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Figure 4.2. The Four bases found in DNA.

2'-deoxyguanosine-5'-triphosphate (dGTP), 2'-deoxycytidine-5'-triphosphate (dCTP), and 2'-deoxythymidine-5'-triphosphate (dTTP).

DNA molecules are very large. The single chromosome of the bacterium Escherichia coli is made up of two strands of DNA that are hydrogen-bonded together to form a single circular molecule comprising 9 million nucleotides. Humans have 46 DNA molecules in each cell, each forming one chromosome. We inherit 23 chromosomes from each parent. Each set of 23 chromosomes encodes a complete copy of our genome and is made up of 6 x 109 nucleotides (or 3 x 109 base pairs—see below). We do not yet know the exact number of genes that encode messenger RNA and therefore proteins in the human genome. The current estimate is in the range of 30,000. Table 4.1 compares the number of predicted messenger RNA genes in the genomes of different organisms. In each organism, there are also approximately 100 genes that code for ribosomal RNAs and transfer RNAs. The role these three types of RNA play in protein synthesis is described in Chapter 8.

Figure 4.3 illustrates the structure of the DNA chain. As nucleotides are added to the chain by the enzyme DNA polymerase (Chapter 5), they lose two phosphate groups. The last (the a phosphate) remains and forms a phosphodiester link between successive deoxyribose residues. The bond forms between the hydroxyl group on the 3' carbon of the deoxyribose of one nucleotide and the a-phosphate group attached to the 5' carbon of the next nucleotide. Adjacent nucleotides are hence joined by a 3'-5' phosphodiester link. The linkage gives rise

Table 4.1. Numbers of Predicted Genes in Various Organisms

Organism

Number of Predicted Genes

Bacterium—Haemophilus influenzae

1,709

Yeast—Saccharomyces cerevisiae

6,241

Fruit fly—Drosophila melannogaster

13,601

Worm—Caenorhabdites elegans

18,424

Plant—Arabidopsis thaliana

25,498

Human—Homo sapiens

-30,000

to the sugar-phosphate backbone of a DNA molecule. A DNA chain has polarity because its two ends are different. In the first nucleotide in the chain, the 5' carbon of the deoxyribose is phosphorylated but otherwise free. This is called the 5' end of the DNA chain. At the other end is a deoxyribose with a free hydroxyl group on its 3' carbon. This is called the 3' end.

The DNA Molecule Is a Double Helix

In 1953 Rosalind Franklin used X-ray diffraction to show that DNA was a helical (i.e., twisted) polymer. James Watson and Francis Crick demonstrated, by building three-dimensional models, that the molecule is a double helix (Fig. 4.4). Two hydrophilic

IN DEPTH 4.1 Gene Number and Complexity

As the genomes of more and more organisms were sequenced, the most surprising feature to emerge was just how few genes supposedly "complex" organisms possess. The first eukaryotic genome to be sequenced was that of the lowly budding yeast, Saccharomyces cerevisiae, the simple unicellular fungus that we use to make bread and beer. S. cerevisiae has about 6000 genes. The fruit fly, Drosophila melanogaster, a much more complex organism with a brain, nervous and digestive systems, and the ability to fly and navigate, on the other hand, has 13,600 genes, or roughly twice the number in a yeast. Even more surprising was the case of the human genome. Prior to the completion of the Human Genome Project predictions of the number of human genes were in the order of 100,000. Surely this complex vertebrate that could send a spaceship to Mars and write War and Peace would need vastly more genes than the fruit fly. In the event, the number of human genes turned out to be much lower than expected, about 30,000, only twice as many genes as in Drosophila.

If complex biological and social achievements are not the result of having more genes, where do they come from? Two factors help the human genome generate a more complex organism. First, having more DNA per gene means that more DNA can be used in enhancer sequences (page 120), allowing more subtle control of where, when, and to what extent a gene is expressed. Second, there is not a straightforward one-to-one relationship between genes and proteins. Alternative splicing (page 118) allows the cell to "cut and paste" a messenger RNA molecule in different ways to produce many different proteins from the same gene. Estimates are that something like 50% of human genes show alternative splicing with the pattern of splicing (the range of proteins produced) varying from tissue to tissue. Drosophila genes also show alternative splicing but those of yeast, which contain few introns (page 98), do not.

5' end base

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phosphodiester link -

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