Lehninger Principles of Biochemistry - Chapter 13: Introduction to Metabolism

Comprehensive vocabulary flashcards covering metabolic pathways, bioenergetics, thermodynamic laws, ATP group transfers, high-energy phosphates, redox reactions, and universal electron carriers from Chapter 13 of Lehninger Principles of Biochemistry.

Catabolism

The degradative phase of metabolism that breaks down energy-containing nutrients into simpler end products, releasing chemical energy.

Anabolism

The biosynthetic or building phase of metabolism that constructs complex cell macromolecules from simple precursor molecules, requiring an input of energy.

Converging Catabolism

A pathway pattern where a diverse variety of starting nutrient molecules (such as carbohydrates, fatty acids, and amino acids) are broken down into common, simple intermediate structures, predominantly acetate ($\text{acetyl-CoA}$).

Diverging Anabolism

A pathway pattern where a few simple precursor molecules (such as acetate) are used to synthesize a wide variety of diverse and complex cellular end products.

First Law of Thermodynamics

The principle of the conservation of energy, which states that total energy remains constant and cannot be created or destroyed during physical or chemical processes.

Second Law of Thermodynamics

The physical law stating that the universe always tends toward increasing disorder or randomness.

Reacting System

The specific collection of matter that is undergoing a particular chemical or physical process, which can be defined as either open or closed.

Open System

A thermodynamic system, such as a living cell or organism, that continuously exchanges both matter and energy with its surroundings.

Universe (Thermodynamics)

The thermodynamic totality consisting of the reacting system and all of its surroundings taken together.

Free Energy ($G$)

A thermodynamic property that expresses the maximum amount of energy capable of doing work during a process occurring at constant temperature and pressure.

Exergonic Reaction

A chemical reaction that proceeds with the release of free energy, characterized by a negative change in free energy ($\Delta G < 0$).

Endergonic Reaction

A non-spontaneous chemical reaction that gains free energy and requires an input of work, characterized by a positive change in free energy ($\Delta G > 0$).

Enthalpy ($H$)

The heat content of a reacting system, which directly reflects the number and kinds of chemical bonds (both covalent and noncovalent) present in reactants and products.

Exothermic Reaction

A chemical reaction that releases heat to its surroundings, characterized by a negative change in enthalpy ($\Delta H < 0$).

Endothermic Reaction

A chemical reaction that absorbs heat from its surroundings, characterized by a positive change in enthalpy ($\Delta H > 0$).

Entropy ($S$)

A quantitative physical expression representing the randomness or state of disorder of the components in a system.

Free-Energy Change Equation

The fundamental thermodynamic equation expressing the change in free energy: $\Delta G = \Delta H - T\Delta S$, where spontaneous reactions are favored by negative $\Delta H$ and positive $\Delta S$.

Biochemical Standard State

A set of reference conditions specifically defined for biological systems: $[H^+] = 10^{-7}\,M$ (pH $7.0$), $[H_2O] = 55.5\,M$, and $[Mg^{2+}] = 1\,mM$, with initial concentrations of other components at $1.0\,M$, temperature at $25^\circ\text{C}$, and pressure at $1\,\text{atm}$.

Standard Transformed Constants ($\Delta G'^\circ$ and $K'_{eq}$)

Physical constants (such as standard transformed free-energy change and standard transformed equilibrium constant) calculated specifically at the biochemical standard state.

Relationship Between $K'_{eq}$ and $\Delta G'^\circ$

The mathematical expression $\Delta G'^\circ = -RT \ln(K'_{eq})$, showing that the standard free-energy change is an alternative way of stating the equilibrium constant.

Actual Free-Energy Change ($\Delta G$)

The variable free-energy change dependent upon prevailing reactant and product concentrations and ambient temperature, given by the relationship $\Delta G = \Delta G'^\circ + RT \ln(Q)$.

Mass-Action Ratio ($Q$)

The ratio of product concentrations to reactant concentrations at any specified instantaneous, non-equilibrium condition during a reaction.

Principle of Additivity of Free Energy

The thermodynamic rule that for sequential chemical reactions, the overall standard free-energy change is equal to the sum of the standard free-energy changes of each individual reaction.

Reaction Coupling

The thermodynamic process in which an unfavorable, endergonic biological reaction is driven in the forward direction by coupling it directly through a shared intermediate to an exergonic reaction, often ATP hydrolysis.

Standard Free Energy of ATP Hydrolysis ($\Delta G'^\circ$)

The standard free-energy change for the reaction $\text{ATP}^{4-} + \text{H}_2\text{O} \rightarrow \text{ADP}^{3-} + \text{HPO}_4^{2-} + \text{H}^+$, which has an intermediate value of $-30.5\,\text{kJ/mol}$.

$$\text{MgATP}^{2-}$$

The specific coordination complex formed between magnesium ions ($\text{Mg}^{2+}$) and ATP in the cytosol, which serves as the true substrate for most enzymes utilizing ATP.

Phosphorylation Potential ($\Delta G_p$)

The actual free energy of hydrolysis of ATP under real intracellular physiological conditions, which varies across cell types and over time.

High-Energy Compounds

Phosphorylated compounds or thioesters whose standard free energy of hydrolysis ($\Delta G'^\circ$) is more negative than $-25\,\text{kJ/mol}$.

Low-Energy Compounds

Phosphorylated biological compounds whose standard free energy of hydrolysis ($\Delta G'^\circ$) is less negative than $-25\,\text{kJ/mol}$.

Phosphoenolpyruvate (PEP)

A high-energy phosphorylated glycolytic intermediate with a $\Delta G'^\circ$ of hydrolysis of $-61.9\,\text{kJ/mol}$, driven by resonance stabilization of inorganic phosphate and keto-enol tautomerization of pyruvate.

1,3-Bisphosphoglycerate (1,3-BPG)

A high-energy acyl phosphate intermediate with a $\Delta G'^\circ$ of hydrolysis of $-49.3\,\text{kJ/mol}$, driven forward by resonance stabilization and ionization of the product, 3-phosphoglycerate.

Thioesters

Molecules containing an acyl group linked to a sulfur atom instead of an oxygen atom in the ester linkage (e.g., acetyl-CoA), yielding a large negative standard free energy of hydrolysis ($\Delta G'^\circ = -31.4\,\text{kJ/mol}$).

Adenylyl Transfer

A nucleophilic attack by a substrate on the $\alpha$-phosphate position of ATP, transferring an adenylate group to the substrate and releasing inorganic pyrophosphate ($\text{PP}_i$).

Nucleoside Diphosphate Kinase

An enzyme that transfers terminal phosphoryl groups from ATP to other nucleoside diphosphates (or deoxynucleoside diphosphates) via a ping-pong mechanism driven by high cellular $[\text{ATP}]/[\text{ADP}]$ ratios.

Electromotive Force (emf)

The quantitative electrical driving force proportional to the difference in electron affinity between two chemical species, which drives spontaneous electron flow through a circuit.

Reducing Agent (Reductant)

The chemical species that donates electrons in an oxidation-reduction reaction and subsequently becomes oxidized.

Oxidizing Agent (Oxidant)

The chemical species that accepts electrons in an oxidation-reduction reaction and subsequently becomes reduced.

Conjugate Redox Pair

An electron donor and its corresponding electron-accepting counterpart participating together in a half-reaction.

Dehydrogenation

A biological oxidation reaction wherein a substrate loses two electrons and two hydrogen ions ($\text{H}^+$), catalyzed by dehydrogenase enzymes.

Standard Reduction Potential ($E'^\circ$)

A quantitative measurement (in volts) of the relative affinity of an electron acceptor in a redox pair for electrons under biochemical standard conditions.

Pyridine Nucleotides

Freely diffusible universal electron coenzymes (nicotinamide adenine dinucleotide, $\text{NAD}^+$, and its phosphorylated form, $\text{NADP}^+$) derived from niacin that undergo reversible reduction of their nicotinamide ring.

NADH Absorbance Peak

The distinct ultraviolet absorbance maximum at $340\,\text{nm}$ exhibited exclusively by reduced pyridine nucleotides (NADH and NADPH), disappearing upon oxidation.

Pellagra

A human disease resulting from a nutritional deficiency of niacin (the precursor of NAD and NADP), characterized clinically by the 'three Ds': dermatitis, diarrhea, and dementia.

Flavoproteins

Enzymes that contain a tightly bound or covalent flavin nucleotide coenzyme (either FMN or FAD) to catalyze oxidation-reduction reactions.

Flavin Nucleotides

Coenzymes derived from the vitamin riboflavin ($\text{FAD}$ and $\text{FMN}$) possessing an isoalloxazine ring that can accept either one electron (forming a semiquinone radical) or two electrons (forming $\text{FADH}_2$ or $\text{FMNH}_2$).