Overview: Gene Structure – Holland-Frei Cancer Medicine …

Genes and Gene Expression

The gene is the fundamental unit of inheritance and the ultimate determinant of all phenotypes. The DNA of a normal human cell contains an estimated 30,000 to 120,000 genes,4,5 but only a fraction of these are used (or expressed) in any particular cell at any given time. For example, genes specific for erythroid cells, such as the hemoglobin genes, are not expressed in brain cells. The identity of each gene expressed in a particular cell at a given time and its level of expression is defined as the transcriptome.

According to the central dogma of molecular biology, a gene exerts its effects by having its DNA transcribed into an mRNA, which is, in turn, translated into a protein, the final effector of the gene's action. Thus, molecular biologists often investigate gene expression or activation, by which is meant the process of transcribing DNA into RNA, or translating RNA into protein. The process of transcription involves creating a perfect RNA copy of the gene using the DNA of the gene as a template. Translation of mRNA into protein is a somewhat more complex process, because the structure of the gene's protein is encoded in the mRNA, and that structural message must be decoded during translation.

Every gene consists of several functional components, each involved in a different facet of the process of gene expression (). Broadly speaking, however, there are two main functional units: the promoter region and the coding region.

Gene expression. A gene's DNA is transcribed into mRNA which is, in turn, translated into protein. The functional components of a gene are schematically diagramed here. Areas of the gene destined to be represented in mature mRNA are called exons, and (more...)

The promoter region controls when and in what tissue a gene is expressed. For example, the promoters of the globin gene are responsible for their expression in erythroid cells and not in brain cells. How is this tissue-specific expression achieved? In the DNA of the gene's promoter region, there are specific structural elements, nucleotide sequences (see Structural Considerations below), that permit the gene to be expressed only in an appropriate cell. These are the elements in the globin gene that instruct an erythroid cell to transcribe globin mRNA from that gene. These structures are referred to as cis-acting elements because they reside on the same molecule of DNA as the gene. In some cases, other tissue type-specific cis-acting elements, called enhancers, reside on the same DNA molecule, but at great distances from the coding region of the gene.6,7 In the appropriate cell, the cis-acting elements bind protein factors that are physically responsible for transcribing the gene. These proteins are called trans-acting factors because they reside in the cell's nucleus, separate from the DNA molecule bearing the gene. For example, brain cells would not have the right trans-acting factors that bind to the -globin promoter, and therefore brain cells would not express globin. They would, however, have trans-acting factors that bind to neuron-specific gene promoters.

The structure of a gene's protein is specified by the gene's coding region. The coding region contains the information that directs an erythroid cell to assemble amino acids in the proper order to make the -globin protein. How is this order of amino acids specified? As described in detail below, DNA is a linear polymer consisting of four distinguishable subunits called nucleotides. In the coding region of a gene, the linear sequence of nucleotides encodes the amino acid sequence of the protein. This genetic code is in triplet form so that every group of three nucleotides encodes a single amino acid. The 64 triplets that can be formed by 4 nucleotides exceed the 20 distinct amino acids used to make proteins. This makes the code degenerate and allows some amino acids to be encoded by several different triplets.8 The nucleotide sequence of any gene can now be determined (see below). By translating the code, one can derive a predicted amino acid sequence for the protein encoded by a gene.

The basic repeating units of the DNA polymer are nucleotides (). Nucleotides consist of an invariant portion, a five-carbon deoxyribose sugar with a phosphate group, and a variable portion, the base. Of the four bases that appear in the nucleotides of DNA, two are purines, adenine (A) and guanine (G), and two are pyrimidines, cytosine (C) and thymine (T). Nucleotides are connected to each other in the polymer through their phosphate groups, leaving the bases free to interact with each other through hydrogen bonding. This base pairing is specific, so that A interacts with T, and C interacts with G. DNA is ordinarily double-stranded, that is, two linear polymers of DNA are aligned so that the bases of the two strands face each other. Base pairing makes this alignment specific so that one DNA strand is a perfectly complementary copy of the other. This complementarity means that each DNA strand carries the information needed to make an exact replica of itself.

Structure of base-paired, double-stranded DNA. Each strand of DNA consists of a backbone of 5-carbon deoxyribose sugars connected to each other through phosphate bonds. Note that as one follows the sequence down the left-hand strand (A to C to G to T), (more...)

In every strand of a DNA polymer, the phosphate substitutions alternate between the 5 and 3 carbons of the deoxyribose molecules. Thus, there is a directionality to DNA: the genetic code reads in the 5 to 3 direction. In double-stranded DNA, the strand that carries the translatable code in the 5 to 3 direction is called the sense strand, while its complementary partner is the antisense strand.

In eukaryotes, the coding regions of most genes are not continuous. Rather, they consist of areas that are transcribed into mRNA, the exons, which are interrupted by stretches of DNA that do not appear in mature mRNA, the introns (see ). The functions of introns are not known with certainty. A purpose of some sort is implied by their conservation in evolution. However, their overall physical structure might be more important than their specific nucleotide sequences, because the nucleotide sequences of introns diverge more rapidly in evolution than do the sequences of exons. Overall, DNA that contains genes comprises a minority of total DNA. Between genes, there are vast stretches of untranscribed DNA that are assumed to play an important structural role.

In the nucleus, DNA is not present as naked nucleic acid. Rather, DNA is found in close association with a number of accessory proteins, such as the histones, and in this form is called chromatin.9 Although many of DNA's accessory proteins have no known specific function, they generally appear to be involved in the correct packaging of DNA. For example, DNA's double helix is ordinarily twisted on itself to form a supercoiled structure.10 This structure must unwind partially during DNA replication and transcription.11 Some of the accessory proteins, for example, topoisomerases and histone acetylases, are involved in regulating this process.

Genes specify the structure of proteins that are responsible for the phenotype associated with a particular gene. While the nucleus of every human cell contains 30,000 to 120,000 genes, only a fraction of them are expressed in any given cell at any given time. The promoter (with or without an enhancer) is the part of the gene that determines when and where it will be expressed. The coding region is the part of the gene that dictates the amino acid sequence of the protein encoded by the gene. DNA is a linear polymer of nucleotides. Ordinarily, the nucleotide bases of one strand of DNA interact with those of another strand (A with T, C with G) to make double-stranded DNA. In the cell's nucleus, DNA is associated with accessory proteins to make the structure called chromatin.

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