Transcription, Translation And Gene Regulation

TRANSCRIPTION The first step taken by the cell to make a protein is to copy, or transcribe, the nucleotide sequence in one strand of the gene into a complementary single-stranded molecule called ribonucleic acid (RNA). Like DNA, RNA is composed of nucleotides, but these nucleotides contain the sugar ribose instead of deoxyribose. Furthermore, in place of thymine, RNA contains uracil (U), which like thymine, pairs with adenine. Hence the RNA bases are A, G, C, and U. The transcription process, which occurs in the cell nucleus, is very similar to the process for replication of DNA because the DNA strand serves as the template for making the RNA copy, which is called a transcript. The RNA transcript, which in many species undergoes some structural modifications, becomes a “working copy” of the in-formation in the gene, a kind of “message” molecule called messenger RNA (mRNA). The mRNA then enters the cytoplasm, where it is used by the cellular machinery to direct the manufacture of a protein. Fig-ure 1-6 summarizes the process of transcription.

TRANSLATION The process of producing a chain of amino acids based on the sequence of nucleotides in the mRNA is called translation. The nucleotide sequence of an mRNA molecule is “read” from one end of the mRNA to the other, in groups of three successive bases. These groups of three are called codons.

          AUU       CCG      UAC       GUA       AAU       UUG

         codon      codon     codon     codon     codon     codon

Because there are four different nucleotides, there are 4 x 4 x 4 = 64 different codons possible, each one coding for an amino acid or a signal to terminate translation. Because only 20 kinds of amino acids are used in the polypeptides that make up proteins, more than one codon may correspond to the same amino acid. For instance, AUU, AUC, and AUA all encode isoleucine, while UUU and UUC code for phenylalanine, and UAG is a translation termination (“stop”) codon.

Protein synthesis takes place on cytoplasmic organelles called ribosomes. A ribosome attaches to one end of an mRNA molecule and moves along the mRNA, catalyzing the assembly of the string of amino acids that will constitute the primary polypeptide chain of the protein. Each kind of amino acid is brought to the assembly process by a small RNA molecule called transfer RNA (tRNA), which is complementary to the mRNA codon that is being read by the ribosome at that point in the assembly.

Trains of ribosomes pass along an mRNA molecule, each member of a train making the same type of polypeptide. At the end of the mRNA, a termination codon causes the ribosome to detach and recycle to another mRNA. The process of translation is shown in Figure 1-7.

GENE REGULATION Let’s take a closer look at the structure of a gene, which determines the final form of the RNA “working copy” as well as the timing of transcription in a particular tissue. Figure 1-8 shows the general structure of a gene. At one end, there is a regulatory region to which various proteins involved in the regulation of the gene’s transcription bind, causing the gene to be transcribed at the right time and in the right amount. A region at the other end of the gene signals the end point of the gene’s transcription. Between these two end regions lies the DNA sequence that will be transcribed to specify the amino acid sequence of a polypeptide.

Gene structure is more complex in eukaryotes than in prokaryotes. Eukaryotes, which include all the multicellular plants and animals, are those organisms whose cells have a membrane-bound nucleus. Prokaryotes are organisms with a simpler cellular structure lacking a nucleus, such as bacteria. In the genes of many eukaryotes, the protein-encoding sequence is interrupted by one or more stretches of DNA called introns. The origin and functions of introns are still unclear. They are excised from the primary transcript during the formation of mRNA. The segments of coding sequence between the introns are called exons.

Some protein-encoding genes are transcribed more or less constantly; these are the “housekeeping” genes that are always needed for basic reactions. Other genes may be rendered unreadable or readable to suit the functions of the organism at particular times and under particular external conditions. The signal that masks or unmasks a gene may come from outside the cell, for example, from a steroid hormone or a nutrient. Alternatively, the signal may come from within the cell as the result of the reading of other genes. In either case, special regulatory sequences in the DNA are directly affected by the signal, and they in turn affect the transcription of the protein-encoding gene. The regulatory substances that serve as signals bind to the regulatory region of the target gene to control the synthesis of transcripts.

Figure 1-9 illustrates the essentials of gene action in a generalized eukaryotic cell. Outside the nucleus of the cell is a complex array of membranous structures, including the endoplasmic reticulum and Golgi apparatus, and organelles such as mitochondria and chloroplasts. The nucleus contains most of the DNA, but note that mitochondria and chloroplasts also contain small chromosomes.

Each gene encodes a separate protein, each with specific functions either within the cell (for example, the purple-rectangle proteins in Figure 1-9) or for export to other parts of the organism (the purple circle proteins). The synthesis of proteins for export (secretory proteins) takes place on ribosomes that are located on the surface of the rough endoplasmic reticulum, a system of large, flattened membrane vesicles. The completed amino acid chains are passed into the lumen of the endoplasmic reticulum, where they fold up spontaneously to take on their three-dimensional structure. The proteins may be modified at this stage, but they eventually enter the chambers of the Golgi apparatus and from there, the secretory vessels, which eventually fuse with the cell membrane and release their contents to the outside.

Proteins destined to function in the cytoplasm and most of the proteins that function in mitochondria and chloroplasts are synthesized in the cytoplasm on ribosomes not bound to membranes. For example, proteins that function as enzymes in the glycolysis pathway follow this route. The proteins destined for organelles are specially tagged to target their insertion into specific organelles. In addition, mitochondria and chloroplasts have their own small circular DNA molecules. The synthesis of proteins encoded by genes on mitochondrial or chloroplast DNA takes place on ribosomes inside the organelles themselves. Therefore the proteins in mitochondria and chloroplasts are of two different origins: either encoded in the nucleus and imported into the organelle or encoded in the organelle and synthesized within the organelle compartment.

Figure 1-9 Simplified view of gene action in a eukaryotic cell.

The basic flow of genetic information is from DNA to RNA to protein. Four types of genes are shown. Gene 1 responds to external regulatory signals and makes a protein for export; gene 2 responds to internal signals and makes a protein for use in the cytoplasm; gene 3 makes a protein to be transported into an organelle; gene 4 is part of the organelle DNA and makes a protein for use inside its own organelle. Most eukaryotic genes contain introns, regions (generally noncoding) that are cut out in the preparation of functional messenger RNA. Note that many organelle genes have introns and that an RNA-synthesizing enzyme is needed for organelle mRNA synthesis. These details have been omitted from the diagram of the organelle for clarity. (Introns will be explained in detail in subsequent chapters.)