Week 13 · Chapter

Chapter 13 — DNA Structure & Replication

Introduction to Biology Free sample edition

The module's primary reading · ~35–45 minutes · Objective 7 (explain the structure and semiconservative replication of DNA, apply Chargaff's rules and complementary base pairing, and trace gene expression through transcription and translation with the genetic code (the central dogma), decoding a sequence from template to protein), with 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) carried forward · Read it first this week; the lecture, the slides, the tutorial, the quiz, and the lab all build on it.

In plain language

Every cell in your body carries the same set of instructions, and this week you learn what those instructions are built like and how a cell copies them. You will picture the double helix (the twisted-ladder shape of a DNA molecule) and learn the one pairing rule that holds its rungs together. You will use that rule to fill in a whole DNA sample from a single number. You will meet the experiment that showed how DNA is copied, where every copy keeps one old strand and gains one new one. And you will see why the copying is so reliable that it rarely makes a mistake.

Why you already care about this

Picture a kitchen counter, a ripe strawberry, and a zip-top bag. You mash the strawberry with a little dish soap and salt, strain the pulp, and pour cold rubbing alcohol gently on top. Soon a white, stringy cloud rises where the two layers meet. You can wind it around a toothpick. That cloud is DNA, many strands of it clumped together, pulled out of a fruit with three things from under the sink.

Those strands are the same molecule that sits in the nucleus of every cell you own. A cell has to copy all of it before it divides, and it gets the copy right almost every time. This week's numbers show how tight the rules are. A sample that is 30% adenine has to be 30% thymine. An A–T rung is held by 2 hydrogen bonds and a G–C rung by 3. And most cultivated strawberries carry 8 sets of chromosomes, which is one reason they give up so much DNA.

So this week is about a shape and a copying job. The shape explains the job: once you see how the ladder is built, you can predict how it copies itself.

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

describe the double helix as a labeled figure, naming its backbone and its base pairs;
explain why a purine always pairs with a pyrimidine and what that does to the helix's width;
write the complement of a short strand, with its 5′ and 3′ ends labeled;
use Chargaff's rules to find all four base percents from one, with every step shown;
place the discoveries that revealed DNA in order, with no invented quotations;
compare the three copying models and explain how one experiment left only the semiconservative one;
name helicase, DNA polymerase, and DNA ligase in order with their jobs;
explain each step of the strawberry DNA extraction.

Carry this line with you: A with T, G with C; complementary, not identical.

Where we are

Already covered: Week 2 introduced the hydrogen bond, Week 3 introduced DNA as a nucleic acid built from nucleotides, and Week 9 placed DNA copying in the S phase, before mitosis. Week 8 added the order-and-location habit: name the stages of a process in order and the place each one runs.
This week: the double helix as a labeled figure, base pairing and Chargaff's rules, the history of the discovery, semiconservative replication and the Meselson and Stahl test, and the three machines that copy DNA.
How they connect: Week 2's hydrogen bonds hold the rungs of the ladder, and Week 3's nucleotides are its building blocks. The copying you learn this week is the work of Week 9's S phase.
Where we're going next: Week 14 follows DNA's instructions out of the nucleus, as a cell reads a gene into RNA and then into a protein.

Week 2 gave you the hydrogen bond, a weak attraction between a slightly positive hydrogen on one molecule and a slightly negative atom on another; one is weak, but many together are strong. Week 3 gave you DNA as a nucleic acid, a long chain of nucleotides with the sugar deoxyribose, and told you that DNA forms a double helix while RNA is a single strand. Week 9 told you that a cell copies its DNA in the S phase, so that each chromosome becomes two identical sister chromatids. This week opens that S phase up and shows you how the copying works, base by base.

1. Picture the double helix: rails and rungs

Think of a rope ladder hanging in a playground, then imagine grabbing the bottom and giving it a slow twist. The two side ropes wind around each other, and the rungs stay level between them. That twisted ladder is the shape of DNA.

The double helix is the shape of a DNA molecule: two strands wound around each other like a twisted ladder, with the sugar-phosphate backbone as the rails and base pairs as the rungs.

Here is the ladder described as a labeled figure, part by part.

The rails. The sugar-phosphate backbone is the rail of each DNA strand, a repeating chain of the sugar deoxyribose joined to phosphate, with the bases sticking inward from it.
The rungs. A base pair is two bases, one on each strand of DNA, joined across the double helix by hydrogen bonds; adenine pairs with thymine and guanine pairs with cytosine.
The glue. Hydrogen bonds hold each rung together: two for an A–T pair and three for a G–C pair. Each one is weak; many together hold the strands tight.
The twist. A full turn of the ladder takes about ten base pairs.

DNA uses four bases, each written with one letter.

Adenine is one of the four bases in DNA, a purine written A, which pairs with thymine through two hydrogen bonds.
Thymine is one of the four bases in DNA, a pyrimidine written T, which pairs with adenine; RNA uses uracil in its place.
Guanine is one of the four bases in DNA, a purine written G, which pairs with cytosine through three hydrogen bonds.
Cytosine is one of the four bases in DNA, a pyrimidine written C, which pairs with guanine.

Worked example — counting the hydrogen bonds in a short stretch. The strand 5′-AATGC-3′ pairs base by base with a partner strand. You count the hydrogen bonds that hold the five rungs.

Sort the rungs. The bases A, A, and T sit in A–T pairs, so there are 3 A–T pairs. The bases G and C sit in G–C pairs, so there are 2 G–C pairs.
Bonds in the A–T pairs. 3 × 2 = 6 hydrogen bonds.
Bonds in the G–C pairs. 2 × 3 = 6 hydrogen bonds.
Total. 6 + 6 = 12 hydrogen bonds.

In words: five rungs, twelve weak bonds, and a stretch rich in G–C pairs is held a little more tightly than one rich in A–T pairs.

Misconception check. Students often write that A pairs with G, or that any base can pair with any other. It is tempting because A and G are the first two letters you meet, and the rule looks like a matter of memory. The cure is to treat the pairing as a fixed rule with no exceptions: A pairs only with T, and G pairs only with C. Say it as two couples, never as a crowd.

Memory hook: rails of sugar and phosphate; rungs of paired bases.

2. Keep the width even: a purine with a pyrimidine

Picture a row of bookends on a shelf, some thick and some thin. If you always set one thick bookend against one thin one, every pair takes up the same space, and the row stays straight. DNA's rungs work the same way.

The four bases come in two sizes.

A purine is a base with a double-ring structure; in DNA the purines are adenine and guanine.
A pyrimidine is a base with a single-ring structure; in DNA the pyrimidines are cytosine and thymine, and every base pair joins one of them to a purine.

Every rung joins one purine to one pyrimidine: A (a purine) with T (a pyrimidine), and G (a purine) with C (a pyrimidine). A double ring plus a single ring always gives the same total size, so every rung is the same length and the helix keeps the same width from end to end.

Worked example — which pairs keep the width even? You test three imagined rungs against the rule.

A with T. A purine with a pyrimidine, so the rung is the standard width. This pair is allowed.
A with G. A purine with a purine, two double rings, so the rung would be too wide. This pair breaks the rule.
C with T. A pyrimidine with a pyrimidine, two single rings, so the rung would be too narrow. This pair breaks the rule too.

In words: one big, one small, every time, and that is why the ladder never bulges or pinches.

Misconception check. Students often think the pairing rule is a list of facts to memorize with no reason behind it. It is tempting because A–T and G–C look like arbitrary couples. But the rule has a structural reason: only a purine-pyrimidine pair fits the fixed width of the ladder, and only the right pair makes the right number of hydrogen bonds. Structure determines function here as everywhere, and the pairing rule is what lets DNA be copied.

Memory hook: one double ring, one single ring, every rung.

3. Read the strands: antiparallel and complementary

Picture two lanes of a highway with traffic running in opposite directions. The lanes run side by side, but the cars in one lane head north while the cars in the other head south. DNA's two strands lie side by side in the same way.

Each strand has a direction, because its two ends are chemically different. The 5′ and 3′ ends are the two chemically different ends of a DNA strand, read five prime and three prime, which give every strand a direction.

Antiparallel means running side by side in opposite directions; the two strands of DNA are antiparallel, so one runs from its 5′ end to its 3′ end while its partner runs from 3′ to 5′.
Complementary strands are two DNA strands whose bases match by the pairing rule, A with T and G with C, so that knowing one strand tells you the other; they are matching partners, not identical copies.

You write a strand's bases in order from one end to the other and label both ends, as in 5′-AATGC-3′.

Worked example — writing a complement. You write the partner of the strand 5′-AATGC-3′.

Pair each base. A pairs with T, A with T, T with A, G with C, and C with G, so the partner's bases in the same positions are T, T, A, C, G.
Label the ends. The partner runs the opposite way, so its end across from the 5′ end is its 3′ end.
Write it out. 5′-AATGC-3′ pairs with 3′-TTACG-5′.

In words: the partner is a mirror by rule, not a copy, and its arrows point the other way.

Misconception check. Students often say the two strands of DNA are identical. It is tempting because both strands are "the same gene" and a copy of DNA is called identical. But the two strands of one helix are complementary: where one has A, the other has T. Two helices made by copying are identical to each other; the two strands inside one helix are partners, not twins. A second slip is to forget the direction. Always label the 5′ and 3′ ends, and flip them for the partner.

Memory hook: partners, not twins; opposite lanes.

4. Apply Chargaff's rules: one percent fixes all four

Think of a dance floor where every person dances in a couple, and every couple pairs one person in red with one person in blue. If you know how many people wear red, you know how many wear blue. DNA's bases are counted the same way.

Chargaff's rules are the pattern that in DNA the percent of adenine equals the percent of thymine and the percent of guanine equals the percent of cytosine; measured samples come out close to equal. Chargaff (1950) reported this from measured samples. In symbols, %A = %T and %G = %C, where %A means the percent of all the bases in a sample that are adenine.

The numbers below are the Chargaff example, an illustrative dataset constructed for this course, not real data. You will see them again in the lecture, the tutorial, the quiz, and the lab.

Percent of each base in one model DNA sample (illustrative, constructed for this course, not real data)
Base	Percent of all bases
Adenine	30%
Thymine	30%
Guanine	20%
Cytosine	20%

Worked example — the Chargaff example. A DNA sample is 30% adenine. You find the other three percents with every step shown.

Thymine. A pairs with T, so the percent of thymine equals the percent of adenine; %T = 30%.
A plus T. 30 + 30 = 60, so A and T together make up 60% of the bases.
G plus C. The four bases make up 100%, so G and C together are 100 − 60 = 40%.
Split evenly. G pairs with C, so the 40% splits evenly; 40 ÷ 2 = 20, so %G = 20% and %C = 20%.
Check the total. 30 + 30 + 20 + 20 = 100, so every base is counted once.
Purines and pyrimidines. The purines are A + G = 30 + 20 = 50%, and the pyrimidines are T + C = 30 + 20 = 50%, because every rung joins one purine to one pyrimidine.

In words: one number, 30% adenine, fixed all four bases, and half of the bases are purines.

Worked example — the second sample. A sample that is 20% adenine gives 20% thymine. Then 20 + 20 = 40; 100 − 40 = 60; and 60 ÷ 2 = 30, so 30% guanine and 30% cytosine. The check is 20 + 20 + 30 + 30 = 100.

In practice (your tools). A free spreadsheet runs this arithmetic once you type the adenine percent. Put the adenine percent in cell B2. In B3 type =B2 for thymine. In B4 type =(100-2*B2)/2 for guanine, and in B5 type =B4 for cytosine. In B6 type =SUM(B2:B5) and check that it reads 100. Then work the same sample by hand and confirm the spreadsheet agrees with you.

Honesty note: real measured samples come out close to these equalities, not exactly on them. The illustrative numbers here land on whole percents so the rule is easy to see; you learn the real measured numbers in words, never as answers to memorize.

Misconception check. Students often set %C equal to %A, writing 30% cytosine for a sample that is 30% adenine. It is tempting because both are "the other letters" once T is filled in. But cytosine matches guanine, not adenine. The cure is to fill the couples in order: first the partner of the base you were given, then the remainder split between the other couple. In the Chargaff example, %C = %G = 20%.

Memory hook: fill the partner, subtract from 100, split the rest.

5. Place the history in order: from transformation to the double helix

Picture a detective story told across several decades, where each investigator hands a clue to the next. No one person solved the case; each step made the next one possible. The discovery of DNA's role and shape ran the same way.

Here are the steps in order. Each name comes with its year and its result, and none of them comes with a quotation, because no quotation from these scientists is pinned for this course.

Griffith (1928) discovered transformation. Transformation is a change in the traits of bacteria caused by a substance taken up from other bacteria; the transforming substance turned out to be DNA.
Avery, MacLeod, and McCarty (1944) showed that the transforming substance is DNA.
Chargaff (1950) reported that adenine matches thymine and guanine matches cytosine.
Hershey and Chase (1952) used labeled bacteriophages to confirm that DNA, not protein, is the genetic material. A bacteriophage is a virus that infects bacteria; labeled bacteriophages showed that DNA, not protein, is the genetic material.
Franklin and Wilkins made X-ray diffraction images of DNA. X-ray diffraction is a method that shines X-rays through a material and reads the pattern they make to learn about its shape; images of DNA made this way helped reveal the double helix.
Watson and Crick (1953) built the double-helix model on that work and on Chargaff's ratios.
The 1962 Nobel Prize went to Crick, Watson, and Wilkins. Franklin had died before it was awarded, and the prize is not given to someone who has died.

Worked example — matching a result to its step. You place each result at the right point in the story.

Labeled viruses that infect bacteria show that DNA, not protein, is the genetic material. That is Hershey and Chase (1952), step 4.
A substance from one kind of bacteria changes another kind. That is Griffith (1928), step 1.
The two strands wind into a helix with paired bases inside. That is Watson and Crick (1953), step 6, built on the X-ray images from step 5.

In words: first the transforming substance was found, then it was named as DNA, then its ratios and images were measured, and only then was its shape built.

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

(a) The discovery of the double helix depended on work by several groups across more than twenty years. Pick one step in the list above and explain how the next step depended on it.
(b) Franklin's images were essential to the model, but the prize went to three others after her death. Explain what this history shows you about how credit in science is shared, using two steps from the list.

Misconception check. Students often attach a famous-sounding quotation to Franklin, Watson, or Crick, because quotations make a story feel real. It is tempting because the story is dramatic and many retellings add lines of dialogue. But a quotation you cannot trace to a pinned source is an invented figure. In this course you state each scientist's result in your own words, with the year, and you leave out any quotation.

Memory hook: transform, name it, measure it, picture it, model it.

6. Compare three copying models

Imagine you need a second copy of a two-page handwritten letter. You could keep the original pages together and write a whole new pair. You could tear each page in half and pair each old half with a new half. Or you could split the two pages apart and write a fresh partner for each old page. Biologists once argued over which of these three plans a cell uses.

DNA replication is the copying of a cell's DNA before it divides, which makes two double helices from one.

Three models were proposed.

The conservative model is a proposed model of DNA replication in which the original double helix stays whole and a completely new double helix is built beside it; the evidence ruled it out.
The dispersive model is a proposed model of DNA replication in which every strand of both copies ends up a patchwork of old and new pieces; the evidence ruled it out.
Semiconservative replication is the way DNA is copied: the double helix unzips, each original strand serves as the pattern for a new partner strand, and every copy ends up half old and half new.

DNA replication is semiconservative. That fits the pairing rule from Section 1: each old strand carries all the information needed to build its partner.

Worked example — the semiconservative count. You follow one double helix through two rounds of copying.

Round one. One double helix copied once gives 2 helices, each with 1 old strand and 1 new strand.
Round two. Each of those 2 helices is copied, giving 2 × 2 = 4 helices.
Sort them. Each of the 2 old strands sits in its own helix with a new partner, so 2 helices are half old and half new and the other 2 are all new.
Share. 2 ÷ 4 = 1⁄2 of the helices still carry an old strand.

In words: the old strands are never thrown away, but each round spreads them across more helices.

Misconception check. Students often call DNA replication conservative, picturing the original helix kept whole like a master copy in a safe. It is tempting because "conserve" sounds like "keep the original safe." But replication is semiconservative: the original helix is split, and each copy keeps one old strand. The "semi" means half.

Memory hook: semi means half old, half new.

7. Test the models: Meselson and Stahl

Picture two loaves of bread that look identical, one made with heavy whole-grain flour and one with light white flour. Drop them in water and the heavy one sinks lower. Meselson and Stahl used the same idea, sorting DNA by density.

Meselson and Stahl (1958) grew bacteria on heavy nitrogen (¹⁵N), then moved them to light nitrogen (¹⁴N), and sorted the DNA by density. Nitrogen is built into every DNA base, so old DNA was heavy and new DNA was light.

Here is what each model predicts, round by round, and what they saw.

After one round of copying. All the DNA formed one band of in-between density. A conservative copy would have given two bands, one heavy and one light, so the single in-between band ruled out the conservative model.
After a second round. An in-between band and a light band appeared. A dispersive copy would have given every helix the same patchwork of old and new pieces, so all the DNA would have sat in one band and no separate light band could appear. The light band ruled out the dispersive model.
The verdict of the evidence. Only the semiconservative model fits both results.

Worked example — reading the bands. You check the second round against your count from Section 6.

Helices after two rounds. 4, from the count in Section 6.
Half old, half new. 2 of them carry one heavy strand and one light strand, so they form the in-between band.
All new. The other 2 carry two light strands, so they form the light band.

In words: two in-between and two light, exactly the two bands Meselson and Stahl saw.

Misconception check. Students often think one experiment "proved" semiconservative replication beyond any question. It is tempting because the result was so clean. But, as Week 1 taught, evidence supports or fails to support a model; it never proves it. The two rounds ruled out the other two models and supported the semiconservative one, and later work has kept supporting it.

Memory hook: one round, one in-between band; two rounds, in-between plus light.

8. Meet the three machines: unzip, add, seal

Think of fixing a long zipper on a jacket. First you pull the two sides apart. Then you fit new teeth along each side, one by one. Then you stitch the fabric shut where you worked in short pieces. A cell copies DNA with three enzymes that do those three jobs, in that order.

Helicase is the enzyme that unzips the double helix during replication by breaking the hydrogen bonds between base pairs.
An origin of replication is a place on a DNA molecule where unzipping, and with it copying, begins.
DNA polymerase is the enzyme that builds a new DNA strand by adding nucleotides that pair with each exposed base, and that checks its own work as it goes.
DNA ligase is the enzyme that seals the sugar-phosphate backbone where a new DNA strand was made in separate pieces.

Written as an ordered chain, the copying is:

helicase unzips → DNA polymerase adds and proofreads → DNA ligase seals

Worked example — matching a job to a machine. You name the enzyme for each event during replication.

The hydrogen bonds between the rungs break at one spot. Helicase, starting at an origin of replication.
A free nucleotide with a C is added across from a G on an exposed strand. DNA polymerase, following the pairing rule.
A short gap in a new strand's backbone is closed. DNA ligase.

In words: unzip, add, seal, and each job belongs to one machine.

Misconception check. Students often say DNA polymerase unzips the helix. It is tempting because polymerase is the famous enzyme and does the most visible work. But helicase unzips, polymerase adds, and ligase seals. A second slip is to mix replication up with protein synthesis. Replication copies DNA into DNA this week; reading DNA into RNA and then protein comes next week.

Memory hook: unzip, add, seal.

9. Explain why copying is so reliable

Imagine copying a long recipe by hand, but with a rule that lets you check every word against its partner on the facing page. You would still slip now and then, but you would catch most slips before the ink dried. DNA copying has two built-in checks like that.

The first check is the pairing rule itself. Because A pairs only with T and G pairs only with C, a single old strand carries all the information for a new one. Polymerase does not have to guess; the exposed base dictates the partner.

The second check is proofreading. Proofreading is the checking DNA polymerase does as it copies, catching and fixing most mispaired nucleotides before they become permanent.

Worked example — following one slip. You follow one copying error through the two checks.

The slip. Across from an exposed A, a G is added by mistake.
The first check. A G across from an A is a purine with a purine, so the rung is the wrong width and the pairing rule is broken.
The second check. DNA polymerase proofreads, removes the wrong G, and adds a T.
The result. The new strand reads the right base, and the copy matches the original.

In words: pairing dictates the partner, and proofreading catches most of the slips that get through.

Caveat: "most" is the honest word. Proofreading catches most slips, not every one, and the rare slip that stays is a change in the DNA. Week 15 returns to those changes and what they do.

Misconception check. Students often assume a copying machine this accurate never makes a mistake. It is tempting because the system works so well. But the system is reliable, not perfect: pairing and proofreading catch most slips, not all of them, and the few that remain become lasting changes in the DNA.

Memory hook: the partner is dictated; the slips are mostly caught.

10. Run the strawberry extraction

Back at the kitchen counter, the strawberry lab makes the double helix something you can hold on a toothpick. Each step has a job, and each job connects to a structure you have already met.

Mash the fruit. Breaking up the tissue exposes more cells to the liquid.
Add soap. Soap breaks open the cell membranes, the phospholipid layers from Week 4, and releases the DNA.
Add salt. Salt helps the DNA strands clump together.
Pour cold alcohol on top. Cold alcohol makes the DNA come out of the liquid as the white strands you can see where the two layers meet.

Strawberries give so much DNA because most cultivated varieties are octoploid. Octoploid means carrying eight sets of chromosomes; most cultivated strawberries are octoploid, which is one reason they yield so much DNA.

Worked example — matching each ingredient to its job. You explain why each step is there.

Without soap. The membranes stay closed, so little DNA is released.
Without salt. The strands do not clump as well, so the cloud is thinner.
Without cold alcohol. The DNA stays dissolved, so you see no white strands at all.

In words: soap opens, salt gathers, and alcohol pulls the DNA out where you can see it.

Misconception check. Students often think the white strands are one DNA molecule, or that they can see the double helix itself. It is tempting because the cloud looks like a single thread. But the cloud is many strands clumped together, far too many and too tangled to see a twist. The helix is a shape you know from the evidence in Sections 5 to 7, not one you see in a cup.

Memory hook: soap opens, salt gathers, alcohol lifts.

Key terms

Double helix — The shape of a DNA molecule: two strands wound around each other like a twisted ladder, with the sugar-phosphate backbone as the rails and base pairs as the rungs. (first used: 1. Picture the double helix: rails and rungs)
Sugar-phosphate backbone — The rail of each DNA strand, a repeating chain of the sugar deoxyribose joined to phosphate, with the bases sticking inward from it. (first used: 1. Picture the double helix: rails and rungs)
Base pair — Two bases, one on each strand of DNA, joined across the double helix by hydrogen bonds; adenine pairs with thymine and guanine pairs with cytosine. (first used: 1. Picture the double helix: rails and rungs)
Adenine — One of the four bases in DNA, a purine written A, which pairs with thymine through two hydrogen bonds. (first used: 1. Picture the double helix: rails and rungs)
Thymine — One of the four bases in DNA, a pyrimidine written T, which pairs with adenine; RNA uses uracil in its place. (first used: 1. Picture the double helix: rails and rungs)
Guanine — One of the four bases in DNA, a purine written G, which pairs with cytosine through three hydrogen bonds. (first used: 1. Picture the double helix: rails and rungs)
Cytosine — One of the four bases in DNA, a pyrimidine written C, which pairs with guanine. (first used: 1. Picture the double helix: rails and rungs)
Purine — A base with a double-ring structure; in DNA the purines are adenine and guanine. (first used: 2. Keep the width even: a purine with a pyrimidine)
Pyrimidine — A base with a single-ring structure; in DNA the pyrimidines are cytosine and thymine, and every base pair joins one of them to a purine. (first used: 2. Keep the width even: a purine with a pyrimidine)
5′ and 3′ ends — The two chemically different ends of a DNA strand, read five prime and three prime, which give every strand a direction. (first used: 3. Read the strands: antiparallel and complementary)
Antiparallel — Running side by side in opposite directions; the two strands of DNA are antiparallel, so one runs from its 5′ end to its 3′ end while its partner runs from 3′ to 5′. (first used: 3. Read the strands: antiparallel and complementary)
Complementary strands — Two DNA strands whose bases match by the pairing rule, A with T and G with C, so that knowing one strand tells you the other; they are matching partners, not identical copies. (first used: 3. Read the strands: antiparallel and complementary)
Chargaff's rules — The pattern that in DNA the percent of adenine equals the percent of thymine and the percent of guanine equals the percent of cytosine; measured samples come out close to equal. (first used: 4. Apply Chargaff's rules: one percent fixes all four)
Transformation — A change in the traits of bacteria caused by a substance taken up from other bacteria; the transforming substance turned out to be DNA. (first used: 5. Place the history in order: from transformation to the double helix)
Bacteriophage — A virus that infects bacteria; labeled bacteriophages showed that DNA, not protein, is the genetic material. (first used: 5. Place the history in order: from transformation to the double helix)
X-ray diffraction — A method that shines X-rays through a material and reads the pattern they make to learn about its shape; images of DNA made this way helped reveal the double helix. (first used: 5. Place the history in order: from transformation to the double helix)
DNA replication — The copying of a cell's DNA before it divides, which makes two double helices from one. (first used: 6. Compare three copying models)
Conservative model — A proposed model of DNA replication in which the original double helix stays whole and a completely new double helix is built beside it; the evidence ruled it out. (first used: 6. Compare three copying models)
Dispersive model — A proposed model of DNA replication in which every strand of both copies ends up a patchwork of old and new pieces; the evidence ruled it out. (first used: 6. Compare three copying models)
Semiconservative replication — The way DNA is copied: the double helix unzips, each original strand serves as the pattern for a new partner strand, and every copy ends up half old and half new. (first used: 6. Compare three copying models)
Helicase — The enzyme that unzips the double helix during replication by breaking the hydrogen bonds between base pairs. (first used: 8. Meet the three machines: unzip, add, seal)
Origin of replication — A place on a DNA molecule where unzipping, and with it copying, begins. (first used: 8. Meet the three machines: unzip, add, seal)
DNA polymerase — The enzyme that builds a new DNA strand by adding nucleotides that pair with each exposed base, and that checks its own work as it goes. (first used: 8. Meet the three machines: unzip, add, seal)
DNA ligase — The enzyme that seals the sugar-phosphate backbone where a new DNA strand was made in separate pieces. (first used: 8. Meet the three machines: unzip, add, seal)
Proofreading — The checking DNA polymerase does as it copies, catching and fixing most mispaired nucleotides before they become permanent. (first used: 9. Explain why copying is so reliable)
Octoploid — Carrying eight sets of chromosomes; most cultivated strawberries are octoploid, which is one reason they yield so much DNA. (first used: 10. Run the strawberry extraction)

Summary

DNA is a double helix: sugar-phosphate rails, base-pair rungs.
A pairs with T by two hydrogen bonds; G pairs with C by three.
Every rung is a purine with a pyrimidine, so the width stays even.
The strands are antiparallel and complementary, not identical.
Chargaff's rules: the percent of A equals T, and G equals C.
Griffith, Avery and colleagues, Chargaff, Hershey and Chase, Franklin and Wilkins, then Watson and Crick, in that order.
Replication is semiconservative: each copy is half old, half new.
Meselson and Stahl's two rounds ruled out the other two models.
Helicase unzips, DNA polymerase adds and proofreads, DNA ligase seals.
Pairing dictates the partner; proofreading catches most slips.

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.

An illustrative DNA sample from a garden pea leaf is 35% guanine. Find the percent of cytosine, adenine, and thymine, and check your total.
Write the complement of the strand 5′-GGATC-3′, label its ends, and count the hydrogen bonds that hold the five rungs.
Suppose DNA copying had been conservative. Describe the bands Meselson and Stahl would have seen after one round of copying, and explain why their actual result ruled this model out.
A study guide you find online states, "DNA polymerase unzips the helix, and then ligase adds the new bases." Explain what is wrong and write the correct order of the three machines.

Answers (worked reasoning — read after attempting)

Cytosine matches guanine, so %C = 35%. G and C together are 35 + 35 = 70%. A and T share the rest: 100 − 70 = 30%, and 30 ÷ 2 = 15, so %A = 15% and %T = 15%. Check: 15 + 15 + 35 + 35 = 100. The slip to avoid is setting %A equal to %G; A matches T.
Pair each base: G with C, G with C, A with T, T with A, C with G, so 5′-GGATC-3′ pairs with 3′-CCTAG-5′. The rungs are 3 G–C pairs (from G, G, and C) and 2 A–T pairs (from A and T). Hydrogen bonds: 3 × 3 = 9 and 2 × 2 = 4, so 9 + 4 = 13.
A conservative copy keeps the old helix whole and builds an all-new one, so after one round there would be one all-heavy helix and one all-light helix: two bands, one heavy and one light. Meselson and Stahl saw a single band of in-between density instead, which means every helix carried one heavy strand and one light strand. That rules out the conservative model.
The statement swaps the jobs. Helicase unzips the helix by breaking the hydrogen bonds; DNA polymerase adds the new nucleotides and proofreads; DNA ligase seals the backbone where a new strand was made in pieces. The correct order is helicase, then DNA polymerase, then DNA ligase.

Next up in this module: the Readings & Resources page, the lecture tutorial, the practice set, and the quiz; next week, the central dogma shows how a cell reads DNA into RNA and then into protein.

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