Читать книгу Snyder and Champness Molecular Genetics of Bacteria - Tina M. Henkin - Страница 242

We have introduced a lot of detail in this chapter, so it is worth reviewing some of the most important concepts and terms. As with any field, molecular genetics has its own jargon, and in order to follow a paper or seminar that includes some molecular genetics, familiarity with this jargon is very helpful.

Figure 2.44 shows a typical gene with a promoter and transcription terminator. The mRNA is transcribed beginning at the promoter and ending at the transcription terminator. The direction on the DNA or RNA is indicated by the direction of the phosphate bonds between the carbons on the ribose or deoxyribose sugars in the backbone of the polynucleotide. These carbons are labeled with a prime to distinguish them from the carbons in the bases of the nucleotides. On one end of the RNA, the 5′ carbon of the terminal nucleotide is not joined to another nucleotide by a phosphate bond. Therefore, this is called the 5′ end. Similarly, the other end is called the 3′ end, because the 3′ carbon of the last nucleotide on this end is not joined to another nucleotide by a phosphate bond. The direction on DNA or RNA from the 5′ end to the 3′ end is called the 5′-to-3′ direction. An RNA polymerase molecule synthesizes mRNA in the 5′-to-3′ direction, moving 3′ to 5′ on the transcribed strand (or template strand) of DNA. The opposite strand of DNA from the transcribed strand has the same sequence and 5′-to-3′ polarity as the RNA, so it is called the coding strand (or nontemplate strand). Sequences of DNA in the region of a gene are usually shown as the sequence of the coding strand. A sequence that is located in the 5′ direction of another sequence on the coding strand is upstream of that sequence, while a sequence in the 3′ direction is downstream. Therefore, the promoter for a gene and the S-D sequences are both upstream of the initiation codon, while the termination codon and the transcription termination sites are both downstream.

The positions of nucleotides in a promoter region are numbered as shown in Figure 2.6. The position of the first nucleotide in the RNA is called the start point and is given the number +1; the distance in nucleotides from this point to another point is numbered negatively or positively, depending on whether the second site is upstream or downstream of the start point, respectively. Note that these definitions can be used to describe only a region of DNA that is known to encode an RNA or protein, where we know which is the coding strand and which is the transcribed strand. Otherwise, what is upstream on one strand of DNA is downstream on the other strand.

Because mRNAs are both made and translated in the 5′-to-3′ direct ion, an mRNA can (and usually will) be translated while it is still being made, at least in bacteria and archaea, in which there is no nuclear membrane separating the DNA from the cytoplasm, where the ribosomes reside. We have discussed how this can lead to phenomena unique to bacteria, such as ρ-dependent polarity, and it is used to regulate expression of some genes in bacteria (see chapter 11).

It is important to distinguish promoters from TIRs and to distinguish transcription termination sites from translation termination sites. Figure 2.44 illustrates this difference. Transcription begins at the promoter and defines the 5′ end of the mRNA, but the place where translation begins, the TIR, can be some distance from the 5′ end. The untranslated region on the 5′ end of an mRNA upstream of the TIR is called the 5′ untranslated region or leader region and can be quite long. Similarly, a nonsense codon in the reading frame for the protein is a translation terminator, not a transcription terminator. The transcription terminator, and therefore the 3′ end of the mRNA, may be some distance downstream from the nonsense codon that terminates transition of the mRNA. The distance from the last termination codon to the 3′ end of the mRNA is the 3′ untranslated region. Polycistronic mRNAs encode more than one polypeptide. These mRNAs have a separate TIR and termination codon for each gene and can have noncoding or untranslated sequences upstream of, downstream of, and between the genes. Eukaryotes generally do not have polycistronic mRNAs, which is related to the dependence on ribosome binding to the 5′ end of the mRNA for translation initiation.