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Term Descriptionfermentation The conversion of rotting fruit or grain into alcohol and CO2 through the action of yeast enzymes under anaerobic conditions. (p. 5)enzyme Protein or RNA biomolecules that function as reaction catalysts to increase the rates of biochemical reactions. (p. 5)biomolecule An...

Description

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Term

Description

fermentation

The conversion of rotting fruit or grain into alcohol and CO2 through the action of yeast enzymes under anaerobic conditions. (p. 5)

enzyme

Protein or RNA biomolecules that function as reaction catalysts to increase the rates of biochemical reactions. (p. 5)

biomolecule

An organic compound essential to living organisms; major types include amino acids, nucleotides, simple sugars, and fatty acids. (p. 7)

macromolecule

An organic polymer such as protein, nucleic acid, or polysaccharide with high molecular weight (from a few thousand to several million daltons). (p. 7)

metabolic pathway

Sequences of biochemical reactions coordinated and controlled by a cell in response to available energy. (p. 7)

signal transduction

Mechanisms that facilitate communication between cells, often initiated through the binding of small molecules (ligands) to proteins called receptors. (p. 7)

ecosystem

A geographic community where different organisms have adapted to share resources and waste management in a linked system of energy flows and nutrient cycles. (p. 8)

angstrom (Å)

A unit of length equal to 10-10 meter typically used to describe the length of a chemical bond. (p. 10)

amino acid

Nitrogen-containing molecules (substituted carboxylic acids) that function as the building blocks for proteins and precursors to numerous nitrogen-containing biomolecules. (p. 11)

protein

A polymer of amino acids represented by an extended polypeptide chain. (p. 11)

polypeptide

A short linear chain of amino acids linked by peptide bonds. (p. 11)

nucleotide

An organic molecule consisting of a purine or pyrimidine base, a five-membered sugar (ribose or deoxyribose), and one to three phosphate groups. (p. 12)

deoxyribonucleic acid (DNA)

A polymeric macromolecule consisting of nucleotides covalently linked through phosphodiester bonds; the biomolecule encoding inheritable genetic information. (p. 12)

ribonucleic acid (RNA)

A nucleic acid polymer consisting of nucleoside monophosphates with unmodified adenine, guanine, cytosine, or uridine nucleotide bases or modified nucleotide bases. (p. 12)

simple sugar

A monomeric carbohydrate used in the cell for functions such as energy storage, structural organization, or cell recognition. (p. 12)

carbohydrate

An organic compound of carbon, hydrogen, and oxygen that can be a simple sugar or a polymer of sugars; the typical formula is (CH2O)n, where n is at least 3. (p. 12)

fatty acid

An organic molecule consisting of a polar carboxyl group covalently linked to a nonpolar extended hydrocarbon chain. (p. 12)

amphipathic

Polar and nonpolar chemical properties contained within the same molecule. (p. 12)

phospholipid

Lipids containing a simple organic molecule attached to a negatively charged phosphoryl group and two fatty acids. (p. 12)

triacylglycerol

A neutral (uncharged) lipid that contains three fatty acid esters covalently linked to glycerol. (p. 13)

polysaccharide

A linear or branched polymer (carbohydrate) of monosaccharide units. (p. 13)

phosphodiester bond

A chemical grouping resulting from two hydroxyl groups in phosphoric acid forming bonds with hydroxyl groups on two other molecules to form ester bonds; the primary linkage

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between nucleotides in DNA and RNA. (p. 13) peptide bond

A covalent bond between the α amino group of one amino acid and the α carboxyl group of another amino acid. (p. 14)

amylose

An α-1,4 linear form of starch. (p. 14)

chitin

A linear polysaccharide consisting of N-acetylglucosamine units linked by β-1,4 glycosidic bonds. Chitin is a major component of insect and crustacean exoskeletons and fungal cell walls. (p. 14)

metabolite

Any of a group of small biomolecules that serve as reactants and products in biochemical reactions within cells. (p. 15)

systems biology

The study of complex chemical reaction networks in cells. (p. 15)

metabolic flux

The rate at which reactants and products are interconverted in a metabolic pathways. (p. 15)

linear metabolic

A metabolic pathway in which each reaction generates only a single product, which is a

pathway

reactant for the next reaction in the pathway. (p. 17)

forked pathway

A metabolic pathway that generates two products, each of which undergoes a different metabolic fate. (p. 17)

cyclic pathway

A metabolic pathway containing several metabolites that regenerate during each turn of the cycle, serving as both reactants and products. (p. 17)

prokaryote

A single-celled organism that lacks a nucleus and other membrane-bound organelles; this category includes all bacteria. (p. 17)

eukaryote

A cell that contains a nucleus and other organelles bounded by membranes, creating microenvironments for biochemical reactions. (p. 17)

capsule

An outer layer, usually of polysaccharides, that surrounds some prokaryotic cells, particularly bacteria. (p. 17)

cytoplasm

A cell's contents within the plasma membrane (but not including the nucleus in eukaryotic cells), including organelles; the site of most cellular activities. (p. 17)

chromosome

A DNA molecule that functions to store and transmit genetic information. (p. 17)

nucleoid

In bacteria, a region containing the chromosome (without any surrounding membrane). (p. 17)

flagellum

An extracellular structure used for cell movement by bacteria and sperm cells. (p. 18)

pilus

A hair-like appendage on the surface of bacteria, used in cell movement and reproduction. (p. 18)

plasmid

A circular DNA molecule that replicates independently of the chromosome; bacterial plasmids encode genes for cell mating, antibiotic resistance, and pathogenesis. (p. 18)

genome

All of the genetic information in a cell or virus contained in DNA or RNA. (p. 18)

chromatin

In eukaryotes, a complex of DNA and proteins that constitutes chromosomes. (p. 18)

nucleus

In eukaryotic cells, a membrane-bound organelle that contains chromosomes. (p. 18)

nucleolus

In eukaryotic cells, a part of the nucleus where ribosomes are assembled from ribosomal RNA and protein. (p. 18)

ribosome

Large RNA-protein complexes that mediate protein synthesis in prokaryotic and eukaryotic cells. (p. 18)

cytoskeleton

In eukaryotic cells, a network of intracellular filaments, consisting of oligomeric proteins, that maintains cell structure. (p. 19)

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mitochondrion pl. mitochondria

The eukaryotic organelle responsible for many of the metabolic reactions involved in energy conversion and production of ATP. (p. 19)

peroxisome

In eukaryotic cells, an organelle containing enzymes for forming or destroying peroxides. (p. 19)

lysosome

In eukaryotic cells, a membrane-bound organelle involved in degradation and detoxification of macromolecules. (p. 19)

chloroplast

In plant cells, an organelle that converts light energy into chemical energy. (p. 19)

vacuole

A membrane-bound organelle in many types of eukaryotic cells, particularly plant cells, that stores metabolites and also isolates molecules that might be harmful to the cell. (p. 19)

endoplasmic

In eukaryotic cells, highly invaginated membrane structures that sequester ribosomes for

reticulum

protein synthesis. (p. 19)

Golgi apparatus

In eukaryotic cells, a membranous structure required for protein translocation within the cell and in facilitating protein secretion at the plasma membrane. (p. 19)

microtubule

Cable-like component of the cytoskeleton that enables an animal cell to move by extending the plasma membrane in one direction while retracting it at the opposite end of the cell. (p. 19)

endosymbiotic

The theory proposing that eukaryotic cells evolved about 1.5 billion years ago as a result of

theory

large predatory cells engulfing aerobic bacteria or cyanobacteria, giving rise to mitochondria and chloroplasts, respectively. (p. 19)

ligand

A small molecule that is often a metabolite, hormone, or peptide and which binds to target proteins and alters their structure and function to control biochemical processes. (p. 20)

base pair

Two nucleotides in nucleic acid chains that are paired by hydrogen bonding, such as C-G, A-T, or A-U. (p. 24)

base stacking

Stabilizing interactions between the aromatic rings of the nucleotide bases within the interior of the DNA helix. (p. 25)

central dogma

The description of information transfer in molecular biology, which flows from DNA to RNA to proteins. (p. 25)

DNA replication

The enzyme-mediated process of doubling the DNA content of a cell during division. (p. 26)

gene

A segment of DNA that codes for a transcribed RNA molecule; the functional unit of heredity. (p. 26)

DNA transcription

The process of generating RNA from a DNA template. (p. 26)

messenger RNA (mRNA)

A molecule of RNA that serves as a template for protein synthesis. (p. 26)

mRNA translation

The process by which a ribosome decodes a molecule of mRNA and synthesizes a corresponding protein. (p. 26)

small nuclear RNA (snRNA)

Small RNA molecules involved in RNA processing. (p. 26)

micro RNA (miRNA)

Genome encoded small RNA molecules that regulate gene expression and mRNA translation. (p. 26)

ribosomal RNA (rRNA)

A type of RNA that forms the major component of ribosomes. (p. 26)

transfer RNA (tRNA)

The adaptor molecule in protein synthesis that delivers an amino acid to the ribosome. (p. 26)

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reverse transcription

The process that converts RNA into DNA, most often related to replication of retroviruses. (p. 27)

transcriptome

The collection of DNA transcripts (RNA products) generated by DNA transcription. (p. 27)

proteome

The complete collection of proteins in a cell or organism. (p. 27)

template strand

A DNA sequence that has the opposite 5′ to 3′ polarity as the corresponding mRNA transcript; it is complementary to the DNA coding strand. (p. 27)

coding strand

A DNA sequence that has the same 5′ to 3′ polarity as the corresponding mRNA transcript; it is complementary to the DNA template strand. (p. 27)

natural selection

The change in the frequency of genes in a population under conditions that favor some genes over others. (p. 28)

wild-type

A fully functional protein-coding sequence without any mutations. (p. 28)

germ-line cell

Cells that give rise to an egg or sperm cell in eukaryotes. (p. 28)

somatic cell

Any cell in an organism other than a germ-line cell. (p. 28)

bioinformatics

The use of computational tools to probe and analyze large data sets of biological information, typically whole genomes or proteomes. (p. 29)

orthologous

One of a set of highly conserved gene sequences that arose from a common ancestral gene

gene

and encode proteins with the same function in different species. (p. 31)

gene duplication

A mechanism by which duplication of a region of DNA containing a gene can lead to evolution of new genetic material. (p. 32)

paralogous

Highly conserved genes within the same species; most often derived from the process of gene

genes

duplication. (p. 32)

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Term bioenergetics

Description Energy conversion processes in biological systems, including transformation of solar energy into chemical energy and interconversion of chemical energy through oxidation and reduction of organic molecules. (p. 40)

homeostasis

The use of energy to maintain a dynamic steady state of an organism that can adjust to changing environmental conditions. (p. 40)

equilibrium

The state of a system in which no net change occurs. (p. 40)

solar energy

Energy produced through thermonuclear reactions in the Sun. (p. 41)

photosynthetic autotroph

An organism that can use photosynthesis to oxidize water and produce oxygen, generating chemical energy in the form of glucose. (p. 41)

aerobic respiration

A set of metabolic processes and reactions that uses oxygen to generate ATP. (p. 41)

heterotroph

An organism that cannot convert solar energy to chemical energy directly, but must depend on nutrients obtained from autotrophs and other heterotrophs as a source of energy. (p. 41)

photosynthesis

The use of solar energy to oxidize water, capture chemical energy, and generate oxygen. (p. 41)

carbon fixation

The conversion of carbon dioxide into other organic compounds, particularly glucose; often considered as part of photosynthesis. (p. 42)

biosphere

All the living organisms on Earth, considered as a whole. (p. 42)

redox reaction

An oxidation–reduction reaction in which electrons are transferred from a compound of lower reduction potential (more negative) to one of higher reduction potential (more positive) as in the electron transport system. (p. 42)

photooxidation

Oxidation caused by light; used particularly for oxidation of chlorophyll, resulting in the transfer of an electron from chlorophyll to an acceptor molecule such as pheophytin. (p. 42)

photophosphorylation

The conversion of ADP to ATP coupled to the transfer of electrons in photosynthesis. (p. 42)

oxidative phosphorylation

A metabolic pathway that oxidizes nutrients, particularly glucose, to generate ATP from ADP. (p. 42)

first law of thermodynamics

In any physical or chemical change, the total amount of energy in the universe remains the same, even though the form of energy may change. (p. 44)

second law of thermodynamics

In the absence of an energy input, all spontaneous processes in the universe tend toward dispersal of energy (disorder), and moreover, the measure of this disorder, called entropy, is always increasing in the universe. (p. 44)

entropy

A measure of the spreading of energy; also a measure of the disorder (randomness) in a system. (p. 44)

enthalpy (H)

The heat content of a system. (p. 44)

bomb calorimeter

A device in which a compound is combusted by a spark at constant volume in the presence of pure oxygen (completely oxidized); the amount of heat exchanged between the reaction chamber and a surrounding water jacket is a measure of enthalpy change. (p. 44)

exothermic

A reaction that releases heat and ΔH < 0. (p. 45)

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endothermic

A reaction that absorbs heat and ΔH > 0. (p. 45)

calorie (cal)

A unit of energy; the amount of heat energy required to raise 1 gram of water by 1 °C using a calorimeter; a Calorie is 103 calories or 1 kilocalorie (kcal), which is equal to 4.184 kilojoules (kJ). (p. 45)

joule (J)

The SI unit of energy; the amount of work done (or energy transferred) when a force of 1 Newton displaces an object by 1 meter in the direction of the force. (p. 45)

Gibbs free energy (G)

A measure of the spontaneity of a reaction, defined as the difference between the enthalpy and entropy of a system at a given temperature (G = H - TS). (p. 48)

exergonic

A chemical reaction that releases energy and is favorable in the direction written with a ΔG < 0. (p. 48)

endergonic

A chemical reaction that requires energy and is unfavorable in the direction written with a ΔG > 0. (p. 48)

standard free energy change (ΔG°)

A reference point for comparing chemical reactions under a defined set of conditions (1 atm pressure, 298 K, 1 M concentration of reactants and products): ΔG° = ΔH° - TΔS° (p. 48)

biochemical standard

Reaction conditions of 1 atm pressure, 298 K temperature, 1 M concentrations of

conditions

reactants and products, pH of 7, and concentration of water at 55.5 M. (p. 48)

equilibrium constant

A measure of the directionality of a reaction under standard conditions, where all

(Keq)

products and reactants start at 1 M and proceed to their equilibrium concentrations. (p. 49)

adenylate system

A group of several phosphoryl transfer reactions that interconvert ATP, ADP, and AMP. (p. 53)

isozymes

Functionally related enzymes encoded by different genes. (p. 54)

isoforms

Functionally distinct proteins transcribed from the same gene. (p. 54)

energy charge (EC)

A measure of the energy state of a cell in terms of ATP, ADP, and AMP ratios: EC = [ATP] + 0.5[ADP] / [ATP] + [ADP] + [AMP] (p. 54)

catabolic pathway

A metabolic pathway that converts energy-rich compounds into energy-depleted compounds, releasing energy for the cell. (p. 55)

anabolic pathway

A metabolic pathway for the biosynthesis of biomolecules from smaller precursors. (p. 55)

hydrogen bond

A weak noncovalent bond in which hydrogen is shared between two electronegative atoms. (p. 57)

proton hopping

A series of hydrogen-bond exchanges between adjacent H2O molecules leading to the transient formation of hydronium ions (H3O+). (p. 58)

ionic interaction

A weak interaction between oppositely charged atoms or groups. (p. 61)

van der Waals

A weak interaction between the dipoles of nearby electrically neutral molecules. (p...