Concept 12.1   There Are Powerful Methods for Sequencing Genomes and Analyzing Gene Products

• To sequence a genome, the chromosomes are cut into overlapping fragments, which are sequenced. Then the fragment sequences are lined up to assemble the DNA sequence of the chromosome. See ANIMATED TUTORIAL 12.1
• High-throughput sequencing involves attaching short, single-stranded DNA fragments to a solid surface. A primer and DNA polymerase are added, and tagged nucleotides are detected by a camera as they are added to the complementary DNA strand. Many sequences can be done in parallel. Review Figure 12.1 and ANIMATED TUTORIAL 12.2
• The analysis of DNA sequences is done by computer. Genomic sequences include protein-coding genes, RNA genes, regulatory sequences, and repeated sequences. Review Figure 12.3
• The proteome is the total protein content of an organism. It can be analyzed using chemical methods that separate and identify proteins. These include two-dimensional electrophoresis, mass spectrometry, and techniques involving antibodies. Review Figure 12.4
• The metabolome is the total content of small molecules in a tissue under particular conditions. These molecules include intermediates in metabolism, hormones and other signaling molecules, and secondary metabolites. Review Figure 12.5

Concept 12.2   Prokaryotic Genomes Are Small, Compact, and Diverse

• Prokaryotic genomes have been studied using functional genomics to determine the roles of various parts of the genome, including the protein-coding genes. Comparative genomics is used to compare sequences among organisms. Review Table 12.1
• Metagenomics is the identification of DNA sequences in environmental samples without first isolating, growing, and identifying the organisms. Review Figure 12.6
• Transposons are sequences of DNA that can move about the genome. Review Figure 12.7
• Transposon mutagenesis can be used to inactivate genes one by one. Then the organism can be tested for survival. In this way, functionally important genes can be identified. Review Figure 12.8

Concept 12.3   Eukaryotic Genomes Are Large and Complex

• Sequences from model organisms have highlighted some common features of eukaryotic genomes. In addition, there are specialized genes such as those for cellular compartmentalization, development, and features unique to plants. Review Figure 12.9, Figure 12.10 and Table 12.2
• Some genes exist as members of gene families. Proteins may be made from these closely related genes at different times and in different tissues. Review Figure 12.11
• Eukaryotic genomes contain various kinds of repeated sequences. Review Table 12.3

Concept 12.4   The Human Genome Sequence Has Many Applications

• The haploid human genome has 3.2 billion bp.
• Only 1.5 percent of the genome codes for proteins; much of the rest consists of repeated sequences.
• Most of the genome is transcribed at some point in some cells.
• Virtually all human genes have introns, and alternative splicing leads to the production of more than one protein per gene.
• Genotyping using single nucleotide polymorphisms (SNPs) can be used to correlate variations in the genome with diseases or drug sensitivity. It may lead to personalized medicine. Review Figure 12.13
• Pharmacogenomics is the analysis of how a person’s genetic makeup affects his or her drug metabolism. Review Figure 12.14
• Short tandem repeats (STRs) are DNA sequences that are variable in length. They can be used to identify individuals. Review Figure 12.15

See ACTIVITY 12.1 for a concept review of this chapter.