AP Biology · Lesson 1

DNA structure and replication

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DNA is two strands of nucleotides. Each nucleotide has a sugar (deoxyribose), a phosphate and a base: A, T, G or C. The sugar of one nucleotide bonds to the phosphate of the next, making a sugar-phosphate backbone with the bases sticking inward. Each strand has a 5' end (a phosphate) and a 3' end (a sugar's hydroxyl group).

The two strands are antiparallel: one runs 5' to 3', and its partner runs 3' to 5'. Bases pair by hydrogen bonds, A with T and G with C. Each pair joins a two-ring base (A or G) to a one-ring base (T or C), so the helix is the same width all along. Because of this pairing, double-stranded DNA has equal amounts of A and T, and equal amounts of G and C.

RNA is usually single-stranded. Its sugar is ribose, and it has uracil (U) where DNA has T. Bacteria keep their main DNA in one circular chromosome and often carry small circular plasmids as well. Eukaryotes have several linear chromosomes, with DNA wound around histone proteins.

DNA copies itself by semiconservative replication: each new helix keeps one old strand and gets one new strand. Helicase unwinds the helix at the replication fork, and topoisomerase relieves the twisting ahead of it. Primase lays down a short RNA primer, because DNA polymerase can only add nucleotides to an existing 3' end. So new DNA always grows 5' to 3'. The leading strand is built in one continuous piece toward the fork. The lagging strand is built away from the fork in short Okazaki fragments. Primers are later replaced with DNA, and ligase seals the gaps. DNA polymerase also proofreads, removing most wrongly paired bases.

Trap New DNA grows only at the 3' end

DNA polymerase cannot start a strand from nothing and cannot add to a 5' end. It reads the template 3' to 5' and builds the new strand 5' to 3'. That one rule explains the primer, the leading strand and the lagging strand's fragments.

Worked example Easy

In a sample of double-stranded DNA, 30 percent of the bases are adenine (A). What percent of the bases are guanine (G)?

  1. 20 percentAnswer
  2. 30 percent
  3. 40 percent
  4. 70 percent

How to solve it

  1. A pairs with T, so T is also 30 percent: A + T = 60 percent.
  2. That leaves 100 - 60 = 40 percent for G and C.
  3. G pairs with C, so G = 40 / 2 = 20 percent.

Why each choice is right or wrong

  • A. Correct. T equals A, so A + T = 60 percent; G and C share the other 40 percent equally, so G is 20 percent.
  • B. Incorrect. 30 percent is the amount of thymine, which pairs with adenine, not the amount of guanine.
  • C. Incorrect. 40 percent is G and C together; G is only half of that because it pairs with C.
  • D. Incorrect. 70 percent is everything except A, which counts T, G and C together, not G alone.

Explain Explain it

Task verbs: determine, explain

To work out a new strand, pair each base (A with T, G with C) and flip the direction: a template read 3' to 5' gives a new strand that runs 5' to 3'. To explain a replication result, name the enzyme involved and the rule it follows, such as polymerase adding only to a 3' end.

Worked example Medium

A template strand reads TACGGA from its 3' end to its 5' end. DNA polymerase builds a new strand on it. Which sequence does the new strand have, written from its 5' end to its 3' end?

  1. TACGGA
  2. ATGCCTAnswer
  3. AUGCCU
  4. TCCGTA

How to solve it

  1. Pair each template base: T with A, A with T, C with G, G with C, G with C, A with T.
  2. That gives ATGCCT, lined up base by base with the template.
  3. The template ran 3' to 5', so the new strand runs 5' to 3': ATGCCT.

Why each choice is right or wrong

  • A. Incorrect. TACGGA repeats the template itself; the new strand must pair with it, not copy it.
  • B. Correct. Pairing T-A, A-T, C-G, G-C, G-C and A-T gives ATGCCT, and the new strand runs 5' to 3' opposite the template.
  • C. Incorrect. AUGCCU contains uracil, which belongs in RNA; DNA polymerase builds DNA with thymine.
  • D. Incorrect. TCCGTA is the right new strand written backward, from its 3' end, but the question asks for it read from 5' to 3'.

Explain Your turn

At a replication fork, one new strand is made in one long piece and the other is made in many short pieces. Explain why, using the direction in which DNA polymerase can build a strand.

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A full answer does this

  • Explains that DNA polymerase can add nucleotides only to the 3' end, so a new strand can grow only in the 5' to 3' direction
  • Explains that because the two template strands are antiparallel, one new strand can grow toward the opening fork continuously, while the other must grow away from the fork and so is built in short pieces as the fork opens

Model answer

DNA polymerase can add nucleotides only to the 3' end of a growing strand, so every new strand grows in the 5' to 3' direction. The two template strands are antiparallel. On one template, growing 5' to 3' means moving toward the fork as it opens, so that leading strand is built in one continuous piece. On the other template, growing 5' to 3' means moving away from the fork. Each time the fork opens further, a new primer is laid down and a new short piece is built, so the lagging strand is made in many fragments.

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