Fundamentals of Molecular Biology. Part 2: Molecular Genetic Mechanisms - A. N. Ogurtsov 2011

The Role of RNA in Translation
Ribosomal RNAs

If the interaction of all components involved in mRNA Translation were to take place in a free solution, the probability of their simultaneous encounter would be negligible, and the polymerization rate would be extremely low. Translation efficiency is ensured by the binding of mRNA and aminoacylated tRNAs to Ribosomes—the most abundant ribonucleoprotein complexes in The Cell, which drive polypeptide elongation at a rate of 3–5 Amino Acids per second.

Consequently, small Proteins consisting of 100–200 Amino acids are synthesized within a minute or less. On the other hand, synthesizing the largest known protein, titin, which is found in Muscles and consists of more than 30,000 amino acid residues, takes 2–3 hours. The cellular "machinery" that performs this task must be both precise and reliable.

Using an Electron microscope, ribosomes were first discovered as small, discrete, RNA-rich particles in Cells that secrete large amounts of proteins. However, their role in METABOLISM/35.html">Protein Biosynthesis remained unclear until a pure ribosomal fraction was isolated. In vitro experiments with radioactively labeled amino acids in such a fraction demonstrated that amino acids are first attached to the growing chains on the ribosome and only later appear in completed proteins.

A ribosome consists of three (in Bacteria) or four (in eukaryotes) different rRNA molecules and several dozen (up to 83) proteins organized into two subunits—large and small (Figure 40).

Ribosomal subunits and rRNA molecules are typically measured in Svedberg units (S), which quantify the sedimentation velocity of suspended particles centrifuged under standard conditions. The small ribosomal subunit contains a single rRNA molecule, known as the small rRNA. The large subunit comprises a large rRNA molecule and a 5S rRNA molecule, with vertebrates possessing an additional 5.8S rRNA molecule.

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Figure 40 - Ribosomal components in PROKARYOTES AND EUKARYOTES

The length of rRNA molecules, the number of proteins in each subunit, and, consequently, the subunit sizes differ between bacterial and Eukaryotic cells. The assembled ribosome sediments at 70S in bacteria and 80S in vertebrates.

Yet far more interesting than these differences is the Structural and functional similarity observed among ribosomes across all organisms. This resemblance is yet another reflection of the common evolutionary Water/144.html">Origin of the fundamental components of biological cells.

To date, The nucleotide sequences of large and small rRNAs have been established for several thousand organisms. Although the primary nucleotide sequences of these rRNAs vary significantly, homologous regions of each RNA type can theoretically form all the helices and loops that establish a conserved three-dimensional Structure for each rRNA across all organisms.

The actual Spatial Structure of bacterial rRNA from Thermus thermophilus was recently determined using X-ray crystallography of the 70S ribosome.

Multiple, relatively small ribosomal proteins are primarily associated with The surface of the rRNA. Although the number of protein molecules in a ribosome vastly exceeds the number of rRNA molecules, the latter account for about 60% of the ribosomal mass.

During translation, the ribosome moves along the mRNA, interacting with numerous protein factors and tRNAs while undergoing major conformational changes.

Despite The complexity of the ribosome, significant progress has been made in determining the overall structure of bacterial ribosomes and identifying their various functional centers. For instance, X-ray crystallographic studies of the 70S ribosome from Thermus thermophilus not only revealed the size and general shape of the ribosomal subunits but also localized the sites where tRNA binds to the ribosome during the elongation of the growing protein chain.

Furthermore, powerful chemical techniques, such as footprinting (specific probing with nucleotide-binding Reagents), have been used to identify specific nucleotide sequences in rRNA that interact with proteins or other RNAs. Half a century after the discovery of ribosomes, their Structure and function in Protein Synthesis have finally become clear.

Conclusions

Genetic information is transcribed from DNA into mRNA in the form of a non-overlapping, degenerate triplet code devoid of punctuation marks.

Each amino acid is encoded by one or more three-nucleotide sequences (codons) in mRNA. Each codon specifies a single amino acid, but Most amino acids are encoded by multiple codons.

The AUG Methionine codon serves as the start codon in most cases, specifying The amino acid at the NH₂-terminus of the protein chain. Three codons (UAA, UAG, UGA) function as stop codons and do not specify any amino acids.

The reading frame—a continuous sequence of codons in mRNA extending from a specific start codon to a stop codon—is translated into a linear sequence of amino acids within a polypeptide chain.

The decoding of the mRNA nucleotide sequence into the Amino Acid Sequence of a protein relies on tRNAs and Aminoacyl-tRNA synthetases.

All tRNAs share a similar three-dimensional structure comprising an acceptor stem for attaching a specific Amino Acid and an anticodon loop bearing a trinucleotide anticodon sequence at its tip. The anticodon can base-pair with the corresponding codon on the mRNA.

Due to wobble base pairing, a tRNA can pair with more than one mRNA codon and, conversely, a given codon can pair with multiple tRNAs. In every case, however, only the correct amino acids are incorporated into the growing polypeptide chain.

Each of the 20 aminoacyl-tRNA synthetases recognizes a single amino acid and covalently attaches it to its cognate tRNA, forming an aminoacyl-tRNA. This reaction activates the amino acid so that it can participate in peptide bond formation.

Both prokaryotic and eukaryotic ribosomes—large ribonucleoprotein complexes where translation takes place—consist of small and large subunits. Each subunit contains a substantial number of diverse proteins and one primary rRNA molecule (small or large). The large subunit also includes one additional 5S rRNA in bacteria and two additional rRNAs in eukaryotic cells (5S and 5.8S in vertebrates).

Homologous rRNAs from many different organisms fold into remarkably similar three-dimensional structures containing numerous loops and binding sites for proteins, mRNAs, and tRNAs. Much smaller ribosomal proteins associate with the peripheral Regions of the rRNA.

Self-Assessment Questions

1. What cellular process is called RNA translation?

2. What is the function of mRNA in translation?

3. What is the function of tRNA in translation?

4. What is the function of ribosomal RNAs in translation?

5. What is The Genetic Code?

6. List the eight Properties of the genetic code.

7. What does the triplet Nature of the genetic code mean?

8. What does the degeneracy of the genetic code mean?

9. For which Two amino acids is the genetic code not degenerate?

10. What are a codon and an anticodon?

11. Which codons are called terminating codons? How many of them are there in the genetic code?

12. Which codons are called nonsense codons?

13. Which codon is called the start codon?

14. What does the unambiguity of the genetic code mean?

15. What does the universality of the genetic code mean?

16. What does the compactness of the genetic code mean?

17. Which Mutations are called conservative mutations?

18. Which mutations are called radical mutations?

19. Which mutations are called missense mutations?

20. What does the non-overlapping nature of the genetic code mean?

21. WHAT IS A reading frame?

22. How many different reading frames can there be? Provide an example.

23. What is the activation of amino acids by aminoacyl-tRNA synthetase?

24. What is the difference between aminoacyl-tRNA and tRNA?

25. What is an anticodon and how does it differ from a codon?

26. What are the Similarities and differences between a codon and an anticodon?

27. Provide Examples of non-standard base pairing between codon and anticodon NUCLEOTIDES.

28. Which codons are referred to as synonymous codons?

29. What is the difference between prokaryotic and eukaryotic ribosomes?