Week 2 · Chapter

Chapter 2 — The Chemistry of Life

Introduction to Biology Free sample edition

The module's primary reading · ~40–50 minutes · Objective 2 (explain the chemistry of life — atoms and the three kinds of chemical bonds, water's polarity and the properties it produces, and the logarithmic pH scale with buffers — and relate the structure of each of the four classes of biological macromolecules (carbohydrates, lipids, proteins, nucleic acids) to its function) · Read it first this week; the lecture, the slides, the tutorial, the quiz, and the lab all build on it.

In plain language

Every living thing is made of tiny pieces called atoms (the smallest units of the substances around you), and four kinds of atom build about 96% of your body. This week you meet the three kinds of chemical bonds (the ways atoms stick to each other) and see why water, one of the simplest molecules, behaves in ways that make life possible, from floating ice to cooling sweat. You will learn to read pH (a number that tells you how acidic or basic a liquid is) and see why a small change in that number, from 7 down to 4, means 1,000 times more acid. You will also see how your body uses a buffer (a system that pushes back against a change in acidity) to keep your blood steady. These ideas are the chemistry under every later week of biology.

Why you already care about this

Picture three things on a kitchen counter. At about pH 2, a cut lemon sits at one end. At about pH 7, a glass of tap water sits in the middle. At about pH 9, a cup of water with a spoonful of baking soda stirred in sits past the middle. They look a lot alike, three clear or pale liquids, but they behave very differently. Lemon juice tastes sharp and sour. Baking-soda water tastes bitter and feels slippery. Tap water tastes like nothing much at all.

Those differences come from chemistry you cannot see. The lemon juice carries far more hydrogen ions than the tap water, and the baking-soda water carries far fewer. How many more? Not a little more. The lemon juice has 10,000,000 times more hydrogen ions than the baking-soda water, and this chapter shows you how to get that number with nothing but counting.

The same chemistry runs inside you. Your blood stays near pH 7.4, your stomach acid sits near pH 1 to 2, and the water that makes up so much of your body cools you, cushions you, and carries everything your cells need. Biology starts with chemistry, and this week you learn the small set of chemistry ideas that biology uses every day.

By the end of this chapter you will be able to:

name the particles inside an atom and tell an atom from a molecule;
sort a bond as covalent, ionic, or hydrogen by the verb that describes it;
explain how water's polarity lets water molecules hydrogen-bond;
match each of water's properties (cohesion, adhesion, high specific heat, evaporative cooling, floating ice, solvent power) to an everyday event;
compare two pH values by counting steps and raising ten to that power, with every step shown;
explain what a buffer does and does not do, using the buffer in your blood.

Carry this line with you: low number, high acid — and every step is tenfold, not one.

Where we are

Already covered: Week 1, The Science of Biology, gave you the characteristics of life, the levels of organization from atom to biosphere, and the controlled experiment, including the drops on a penny.
This week: atoms, elements, and molecules; the three bonds; water's polarity and its properties; the pH scale; and buffers.
How they connect: Week 1's ladder of organization starts with atoms and molecules, and this week zooms in on those bottom rungs; the penny result from Week 1 finally gets its explanation.
Where we're going next: Week 3, Biological Macromolecules, uses these bonds and this water to build the large molecules of life: carbohydrates, lipids, proteins, and nucleic acids.

Week 1 left you with a puzzle. A penny held an average of 30 drops of plain water but only 14 drops of soapy water. You read that experiment for its variables, and you were told the reason would wait. This week the reason arrives. If a word from Week 1 is fuzzy, here is the one you need most: an emergent property is an ability that appears at one level of organization but not in its separate parts. Water has several emergent properties, and every one of them comes from how its molecules attract each other. Next, you will start at the very bottom of the ladder, with the atom.

1. Build from atoms: elements, atoms, and molecules

Think about a set of toy building bricks. A few kinds of brick, snapped together in different ways, can make a car, a house, or a tree. Matter works the same way. A small number of kinds of pieces, joined in different ways, make everything from a raindrop to a redwood.

The pieces are atoms. An atom is the smallest unit of an element that still has that element's properties, built from protons and neutrons in a central nucleus with electrons around it. Each atom is built from three kinds of particles:

A proton is a positively charged particle in an atom's nucleus; the number of protons decides which element the atom is.
A neutron is a particle with no charge that sits in an atom's nucleus beside the protons.
An electron is a negatively charged particle that moves around an atom's nucleus; electrons are the particles atoms share or transfer when they form bonds.

Keep the electrons in mind. They are the part of the atom that does the bonding, so they will matter in every section that follows.

An element is a pure substance made of only one kind of atom, such as oxygen, carbon, hydrogen, or nitrogen. Those four are the big ones for life. Together they make up about 96% of your body by mass. Phosphorus and sulfur are the other two of the six elements of life.

Worked example — the elements of life. Your body by mass is about 65% oxygen, 18% carbon, 10% hydrogen, and 3% nitrogen. Add them, one at a time:

Start with oxygen and carbon: 65 + 18 = 83.
Add hydrogen: 83 + 10 = 93.
Add nitrogen: 93 + 3 = 96.

So oxygen, carbon, hydrogen, and nitrogen together make up about 96% of your body by mass. In words: four elements build almost all of you, and everything else, calcium, iron, and the rest, shares the last few percent. These are rounded figures, so treat them as approximate.

Atoms rarely sit alone. They join. A molecule is two or more atoms joined by chemical bonds, such as H₂O, which is one oxygen atom bonded to two hydrogen atoms. The small 2 after the H tells you there are two hydrogen atoms.

Worked example — atom or molecule? Sort four things.

H. One hydrogen atom on its own. It is an atom.
H₂O. Two hydrogen atoms and one oxygen atom joined by bonds. It is a molecule.
O. One oxygen atom on its own. It is an atom.
O₂. Two oxygen atoms joined by a bond, the oxygen you breathe. It is a molecule.

In words: one atom alone is an atom; two or more atoms joined by bonds make a molecule, even when both atoms are the same element.

Misconception check. Students often use "atom" and "molecule" as if they meant the same thing, saying "a water atom," for example. The slip is tempting because both words name something too small to see. The cure is to count: one atom alone is an atom, and two or more atoms bonded together are a molecule. There is no such thing as a water atom; water is a molecule built from three atoms.

Memory hook: an atom is one brick; a molecule is bricks snapped together.

2. Sort the three bonds: share, transfer, attract

Picture three ways two people can hold on to the same thing. They can both grip one rope and share it. One can hand the rope over completely, and then the two are still drawn to each other. Or they can stand near each other with a light, easy pull, like two magnets that barely touch. Atoms and molecules hold on to each other in three ways that match those pictures, and each one has its own verb.

Covalent bonds share. A covalent bond is a strong bond in which two atoms share a pair of electrons, like the bonds that hold the hydrogens to the oxygen inside a water molecule. Sharing is strong. The bonds inside a water molecule do not come apart when you pour a glass of water.

Ionic bonds transfer. First you need one more word. An ion is an atom that has gained or lost one or more electrons and so carries an electric charge, such as Na⁺ or Cl⁻. An ionic bond is a bond formed when one atom transfers an electron to another and the two oppositely charged ions attract, as sodium and chloride do in table salt. Sodium gives up an electron and becomes Na⁺. Chlorine takes that electron and becomes the chloride ion, Cl⁻. Opposite charges attract, and the two ions hold together.

Hydrogen bonds attract, weakly. A hydrogen bond is a weak attraction between a slightly positive hydrogen on one molecule and a slightly negative atom, such as oxygen, on another; one is weak, but many together are powerful. Think of a strip of hook-and-loop fastener. One tiny hook pulls off with no effort. Thousands of hooks together hold a shoe on your foot.

Worked example — name the bond. Decide which bond is at work in each case, using the verb.

Inside one water molecule, holding a hydrogen to the oxygen. The two atoms share a pair of electrons. Share means covalent.
Holding the sodium and the chloride together in a grain of table salt. Sodium handed an electron to chlorine, and the charged ions attract. Transfer means ionic.
Between two neighboring water molecules in a glass. A slightly positive hydrogen on one molecule is drawn to the slightly negative oxygen on the next. A weak attraction between molecules means hydrogen bond.

In words: share is covalent, transfer is ionic, and a weak pull between molecules is a hydrogen bond.

Misconception check. Students often say "ionic bonds share electrons." The mix-up is tempting because both covalent and ionic bonds involve electrons moving between atoms. But the verbs are different, and the verb is the whole point. Covalent bonds share a pair of electrons. Ionic bonds transfer an electron, and then the charged ions attract. If nothing was handed over, it is not ionic.

Memory hook: three bonds, three verbs — share, give away, cling.

3. Picture water: why polarity matters

Imagine two people sharing a blanket on a cold night, and one of them keeps pulling it to their side. They are still sharing, but the sharing is uneven. One side ends up warm and the other side ends up a little cold. Water's electrons are shared the same way.

Here is the water molecule described as a labeled figure. In the middle sits one oxygen atom. Two hydrogen atoms are attached to it, each by a covalent bond. The oxygen is labeled δ−, which means a slight negative charge. Each hydrogen is labeled δ+, which means a slight positive charge. The δ symbol is the Greek letter delta, and here it means "slightly."

Why the labels? Oxygen pulls the shared electrons toward itself more strongly than hydrogen does. The electrons spend more time near the oxygen, so the oxygen end turns slightly negative and the hydrogen ends turn slightly positive. The whole molecule is still neutral, but its charge is lopsided.

Polarity is an uneven spread of charge across a molecule, as in water, where oxygen pulls the shared electrons toward itself and becomes slightly negative while the hydrogens become slightly positive. A molecule with this uneven spread is called polar.

Polarity is what makes the hydrogen bond possible. The δ+ hydrogen of one water molecule is drawn to the δ− oxygen of a neighbor. Each water molecule can link to its neighbors this way, so a glass of water is a crowd of molecules constantly forming and breaking hydrogen bonds with each other.

Worked example — read the figure. Look at the labeled water molecule and answer three questions.

Which atom pulls the shared electrons harder? The oxygen, which is why it carries the δ− label.
Which ends are slightly positive? The two hydrogens, each labeled δ+.
Where would a neighboring water molecule's oxygen be drawn? Toward one of these hydrogens, because δ− attracts δ+. That attraction is a hydrogen bond.

In words: oxygen hogs the electrons, the hydrogens are left slightly positive, and opposite partial charges on neighboring molecules pull together.

Misconception check. Students often think the hydrogen bond is the bond inside a water molecule that holds a hydrogen to its oxygen. The mix-up is tempting because both bonds involve the same hydrogen atom. The cure is to ask where the bond sits. Inside one molecule, the hydrogen and oxygen share electrons, so that bond is covalent and strong. Between two molecules, a δ+ hydrogen is drawn to a δ− oxygen, and that weak pull is the hydrogen bond.

Memory hook: inside, a firm share; between neighbors, a gentle pull.

4. Trace water's properties back to hydrogen bonds

Every property in this section is an emergent property. No single water molecule has surface tension or cools a body. Those abilities appear only when many water molecules hydrogen-bond together. Each property below answers the same question: what are the hydrogen bonds doing?

Cohesion: water sticks to water. Cohesion is the attraction of water molecules to each other through hydrogen bonds, which produces surface tension and helps hold a column of water together inside a plant. At the top of a pond, the molecules cling to each other so tightly that the surface acts like a stretched sheet. Surface tension is the tight, skin-like surface that forms where water meets air because the water molecules at the surface cling to each other. A water strider, a small insect, can stand on a pond because surface tension holds it up. Inside a tall plant, cohesion keeps the thin columns of water in its vessels from breaking apart as water is drawn up toward the leaves.

Now the Week 1 puzzle. In the illustrative penny experiment, plain water averaged 30 drops and soapy water averaged 14 drops. Here is why. Plain water's cohesion builds strong surface tension, so the drops pile into a tall dome before it spills. Soap lowers water's surface tension by getting between the water molecules and disrupting their hydrogen bonds. With less surface tension, the dome breaks sooner. The 16-drop gap is cohesion, measured.

Adhesion: water sticks to other things. Adhesion is the attraction of water molecules to a different surface, such as the wall of a narrow tube or a plant's vessels. Dip the corner of a paper towel into a glass of water and watch the wet line creep upward. Capillary action is the climb of water up a narrow tube or through a paper towel, as adhesion pulls water along the surface and cohesion drags more water behind it. The two properties work as a team: adhesion grabs the wall, and cohesion pulls the rest of the water along.

High specific heat: water resists temperature change. Specific heat is the amount of heat a substance must absorb to raise its temperature; water's is high, so oceans and bodies change temperature slowly. Hydrogen bonds hold water molecules to each other, so heat has to loosen those bonds before the molecules can speed up. That is why a large lake or an ocean stays cooler than the air on a hot afternoon, and why your mostly-water body does not swing wildly in temperature when the weather changes.

Evaporative cooling: sweat cools you. Evaporative cooling is the cooling of a surface as its fastest-moving water molecules escape as vapor and carry heat away, which is how sweating cools the body. On a hot hike, sweat spreads on your skin. The water molecules moving fast enough to break their hydrogen bonds escape into the air, and they take heat with them. What stays behind on your skin is cooler.

Floating ice: frozen water is less dense. Drop an ice cube into a glass of water and it bobs at the top. When water freezes, hydrogen bonds lock each molecule into place, holding the molecules farther apart than in liquid water. Ice is therefore less dense than liquid water, and it floats. Because ice floats, a pond freezes from the top down, and fish keep living in the liquid water under the ice.

Solvent power: water dissolves the stuff of life. A solvent is the substance that other substances dissolve in; water dissolves so many charged and polar substances that it is the medium of every cell. Stir sugar into a glass of iced tea and it disappears. Water molecules crowd around each sugar molecule, their partial charges attracted to the sugar's, and pull it into the liquid. The molecules of life are built and dissolved in water, and next week's macromolecules are no exception.

Worked example — match the property. Name the property of water behind each event.

A water strider stands on a pond's surface. Water molecules cling to each other at the surface. That is cohesion, through surface tension.
Fish stay alive under a frozen pond. The ice on top floats because hydrogen bonds hold frozen molecules farther apart. That is floating ice.
Sugar vanishes into iced tea. Water molecules surround the sugar and pull it into the liquid. That is solvent power.
A paper towel's wet line climbs upward. Water clings to the towel's fibers and drags more water along. That is adhesion working with cohesion, the team called capillary action.

In words: every one of these events traces back to the same cause, hydrogen bonds between polar water molecules.

Misconception check. Two slips show up again and again. First, students swap cohesion and adhesion. Use the prefixes: co- means together, so cohesion is water with water; ad- means toward something else, so adhesion is water attached to another surface. Second, students say "ice floats because it is lighter," with no reason given. The reason is the hydrogen bonds: freezing locks the molecules farther apart, so the same mass takes up more room and ice is less dense.

Memory hook: co is water with water; ad is water attached to something else.

5. Count the steps: reading the pH scale

Imagine a video game where each new level multiplies your points by ten. Level 3 is not a little ahead of level 2; it holds ten times as many points. The pH scale is built the same way, and it is the most common place students go wrong this week.

Start with the particle the scale measures. A hydrogen ion, H⁺, is a hydrogen atom that has lost its electron. The more hydrogen ions a liquid carries, the more acidic it is.

The word for this measure is pH. It is a measure of hydrogen-ion concentration on an inverse logarithmic scale from 0 to 14, where 7 is neutral, a lower number means more hydrogen ions, and each whole unit is a tenfold change. As a formula, pH = −log[H⁺], where [H⁺] is the hydrogen-ion concentration in moles per liter (written M).

Read the scale with three anchors:

An acid is a substance that raises the hydrogen-ion concentration of a solution, giving it a pH below 7, such as lemon juice or vinegar.
A base is a substance that lowers the hydrogen-ion concentration of a solution, giving it a pH above 7, such as a baking-soda solution. A base raises the share of hydroxide ions, OH⁻, as it lowers the share of H⁺.
Pure water is neutral at pH 7, with a hydrogen-ion concentration of 1 × 10⁻⁷ moles per liter.

"Inverse" means the number goes down as the hydrogen ions go up. That is why the shortcut is low number, high acid. "Logarithmic" means each whole step is a multiply-by-ten step. You never subtract pH values to compare them. You count the whole-unit steps, and then you raise ten to that power.

The pH ladder: approximate pH of four household liquids and two body fluids, with each one's class
Liquid	Approximate pH	Class
Stomach acid	1 to 2	acid
Lemon juice	2	acid
White vinegar	3	acid
Tap water	7	neutral
Blood	7.4	slightly basic
Baking-soda solution	9	base

Honesty note: the household values are approximate and vary by brand, so what matters is the class (acid, neutral, or base), the direction (lower is more acidic), and the tenfold-step arithmetic, never one brand's exact pH.

Worked example — the pH ladder. Work each comparison in two moves: count the steps, then raise ten.

Classify. Lemon juice (about pH 2) and white vinegar (about pH 3) sit below 7, so they are acids. Tap water (about pH 7) is neutral. Baking-soda solution (about pH 9) sits above 7, so it is a base.
pH 4 versus pH 7. Count the steps from 4 up to 7: 4 to 5, 5 to 6, 6 to 7. That is three steps. Raise ten to the third power: 10³ = 10 × 10 × 10 = 1,000. So pH 4 has 1,000 times more hydrogen ions than pH 7.
Vinegar versus tap water, pH 3 versus pH 7. Count the steps from 3 up to 7: four steps. Raise ten: 10⁴ = 10,000. The vinegar has 10,000 times more hydrogen ions than the tap water.
Lemon juice versus baking-soda solution, pH 2 versus pH 9. Count the steps from 2 up to 9: seven steps. Raise ten: 10⁷ = 10,000,000. The lemon juice has 10,000,000 times more hydrogen ions than the baking-soda solution.
pH 2 versus pH 4. Count the steps from 2 up to 4: two steps. Raise ten: 10² = 100. pH 2 has 100 times more hydrogen ions than pH 4.
Read the concentration. Because [H⁺] = 10^(−pH), pH 3 means 1 × 10⁻³ M and pH 7 means 1 × 10⁻⁷ M. The exponents are four steps apart, which matches the 10,000 times from step 3.

In words: on the pH scale, every whole step multiplies the hydrogen ions by ten, so a gap of a few steps is a gap of thousands or more. Put another way, pH 4 versus pH 7 is a 1,000-fold gap, not a small nudge. A cook choosing between vinegar and tap water for a pickle brine is choosing a liquid with 10,000 times more hydrogen ions.

This week's lab as a controlled test. In the Red-Cabbage pH Indicator lab, you brew an indicator from red cabbage, add it to five household liquids, and sort each liquid as acid, neutral, or base. The cabbage's pigments change color with pH, turning toward red or pink-purple in acids and toward blue-green or greenish-yellow in bases. Read it with Week 1's tools. The independent variable is which liquid you test. The dependent variable is the indicator's color, which you record in words and translate into a class. The controlled variables are the same amount of indicator and the same amount of liquid in every cup. Tap water, near neutral, serves as your reference cup. If color is hard for you to judge, the free PhET pH Scale simulation is a virtual alternative that shows each liquid's pH as a number.

Misconception check. Two slips go together. First, students often think "a higher pH means more acidic." It is the reverse: lower pH means more hydrogen ions, so low number, high acid. Second, students read the pH scale like a ruler and say "pH 4 is a bit more acidic than pH 7." It is not a bit. Three steps means 10³ = 1,000 times more hydrogen ions. Count the steps, then raise ten, every time.

Memory hook: low number, high acid; each step, times ten.

6. Explain buffers: resist, never prevent

Think about a car's shock absorbers on a bumpy road. They do not make the bumps disappear. They soak up most of each jolt so the ride stays smooth. Hit a deep enough pothole, though, and you still feel it. A buffer does the same job for pH.

A buffer is a system that resists a change in pH by taking up or releasing hydrogen ions; it slows a change but never prevents one, and it can be overwhelmed. The verb matters. A buffer resists. It does not prevent.

Your blood carries one of the most important buffers in your body, the carbonic acid / bicarbonate system, and it holds your blood near pH 7.4. That steadiness is homeostasis at the chemical level, the regulation of the inside of your body that Week 1 listed among the characteristics of life.

Worked example — the blood buffer at work. Follow the buffer in both directions.

Blood starts to turn more acidic, with extra hydrogen ions arriving. Bicarbonate ions take up the excess hydrogen ions and become carbonic acid. Fewer free hydrogen ions remain, so the pH drops much less than it would have.
Blood starts to drift basic, with too few hydrogen ions. Carbonic acid gives hydrogen ions back. The pH rises much less than it would have.
Clearing the extra. Carbonic acid breaks down into water and carbon dioxide, and your lungs breathe the carbon dioxide out.

In words: the buffer acts like a hydrogen-ion bank, taking deposits when there are too many and making withdrawals when there are too few, so the blood stays near pH 7.4. Caveat: the bank has limits. A large enough flood of acid or base can overwhelm a buffer, and then the pH does change.

Misconception check. Students often think "a buffer prevents any pH change." The idea is tempting because blood pH stays so steady. But a buffer only resists change; it slows the shift and keeps it small. Add enough acid or base and the buffer runs out of capacity, and the pH moves. Say resists, never prevents.

Memory hook: a buffer is a shock absorber, not a wall.

Key terms

Atom — The smallest unit of an element that still has that element's properties, built from protons and neutrons in a central nucleus with electrons around it. (first used: 1. Build from atoms: elements, atoms, and molecules)
Proton — A positively charged particle in an atom's nucleus; the number of protons decides which element the atom is. (first used: 1. Build from atoms: elements, atoms, and molecules)
Neutron — A particle with no charge that sits in an atom's nucleus beside the protons. (first used: 1. Build from atoms: elements, atoms, and molecules)
Electron — A negatively charged particle that moves around an atom's nucleus; electrons are the particles atoms share or transfer when they form bonds. (first used: 1. Build from atoms: elements, atoms, and molecules)
Element — A pure substance made of only one kind of atom, such as oxygen, carbon, hydrogen, or nitrogen. (first used: 1. Build from atoms: elements, atoms, and molecules)
Molecule — Two or more atoms joined by chemical bonds, such as H₂O, which is one oxygen atom bonded to two hydrogen atoms. (first used: 1. Build from atoms: elements, atoms, and molecules)
Covalent bond — A strong bond in which two atoms share a pair of electrons, like the bonds that hold the hydrogens to the oxygen inside a water molecule. (first used: 2. Sort the three bonds: share, transfer, attract)
Ion — An atom that has gained or lost one or more electrons and so carries an electric charge, such as Na⁺ or Cl⁻. (first used: 2. Sort the three bonds: share, transfer, attract)
Ionic bond — A bond formed when one atom transfers an electron to another and the two oppositely charged ions attract, as sodium and chloride do in table salt. (first used: 2. Sort the three bonds: share, transfer, attract)
Hydrogen bond — A weak attraction between a slightly positive hydrogen on one molecule and a slightly negative atom, such as oxygen, on another; one is weak, but many together are powerful. (first used: 2. Sort the three bonds: share, transfer, attract)
Polarity — An uneven spread of charge across a molecule, as in water, where oxygen pulls the shared electrons toward itself and becomes slightly negative while the hydrogens become slightly positive. (first used: 3. Picture water: why polarity matters)
Cohesion — The attraction of water molecules to each other through hydrogen bonds, which produces surface tension and helps hold a column of water together inside a plant. (first used: 4. Trace water's properties back to hydrogen bonds)
Surface tension — The tight, skin-like surface that forms where water meets air because the water molecules at the surface cling to each other. (first used: 4. Trace water's properties back to hydrogen bonds)
Adhesion — The attraction of water molecules to a different surface, such as the wall of a narrow tube or a plant's vessels. (first used: 4. Trace water's properties back to hydrogen bonds)
Capillary action — The climb of water up a narrow tube or through a paper towel, as adhesion pulls water along the surface and cohesion drags more water behind it. (first used: 4. Trace water's properties back to hydrogen bonds)
Specific heat — The amount of heat a substance must absorb to raise its temperature; water's is high, so oceans and bodies change temperature slowly. (first used: 4. Trace water's properties back to hydrogen bonds)
Evaporative cooling — The cooling of a surface as its fastest-moving water molecules escape as vapor and carry heat away, which is how sweating cools the body. (first used: 4. Trace water's properties back to hydrogen bonds)
Solvent — The substance that other substances dissolve in; water dissolves so many charged and polar substances that it is the medium of every cell. (first used: 4. Trace water's properties back to hydrogen bonds)
pH — A measure of hydrogen-ion concentration on an inverse logarithmic scale from 0 to 14, where 7 is neutral, a lower number means more hydrogen ions, and each whole unit is a tenfold change. (first used: 5. Count the steps: reading the pH scale)
Acid — A substance that raises the hydrogen-ion concentration of a solution, giving it a pH below 7, such as lemon juice or vinegar. (first used: 5. Count the steps: reading the pH scale)
Base — A substance that lowers the hydrogen-ion concentration of a solution, giving it a pH above 7, such as a baking-soda solution. (first used: 5. Count the steps: reading the pH scale)
Buffer — A system that resists a change in pH by taking up or releasing hydrogen ions; it slows a change but never prevents one, and it can be overwhelmed. (first used: 6. Explain buffers: resist, never prevent)

Summary

Atoms are built from protons, neutrons, and electrons; an element is one kind of atom.
Oxygen, carbon, hydrogen, and nitrogen make up about 96% of the body by mass.
One atom alone is an atom; two or more bonded atoms make a molecule.
Covalent bonds share electrons, ionic bonds transfer them, and hydrogen bonds weakly attract.
Water is polar: its oxygen is slightly negative and its hydrogens slightly positive.
Hydrogen bonds between water molecules produce cohesion, adhesion, high specific heat, evaporative cooling, floating ice, and solvent power.
Lower pH means more hydrogen ions; each whole pH step is a tenfold change.
To compare two pH values, count the steps, then raise ten to that power.
A buffer resists a pH change but never prevents one; blood's buffer holds it near pH 7.4.

Check your understanding

Work these before looking at the answers — they are ungraded, and the answers (with reasoning) are at the bottom of the page.

In an illustrative test made up for this question, a cup of black coffee reads pH 5 and a cup of soapy dishwater reads pH 10. Which liquid is more acidic, and how many times more hydrogen ions does it carry?
Sort each as an atom or a molecule: C, N₂, CO₂, and O. Then name the bond that holds the two nitrogen atoms in N₂ together, and explain how you know.
A florist stands a cut celery stalk in a glass of colored water, and after a while the color shows up in the leaves. Which two properties of water move the water up the stalk, and what does each one do?
A classmate says, "Our blood has a buffer, so a sour drink cannot change its pH at all." Explain what is right and what is wrong in that statement.

Answers (worked reasoning — read after attempting)

The coffee is more acidic, because its pH is the lower number: low number, high acid. Count the steps from 5 up to 10: 5 to 6, 6 to 7, 7 to 8, 8 to 9, 9 to 10. That is five steps. Raise ten to the fifth power: 10⁵ = 100,000. So the coffee carries 100,000 times more hydrogen ions than the dishwater. If you wrote "5 more" or "twice as many," you read the scale as a ruler; each step is times ten.
C is one carbon atom, so it is an atom. O is one oxygen atom, so it is an atom. N₂ is two nitrogen atoms bonded together, so it is a molecule. CO₂ is one carbon and two oxygen atoms bonded together, so it is a molecule. The two nitrogen atoms in N₂ are the same element, so neither one would pull an electron away from the other to make ions; they share electrons, and sharing means a covalent bond.
Adhesion and cohesion, working together as capillary action. Adhesion is water clinging to the walls of the stalk's narrow vessels, which pulls the water up along those walls. Cohesion is water clinging to water, which drags the rest of the column up behind it without the column breaking.
What is right: blood does have a buffer, the carbonic acid / bicarbonate system, and it does push back against a change by taking up extra hydrogen ions. What is wrong is "cannot change its pH at all." A buffer resists a change; it never prevents one. It keeps the change small, and a large enough load of acid could overwhelm it.

Next up in this module: the lecture, the slide deck, the Readings & Resources page, the tutorial, the practice set, and the quiz — and next week the build-and-break rule assembles big molecules in water.

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