The Study of Life and the Chemistry of Life

This is Unit One of Biology, Part Three of four. Part Two ended with the phylogenetic tree, and with it the study of life. This part takes up the chemistry every one of those levels is built from. It opens where the book starts over. Matter occupies space and has mass, an element is matter no ordinary reaction breaks down further, and inside one atom a nucleus of protons and neutrons sits in mostly empty space. One count fixes the element and another is free to vary. That variation is what isotopes are, some of them decay at a fixed rate, and a worked entry reads that rate backward into elapsed time. Electrons decide which atoms bond, and how. Five attractions follow, and they sort by one question: what happened to the electrons. Water then takes six entries with one property behind all of them. The part closes on the p H scale, acids, bases, and a buffer worked through inside the body. By the end you will be able to do five things. One: say what an element is, what sits inside one atom, and which count fixes the element. Two: say what isotopes vary, and how a fixed decay rate gives elapsed time. Three: sort the bonds by what happens to the electrons. Four: trace water's behavior back to its polarity. Five: read the p H scale, and say how a buffer holds blood in its range.

The unit now leaves structure for chemistry and does not come back. Three entries open it: what an element is, what sits inside one atom, and which particle decides the element.

Where chemistry starts.

Bio 0111 Matter and Elements

Matter occupies space and has mass; an element is matter that ordinary reactions cannot break into simpler substances. Carbon, oxygen, hydrogen and nitrogen make up most of a living organism. It is defined by what a reaction cannot do to it, not by how common it is.

Inside one atom.

Bio 0113 Atomic Structure

An atom has a nucleus of protons and neutrons, with electrons in the space around it. A proton carries a positive charge, a neutron none, an electron a negative charge equal and opposite to a proton's. Nearly all of an atom's volume is empty space, and its mass is not spread evenly.

Counting the particles.

Bio 0115 Atomic Number and Mass Number

The atomic number counts an atom's protons; the mass number counts protons and neutrons together. Carbon's atomic number is six, so every carbon atom has six protons whatever its neutron count. The atomic number identifies the element; the mass number can vary within it.

Three entries following from the last. If the mass number can vary while the element does not, some atoms of an element differ from others; some of those break down at a fixed rate; and a fixed rate is a clock.

Same element, different mass.

Bio 0117 Isotopes

Isotopes are atoms of one element sharing the same number of protons but differing in neutrons. Carbon twelve has six neutrons and carbon fourteen has eight, and both are carbon. A differing neutron count changes an atom's mass, not the element it belongs to.

The ones that break down.

Bio 0119 Radioactive Isotopes and Half-Life

A radioactive isotope decays at a fixed rate; its half-life is the time for half a starting amount to decay. Carbon fourteen decays to nitrogen fourteen with a half-life near 5,730 years, and that rate never changes. A half-life is a rate, not a countdown — half of what remains decays in the next one.

A worked procedure on a real sample.

Bio 0122 Dating a Fossil by Isotope Decay

A living organism holds the atmosphere's ratio of carbon fourteen to carbon twelve while it takes carbon in. At death the intake stops, the carbon fourteen decays toward nitrogen fourteen at its half-life of about 5,730 years, and the carbon twelve stays put. Half the living ratio means one half-life; a quarter means two, near 11,460 years. Past about nine half-lives too little remains to measure, so the method stops at roughly 50,000 years. The estimate is only as reliable as the assumption that the sample exchanged no carbon after death.

Four entries on one idea: an atom's outer electrons decide what it does. The first gives the rule they follow, the second what an atom becomes when it gains or loses one, and the last two the ways atoms hold together.

The rule electrons follow.

Bio 0125 Electron Shells and the Octet Rule

Electrons occupy shells at increasing distances from the nucleus, and the octet rule favors eight in the outer shell. Neon holds eight there and rarely reacts; sodium holds one and readily gives it up. It is a stability rule, not a hard limit — the innermost shell is stable at two electrons.

Gaining or losing one.

Bio 0127 Ions

An ion is an atom that has gained or lost electrons, leaving it with a net electric charge. Sodium loses its single outer electron and becomes positively charged; chlorine gains one and becomes negatively charged. The charge comes from an imbalance between protons and electrons, never from a change in proton count.

What opposite charges do.

Bio 0129 Ionic Bonds

An ionic bond forms when a positively charged ion and a negatively charged ion attract and hold together by their opposite charges. Sodium and chloride ions pack into the crystal lattice of table salt. Charge attraction alone holds them — no electron is shared.

The other way to hold.

Bio 0131 Covalent Bonds

A covalent bond forms when two atoms share one or more pairs of electrons. Two hydrogen atoms share a pair to form a hydrogen molecule, each filling its outer shell. Sharing is what separates a covalent bond from an ionic one, where electrons transfer completely instead.

Four entries that grade what came before. Sharing admits degrees: even, uneven, and uneven enough to leave partial charges on a molecule. Those charges produce two attractions between molecules, far weaker than the bonds inside them, and doing structural work anyway.

Sharing, unevenly.

Bio 0133 Polar Covalent Bonds

A polar covalent bond shares electrons unevenly, because one atom pulls them closer. In a water molecule, oxygen pulls harder than hydrogen, leaving oxygen slightly negative and each hydrogen slightly positive. It still shares — unevenness is a matter of degree, not a switch to an ionic bond.

Sharing, evenly.

Bio 0135 Nonpolar Covalent Bonds

A nonpolar covalent bond shares electrons evenly because both atoms pull with about equal strength. Two atoms of the same element, as in the hydrogen molecule, leave neither with a partial charge. The book then relaxes its own line: similar but non-identical atoms, carbon and hydrogen among them, count as nonpolar in practice.

Between polar molecules.

Bio 0137 Hydrogen Bonds

A hydrogen bond is a weak attraction between a slightly positive hydrogen and a slightly negative atom, on a neighboring molecule or a distant part of the same one. One water molecule's positive hydrogen is drawn to a neighbor's negative oxygen. It is far weaker than a covalent bond within a molecule.

Weaker still.

Bio 0139 Van der Waals Interactions

Van der Waals interactions are weak, brief attractions caused by temporary shifts in a molecule's electron distribution. Two nonpolar molecules passing close feel a fleeting pull as their electrons bunch to one side. They are weaker and shorter-lived than a hydrogen bond, but across many contact points they add up to structural strength.

Six entries close this part, and they are one argument rather than six facts. Water's polarity lets each molecule hydrogen-bond to several neighbors. Everything after — surface tension, slow warming, cooling by evaporation, dissolving, floating ice — is that same bonding from another side.

The property itself.

Bio 0142 Water's Polarity

Water is a polar molecule, carrying a partial negative charge near its oxygen and a partial positive charge near each hydrogen. That lets one molecule hydrogen-bond to several neighbors at once, forming a loose, shifting network. Polarity, not size or abundance, is behind nearly every distinctive behavior water shows.

Sticking, two ways.

Bio 0144 Cohesion and Adhesion

Cohesion is water's tendency to stick to itself through hydrogen bonds; adhesion is its tendency to stick to other polar surfaces. A water strider is held up by cohesion at the surface, while water climbing a thin glass tube shows adhesion. The same hydrogen bonding produces both.

Why water warms slowly.

Bio 0146 Water's High Heat Capacity

Water has a high heat capacity: raising its temperature takes a large amount of energy, because much of that energy first breaks hydrogen bonds. A large lake warms and cools far more slowly across a day than the dry land beside it. Heat capacity concerns changing temperature, not changing state.

And why sweat cools.

Bio 0148 Water's Heat of Vaporization

Water's heat of vaporization is the large amount of energy required to turn one gram of liquid water into vapor, because hydrogen bonds must break first. Sweat evaporating from skin carries a large amount of body heat away. Vaporization removes heat from the surface it leaves, which is why evaporation cools.

What water carries.

Bio 0150 Water as a Solvent

Water dissolves many substances because its polar molecules surround and separate charged or polar particles. Table salt dissolves as water molecules surround each sodium and chloride ion and pull the ionic lattice apart. Polar and ionic substances dissolve well; nonpolar substances such as oil resist mixing in.

The solid form.

Bio 0152 Why Ice Floats

Ice is less dense than liquid water because its hydrogen bonds lock into a rigid, spaced-out lattice as water freezes, so the same mass takes up more space and the cube floats. Ice floating is unusual among solids, most of which are denser than their liquid form.

Three entries: the scale, then the two kinds of substance that move a solution along it. Both definitions are stated in hydrogen ion concentration, because both entries warn against the sensory ones students arrive with — sour, bitter, corrosive.

The scale itself.

Bio 0155 The pH Scale

The p H scale measures how acidic or basic a solution is from its hydrogen ion concentration, running zero to fourteen with seven neutral. Pure water sits at p H seven, and more free hydrogen ions than pure water reads below seven. Each whole step is a tenfold change, not an even one.

What pushes it down.

Bio 0157 Acids

An acid increases the concentration of hydrogen ions in a solution, lowering its p H. Dissolved carbon dioxide forms carbonic acid in rainwater, raising its free hydrogen ions and taking it below seven. An acid is defined by what it adds, not by how it tastes or what it dissolves.

What pushes it up.

Bio 0159 Bases

A base decreases the concentration of hydrogen ions, raising p H. Baking soda added to water lowers the free hydrogen ions in the mixture and takes its p H above seven. A base need not contain hydroxide or taste bitter — lowering hydrogen ion concentration is the whole requirement.

Two entries, the second a worked procedure that runs long on its own. A buffer is a matched pair, and the blood entry is where the pair becomes visible: one reaction running whichever way the blood needs.

What resists the swing.

Bio 0161 Buffers

A buffer resists a change in p H by absorbing or releasing hydrogen ions as conditions shift. A bicarbonate buffer in lake water absorbs excess hydrogen ions from runoff, holding the water in a range fish can survive. A buffer moderates within a working range; it does not hold p H fixed.

The buffer worked through, inside the body.

Bio 0164 Buffering Blood pH, Worked

The matched pair is carbonic acid and bicarbonate: carbon dioxide from ordinary metabolism combines with water to form carbonic acid, a weak acid, which can release a hydrogen ion and become bicarbonate, a weak base. Both forms sit in the blood together, and the reaction runs in either direction as the blood needs. The lungs reinforce it: carbonic acid also breaks down into carbon dioxide and water, and exhaling that carbon dioxide pulls the system toward absorbing more acid. A buffer works by shifting a reaction back and forth, not by neutralizing every hydrogen ion outright.

Five things to carry out of Part Three. Matter occupies space and has mass, and an element is matter that ordinary reactions cannot break into anything simpler. An atom holds protons and neutrons in a nucleus with electrons around it, and nearly all of its volume is empty. The atomic number counts protons and fixes the element; the mass number counts protons and neutrons together and can vary. Isotopes are that variation — carbon twelve with six neutrons, carbon fourteen with eight, both of them carbon. A radioactive isotope decays at a fixed rate, and its half-life is the time for half a starting amount to decay. Reading what remains against that rate gives elapsed time, workable to about nine half-lives and no further. Sort the bonds by what happens to the electrons. Transferred outright: ionic. Shared evenly: nonpolar covalent. Shared unevenly: polar covalent, which leaves partial charges behind. Those charges make hydrogen bonds between molecules, and weaker still are van der Waals interactions, which need no permanent polarity. Water is one property with a list of consequences. Polarity gives hydrogen bonding; hydrogen bonding gives cohesion and adhesion, a high heat capacity, a high heat of vaporization, water's reach as a solvent, and floating ice. The p H scale reads hydrogen ion concentration from zero to fourteen with seven neutral, and one whole step is a tenfold change. An acid raises that concentration and a base lowers it, neither of them defined by taste. A buffer absorbs or releases hydrogen ions to hold a working range, and in blood the carbonic acid and bicarbonate pair runs whichever way is needed. Part Four turns to the large carbon molecules that living structure is built from, and to the two reactions that assemble and dismantle every one of them.