Week 3 · Chapter

Chapter 3 — Biological Macromolecules

Introduction to Biology Free sample edition

The module's primary reading · ~35–45 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 built from a few kinds of very large molecules, and this week you meet all four of them. You will learn how cells snap small pieces together into long chains, and how they take those chains apart again with water. You will meet carbohydrates (sugars and chains of sugars, such as starch) and lipids (fats, oils, and their relatives, which avoid water). You will also meet proteins (chains of amino acids that fold into working shapes) and nucleic acids (DNA and RNA, which store a cell's instructions). Most of all, you will see the idea that runs through this whole course: structure determines function (a molecule's shape decides the job it can do).

Why you already care about this

Put a plain cracker on your tongue and chew it slowly. At first it tastes like flour and salt. After a while it starts to taste a little sweet. Nothing sweet was added. Something in your mouth changed the cracker while you chewed.

That small change is the subject of this week. The cracker is full of starch, a long chain of sugar units. Your saliva carries a protein that cuts that chain into smaller sugar pieces, and those smaller pieces taste sweet. A chain was built in a plant; a chain was broken in your mouth. Every big molecule in your body is built and broken the same two ways. Your body runs on 4 classes of these molecules, your proteins are built from 20 kinds of amino acid, and a single swap among roughly 600 amino acids can cause a disease.

You meet these molecules every day without naming them. A food label lists carbohydrate, fat, and protein. An egg white turns from clear to solid white in a hot pan. This chapter gives those everyday things their biology.

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

explain how dehydration synthesis builds a polymer and how hydrolysis breaks one, and count the water molecules each step removes or adds;
sort a molecule into one of the four classes and name each class's building block and job;
explain why starch and cellulose behave so differently even though both are built from glucose;
explain why lipids are not polymers, and tell a saturated fat from an unsaturated one by the shape of its tails;
put the four levels of protein structure in order and explain what denaturation does and does not change;
explain how one changed amino acid in hemoglobin leads to sickle cell disease;
tell DNA from RNA by sugar, base, and number of strands;
read an iodine starch test for each food and explain the color from the molecule's shape.

Carry this line with you: the shape is the job — change one, and you change the other.

Where we are

Already covered: Week 1 set up how biologists test a claim with a controlled experiment; Week 2 covered atoms, bonds, water, and pH.
This week: the four classes of large biological molecules, how they are built and broken, and the rule that structure determines function.
How they connect: these molecules are built from the atoms and bonds of Week 2, they are assembled and digested in water, and you test them with a control group exactly as Week 1 taught.
Where we're going next: Week 4, Cell Structure & Function, puts these molecules to work inside the cell, starting with the membrane that phospholipids build.

Week 1 gave you the habit of comparing a test against a control, and you will use it again in this week's starch test, where plain water is the control. Week 2 gave you the pieces. Covalent bonds, in which two atoms share a pair of electrons, hold each of these big molecules together. Hydrogen bonds, the weak attractions you met with water, help a protein hold its folded shape. Water is the medium every reaction in this chapter runs in. Next week you will see these molecules become the parts of a cell.

1. Build and break: monomers, polymers, and water

Think of a string of paper clips. Each clip is one small unit. Hook enough of them together and you get a long chain. Unhook them and you are back to single clips. Cells build their largest molecules in the same way.

Biologists call the big molecules of life macromolecules. A macromolecule is a large biological molecule, and living things build four classes of them: carbohydrates, lipids, proteins, and nucleic acids. Three of the four classes are chains.

A monomer is one small building-block unit that can be joined to others like it to make a larger molecule, such as a glucose unit or an amino acid.
A polymer is a long chain of monomers joined by bonds, such as starch, a protein, or a strand of DNA.

Your cells use two reactions with every polymer, and both involve water (H₂O).

Dehydration synthesis is the reaction that builds a polymer by joining two monomers and removing one water molecule for each new bond. "Dehydration" means losing water, and "synthesis" means building.
Hydrolysis is the reaction that breaks a polymer apart by adding a water molecule back across a bond. "Hydro" means water, and "lysis" means splitting.

Each new bond you count costs one water molecule to make and takes one water molecule to break. Enzymes, a kind of protein you will meet properly in Week 5, speed up both reactions.

Worked example — counting the water. Starch is a polysaccharide built from glucose. Take a short stretch of it: 3 glucose units joined in a row.

Count the bonds. Each bond sits between two neighbors, so a row of units always has one fewer bond than units. Joining 3 glucose units in a row makes 3 − 1 = 2 new bonds.
Count the water removed. Dehydration synthesis removes one water molecule per new bond, so 2 water molecules are removed.
Break it again. Hydrolysis of that short chain adds the 2 water molecules back, one per bond, and returns 3 single glucose units.

In words: a chain of 3 units has 2 bonds, so building it removes 2 waters and breaking it adds the same 2 waters back. A longer chain costs you more water: a row of 5 units removes 4 waters versus 2 for a row of 3, twice as many.

Digestion is hydrolysis. When you eat, your body breaks the polymers in your food into monomers it can absorb. That is the cracker on your tongue. Chewing a cracker turns it sweet because amylase in saliva hydrolyzes starch toward maltose and glucose, which is hydrolysis at work. The starch chain is cut at its bonds, with water added at each cut.

Misconception check. Students often swap the two reactions and say that hydrolysis builds. The names are easy to blur because both contain a word for water. The cure is the direction of the water. Building a chain removes water, so it is dehydration synthesis. Breaking a chain adds water, so it is hydrolysis. If water goes in, the chain comes apart.

Memory hook: build by removing water; break by adding water.

2. Sort the four classes of macromolecules

Picture the nutrition label on a granola bar. It lists total carbohydrate, total fat, and protein, each in grams. That label names three of the four classes of macromolecules. The fourth, the nucleic acids, is in the food too, inside every cell of the oats and nuts, but labels do not list it.

The four classes of large biological molecules are:

The four classes of macromolecules, with each class's building block and main jobs
Class	Building block	Main jobs
Carbohydrates	monosaccharides (single sugar units, such as glucose)	fuel and stored fuel; structural fiber
Lipids	not one repeating monomer; for example, glycerol and fatty acids	fats and oils; membranes (phospholipids); steroids such as cholesterol
Proteins	amino acids	enzymes, structure, transport, defense, signaling
Nucleic acids	nucleotides	storing and passing on the cell's instructions

Every living thing, from a bacterium to an oak tree to you, builds itself from these same four classes. In Week 1 you met that shared set of building-block molecules as one of the pieces of evidence that all living things descend from common ancestors.

Worked example — sort four molecules. You place each molecule in its class by asking what it is built from.

Glycogen. It is a chain of sugar units, so it is a carbohydrate.
Olive oil. It is an oil, a fat that avoids water, so it is a lipid.
An enzyme. Enzymes are one of the jobs proteins do, so it is a protein.
A strand of DNA. DNA is built from nucleotides, so it is a nucleic acid.

In words: ask what the molecule is built from, and the building block names the class.

Misconception check. Students often think all four classes are polymers built the same way. The idea is tempting because three of the four really are chains. But lipids are the exception, as Section 4 shows: a fat is an assembly of a few parts, not a long chain of one repeating monomer. Sort lipids by their dislike of water, not by a chain.

Memory hook: four classes, one question: what is it built from?

3. Climb the carbohydrate ladder: one sugar to many

Think about the difference between a spoonful of table sugar, a baked potato, and the dietary fiber listed on a cereal box. All three are carbohydrate. Only the sugar tastes sweet; the potato is soft and starchy; the fiber is tough. The difference is in how the sugar units are joined.

A carbohydrate is a member of the class of macromolecules made of sugar units, from single sugars such as glucose to long chains such as starch and cellulose. Carbohydrates climb a three-rung ladder:

monosaccharide → disaccharide → polysaccharide

A monosaccharide is a single sugar unit, such as glucose; it is the monomer of carbohydrates.
A disaccharide is a sugar made of two sugar units joined together, such as table sugar (sucrose).
A polysaccharide is a carbohydrate made of many sugar units joined in a chain, such as starch or cellulose.

Glucose is a single sugar unit that cells use for fuel and that serves as the monomer of both starch and cellulose. Here is the surprise of the week. You can build two very different polysaccharides from the very same monomer.

Starch is a polysaccharide built from glucose that plants use as stored fuel; its coiled chain turns iodine blue-black.
Cellulose is a polysaccharide built from glucose linked differently from starch, which gives plants structural fiber and is the dietary fiber in food.

Starch and cellulose share a monomer. What differs is the way the glucose units are linked, and that difference changes the shape of the whole chain. Starch coils, and amylase can hydrolyze it toward glucose for fuel. Cellulose forms tough structural fiber, and it is the dietary fiber on a food label.

Worked example — which rung? You place each sugar on the ladder by counting its units.

Glucose, one unit. Monosaccharide.
Sucrose, table sugar, two units. Disaccharide.
Starch, a long chain of glucose. Polysaccharide.
Cellulose, a long chain of glucose linked another way. Polysaccharide.

In words: count the sugar units. One is a monosaccharide, two is a disaccharide, and many is a polysaccharide.

Misconception check. Students often think all carbs are sugar, so "low in sugar" must mean "low in carbohydrate." The idea is tempting because sweet foods are the carbs we notice. But cellulose is a carbohydrate and is the dietary fiber, and starch is a carbohydrate that does not taste sweet until it is broken down. Sugar is only the bottom two rungs of the ladder.

Memory hook: same glucose, different links, different jobs.

4. Lipids: the class that is not a chain

Leave a stick of butter and a bottle of cooking oil on a cool counter. The butter stays a solid block. The oil pours. Both are mostly fat, and neither dissolves in water. The reason one is solid and the other is liquid is the shape of their tails.

A lipid is a member of the class of macromolecules grouped by being water-fearing rather than by a repeating monomer, including fats and oils, phospholipids, and steroids; lipids are not polymers. There are three kinds you need this week.

Fats and oils. A triglyceride is a fat or an oil, assembled from one glycerol and three fatty acids rather than from a chain of one repeating monomer. A fatty acid is a long carbon-and-hydrogen tail that attaches to glycerol in a fat or an oil; three of them join one glycerol in a triglyceride. Picture a capital letter E: the upright stroke is the glycerol, and the three arms are the fatty-acid tails.

The tails come in two shapes.

A saturated fatty acid has only single carbon-carbon bonds, and its straight tail packs tightly, so fats made of such tails stay solid.
An unsaturated fatty acid has at least one carbon-carbon double bond that puts a kink in its tail, so fats made of such tails stay liquid.

If you picture the tails, straight ones stack like pencils in a box. Kinked tails jostle like bent sticks and cannot pack close, so the fat flows.

Phospholipids. A phospholipid is a lipid with a water-loving, phosphate-containing head and two water-fearing fatty-acid tails; it is the main building block of a cell membrane. One end of the molecule likes water and the other end avoids it. That split personality is the reason a membrane can exist at all, and next week's membrane is built from it.

Steroids. A steroid is a lipid built on four fused carbon rings, such as cholesterol. A steroid looks nothing like a fat, yet it is a lipid, because lipids are grouped by avoiding water and not by a shared monomer.

Worked example — reading a triglyceride. You describe a fat that stays solid at room temperature.

Parts. One glycerol plus three fatty acids: 1 + 3 = 4 parts in one triglyceride.
Polymer or not? Not a polymer. The four parts are two different kinds of molecule, not a chain of one repeating monomer.
Tail shape. It stays solid, so its tails are mostly straight, saturated tails that pack tightly.
Its oily cousin. A cooking oil that pours has kinked, unsaturated tails that cannot pack.

In words: a triglyceride is an assembly of four parts, and the shape of its three tails decides whether it is a solid fat or a liquid oil.

Misconception check. Students often think lipids are polymers like the other three classes. The idea is tempting because a triglyceride has repeating-looking tails. But a triglyceride is one glycerol plus three fatty acids, an assembly of a few parts, not a long chain of one repeating monomer. And a steroid, with its four rings, has no chain at all.

Memory hook: lipids are a club for water-fearers, not a chain.

5. Build proteins and fold them in four levels

Watch an egg white in a hot pan. It starts clear and runny. Soon it turns solid and white, and no amount of cooling turns it back. Egg white carries a protein called albumin, and the heat changed that protein's shape. To see why shape matters so much, start with how a protein is built.

A protein is a member of the class of macromolecules built from amino acids joined by peptide bonds, which do jobs such as speeding reactions, building structure, carrying substances, defending the body, and sending signals.

An amino acid is the monomer of proteins; cells build proteins from 20 common kinds.
A peptide bond is the bond that joins one amino acid to the next in a protein chain, formed by dehydration synthesis.

The job list is long. Proteins work as enzymes, as structure, in transport, in defense, and in signaling. Twenty kinds of amino acid, arranged in different orders and lengths, make every one of those proteins possible, much as a short alphabet spells every word in a dictionary.

A chain of amino acids does not stay a floppy string. It folds, and biologists describe that folding at four levels, always in this order:

Primary structure — the first level of protein structure: the exact order of amino acids in the chain.
Secondary structure — the second level of protein structure: local coils and folds of the chain, the helix and the pleated sheet, held by hydrogen bonds.
Tertiary structure — the third level of protein structure: the overall three-dimensional fold of one complete chain.
Quaternary structure — the fourth level of protein structure: two or more folded chains assembled into one working protein.

Not every protein reaches the fourth level; quaternary structure applies only to proteins made of more than one chain.

Denaturation is the loss of a protein's three-dimensional shape, and with it its function, caused by heat, a change in pH, or certain chemicals; the amino-acid sequence stays intact. That is the egg white. Cooking turns the egg-white protein permanently solid and white, because heat undid its fold. Some proteins can fold back once normal conditions return, but many cannot.

Worked example — what does denaturation change? You heat a protein made of two folded chains until it loses its shape.

Primary structure. Unchanged. The amino acids are still in the same order, joined by the same peptide bonds.
Secondary structure. Lost. The local helices and sheets come undone.
Tertiary structure. Lost. Each chain's overall fold is gone.
Quaternary structure. Lost. The two chains no longer fit together as one working protein.
Function. Lost, because the job depended on the shape.

In words: denaturation keeps the sequence and loses the shape, and losing the shape loses the job.

Misconception check. Two slips are common here. First, students list the four levels out of order; the cure is to build up from the chain (sequence, then local coils, then the whole fold, then several chains together). Second, students read denaturation as breaking the chain into pieces. It is not. The fold is lost; the sequence is intact. Breaking the chain is hydrolysis, which is a different event.

Memory hook: sequence, coil, fold, assemble.

6. See one amino acid change the job: sickle cell disease

Think of a sentence where one letter changes: "the cat sat" becomes "the cot sat." One letter, and the meaning shifts. A protein can behave the same way.

Hemoglobin is the protein packed inside your red blood cells. Sickle cell disease is a disease in which valine takes the place of glutamic acid at position 6 of hemoglobin's beta chain. As a result, the protein links into fibers when oxygen is low and bends red blood cells into a rigid crescent.

Worked example — one change, traced from structure to function. You follow the change one level at a time, from your hemoglobin's sequence to your red blood cells.

Primary structure. At position 6 of the beta chain, valine (Val) sits where glutamic acid (Glu) normally sits. That is one change out of roughly 600 amino acids, counting all four chains of hemoglobin.
Shape. The altered hemoglobin links into long fibers when oxygen is low.
The cell. Those fibers bend the red blood cell into a rigid crescent, the sickle shape that gives the disease its name.
The body. Rigid crescent cells can block small blood vessels.

In words: one amino acid in about 600 changed, and the change ran all the way up from the sequence to the shape of a whole cell.

This is the clearest case of the course's spine you will meet. The order of amino acids is information. Change one, and the fold can change; change the fold, and the job can break. Caveat: this chapter teaches sickle cell disease only as a structure-to-function case. How the change is inherited waits for the genetics weeks later in the course.

Misconception check. Students often think the amino-acid order does not really matter, as long as the right kinds of amino acids are present. The idea is tempting because a single swap sounds too small to matter in a chain of hundreds. Sickle cell disease is the cure for that belief. The order is the information; one wrong amino acid can change the fold and break the job.

Memory hook: the order is the information.

Pause and reflect. Choose one of these two prompts and think it through, or jot a few sentences in your notes.

(a) Think of an object you use every day whose job depends on its exact shape, such as a key or a zipper. What would happen if one small part of that shape changed?
(b) Think of a food you cook or prepare. Which of the four classes of macromolecules does it contain, and how might heat change one of them?

7. Tell DNA from RNA

Think of a master recipe book kept on a shelf and a single recipe card copied out to use at the stove. The book is the safe, complete store; the card is a working copy. The two kinds of nucleic acid split their work in a similar way.

A nucleic acid is a member of the class of macromolecules, DNA and RNA, built from nucleotides, which store and pass on a cell's instructions. A nucleotide is the monomer of nucleic acids, made of a sugar, a phosphate, and a base.

The two nucleic acids differ in three ways you can check:

DNA (deoxyribonucleic acid) is the nucleic acid with the sugar deoxyribose and the bases adenine, thymine, guanine, and cytosine, usually built as a two-stranded double helix.
RNA (ribonucleic acid) is the nucleic acid with the sugar ribose, which uses uracil where DNA uses thymine and is usually a single strand.

DNA and RNA compared by sugar, the base that differs, and number of strands
Feature	DNA	RNA
Sugar	deoxyribose	ribose
Base that differs	thymine	uracil (in place of thymine)
Strands	two, as a double helix	usually one

Nucleic acids store and transmit instructions. For this week, one sentence is enough about how: the base sequence is a code for the amino-acid sequence. The full story of how a cell reads that code comes much later in the course.

Worked example — DNA or RNA? You decide which nucleic acid each description fits.

A single strand that contains uracil. RNA, because uracil is RNA's base.
A double helix with the sugar deoxyribose. DNA.
A strand that contains thymine. DNA, because RNA uses uracil in place of thymine.

In words: check the sugar, the base, and the number of strands, and any one of the three can decide it.

Misconception check. Students often write that RNA contains thymine. The slip is tempting because DNA and RNA share three of their four bases. But RNA uses uracil where DNA uses thymine. If you see a T in RNA, something has gone wrong.

Memory hook: DNA has the T; RNA has the U.

8. Read the iodine starch test: structure determines function

Set out five small dishes on a kitchen counter: a piece of bread, a slice of raw potato, some sugar water, a spoonful of cooking oil, and a slice of fruit. Add a sixth dish of plain water. Now put a drop of iodine solution on each one and watch the colors.

Iodine solution starts amber, an orange-brown color. When it meets starch it turns blue-black, because iodine fits inside the coiled starch chain. The test reads starch's shape. That makes it a small proof of the idea this whole course hangs on.

Structure determines function is the principle that the shape of a molecule, cell, or organ decides what job it can do, so a change in shape can change or break the job. You saw it with starch and cellulose, with saturated and unsaturated tails, with the egg white, and with hemoglobin. The iodine test shows it once more, in a dish on your counter.

The results below are an illustrative, qualitative set of results built for this course, not real data. Your own foods at home may differ a little.

Iodine color on five foods and a plain-water control (illustrative, qualitative results built for this course, not real data)
Sample	Iodine color	Starch?
Plain water (negative control)	amber	no
Bread	blue-black	present
Potato	blue-black	present
Sugar water	amber	no
Cooking oil	amber	no
Fruit	amber or faint	little free starch

A negative control is a sample known to lack what a test detects, such as plain water in an iodine starch test, which shows the color a no result should give. It is the control group of Week 1, applied to a color test.

Worked example — the iodine starch test. You read every dish against your control.

Negative control. A drop of iodine on plain water stays amber (orange-brown), because water has no starch; every other color is compared against this one.
Bread. Turns blue-black, so starch is present.
Potato. Turns blue-black, so starch is present.
Sugar water. Stays amber, so there is no starch. Table sugar (sucrose) is a disaccharide, not a polysaccharide, so iodine cannot detect it; finding the sugar would take a different test.
Cooking oil. Stays amber, so there is no starch; oil is a lipid.
Fruit. Stays amber or changes faintly, so there is little free starch.
Tally. 2 of the 5 foods turn blue-black (bread and potato), 2 stay amber (sugar water and cooking oil), and 1 is faint (fruit); 2 + 2 + 1 = 5.

In words: only the foods with starch's coiled chain turn the iodine blue-black, so the test is reading a shape, not the taste on your tongue.

Notice what the test can and cannot tell you, and keep it in mind for your lab. Honesty note: an amber result means "no starch," not "no carbohydrate." The sugar water is full of carbohydrate, yet it stays amber, because its sugar is a two-unit disaccharide with no coil for iodine to fit inside.

Misconception check. Students often think a sweet food should turn iodine blue-black, because sweet things are full of carbohydrate. The idea is tempting because "starch" and "sugar" both sound like carbs. But iodine reads starch's coiled shape, not sweetness. A sweet taste or a high sugar content does not turn iodine blue-black.

Memory hook: iodine reads the coil, not the sugar.

Key terms

Macromolecule — A large biological molecule; living things build four classes of them: carbohydrates, lipids, proteins, and nucleic acids. (first used: 1. Build and break: monomers, polymers, and water)
Monomer — One small building-block unit that can be joined to others like it to make a larger molecule, such as a glucose unit or an amino acid. (first used: 1. Build and break: monomers, polymers, and water)
Polymer — A long chain of monomers joined by bonds, such as starch, a protein, or a strand of DNA. (first used: 1. Build and break: monomers, polymers, and water)
Dehydration synthesis — The reaction that builds a polymer by joining two monomers and removing one water molecule for each new bond. (first used: 1. Build and break: monomers, polymers, and water)
Hydrolysis — The reaction that breaks a polymer apart by adding a water molecule back across a bond; digestion is hydrolysis. (first used: 1. Build and break: monomers, polymers, and water)
Carbohydrate — The class of macromolecules made of sugar units, from single sugars such as glucose to long chains such as starch and cellulose. (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Monosaccharide — A single sugar unit, such as glucose; the monomer of carbohydrates. (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Disaccharide — A sugar made of two sugar units joined together, such as table sugar (sucrose). (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Polysaccharide — A carbohydrate made of many sugar units joined in a chain, such as starch or cellulose. (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Glucose — A single sugar unit that cells use for fuel and that serves as the monomer of both starch and cellulose. (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Starch — A polysaccharide built from glucose that plants use as stored fuel; its coiled chain turns iodine blue-black. (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Cellulose — A polysaccharide built from glucose linked differently from starch, which gives plants structural fiber and is the dietary fiber in food. (first used: 3. Climb the carbohydrate ladder: one sugar to many)
Lipid — The class of macromolecules grouped by being water-fearing rather than by a repeating monomer, including fats and oils, phospholipids, and steroids; lipids are not polymers. (first used: 4. Lipids: the class that is not a chain)
Triglyceride — A fat or an oil, assembled from one glycerol and three fatty acids rather than from a chain of one repeating monomer. (first used: 4. Lipids: the class that is not a chain)
Fatty acid — A long carbon-and-hydrogen tail that attaches to glycerol in a fat or an oil; three of them join one glycerol in a triglyceride. (first used: 4. Lipids: the class that is not a chain)
Saturated fatty acid — A fatty acid with only single carbon-carbon bonds, whose straight tail packs tightly, so fats made of such tails stay solid. (first used: 4. Lipids: the class that is not a chain)
Unsaturated fatty acid — A fatty acid with at least one carbon-carbon double bond that puts a kink in its tail, so fats made of such tails stay liquid. (first used: 4. Lipids: the class that is not a chain)
Phospholipid — A lipid with a water-loving, phosphate-containing head and two water-fearing fatty-acid tails; the main building block of a cell membrane. (first used: 4. Lipids: the class that is not a chain)
Steroid — A lipid built on four fused carbon rings, such as cholesterol. (first used: 4. Lipids: the class that is not a chain)
Protein — The class of macromolecules built from amino acids joined by peptide bonds, which do jobs such as speeding reactions, building structure, carrying substances, defending the body, and sending signals. (first used: 5. Build proteins and fold them in four levels)
Amino acid — The monomer of proteins; cells build proteins from 20 common kinds. (first used: 5. Build proteins and fold them in four levels)
Peptide bond — The bond that joins one amino acid to the next in a protein chain, formed by dehydration synthesis. (first used: 5. Build proteins and fold them in four levels)
Primary structure — The first level of protein structure: the exact order of amino acids in the chain. (first used: 5. Build proteins and fold them in four levels)
Secondary structure — The second level of protein structure: local coils and folds of the chain, the helix and the pleated sheet, held by hydrogen bonds. (first used: 5. Build proteins and fold them in four levels)
Tertiary structure — The third level of protein structure: the overall three-dimensional fold of one complete chain. (first used: 5. Build proteins and fold them in four levels)
Quaternary structure — The fourth level of protein structure: two or more folded chains assembled into one working protein. (first used: 5. Build proteins and fold them in four levels)
Denaturation — The loss of a protein's three-dimensional shape, and with it its function, caused by heat, a change in pH, or certain chemicals; the amino-acid sequence stays intact. (first used: 5. Build proteins and fold them in four levels)
Sickle cell disease — A disease in which valine takes the place of glutamic acid at position 6 of hemoglobin's beta chain, so the protein links into fibers when oxygen is low and bends red blood cells into a rigid crescent. (first used: 6. See one amino acid change the job: sickle cell disease)
Nucleic acid — The class of macromolecules, DNA and RNA, built from nucleotides, which store and pass on a cell's instructions. (first used: 7. Tell DNA from RNA)
Nucleotide — The monomer of nucleic acids, made of a sugar, a phosphate, and a base. (first used: 7. Tell DNA from RNA)
DNA — Deoxyribonucleic acid: the nucleic acid with the sugar deoxyribose and the bases adenine, thymine, guanine, and cytosine, usually built as a two-stranded double helix. (first used: 7. Tell DNA from RNA)
RNA — Ribonucleic acid: the nucleic acid with the sugar ribose, which uses uracil where DNA uses thymine and is usually a single strand. (first used: 7. Tell DNA from RNA)
Structure determines function — The principle that the shape of a molecule, cell, or organ decides what job it can do, so a change in shape can change or break the job. (first used: 8. Read the iodine starch test: structure determines function)
Negative control — A sample known to lack what a test detects, such as plain water in an iodine starch test, which shows the color a no result should give. (first used: 8. Read the iodine starch test: structure determines function)

Summary

Dehydration synthesis builds a polymer and removes one water per new bond.
Hydrolysis breaks a polymer and adds one water per bond; digestion is hydrolysis.
The four classes are carbohydrates, lipids, proteins, and nucleic acids.
Starch and cellulose are both built from glucose, linked differently.
Lipids are not polymers; a triglyceride is one glycerol and three fatty acids.
Straight saturated tails make solid fats; kinked unsaturated tails make liquid oils.
Proteins are chains of 20 common amino acids that fold in four levels, in order.
Denaturation loses the shape and the job but keeps the sequence.
In sickle cell disease, one amino acid change alters hemoglobin's behavior.
DNA has deoxyribose, thymine, and two strands; RNA has ribose, uracil, and one strand.
Structure determines function; iodine reads starch's coil, not sweetness.

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.

A cell builds a short chain of 6 glucose units in a row. How many water molecules does dehydration synthesis remove to build it, and how many water molecules does hydrolysis add to break it completely back into single glucose units?
Sort each molecule into its class: sucrose, cholesterol, a strand of RNA, and a phospholipid. For any lipid, say why it counts as a lipid even though it is not a polymer.
A protein chain of 150 amino acids (an illustrative example) is heated until it loses its function. Which level of structure is still intact, and how many peptide bonds are still in the chain?
A friend at the gym puts a drop of iodine on a sweet sports drink. It stays amber. The friend says, "So this drink has no carbohydrate." What is wrong with that conclusion?

Answers (worked reasoning — read after attempting)

A row of units has one fewer bond than units, so 6 glucose units have 6 − 1 = 5 bonds. Dehydration synthesis removes one water per bond, so it removes 5 water molecules. Hydrolysis adds one water per bond to break the chain apart, so it adds the same 5 water molecules back. Building and breaking trade the same number of waters, in opposite directions.
Sucrose is a carbohydrate (a disaccharide, two sugar units). Cholesterol is a lipid (a steroid, built on four fused rings). The strand of RNA is a nucleic acid. The phospholipid is a lipid. Cholesterol and the phospholipid count as lipids because lipids are grouped by being water-fearing, not by a chain of one repeating monomer.
The primary structure, the order of amino acids, is still intact. Heat denatures the protein, which undoes its fold but does not break the chain. A row of 150 amino acids has 150 − 1 = 149 peptide bonds, and all 149 are still there. The protein lost its function because it lost its shape, not its sequence.
Iodine detects only starch, by fitting inside starch's coiled chain. The drink's sweetness comes from sugars, and sugars are carbohydrates too. An amber result means "no starch," not "no carbohydrate." Finding the sugar would take a different test, not iodine.

Next up in this module: the Readings & Resources page, the lecture tutorial, the practice set, and the quiz — and next week the phospholipid becomes the cell membrane under the fluid mosaic model.

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