DNA Structure & Replication

Nucleic acids (DNA and RNA) are one of the four main classes of macromolecules — large organic molecules containing mainly carbon, hydrogen, oxygen and nitrogen — alongside proteins, carbohydrates and lipids. Before examining DNA in detail, it is helpful to see how genetic information is organised. There are three fundamental units, arranged in a hierarchy:

1. DNA - the chemical unit of genetic information.
2. Genes - the functional units of genetic information. A gene is a specific sequence of DNA that determines protein synthesis, the characteristics of an organism, and inheritance from one generation to the next.
3. Chromosomes - the structural units of genetic information. Each chromosome is one large, discrete double-helix DNA molecule, and each chromosome carries many genes.

DEOXYRIBONUCLEIC ACID

DNA (deoxyribonucleic acid) is made of small repeating subunits called nucleotides, joined one after another into a chain. Each nucleotide contains three components:

1. A deoxyribose sugar
2. A phosphate group
3. A nitrogenous base - adenine (A), thymine (T), guanine (G) or cytosine (C)

One nucleotide - the basic unit of DNA: a phosphate group and a nitrogenous base attached to a deoxyribose sugar.

Nucleotides join sugar-to-phosphate, so each strand of DNA has a continuous sugar-phosphate backbone with the bases attached along it. A strand built this way is called a polynucleotide, and the order of the bases along the backbone is the genetic information itself.

THE DOUBLE HELIX AND COMPLEMENTARY BASE PAIRING

The structure of DNA is described as a double helix: two polynucleotide strands twisted around one another. The strands are antiparallel - they run in opposite directions, one in the $5'\to3'$ direction and the other $3'\to5'$. The strands are joined by weak bonds (hydrogen bonds) between pairs of bases. Each base can only bind one partner - this is called complementary base pairing:

• Adenine (A) pairs only with thymine (T) - held by two hydrogen bonds.
• Guanine (G) pairs only with cytosine (C) - held by three hydrogen bonds.

Two antiparallel strands joined by complementary base pairs: A-T (two hydrogen bonds) and G-C (three hydrogen bonds).

Each hydrogen bond is individually weak, and this is important: the two strands can be separated (for replication and transcription) without breaking the strong covalent bonds of the sugar-phosphate backbones, and can rejoin afterwards.

CHROMATIN AND CHROMOSOMES

When a eukaryotic cell is not dividing, its DNA is wound around proteins called histones to form long thread-like material called chromatin. When the cell prepares to divide, the chromatin condenses into short, compact structures - the chromosomes. After replication, a chromosome consists of two identical copies called sister chromatids, joined at a point called the centromere; the chromatids separate during cell division.

The ends of each linear chromosome are capped by telomeres, protective sequences that prevent genetic information from being lost during copying. Telomeres shorten with every division, which is why a typical human cell can divide only about 50-70 times.

Human cells contain 46 chromosomes, arranged as 23 homologous pairs (a dog has 78 chromosomes in 39 pairs). One pair, the sex chromosomes, determines sex: males have the XY pair and females the XX pair. The other 22 pairs are called autosomes and determine most other characteristics. The two members of a homologous pair carry alleles of the same genes at the same positions - one chromosome inherited from each parent. A photograph of the complete, stained set of chromosomes is called a karyotype. The Human Genome Project went further and localised individual genes to specific chromosomes.

DNA IN PROKARYOTES AND EUKARYOTES

• Eukaryotes (cells about 10-100 μm) - multiple long linear chromosomes, wound around histones, held inside the nucleus; small circular DNA molecules also occur in mitochondria and chloroplasts.
• Prokaryotes (cells about 1-10 μm) - a single circular chromosome, generally not bound to histones, coiled into a region of the cytosol called the nucleoid region; many also carry small extra loops of DNA called plasmids.

Circular DNA has several advantages: it is more energy-efficient to maintain, it contains few repeated sequences and no introns (so less processing is needed to make proteins), and it needs no telomeres - which is one reason prokaryotic cells can divide indefinitely.

SEMI-CONSERVATIVE REPLICATION

In addition to storing information for protein synthesis, DNA can replicate. Replication must occur before a cell can divide, and cell division is required for growth, repair and reproduction. The three essential stages are:

1. Enzymes unwind the double helix and separate the two strands, exposing the bases. Each strand now acts as a template for a new strand.
2. Free nucleotides in the nucleus bind to their complementary bases on each template strand (specific base-pairing), and an enzyme joins them into a growing new strand.
3. The two new double helices twist up again. Each molecule contains one original strand and one newly made strand - which is why the process is called semi-conservative replication.

The enzymes involved, in order of action, are:

1. Helicase - unwinds the helix and breaks the weak hydrogen bonds, exposing the two template strands.
2. DNA primase - lays down a short single-stranded RNA primer at the $3'$ end of the template, marking where replication begins.
3. DNA polymerase - adds free complementary nucleotides (each a complete nucleotide: sugar, phosphate and base), always building in the $5'\to3'$ direction.
4. DNA ligase - seals the sugar-phosphate backbone of the new strand.

Because DNA polymerase can only build in the $5'\to3'$ direction, the two new strands are made differently:

• Leading strand - synthesised continuously, following the replication fork.
• Lagging strand - synthesised in short fragments, each started with its own primer; DNA ligase later joins the fragments into one continuous strand.

The replication fork. Each old strand (solid) templates a new strand (dashed); the leading strand grows continuously while the lagging strand is built in primer-started fragments.

In summary: one parent DNA molecule → two identical DNA molecules, each containing one original strand and one new strand.

Because base pairing is strictly complementary, the base sequence is conserved: each daughter molecule is identical to the original. In eukaryotes, replication takes place in the nucleus; in prokaryotes, in the nucleoid region of the cytoplasm.