4 DNA Structure and Replication

DNA structure and genome organization

DNA, or deoxyribonucleic acid, stores hereditary information in the order of its nucleotide bases. Each nucleotide consists of a deoxyribose sugar, a phosphate group, and one base: adenine (A), thymine (T), guanine (G), or cytosine (C). Nucleotides are joined by covalent phosphodiester bonds, forming a sugar–phosphate backbone.

Each DNA strand has a direction, labeled $5′ \to 3′$. In most cells, two strands coil into a double helix and run antiparallel: one runs $5′ \to 3′$, while its partner runs $3′ \to 5′$. The bases pair specifically: A with T, and G with C, through hydrogen bonds. Because the sequence of one strand determines the sequence of its partner, either strand can serve as a template for copying DNA.

A genome is an organism’s complete set of genetic material. It includes genes as well as DNA sequences that do not encode proteins, including regulatory and structural sequences.

Genome organization differs among organisms:

• Bacteria and archaea keep their DNA in a nucleoid rather than a membrane-bound nucleus. Many have a main circular chromosome, though linear chromosomes also occur. Some also have plasmids: smaller DNA molecules that can replicate separately or sometimes integrate into a chromosome. DNA-binding proteins and supercoiling help compact and organize this DNA.

• Eukaryotes organize DNA into multiple, usually linear chromosomes in the nucleus. DNA wraps around histone proteins to form nucleosomes, the basic units of chromatin. A nucleosome core contains about $147$ base pairs of DNA wrapped around a histone protein complex. Chromatin both compacts DNA and helps organize access to it; its structure is dynamic.

• Telomeres are repetitive DNA sequences associated with proteins that protect the ends of linear eukaryotic chromosomes. They matter when those chromosome ends are copied.

The complementary, antiparallel structure of DNA explains how each strand can guide the production of a matching partner.

Starting DNA replication

Before a cell divides, it copies its DNA so each daughter cell can receive a genome. Replication is semiconservative: each resulting DNA double helix contains one original strand and one newly made strand.

Replication begins at specific DNA sites called origins. The DNA opens at an origin to form a replication bubble, with two replication forks that typically move in opposite directions. Bacterial chromosomes often have one origin, while eukaryotic chromosomes use many origins to copy their much larger genomes in time.

Initiator proteins recognize origins and help assemble the replication machinery. Helicase separates the DNA strands. Single-strand DNA-binding proteins keep the exposed strands from pairing again; these are called SSB in bacteria and RPA in eukaryotes. As helicase unwinds the DNA, twisting strain builds ahead of the fork. Topoisomerases relieve this strain by temporarily cutting and rejoining DNA.

In eukaryotic cells, origins are licensed before DNA synthesis and activated during S phase. This two-step control helps ensure each region of the genome is replicated once per cell cycle.

Takeaway: Origins establish where copying begins, while the machinery at each fork opens and stabilizes the DNA template.

Building new DNA strands

DNA polymerases build new DNA by matching each incoming nucleotide to the exposed template strand. A DNA polymerase can extend DNA only in the $5′ \to 3′$ direction, so it needs a short starting strand called a primer. Primase makes RNA primers; in eukaryotes, primase works as part of a complex that also begins DNA synthesis. A sliding clamp helps keep DNA polymerase attached to its template so synthesis can proceed efficiently.

The two template strands run in opposite directions, so their new partner strands are made differently at each fork:

• The leading strand is synthesized continuously in the direction the fork advances.

• The lagging strand is synthesized discontinuously, away from the advancing fork. It is made in short sections called Okazaki fragments, and each fragment begins with a new RNA primer.

After the fragments are made, enzymes remove the RNA primers and replace them with DNA. DNA ligase seals the remaining breaks in the sugar–phosphate backbone, joining the sections into a continuous strand.

Takeaway: Polymerase’s direction of synthesis means one strand can be built continuously while the other must be assembled in fragments.

Accuracy and completion

DNA polymerases select nucleotides by complementary base pairing. Many can also proofread newly made DNA by removing a wrongly paired nucleotide before synthesis continues. Base selection and proofreading make replication highly accurate.

Replication ends when replication forks meet or reach the ends of the DNA molecule. Linear eukaryotic chromosomes present a special challenge: the final RNA primer on the lagging strand cannot be replaced in the usual way at a chromosome end. In certain cells, telomerase can extend telomeric DNA, helping maintain those chromosome ends.

Together, complementary base pairing, proofreading, primer replacement, and ligation produce complete DNA molecules while preserving the original strands as templates.