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Week 2 · Chapter

Chapter 2 — The Chemistry of Life

Human Anatomy and Physiology I Free sample edition

The module's primary reading · ~40–50 minutes · Objective 2 (relate the chemistry of the body to its function — atoms and the three bond types, water's properties, the logarithmic pH scale with the blood's buffered range, and the four classes of organic compounds — and explain the cell's membrane, organelles, and transport (diffusion, osmosis and tonicity, active transport, and bulk transport), the overview of how a cell makes ATP, and how a gene is read into a protein), Objective 1 (use the language of the body correctly — the anatomical position, the directional-term pairs, the three body planes, and the body cavities and abdominal regions — distinguish anatomy from physiology, climb the levels of structural organization, list the functions and requirements of human life, and trace a homeostatic feedback loop through its receptor, control center, and effector, telling negative feedback from positive feedback) · Read it first this week; the lecture, the slides, the tutorial, the quiz, and the lab all build on it.

In plain language

Your body is built from atoms (the tiny units every substance is made of), and four kinds of atom make up about 96% of your mass. Atoms hold together through chemical bonds (the ways atoms hand over or share their outer particles), and the bonds in water explain why water can dissolve salt, soak up heat, and cushion a joint. This week you also learn to read pH (a number that tells you how acidic or basic a liquid is) and to see why a change of 3 units on that scale means 1,000 times more acid. Your blood stays inside a narrow pH band, and a buffer (a pair of chemicals that pushes back against a change in acidity) helps keep it there. Every later week, from the cell to the nerve impulse, runs on this chemistry.

Why you already care about this

Stir 1 spoonful of table salt into a pot of soup and watch it vanish. Run a hot trail on a summer afternoon and feel the sweat cool your skin. Look at a lab report from a clinic and find a line for blood pH reading 7.4. The normal band printed beside it runs from 7.35 to 7.45. Those three moments look unrelated. They are the same subject.

The salt vanishes because water pulls its charged pieces apart. The sweat cools you because water soaks up a lot of heat. The blood value sits in its narrow band because your body defends it every second, with chemistry and with your breathing. Water can be up to about 60% of an adult's body mass, so the chemistry of water is the chemistry of you.

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

name the three particles in an atom and say which one decides the element;
sort a bond as ionic, covalent, or hydrogen by what happens to the electrons;
link each of water's four jobs in the body to its polarity;
compare two whole-number pH values by counting the steps and then raising ten to that power, with every step shown;
read a blood pH value against the range 7.35 to 7.45 and name the departure on each side;
match each class of organic compound to its building block and explain why a protein's shape decides its job.

Carry this line with you: count the steps, then raise ten — a pH scale is not a ruler.

Where we are

Already covered: Week 1, Body Organization, Homeostasis & Anatomical Terminology, gave you the levels of organization and homeostasis: a set point, a normal range, and negative feedback.
This week: atoms, the three bonds, water's four jobs, the pH scale, buffers, and the organic compounds with ATP.
How they connect: this week zooms in on Week 1's chemical level, and Week 1's homeostasis returns as the blood's pH range.
Where we're going next: Week 3, The Cell & Membrane Transport, moves water and ions across the cell's membrane.

In Week 1 you met the chemical level as the first rung of the ladder. You also learned that your body holds a regulated variable near a set point, inside a normal range, by negative feedback that reverses a change. The first rung is where this chapter starts, and the feedback idea comes back in Section 5, where your blood's pH is the variable being held steady. Next, you start with the smallest piece: the atom.

1. Build up from atoms: protons name the element

Think of a box of beads in three kinds. One kind carries a plus sign, one carries nothing, and one carries a minus sign. Every atom in your body, and in the salt on your table, is built from those three kinds of particle.

A proton is a positively charged particle in an atom's nucleus; the count of protons decides which element the atom is.
A neutron is an uncharged particle that sits in an atom's nucleus alongside the protons.
An electron is a negatively charged particle around an atom's nucleus; atoms transfer or share electrons when they form bonds.

An atom is the smallest unit of an element, built from protons and neutrons in a central nucleus with electrons around it. An element is a substance made of one kind of atom, identified by the number of protons in each atom's nucleus. That count has its own name. The atomic number is the count of protons in the nucleus of an atom, the number that identifies its element. Change the number of protons and you have a different element. Change the number of electrons and you still have the same element, now carrying a charge.

Four elements do most of the work in your body: oxygen, carbon, hydrogen, and nitrogen. Six more get named now because later weeks need them: calcium, phosphorus, potassium, sodium, chlorine, and magnesium. The bone, nerve, and muscle weeks will use them as charged particles, so their names will come back.

Worked example — the four big elements. By mass, your body is about 65% oxygen, 18% carbon, 10% hydrogen, and 3% nitrogen. Add them one at a time:

Oxygen plus carbon: 65 + 18 = 83.
Add hydrogen: 83 + 10 = 93.
Add nitrogen: 93 + 3 = 96.

So oxygen, carbon, hydrogen, and nitrogen make up about 96% of body mass. In words: four elements build almost all of you, and every other element shares the last few percent. Honesty note: these are rounded figures, so treat each one as "about."

Misconception check. Students often think the number of electrons decides the element, because electrons are the particles that move during a bond. It is the protons. A sodium atom that gives away one electron is still sodium; it has become a charged sodium ion. If you want to know which element you have, count the protons.

Memory hook: count protons for identity; follow electrons for bonding.

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

Picture three ways you and a friend can deal with one concert ticket. You hand the ticket over. You both hold it together. Or you stand near each other, pulled together by a weak attraction while each of you keeps a ticket of your own. Atoms bond in those three ways.

An ion is an atom that has given away or taken electrons and so carries an electric charge, such as Na⁺ or Cl⁻. An ionic bond is a bond in which one atom transfers an electron to another and the two oppositely charged ions attract, as sodium and chloride do in table salt. Sodium gives one electron to chlorine. Sodium becomes Na⁺, chlorine becomes Cl⁻, and the opposite charges hold together.

A covalent bond is a bond in which two atoms share one or more pairs of electrons. Sharing comes in two kinds. A nonpolar covalent bond is a covalent bond in which the two atoms share their electrons evenly, so neither end carries a partial charge. A polar covalent bond is a covalent bond in which one atom pulls the shared electrons closer, leaving that end slightly negative and the other end slightly positive, as inside a water molecule. Chemists mark those slight charges δ− and δ+.

A hydrogen bond is a weak attraction between a slightly positive hydrogen on one molecule and an electronegative atom on a neighboring molecule, drawn as a dotted line. "Electronegative" means the atom pulls hard on shared electrons, the way the oxygen in water does. The dotted line is a reminder that this bond is weak.

Worked example — name the bond. Read what the electrons do, then name the bond.

In a kitchen, a pinch of salt holds Na⁺ and Cl⁻ together. One atom transferred an electron, so the bond is ionic.
Inside one water molecule, the oxygen and each hydrogen share a pair of electrons, and the oxygen pulls them closer. Sharing, unevenly, means a polar covalent bond.
Two atoms of the same element share a pair of electrons. Neither pulls harder, so the sharing is even and the bond is nonpolar covalent.
A δ+ hydrogen on one water molecule is drawn to the δ− oxygen of the next molecule. Nothing is shared or handed over between them; it is a weak pull between molecules, so it is a hydrogen bond.

Misconception check. Students often think the hydrogen bond is the bond inside a water molecule, because the same hydrogen atom shows up in both. Ask where the bond sits. Inside one molecule, oxygen and hydrogen share electrons, so that bond is polar covalent. Between two molecules, a weak attraction pulls a δ+ hydrogen toward a δ− oxygen, and that is the hydrogen bond.

Carry-line: ionic transfers; covalent shares; hydrogen bonds attract between molecules.

3. Picture water: polarity and four jobs

Imagine you are looking at a labeled drawing of one water molecule, H₂O. In the center sits a large oxygen atom marked δ−. Two smaller hydrogen atoms sit off to one side of it, each marked δ+, each joined to the oxygen by a short solid line for its polar covalent bond. Around the molecule, dotted lines reach out to neighboring water molecules. Those dotted lines are hydrogen bonds.

The oxygen pulls the shared electrons toward itself, so one side of the molecule is slightly negative and the other slightly positive. Polarity is an uneven spread of charge across a molecule, so one end is slightly negative and the other slightly positive. Almost everything useful about water follows from it.

Water does four jobs in your body:

The solvent. A solvent is the liquid in which other substances dissolve; water is the body's solvent, and its reactions happen in it. When salt enters the water of your blood plasma, the slightly negative oxygen ends are drawn toward each Na⁺ and the slightly positive hydrogen ends toward each Cl⁻, which pulls the ions apart and keeps them apart.
The heat sink. Water absorbs heat with little rise in its own temperature. When sweat evaporates from a runner's skin on a hot trail, it carries heat away with it.
The lubricant. Water is the main ingredient of the slippery fluids between moving parts, such as the synovial fluid inside a knee joint and the pleural fluid around the lungs.
The reactant. Water takes part in reactions. Hydrolysis is a reaction that consumes a water molecule to split a larger molecule into smaller pieces. Dehydration synthesis is a reaction that joins two smaller molecules into a larger one and produces a water molecule as it does.

Water is up to about 60% of an adult's body mass, so every one of those jobs runs all day in your tissues, the way the salt in your soup stays dissolved.

Worked example — match the job. For each moment, name the job water is doing.

Salt stirred into soup disappears from view. The ions were pulled apart and surrounded, so water is acting as the solvent.
A hiker's skin cools as sweat evaporates. Water soaked up heat and carried it away, so water is acting as the heat sink.
A knee bends smoothly again and again on a stair climb. The fluid in the joint lets the surfaces glide, so water is acting as the lubricant.
A large molecule is split into two smaller ones, and a water molecule is used up. That is hydrolysis, so water is acting as a reactant.

Misconception check. Students often swap hydrolysis and dehydration synthesis because both names mention water. Read the word parts. Hydro-lysis means water-splitting: water goes in and a large molecule breaks apart. Dehydration synthesis means building while losing water: two small molecules join and a water molecule comes out.

Memory hook: one bent molecule; four jobs.

4. Count the steps: reading the pH scale

Two cups of clear liquid on your counter can look the same and still be very different. What separates them is how many hydrogen ions, H⁺, each one carries. pH is a measure of hydrogen-ion concentration on an inverse logarithmic scale from 0 to 14, with 7 neutral and each whole unit a tenfold change.

Two words in that definition do the heavy lifting. "Inverse" means the scale runs backward: a lower pH means more hydrogen ions, so a lower number is more acidic. "Logarithmic" means each whole step multiplies. One step down the scale is ten times more hydrogen ions, not one more unit of them.

So the method has two moves, every time. First, count the whole-unit steps between the two values. Second, raise ten to that power.

Worked example — Dataset B, the pH step pair. Compare pH 4 with pH 7.

Count the steps: from 4 up to 7 is 4 to 5, 5 to 6, and 6 to 7, which is three whole-unit steps.
Raise ten: 10³ = 10 × 10 × 10 = 1,000, so pH 4 has 1,000 times more hydrogen ions than pH 7.

Now the companion pair, pH 5 vs. pH 7. From 5 up to 7 is two steps, so 10² = 10 × 10 = 100 times more hydrogen ions at pH 5, never 20. And the smallest case, pH 4 vs. pH 5: one whole-unit step, so 10¹ = 10 times more hydrogen ions at pH 4.

Say it in words: pH 4 versus pH 7 is a 1,000-fold difference, though the two numbers look only three apart. That is why the clinic report in the opening prints such a narrow band, and why you count before you compare.

Misconception check. Three slips travel together. Students often say "pH 4 is three times more acidic than pH 7"; it is 1,000 times, because each of the three steps multiplies by ten. Students often say two units is "twentyfold"; it is 100-fold, because 10 × 10 is 100, not 10 + 10. And students often think "a higher pH means more acidic"; it is the reverse, because the scale is inverse. Count the steps, then raise ten, and read low numbers as more acid.

Caveat: the step rule in this course is worked on whole-unit steps only. A step of a fraction of a unit is described in words, as you will see in the next section.

5. Hold the line: acids, bases, and buffers

Picture yourself in a crowded stairwell, climbing four flights with everyone else. Your leg muscles work hard, and working muscle makes carbon dioxide, CO₂, as waste. That CO₂ meets the water in your blood and makes carbonic acid, H₂CO₃. Acid in the blood is the kind of change homeostasis has to answer.

An acid is a substance that adds hydrogen ions to a solution; an acidic solution sits below pH 7. A base is a substance that adds hydroxide ions, OH⁻, to a solution or takes up hydrogen ions; a basic solution sits above pH 7.

Your blood is held between 7.35 and 7.45, typically 7.4, a little on the basic side of neutral. That band is a normal range in exactly the Week 1 sense, and your body defends it the Week 1 way, by reversing a change. Your breathing on that hot trail run, faster and deeper, is part of the defense.

The first defense is a buffer. A buffer is a weak acid paired with its conjugate base that absorbs small additions of acid or base and so resists a change in pH. In blood, the main buffer is the bicarbonate system, with bicarbonate, HCO₃⁻, as its base half. When extra hydrogen ions arrive, the base half takes some of them up. The second defense is your breathing, which carries CO₂ out of your body. Working muscle makes CO₂, CO₂ makes carbonic acid, and buffers and breathing hold the line.

When the line does not hold, the departure has a name on each side. Acidosis is a blood pH below the defended range of 7.35 to 7.45, on the acidic side. Alkalosis is a blood pH above the defended range of 7.35 to 7.45, on the basic side. Those two names are the clinical connection for this week, and they illustrate one thing: the range is narrow, and leaving it on either side matters.

Worked example — read the chart. An illustrative chart value reads 7.0.

Compare it to the range: 7.0 is below 7.35, so it falls on the acidosis side.
Find the drop from typical: 7.4 − 7.0 = 0.4 of a unit.
Describe it in words: the drop is a meaningful rise in hydrogen ions. Because it is a fraction of a unit, this course describes it in words and never turns it into a fold figure.

Misconception check. Students often think a buffer holds blood at exactly pH 7, or never lets the pH change at all. Neither is right. The blood is held near 7.4, not at neutral 7. A buffer resists a change and keeps it small; it does not forbid one. Overwhelm the buffer and the pH leaves the range, and that is acidosis or alkalosis.

Limitation: this week names the departures and stops there. How each one arises in a particular body is a question for later courses, not for this chapter.

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

6. Name the building blocks: organic compounds and ATP

Think of four sets of building toys on your floor, each with its own kind of piece. The molecules of life sort the same way. Four classes of organic compound build your body, and three of them are made from one repeating kind of piece.

A carbohydrate is an organic compound built from sugar units called monosaccharides. A monosaccharide is a single sugar unit, the building block of carbohydrates.
A lipid is an organic compound, such as a triglyceride, that is not built from one single repeating building block. A triglyceride is a lipid made of one glycerol joined to fatty acids.
A protein is an organic compound made of a chain of amino acids folded into a shape that decides its job. An amino acid is the building block of proteins; 20 kinds make up nearly all human proteins.
A nucleic acid is an organic compound built as a chain of nucleotides, the fourth class of organic compound in the body. A nucleotide is the building block of nucleic acids.

Proteins earn extra attention from you, because structure determines function here more plainly than anywhere. The order of the amino acids, the sequence, sets how the chain folds. The fold sets the shape, and the shape sets the job. Proteins are the body's workers, and one job they do is serving as enzymes; how enzymes work is outside this course.

Denaturation is the unfolding of a protein's shape by heat, a change in pH, or another physical or chemical stress, which can cost the protein its function. A very high body temperature during a fever can loosen a protein's shape this way. The sequence of amino acids stays the same, but the fold, and with it the job, can be lost.

ATP is adenosine triphosphate, a molecule of adenine, ribose, and three phosphate groups that releases usable energy when one phosphate group is split off. Think of it as spendable money in your pocket, not savings. Next week's sodium-potassium pump spends it, and so does every muscle contraction you will study later in the course.

Worked example — match the block. For each molecule, name its class and its building block.

A chain of amino acids folded into a channel shape: a protein, built from amino acids.
One glycerol joined to fatty acids: a triglyceride, which is a lipid, with no single repeating monomer.
A long chain of sugar units: a carbohydrate, built from monosaccharides.
A long chain of nucleotides: a nucleic acid, built from nucleotides.

Misconception check. Students often give lipids a single monomer, the way the other three classes have one. A triglyceride is glycerol plus fatty acids, two different kinds of piece, so there is no single repeating building block for lipids. If a list of "four classes, four monomers" looks too tidy, the lipid row is where it breaks.

Key terms

Proton — A positively charged particle in an atom's nucleus; the count of protons decides which element the atom is. (first used: 1. Build up from atoms: protons name the element)
Neutron — An uncharged particle that sits in an atom's nucleus alongside the protons. (first used: 1. Build up from atoms: protons name the element)
Electron — A negatively charged particle around an atom's nucleus; atoms transfer or share electrons when they form bonds. (first used: 1. Build up from atoms: protons name the element)
Atom — The smallest unit of an element, built from protons and neutrons in a central nucleus with electrons around it. (first used: 1. Build up from atoms: protons name the element)
Element — A substance made of one kind of atom, identified by the number of protons in each atom's nucleus. (first used: 1. Build up from atoms: protons name the element)
Atomic number — The count of protons in the nucleus of an atom, the number that identifies its element. (first used: 1. Build up from atoms: protons name the element)
Ion — An atom that has given away or taken electrons and so carries an electric charge, such as Na⁺ or Cl⁻. (first used: 2. Sort the three bonds: transfer, share, attract)
Ionic bond — A bond in which 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: transfer, share, attract)
Covalent bond — A bond in which two atoms share one or more pairs of electrons. (first used: 2. Sort the three bonds: transfer, share, attract)
Nonpolar covalent bond — A covalent bond in which the two atoms share their electrons evenly, so neither end carries a partial charge. (first used: 2. Sort the three bonds: transfer, share, attract)
Polar covalent bond — A covalent bond in which one atom pulls the shared electrons closer, leaving that end slightly negative and the other end slightly positive, as inside a water molecule. (first used: 2. Sort the three bonds: transfer, share, attract)
Hydrogen bond — A weak attraction between a slightly positive hydrogen on one molecule and an electronegative atom on a neighboring molecule, drawn as a dotted line. (first used: 2. Sort the three bonds: transfer, share, attract)
Polarity — An uneven spread of charge across a molecule, so one end is slightly negative and the other slightly positive. (first used: 3. Picture water: polarity and four jobs)
Solvent — The liquid in which other substances dissolve; water is the body's solvent, and its reactions happen in it. (first used: 3. Picture water: polarity and four jobs)
Hydrolysis — A reaction that consumes a water molecule to split a larger molecule into smaller pieces. (first used: 3. Picture water: polarity and four jobs)
Dehydration synthesis — A reaction that joins two smaller molecules into a larger one and produces a water molecule as it does. (first used: 3. Picture water: polarity and four jobs)
pH — A measure of hydrogen-ion concentration on an inverse logarithmic scale from 0 to 14, with 7 neutral and each whole unit a tenfold change. (first used: 4. Count the steps: reading the pH scale)
Acid — A substance that adds hydrogen ions to a solution; an acidic solution sits below pH 7. (first used: 5. Hold the line: acids, bases, and buffers)
Base — A substance that adds hydroxide ions to a solution or takes up hydrogen ions; a basic solution sits above pH 7. (first used: 5. Hold the line: acids, bases, and buffers)
Buffer — A weak acid paired with its conjugate base that absorbs small additions of acid or base and so resists a change in pH. (first used: 5. Hold the line: acids, bases, and buffers)
Acidosis — A blood pH below the defended range of 7.35 to 7.45, on the acidic side. (first used: 5. Hold the line: acids, bases, and buffers)
Alkalosis — A blood pH above the defended range of 7.35 to 7.45, on the basic side. (first used: 5. Hold the line: acids, bases, and buffers)
Carbohydrate — An organic compound built from sugar units called monosaccharides. (first used: 6. Name the building blocks: organic compounds and ATP)
Monosaccharide — A single sugar unit, the building block of carbohydrates. (first used: 6. Name the building blocks: organic compounds and ATP)
Lipid — An organic compound, such as a triglyceride, that is not built from one single repeating building block. (first used: 6. Name the building blocks: organic compounds and ATP)
Triglyceride — A lipid made of one glycerol joined to fatty acids. (first used: 6. Name the building blocks: organic compounds and ATP)
Protein — An organic compound made of a chain of amino acids folded into a shape that decides its job. (first used: 6. Name the building blocks: organic compounds and ATP)
Amino acid — The building block of proteins; 20 kinds make up nearly all human proteins. (first used: 6. Name the building blocks: organic compounds and ATP)
Nucleic acid — An organic compound built as a chain of nucleotides, the fourth class of organic compound in the body. (first used: 6. Name the building blocks: organic compounds and ATP)
Nucleotide — The building block of nucleic acids. (first used: 6. Name the building blocks: organic compounds and ATP)
Denaturation — The unfolding of a protein's shape by heat, a change in pH, or another physical or chemical stress, which can cost the protein its function. (first used: 6. Name the building blocks: organic compounds and ATP)
ATP — Adenosine triphosphate, a molecule of adenine, ribose, and three phosphate groups that releases usable energy when one phosphate group is split off. (first used: 6. Name the building blocks: organic compounds and ATP)

Summary

The number of protons, the atomic number, identifies an element.
Oxygen, carbon, hydrogen, and nitrogen make up about 96% of body mass.
An ionic bond transfers an electron; a covalent bond shares electron pairs.
A hydrogen bond is a weak attraction between molecules, not the bond inside water.
Water's polarity makes it a solvent, a heat sink, a lubricant, and a reactant.
To compare two pH values, count the whole-unit steps, then raise ten to that power.
Lower pH means more hydrogen ions and more acid.
Blood is held between 7.35 and 7.45; below is acidosis, above is alkalosis.
A buffer resists a pH change; it does not forbid one.
A protein's sequence sets its shape, and its shape sets its job.
ATP releases usable energy when one phosphate group is split off.

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 pair made up for this question, a rain-barrel sample reads pH 6 and a garden-pond sample reads pH 8. Which sample carries more hydrogen ions, and how many times more?
In a second illustrative pair, a fish-tank sample reads pH 2 and a second sample reads pH 6. Someone reads the difference as "4 times more acidic." Work the comparison and correct the reading.
An illustrative chemistry-kit card describes two atoms that each have 11 protons, but one has 11 electrons and the other has 10. Are they the same element? What is different about the second one?
A study flash card reads: "When a protein denatures, it loses its amino acids, so its sequence changes and its job goes with it." Using this week's definition of denaturation, say what is right and what is wrong about that card.

Answers (worked reasoning — read after attempting)

The rain-barrel sample carries more, because its pH is the lower number and a lower pH means more hydrogen ions. Count the steps from 6 up to 8: 6 to 7 and 7 to 8, which is two steps. Raise ten: 10² = 10 × 10 = 100. So the rain-barrel sample carries 100 times more hydrogen ions than the pond sample.
Count the steps from 2 up to 6: 2 to 3, 3 to 4, 4 to 5, and 5 to 6, which is four steps. Raise ten: 10⁴ = 10 × 10 × 10 × 10 = 10,000. So the pH 2 sample carries 10,000 times more hydrogen ions, not 4 times. "4 times" reads the scale like a ruler; each step multiplies by ten.
Yes, they are the same element, because both have 11 protons, and the count of protons decides the element. The second one has given away one electron, so it carries a charge of plus one. It is an ion of that element, not a different element.
What is right: a denatured protein can lose its job, because denaturation unfolds the shape and the shape sets the job. What is wrong: the protein does not lose its amino acids, and its sequence does not change. Denaturation unfolds the fold and leaves the chain of amino acids as it was; the shape, and with it the function, is what can be lost.

Next up in this module: the lecture, the slides, the Readings & Resources page, the tutorial, the practice set, and the quiz; next week the membrane model puts these bonds to work.

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