Chapter 17

Genes control cellular metabolism by serving as the blueprints for the primary structure of enzymes that in turn affect the rate of other chemical reactions. In eukaryotes, DNA serves as the template for the production of messenger RNA (mRNA). All RNA is produced via a process called transcription. At ribosomes, the mRNA is translated into a series of amino acids bound together by peptide bonds thereby forming a polypeptide. This process is called translation (Fig. 17.3). The actual directions necessary for the production of a polypeptide are provided by the sequence of nucleotides along the mRNA, and that sequence is determined from forming the RNA complement of one of the DNA strands (the template strand) at a particular genetic locus. Three sequential nucleotides along the mRNA molecule provide an unambiguous message (a codon) for a particular Amino Acid. The association of codons with their appropriate amino acids is referred to as the Genetic Code. Because each codon is three nucleotides long it is referred to as being a triplet code. (Fig. 17.4, 17.5)

There are great similarities between both transcription and translation in eukaryotes and prokaryotes. One difference is due to the absense of a nuclear envelope in prokaryotes. As the mRNA transcript is being produced in prokaryotes, ribosomes assemble around the RNA strand and begin translating it (even before transcription is complete). (Fig. 17.7) Therefore, the RNA translated is an exact complement of the template DNA strand. In eukaryotes, the RNA transcribed is first processed in the nucleus before it migrates through a nucleopore into the cytosol where translation takes place (Fig. 17.8). This processing involves removing internal segments (introns) of the RNA and splicing together the remaining segments (exons). A large structure in the nucleus called the spliceosome aids in this splicing process for pre-mRNA molecules. Processing also involves added a methyl guanosine cap to the 5' end and a polyA tail to the 3' end of the mRNA. (Fig. 17.9, 17.10)

The enzyme that forms the RNA molecule is RNA polymerase. RNA always reads the template DNA strand in a 3' to 5' direction. That means the RNA is synthesized in a 5' to 3' direction. At any genetic locus only one of the DNA strands has a meaningful message, it is referred to as the template strand, the other strand the nontemplate strand will be almost identical to the RNA molecule transcribed except that it has a T instead of a U and deoxyribose sugar instead of ribose. Along the same double stranded DNA molecule one strand may be the template for one locus and the other strand the template for a different locus. The appropriate strand to serve as the template at any locus is identified by a DNA sequence associated with that locus called the promoter. RNA recognizes where to begin transcription along the double stranded DNA molecule differently in prokaryotes versus eukaryotes. In prokaryotes, RNA polymerase recognizes the promoter, attaches there, unzippers a short region of the DNA and begins transcribing the template about 10 bases downstream from the attachment site. In eukaryotes, an assemblage of proteins (transcription factors) recognize and attach to the promoter. The RNA polymerase recognizes the assemblage of transcription factors and attaches to this assemblage. From this site, RNA begins transcription about 30 bases downstream of the attachment site. The RNA polymerase continues along the template until a termination signal is produced. After the transcription termination signal is reached the RNA discharges from the DNA and transcription is terminated. This termination process differs a bit between prokaryotes and eukaryotes.

The genetic code is provided in Fig.17.4. Note that there are 64 possible combinations of 4 bases taken 3 at a time. Of these 64 possible codons, three of them are stop signals for translation. Note that there is only one codon, AUG, for methionine which is always the first amino acid positioned at the amino end of the polypeptide chain. Some amino acids are coded for by more than one codon, but any codon codes for only one amino acid. This can be restated as: the code is redundant but unambiguous. Note that the redundancy of the genetic code is such that the identity of the third base position is unimportant or it is only important whether this third position contains a purine or pyrimidine. With minor exceptions, all living organisms utilize the same genetic code, so the code is effectively universal. The mRNA consists of a continuous stretch of nucleotides that that are read sequentially in sets of three nucleotides. Therefore codons are not set off from each other (e.g., they do not have the analogues of commas).

Other types of RNA are important for translation. A short length of RNA that folds on itself forming a complex three-dimensional structure and serves to bring the appropriate amino acids to the ribosomes is called tRNA. (Fig. 17.14) The tRNA molecule has three loops, one of them containing the anticodon region which will bond with the codon it is complementary with based on hydrogen bonding. Before the tRNA arrives at a ribosome it must be first charged with an amino acid. This charging occurs with the assistance of a specific aminoacyl-tRNA synthetase enzyme for each amino acid. The appropriate amino acid is bound to the 3' end of the tRNA molecule. (Fig. 17.15)

Ribosomes are made up of proteins and ribosomal RNA (rRNA). In the cytosol, the ribosome is normally found as two separate units the large and small subunits. When assembled the ribosome has three regions, referred to as the E,P, and A windows, that functionally interact with tRNAs and mRNA during translation. (Fig. 17.16)

Translation is broken down into initiation, elongation and termination. Initiation involves the mRNA binding to the small ribosomal subunit such that AUG is positioned in the P site. A charged tRNA containing methionine positions its anticodon opposite the AUG codon. A set of three protein initiation factors bind to the ribosomal subunit and then the large subunit combines with this complex forming the functional ribosome/mRNA complex. The A site is at first empty of any charged tRNA, but does contain the second codon contained on the mRNA. As the first step in elongation, this second codon attracts the appropriate charged tRNA thereby positioning the second amino acid's amino group adjacent to the carboxyl group of the first amino acid. A peptide bond forms between these amino acids forming a dipeptide. Once the peptide bond forms the tRNA in the P site is discharged of its amino acid. Translocation then causes the ribosome to move three nucleotides down the mRNA in a 5'to3' direction. This positions the codon that had been in the A site and its associated tRNA (now charged with a dipeptide) into the P site. The codon that had been in the P site and its associated discharged tRNA are simultaneously moved to the E site where the tRNA is released. A new codon has moved into the A site, and awaits the continuing process. This process continues until a stop signal arrives in the A site. A release factor binds with the stop signal and releases the polypeptide. (Fig. 17.17, 17.18, 17.19)

The growing polypeptide's primary structure is determined by the message on the mRNA. Its three-dimension structure is often influenced by the presence of chaperone proteins. After translation some amino acids may be removed or the side chains modified enzymatically.

Proteins destined to remain in the cytosol are made on free ribosomes. Proteins destined for membranes or secretion are synthesized on ribosomes bound to the endoplasmic reticulum. A signal-recognition particle binds to a signal sequence at the leading end of the growing polypeptide, enabling the ribosome to bind to the endoplasmic reticulum (fig. 17.21). Other signal sequences target proteins for mitochondria or chloroplasts.