39.3 A Ribosome Is a Ribonucleoprotein Particle Made of Two Subunits

We now turn to ribosomes, the molecular machines that coordinate the interplay of aminoacyl-tRNAs, mRNA, and proteins that results in protein synthesis. An E. coli ribosome is a ribonucleoprotein assembly with a mass of about 2.7 MDa, a diameter of approximately 250 Å, and a sedimentation coefficient of 70S. The 20,000 ribosomes in a bacterial cell constitute nearly a fourth of its mass.

A ribosome can be dissociated into a large subunit (50S) and a small subunit (30S) (Figure 39.7). These subunits can be further dissociated into their constituent proteins and RNAs. The small subunit contains 21 different proteins (referred to as S1 through S21) and a 16S RNA molecule. The large subunit contains 34 different proteins (L1 through L34) and two RNA molecules, a 23S and a 5S species.

Figure 39.7: Figure 39.7 The ribosome at high resolution. Detailed models of the ribosome based on the results of x-ray crystallographic studies of the 70S ribosome and the 30S and 50S subunits. (Left) View of the part of the 50S subunit that interacts with the 30S subunit; (center) side view of the 70S ribosome; (right) view of the part of the 30S subunit that interacts with the 50S subunit. 23S RNA is shown in yellow, 5S RNA in orange, 16S RNA in green, proteins of the 50S subunit in red, and proteins of the 30S subunit in blue. Notice that the interface between the 50S and the 30S subunits consists entirely of RNA.

Ribosomal RNAs Play a Central Role in Protein Synthesis

The prefix ribo in the name ribosome is apt, because RNA constitutes nearly two-thirds of the mass of these large molecular assemblies. The three RNAs present—5S, 16S, and 23S—are critical for ribosomal architecture and function. These ribosomal RNAs (rRNAs) are folded into complex structures with many short duplex regions (Figure 39.8).

Figure 39.8: Ribosomal RNA folding pattern. (A) The secondary structure of 16S ribosomal RNA deduced from sequence comparison and the results of chemical studies. (B) The tertiary structure of 16S RNA determined by x-ray crystallography.

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For many years, the protein components of ribosomes were thought to orchestrate protein synthesis, with the RNA components serving primarily as structural scaffolding. But this idea raised a perplexing evolutionary “chicken-and-egg” question: Namely, how can complex proteins be synthesized if complex proteins are required for protein synthesis? The discovery of catalytic RNA made biochemists receptive to the possibility that RNA plays a much more active role in ribosomal function. Detailed structural analyses make it clear that the key catalytic sites in the ribosome are composed almost entirely of RNA. Contributions from the proteins are minor. The almost inescapable conclusion is that, early in the evolution of life, the ribosome initially consisted only of RNA and that the proteins were added later to fine-tune its functional properties. This conclusion has the pleasing consequence of dodging the chicken-and-egg question.

Messenger RNA Is Translated in the 5′-to-3′ Direction

The sequence of amino acids in a protein is translated from the nucleotide sequence in mRNA, and the direction of translation is 5′ → 3′. The direction of translation has significant consequences. Recall that transcription also is in the 5′ → 3′ direction. If the direction of translation were opposite that of transcription, only fully synthesized mRNA could be translated. In contrast, because the directions are the same, mRNA can be translated while it is being synthesized. In bacteria, almost no time is lost between transcription and translation. The 5′ end of mRNA interacts with ribosomes very soon after it is made, much before the 3′ end of the mRNA molecule is finished. A key feature of bacterial gene expression is that translation and transcription are closely coupled in space and time. Many ribosomes can be translating an mRNA molecule simultaneously. This parallel synthesis markedly increases the efficiency of mRNA translation. The group of ribosomes bound to an mRNA molecule is called a polyribosome or a polysome (Figure 39.9).

Figure 39.9: Polysomes. Transcription of a segment of DNA from E. coli generates mRNA molecules that are immediately translated by multiple ribosomes.

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