Lecture: The Chemistry of Life
Lecture script · about 15–20 minutes spoken · Week 2
Opening
Stir a spoonful of salt into a pot of soup and it vanishes. Run a hot trail and your sweat cools you down. Open a clinic lab report and there's a line for blood pH, reading 7.4, with a narrow normal band beside it, 7.35 to 7.45. A future nurse reading that chart, a runner on that trail, and a cook at that stove are all meeting the same chemistry, and this lecture is about that chemistry.
In Week 1, you climbed the levels of structural organization, from the chemical level all the way up to the whole organism. You also met homeostasis: the body holds a regulated variable near a set point, inside a normal range, using negative feedback that reverses a change. In this lecture we stand on the bottom rung of that ladder, the chemical level, and we look closely at what's there. Homeostasis comes back too, because your blood's pH is one of the variables your body defends hardest.
Next week, in Week 3, the cell and its membrane take over, and they lean on every idea in this lecture. So here's the plan. We'll start with the atom, then the three bonds, then water, then pH, then buffers, and we'll finish with the four classes of organic compounds and the energy molecule called ATP.
1. Atoms and elements
Picture a box of beads in three kinds. One kind carries a plus sign. One carries nothing. One carries a minus sign. Every atom in your body is built from those three kinds of particle.
The plus beads are protons. A proton is a positively charged particle in an atom's nucleus; the count of protons decides which element the atom is. The uncharged beads are neutrons. A neutron is an uncharged particle that sits in an atom's nucleus alongside the protons. And the minus beads are electrons. An electron is a negatively charged particle around an atom's nucleus; atoms transfer or share electrons when they form bonds.
Put them together and you have an atom, 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 gets 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 protons and you've changed the element. Change the 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. By mass, you're 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 build about 96% of you. These are rounded figures, so hold them as "about."
I also want you to hear six more names now: calcium, phosphorus, potassium, sodium, chlorine, and magnesium. The bone, nerve, and muscle weeks will use them as charged particles, so they'll be back.
Pause and try this. A sodium atom gives away one of its electrons. Is it still sodium, or has it become a different element?
Think about which particle decides the element.
Here's the answer. It's still sodium. The protons decide the element, and the protons didn't change. Losing an electron gives the atom a charge, so it's now a sodium ion, but its identity is the same.
2. Three bonds: transfer, share, attract
Think about three ways you and a friend could handle one concert ticket. You could hand it over. You could both hold it together. Or you could each keep your own ticket and stand close, pulled together by a weak attraction. Atoms bond in those same three ways, and the trick to sorting them is to ask what the electrons are doing.
First, handing over. An ion is an atom that has given away or taken electrons and so carries an electric charge. 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 a positive sodium ion, chlorine becomes a negative chloride ion, and the opposite charges hold on to each other.
Second, sharing. A covalent bond is a bond in which two atoms share one or more pairs of electrons. Sharing can be fair or lopsided. In a nonpolar covalent bond, the two atoms share their electrons evenly, so neither end carries a partial charge. In a polar covalent bond, one atom pulls the shared electrons closer, leaving that end slightly negative and the other end slightly positive, as inside a water molecule. Chemists write those slight charges as delta minus and delta plus.
Third, a weak pull between molecules. 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 oxygen does. The dotted line is a reminder that this bond is weak.
Here's the trap I want you to see coming. The bonds inside one water molecule are polar covalent. The hydrogen bonds sit between molecules. Same hydrogen atom, two different bonds, two different places.
Pause and try this. Inside a single water molecule, what kind of bond holds a hydrogen to the oxygen?
Ask yourself whether the electrons are shared or handed over.
Here's the answer. It's a polar covalent bond. The oxygen and the hydrogen share a pair of electrons, and the oxygen pulls them closer, so the sharing is uneven. A hydrogen bond would be the weak pull from that hydrogen to the oxygen of the next molecule over.
3. Water and its four jobs
Let me describe one water molecule for you in words. In the middle sits a large oxygen atom, slightly negative. Two smaller hydrogen atoms sit off to one side of it, each slightly positive, each tied to the oxygen by a polar covalent bond. Around the molecule, dotted lines reach out to its neighbors. Those are the hydrogen bonds.
That uneven charge has a name. Polarity is an uneven spread of charge across a molecule, so one end is slightly negative and the other slightly positive. Water's polarity explains four jobs it does in your body.
Job one, 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 to the sodium ions and the slightly positive hydrogen ends to the chloride ions, and the salt comes apart.
Job two, the heat sink. Water absorbs heat with little rise in its own temperature. On that hot trail, sweat leaves your skin and carries heat away with it.
Job three, the lubricant. Water is the main ingredient of the slippery fluids between moving parts, like the synovial fluid in your knee and the pleural fluid around your lungs.
Job four, the reactant. 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. Hydro-lysis, water-splitting. Dehydration, losing water while you build.
Water is up to about 60% of an adult's body mass, so those four jobs run all day in your tissues.
Pause and try this. A runner's skin cools as sweat leaves it on a hot afternoon. Which of water's four jobs is that?
Pick one: solvent, heat sink, lubricant, or reactant.
Here's the answer. It's the heat sink. Water soaks up heat with little rise in its own temperature, and when the sweat leaves your skin it takes that heat along. The other three jobs are real, but they're not what's cooling the runner.
4. Counting pH steps
Two cups of clear liquid can look identical and still be very different, and what separates them is how many hydrogen ions 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 step multiplies. One whole step is ten times as many hydrogen ions, not one more.
So the method is two moves, every time. Count the whole-unit steps. Then raise ten to that power.
Let's do the pinned pair together: pH 4 compared with pH 7. Count up from 4. Four to 5 is one step, 5 to 6 is two, 6 to 7 is three. That's three steps. Now raise ten to the third power: ten times ten times ten, which is 1,000. So pH 4 carries 1,000 times more hydrogen ions than pH 7. The numbers look three apart. The difference is 1,000-fold.
That's the most common wrong turn in this topic. People say pH 4 is three times more acidic than pH 7, because they read the scale like a ruler. It isn't a ruler. Each step multiplies by ten.
One more pinned fact helps. A single whole step, pH 4 against pH 5, is 10 times more hydrogen ions at pH 4.
Pause and try this. Compare pH 5 with pH 7. How many times more hydrogen ions does pH 5 carry?
Count first, then raise ten.
Here's the answer. It's 100 times. From 5 up to 7 is two steps, and ten times ten is 100. If you said 20, you added the two tens instead of multiplying them; on this scale the steps multiply, so it's 100 and never 20.
5. Acids, bases, and buffers
Picture yourself climbing a long stairwell with a crowd. Your leg muscles work hard, and working muscle makes carbon dioxide as waste. That carbon dioxide meets the water in your blood and makes carbonic acid. So exercise adds acid to your blood, and that's exactly the kind of change homeostasis has to answer.
First, the two words. 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 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's a normal range in the Week 1 sense, and your body defends it the Week 1 way, by reversing a change.
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 your blood, the main buffer is the bicarbonate system. When extra hydrogen ions show up, the bicarbonate takes some of them up. The second defense is your breathing, which carries carbon dioxide out of your body. Working muscle makes carbon dioxide, carbon dioxide makes carbonic acid, and buffers and breathing hold the line.
When the line doesn't hold, each side has a name. 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 names are this week's clinical connection, and they illustrate one thing: the range is narrow, and leaving it on either side matters.
Now a reading. Suppose an illustrative chart shows 7.0. It's below 7.35, so it sits on the acidosis side. The drop from 7.4 is 0.4 of a unit. Because that's a fraction of a step, we describe it in words, as a meaningful rise in hydrogen ions, and we don't turn it into a fold figure.
Pause and try this. A blood pH reading sits above 7.45. Which name goes with that departure?
Remember which way is basic.
Here's the answer. It's alkalosis. Above 7.45 is past the top of the range, toward the basic side. Below 7.35 would be acidosis. And notice the buffer didn't hold the blood at exactly 7; it holds it near 7.4, and it resists change rather than forbidding it.
6. Organic compounds and ATP
Think of four bins of building toys, each with its own kind of piece. The big molecules of life sort the same way. Four classes of organic compound build your body.
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 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, and 20 kinds make up nearly all human proteins. A nucleic acid is an organic compound built as a chain of nucleotides, and a nucleotide is its building block.
Then there's the odd one out. 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. Two different kinds of piece, so no single monomer.
Proteins deserve a closer look, because structure determines function here more plainly than anywhere. The order of the amino acids sets how the chain folds. The fold sets the shape. The shape sets the job. One job proteins do is serving as enzymes, though 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 fever can loosen a protein's shape this way. The amino acids stay in the same order, but the fold, and with it the job, can be lost.
Last, the energy molecule. 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 spending money, not savings. Next week's sodium-potassium pump spends it, and so does every muscle contraction later in the course.
Pause and try this. Carbohydrates are built from monosaccharides and proteins from amino acids. What is the single repeating building block of a triglyceride?
Think about how many different kinds of piece go into it.
Here's the answer. There isn't one. A triglyceride is glycerol plus fatty acids, two different kinds of piece, so lipids have no single repeating monomer. That's the row that breaks the tidy pattern of four classes and four building blocks.
Closing
Let me pull it together in the order we built it. The protons in an atom's nucleus decide the element, and four elements make up about 96% of your body. Ionic bonds transfer an electron, covalent bonds share electron pairs, and hydrogen bonds are a weak pull between molecules. Water is polar, and that makes it a solvent, a heat sink, a lubricant, and a reactant. On the pH scale you count the steps and then raise ten, so pH 4 against pH 7 is 1,000 times. Your blood is held between 7.35 and 7.45 by buffers and breathing, with acidosis below and alkalosis above. And a protein's sequence sets its shape, its shape sets its job, and ATP pays for the work.
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 A&P Lab & Inquiry has you measure the acidity of six liquids in a free pH simulation. In Week 3, The Cell & Membrane Transport, you'll see the cell's membrane decide what crosses its border, using the water and the bonds from this lecture.
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