Introduction to Molecular Biology: From Cells to Atoms - Anthony Rees, Michael Sternberg 2002

Nucleic Acids and Genes
The Translational Apparatus of the Cell

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Fig. 24.1.

Translation is The process of mRNA decoding, whereby the information encoded in The nucleotide sequence of an mRNA is translated into the Amino Acid Sequence of a protein. This section outlines the translational machinery of The Cell, while The Mechanism of translation is discussed in detail in Chapter 25.

Protein Synthesis proceeds via the sequential polycondensation of individual amino acid residues, starting from the amino (N)-terminus of the polypeptide chain and extending toward the carboxyl (C)-terminus. Consequently, mRNA decoding occurs in the 5' -> 3' direction.

Decoding relies on the specific binding of the anticodon of a Transfer RNA (tRNA) to the corresponding codon of the mRNA (Chapter 19). Prior to this codon-anticodon recognition, the appropriate amino acid residue is attached to the tRNA, forming an aminoacyl-tRNA. This process is known as tRNA activation. Protein synthesis takes place on the ribosome. All stages of this process are facilitated by a multitude of various Enzymes and other Proteins (such as initiation factors, for example) (Chapter 25).

tRNA activation involves the attachment of an amino acid to the 3'-terminal adenosine of the tRNA molecule, yielding an aminoacyl-tRNA. This process is catalyzed by an aminoacyl-tRNA synthetase, with at least one such catalytic enzyme existing for each amino acid. The energy required for this process is provided by ATP Hydrolysis. The reaction can be represented as follows:

In an aminoacyl-tRNA, The amino acid is linked via an ester bond (—O—) to either the 2'- or 3'-OH group of adenosine (Fig. 24.2). The binding of an aminoacyl-tRNA synthetase to its specific cognate amino acid is executed with extremely high fidelity: misactivation of a tRNA would result in the incorporation of an incorrect amino acid into the polypeptide chain at that position. There is an additional proofreading mechanism, often referred to as an editing mechanism, which ensures activation accuracy; it works by having the respective synthetase automatically catalyze the deacylation of any incorrectly activated tRNA, causing it to dissociate into its original components—namely, the free Amino Acid and free tRNA.

Fig. 24.2.

The ribosome is an organelle composed of two subunits where protein synthesis takes place. Each subunit represents a complex assembly of proteins and RNA molecules. Throughout the entire process of protein synthesis, the growing polypeptide chain, the mRNA, and the incoming aminoacyl-tRNA remain attached to the ribosome. The sedimentation coefficient of prokaryotic Ribosomes from *E. coli* is approximately 70S, whereas cytoplasmic ribosomes in eukaryotes have a sedimentation coefficient of 80S. Mitochondria and METABOLISM/14.html">Chloroplasts—Organelles found in Eukaryotic Cells—contain their own ribosomes with a sedimentation coefficient of 70S, which closely resemble prokaryotic ribosomes.

Dissociation of the ribosome into large and small subunits *in vitro* occurs at low Mg²⁺ concentrations. The prokaryotic 70S ribosome consists of 50S and 30S subunits, whereas the eukaryotic 80S ribosome comprises 60S and 40S subunits. Under appropriate chemical Treatment, these subunits can, in turn, dissociate into their constituent parts—protein and rRNA (Fig. 24.3). The rRNA-to-protein weight ratio for prokaryotic and eukaryotic ribosomes is 2:1 and 1:1, respectively.

The nucleotide sequences of several rRNA molecules have been determined. Analysis of these sequences has revealed regions capable of base pairing that can participate in Secondary Structure formation, much like the stem structures found in tRNA molecules (Chapter 19).

Many ribosomal proteins are basic due to the high proportion of Arg⁺ and Lys⁺ side chains. It is highly probable that many of these positively charged groups interact with the negatively charged phosphate groups of the rRNA molecules, thereby stabilizing the protein-nucleic acid complex.

Fig. 24.3.

The self-assembly of an entire functional ribosome from its component proteins and rRNA has been successfully achieved *in vitro*. This demonstrates that the complex STRUCTURE OF THE ribosome is determined exclusively by the interactions among its constituent molecules.

The structure of the ribosome has been studied using Electron Microscopy. Figure 24.4 shows two mutually perpendicular projections of an *E. coli* 70S ribosome. The overall dimensions of prokaryotic ribosomes are approximately 20 nm at their smallest axis and 30 nm at their largest. The larger (80S) eukaryotic ribosomes are morphologically similar to their prokaryotic counterparts, but are approximately 1.15 times larger in every dimension (23 nm × 35 nm, respectively).

Fig. 24.4

Ribosomal binding sites are specific regions where various molecules involved in translation attach. A narrow cleft remains between the large and small ribosomal subunits (Fig. 24.4), which is occupied by the mRNA molecule. Upon arriving at the ribosome, each incoming aminoacyl-tRNA binds to a site designated as the A site. Another site, denoted as the P site, binds the peptidyl-tRNA molecule that carries the nascent polypeptide chain (Chapter 25).

A polysome, or polyribosome, is an mRNA molecule with multiple active ribosomes translating it simultaneously, with each synthesizing a protein molecule (Fig. 24.1).

Broadly speaking, protein synthesis initiates when a complex forms consisting of the large and small ribosomal subunits, an mRNA molecule, and the appropriate aminoacyl-tRNA. The intact ribosome then translocates along the mRNA from the 5' to the 3' end. This movement is accompanied by the elongation of the polypeptide chain. Once the Synthesis of the polypeptide chain is fully completed, it is released from the ribosome, which in turn detaches from the mRNA and dissociates into its large and small subunits. These subunits are then free to participate in the synthesis of another protein molecule; the entire process is described in detail in the following chapter.