Chapter 27: Genomics

• Genomics is the study of whole sets of genes and their functions.

• A genetic map shows the physical location of markers, identifiable DNA sequences (some within genes, some within noncoding DNA) that are known to be inherited. In the human genome, the markers were an average of 1 million nucleotides apart.

  • This is known as a genetic map because the order and locations of the markers are established by genetic studies of inheritance in related individuals.

• With the exception of large areas of repetitive DNA, the DNA base sequences of all chromosomes have been examined. The HGP utilized a series of progressively more detailed maps to create a collection of DNA fragments with known location.

• Celera began by randomly fragmenting all of the DNA without first placing it within the framework of a map. ^^In both groups the fragments were cloned, labelled, ordered, and the individual sequences assembled by computers^^.

• The results of the two projects are generally supportive of each other. There are about 3 billion base pairs and about 19,000 genes in the human genome. The bulk of the genome consists of noncoding, repetitive sequences. About 200 of the human genes are identical to those in bacteria.

• Telomeres are the ends of chromosomes; in humans, telomeres contain long series of repeating groups of nucleotides.

• As the DNA in each chromosome is duplicated in preparation for cell division, the two copies remain joined together at a constricted point in the middle of the chromosome; this is the centromere. The duplicated chromosomes bound together at the centromere are known as sister chromatids.

• Telomerase is the enzyme responsible for adding telomeres to DNA. It is active during embryonic development. In adults, telomerase is only active in the germ cells destined to become egg and sperm. Under normal, healthy conditions, ^^telomerase is not active in other adult cells (the somatic cells).^^

• In addition to the noncoding telomeres, centromeres, and introns along a chromosome, there are noncoding promoter sequences, which are regulatory regions of DNA that determine which of its genes are turned on.

• All of your cells (except red blood cells) contain all of your genes, but only the genes needed by any individual cell will be activated in that cell.

• An error in base sequence that is carried along during DNA replication is called a mutation. Mutation commonly refers to variations in DNA sequence found in a very small number of individuals of a species.

  • Some mutations result from spontaneous and random events. Others are induced by exposure to a mutagen—an external agent that can cause a mutation. Viruses, chemicals, and ionizing radiation can all be mutagenic.
  • The biological effects of incorporating an incorrect amino acid into a protein range from negligible to catastrophic, depending on both the nature and location of the change.

• Mutations, or sometimes the combination of several mutations, can also produce vulnerability to certain diseases, which may or may not develop in an individual.

• Polymorphisms are also variations in the nucleotide sequence of DNA within a given population. Most polymorphisms are simply differences in the DNA sequence between individuals due to geographical and ethnic differences and are part of the biodiversity exhibited by life on earth.

  • While the vast majority of polymorphisms recorded have neither advantageous nor deleterious effects, some do and have been shown to give rise to various disease states.

• Recombinant DNA is the DNA that contains two or more DNA segments not found together in nature.

• Using recombinant DNA technology, it is possible to cut a gene out of one organism and splice it into (recombine it with) the DNA of a second organism.

  • Bacteria provide excellent hosts for recombinant DNA. Bacterial cells, unlike the cells of higher organisms, contain part of their DNA in small circular pieces called plasmids, each of which carries just a few genes.

• Plasmids are extremely easy to isolate, several copies of each plasmid may be present in a cell, and each plasmid replicates through the normal basepairing pathway.

• The ease of isolating and manipulating plasmids plus the rapid replication of bacteria create ideal conditions for production of recombinant DNA and the proteins whose synthesis it directs in bacteria.

• To prepare a plasmid for insertion of a foreign gene, the plasmid is cut open with a bacterial enzyme, known as a restriction endonuclease or restriction enzyme, that recognizes a specific sequence in a DNA molecule and cleaves between the same two nucleotides in that sequence.

  • This restriction enzyme makes its cut at the same spot in the sequence of both strands of the double-stranded DNA when read in the same 5′ to 3′ direction.
  • As a result, the cut is offset so that both DNA strands are left with a few unpaired bases on each end. These groups of unpaired bases are known as sticky ends because they are available to match up with complementary base sequences.

• Mapping the human genome holds major promise for applications in health and medicine. Drugs can be precisely chosen based on a patient’s own DNA, thereby avoiding drugs that are ineffective or toxic for that individual.

  • Perhaps one day inherited diseases will be prevented or cured by gene therapy. By genetic modification of crop plants and farm animals, the productivity, marketability, and health benefits of these products can be enhanced.

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