Prokaryotic mRNA

All mRNA molecules are subject to attack by RNases, and this degradation is an essential aspect of the regulation of gene expression. Proteins are not made when they are not needed, and the rate of protein synthesis is determined by 

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At their 3 end, most eukaryotic mRNAs have a string of 80 to 250 A residues, making up the poly(A) tail. This tail serves as a binding site for one or more specific proteins. The poly(A) tail and its associated proteins probably help protect mRNA from enzymatic destruction. Many prokaryotic mRNAs also acquire poly(A) tails, but these tails stimulate decay of mRNA rather than protecting it from degradation. 

A primary transcript is a linear copy of a transcriptional unit—the segment of DNA between specific initiation and termination sequences. The primary transcripts of both prokaryotic and eukaryotic tRNAs and rRNAs are post-transcriptionally modified by cleavage of the original transcripts by ribonucleases. tRNAs are then further modified to help give each species its unique identity. In contrast, prokaryotic mRNA is generally identical to its primary transcript, whereas eukaryotic nrRNA is extensively modified posttranscriptionally. 

The pathway of protein synthesis translates the three-letter alphabet of nucleotide sequences on mRNA into the twenty-letter alphabet of amino acids that constitute proteins. The mRNA is translated from its 5 -end to its 3 -end, producing a protein synthesized from its amino-terminal end to its carboxyl-terminal end. Prokaryotic mRNAs often have several coding regions, that is, they are polycistronic (see p. 420). Each coding region has its own initiation codon and produces a separate species of polypeptide. In contrast, each eukaryotic mRNA codes for only one polypeptide chain, that is, it is monocistronic. The process of translation is divided into three separate steps initiation, elongation, and termination. The polypeptide chains produced may be modified by posttranslational modification. Eukaryotic protein synthesis resembles that of prokaryotes in most details. [Note Individual differences are mentioned in the text.]... 

Complementary binding between prokaryotic mRNA Shine-Dalgamo sequence and 16S rRNA. 

Prokaryotic mRNA is generally identical to its primary transcript, whereas eukaryotic mRNA is extensively modified posttranscriptionally. For example, a 7-methyl-guanosine "cap" is attached to the 5-terminal end of the mRNA through a triphosphate linkage by guanylyl-transferase. A long poly-Atail—not transcribed from the DNA—is attached to the 3 -end of most mRNAs. Many eukaryotic mRNAs also contain introns that must be removed to make the mRNA functional. Their removal requires small nuclear RNAs. 

Polycistronic messenger RNA. In prokaryotes, an RNA that contains two or more cistrons note that only in prokaryotic mRNAs can more than one cis-tron be utilized by the translation system to generate individual proteins. 

In contrast to prokaryotic mRNAs, mRNAs from various eukaryotic cells and viruses have been found to contain a terminal 7-methylguanosine (m7G) residue linked from its 5 -position through a triphosphate bridge which was presented commonly as shown in the following Scheme 1. ... 

The cap protects the 5 end of the primary transcript against attack by ribonu-cleases that have specificity for 3 5 phosphodiester bonds and so cannot hydrolyze the 5 5 bond in the cap structure. In addition, the cap plays a role in the initiation step of protein synthesis in eukaryotes. Only RNA transcripts from eukaryotic protein-coding genes become capped prokaryotic mRNA and eukaryotic rRNA and tRNAs are uncapped. 

In eukaryotes, each mRNA is monocistronic, that is, discounting any subsequent post-translational cleavage reactions that may occur, the mRNA encodes a single protein. In prokaryotes, many mRNAs are polycistronic, that is they encode several proteins. Each coding sequence in a prokaryotic mRNA has its own initiation and termination codons. 

Prokaryotic mRNA is polycitronic, whereas eukaryotic mRNA tends to be monocitronic. 

Prokaryotic ribosomes attach to the nascent mRNA while it is still being transcribed. Because transcription and translation are coupled, prokaryotic mRNAs undergo little modification and processing before being used as templates for protein synthesis. Prokaryotic tRNA and rRNA are transcribed in units larger than those ultimately used and must be processed to generate the functional molecules. The processing of these and the eukaryotic primary transcripts, almost all of which require modification, is discussed in a later section. 

Prokaryotic mRNAs function in translation with no processing, whereas a very complex process is used by eukaryotes to produce a mature, functional mRNA. 

Prokaryotic mRNAs function in translation with no processing. 

Because prokaryotic mRNAs are not compartmentalized and not processed, translation can begin before the mRNA synthesis is complete. 

In addition, several ribosomes can independently and simultaneously translate a mRNA molecule and, hence, synthesize several identical polypeptide chains concurrently (Figure 12.3). Such clusters or groups of ribosomes are called polyribosomes or polysomes. The number of attached ribosomes depends on the size of the mRNA and how frequently ribosomes can initiate at the start of a gene sequence. Because RNA transcription and translation are neither temporally nor spatially separated in prokaryotes, it is possible for translation to begin before transcription is completed. However, we have already noted that prokaryotic mRNAs have short half-lives this is probably a result of their continuous degra-... 

The polycistronic structure of prokaryotic mRNA presents another intriguing prospect. In some cases, a downstream cistron lacking a strong (or exposed) RBS is... 

Translation in prokaryotes begins with the formation of the ribosome complex at a defined position on the mRNA, termed the Shine-Delgamo sequence, or the ribosome binding site (RBS). In prokaryotic mRNA, this is a relatively small (4-7 nucleotides) region rich in purine nucleotides located less than 10 nucleotides to the 5 side of the translational start site (Fig. 23-3). This Shine-Delgarno sequence is complementary to the 16S ribosomal RNA (rRNA) associated with the 30S ribosomal subunit, and directs it to bind the mRNA at that position. The 3 OS ribosomal subunit will not bind this region on the mRNA without the aid of an associated protein called initiation factor 3 (IF-3). The 30S ribosomal subunit will bind the mRNA in such a manner that the peptidyl (P) site of the complex is occupied by a specialized codon with the sequence, AUG. It is at this AUG start codon where translation will eventually begin. 

Different in vitro translation systems are used depending on whether the mRNA is of prokaryotic or eukaryotic origin. For eukaryotic mRNA, translation kits from reticulocyte lysates or wheat germ extract are recommended, and for prokaryotic mRNA, the E. coli 30 S supernatant, all of which are commercially available. These translation kits can be supplemented with [3H]-leudne or... 

Proteins are synthesized in the amino-to-carboxyl direction, and mRNA is translated in the 5 —> 3 direction. The start signal on prokaryotic mRNA is AUG (or GUG) preceded by a purine-rich sequence that can base-pair with 16S rRNA. 

Protein synthesis takes place in three phases initiation, elongation, and termination. In prokaryotes, mRNA, formylmethionyl-tRNAf (the special initiator tRNA that recognizes AUG), and a 308 ribosomal suhunit come together with the assistance of initiation factors to form a 308 initiation complex. A 508 rihosomal suhunit then joins this complex to form a 708 initiation complex, in which fMet-tRNAf occupies the P site of the rihosome. 

Eukaryotic mRNAs dilfer from prokaryotic mRNAs in several respects (Figure 25-2). Eukaryotie genes invariably contain information for only a single polypeptide but each gene may consist of millions of nucleotides because eukaryotic genes contain introns and exons. The mRNA that is transcribed (primary transcript) is processed in several ways ... 

Structures of prokaryotic and eukaryotic primary transcripts (mRNAs). Prokaryotic mRNAs are polygenic, do not contain introns or exons, and are short lived in the cell. Eukaryotic mRNAs are monogenic, contain introns and exons, and usually are long lived in the cell. 

Many prokaryotic mRNA molecules are polycistronic and contain coding sequences for several polypeptides. Thus, a polycistronic mRNA molecule must possess a... 

In prokaryotes, mRNA synthesis can be controlled simply by regulating initiation of transcription. In eukaryotes, mRNA is formed from a primary transcript followed by a series of processing events (e.g., intron excision, polyadenylylation). Eukaryotes regulate not only transcription initiation but the various stages of processing as well. 

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