Unit 1 Beta

Chemistry of Life: the one-page sheet

1.1 Structure of Water and Hydrogen Bonding

Oxygen pulls shared electrons harder than hydrogen, and the water molecule is bent, so water is polar: a δ− oxygen end and δ+ hydrogen ends. Opposite partial charges on neighboring molecules attract, forming hydrogen bonds. Those bonds explain cohesion and surface tension, adhesion and capillary action, water's high specific heat and high heat of vaporization, why ice floats, and why water dissolves ions and polar molecules but not oil. Water also splits into a few hydrogen and hydroxide ions; pH measures the hydrogen ions, and buffers keep pH steady.

A covalent bond joins atoms inside one molecule by sharing electrons. A hydrogen bond is a weaker attraction between a δ+ hydrogen and a δ− atom such as oxygen or nitrogen, usually on a different molecule.
Cohesion is water attracting water; adhesion is water attracting a different polar or charged surface. Water climbs a narrow tube when adhesion pulls it up the walls and cohesion drags the rest of the column along.
Specific heat is about changing temperature; heat of vaporization is about changing from liquid to gas. Hydrogen bonds make both unusually high for water, so water warms slowly and evaporation cools strongly.
A polar or charged substance is hydrophilic and dissolves in water. A nonpolar one, such as oil, is hydrophobic: water molecules bond to each other instead and push it aside.
pH measures hydrogen ion concentration on a scale where each whole step is a tenfold change. A buffer takes up or releases hydrogen ions, so the pH of a solution changes much less when acid or base is added.

The shared electrons spend more time near oxygen, so the oxygen end of a water molecule carries a partial negative charge (δ−) and each hydrogen a partial positive charge (δ+). The charges do not cancel out: water is a polar molecule with a negative end and a positive end. The δ+ hydrogen of one molecule is drawn to the δ− oxygen of another, forming a hydrogen bond; each water molecule can hold up to four. Water clings to itself (cohesion, surface tension) and to charged or polar surfaces (adhesion), and it takes extra energy to speed its molecules up or pull them into the air. Water warms slowly (high specific heat) and evaporating water carries away a large amount of heat (high heat of vaporization), which steadies temperatures in bodies, lakes and coasts. Salts and polar substances dissolve in water, which is why most of the chemistry of a cell takes place in water.

potential energy: Kinetic energy is energy of motion (temperature measures how fast molecules move). Potential energy is stored energy, such as the energy in the arrangement of attracting particles; chemical energy is potential energy stored in the bonds of molecules.
atom: The smallest unit of a chemical substance: a dense center of positively charged protons and uncharged neutrons, surrounded by negatively charged electrons. Atoms bond to each other through their electrons.
molecule: Two or more atoms held together by covalent bonds, such as H2O (one oxygen and two hydrogens).
covalent bond: A bond in which two atoms share a pair of electrons. Sharing two pairs makes a double bond, three pairs a triple bond. Covalent bonds hold the atoms of a molecule together.
electronegativity: How strongly an atom pulls on the electrons it shares in a covalent bond. Oxygen and nitrogen are highly electronegative; carbon and hydrogen are not.
polar covalent bond: A covalent bond in which electrons are shared unequally, because one atom is more electronegative (O–H, N–H). In a nonpolar covalent bond (C–H, C–C) they are shared about equally.
polarity: Uneven distribution of charge in a molecule: one end carries a partial negative charge (δ−) and another a partial positive charge (δ+). Water is polar; oil is nonpolar.
ion: An atom or group of atoms with an electric charge because it has gained electrons (a negative anion, such as Cl−) or lost electrons (a positive cation, such as Na+).
ionic bond: The attraction between oppositely charged ions, as between Na+ and Cl− in table salt. A solid held together this way is an ionic compound, or salt.
hydrogen bond: A weak attraction between a partially positive hydrogen atom (bonded to O or N) and a partially negative atom, such as oxygen or nitrogen, in another molecule or another part of the same large molecule.
water molecule: H2O: one oxygen covalently bonded to two hydrogens in a bent shape. The oxygen end is partly negative and the hydrogen ends partly positive, so each molecule can hydrogen-bond with up to four neighbors.
cohesion: Water molecules attracting each other through hydrogen bonds. It produces surface tension and holds the water column together in plants.
surface tension: The resistance of a liquid's surface to being stretched or broken, caused by cohesion among the molecules at the surface. Water's is very high.
adhesion: Water molecules attracting a different polar or charged surface, such as glass, paper or the walls of xylem.
capillary action: The rise of water in a narrow tube or porous material: adhesion pulls water up the walls and cohesion pulls the rest of the water along.
specific heat: The energy needed to raise the temperature of 1 gram of a substance by 1 °C. Water's is high (4.18 J/g·°C) because heat must break hydrogen bonds before molecules move faster.
heat of vaporization: The energy needed to turn 1 gram of a liquid into a gas. Water's is high (about 2,260 J/g at 100 °C) because an escaping molecule must break all its hydrogen bonds.
evaporative cooling: The cooling of a surface as a liquid evaporates from it: the fastest molecules escape and carry energy away, leaving slower, cooler molecules behind. Sweating and transpiration cool this way.
density of ice: Ice is about 9% less dense than liquid water because hydrogen bonds lock its molecules into an open lattice, so ice floats and lakes freeze from the top down.
xylem: The plant tissue of narrow, hollow tubes that carries water and dissolved minerals from the roots up to the leaves.
stomata: Tiny pores, mostly on the undersides of leaves (one is a stoma), each opened and closed by a pair of guard cells. Water vapor leaves and carbon dioxide enters through them.
transpiration: The loss of water vapor from a plant, mostly through open stomata. Evaporation at the leaf pulls a cohesive column of water up the xylem.
solvent: The substance in which other substances dissolve. Water dissolves ions and polar molecules, so it is the solvent for most of the chemistry in cells.
solute: A substance dissolved in a solvent. A solute spread evenly through a solvent makes a solution; with water as the solvent it is an aqueous solution.
hydrophilic: "Water-loving": polar or charged, so it attracts water and usually dissolves in it. Salt and sugar are hydrophilic.
hydrophobic: "Water-avoiding": nonpolar, so it does not attract water and does not dissolve in it. Water molecules bond to each other and push hydrophobic molecules together, as with oil drops.
hydrogen ion: H+, a hydrogen atom without its electron (a bare proton). Water splits into a few H+ and hydroxide ions (OH−); the H+ concentration sets the pH.
pH: A measure of hydrogen ion concentration: pH = −log[H+]. pH 7 is neutral, below 7 is acidic, above 7 is alkaline (basic), and each whole unit is a tenfold change in [H+].
acid: A substance that adds hydrogen ions (H+) to a solution and lowers its pH, such as hydrochloric acid.
base (chemistry): A substance that lowers the hydrogen ion concentration of a solution, by taking up H+ or adding hydroxide ions (OH−), and raises its pH.
buffer: A pair of substances that takes up hydrogen ions when they are added and releases them when they are removed, so pH changes little. Blood's main buffer is carbonic acid and bicarbonate.

1.2 Elements of Life

Organisms build their molecules from atoms they take in; atoms are recycled, never made new. Carbon's four bonds make chains, branches and rings, and functional groups such as hydroxyl, carboxyl, amino, phosphate and sulfhydryl give each molecule its chemistry. Nitrogen goes into proteins and nucleic acids; phosphorus into nucleic acids, ATP and some lipids; sulfur into some amino acids. Photosynthesis and cellular respiration cycle carbon, hydrogen and oxygen between the air, water and living things.

An element is a substance made of one kind of atom. Six of them, carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur (CHONPS), make up about 98% of the mass of a living thing.
Isotopes are atoms of one element with different numbers of neutrons. They behave the same in chemistry, so a radioactive or heavy isotope can be fed to cells and traced into the molecules that use that element.
Organic molecules are built on carbon skeletons. Small attached groups of atoms, the functional groups, give each molecule its chemistry: –OH is polar, –COOH acts as an acid, –NH₂ as a base.
Which element is in which molecule: N in proteins and nucleic acids; P in nucleic acids, ATP and some lipids; S in some amino acids, so in many proteins. Sugars and fats are mostly C, H and O.

They must take in atoms from their surroundings, because atoms are not created or destroyed in living things; they are only rearranged. Carbon atoms link into chains, branches and rings: the carbon skeletons of every large biological molecule. Organisms must take in nitrogen and phosphorus (plants from the soil, animals from food) or they cannot build these molecules or grow. Sulfur is needed to build many proteins; together the core elements of life are C, H, O, N, P and S. The same atoms cycle between air, water and organisms again and again: matter is recycled, while energy flows through.

element: A pure substance made of one kind of atom, defined by its number of protons. Carbon, oxygen and nitrogen are elements.
isotope: One of two or more forms of an element whose atoms have the same number of protons but different numbers of neutrons. Radioactive isotopes, such as phosphorus-32, can be traced through cells because they behave chemically like the ordinary atoms.
elements of life: Carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur (CHONPS), which together make up about 98% of the mass of living things.
recycling of matter: Atoms are not created or destroyed by living things: organisms take them in from the environment, rearrange them into new molecules and return them, so the same atoms cycle through air, water and organisms.
organic molecule: A molecule built on a skeleton of carbon atoms, usually bonded to hydrogen. Water, carbon dioxide and salts are inorganic molecules.
carbon skeleton: The chain, branched chain or ring of carbon atoms that forms the framework of an organic molecule. A molecule of only carbon and hydrogen is a hydrocarbon.
isomer: One of two or more molecules with the same chemical formula but different arrangements of atoms, and so different shapes and properties.
functional group: A small cluster of atoms attached to a carbon skeleton that gives a molecule its chemical behavior, such as hydroxyl (–OH) or carboxyl (–COOH).
hydroxyl group: –OH: a polar group that hydrogen-bonds with water and makes molecules such as sugars more soluble.
carboxyl group: –COOH: an acidic group that releases a hydrogen ion and becomes –COO−. Every amino acid has one.
amino group: –NH2: a basic group that picks up a hydrogen ion and becomes –NH3+. Every amino acid has one.
phosphate group: A phosphorus atom bonded to four oxygens, carrying negative charge. Phosphate groups are part of nucleic acids, ATP and some lipids.
sulfhydryl group: –SH: a sulfur-containing group. Two sulfhydryl groups can bond to each other, linking parts of a protein. It is found in the amino acid cysteine.
methyl group: –CH3: a nonpolar group of one carbon and three hydrogens.
carbonyl group: C=O: a carbon double-bonded to an oxygen; a polar group found in sugars.
carbohydrate: A sugar or a larger molecule built from sugars, made of carbon, hydrogen and oxygen. Carbohydrates store energy and build structures.
lipid: A fat, oil or related molecule, made mostly of carbon and hydrogen, that does not dissolve in water because it is largely nonpolar.
amino acid: The building block of proteins: a small molecule with an amino group and a carboxyl group. Every amino acid contains nitrogen; a few also contain sulfur.
protein: A large molecule made of one or more chains of amino acids; proteins do most of the work in cells.
nucleic acid: A large molecule that stores or helps use the information in genes, such as DNA. Nucleic acids contain carbon, hydrogen, oxygen, nitrogen and phosphorus.
ATP: Adenosine triphosphate: the molecule cells use to carry energy from where it is released to where it is used. It contains three phosphate groups.
photosynthesis: The process by which plants, algae and some bacteria use the energy of light to build sugar from carbon dioxide and water, releasing oxygen.
cellular respiration: The process by which cells break down sugar, usually with oxygen, releasing carbon dioxide and water and capturing the energy as ATP.
nitrogen in biological molecules: Organisms need nitrogen to build proteins (every amino acid contains it) and nucleic acids.
phosphorus in biological molecules: Organisms need phosphorus to build nucleic acids, ATP and some lipids, all of which contain phosphate groups.
sulfur in biological molecules: Organisms need sulfur because some amino acids, such as cysteine, contain it, so it is part of many proteins.

1.3 Introduction to Macromolecules

Macromolecules are large molecules; most are polymers, chains of monomers joined by covalent bonds. Dehydration synthesis joins two monomers by removing an –OH from one and an –H from the other as water; hydrolysis breaks the bond by adding water back. A chain of n monomers needs n − 1 bonds. Enzymes speed up both reactions. Carbohydrates, proteins and nucleic acids are polymers; lipids are not. How the monomers are arranged sets a molecule's shape, and its shape sets its function.

A monomer is one building block; a polymer is a long chain of monomers joined by covalent bonds. Carbohydrates, proteins and nucleic acids are polymers; lipids are large molecules but not chains of repeating units.
Dehydration synthesis builds: monomer + monomer → longer chain + water. Hydrolysis breaks: polymer + water → shorter pieces. "Dehydration" means water is removed; "hydro-lysis" means splitting with water.
Counting rule: a straight chain of n monomers has n − 1 links, so making it releases n − 1 water molecules and breaking it down completely uses n − 1.
Structure determines function: the same monomers, linked in a different order or a different way, give molecules with different shapes, and shape decides what a molecule can do.

They build large molecules (polymers) by linking small, similar units (monomers) into chains. The –OH and –H leave together as a water molecule, and a new covalent bond links the two monomers: dehydration synthesis. A straight chain of n monomers is held together by n − 1 bonds and its synthesis releases n − 1 water molecules. The –H goes to one monomer and the –OH to the other, the bond breaks, and the monomers are freed: hydrolysis. Enzymes, proteins that speed up reactions, carry out dehydration synthesis and hydrolysis fast enough for life.

macromolecule: A very large biological molecule, usually thousands of atoms. Carbohydrates, proteins and nucleic acids are macromolecules built as polymers; large lipids are macromolecules that are not polymers.
monomer: A small molecule that can link with others like it to form a polymer; one building block.
polymer: A large molecule made of many monomers joined in a chain by covalent bonds.
chemical reaction: A process that breaks some chemical bonds and forms new ones, turning reactants into products. Atoms are rearranged, not created or destroyed.
dehydration synthesis: A reaction that joins two monomers with a covalent bond by removing an –OH from one and an –H from the other, which leave as a water molecule. Also called a condensation reaction.
hydrolysis: A reaction that breaks the bond between two monomers by adding a water molecule: the –H goes to one monomer and the –OH to the other.
enzyme: A protein that speeds up a chemical reaction, such as the hydrolysis of a polymer, without being used up. Enzymes are taught in full in Unit 3.
structure determines function: The principle that a molecule's (or a cell's, or an organ's) structure, especially its shape, determines what it can do.

1.4 Carbohydrates

Carbohydrates are built from monosaccharides such as glucose, fructose and galactose. Glycosidic bonds, made by dehydration synthesis, join them into disaccharides (sucrose, lactose, maltose) and polysaccharides. Starch and glycogen are coiled, branched chains of α-glucose that store energy. Cellulose is straight chains of β-glucose that hydrogen-bond into fibers in plant cell walls, and chitin is a similar structural polymer that contains nitrogen. The α or β link changes shape, and shape decides function and digestibility.

Monosaccharides (glucose, fructose, galactose) are single sugars; disaccharides are two joined by a glycosidic bond (sucrose = glucose + fructose; lactose = glucose + galactose; maltose = glucose + glucose); polysaccharides are long chains.
Storage polysaccharides: starch (plants) and glycogen (animals, in liver and muscle), both α-glucose, coiled and branched. Structural polysaccharides: cellulose (plant cell walls, β-glucose) and chitin (insect exoskeletons and the walls of fungi, a β-linked sugar that contains nitrogen).
Same monomer, different bond, different job: starch and cellulose are both pure glucose. The α or β link changes the chain's shape, and shape decides both its role and which enzymes can break it.

It dissolves easily in water and is the monomer from which larger carbohydrates are built. Two sugars make a disaccharide (such as sucrose); hundreds or thousands make a polysaccharide. Bonds between α-glucose units give a chain that coils (starch, glycogen); bonds between β-glucose units give a straight chain with every other unit flipped (cellulose). Starch in plants and glycogen in animals store glucose that enzymes can quickly hydrolyze when energy is needed. Cellulose forms strong fibers in plant cell walls; enzymes that cut α bonds do not fit β bonds, so most animals cannot digest it.

monosaccharide: A single sugar unit, the monomer of carbohydrates, such as glucose, fructose or galactose. Also called a simple sugar.
glucose: C6H12O6, the six-carbon sugar that cells break down for energy, that photosynthesis makes, and that forms starch, glycogen and cellulose.
fructose: Fructose and galactose: six-carbon sugars with the same formula as glucose (C6H12O6) but different structures (isomers of glucose).
alpha glucose: The two ring forms of glucose. In alpha glucose the –OH on carbon 1 points below the ring; in beta glucose it points above. Starch and glycogen are built from alpha glucose, cellulose from beta glucose.
glycosidic bond: The covalent bond, an oxygen bridge, that joins two sugar units. It forms by dehydration synthesis and is broken by hydrolysis.
disaccharide: Two monosaccharides joined by a glycosidic bond: sucrose (glucose + fructose), lactose (glucose + galactose) or maltose (glucose + glucose).
polysaccharide: A carbohydrate polymer of many monosaccharides joined by glycosidic bonds, such as starch, glycogen, cellulose or chitin.
starch: The energy-storage polysaccharide of plants: chains of alpha glucose that coil (amylose) or coil and branch (amylopectin).
glycogen: The energy-storage polysaccharide of animals and fungi: highly branched chains of alpha glucose, stored mainly in the liver and muscles.
cell wall: A stiff layer outside the cell of plants (and of fungi and many bacteria) that supports the cell. Plant cell walls are made mostly of cellulose fibers.
cellulose: A structural polysaccharide of beta glucose. Its straight chains hydrogen-bond side by side into strong fibers that make up plant cell walls; humans cannot digest it (dietary fiber).
chitin: A structural polysaccharide of beta-linked, nitrogen-containing sugars that forms the exoskeletons of insects and crabs and the walls of fungi.
energy storage polysaccharide: Storage polysaccharides (starch, glycogen) are coiled, branched chains of alpha glucose that enzymes break down quickly; structural polysaccharides (cellulose, chitin) are straight beta-linked chains bonded into fibers.

1.5 Lipids

Lipids are mostly nonpolar, so they are hydrophobic. Triglycerides (glycerol plus three fatty acids) store energy densely. Saturated fatty acids are straight and pack tightly, so they are solid at room temperature; cis double bonds in unsaturated fatty acids kink the chains, so they are liquid. Phospholipids have a hydrophilic head and two hydrophobic tails and form the bilayers of cell membranes. Steroids such as cholesterol and steroid hormones are built on four fused rings.

A triglyceride (fat or oil) is glycerol + three fatty acids, joined by dehydration synthesis (three waters released). Lipids are not polymers: there is no repeating chain of monomers.
Saturated: no C=C double bonds, chains "saturated" with hydrogen, straight, solid at room temperature (animal fats). Unsaturated: one or more C=C double bonds, kinked, liquid (plant and fish oils).
Phospholipids are amphipathic: a hydrophilic head and hydrophobic tails. That is why they form bilayers, and cell membranes are phospholipid bilayers.
Steroids are lipids built from four fused carbon rings. Cholesterol sits in animal cell membranes; steroid hormones such as testosterone and estrogen act as signals.

Lipids are hydrophobic: they do not dissolve in water, and water pushes them together. Straight chains pack tightly side by side, attract each other strongly, and need more heat to melt: saturated fats such as butter are solid at room temperature. Kinked chains cannot pack tightly, attract each other less and melt at lower temperatures: unsaturated fats such as olive oil are liquid. In water, phospholipids arrange themselves into a bilayer, heads facing the water on both sides and tails hidden in the middle: the basic structure of every cell membrane. They store about twice as much energy per gram as carbohydrates, which makes fat the body's long-term energy store.

fatty acid: A long hydrocarbon chain (the hydrocarbon tail) with a carboxyl group at one end; the building block of fats, oils and phospholipids.
triglyceride: A fat or oil molecule: glycerol joined to three fatty acids, made by dehydration synthesis (releasing three waters). The main long-term energy store.
saturated fatty acid: A fatty acid with only single carbon-carbon bonds, so it carries as much hydrogen as possible and its chain is straight. Saturated fats pack tightly and are solid at room temperature.
unsaturated fatty acid: A fatty acid with one or more carbon-carbon double bonds. A cis double bond kinks the chain, so unsaturated fats pack loosely and are liquid (oils) at room temperature.
phospholipid: A lipid made of glycerol, two fatty acid tails and a phosphate-containing head. Its hydrophilic head and hydrophobic tails make it form bilayers in water.
amphipathic: Having both a hydrophilic (water-loving) part and a hydrophobic (water-avoiding) part, like a phospholipid with its polar head and nonpolar tails.
lipid bilayer: A double layer of phospholipids in water, with the hydrophobic tails facing each other in the middle and the hydrophilic heads facing the water on both sides.
membrane: A thin boundary, built on a phospholipid bilayer, that encloses a cell (the cell membrane) or a space inside it. Membranes are taught in full in Unit 2.
steroid: A lipid whose carbon skeleton is four fused rings, such as cholesterol, testosterone and estrogen.
cholesterol: A steroid found in animal cell membranes, where it steadies the membrane against temperature changes; the starting molecule for steroid hormones.
steroid hormone: A hormone that is a steroid, such as testosterone or estrogen. Being hydrophobic, it can pass through the lipid bilayer of a cell membrane.
energy density of fats: Fats store about 37 kJ per gram, more than twice as much as carbohydrates (about 17 kJ per gram), because their chains are rich in C–H bonds and low in oxygen.

1.6 Nucleic Acids

Nucleic acids are polymers of nucleotides, each a phosphate, a five-carbon sugar and a nitrogenous base. Phosphates link the sugars into a backbone with a 5′ end and a 3′ end. DNA (deoxyribose; A, T, G, C) is usually a double helix of two antiparallel strands held together by hydrogen bonds between complementary bases, A with T and G with C. RNA (ribose; A, U, G, C) is usually single-stranded. The order of bases carries genetic information, and genes are stretches of that sequence.

DNA vs RNA: DNA has deoxyribose, thymine (T) and is usually double-stranded; RNA has ribose (one more –OH), uracil (U) instead of T, and is usually single-stranded.
Complementary base pairing: A pairs with T (or U in RNA) through two hydrogen bonds; G pairs with C through three. In double-stranded DNA, %A = %T and %G = %C.
Antiparallel: one strand runs 5′→3′, its partner 3′→5′. Always write a sequence from its 5′ end; the partner of 5′-ATG-3′ is 5′-CAT-3′.
The strands are held together by hydrogen bonds (weak, easy to separate by heating) but each strand is held together by covalent bonds in its backbone (strong, intact when strands separate).

It is the monomer of DNA and RNA; DNA nucleotides carry deoxyribose and one of A, T, G or C, RNA nucleotides carry ribose and one of A, U, G or C. The nucleotides form a strand with a sugar-phosphate backbone and bases sticking out to one side; the strand has two different ends, 5′ and 3′. Two strands can join base to base only where their sequences are complementary: every A opposite a T, every G opposite a C. DNA is two antiparallel strands twisted into a double helix, with the backbones outside and the paired bases inside. The base sequence carries information; a gene is a stretch of DNA whose sequence the cell uses, and complementary pairing lets each strand be copied.

five-carbon sugar: A sugar with five carbon atoms, such as ribose and deoxyribose; the sugar part of every nucleotide. Its carbons are numbered 1′ to 5′.
deoxyribose: The five-carbon sugar in DNA nucleotides; it lacks the –OH group that ribose has on carbon 2′.
ribose: The five-carbon sugar in RNA nucleotides; it has an –OH group on carbon 2′.
nitrogenous base: The nitrogen-containing ring molecule attached to the sugar of a nucleotide: adenine, guanine, cytosine, thymine (DNA only) or uracil (RNA only). Its order along a strand carries information.
adenine: The four bases of DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). A pairs with T, and G with C.
uracil: The base (U) that takes the place of thymine in RNA; it pairs with adenine.
nucleotide: The monomer of nucleic acids: a phosphate group, a five-carbon sugar and a nitrogenous base.
sugar-phosphate backbone: The repeating sugar–phosphate–sugar chain of a nucleic acid strand, held together by covalent phosphodiester bonds formed by dehydration synthesis; the bases stick out from it.
5' end: The two different ends of a nucleic acid strand: the 5′ end (free phosphate on a 5′ carbon) and the 3′ end (free –OH on a 3′ carbon). Sequences are written 5′ to 3′, and strands grow at the 3′ end.
DNA: Deoxyribonucleic acid: a nucleic acid of deoxyribose nucleotides with the bases A, T, G and C, usually a double helix; it stores genetic information.
RNA: Ribonucleic acid: a nucleic acid of ribose nucleotides with the bases A, U, G and C, usually single-stranded; it has several roles in using genetic information.
complementary base pairing: The rule that bases on opposite strands pair A with T (or U in RNA) by two hydrogen bonds and G with C by three, so the sequence of one strand fixes the sequence of the other.
double helix: The shape of DNA: two antiparallel strands twisted around each other, with the sugar-phosphate backbones outside and the base pairs inside, like a twisted ladder.
antiparallel: Running in opposite directions: in double-stranded DNA one strand runs 5′ to 3′ and its partner 3′ to 5′.
single-stranded: Made of one nucleotide strand, as most RNA is. Double-stranded nucleic acid, as most DNA is, has two complementary strands paired by hydrogen bonds.
genetic information: The information carried by the order (sequence) of bases in DNA or RNA.
gene: A stretch of DNA whose base sequence the cell uses, often as the instructions for building a particular protein.

1.7 Proteins

Proteins are polymers of amino acids joined by peptide bonds. The sequence (primary structure) determines how the chain folds: backbone hydrogen bonds make α helices and β pleated sheets (secondary structure); interactions among R groups, especially nonpolar side chains clustering away from water, fold the whole chain into its 3-D shape (tertiary structure); and some proteins combine several chains (quaternary structure). A protein's shape determines its function, so changing a single amino acid or denaturing the protein can stop it from working.

Primary = sequence (peptide bonds). Secondary = helices and sheets (backbone hydrogen bonds). Tertiary = overall 3-D fold (R-group interactions). Quaternary = several chains together (as in hemoglobin's four subunits).
R-group chemistry drives folding: nonpolar side chains cluster inside (hydrophobic interactions), polar and charged ones face the water, opposite charges form ionic bonds, and two cysteines can form a covalent disulfide bridge.
Denaturation unfolds a protein by breaking the weak bonds of its higher levels of structure. The peptide bonds survive, so the primary structure is unchanged, but the shape, and the function, are lost.

Amino acids differ only in their R groups, which may be nonpolar, polar, or charged (acidic or basic). A polypeptide forms, with an amino end (N-terminus) and a carboxyl end (C-terminus); its order of amino acids is its primary structure. Parts of the chain coil into α helices or fold into β pleated sheets: secondary structure. The whole chain folds into one specific 3-D shape: tertiary structure. Some proteins join two or more folded chains: quaternary structure. Changing one amino acid, or changing temperature or pH enough to break the weak bonds (denaturation), can change the shape and stop the protein from working.

R group: The side chain that makes each of the 20 amino acids different, attached to the central carbon alongside the amino group, carboxyl group and hydrogen.
nonpolar side chain: The chemical families of R groups: nonpolar (hydrophobic), polar uncharged (hydrophilic), and charged, either acidic (negative) or basic (positive). Their interactions drive folding.
peptide bond: The covalent bond between the carboxyl group of one amino acid and the amino group of the next, formed by dehydration synthesis. A short chain of amino acids is a peptide.
polypeptide: A chain of amino acids joined by peptide bonds, with a free amino group at one end (amino end, N-terminus) and a free carboxyl group at the other (carboxyl end, C-terminus).
primary structure: The sequence of amino acids in a polypeptide, held by peptide bonds and set by the gene for that protein.
secondary structure: Local coils (alpha helix) and folds (beta pleated sheet) in a polypeptide, held by hydrogen bonds between C=O and N–H groups of the backbone.
hydrophobic interaction: The clustering of nonpolar side chains away from water in the core of a folded protein; water molecules bond to each other and push the nonpolar groups together.
disulfide bridge: A covalent S–S bond between the sulfhydryl groups of two cysteine side chains, which locks parts of a folded protein together.
protein folding: The process by which a polypeptide takes on its working 3-D shape, driven by its sequence; chaperone proteins help many chains fold correctly in cells.
tertiary structure: The overall three-dimensional shape of one polypeptide, held by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bridges between side chains. A change in this shape is a conformational change.
quaternary structure: The arrangement of two or more folded polypeptides (subunits) in one functional protein, such as the four subunits of hemoglobin.
denaturation: The loss of a protein's shape when heat, extreme pH or certain chemicals break the bonds of its secondary, tertiary and quaternary structure. Peptide bonds survive, but the protein stops working.
structural protein: Proteins' jobs follow from their shapes: enzymes speed reactions, structural proteins such as collagen support tissues, hemoglobin carries oxygen, and motor proteins produce movement.
sequence determines shape: The principle that a protein's amino acid sequence determines how it folds, and its folded shape determines its function.