Gene expression may be controlled at multiple levels

extensively modified before it is translated; a 5' cap is added, the 3' end is cleaved and polyadenylated, and introns are removed (see Chapter 14). These modifications determine the stability of the mRNA, whether mRNA can be translated, the rate of translation, and the amino acid sequence of the protein produced. There is growing evidence that a number of regulatory mechanisms in eukary-otic cells operate at the level of mRNA processing.

A fourth point for the control of gene expression is the regulation of RNA stability. The amount of protein produced depends not only on the amount of mRNA synthesized, but also on the rate at which the mRNA is degraded; so RNA stability plays an important role in gene expression. A fifth point of gene regulation is at the level of translation, a complex process requiring a large number of enzymes, protein factors, and RNA molecules (Chapter 15).

All of these factors, as well as the availability of amino acids and sequences in mRNA, influence the rate at which proteins are produced and therefore provide points at which gene expression may be controlled.

Finally, many proteins are modified after translation (Chapter 13), and these modifications affect whether the proteins become active; so genes can be regulated through processes that affect posttranscriptional modification. Gene expression may be affected by regulatory activities at any or all of these points.

Concepts]"

Gene expression may be controlled at any of a number of points along the molecular pathway from DNA to protein, including gene structure, transcription, mRNA processing, RNA stability, translation, and posttranslational modification.

Genes and Regulatory Elements

In our consideration of gene regulation, it will be necessary to distinguish between the DNA sequences that are transcribed and the DNA sequences that regulate the expression of other sequences. We will refer to any DNA sequence that is transcribed into an RNA molecule as a gene. According to this definition, genes include DNA sequences that encode proteins, as well as sequences that encode rRNA, tRNA, snRNA, and other types of RNA. Structural genes encode proteins that are used in metabolism or biosynthesis or that play a structural role in the cell. Regulatory genes are genes whose products, either RNA or proteins, interact with other sequences and affect their transcription or translation. In many cases, the products of regulatory genes are DNA-binding proteins.

We will also encounter DNA sequences that are not transcribed at all but still play a role in regulating other nucleotide sequences. These regulatory elements affect the expression of sequences to which they are physically linked. Much of gene regulation takes place through the action of proteins produced by regulatory genes that recognize and bind to regulatory elements.

Concepts]"

Genes are DNA sequences that are transcribed into RNA. Regulatory elements are DNA sequences that are not transcribed but affect the expression of genes.

DNA-Binding Proteins

Much of gene regulation is accomplished by proteins that bind to DNA sequences and influence their expression. These regulatory proteins generally have discrete functional

(a) Helix-turn-helix (b) Zinc fingers (c) Steroid receptor

Helix Turn Helix

DNA- Turn Dimer-

binding helix binding helix

DNA- Turn Dimer-

binding helix binding helix

(d) Leucine zipper

(a) Helix-turn-helix (b) Zinc fingers (c) Steroid receptor

Helix Turn Helix

(e) Helix-loop-helix

(f) Homeodomain

(d) Leucine zipper

(e) Helix-loop-helix

(f) Homeodomain

16.2 DNA-binding proteins can be grouped into several types on the basis of their structure, or motif. (a) The helix-turn-helix DNA motif consists of two alpha helices connected by a turn. (b) The zinc-finger motif consists of a loop of amino acids containing a single zinc ion. Most proteins containing zinc fingers have several repeats of the zinc-finger motif. Each zinc finger fits into the major groove of DNA and forms hydrogen bonds with bases in the DNA. (c) The steroid receptor binding motif has two alpha helices, each with a zinc ion surrounded by four cysteine residues. The two alpha helices are perpendicular to one another: one fits into the major groove of the double helix, whereas the other is parallel to the DNA. (d) The leucine-zipper motif consists of a helix of leucine nucleotides and an arm of basic amino acids. DNA-binding proteins usually have two polypeptides; the leucine nucleotides of the two polypeptides face one another, whereas the basic amino acids bind to the DNA. (e) The helix-loop-helix binding motif consists of two alpha helices separated by a loop of amino acids. Two polypeptide chains with this motif join to form a functional DNA-binding protein. A highly basic set of amino acids in one of the helices binds to the DNA. (f) The homeodomain motif consists of three alpha helices; the third helix fits in a major groove of DNA.

parts—called domains, typically consisting of 60 to 90 amino acids—that are responsible for binding to DNA. Within a domain, only a few amino acids actually make contact with the DNA. These amino acids (most commonly asparagine, glutamine, glycine, lysine, and arginine) often form hydrogen bonds with the bases or interact with the sugar-phosphate backbone of the DNA. Many regulatory proteins have additional domains that can bind other molecules such as other regulatory proteins.

DNA-binding proteins can be grouped into several distinct types on the basis of a characteristic structure, called a motif, found within the binding domain. Motifs are simple structures, such as alpha helices, that can fit into the major groove of the DNA. Some common DNA-binding motifs are illustrated in 4 Figure 16.2 and are summarized in Table 16.1.

www.whfreeman.com/pierce Molecular images of several DNA-binding proteins

Table 16.1 Common DNA-binding motifs

Motif

Location

Characteristics

Binding Site in DNA

Helix-turn-helix

Bacterial regulatory proteins; related motifs in eukaryotic proteins

Two alpha helices

Major groove

Zinc-finger

Eukaryotic regulatory and other proteins

Loop of amino acids with zinc at base

Major groove

Steroid receptor

Eukaryotic proteins

Two perpendicular alpha helices with zinc surrounded by four cysteine residues

Major groove and DNA backbone

Leucine-zipper

Eukaryotic

Helix of leucine residues and

Two adjacent

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