ZOOHCC - 501: Molecular Biology (Theory)
Unit 3: Transcription and Regulatory RNAs
ribosomal RNA (rRNA)
Ribosomal RNA (rRNA), an intracellular molecule that forms part of the protein-synthesizing organelle known as the ribosome, is transported to the cytoplasm and helps convert messenger RNA (mRNA) information into protein. The three main types of RNA found in cells are rRNA, mRNA, and transfer RNA (tRNA).
rRNA molecules are synthesized in a specialized region of the cell nucleus called the nucleolus. The nucleolus appears as a dense region within the cell nucleus and contains genes encoding rRNA. Encoded rRNAs vary in size and are classified as either large or small. Each ribosome contains at least one large rRNA and at least one small rRNA. In the nucleolus, large and small rRNA associate with ribosomal proteins to form the large and small ribosomal subunits (eg, 50S and 30S, respectively, in bacteria). (These subunits are commonly named for their sedimentation velocity in a centrifuge and are measured in Svedberg units [S].) Ribosomal proteins are synthesized in the cytoplasm and transported to the nucleus, where they are assembled in the nucleolus. can be Subunits are then returned to the cytoplasm for final assembly.
rRNA forms extensive secondary structures and plays an active role in recognizing conserved portions of mRNA and tRNA. In eukaryotes (organisms with distinct nuclei), a single cell can have 50-5,000 sets of rRNA genes and up to 10 million ribosomes. In contrast, prokaryotes (organisms without a nucleus) generally have a smaller set of rRNA genes and ribosomes per cell. For example, in the bacterium Escherichia coli, seven copies of the rRNA gene synthesize approximately 15,000 ribosomes per cell.
There is a fundamental difference between prokaryotes in the archaeal and bacterial domains. These differences are reflected not only in the use of lipids, cell wall composition, and different metabolic pathways, but also in rRNA sequences. Bacterial and archaeal rRNAs are not only different from each other, but also from eukaryotic rRNAs. This information is important in understanding the evolutionary origins of these organisms. This is because it suggests that the bacterial and archaeal lineages diverged from a common ancestor sometime before eukaryotic evolution.
rRNA synthesis
Ribosome synthesis is a highly complex and coordinated process involving over 200 assembly factors. Synthesis and processing of ribosomal components occurs not only in the nucleolus, but also in the nucleoplasm and cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNA by different RNA polymerases. Primary transcripts undergo extensive processing and modification before being bound and folded by ribosomal proteins and assembly factors imported from the cytoplasm. Extensive modification of ribosomal RNA by snoRNPs is another distinguishing feature of eukaryotic ribosomes. Individual modified bases do not appear to have specific functions, and all modifications together stabilize a specific conformation of ribosomal RNA. Moreover, these modified bases are more concentrated in functional regions of rRNA and regulate translational ribosomal activity.
Both rRNA modification and pre-rRNA processing occur in the nucleolus. This is because both steps require components found only in the nucleolus. While snoRNPs chemically modify rRNA, other 'nucleolar proteins' hydrolyze the transcribed 'spacer RNA' of the precursor RNA into cleaved 18S, 5.8S, and 28S rRNAs. increase. Generation of mature rRNA returns free nucleolar proteins to the nucleolar pool for recycling.
Cations such as magnesium ions (Mg2+) play an important role in maintaining the structure of the ribosome. During experiments, ribosomes dissociate into subunits when Mg2+ is removed. Although the exact role of Mg2+ remains unclear, it is plausible that cations interact with the ionized phosphate of RNA so that he bridges the two ribosomal subunits.
After ribosome assembly is complete, some ribosomes are bound to the intracellular membrane, mainly the endoplasmic reticulum, while free ribosomes are distributed throughout the cytoplasm.
Structure of rRNA
tRNA Synthesis
Transfer ribonucleic acid (tRNA) is synthesized from the tRNA gene, primarily by transcription by RNA polymerase, and undergoes several steps of processing, splicing, CCA addition, and post-transcriptional modification into its mature form. Primary transcripts of tRNA genes contain 5' and 3' extra sequences that are removed by various causative nucleases and, in some cases, introns that are spliced out by specific endonucleases. The two resulting fragments are joined by RNA ligase. The CCA sequence present at the 3' end of all mature tRNAs is not encoded by the tRNA genes of some species and is added post-transcriptionally by CCA-adding enzymes. All mature tRNA molecules contain modified nucleotides produced by modification enzymes thought to be involved in stabilizing the tRNA structure, deciphering its properties, and proper processing. The concentration of individual tRNA molecules is controlled to maintain cellular function.
One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for approximately 20% of the total bases in the molecule. Collectively, these unusual bases protect tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by specific enzymes after transcription. All of these enzymes have unique base and site specificities. Methylation, the most common chemical modification, is performed by at least nine different enzymes, with three enzymes at different positions dedicated to guanine methylation.
The nature and location of these modified bases vary by species. Therefore, there are some bases that are exclusive to eukaryotes or prokaryotes. For example, adenine thiolation is observed only in prokaryotes, whereas cytosine methylation is restricted to eukaryotes. Overall, eukaryotic tRNAs are more extensively modified than prokaryotic ones. Although the nature of the alterations varies, some regions of tRNA are always significantly altered. Each of the three stem-loop regions, or "arms," of tRNA has modified bases that serve a unique purpose. The TΨC arm is named for the presence of the nucleotides thymine, pseudouridine, and cytosine, which are recognized by the ribosome during translation. The DHU or D arm containing the modified pyrimidine dihydrouracil serves as the recognition site for the enzyme aminoacyl-tRNA synthetase, which catalyzes the covalent addition of amino acids to tRNA. Anticodon loops often have a cuein base that is a modified guanine. This base forms a wobble pair with the codon sequence on the mRNA. H. Forms base pairs that do not follow the Watson-Crick base pairing rules. tRNA usually binds "loosely" to mRNA at the third codon position. This allows for multiple types of non-Watson-Crick base pairs or wobble bases at the third codon position. The presence of a cuein in the first position of the anticodon, paired with the third position of the codon, has been observed to improve the translational fidelity of tRNA.
Structure of transfer RNA
Like all molecules of the nucleic acid family, transfer RNA is composed of nucleotides. Nucleotides contain a sugar, a phosphate group, and a nitrogenous base. In RNA, the sugar used is ribose and the base can be A, U, C, or G. Although not shown much in the diagram, it should be remembered that As, Us, Cs, and Gs have this complete nucleotide structure, with a ribose sugar and a phosphate group, respectively.
A tRNA structure is the structure of an RNA strand folded into a series of loops. Amino acids are attached at one end, shown in blue in the diagram as the acceptor stem. At the opposite end are groups of three nucleotides called anticodons. Anticodons are adapted to mRNA sequences by the ribosome. The ribosome transfers (attaches) an amino acid to the growing polypeptide chain, at which point the tRNA molecule can be considered empty. However, it is reusable and can accommodate another amino acid of the same type.
Key points:
tRNAs are synthesized from the tRNA gene by RNA polymerase and matured by processing, splicing, CCA addition, and post-transcriptional modifications.
tRNA synthesis is controlled by promoter activity and specific factors (ppGpp and/or pppGpp in prokaryotes and Maf1 in eukaryotes), depending on the nutritional status of the cell.
The relative amount of tRNA is regulated by several factors. tRNA gene copy number, transcriptional activity above, and tRNA degradation by various nucleases.
The primary transcript of the tRNA gene contains 5' and 3' extra sequences that are removed by various causative nucleases.
In some cases, tRNA transcripts contain introns spliced out by specific endonucleases, and the two resulting fragments are joined by RNA ligase. CCA-adding enzymes regulate the amount of active tRNA by repairing the CCA sequence at the C-terminus of tRNA.
tRNA has various modified nucleotides introduced by modifying the enzyme during or after the processing, splicing, and transport steps.
Several modifications of tRNA play important roles in the translation process, including: B. Enhancement, elongation, restriction and/or alteration of codon-anticodon interactions, stabilization of tRNA structure, recognition by aminoacyl-tRNA synthetase, etc.
