Chemical Elements and Compounds
         Matter consists of chemical elements in pure form and in combinations called compounds
         Life requires about 25 chemical elements

    Atoms and Molecules
         Atomic structure determines the behavior of an element
         Atoms combine by chemical bonding to form molecules
         Weak chemical bonds play important roles in the chemistry of life
         A molecule's biological function is related to its shape
         Chemical reactions make and break chemical bonds

Chapter 2 Vocabulary

matter - anything that takes up space and has mass.

element - any substance that cannot be broken down to any other substance.

compound - a chemical combination, in a fixed ratio, of two or more elements.

trace element - an element indispensable for life but required in extremely minute amounts.

atom - the smallest unit of matter that retains the properties of an element.

neutron - an electrically neutral particle (a particle having no electrical charge), found in the atom.

proton - a subatomic particle with a single positive electrical charge, found in the nucleus of the atom

electron - a particle with a single negative charge; one or more electrons orbit the nucleus of the atom.

Atomic nucleus - an atom's central core, containing protons and neutrons.

dalton (DAWL-ton) - the atomic mass unit; a measure of mass for atoms and subatomic particles.

atomic number - the number of protons in the nucleus of an atom, unique for each element and designated by a subscript to the left of the  elemental symbol.

mass number - the sum of the number of protons and neutrons in an atom's nucleus.

atomic weight - the total atomic mass, which is the mass in grams of one mole of the atom.

isotope (EYE-so-tope) - one of several atomic forms of an element, each containing a different number of neutrons and thus differing in atomic mass.

radioactive isotope - an isotope, an atomic form of a chemical element, that is unstable; the nucleus decays spontaneously, giving off detectable particles and energy.

energy - the capacity to do work by moving matter against an opposing force.

potential energy - the energy stored by matter as a result of its location or spatial arrangement.

electron shell - an energy level at which an electron orbits the nucleus of an atom.

Orbital - the three dimensional space where an electron is found 90 % of the time.

Valence electrons - the outermost electrons which determine the chemical properties of an atom

valence shell - the outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom.

chemical bond - An attraction between two atoms resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms; the bonded atoms gain complete outer electron shells.

covalent bond (koh-VAY-lent) - a type of strong chemical bond in which two atoms share one pair of electrons in a mutual valence shell.

molecule - two or more atoms held together by chemical bonds.

structural formula - a type of molecular notation in which the constituent atoms are joined by lines representing covalent bonds.

molecular formula - a type of molecular notation indicating only the quantity of the constituent atoms.

Double covalent bond - the sharing of two pairs of valence electrons

Valence - the bonding capacity which equals the number of unpaired electrons.

electronegativity - the tendency for an atom to pull electrons toward itself.

nonpolar covalent bond - a type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity.

polar covalent bond - a type of covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

ion (EYE-on) - an atom that has gained or lost electrons, thus acquiring a charge.

cation (KAT-eye-on) - an ion with a positive charge, produced by the loss of one or more electrons.

anion (AN-eye-on) - a negatively charged ion.

ionic bond (eye-ON-ik) - a chemical bond resulting from the attraction between oppositly charged ions.

hydrogen bond - a type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.

Van der Waals interactions - weak attractions between molecules or parts of molecules that are brought abour by localized charge fluctuations.

reactant - a starting material in a chemical reaction.

products - the final material in a chemical reaction.

chemical equilibrium - in a reversible chemical reaction, the point at which the rate of the forward reaction equals the rate of the reverse reaction.

    Effects of Water’s Polarity
          The polarity of water molecules results in hydrogen bonding
          Organisms depend on the cohesion of water molecules
          Water moderates temperatures on Earth
          Oceans and lakes don’t freeze because ice floats
          Water is the solvent of life

     Dissociation of Water Molecules
          Organisms are sensitive to changes in pH
          Acid precipitation threatens the fitness of the environment

Chapter 3 Vocabulary

cohesion - the binding together of like molecules, often by hydrogen bonds.

adhesion - the tendency of different kinds of molecules to stick together.

surface tension - a measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules.

kinetic energy (kih-NET-ik) - the energy of motion, which is directly related to the speed of that motion. Moving matter does work by transferring some of its kinetic energy to other matter.

heat - the total amount of kinetic energy due to molecular motion in a body of matter. Heat is energy in its most random form.

temperature - a measure of the intensity of heat in degrees, reflecting the average kinetic energy of the molecules.

calorie (cal) - the amount of heat energy required to raise the temperature of 1 g of water 1° C; the amount of heat energy that 1 g of water releases when it cools by 1° C. The Calorie (with a capital C), usually used to indicate the energy content of food, is a kilocalorie.

kilocalorie (kcal) - a thousand calories; the amount of heat energy required to raise the temperature of 1 kg of water 1° C.

joule (J) - a unit of energy: 1 J = 0.239 cal; 1 cal = 4.184 J.

specific heat - the amount of heat that must be absorbed or lost for 1 g of a substance to change its temp. 1° C.

heat of vaporization - the quantity of heat a liquid must absorb for 1 g of it to be converted from a liquid to the gaseous state.

evaporative cooling - the property of a liquid whereby the surface becomes cooler during evaporation, owing to a loss of highly kinetic molecules to the gaseous state.

solution - a homogeneous, liquid mixture of two or more substances.

solvent - the dissolving agent of a solution. Water is the most versatile solvent known.

solute (SOL-yoot) a substance that is dissolved in a solution.

aqueous solution (AY-kwee-us) - a solution in which water is the solvent.

hydrophilic (HY-droh-FIL-ik) - having an affinity for water.

hydrophobic (HY-droh-FOH-bik) - having an aversion to water; tending to coalesce and form droplets in water.

mole - the number of grams of a substance that equals its molecular weight in daltons and contains Avogadro's number of molecules.

molecular weight

molarity - a common measure of solute concentration, referring to the number of moles of solute in 1 L of solution.

     The Importance of Carbon
        Organic chemistry is the study of carbon chemistry
          Carbon molecules are the most versatile building blocks of molecules
          Variation in carbon skeletons contributes to the diversity of organic molecules

      Functional Groups
          Functional groups also contribute to the molecular diversity of life
          The chemical elements of life: a review

Chapter 4 Vocabulary

organic chemistry- the study of carbon compounds (organic compounds).

hydrocarbon (HY-droh-kar-bon) - an organic molecule consisting only of carbon and hydrogen.

isomer (EYE-sum-ur) - one of several organic compounds with the same molecular formula but different structures and therefore different properties. The three types are structural isomers, geometric isomers, and enantiomers.

enantiomer (eh-NAN-she-uh-mer) - one of a pair of molecules that are mirror-image isomers of each other.

functional group - a specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.

hydroxyl group (hy-DROKS-ul) - a functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols.

alcohols - organic compounds containing hydroxyl groups

carbonyl group (KAR-buh-nil) - a functional group present in aldehydes and ketones, consisting of a carbon atom double-bonded to an oxygen atom.

aldehyde (AL-duh-hyde) - an organic molecule with a carbonyl group located at the end of the carbon skeleton.

ketone - organic compounds where the carbonyl group is not at the end of a carbon skeleton

carboxyl group (kar-BOX-ul) - a functional group present in organic acids, consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group.

amino group - a functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1.

amines - organic compounds containing an amino group

sulfhydryl group - the organic functional group which consists of a sulfur atom bonded to an atom of hydrogen

thiols - organic compounds containing sulfhydryls

phosphate group (FOS-fate) - a functional group important in energy transfer.

monosaccharide (MON-oh-SAK-ur-ide) - the simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides. Also known as simple sugars, the molecular formulas of monosaccharides are generally some multiple of CH2O.

    Polymer Principles
         Most macromolecules are polymers
         An immense variety of polymers can be built from a small set of monomers

    Carbohydrates - Fuel and Building Material
         Sugars, the smallest carbohydrates, serve as fuel
         Matter consists of chemical elements in and carbon sources
         Polysaccharides, the polymers of sugars, have storage and structural roles

    Lipids - Diverse Hydrophobic Molecules
         Fats store large amounts of energy
         Phospholipids are major components of cell membranes
         Steroids include cholesterol and certain hormones

    Proteins - The Molecular Tools of the Cell
         A polypeptide is a polymer of amino acids connected in a specific sequence
         A protein’s function depends on its specific conformation

    Nucleic Acids - Informational Polymers
         Nucleic acids store and transmit hereditary information
         A nucleic acid strand is a polymer of nucleotides
         Inheritance is based on replication of the DNA double helix
         We can use DNA and proteins as tape measures of evolution

Chapter  5 Vocabulary

polymer (POL-eh-mur) - a large molecule consisting of many identical or similar monomers linked together.

monomer (MON-uh-mer) - the subunit that serves as the building block of a polymer.

condensation reaction A reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water; also called dehydration reaction.

dehydration reaction - when monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule

hydrolysis (hy-DROL-eh-sis) - a chemical process that lyses or splits molecules by the addition of water; an essential process in digestion.

carbohydrate (KAR-bo-HY-drate) - a sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides).

disaccharide (dy-SAK-ur-ide) - a double sugar, consisting of two monosaccharides joined by dehydration synthesis.

glycosidic linkage - a covalent bond formed between two monosaccharides by a dehydration eraction.

polysaccharide (POL-ee-SAK-ur-ide) - a polymer of up to over a thousand monosaccharides, formed by condensation synthesis.

starch - a storage polysaccharide in plants consisting entirely of glucose.

glycogen (GLY-koh-jen) - an extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.

cellulose (SELL-yoo-lose) - a structural polysaccharide of cell walls, consisting of glucose monomers joined by (-1, 4-glycosidic linkages.

lipid (LIH-pid) - one of a family of compounds, including fats, phospholipids, and steroids, that are insoluble in water.

fat (triacylglycerol) (tri-AH-sil-GLIS-er-all) - a biological compound consisting of three fatty acids linked to one glycerol molecule.

fatty acid - a long carbon chain carboxylic acid. Fatty acids vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form fat.

triacylglycerol - the resulting fat from the joining of three fatty acids to glycerol by an ester linkage

saturated fatty acid - a fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.

unsaturated fatty acid - a fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.

phospholipids (FOS-foh-LIP-ids) - molecules that constitute the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail.

steroids - a class of lipids characterized by a carbon skeleton consisting of four rings with various functional groups attached.

cholesterol (kol-ESS-teh-rol) - a steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids.

conformation - the unique three dimensional shape of proteins

polypeptide (POL-ee-PEP-tide) - a polymer (chain) of many amino acids linked together by peptide bonds.

amino acid (uh-MEE-noh) - an organic molecule possessing both carboxyl and amino groups. Amino acids serve as the monomers of proteins.peptidesbonds

primary structure - the level of protein structure referring to the specific sequence of amino acids.

secondary structure - the localized, repetitive folding of the polypeptide backbone of a protein due to hydrogen bond formation between peptide linkages.

alpha helix - a spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

pleated sheet - one form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

tertiary structure (TUR-shee-air-ee) - irregular contortions of a protein molecule due to interactions of side chains involved in hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges.

hydrophobic interaction - a type of weak chemical bond formed when molecules that do not mix with water coalesce to exclude the water.

disulfide bridges - strong covalent bonds formed where two cystiene monomers are broguht close together by the folding of the protein.

quaternary structure (KWAT-ur-nair-ee) - the particular shape of a complex, aggregate protein, defined by the characteristic three-dimensional arrangement of its constituent subunits, each a polypeptide.

Denaturation - the unraveling of a protein causing the loss of native conformers

chaperone proteins - molecules that function as temporary braces in assisting the folding of other proteins

deoxyribonucleic acid (DNA) (DEE-oks-ee-ry-boh-noo-KLAY-ik) - a double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins.

ribonucleic acid (RNA) (RY-boh-noo-KLAY-ik) - a single-stranded nucleic acid molecule involved in protein synthesis, the structure of which is specified by DNA.

nucleotide (NOO-klee-oh-tide) - the building block of a nucleic acid, consisting of a five-carbon sugar covently bonded to a nitrogenous base and a phosphate group.

pyrimidine - family of nitrogenous bases; Six-membered ring of carbon and nitrogen atoms; cytocine, thymine, and uracil

purines - family of nitrogenous bases; Six-membered ring of carbon fused to a five-membered ring; adenine and guanine

ribose - rhe sugar component of RNA.

deoxyribose - the sugar component of DNA, having one less hydroxyl group than ribose, the sugar component of RNA.

polynucleotide (POL-ee-NOO-klee-oh-tide) - a polymer made up of many nucleotides covalently bonded together.

double helix - the form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

    Metabolism, Energy, and Life
         The chemistry of life is organized into metabolic pathways
         Organisms transform energy
         The energy transformations of life are subject to two laws of
         thermodynamics
         Organisms live at the expense of free energy
         ATP powers cellular work by coupling exergonic reactions to endergonic
         reactions

    Enzymes
         Enzymes speed up metabolic reactions by lowering energy barriers
         Enzymes are substrate-specific
         The active site is an enzyme's catalytic center
         A cell's physical and chemical environment affects enzyme activity

    The Control of Metabolism
         Metabolic control often depends on allosteric regulation
         The localization of enzymes within a cell helps order metabolism
         The theme of emergent properties is manifest in the chemistry of life: a
         review

Chapter 6 Vocabulary

catabolic pathway (KAT-uh-BOL-ik) - a metabolic pathway that releases energy by breaking down complex molecules into simpler compounds.

anabolic pathways - a metabolic pathway that consumes energy to build complicated molecules from simpler ones

bioenergetics - the study of how organisms manage their energy resources.

energy of activation (EA) - the amount of energy that reactants must absorb before a chemical reaction will start.

kinetic energy (kih-NET-ik) - the energy of motion, which is directly related to the speed of that motion. Moving matter does work by transferring some of its kinetic energy to other matter.

potential energy - the energy stored by matter as a result of its location or spatial arrangement.

thermodynamics - the study of the energy transformation that occurs in a collection of matter

first law of thermodynamics

second law of thermodynamics - the principle whereby every energy transfer or transformation increases the entropy of the universe. Ordered forms of energy are at least partly converted to heat, and in spontaneous reactions, the free energy of the system also decreases.

entropy (EN-truh-pee) - a quantitative measure of disorder or randomness, symbolized by S.

free energy - a quantity of energy that interrelates entropy (S) and the system's total energy (H); symbolized by G. The change in free energy of a system is calculated by the equation G = (H - T(S, where T is absolute temperature.

exergonic reaction (EKS-ur-GON-ik) - a spontaneous chemical reaction in which there is a net release of free energy.

endergonic reaction (EN-dur-GON-ik) - a nonspontaneous chemical reaction in which free energy is absorbed from the surroundings.

metabolic equalibrium

energy coupling - the use of an exergonic process to drive an endergonic one.

ATP (adenosine triphosphate) (uh-DEN-oh-sin try-FOS-fate) - an adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells.

phosphorylated intermediate - the recipient of the phosphate group in ATP hydrolysis.

enzyme - a class of proteins serving as catalysts, chemical agents that change the rate of a reaction without being consumed by the reaction.

catalyst - a chemical agent that changes the rate of a reaction without being consumed by the reaction.

free energy of activation - the initial investment of energy necessary to start a chemical reaction; also called activation energy

substrate - the substance on which an enzyme works.

active site - the specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds.

induced fit - the change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate.

cofactor - any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.

coenzyme (ko-EN-zyme) - an organic molecule serving as a cofactor. Most vitamins function as coenzymes in important metabolic reactions.

competitive inhibitor -a substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics.

noncompetitive inhibitor - a substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate.

allosteric site (AL-oh-STEER-ik) - a specific receptor site on an enzyme molecule remote from the active site. Molecules bind to the allosteric site and change the shape of the active site, making it either more or less receptive to the substrate.

feedback inhibition - a method of metabolic control in which the end-product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

cooperativity (koh-OP-ur-uh-TIV-eh-tee) - an interaction of the constituent subunits of a protein causing a conformational change in one subunit to be transmitted to all the others.