PO₄³⁻ used to make ATP, nucleic acids, and phospholipids.

Purine Bases

Adenine and guanine (two-ring structures).

Pyrimidine Bases

Uracil, cytosine, and thymine (single-ring structures).

Nucleoside

Base + sugar component of nucleic acids.

Nucleotide

Nucleoside + phosphate group; building blocks of DNA/RNA.

Lipid Biosynthesis

Fatty acids synthesized from acetyl-CoA, malonyl-CoA, and NADPH.

Triacylglycerol

Storage lipid made from three fatty acids and glycerol.

Phospholipid

Membrane lipid with glycerol, two fatty acids, and phosphate group.

Integration of Metabolism

Catabolism provides ATP, reducing power, and precursors; anabolism uses them for biosynthesis to maintain balance and growth.