DNA and the Central Dogma of Human Genetics
The regulation of cellular growth and function in all human tissue is dependent on the activities of specific protein molecules. In turn, protein activity is dependent on the expression of the genes that contain the correct DNA sequence for protein synthesis. The DNA molecule is a double-stranded helix. Each strand is composed of a sequence of four nucleotide bases—adenine (A), guanine (G), cytosine (C), and thymine (T)—joined to a sugar and a phosphate. The order of the bases in the DNA sequence forms the genetic code that directs the expression of genes. The double-stranded helix is formed as a result of hydrogen bonding between the nucleotide bases of opposite strands. The bonding is specific, such that A always pairs with T, and G always pairs with C. The specificity of the hydrogen bonding is the molecular basis of the accurate copying of the DNA sequence that is required during the processes of DNA replication (necessary for cell division) and transcription of DNA into RNA (necessary for gene expression and protein synthesis; Fig. 1.1.1 ).
Gene expression begins with the recognition of a particular DNA sequence called the promoter sequence as the start site for RNA synthesis by the enzyme RNA polymerase. The RNA polymerase “reads” the DNA sequence and assembles a strand of RNA that is complementary to the DNA sequence. RNA is a single-stranded nucleic acid composed of the same nucleotide bases as DNA, except that uracil takes the place of thymine. Human genes (and genes found in other eukaryotic organisms) contain many DNA sequences that are not translated into polypeptides and proteins. These sequences are called intervening sequences or introns. Introns do not have any known specific function, and although they are transcribed into RNA by RNA polymerase, they are spliced out of the initial RNA product (termed heteronuclear RNA, or hnRNA) to form the completed messenger RNA (mRNA). Untranslated RNA may have specific functions. For example, antisense RNA and micro RNAs (miRNA) appear to regulate expression of genes. The mRNA is the template for protein synthesis. Proteins consist of one or more polypeptide chains, which are sequences of specific amino acids. The sequence of bases in the mRNA directs the order of amino acids that make up the polypeptide chain. Individual amino acids are encoded by units of three mRNA bases, termed codons. Transfer RNA (tRNA) molecules bind specific amino acids and recognize the corresponding three-base codon in the mRNA. Cellular organelles called ribosomes bind the mRNA in such a configuration that the RNA sequence is accessible to tRNA molecules and the amino acids are aligned to form the polypeptide. The polypeptide chain may be processed by a number of other chemical reactions to form the mature protein ( Fig. 1.1.2 ).
Human Genome
Human DNA is packaged as chromosomes located in the nuclei of cells. Chromosomes are composed of individual strands of DNA wound about proteins called histones. The complex winding and coiling process culminates in the formation of a chromosome. The entire collection of human chromosomes includes 22 paired autosomes and two sex chromosomes. Women have two copies of the X chromosome, and men have one X and one Y chromosome ( Fig. 1.1.3 ).
The set consisting of one of each autosome as well as both sex chromosomes is called the human genome. The chromosomal molecules of DNA from one human genome, if arranged in tandem end to end, contain approximately 3.2 billion base pairs (bp). The Human Genome Project was formally begun in 1990 with the defined goals to: identify all the approximately 20,000–25,000 genes in human DNA; determine the sequences of the 3 billion chemical base pairs that make up human DNA; store this information in publicly available databases; improve tools for data analysis; transfer related technologies to the private sector; and address the ethical, legal, and social issues that may arise from the project. One of the most important goals, the complete sequence of the human genome, was completed in draft form in 2001. Catalogs of variation in the human genome sequence have also been completed, with the microsatellite repeat map in 1994, the release of the HapMap from the International HapMap Consortium in 2004, and more recently a catalog of variants from the 1000 genomes project. dbSNP ( https://www-ncbi-nlm-nih-gov.easyaccess1.lib.cuhk.edu.hk/projects/SNP/ ) is a database listing single nucleotide polymorphisms (SNPs) that are single-letter variations in a DNA base sequence. SNPs are bound together to form haplotypes, which are blocks of SNPs that are commonly inherited together. This binding occurs through the phenomenon of linkage disequilibrium. Within a haplotype block, which may extend for 10,000–100,000 bases of DNA, the analysis of only a subset of all SNPs may “tag” the entire haplotype. The International HapMap project has performed an initial characterization of the linkage disequilibrium patterns between SNPs in multiple different populations. The SNP haplotype blocks identified can be examined for association with human disease, especially common disorders with complex inheritance. Knowledge about the effects of DNA variations among individuals can lead to new ways to diagnose, treat, and prevent human disease. This approach has been used successfully to identify the risk loci for age-related macular degeneration, myopia, primary open-angle glaucoma, and Fuchs’ endothelial dystrophy.
Mitosis and Meiosis
In order for cells to divide, the entire DNA sequence must be copied so that each daughter cell can receive a complete complement of DNA. The growth phase of the cell cycle terminates with the separation of the two sister chromatids of each chromosome, and the cell divides during mitosis. Before cell division, the complete DNA sequence is copied by the enzyme DNA polymerase in a process called DNA replication. DNA polymerase is an enzyme capable of the synthesis of new strands of DNA using the exact sequence of the original DNA as a template. Once the DNA is copied, the old and new copies of the chromosomes form their respective pairs, and the cell divides such that one copy of each chromosome pair belongs to each cell ( Fig. 1.1.4 ). Mitotic cell division produces a daughter cell that is an exact replica of the dividing cell.
Meiotic cell division is a special type of cell division that results in a reduction of the genetic material in the daughter cells, which become the reproductive cells—eggs (women) and sperm (men). Meiosis begins with DNA replication, followed by a pairing of the maternal and paternal chromosomes (homologous pairing) and an exchange of genetic material between chromosomes by recombination ( Fig. 1.1.5 ). The homologous chromosome pairs line up on the microtubule spindle and divide such that the maternal and paternal copies of the doubled chromosomes are distributed to separate daughter cells. A second cell division occurs, and the doubled chromosomes divide, which results in daughter cells that have half the genetic material of somatic (tissue) cells.
Mitosis and Meiosis
In order for cells to divide, the entire DNA sequence must be copied so that each daughter cell can receive a complete complement of DNA. The growth phase of the cell cycle terminates with the separation of the two sister chromatids of each chromosome, and the cell divides during mitosis. Before cell division, the complete DNA sequence is copied by the enzyme DNA polymerase in a process called DNA replication. DNA polymerase is an enzyme capable of the synthesis of new strands of DNA using the exact sequence of the original DNA as a template. Once the DNA is copied, the old and new copies of the chromosomes form their respective pairs, and the cell divides such that one copy of each chromosome pair belongs to each cell ( Fig. 1.1.4 ). Mitotic cell division produces a daughter cell that is an exact replica of the dividing cell.
Meiotic cell division is a special type of cell division that results in a reduction of the genetic material in the daughter cells, which become the reproductive cells—eggs (women) and sperm (men). Meiosis begins with DNA replication, followed by a pairing of the maternal and paternal chromosomes (homologous pairing) and an exchange of genetic material between chromosomes by recombination ( Fig. 1.1.5 ). The homologous chromosome pairs line up on the microtubule spindle and divide such that the maternal and paternal copies of the doubled chromosomes are distributed to separate daughter cells. A second cell division occurs, and the doubled chromosomes divide, which results in daughter cells that have half the genetic material of somatic (tissue) cells.
Basic Mendelian Principles
Two important rules central to human genetics emerged from the work of Gregor Mendel, a nineteenth century Austrian monk. The first is the principle of segregation, which states that genes exist in pairs and that only one member of each pair is transmitted to the offspring of a mating couple. The principle of segregation describes the behavior of chromosomes in meiosis. Mendel’s second rule is the law of independent assortment, which states that genes at different loci are transmitted independently. This work also demonstrated the concepts of dominant and recessive traits. Mendel found that certain traits were dominant and could mask the presence of a recessive gene.
At the same time that Mendel observed that most traits segregate independently, according to the law of independent assortment, he unexpectedly found that some traits frequently segregate together. The physical arrangement of genes in a linear array along a chromosome is the explanation for this surprising observation. On average, a recombination event occurs once or twice between two paired homologous chromosomes during meiosis ( Fig. 1.1.6 ). Most observable traits, by chance, are located far away from one another on a chromosome, such that recombination is likely to occur between them, or they are located on entirely different chromosomes. If two traits are on separate chromosomes, or a recombination event is likely to occur between them on the same chromosome, the resultant gamete formed during meiosis has a 50% chance of inheriting different alleles from each loci, and the two traits respect the law of independent assortment. If, however, the loci for these two traits are close together on a chromosome, with the result that a recombination event occurs between them only rarely, the alleles at each loci are passed to descendent gametes “in phase.” This means that the particular alleles present at each loci in the offspring reflect the orientation in the parent, and the traits appear to be “linked.” For example, in Mendel’s study of pea plants, curly leaves were always found with pink flowers, even though the genes for curly leaves and pink flowers are located at distinct loci. These traits are linked, because the curly leaf gene and the pink-flower gene are located close to each other on a chromosome, and a recombination event only rarely occurs between them. Recombination and linkage are the fundamental concepts behind genetic linkage analysis.
Mutations
Mutations are changes in the gene DNA sequence that result in a biologically significant change in the function of the encoded protein. If a particular gene is mutated, the protein product might not be produced, or it might be produced but function poorly or even pathologically (dominant negative effect). Point mutations (the substitution of a single base pair) are the most common mutations encountered in human genetics. Missense mutations are point mutations that cause a change in the amino acid sequence of the polypeptide chain. The severity of the missense mutation is dependent on the chemical properties of the switched amino acids and on the importance of a particular amino acid in the function of the mature protein. Point mutations also may decrease the level of polypeptide production because they interrupt the promoter sequence, splice site sequences, or create a premature stop codon.
Gene expression can be affected by the insertion or deletion of large blocks of DNA sequence. These types of mutations are less common than point mutations but may result in a more severe change in the activity of the protein product. A specific category of insertion mutations is the expansion of trinucleotide repeats found in patients affected by certain neurodegenerative disorders. An interesting clinical phenomenon, “anticipation,” was understood on a molecular level with the discovery of trinucleotide repeats as the cause of myotonic dystrophy. Frequently, offspring with myotonic dystrophy were affected more severely and at an earlier age than their affected parents and grandparents. Examination of the disease-causing trinucleotide repeat in affected pedigrees demonstrated that the severity of the disease correlated with the number of repeats found in the myotonic dystrophy gene in affected individuals. This phenomenon has been observed in a number of other diseases, including Huntington’s disease.
Chromosomal rearrangements may result in breaks in specific genes that cause an interruption in the DNA sequence. Usually, the break in DNA sequence results in a truncated, unstable, dysfunctional protein product. Occasionally, the broken gene fuses with another gene to cause a “fusion polypeptide product,” which may have a novel activity in the cell. Often, such a novel activity results in an abnormality in the function of the cell. An example of such a fusion protein is the product of the chromosome 9;22 translocation that is associated with many cases of leukemia ( Fig. 1.1.7 ).
A set consisting of one of each autosome as well as an X or a Y chromosome is called a haploid set of chromosomes. The normal complement of two copies of each gene (or two copies of each chromosome) is called diploidy. Rarely, as a result of abnormal chromosome separation during cell division, a cell or organism may have three copies of each chromosome, which is called triploidy. A triploid human is not viable, but some patients have an extra chromosome or an extra segment of a chromosome. In such a situation, the abnormality is called trisomy for the chromosome involved. For example, patients with Down syndrome have three copies of chromosome 21, also referred to as trisomy 21.
If one copy of a pair of chromosomes is absent, the defect is called haploidy. Deletions of the X chromosome are frequently the cause of Duchenne’s muscular dystrophy.
Polymorphisms are changes in DNA sequence that don’t have a significant biological effect. These DNA sequence variants may modify disease processes, but alone are not sufficient to cause disease. Human DNA sequence is highly variable and includes single nucleotide polymorphisms (SNPs), microsatellite repeat polymorphisms (20–50 bp repeats of CA or GT sequence), variable number of tandem repeat polymorphisms (VNTR, repeats of 50–100 bp of DNA), or larger insertion deletions.
Genes and Phenotypes
The relationship between genes and phenotypes is complex. More than one genetic defect can lead to the same clinical phenotype (genetic heterogeneity), and different phenotypes can result from the same genetic defect (variable expressivity). Retinitis pigmentosa is an excellent example of genetic heterogeneity, as it may be inherited as an X-linked, autosomal dominant, autosomal recessive, or digenic trait, and more than 200 causative genes have been identified. Other ocular disorders that are genetically heterogeneous include congenital cataract, glaucoma, and age-related macular degeneration. Different genes may contribute to a common phenotype because they affect different steps in a common pathway. Understanding the role of each gene in the disease process can help define the cellular mechanisms that are responsible for the disease.
For many genes, a single mutation that alters a critical site in the protein results in an abnormal phenotype. For some diseases, the resulting phenotypes are remarkably similar regardless of the nature of the mutation. For example, a wide variety of mutations in RB1 cause retinoblastoma. Other diseases, however, exhibit variable expressivity, in which an individual’s mutation may be responsible for severe disease, mild disease, or disease that is not clinically detectable (incomplete penetrance). There are many examples of ocular disease demonstrating variable expressivity, including Kjer’s autosomal dominant optic atrophy, Axenfeld–Rieger syndrome, and aniridia.
Different mutations in the same gene can also result in different phenotypes (allelic heterogeneity). Allelic heterogeneity accounts for the different phenotypes of dominant corneal stromal dystrophies caused by mutations in the TGFB1/BIGH3. The phenotypic expression of a mutation may depend on its location within a gene. Such variable expressivity based on the location of the mutation is exemplified by mutations in the rds gene, which may cause typical autosomal dominant retinitis pigmentosa or macular dystrophy depending on the position of the genetic defect.
Patterns of Human Inheritance
The most common patterns of human inheritance are autosomal dominant, autosomal recessive, X-linked recessive, and mitochondrial. Fig. 1.1.8 shows examples of these four inheritance patterns. Other inheritance patterns less commonly encountered in human disease include X-linked dominant, digenic inheritance (polygenic), pseudodominance, and imprinting. Fig. 1.1.9 defines the notation and symbols used in pedigree construction.
Stay updated, free articles. Join our Telegram channel
Full access? Get Clinical Tree
