Chemistry of Life

Main notes

Every living thing runs on chemistry. The behavior of atoms and the bonds that hold them together explain how cells store energy, build and break molecules, and keep internal conditions steady. This chapter lays the chemical foundation for the next topic, in which those molecules assemble into the large structures of the cell. It also connects forward to metabolism, membrane transport, and every process that keeps an organism alive.

Atomic Structure

Matter is made of atoms, and each atom is built from three kinds of particles. Protons carry a positive charge and sit in the nucleus, the dense center of the atom. Neutrons are uncharged and also sit in the nucleus, while electrons carry a negative charge and move in regions around the nucleus called electron shells. The atomic number is the number of protons in the nucleus, and it defines which element an atom is: hydrogen has atomic number 1, carbon 6, nitrogen 7, and oxygen 8. The mass number is the sum of protons plus neutrons. Atoms of the same element that differ in neutron number are called isotopes; carbon-12 and carbon-14 are isotopes of carbon.

Electrons occupy shells of increasing energy, and the outermost shell, the valence shell, determines how the atom reacts. The first shell holds up to two electrons and the second holds up to eight. Atoms are most stable when the valence shell is full, a tendency known as the octet rule. This drive to fill the valence shell is the root of every kind of chemical bond.

Common Mistake: The atomic number is the proton count, not the mass number. An atom can gain or lose neutrons and remain the same element, but gaining or losing a proton turns it into a different element entirely.

ELI-10

Think of an atom as a crowd: a small, heavy group of people stands at the center while tiny children race around them in circles. The heavy group is the nucleus and the running children are the electrons. The children can only run at certain distances, and each ring of distance holds a set number of children. An atom likes its rings exactly full, and this wish is what pushes atoms to join with other atoms. Counting the heavy people at the center tells you which atom you are looking at.

Bonding Types

Atoms bond because filled valence shells are more stable than half-filled ones. Electronegativity is the pull an atom exerts on shared electrons, and it increases across the periodic table and up the groups. When the electronegativity difference is large, the more electronegative atom strips electrons away entirely, creating charged particles called ions. The oppositely charged ions then attract each other in an ionic bond, as in sodium chloride, table salt.

Covalent bonds form when atoms share electrons instead of transferring them. In a nonpolar covalent bond the electrons are shared equally, as in molecular oxygen, because the two atoms have equal electronegativity. In a polar covalent bond the more electronegative atom pulls the shared electrons closer, giving one end of the molecule a slight negative charge and the other end a slight positive charge; water is the classic example. Atoms can share one, two, or three electron pairs, producing single, double, or triple bonds, and carbon's ability to form four covalent bonds is the backbone of organic chemistry.

Hydrogen bonds are weak attractions between a hydrogen atom already covalently bonded to nitrogen or oxygen and a nearby electronegative atom. They are not true bonds, yet they form and break constantly, and they are what stick water molecules to one another. Even weaker are van der Waals interactions, momentary attractions that arise when the electrons of a molecule happen to cluster to one side.

Common Mistake: A hydrogen bond is often mistaken for a bond inside a molecule. It is an attraction between molecules, and it is far weaker than the covalent bonds that hold atoms together within one molecule.

ELI-10

Two children can share a ball by holding it together, which is a covalent bond. One child can also snatch the ball away completely, which is an ionic bond, and then the child without the ball stays close because of the quarrel. A hydrogen bond is more like two kids standing near a magnet: the pull exists but it is gentle. These gentle pulls are weak on their own, yet thousands of them together can hold big structures together. Sharing, snatching, and gentle pulling are the three main ways atoms stick.

Water Properties

Water is the solvent of life, and nearly every property that makes it so comes from its polarity. Each water molecule is bent, with the oxygen end slightly negative and the hydrogen ends slightly positive, so neighboring molecules pull on one another through hydrogen bonds. Cohesion is the tendency of water molecules to stick to each other, which produces surface tension, while adhesion is the tendency to stick to other surfaces, which helps water climb upward through narrow plant vessels.

Water also resists temperature change. Its high specific heat means a great deal of energy is needed to raise its temperature, because the energy goes into breaking hydrogen bonds instead of speeding up the molecules. Its high heat of vaporization means evaporation removes a large amount of heat, which is why sweating cools the body. As a solvent, water surrounds and separates charged and polar solutes, while nonpolar molecules such as oils do not dissolve in it. Finally, ice floats: solid water is less dense than liquid water because hydrogen bonds hold the molecules in an open lattice, and this is why ponds freeze from the top down and aquatic life survives the winter.

Common Mistake: Polar does not mean charged overall. A water molecule has charged regions, but its total charge is zero; the partial charges arise from unequal sharing of electrons, not from a net charge.

ELI-10

Picture water molecules as dancers holding hands. Each dancer can grab only a few neighbors at a time, and the grabbing is the hydrogen bonding. When you heat the water, the dancers refuse to let go right away, which is why water warms up slowly. When water freezes, the dancers lock arms in a wide open circle, which spreads them out and makes ice lighter than water. Because ice floats, fish stay safe under the frozen top layer of a pond in winter.

pH and Buffers

Water molecules occasionally split apart into hydrogen ions, H+, and hydroxide ions, OH-. The pH scale measures the hydrogen ion concentration of a solution and runs from 0 to 14, with 7 neutral. Solutions below 7 are acids, which release hydrogen ions, and solutions above 7 are bases, which accept hydrogen ions or release hydroxide ions. Because pH is a negative logarithm, each whole-number change represents a tenfold change in hydrogen ion concentration: pH 5 is ten times more acidic than pH 6 and one hundred times more acidic than pH 7.

Biological fluids stay within narrow ranges, and human blood is held near pH 7.4. Buffers are substances that resist pH change by accepting hydrogen ions when the solution turns too acidic and releasing them when it turns too basic. The carbonic acid-bicarbonate system is the main buffer of human blood, keeping it between about 7.35 and 7.45. A buffer works through a paired reaction that runs in both directions:

1. Hydrogen ions enter the blood, making it more acidic.
2. Bicarbonate ions take up the excess hydrogen ions.
3. Carbonic acid forms, and the pH barely moves.
4. If the blood turns too basic, carbonic acid releases hydrogen ions.
5. The paired reaction keeps shifting until the pH returns near 7.4.

Common Mistake: Acid strength is not the same as acid concentration. A strong acid releases nearly all of its hydrogen ions while a weak acid releases only a fraction, but either can be diluted in water to a low concentration.

ELI-10

Think of pH as a number line from zero to fourteen that shows how many acid particles are floating in a liquid. A low number means many acid particles, and a high number means few, with seven in the middle. Moving one step on the line means ten times more acid particles, so the line is not even like a ruler. A buffer is like a sponge for acid particles: it soaks them up when there are too many and squeezes them out when there are too few. Blood uses such a sponge to stay near the number seven.

Functional Groups

Organic molecules are built on carbon skeletons, and the small clusters of atoms that give each molecule its chemical personality are the functional groups. Every functional group behaves predictably no matter which molecule carries it, so learning a handful of them explains the chemistry of a vast number of biological molecules.

The hydroxyl group (OH) is polar and hydrophilic, so molecules that carry it tend to dissolve in water. The carbonyl group (C=O) is a carbon double-bonded to an oxygen, found at the end of a carbon chain as an aldehyde or inside the chain as a ketone. The carboxyl group (COOH) acts as an acid, releasing a hydrogen ion in water. The amino group (NH2) acts as a base, accepting a hydrogen ion. The phosphate group (PO4) is strongly acidic, carries a negative charge, and its transfer is how cells store and release energy. The sulfhydryl group (SH) can form links between parts of molecules, and the methyl group (CH3) is nonpolar and hydrophobic, often used by cells to modify gene expression.

Common Mistake: A functional group is not a whole molecule. It is only a small reactive part, and the rest of the molecule, its carbon skeleton, also shapes how the molecule behaves.

ELI-10

Think of functional groups as different shaped keys that can be attached to a block. Each key shape does its own job: one key makes the block dissolve in water, another makes the block donate a sour particle, and another makes the block stay away from water. The same key behaves the same way no matter which block it is on. Chemists can predict how a molecule behaves just by reading its keys. That is why memorizing a handful of keys unlocks the chemistry of countless molecules.

High-Yield:

• Know the three subatomic particles: their charge, their mass, and where they sit.
• Every unit of pH is a tenfold change, so small pH shifts mean large concentration changes.
• Hydrogen bonds explain water's cohesion, high specific heat, and floating ice.
• Electronegativity differences decide whether a bond is ionic, polar covalent, or nonpolar covalent.
• Functional groups dictate a molecule's polarity, acidity, and solubility.

Quick Review

• An atom's atomic number is its proton count, the mass number adds the neutrons, and isotopes differ only in neutrons.
• Atoms react to fill their valence shells, and this drive produces ionic, covalent, and hydrogen bonds.
• Ionic bonds transfer electrons, covalent bonds share them, and hydrogen bonds are weak attractions between molecules.
• Water's polarity creates cohesion, adhesion, a high specific heat, and a powerful solvent.
• Ice floats because hydrogen bonds spread the molecules into an open lattice.
• The pH scale runs from 0 to 14, with 7 neutral and each unit a tenfold change in hydrogen ion concentration.
• Buffers such as the bicarbonate system hold human blood near pH 7.4.
• Functional groups determine whether a molecule is polar, acidic, basic, or hydrophobic.

Key terms

Key terms are emphasized and defined within the main notes.

Important formulas or processes

See the formulas, procedures, and process blocks in the main notes where applicable.

Common mistakes

See the labeled common-mistake callouts in the main notes where present.