Lecture: DNA Structure & Replication
Lecture script · about 15–20 minutes spoken · Week 13
Opening
Picture a kitchen counter and a ripe strawberry. You mash it with a little dish soap and salt, strain the pulp, and pour cold rubbing alcohol gently on top. A white, stringy cloud rises where the two layers meet. That cloud is DNA, many strands of it clumped together, and you pulled it out of a fruit with things from under the sink.
Those strands are the same molecule that sits in every one of your cells. A nursing student will one day read a genetic test built on it, and a crime-lab technician handles it every shift. Every cell has to copy all of its DNA before it divides, and it gets the copy right almost every time.
Here's where we are. In Week 2 you met the hydrogen bond, a weak attraction that gets strong in large numbers. In Week 3 you met DNA as a nucleic acid built from nucleotides. In Week 9 you learned that a cell copies its DNA in the S phase, before mitosis. In this lecture I'll open that S phase up: the twisted ladder, its pairing rule, the history, and the copying itself. Next week, in Week 14, you follow DNA's instructions out to a protein.
1. The double helix: rails and rungs
Picture a rope ladder in a playground. Grab the bottom and give it a slow twist. The two side ropes wind around each other, and the rungs stay level between them. That's 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. The rails are the 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. The rungs are base pairs. 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 four bases go by single letters: A for adenine, T for thymine, G for guanine, and C for cytosine. The rule is short. A pairs with T. G pairs with C.
What holds a rung together? Hydrogen bonds, the same weak attractions you met in Week 2. An A and T pair is held by two of them. A G and C pair is held by three. Each bond is weak, but many together hold the strands tight. And the ladder twists as it goes: a full turn takes about ten base pairs.
Let me count one short stretch. The strand A, A, T, G, C has five rungs. Three of them are A and T pairs, so that's 3 times 2, which is 6 bonds. Two of them are G and C pairs, so that's 2 times 3, which is 6 more. That's 12 hydrogen bonds in all.
Pause and try this. Which rung is held more tightly, an A and T pair or a G and C pair?
Count the bonds in each kind of rung.
Here's the answer. The G and C pair is held more tightly. It has three hydrogen bonds, and the A and T pair has two.
2. One double ring, one single ring
Think 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.
Now look at the pairing rule again with that in mind. A is a purine and T is a pyrimidine. G is a purine and C is a pyrimidine. So every rung is one double ring plus one single ring. That always adds up to the same width, and so the helix keeps the same width from one end to the other. If two purines tried to pair, the rung would bulge. If two pyrimidines tried, it would pinch.
That's structure determines function, the course's spine, once more. The pairing rule isn't a random list of couples. It's the only arrangement that fits the ladder, and it's what lets DNA be copied.
Pause and try this. Someone proposes a rung made of adenine and guanine. Why won't it fit?
Think about how many rings each base has.
Here's the answer. Adenine and guanine are both purines, with two rings each. Two double rings make a rung that's too wide for the ladder.
3. Strands with a direction
Picture a two-lane road with traffic going opposite ways. The lanes run side by side, but one heads north and the other heads south. DNA's two strands lie together in the same way.
Each strand has a direction, because its two ends are 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. The two strands run opposite ways, and we call that antiparallel. 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′.
Here's the most important idea in this section. The two strands are not identical. 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.
Take the strand that reads, from its five prime end, A, A, T, G, C. Pair each base, and the partner reads T, T, A, C, G, starting at its three prime end because it runs the other way. One strand gave you the other.
Pause and try this. Someone says the two strands of one DNA molecule are identical copies. What's the better word?
Think about what sits across from an A.
Here's the answer. The better word is complementary. Across from every A sits a T, so the strands are matching partners, not twins.
4. Chargaff's rules: one number fixes four
Think of a dance floor where 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. Bases in DNA 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 reported this in 1950 from measured samples.
Let me work the Chargaff example you'll see all week. It's an illustrative sample, made up for this course, not real data. The sample is 30% adenine. A pairs with T, so thymine is also 30%. Together, A and T are 30 plus 30, which is 60%. All four bases make 100%, so G and C together are 100 minus 60, which is 40%. G pairs with C, so that 40% splits evenly: 40 divided by 2 is 20. Guanine is 20%, and cytosine is 20%. Check it: 30 plus 30 plus 20 plus 20 is 100.
Here's a second sample. If it's 20% adenine, then it's 20% thymine. That's 40% for A and T, which leaves 60% for G and C, so 30% guanine and 30% cytosine.
One honest note. Real measured samples come out close to these equalities, not exactly on them. So you learn the real numbers in words, and you use the clean ones to practice the rule.
Pause and try this. In the first sample, someone writes that cytosine is 30%, the same as adenine. What went wrong?
Ask yourself which base cytosine pairs with.
Here's the answer. Cytosine matches guanine, not adenine. Guanine is 20%, so cytosine is 20% too.
5. The history, in order
Picture a detective story where each investigator hands a clue to the next. The discovery of DNA's job and shape ran that way. I'll give you each step with its year and result, and no quotations, because none is pinned for this course.
In 1928 Griffith 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. In 1944 Avery, MacLeod, and McCarty showed that the transforming substance is DNA. In 1950 Chargaff reported his base ratios. In 1952 Hershey and Chase used labeled viruses that infect bacteria, called bacteriophages, to confirm that DNA, not protein, is the genetic material.
Then came the shape. Franklin and Wilkins made X-ray diffraction images of DNA, patterns made by shining X-rays through it. In 1953 Watson and Crick 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 isn't given to someone who has died.
Pause and try this. Which came first, the double-helix model or the finding that the transforming substance is DNA?
Line up the two years.
Here's the answer. The transforming substance was shown to be DNA in 1944. The double-helix model came later, in 1953.
6. Three ways to copy
Imagine copying a two-page letter. You could keep both pages and write a whole new pair. You could mix old scraps with new ones. Or you could split the pages and write a fresh partner for each. Biologists once argued over which plan 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 on the table. In the conservative model, the original double helix stays whole and a completely new double helix is built beside it. In the dispersive model, every strand of both copies ends up a patchwork of old and new pieces. And in semiconservative replication, 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 what you learned in Section 3: one strand tells you the other, so each old strand carries everything needed to build its partner.
Let me count two rounds. One double helix copied once gives 2 helices, each with one old strand and one new. Copy those again and you get 4 helices. Only 2 of them still carry an old strand. So half of them hold on to an original strand, and half are all new.
Pause and try this. Someone says replication is conservative because the cell keeps its original DNA safe. What's the correct name, and what does it mean?
Think about what "semi" means.
Here's the answer. It's semiconservative. Each new helix keeps one old strand and gains one new strand, so it's half old and half new.
7. The test that settled it
Picture two loaves that look alike, one dense and heavy, one light and airy. Meselson and Stahl sorted DNA the same way, by how dense it was.
In 1958 Meselson and Stahl grew bacteria on a heavy form of nitrogen, then moved them to the ordinary light form, and sorted the DNA by density. Nitrogen is built into every DNA base, so old DNA was heavy and new DNA was light.
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 kept all the DNA in one mixed band, with no separate light band. So that light band ruled out the dispersive model. Only the semiconservative model fits both results.
Pause and try this. After one round, why does a single in-between band rule out the conservative model?
Picture what a conservative copy would leave behind.
Here's the answer. A conservative copy keeps one all-heavy helix and builds one all-light helix, which would make two separate bands. One in-between band means every helix had one old strand and one new.
8. Three machines: unzip, add, seal
Think about 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 doing 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. It starts at an origin of replication, a place on a DNA molecule where unzipping, and with it copying, begins. Next, 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. Last, DNA ligase is the enzyme that seals the sugar-phosphate backbone where a new DNA strand was made in separate pieces.
So the order is a fact: unzip, add, seal.
Pause and try this. Someone says DNA polymerase unzips the helix. Which enzyme really does it?
Run the three jobs in order.
Here's the answer. Helicase unzips. Polymerase adds the new nucleotides, and ligase seals the backbone.
9. Why copying is so reliable
Imagine copying a recipe by hand while checking every word against a facing page. You'd still slip, but you'd catch most slips. DNA copying has two checks like that.
The first check is the pairing rule. Because A pairs only with T and G pairs only with C, the exposed base dictates the partner. Polymerase doesn't have to guess.
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. Say a G is set across from an A by mistake. That's two purines in one rung, the wrong fit. Polymerase catches it, takes the G out, and puts in a T.
Notice the honest word there: most. Pairing and proofreading catch most slips, not every one. The rare slip that stays is a lasting change in the DNA, and Week 15 comes back to those changes. Replication copies DNA into DNA; reading DNA into protein is next week's story.
Pause and try this. Name the two checks that make DNA copying so reliable.
One is a rule, and one is a job.
Here's the answer. The pairing rule dictates each partner, and DNA polymerase's proofreading catches most of the slips that get through.
10. The strawberry, explained
Back to the kitchen counter. Now that you know the molecule, each step of the strawberry lab has a job. Soap breaks open the cell membranes, the phospholipid layers from Week 4, and releases the DNA. Salt helps the DNA strands clump together. Cold alcohol makes the DNA come out of the liquid, and that's the white cloud you see where the layers meet.
Why a strawberry? Most cultivated strawberries are octoploid. Octoploid means carrying eight sets of chromosomes; most cultivated strawberries are octoploid, which is one reason they yield so much DNA. More sets of chromosomes means more DNA in every cell.
One caution. The white cloud is many strands tangled together, so you can't see the twist of the helix in it. You know that shape from the evidence, not from a cup.
Pause and try this. If you skip the cold alcohol, what do you expect to see?
Think about what the alcohol does to the DNA.
Here's the answer. You'd see no white strands. Without the cold alcohol, the DNA stays dissolved in the liquid.
Closing
Let me pull it together, in order. 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. The strands are antiparallel and complementary, not identical. Chargaff's rules turn 30% adenine into 30% thymine, 20% guanine, and 20% cytosine. The history runs from Griffith in 1928 to Watson and Crick in 1953. Replication is semiconservative, as Meselson and Stahl showed. Helicase unzips, polymerase adds and proofreads, and ligase seals. And soap, salt, and cold alcohol pull DNA out of a strawberry.
Next in this module, read the Readings & Resources page, then work through the lecture tutorial, the practice set, and the quiz, and then the discussion and the assignment. Next week, in Week 14, you follow a gene from DNA to RNA to protein in gene expression.
Built with The Course Maker · samples.thecoursemaker.com