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Modern Genetic Analysis Chapter 3. Gene Function
Genes and RNA

As we have discussed previously, the initial products of all genes are ribonucleic acids (RNAs). RNA is produced by a process that copies the nucleotide sequence in DNA. Since this process is reminiscent of transcribing (copying) written words, the synthesis of RNA is called transcription. The DNA is said to be transcribed into RNA, and the RNA is called a transcript. As we shall see, the process by which RNAs are transcribed from genes has some similarities with the way new DNA is synthesized during DNA replication, but there are also important differences.

One way to think about the different biological roles of DNA and RNA is to consider that the DNA (that is, the genome) is the instruction manual for producing all the RNAs that the cell needs, whereas RNA is the erasable readout of those parts of the manual relevant to any given task. We looked at DNA previously. To understand the roles that RNAs play in the cell, let's first consider their general chemical features.

Properties of RNA

Although RNA and DNA are both nucleic acids, RNA differs in several important ways:

1. RNA is a single-stranded nucleotide chain, not a double helix. One consequence of this is that RNA can form a much greater variety of complex three-dimensional molecular shapes than can double-stranded DNA. We will consider this in more detail later in the chapter.
2. RNA has ribose sugar in its nucleotides, rather than deoxyribose. As the names suggest, the two sugars differ in the presence or absence of just one oxygen atom. Analogous to the individual strands of DNA, there is a phosphate-ribose backbone to RNA, with a base covalently linked to the 1 position on each ribose.
3. RNA nucleotides carry the bases adenine, guanine, and cytosine, but the pyrimidine base uracil (abbreviated U) is found in place of thymine.

However, uracil forms hydrogen bonds with adenine just as thymine does.

Classes of RNA

RNAs can be grouped into two general classes. Some RNAs are intermediaries in the process of decoding genes into polypeptide chains. We will refer to these RNAs as "informational" RNAs. In the other class, the RNA itself is the final, functional product. We will refer to these RNAs as "functional" RNAs.

Informational RNAs.

For the vast majority of genes, the RNA is only an intermediate in the synthesis of the ultimate functional product, which is a protein. The informational RNA of this vast majority of genes is always messenger RNA (mRNA).

In prokaryotes, the transcript, as it is synthesized directly from the DNA (the primary transcript), is the mRNA. In eukaryotes, however, the primary transcript is processed through modification of the 5 and 3 ends and removal of pieces of the primary transcript (introns). At the end of this pre-mRNA processing, an mRNA is produced. We will discuss these steps in producing mRNAs later in this chapter.

The sequence of nucleotides in mRNA is converted into the sequence of amino acids in a polypeptide chain by a process called translation. In this connection the word translation is used in much the same way as we use it in translating a foreign language: the cell has a way of translating the language of RNA into the language of polypeptides. Proteins are made up of one or more polypeptide chains.

Functional RNAs.

As more is learned about the intimate details of cell biology, we have come to realize that functional RNAs play many diverse roles. Again, it's important to emphasize that for these functional RNAs, their action is purely at the level of the RNA; they are never translated into polypeptides. Each class of functional RNA is encoded by a relatively small number of genes (a few tens to a few hundred at most).

The main classes of functional RNAs contribute to various steps in the informational processing of DNA to protein. Two such classes of functional RNAs are found in all organisms: transfer RNAs and ribosomal RNAs.

Transfer RNA (tRNA) molecules act as transporters that bring amino acids to the mRNA during the process of translation (protein synthesis). The tRNAs are general components of the translation machinery; they can bring amino acids to the mRNA of any protein-coding gene.

Ribosomal RNAs (rRNAs) are components of ribosomes, which are large macromolecular assemblies that act as guides to coordinate the assembly of the amino acid chain of a protein. Ribosomes are composed of several types of rRNA and about 100 different proteins. As in the case of tRNA, the rRNAs are general translational components that can be used to translate the mRNA of any protein-coding gene.

Two other classes of functional RNAs involved in information processing are specific to eukaryotes. Small nuclear RNAs (snRNAs) are involved in the splicing of pre-mRNAs into messenger RNAs in the eukaryotic cell's nucleus. Several different snRNAs, together with several protein subunits, form a macromolecular assembly called an snRNP (small ribonucleoprotein particle). Small cytoplasmic RNAs (scRNAs) are involved in protein trafficking within the eukaryotic cell. Specifically, they ensure that polypeptides destined, for example, to be secreted from the cell are inserted into one of the membrane compartments of the cell (the rough endoplasmic reticulum). This begins the process of protein secretion.

MESSAGE
There are two types of genes, those coding for protein (the majority) and those encoding functional RNAs.

All DNA and RNA function is based on two key elements:

1. Complementary bases in single-stranded nucleo-tide chains can hydrogen-bond to form double-stranded structures.
2. Particular base sequences in single-stranded or double-stranded nucleic acids can be recognized by specific nucleic acidbinding proteins. (These proteins are themselves encoded by genes, but their function is to act on other genes.)

We shall see these two properties at work throughout the detailed discussions of transcription and translation that follow.

MESSAGE
The transactions of DNA and RNA are based on complementarity of base sequences and on attachment of various nucleic acidbinding proteins to specific sites.

© 1999 by W. H. Freeman and Company. All rights reserved.