Lehninger Principles of Biochemistry: Chapter 13 Key Terms

autotroph

An organism that can synthesize its own complex molecules from very simple carbon and nitrogen sources, such as carbon dioxide and ammonia.

heterotroph

An organism that requires complex nutrient molecules, such as glucose, as a source of energy and carbon.

metabolism

The entire set of enzyme-catalyzed transformations of organic molecule in living cells; the sum of anabolism and catabolism.

metabolic pathways

Linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes.

metabolite

A chemical intermediate in the enzyme-catalyzed reactions of metabolism.

intermediary metabolism

In cells, the enzyme-catalyzed reactions that extract chemical energy from nutrient molecules and use it to synthesize and assemble cell components.

catabolism

The phase of intermediary metabolism concerned with the energy-yielding degradation of nutrient molecules.

anabolism

The phase of intermediary metabolism that is concerned with the energy-requiring biosynthesis of cell components from smaller precursors.

standard transformed constants

Used to calculate standard transformed Gibbs energies of formation and standard transformed enthalpies of formation of 53 reactants (sums of species) at 298.15 K, pH 7, and ionic strengths of 0, 0.1, and 0.25 ᴍ.

homolytic cleavage

The breaking of a covalent bond in such a way that each fragment gets one of the shared electrons.

radical

An atom or group of atoms possessing an unpaired electron; also called a free radical.

heterolytic cleavage

The process of cleaving a covalent bond where one previously bonded species takes both original bonding electrons from the other species.

nucleophile

an electron-rich group with a strong tendency to donate electrons to an electron-deficient nucleus (electrophile); the entering reactant in a bimolecular substitution reaction.

electrophile

An electron-deficient group with a strong tendency to accept electrons from an electron-rich group (nucleophile).

carbanion

A negatively charged carbon atom.

carbocation

A positively charged carbon atom; also called a carbonium ion.

aldol condensation

A condensation reaction in organic chemistry in which an enol or an enolate ion reacts with a carbonyl compound to form a β-hydroxyaldehyde or β-hydroxyketone (an aldol reaction), followed by dehydration to give a conjugated enone.

Claisen condensation

A carbon-carbon bond forming reaction that occurs between two esters or one ester and another carbonyl compound in the presence of a strong base, resulting in a β-keto ester or a β-diketone.

kinases

Enzymes that catalyze phosphorylation of certain molecules by ATP.

phosphorylation potential (∆Gᵩ)

The actual free-energy change of ATP hydrolysis under the nonstandard conditions prevailing in a cell.

thioester

An ester of a carboxylic acid with a thiol or mercaptan.

adenylylation

Now known as AMPylation, is a process in which adenosine monophosphate (AMP) molecule is covalently attached to a protein side chain, altering the function of the protein.

inorganic pyrophosphatase

An enzyme that hydrolyzes a molecule of inorganic pyrophosphate to yield two molecules of (ortho) phosphate; also known as pyrophosphatase.

nucleoside diphosphate kinase

An enzyme that catalyzes the transfer of the terminal phosphate of a nucleoside 5'-triphosphate to a nucleoside 5'-diphosphate.

adenylate kinase

A phosphotransferase enzyme that catalyzes the interconversion of adenine nucleotides (ATP, ADP, and AMP). By constantly monitoring phosphate nucleotide levels inside the cell, plays an important role in cellular energy homeostasis; also known as ADK or myokinase.

creatine kinase

Catalyses the conversion of creatine and utilizes adenosine triphosphate to create phosphocreatine and adenosine diphosphate.

phosphagens

Also known as macroergic compounds, are high energy storage compounds, also known as high-energy phosphate compounds, chiefly found in muscular tissue in animals.

polyphosphate kinase-1, kinase-2

An enzyme that catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate moieties.

electromotive force (emf)

A difference in potential that tends to give rise to an electric current; the electrical intensity or "pressure" developed by a source of electrical energy such as a battery or generator.

conjugate redox pair

An electron donor and its corresponding electron acceptor; for example, Cu⁺ (donor) and Cu²⁺ (acceptor), or NADH (donor) and NAD⁺ (acceptor).

dehydrogenation

A chemical reaction that involves the removal of hydrogen from an organic molecule.

dehydrogenases

Enzymes that catalyze the removal of pairs of hydrogen atoms from substrates.

reducing equivalent

A general term for an electron or an electron equivalent in the form of a hydrogen atom or a hydride ion.

standard reduction potential (E'°)

The electromotive force exhibited at an electrode by 1 ᴍ concentration. ∆G'° denotes the standard free-energy change at pH 7.0 in 55.5 ᴍ water.

pyridine nucleotide

A nucleotide coenzyme containing the pyridine derivative nicotinamide; NAD or NADP.

oxidoreductase

An enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor. This group of enzymes usually utilizes NADP or NAD+ as cofactors.

flavoprotein

An enzyme containing a flavin nucleotide as a tightly bound prosthetic group.

flavin nucleotides

Nucleotide coenzymes (FMN and FAD) containing riboflavin.

cryptochrome

A class of flavoproteins that are sensitive to blue light; involved in the circadian rhythms of plants and animals, and possibly also in the sensing of magnetic fields in a number of species.

photolyase

DNA repair enzymes that repair damage caused by exposure to ultraviolet light. These enzymes require visible light (from the violet/blue end of the spectrum) both for their own activation and for the actual DNA repair.