R rna
- 1. Ribosomal Ribonucleic Acid (rRNA) To: Dr. Smita Rastogi Verma Presented By: Sandeep Kumar (2K19/BT/043)
- 2. Ribosomal Ribonucleic Acid (rRNA) rRNA is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins by mass.
- 3. Structure The primary structure of rRNA sequences can vary across organisms, base-pairing within these sequences commonly forms stem-loop configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional rRNA structures that are similar across species. Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. These ribosomal proteins contain basic residues (as opposed to acidic residues) and aromatic residues (i.e. phenylalanine, tyrosine and tryptophan) allowing them to form chemical interactions with their associated RNA regions, such as stacking interactions. An example of a fully-assembled small subunit of ribosomal RNA in prokaryotes, specifically Thermus Thermophilus. The actual ribosomal RNA (16S) is shown coiled in orange with ribosomal proteins attaching in blue.
- 4. Ribosomal proteins can also cross-link to the sugar-phosphate backbone of rRNA with binding sites that consist of basic residues (i.e. lysine and arginine). All ribosomal proteins (including the specific sequences that bind to rRNA) have been identified. Ribosomal RNA organizes into two ribosomal subunits: the large ribosomal subunit (LSU) and small ribosomal subunit (SSU). Between these subunits, the rRNA types used to form the subunit differ
- 5. Subunits and associated Ribosomal RNA Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits, one large and one small. Type Size Large subunit (LSU rRNA) Small subunit (SSU rRNA) Prokaryotic 70S 50S (5S : 120 nt, 23S : 2906 nt) 30S (16S : 1542 nt) Eukaryotic 80S 60S (5S : 121 nt, 5.8S : 156 nt, 28S : 5070 nt) 40S (18S : 1869 nt) Note that "nt" represents the length of the rRNA type in nucleotides and the "S" (such as in "16S) represents Svedberg units.
- 6. In the ribosomes of prokaryotes such as bacteria, the SSU contains a single small rRNA molecule (~1500 nucleotides) while the LSU contains one single small rRNA and a single large rRNA molecule (~3000 nucleotides). These are combined with ~50 ribosomal proteins to form ribosomal subunits. . There are three types of rRNA found in prokaryotic ribosomes: 23S and 5S rRNA in the LSU and 16S rRNA in the SSU. In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. In Prokaryotes Example of typical rDNA sequence found repeated throughout the genome, specifically of the internal transcribed spacer between 16S and 23S found in bacteria.
- 7. The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal RNAs). Therefore it can be deduced that in both bacteria and archaea there is one rRNA gene that codes for all three rRNA types :16S, 23S and 5S. Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon. As shown by the image, There is an internal transcribed spacer between 16S and 23S rRNA genes. There may be one or more copies of the operon, dispersed in the genome (for example, Escherichia coli has seven). Typically in bacteria there are between one and fifteen copies. Archaea contains either a single rRNA gene operon or up to four copies of the same operon. The 3' end of the 16S ribosomal RNA (in a ribosome) recognizes a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence.
- 8. In the ribosomes of eukaryotes such as humans, the SSU contains a single small rRNA (~1800 nucleotides) while the LSU contains two small rRNAs and one molecule of large rRNA (~5000 nucleotides). Eukaryotic rRNA has over 70 ribosomal proteins which interact to form larger and more polymorphic ribosomal units in comparison to prokaryotes. There are four types of rRNA in eukaryotes: 3 species in the LSU and 1 in the SSU. Yeast has been the traditional model for observation of eukaryotic rRNA behavior and processes, leading to a deficit in diversification of research. In yeast, the LSU contains the 5S, 5.8S and 28S rRNAs. The combined 5.8S and 28S are roughly equivalent in size and function to the prokaryotic 23S rRNA subtype, minus expansion segments (ESs) that are localized to the surface of the ribosome which were thought to occur only in eukaryotes. In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats. In Eukaryotes
- 9. In humans, approximately 300–400 repeats are present in five clusters, located on chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 21 (RNR4) and 22 (RNR5). Humans have 10 clusters of genomic rDNA which in total make up less than 0.5% of the human genome. Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules and 4 types of cytoplasmic rRNA (the 28S, 5.8S, 18S, and 5S subunits). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers. The first spacer corresponds to the one found in bacteria and archaea, and the other spacers an insertion into what was the 23S rRNAin prokaryotes. The 45S rDNA is organized into 5 clusters (each has 30–40 repeats) on chromosomes 13, 14, 15, 21, and 22. Diagram of ribosomal RNA types and how they combine to create the ribosomal subunits.
- 10. These are transcribed by RNA polymerase I. The DNA for the 5S subunit occurs in tandem arrays (~200–300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by RNA polymerase III. The 18S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5.8S and 28S in mammals, 25S in plants, rRNAs). The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystall- ographyThe secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown. Small subunit ribosomal RNA, 5' domain taken from the Rfam database. This example is RF00177, a fragment from an uncultured bacterium.
- 11. Functions of rRNA Universally conserved secondary structural elements in rRNA among different species show that these sequences are some of the oldest discovered. They serve critical roles in forming the catalytic sites of translation of mRNA. During translation of mRNA, rRNA functions to bind both mRNA and tRNA to facilitate the process of translating mRNA's codon sequence into amino acids. rRNA initiates the catalysis of protein synthesis when tRNA is sandwiched between the SSU and LSU. In the SSU, the mRNA interacts with the anticodons of the tRNA. In the LSU, the amino acid acceptor stem of the tRNA interacts with the LSU rRNA. The ribosome catalyzes ester-amide exchange, transferring the C-terminus of a nascent peptide from a tRNA to the amine of an amino acid. These processes are able occur due to sites within the ribosome in which these molecules can bind, formed by the rRNA stem-loops. A ribosome has three of these binding sites called the A, P and E sites:
- 12. • In general, the A (aminoacyl) site contains an aminoacyl-tRNA (a tRNA esterified to an amino acid on the 3' end). • The P (peptidyl) site contains a tRNA esterified to the nascent peptide. The free amino (NH2) group of the A site tRNA attacks the ester linkage of P site tRNA, causing transfer of the nascent peptide to the amino acid in the A site. This reaction is takes place in the peptidyl transferase center. • The E (exit) site contains a tRNA that has been discharged, with a free 3' end (with no amino acid or nascent peptide). A single mRNA can be translated simultaneously by multiple ribosomes. This is called a polysome. A simplified depiction of a ribosome (with SSU and LSU artificially detached here for visualization purposes) depicting the A and P sites and both the small and large ribosomal subunits operating in conjunction.
- 13. In prokaryotes, much work has been done to further identify the importance of rRNA in translation of mRNA. For example, it has been found that the A site consists primarily of 16S rRNA. Apart from various protein elements that interact with tRNA at this site, it is hypothesized that if these proteins were removed without altering ribosomal structure, the site would continue to function normally. In the P site, through the observation of crystal structures it has been shown the 3' end of 16s rRNA can fold into the site as if a molecule of mRNA. This results in intermolecular interactions that stabilize the subunits. Similarly, like the A site, the P site primarily contains rRNA with few proteins. The peptidyl transferase center, for example, is formed by nucleotides from the 23S rRNA subunit. In fact, the peptidyl transferase center contains no proteins, and is entirely initiated by the presence of rRNA. Unlike the A and P sites, the E site contains more proteins. Because proteins are not essential for the functioning of the A and P sites, the E site molecular composition shows that it is perhaps evolved later. In primitive ribosomes, it is likely that tRNAs exited from the P site. Additionally, it has been shown that E-site tRNA bind with both the 16S and 23S rRNA subunits.