Lecture: The Chemistry of Life
Lecture script · about 15–20 minutes spoken · Week 2
Opening
Picture three cups on a kitchen counter. One holds lemon juice. One holds tap water. One holds water with a spoonful of baking soda stirred in. They look a lot alike, but they behave very differently, and by the end of this lecture you'll be able to say how differently with a number. A nursing student reading blood chemistry, a home cook puzzling over lemon and baking soda, and a gardener watching water climb into leaves all meet this chemistry.
In Week 1, you met the characteristics of life, the ladder of organization from atom to biosphere, and the controlled experiment. You also met a puzzle. A penny held an average of 30 drops of plain water but only 14 drops of soapy water, and I promised the reason would come later. It comes in this lecture. This week we zoom in on the bottom rungs of that ladder, the atoms and molecules, because everything a cell does is built on them. Next week, in Week 3, those same bonds and that same water will build the big molecules of life.
We'll go from atoms to bonds to water, then to the pH scale and the buffers that keep your blood steady.
1. Atoms, elements, and molecules
Think about a box of toy building bricks. There are only a few kinds of brick, but snap them together in different ways and you can build 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.
Those 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. A proton carries a positive charge, and the number of protons decides which element the atom is. A neutron carries no charge and sits in the nucleus beside the protons. An electron carries a negative charge and moves around the nucleus. Keep your eye on the electrons, because they're the part of the atom that does the bonding.
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. Your body by mass is about 65% oxygen, 18% carbon, 10% hydrogen, and 3% nitrogen. Add oxygen and carbon and you get 83. Add hydrogen and you're at 93. Add nitrogen and you reach 96. So those four elements build about 96% of you. Phosphorus and sulfur are the other two of the six elements of life. 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. A single hydrogen atom on its own is an atom. Two hydrogens bonded to an oxygen make a molecule of water.
Pause and try this. The oxygen you breathe is two oxygen atoms bonded together. Is that an atom or a molecule?
Count the atoms before you decide.
Here's the answer. It's a molecule, because two atoms are joined by a bond, even though both atoms are the same element. One atom alone is an atom; two or more bonded together make a molecule. That's also why there's no such thing as "a water atom." Water is a molecule built from three atoms.
2. The three bonds: share, transfer, attract
Picture three ways two people can hold on to the same rope. They can both grip it and share it. One can hand it over completely, and then the two are still drawn to each other. Or they can stand close 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.
The first verb is 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 don't come apart when you pour a glass of water.
The second verb is transfer. To follow it, 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. 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 a positive sodium ion. Chlorine takes that electron and becomes a negative chloride ion. Opposite charges attract, and the two ions hold together.
The third verb is attract, gently. 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 about a strip of hook-and-loop fastener on a shoe. One tiny hook pulls loose with no effort. Many hooks together hold the shoe on your foot.
Pause and try this. In a grain of table salt, sodium has handed an electron to chlorine. Which bond is that?
Find the verb in the question.
Here's the answer. It's an ionic bond, because the electron was handed over, and handing over is transfer. A common slip is to say ionic bonds share electrons. They don't. Covalent bonds share; ionic bonds transfer and then the charged ions attract.
3. Water's polarity
Imagine two people sharing a blanket on a cold night, and one of them keeps tugging it toward their side. They're still sharing, but the sharing is uneven. One person ends up warm and the other ends up a little cold. Water shares its electrons the same uneven way.
Let me describe the water molecule as a labeled figure, in words. In the middle sits one oxygen atom. Two hydrogen atoms are attached to it, each by a covalent bond. The oxygen carries a label that reads delta minus, which means a slight negative charge. Each hydrogen carries a label that reads delta plus, which means a slight positive charge. Delta is a Greek letter, 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 molecule as a whole 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.
Here's why polarity matters so much. The slightly positive hydrogen of one water molecule is drawn to the slightly negative oxygen of a neighbor. That pull is a hydrogen bond. So a glass of water is a crowd of molecules, each one linking to its neighbors, constantly making and breaking hydrogen bonds.
Pause and try this. Inside one water molecule, a hydrogen is held to its oxygen. Is that a hydrogen bond or a covalent bond?
Think about where the bond sits.
Here's the answer. It's a covalent bond, because inside one molecule the hydrogen and the oxygen share a pair of electrons. The hydrogen bond is the weak pull between two different water molecules. Inside, a firm share; between neighbors, a gentle pull.
4. Water's emergent properties
In Week 1 you met the idea of an emergent property, an ability that appears at one level of organization but not in its separate parts. Water is full of them. No single water molecule has surface tension or cools your skin. Those abilities appear only when many water molecules hydrogen-bond together. So for every property I'm about to name, ask one question: what are the hydrogen bonds doing?
Start with cohesion. 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 surface of a pond, the molecules cling to each other so tightly that the surface acts like a stretched sheet. A water strider, a small insect, can stand on a pond because of it. Inside a tall plant, cohesion keeps the thin columns of water from breaking as water is drawn up toward the leaves.
Now the penny. Plain water averaged 30 drops; soapy water averaged 14. Plain water's cohesion builds strong surface tension, so the drops pile into a tall dome before it spills. Soap gets between the water molecules and disrupts their hydrogen bonds, which lowers surface tension, so the dome breaks sooner. That gap of 16 drops is cohesion, measured.
Next comes adhesion. 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 water and the wet line creeps upward. That climb is capillary action: adhesion grabs the fibers, and cohesion drags more water along behind.
Water also resists temperature change. Its specific heat, the amount of heat a substance must absorb to raise its temperature, is high, so oceans and bodies change temperature slowly. Hydrogen bonds hold the molecules to each other, so heat has to loosen those bonds before the molecules can speed up.
Then there's sweat. Evaporative cooling is the cooling of a surface as its fastest-moving water molecules escape as vapor and carry heat away. On a hot hike, the fastest molecules in your sweat break free into the air and take heat with them, and the skin they leave behind is cooler.
Ice is the strange one. When water freezes, hydrogen bonds lock each molecule into place, holding them farther apart than in liquid water. So ice is 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 underneath.
Last, water is a superb solvent, the substance other substances dissolve in. Stir sugar into iced tea and it vanishes, because water molecules crowd around each sugar molecule and pull it into the liquid. The molecules of life are built and dissolved in water.
Pause and try this. A water strider stands on a pond, and a paper towel soaks water upward. Which one is cohesion, and which one leans on adhesion?
Sort them by what the water is clinging to.
Here's the answer. The water strider is cohesion, because the water at the surface is clinging to other water. The paper towel leans on adhesion, because the water is clinging to the towel's fibers, with cohesion pulling the rest along. The prefixes help: co means together, so water with water; ad means toward something else, so water attached to another surface.
5. The pH scale
Imagine a video game where each new level multiplies your points by ten. Level 3 isn't a little ahead of level 2; it holds ten times as many points. The pH scale is built the same way, and it's the week's most common stumble.
A hydrogen ion is a hydrogen atom that has lost its electron, and the more hydrogen ions a liquid carries, the more acidic it is. The word for this measure is pH. It's 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. Pure water sits at pH 7, with a hydrogen-ion concentration of 1 times 10 to the minus 7 moles per liter. An acid gives a pH below 7, like lemon juice at about 2 or white vinegar at about 3. A base gives a pH above 7, like a baking-soda solution at about 9. Inverse means the number goes down as the acid goes up. So here's the phrase to remember: low number, high acid.
Logarithmic means each whole step multiplies the hydrogen ions by ten. So you never subtract two pH values to compare them. You count the whole-unit steps, and then you raise ten to that power. Take pH 4 against pH 7. Count from 4 up to 7: 4 to 5, 5 to 6, 6 to 7. That's three steps. Ten to the third power is ten times ten times ten, which is 1,000. So pH 4 has 1,000 times more hydrogen ions than pH 7. Not a bit more; 1,000 times more.
Now lemon juice against baking-soda solution, pH 2 against pH 9. Count from 2 up to 9 and you get seven steps. Ten to the seventh power is 10,000,000. The lemon juice carries 10,000,000 times more hydrogen ions than the baking-soda water, from a gap that looks like only a few units.
Two more anchors help. Your blood sits near pH 7.4, a little above neutral, and stomach acid sits at about pH 1 to 2, strongly acidic. Household values are approximate and vary by brand, so the class, the direction, and the counting are what matter.
Pause and try this. White vinegar sits at about pH 3 and tap water at about pH 7. How many times more hydrogen ions does the vinegar carry?
Count the steps first, then raise ten.
Here's the answer. From 3 up to 7 is four steps, and ten to the fourth power is 10,000, so the vinegar carries 10,000 times more hydrogen ions than the tap water. If you were tempted to say "4 more" or "a little more," that's the ruler trap. Each step is times ten, not plus one.
6. Buffers
Think about the shock absorbers on a car rolling down a bumpy road. They don't 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 that 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. Listen to the verb. A buffer resists. It doesn't prevent.
Your blood carries one of the most important buffers in your body, the carbonic acid and bicarbonate system, and it holds your blood near pH 7.4. When extra hydrogen ions arrive and blood starts to turn more acidic, bicarbonate ions take them up and become carbonic acid, so the pH drops much less than it would have. When blood drifts the other way, carbonic acid gives hydrogen ions back. Carbonic acid also breaks down into water and carbon dioxide, and your lungs breathe the carbon dioxide out. Think of it as a hydrogen-ion bank that takes deposits when there are too many and makes withdrawals when there are too few. That steadiness is homeostasis at the chemical level, one of the characteristics of life from Week 1.
Pause and try this. Someone says, "My blood has a buffer, so a sour drink can't change its pH at all." What's the one word in that claim that needs fixing?
Think about what a shock absorber can and can't do.
Here's the answer. The trouble is "at all," because a buffer resists a change; it never prevents one. It keeps the change small, and a large enough load of acid or base could overwhelm it. Say resists, never prevents.
Closing
Let me pull it together in the order we built it. Atoms are made of protons, neutrons, and electrons, and four elements build about 96% of your body; one atom alone is an atom, and bonded atoms make a molecule. Covalent bonds share, ionic bonds transfer, and hydrogen bonds gently attract. Water is polar, slightly negative at the oxygen and slightly positive at the hydrogens, and that's why its molecules hydrogen-bond. Those hydrogen bonds give water its remarkable properties and explain the penny. On the pH scale, low number means high acid, and every whole step is a tenfold change, so you count the steps and then raise ten. And a buffer resists a change in pH but never prevents one.
Next in this module come the slide deck, the Readings & Resources page, the lecture tutorial, the practice set, the quiz, the discussion, and the assignment. Then the Biology Lab & Inquiry puts the pH scale to work with a red-cabbage indicator you brew yourself. In Week 3, Biological Macromolecules, you'll see how cells use these bonds, in water, to build carbohydrates, lipids, proteins, and nucleic acids.
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