From our discussion thus far, it is clear that the genes control both the physical and chemical functions of the cells. However, the degree of activation of respective genes must also be controlled; otherwise, some parts of the cell might overgrow or some chemical reactions might overact until they kill the cell. Each cell has powerful internal feedback control mechanisms that keep the various functional operations of the cell in step with one another. For each gene (approximately 30,000 genes in all), at least one such feedback mechanism exists.

There are basically two methods by which the bio chemical activities in the cell are controlled: (1) genetic regulation, in which the degree of activation of the genes and the formation of gene products are themselves controlled, and (2) enzyme regulation, in which the activity levels of already formed enzymes in the cell are controlled.

Genetic Regulation

 Genetic regulation, or regulation of gene expression, covers the entire process from transcription of the genetic code in the nucleus to the formation of proteins in the cytoplasm. Regulation of gene expression provides all living organisms with the ability to respond to changes in their environment. In animals that have many different types of cells, tissues, and organs, differential regulation of gene expression also permits the many different cell types in the body to each perform their specialized functions. Although a cardiac myocyte contains the same genetic code as a renal tubular epithelia cell, many genes are expressed in cardiac cells that are not expressed in renal tubular cells. The ultimate measure of gene “expression” is whether (and how much) of the gene products (proteins) are produced because proteins carry out cell functions specified by the genes. Regulation of gene expression can occur at any point in the pathways of transcription, RNA processing, and translation.

The Promoter Controls Gene Expression. Synthesis of cellular proteins is a complex process that starts with the transcription of DNA into RNA. The transcription of DNA is controlled by regulatory elements found in the promoter of a gene (Figure 1). In eukaryotes, which includes all mammals, the basal promoter consists of a sequence of seven bases (TATAAAA) called the TATA box, the binding site for the TATA-binding protein and several other important transcription factors that are collectively referred to as the transcription factor IID complex. In addition to the transcription factor IID complex, this region is where transcription factor IIB binds to both the DNA and RNA polymerase 2 to facilitate transcription of the DNA into RNA. This basal promoter is found in all protein-coding genes, and the polymerase must bind with this basal promoter before it can begin traveling along the DNA strand to synthesize RNA. The upstream promoter is located farther upstream from the transcription start site and contains several binding sites for positive or negative transcription factors that can affect transcription through interactions with proteins bound to the basal promoter. The structure and transcription factor binding sites in the upstream promoter vary from gene to gene to give rise to the different expression patterns of genes in different tissues.

Fig1. Gene transcription in eukaryotic cells. A complex  arrangement of multiple clustered enhancer modules is interspersed  with insulator elements, which can be located either upstream or  downstream of a basal promoter containing TATA box (TATA), proximal promoter elements (response elements, RE), and initiator  sequences (INR).

Transcription of genes in eukaryotes is also influenced by enhancers, which are regions of DNA that can bind transcription factors. Enhancers can be located a great distance from the gene they act on or even on a different chromosome. They can also be located either upstream or downstream of the gene that they regulate. Although enhancers may be located far away from their target gene, they may be relatively close when DNA is coiled in the nucleus. It is estimated that there are 110,000 gene enhancer sequences in the human genome.

In the organization of the chromosome, it is important to separate active genes that are being transcribed from genes that are repressed. This separation can be challenging because multiple genes may be located close together on the chromosome. This separation is achieved by chromosomal insulators. These insulators are gene sequences that provide a barrier so that a specific gene is isolated against transcriptional influences from surrounding genes. Insulators can vary greatly in their DNA sequence and the proteins that bind to them. One way an insulator activity can be modulated is by DNA methylation, which is the case for the mammalian insulin-like growth factor 2 (IGF-2) gene. The mother’s allele has an insulator between the enhancer and promoter of the gene that allows for the binding of a transcriptional repressor. However, the paternal DNA sequence is methylated such that the transcriptional repressor cannot bind to the insulator and the IGF-2 gene is expressed from the paternal copy of the gene.

Other Mechanisms for Control of Transcription by the Promoter. Variations in the basic mechanism for control of the promoter have been rapidly discovered in the past 2 decades. Without giving details, let us list some of them:

1. A promoter is frequently controlled by transcription factors located elsewhere in the genome. That is, the regulatory gene causes the formation of a regulatory protein that in turn acts either as an activator or a repressor of transcription.

 2. Occasionally, many different promoters are controlled at the same time by the same regulatory protein. In some instances, the same regulatory protein functions as an activator for one promoter and as a repressor for another promoter.

3. Some proteins are controlled not at the starting point of transcription on the DNA strand but farther along the strand. Sometimes the control is not even at the DNA strand itself but during the processing of the RNA molecules in the nucleus before they are released into the cytoplasm; control may also occur at the level of protein formation in the cytoplasm during RNA translation by the ribosomes.

 4. In nucleated cells, the nuclear DNA is packaged in specific structural units, the chromosomes. Within each chromosome, the DNA is wound around small proteins called histones, which in turn are held tightly together in a compacted state by still other proteins. As long as the DNA is in this compacted state, it cannot function to form RNA. However, multiple control mechanisms are being discovered that can cause selected areas of chromosomes to become decompacted one part at a time so that partial RNA transcription can occur. Even then, specific transcriptor factors control the actual rate of transcription by the promoter in the chromosome. Thus, still higher orders of control are used to establish proper cell function. In addition, signals from outside the cell, such as some of the body’s hormones, can activate specific chromosomal areas and specific transcription factors, thus controlling the chemical machinery for function of the cell.

Because there are more than 30,000 different genes in each human cell, the large number of ways in which genetic activity can be controlled is not surprising. The gene control systems are especially important for controlling intracellular concentrations of amino acids, amino acid derivatives, and intermediate substrates and products of carbohydrate, lipid, and protein metabolism.  

Control of Intracellular Function by Enzyme Regulation

 In addition to control of cell function by genetic regulation, cell activities are also controlled by intracellular inhibitors or activators that act directly on specific intra cellular enzymes. Thus, enzyme regulation represents a second category of mechanisms by which cellular bio chemical functions can be controlled. Enzyme Inhibition. Some chemical substances formed in the cell have direct feedback effects to inhibit the specific enzyme systems that synthesize them. Almost always the synthesized product acts on the first enzyme in a sequence, rather than on the subsequent enzymes, usually binding directly with the enzyme and causing an allosteric conformational change that inactivates it. One can readily recognize the importance of inactivating the first enzyme because this prevents buildup of intermediary products that are not used.

Enzyme inhibition is another example of negative feedback control; it is responsible for controlling intracellular concentrations of multiple amino acids, purines, pyrimidines, vitamins, and other substances.

Enzyme Activation. Enzymes that are normally inactive often can be activated when needed. An example of this phenomenon occurs when most of the ATP has been depleted in a cell. In this case, a considerable amount of cyclic adenosine monophosphate (cAMP) begins to be formed as a breakdown product of ATP; the presence of this cAMP, in turn, immediately activates the glycogen splitting enzyme phosphorylase, liberating glucose molecules that are rapidly metabolized, with their energy used for replenishment of the ATP stores. Thus, cAMP acts as an enzyme activator for the enzyme phosphorylase and thereby helps control intracellular ATP concentration.

Another interesting instance of both enzyme inhibition and enzyme activation occurs in the formation of the purines and pyrimidines. These substances are needed by the cell in approximately equal quantities for formation of DNA and RNA. When purines are formed, they inhibit the enzymes that are required for formation of additional purines. However, they activate the enzymes for formation of pyrimidines. Conversely, the pyrimidines inhibit their own enzymes but activate the purine enzymes. In this way, there is continual cross-feed between the synthesizing systems for these two substances, resulting in almost exactly equal amounts of the two substances in the cells at all times.

Summary. There are two principal mechanisms by which cells control proper proportions and quantities of different cellular constituents: (1) genetic regulation and (2) enzyme regulation. The genes can be either activated or inhibited, and likewise, the enzyme systems can be either activated or inhibited. These regulatory mechanisms most often function as feedback control systems that continually monitor the cell’s biochemical composition and make corrections as needed. However, on occasion, substances from without the cell (especially some of the hormones discussed throughout this text) also control the intracellular biochemical reactions by activating or inhibiting one or more of the intracellular control systems.