The Chemistry of Life and Biological Macromolecules

Every living thing, from a soil bacterium to a redwood to you, is a chemical system that obeys the same rules as a beaker of salt water. The difference is organization: a small set of elements, held together by a handful of bond types and dissolved in water, assembles into the four great families of large molecules that store energy, build structures, speed reactions and carry hereditary information. Master this chemistry now and almost every later topic in biology, from enzymes to genetics to ecology, becomes a matter of applying ideas you already own.

Section 1Atoms, bonds and the properties of water

Matter, elements and the atom

Matter is anything that takes up space and has mass. All matter is made of elements, substances that cannot be broken down into other substances by ordinary chemical reactions. About 92 elements occur naturally, yet only four, oxygen, carbon, hydrogen and nitrogen, make up about 96 percent of the mass of the human body. Calcium, phosphorus, potassium, sulfur, sodium, chlorine and magnesium account for most of the remaining 4 percent. Trace elements such as iron, iodine, zinc and copper are needed only in tiny amounts, but they are essential: iodine is built into thyroid hormone, and iron sits at the center of the heme group that carries oxygen in hemoglobin. A compound is a substance made of two or more elements in a fixed ratio, and it usually has properties quite unlike its parts. Sodium is an explosive metal and chlorine a poisonous gas, but sodium chloride is table salt.

The smallest unit of an element that keeps its chemical properties is the atom. Atoms have a dense central nucleus holding positively charged protons and uncharged neutrons, surrounded by a cloud of negatively charged electrons. Protons and neutrons each have a mass of about 1 dalton (1 atomic mass unit); an electron has about 1/1,840 of that mass, so electrons contribute almost nothing to mass but nearly everything to chemistry.

• The atomic number is the number of protons. It defines the element: every carbon atom has 6 protons.
• The mass number is protons plus neutrons. Common carbon has 6 protons and 6 neutrons, mass number 12.
• In a neutral atom, the number of electrons equals the number of protons.

Isotopes and radioactivity

Atoms of one element can differ in their number of neutrons. These forms are isotopes. Carbon-12 is about 99 percent of natural carbon, carbon-13 about 1 percent, and carbon-14 is present in trace amounts. Isotopes of an element behave almost identically in chemical reactions because chemistry depends on electrons, not neutrons. Some isotopes have unstable nuclei that decay spontaneously, giving off particles and energy; these are radioactive isotopes. Each decays at a fixed rate measured as a half-life, the time for half of a sample to decay. Carbon-14 has a half-life of about 5,730 years, which makes it useful for dating organic remains up to roughly 50,000 years old. In research, radioactive tracers let biologists follow atoms through metabolic pathways, as in the classic experiments that traced carbon through photosynthesis and showed that DNA, not protein, enters bacteria during viral infection.

Electrons, shells and valence

Electrons occupy energy levels, often drawn as shells around the nucleus. The first shell holds up to 2 electrons; the second and third each hold up to 8 for the elements that matter most in biology. The electrons in the outermost occupied shell are valence electrons, and they determine how an atom reacts. Atoms are most stable when their valence shell is full. Helium, neon and argon already have full shells and are inert. Other atoms reach stability by sharing, gaining or losing electrons. The number of unpaired valence electrons an atom usually shares gives its valence, the number of covalent bonds it typically forms: hydrogen 1, oxygen 2, nitrogen 3 and carbon 4. Remembering "HONC 1234" lets you check almost any biological structure for a missing or extra bond.

Covalent bonds and electronegativity

A covalent bond is a shared pair of valence electrons. Two hydrogen atoms share one pair to form H₂ (a single bond); two oxygen atoms share two pairs to form O₂ (a double bond). A molecule is two or more atoms held together by covalent bonds. Covalent bonds are strong, and the bonds within biological molecules do not break at body temperature without the help of enzymes.

Atoms differ in how strongly they pull shared electrons toward themselves, a property called electronegativity. Oxygen and nitrogen are highly electronegative; carbon and hydrogen are similar to each other and much less so. When two atoms of similar electronegativity share electrons, the sharing is equal and the bond is nonpolar covalent (C to C, C to H). When one atom is much more electronegative, the electrons spend more time near it, giving it a partial negative charge (written δ−) and leaving the other atom with a partial positive charge (δ+). Such a bond is polar covalent (O to H, N to H). The polarity of the O to H bonds in water is the single fact that explains most of what makes water special.

Ionic bonds, hydrogen bonds and weak interactions

When the difference in electronegativity is very large, one atom strips an electron from the other. Sodium gives up its single valence electron to chlorine; sodium becomes a cation (Na⁺) and chlorine an anion (Cl⁻). The attraction between oppositely charged ions is an ionic bond. Ionic compounds such as NaCl form crystals when dry, but in water the ions separate and are surrounded by water molecules, so ionic bonds are weak in the watery interior of a cell.

A hydrogen bond forms when a hydrogen atom that is covalently bonded to an electronegative atom (O or N) is attracted to another electronegative atom nearby. A hydrogen bond is about 5 to 10 percent as strong as a covalent bond, but biology runs on huge numbers of them. They hold the two strands of DNA together, shape proteins, and link water molecules into a constantly shifting network. Their weakness is a feature: hydrogen bonds can form and break quickly, letting DNA unzip for copying and enzymes bind and release substrates.

Van der Waals interactions are even weaker attractions that arise because electrons are always moving, creating fleeting regions of slight charge on any molecule. They matter only when molecules fit very closely, but many together are significant. Geckos cling to glass largely through van der Waals forces between millions of tiny hairs on their toes and the surface. The hydrophobic effect, the tendency of nonpolar molecules to cluster together in water, is not really a bond at all; it results from water molecules hydrogen bonding with each other and excluding the nonpolar substances. It is one of the main forces that folds proteins and builds membranes.

Molecular shape follows from bonding. When an atom forms covalent bonds, its valence orbitals rearrange into a geometry: carbon with four single bonds is tetrahedral, with bond angles of about 109.5 degrees, and water is bent, with an angle of about 104.5 degrees. Shape matters because molecules recognize each other by fit. Morphine and the body's own endorphins have similar shapes, which is why both bind the same opioid receptors in the brain.

Chemical reactions

A chemical reaction makes and breaks bonds, converting reactants into products. Matter is conserved: the same atoms appear on both sides of a balanced equation. Photosynthesis, for example, can be summarized as 6 CO₂ + 6 H₂O → C₆H₁₂O₆ + 6 O₂. Many reactions are reversible, and they proceed until the forward and reverse rates are equal, a state called chemical equilibrium. At equilibrium the concentrations stop changing, but they are not necessarily equal. Adding reactant or removing product pushes the reaction forward, an idea you will use often when you study metabolism.

Water: a polar molecule

Water (H₂O) is bent, with oxygen at the vertex. Oxygen pulls the shared electrons toward itself, so the oxygen end carries a partial negative charge and each hydrogen a partial positive charge. Because of this polarity, each water molecule can hydrogen bond with up to four neighbors. In liquid water these hydrogen bonds last only trillionths of a second, constantly breaking and reforming, but at any moment most molecules are hydrogen bonded to several others. Four emergent properties follow, and each is essential for life.

Four emergent properties of water

1. Cohesion and adhesion. Hydrogen bonds hold water molecules to each other, a property called cohesion. Cohesion gives water a high surface tension, which lets a water strider walk across a pond. Adhesion is the attraction of water to other polar surfaces. In plants, cohesion holds the column of water together inside the narrow xylem tubes while adhesion to the cell walls resists gravity, so evaporation from leaves can pull water up from the roots of a tree many meters tall.

2. Moderation of temperature. Water has a high specific heat: it takes 1 calorie to raise 1 gram of water by 1 °C, far more than for most substances. The reason is that much of the heat added first goes into breaking hydrogen bonds rather than speeding molecules up. Oceans and lakes therefore warm and cool slowly, stabilizing coastal climates, and the water that makes up 60 percent or more of a body buffers it against rapid temperature swings. Water also has a high heat of vaporization: about 580 calories are needed to evaporate 1 gram at body temperature. Because the fastest, most energetic molecules leave first, the remaining liquid cools. This evaporative cooling is why sweating cools you and why transpiration keeps leaves from overheating in the sun.

3. Floating ice. Most substances are densest as solids, but water is densest at about 4 °C. As water freezes, each molecule locks into hydrogen bonds with four neighbors in an open crystal lattice, so ice is about 10 percent less dense than liquid water and floats. Floating ice insulates the water below. If ice sank, lakes and seas would freeze from the bottom up and much aquatic life could not survive winter.

4. A versatile solvent. A solution is a uniform mixture of a solute dissolved in a solvent; when water is the solvent it is an aqueous solution. Water dissolves ionic compounds by surrounding each ion with a hydration shell, and it dissolves polar molecules such as sugars by hydrogen bonding with their polar groups. Substances that interact readily with water are hydrophilic; nonpolar substances such as oils are hydrophobic. Some hydrophilic substances, such as large proteins, do not truly dissolve but stay suspended as a colloid.

Chemists count molecules by the mole, which is 6.02 × 10²³ particles (Avogadro's number). One mole of a substance has a mass in grams equal to its molecular mass in daltons. Glucose (C₆H₁₂O₆) has a molecular mass of 180 daltons, so 180 grams is 1 mole. A 1 molar (1 M) solution has 1 mole of solute per liter of solution.

Acids, bases and pH

A small fraction of water molecules dissociate: one hydrogen leaves its electron behind and transfers to a neighbor as a proton, producing a hydronium ion (H₃O⁺, usually written H⁺) and a hydroxide ion (OH⁻). In pure water at 25 °C, [H⁺] = [OH⁻] = 10⁻⁷ M, and their product is always 10⁻¹⁴. An acid increases [H⁺] (hydrochloric acid releases H⁺ completely); a base decreases it, either by accepting H⁺ (ammonia) or by releasing OH⁻ (sodium hydroxide).

The pH is the negative base-10 logarithm of the hydrogen ion concentration: pH = −log[H⁺]. Pure water is pH 7, neutral. Acidic solutions are below 7 and basic (alkaline) ones are above. Because the scale is logarithmic, each unit is a tenfold change: pH 4 has 10 times the H⁺ of pH 5 and 1,000 times that of pH 7. Most cells keep their interior near pH 7, and human blood is held between 7.35 and 7.45. Stomach fluid is about pH 2, while the small intestine is slightly basic.

Living fluids resist pH change because of buffers, substances that take up H⁺ when it is in excess and release it when it is scarce. The most important buffer in blood is the carbonic acid and bicarbonate system:

CO₂ + H₂O ⇌ H₂CO₃ ⇌ HCO₃⁻ + H⁺

If H⁺ rises, the reaction shifts left as bicarbonate absorbs it; if H⁺ falls, carbonic acid dissociates to replace it. The lungs adjust CO₂ and the kidneys adjust bicarbonate, giving two levers for long term control.

Section 2Carbon and functional groups

Why carbon?

Apart from water, nearly every molecule in a cell is built on a skeleton of carbon. Compounds containing carbon bonded to hydrogen are called organic compounds; the name dates from a time when chemists thought only living things could make them. In 1828 a chemist synthesized urea from inorganic starting materials, and in 1953 Stanley Miller showed that amino acids form when electric sparks pass through a mixture of simple gases thought to resemble the early atmosphere. These experiments helped replace the idea of a special "vital force" with mechanism: life is built from the same atoms and obeys the same laws as nonliving matter.

Carbon's power comes from its four valence electrons. It forms four covalent bonds, so it can link to four other atoms in different directions. Carbon atoms bond readily to each other, producing chains, branches and rings of almost any length, and they can share one, two or three electron pairs. Each carbon with four single bonds sits at the center of a tetrahedron, giving organic molecules three dimensional shape. When two carbons are joined by a double bond, the atoms attached to them lie in one flat plane and the bond cannot rotate, which locks part of the molecule in place.

Hydrocarbons and carbon skeletons

Hydrocarbons contain only carbon and hydrogen. Their C to H bonds are nonpolar, so hydrocarbons are hydrophobic, and those bonds store a great deal of energy that is released when they are burned or, in cells, oxidized. The fatty acid tails of fats are long hydrocarbon chains, which is why fats are such rich fuel. Carbon skeletons vary in four ways: length, branching, the position of double bonds and the presence of rings.

Isomers

Isomers are compounds with the same molecular formula but different structures, and therefore different properties. There are three kinds that biology students must know:

• Structural isomers differ in the covalent arrangement of their atoms. Glucose and fructose are both C₆H₁₂O₆, but glucose has an aldehyde group and fructose a ketone.
• Cis trans isomers (geometric isomers) have the same bonds but differ in arrangement around a double bond. In the cis form, the two groups of interest are on the same side; in the trans form, on opposite sides. Retinal, the light-sensing molecule of the eye, switches from cis to trans when it absorbs a photon, and that change in shape starts vision.
• Enantiomers are mirror images that cannot be superimposed, like left and right hands. They arise around an asymmetric carbon, a carbon bonded to four different groups. Cells usually make and use only one enantiomer. Proteins are built from L amino acids, and most natural sugars are D sugars.

The chemical groups most important to life

The carbon skeleton gives a molecule its general shape, but small clusters of atoms attached to it, called functional groups, usually determine its chemical behavior. A functional group behaves much the same way whatever molecule it is on, so learning seven groups lets you predict the properties of thousands of compounds. The male and female sex hormones testosterone and estradiol share the same four-ring steroid skeleton and differ only in a few functional groups, yet they drive very different development.

At the near-neutral pH of a cell, carboxyl groups usually exist as ionized −COO⁻ and amino groups as −NH₃⁺. A free amino acid in the cytoplasm therefore carries both a positive and a negative charge, which makes it very water soluble. Phosphate groups carry two negative charges when at the end of a molecule, and the repulsion between closely packed phosphates is part of why ATP stores useful energy.

ATP: an important source of energy for cellular processes

Adenosine triphosphate (ATP) consists of the nitrogenous base adenine, the five-carbon sugar ribose and a chain of three phosphate groups. When water breaks the bond to the terminal phosphate (hydrolysis), ATP becomes ADP (adenosine diphosphate) plus inorganic phosphate (P_i), and energy is released. Cells couple this release to work: transferring the phosphate to another molecule changes that molecule's shape or reactivity, driving muscle contraction, active transport and synthesis. Cells regenerate ATP from ADP and P_i using energy from food, a cycle you will follow in detail in the chapter on cellular respiration.

Section 3Carbohydrates and lipids

Macromolecules, polymers and monomers

Carbohydrates, proteins and nucleic acids are polymers, long molecules built by linking many similar or identical building blocks called monomers. Lipids are large molecules too, but they are not true polymers. Cells use the same two reactions to build and dismantle all polymers. In dehydration synthesis (a condensation reaction), two monomers are joined by a covalent bond and a molecule of water is released: one monomer gives up a hydroxyl and the other a hydrogen. Hydrolysis is the reverse: water is added across the bond, breaking it. Digestion is mostly hydrolysis, as enzymes in your gut break starch, proteins and fats into monomers small enough to absorb. Both reactions are catalyzed by specific enzymes.

Monosaccharides and disaccharides

Carbohydrates include sugars and their polymers, and many have the general formula (CH₂O)_n. The simplest are monosaccharides, which carry a carbonyl group and several hydroxyl groups. They are classified by the position of the carbonyl, as aldoses (aldehyde, at carbon 1) or ketoses (ketone, inside the chain), and by the number of carbons: trioses (3), pentoses (5) and hexoses (6). Glucose and galactose are aldohexoses that differ only in the arrangement around one asymmetric carbon; fructose is a ketohexose. Ribose and deoxyribose are pentoses found in RNA and DNA. In water, most five and six carbon sugars form rings, because a hydroxyl group reacts with the carbonyl of the same molecule. Ring closure creates a new asymmetric carbon (carbon 1 in glucose) whose hydroxyl can point below the ring (the alpha form) or above it (the beta form). This tiny difference has enormous consequences.

A disaccharide forms when a dehydration reaction joins two monosaccharides by a glycosidic linkage. Maltose is glucose plus glucose (malt sugar, from starch breakdown). Sucrose, table sugar, is glucose plus fructose and is the form in which plants move sugar through their phloem. Lactose, milk sugar, is glucose plus galactose.

Polysaccharides: storage and structure

Polysaccharides are polymers of hundreds to thousands of monosaccharides. Their function depends on which sugar they use and how the units are linked.

• Starch is the main storage polysaccharide of plants, kept in plastids. It is made of alpha glucose. Amylose is unbranched and coils into a helix; amylopectin has branches every 24 to 30 units. Animals, including humans, have enzymes that hydrolyze the alpha linkages of starch.
• Glycogen is the storage polysaccharide of animals, stored mainly in liver and skeletal muscle. It resembles amylopectin but is more highly branched (about every 8 to 12 units), so enzymes can release glucose quickly from many branch tips at once. Your glycogen stores last only about a day without eating.
• Cellulose, the main component of plant cell walls, is the most abundant organic compound on Earth. It is made of beta glucose. Because of the beta linkage, every other glucose is flipped, and the chains stay straight. Parallel cellulose chains hydrogen bond to each other, forming strong microfibrils.
• Chitin forms the exoskeleton of arthropods and the cell walls of fungi. It is like cellulose, but each glucose carries a nitrogen-containing group. Chitin is tough and is also used to make absorbable surgical thread.

The enzymes that digest starch cannot break the beta linkages of cellulose, so for humans cellulose passes through the gut as insoluble fiber, which helps move material through the intestine. Cows, termites and other herbivores digest cellulose only with help from microbes in their gut that make cellulase.

Lipids: a diverse hydrophobic group

Lipids are grouped together not by a common monomer but by a shared property: they mix poorly, if at all, with water, because they consist mostly of hydrocarbon regions. The three most important kinds are fats, phospholipids and steroids.

A fat, or triglyceride, is built from one glycerol (a three-carbon alcohol) and three fatty acids. Each fatty acid is a long hydrocarbon chain, usually 16 or 18 carbons, with a carboxyl group at one end. Dehydration reactions link each fatty acid to glycerol by an ester linkage. Fats are excellent energy stores: a gram of fat stores more than twice the energy of a gram of carbohydrate (about 9 versus 4 kilocalories), because fats are rich in energy-storing C to H bonds and are stored without water. Adipose tissue also cushions organs and insulates the body.

A saturated fatty acid has no carbon to carbon double bonds; it holds as many hydrogens as possible and its chain is straight. Straight chains pack tightly, so saturated fats such as butter and lard are solid at room temperature. An unsaturated fatty acid has one or more double bonds, usually in the cis form, which puts a kink in the chain. Kinked chains cannot pack closely, so plant and fish oils stay liquid. Hydrogenation adds hydrogen to unsaturated oils to make them solid, and partial hydrogenation also creates trans fats, which have trans double bonds and straight chains. Trans fats raise LDL cholesterol and the risk of heart disease even more than saturated fats, and many countries have banned or sharply limited them. Omega-3 fatty acids, which have a double bond three carbons from the tail end, are essential fatty acids that the body cannot make.

Phospholipids and steroids

A phospholipid has only two fatty acids attached to glycerol; the third carbon carries a negatively charged phosphate group, usually linked to another small charged or polar molecule such as choline. The result is amphipathic: a hydrophilic head and two hydrophobic tails. In water, phospholipids self-assemble into a bilayer, heads facing the water on both sides and tails tucked inside, away from water. That bilayer is the basic fabric of every cell membrane, as Chapter 2 explains.

Steroids are lipids whose carbon skeleton is four fused rings. Cholesterol is a component of animal cell membranes, where it modulates fluidity, and it is the precursor from which animals make other steroids, including the sex hormones (estrogens, testosterone), the adrenal hormones (cortisol, aldosterone) and vitamin D. High blood levels of cholesterol carried in LDL particles contribute to atherosclerosis. Waxes, made of a fatty acid joined to a long chain alcohol, waterproof leaves, feathers and insect cuticles.

Section 4Proteins: structure and folding

The many jobs of proteins

Proteins account for more than half the dry mass of most cells, and they do nearly everything. Enzymes are protein catalysts that speed reactions without being used up. Structural proteins (collagen, keratin, silk) give strength; transport proteins (hemoglobin, membrane channels) move substances; contractile proteins (actin, myosin) produce movement; storage proteins (ovalbumin in egg white, casein in milk) hold amino acids; hormones such as insulin carry signals; receptor proteins detect them; and defensive proteins such as antibodies recognize invaders. All of this variety comes from one kind of polymer: a chain of amino acids folded into a specific shape.

Amino acids

An amino acid has a central carbon (the alpha carbon) bonded to four partners: an amino group, a carboxyl group, a hydrogen atom and a variable side chain, or R group. Cells use 20 standard amino acids, and the R group is what makes each one different. Side chains fall into broad classes:

Two amino acids are special. Cysteine has a sulfhydryl group, and two cysteines can form a covalent disulfide bridge. Proline's side chain loops back to bond its own amino nitrogen, making a rigid kink that often breaks helices. Humans can make about 11 of the 20; the other 9 are essential amino acids that must come from the diet.

Peptide bonds and polypeptides

A dehydration reaction joins the carboxyl group of one amino acid to the amino group of the next, forming a peptide bond. A chain of amino acids is a polypeptide. The repeating N to C to C sequence is the backbone, with the R groups sticking out from it. A polypeptide has direction: one end has a free amino group (the N-terminus) and the other a free carboxyl group (the C-terminus), and ribosomes always build chains from N to C. A protein is one or more polypeptides folded into a functional shape. With 20 choices at every position, a chain of just 100 amino acids could have 20¹⁰⁰ possible sequences, more than the number of atoms in the observable universe.

Four levels of protein structure

Primary structure is the sequence of amino acids, written from N to C terminus. It is dictated by the gene. Everything else follows from it, because the sequence determines which interactions are possible.

Secondary structure is local coiling or folding stabilized by hydrogen bonds between backbone atoms, specifically between the carbonyl oxygen of one peptide bond and the N to H hydrogen of another. Side chains are not involved. The two main forms are the alpha helix, a coil with a hydrogen bond between every fourth amino acid, and the beta pleated sheet, in which two or more stretches of chain lie side by side, connected by hydrogen bonds. Keratin of hair is mostly alpha helix; spider silk owes its strength to many beta sheets.

Tertiary structure is the overall three dimensional shape of one polypeptide, produced by interactions between R groups. Hydrophobic side chains cluster in the center, away from water (the hydrophobic effect), where van der Waals interactions hold them together. Polar and charged side chains form hydrogen bonds and ionic bonds with each other and with water. Covalent disulfide bridges between cysteines act like rivets that lock the shape.

Quaternary structure exists only in proteins made of more than one polypeptide, and it describes how those subunits fit together. Hemoglobin has four subunits (two alpha and two beta chains), each carrying a heme group; collagen is three helical chains wound into a rope like triple helix.

Sequence, shape and disease

Because shape depends on sequence, even one amino acid change can matter. In sickle cell disease, the sixth amino acid of the hemoglobin beta chain is valine instead of glutamate. Swapping a charged side chain for a hydrophobic one creates a sticky patch on the surface. When oxygen is low, the altered hemoglobin molecules stick together into long fibers that deform red blood cells into a sickle shape. Sickled cells clog small vessels and break down early, causing pain crises and anemia. People who carry one copy of the allele are partly protected from malaria, which explains why the allele is common where malaria is common.

Folding, chaperones and denaturation

A protein's shape is the lowest energy arrangement its sequence allows under cellular conditions, but reaching it is not always easy. Many proteins fold with the help of chaperonins (molecular chaperones), barrel shaped protein complexes that shelter a new polypeptide from the crowded cytoplasm while it folds. Chaperones do not specify the final shape; they prevent wrong interactions along the way.

If the pH, salt concentration or temperature changes enough, the weak bonds holding secondary, tertiary and quaternary structure break, and the protein unravels. This loss of shape is denaturation, and a denatured protein loses its function. The primary structure, held by covalent peptide bonds, survives. Cooking an egg denatures albumin, turning it from clear to white and solid. A high fever is dangerous partly because some proteins begin to denature. In a classic experiment, the enzyme ribonuclease was denatured with chemicals and then, when the chemicals were removed, refolded on its own into its active shape. That result showed that the information for folding lies in the primary structure. Today, computer models trained on known structures can predict how a sequence will fold with remarkable accuracy, though experimental methods such as X-ray crystallography and cryo-electron microscopy remain the gold standard.

Section 5Nucleic acids and the flow of information

Genes and the central dogma

The amino acid sequence of every protein is encoded in a gene, a stretch of deoxyribonucleic acid (DNA). DNA does not build proteins directly. In eukaryotes, it stays in the nucleus, and its information is first copied into messenger RNA (mRNA), a ribonucleic acid, in a process called transcription. The mRNA moves to the cytoplasm, where ribosomes read it and assemble the polypeptide in translation. When a cell divides, its DNA is copied by replication so each daughter cell receives a full set. This flow, DNA to RNA to protein, is the central dogma of molecular biology. There are exceptions: retroviruses such as HIV use the enzyme reverse transcriptase to copy RNA into DNA, and many RNA molecules (ribosomal RNA, transfer RNA, microRNAs) do their jobs without ever being translated.

Nucleotides

Nucleic acids are polymers called polynucleotides, built from monomers called nucleotides. Each nucleotide has three parts: a five-carbon sugar (a pentose), a nitrogenous base and one to three phosphate groups. The sugar plus base, without phosphate, is a nucleoside. The carbons of the sugar are numbered with primes (1′ to 5′) to tell them apart from the atoms of the base. The base attaches to the 1′ carbon and the phosphate to the 5′ carbon.

• The sugar in DNA is deoxyribose, which lacks the oxygen on the 2′ carbon. The sugar in RNA is ribose, which has an OH there. That extra hydroxyl makes RNA more chemically reactive and less stable than DNA, one reason DNA is the long-term storage form.
• The bases come in two families. Pyrimidines have a single six-membered ring: cytosine (C), thymine (T), found only in DNA, and uracil (U), found only in RNA. Purines are larger, with a six-membered ring fused to a five-membered ring: adenine (A) and guanine (G).

The sugar phosphate backbone

Nucleotides are joined by dehydration reactions that link the phosphate on the 5′ carbon of one nucleotide to the hydroxyl on the 3′ carbon of the next. The resulting phosphodiester linkage creates a repeating sugar phosphate backbone with the bases projecting from it. Like a polypeptide, a polynucleotide has direction: one end has a free phosphate on a 5′ carbon (the 5′ end) and the other a free hydroxyl on a 3′ carbon (the 3′ end). Sequences are written 5′ to 3′, and new nucleotides are always added to the 3′ end. The sequence of bases along a gene is unique to that gene and carries its information.

The double helix

RNA usually exists as a single strand, though it can fold back on itself where complementary stretches pair, giving molecules such as transfer RNA a precise three dimensional shape. DNA is a double helix: two polynucleotide strands wound around an imaginary axis, with the backbones on the outside and the bases paired in the interior. Several features are essential:

• The strands are antiparallel: they run in opposite 5′ to 3′ directions, like the lanes of a two-way road.
• Bases pair by hydrogen bonding in a fixed way, called complementary base pairing: A with T (two hydrogen bonds) and G with C (three hydrogen bonds). In RNA, A pairs with U. Each pair joins a purine to a pyrimidine, so the helix has a uniform width of about 2 nanometers.
• Because of pairing, the two strands are complementary: knowing one sequence tells you the other. That is the basis for accurate copying during replication. It also explains Chargaff's rules: in any double-stranded DNA, the amount of A equals T and the amount of G equals C.
• The helix makes one full turn about every 10 base pairs (3.4 nm). Regions rich in G and C, with three hydrogen bonds per pair, are harder to separate than regions rich in A and T.

Other jobs for nucleotides

Nucleotides are not only building blocks. ATP is the cell's energy currency; GTP powers protein synthesis and signaling; cyclic AMP is a second messenger inside cells; and the electron carriers NAD⁺ and FAD, central to respiration, are nucleotide derivatives. Some RNA molecules, called ribozymes, act as catalysts. The ribosome's peptide-bond-forming center is RNA, a clue that early life may have used RNA for both information and catalysis.

DNA, proteins and evolution

Because genes are passed from parents to offspring, closely related species share more of their DNA and protein sequences than distantly related ones. Comparing sequences, the field of molecular systematics, lets biologists build family trees of life. Human and chimpanzee genomes differ by only about 1 to 2 percent in the stretches that can be aligned. Modern genomics sequences entire genomes quickly and cheaply, and bioinformatics uses computers to store and compare that flood of data, opening approaches to medicine and evolution that were unimaginable a generation ago.

Words worth knowing