bioquimicaIII b

bioquimicaIII b

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Control of Gene Expression

Concept Outline

16.1Gene expression is controlled by regulating transcription.

An Overview of Transcriptional Control.In bacteria transcription is regulated by controlling access of RNA polymerase to the promoter in a flexible and reversible way; eukaryotes by contrast regulate many of their genes by turning them on and off in a more permanent fashion.

16.2Regulatory proteins read DNA without unwinding it.

How to Read a Helix without Unwinding It. Regulatory proteins slide special segments called DNA- binding motifs along the major groove of the DNA helix, reading the sides of the bases.

Four Important DNA-Binding Motifs.DNA-binding proteins contain structural motifs such as the helix-turnhelix which fit into the major groove of the DNA helix.

16.3Bacteria limit transcription by blocking RNA polymerase.

Controlling Transcription Initiation. Repressor proteins inhibit RNA polymerase’s access to the promoter, while activators facilitate its binding.

16.4Transcriptional control in eukaryotes operates at a distance.

Designing a Complex Gene Control System. Eukaryotic genes use a complex collection of transcription factors and enhancers to aid the polymerase in transcription.

The Effect of Chromosome Structure on Gene Regulation.The tight packaging of eukaryotic DNA into nucleosomes does not interfere with gene expression.

Posttranscriptional Control in Eukaryotes.Gene expression can be controlled at a variety of levels after transcription.

In an orchestra, all of the instruments do not play all the time; if they did, all they would produce is noise. In- stead, a musical score determines which instruments in the orchestra play when. Similarly, all of the genes in an organism are not expressed at the same time, each gene producing the protein it encodes full tilt. Instead, different genes are expressed at different times, with a genetic score written in regulatory regions of the DNA determining which genes are active when (figure 16.1).

FIGURE 16.1 Chromosome puffs.In this chromosome of the fly Drosophila melanogaster,individual active genes can be visualized as “puffs” on the chromosomes. The RNA being transcribed from the DNA template has been radioactively labeled, and the dark specks indicate its position on the chromosome.

the maintenance of a constant internal environment—is considered by many to be the hallmark of multicellular organisms. Although cells in such organisms still respond to signals in their immediate environment (such as growth factors and hormones) by altering gene expression, in doing so they participate in regulating the body as a whole. In multicellular organisms with relatively constant internal environments, the primary function of gene control in a cell is not to respond to that cell’s immediate environment, but rather to participate in regulating the body as a whole.

Some of these changes in gene expression compensate for changes in the physiological condition of the body. Others mediate the decisions that producethe body, ensuring that the right genes are expressed in the right cells at the right time during development. The growth and development of multicellular organisms entail a long series of biochemical reactions, each catalyzed by a specific enzyme. Once a particular developmental change has occurred, these enzymes cease to be active, lest they disrupt the events that must follow. To produce these enzymes, genes are transcribed in a carefully prescribed order, each for a specified period of time. In fact, many genes are activated only once, producing irreversible effects. In many animals, for example, stem cellsdevelop into differentiated tissues like skin cells or red blood cells, following a fixed genetic program that often leads to programmed cell death. The one-time expression of the genes that guide this program is fundamentally different from the reversible metabolic adjustments bacterial cells make to the environment. In all multicellular organisms, changes in gene expression within particular cells serve the needs of the whole organism, rather than the survival of individual cells.

Posttranscriptional Control

Gene expression can be regulated at many levels. By far the most common form of regulation in both bacteria and eukaryotes is transcriptional control,that is, control of the transcription of particular genes by RNA polymerase. Other less common forms of control occur after transcription, influencing the mRNA that is produced from the genes or the activity of the proteins encoded by the mRNA. These controls, collectively referred to as posttranscriptional controls,will be discussed briefly later in this chapter.

Gene expression is controlled at the transcriptional and posttranscriptional levels. Transcriptional control, more common, is effected by the binding of proteins to regulatory sequences within the DNA.

314Part VMolecular Genetics

An Overview of Transcriptional Control

Control of gene expression is essential to all organisms. In bacteria, it allows the cell to take advantage of changing environmental conditions. In multicellular organisms, it is critical for directing development and maintaining homeostasis.

Regulating Promoter Access

One way to control transcription is to regulate the initiation of transcription. In order for a gene to be transcribed, RNA polymerase must have access to the DNA helix and must be capable of binding to the gene’s promoter,a specific sequence of nucleotides at one end of the gene that tells the polymerase where to begin transcribing. How is the initiation of transcription regulated? Protein-binding nucleotide sequences on the DNA regulate the initiation of transcription by modulating the ability of RNA polymerase to bind to the promoter. These protein-binding sites are usually only 10 to 15 nucleotides in length (even a large regulatory protein has a “footprint,” or binding area, of only about 20 nucleotides). Hundreds of these regulatory sequences have been characterized, and each provides a binding site for a specific protein able to recognize the sequence. Binding the protein to the regulatory sequence either blockstranscription by getting in the way of RNA polymerase, or stimulates transcription by facilitating the binding of RNA polymerase to the promoter.

Transcriptional Control in Prokaryotes

Control of gene expression is accomplished very differently in bacteria than in the cells of complex multicellular organisms. Bacterial cells have been shaped by evolution to grow and divide as rapidly as possible, enabling them to exploit transient resources. In bacteria, the primary function of gene control is to adjust the cell’s activities to its immediate environment. Changes in gene expression alter which enzymes are present in the cell in response to the quantity and type of available nutrients and the amount of oxygen present. Almost all of these changes are fully reversible, allowing the cell to adjust its enzyme levels up or down as the environment changes.

Transcriptional Control in Eukaryotes

The cells of multicellular organisms, on the other hand, have been shaped by evolution to be protected from transient changes in their immediate environment. Most of them experience fairly constant conditions. Indeed, homeostasis—

16.1Gene expression is controlled by regulating transcription.

How to Read a Helix without Unwinding It

It is the ability of certain proteins to bind to specificDNA regulatory sequences that provides the basic tool of gene regulation, the key ability that makes transcriptional control possible. To understand how cells control gene expression, it is first necessary to gain a clear picture of this molecular recognition process.

Looking into the Major Groove

Molecular biologists used to think that the DNA helix had to unwind before proteins could distinguish one DNA sequence from another; only in this way, they reasoned, could regulatory proteins gain access to the hydrogen bonds between base-pairs. We now know it is unnecessary for the helix to unwind because proteins can bind to its outside surface, where the edges of the base-pairs are exposed. Careful inspection of a DNA molecule reveals two helical grooves winding round the molecule, one deeper than the other. Within the deeper groove, called the major groove,the nucleotides’ hydrophobic methyl groups, hydrogen atoms, and hydrogen bond donors and acceptors protrude. The pattern created by these chemical groups is unique for each of the four possible base-pair arrangements, providing a ready way for a protein nestled in the groove to read the sequence of bases (figure 16.2).

DNA-Binding Motifs

Protein-DNA recognition is an area of active research; so far, the structures of over 30 regulatory proteins have been analyzed. Although each protein is unique in its fine details, the part of the protein that actually binds to the DNA is much less variable. Almost all of these proteins employ one of a small set of structural,or DNA-binding, motifs,particular bends of the protein chain that permit it to interlock with the major groove of the DNA helix.

Regulatory proteins identify specific sequences on the DNA double helix, without unwinding it, by inserting DNA-binding motifs into the major groove of the double helix where the edges of the bases protrude.

Chapter 16Control of Gene Expression315

16.2Regulatory proteins read DNA without unwinding it.

Minor groove

Major groove

Sugar

Phosphate OH

CH3HH N

Minor groove

Major groove

Key: = Hydrogen bond donors

= Hydrogen bond acceptors

= Hydrophobic methyl group

= Hydrogen atoms unable to form hydrogen bonds

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