When it comes to the inner workings of our cells, the tiny but mighty ribosomes are an essential part of the puzzle. These incredible molecular machines are responsible for the translation step of the central dogma. Ribosomes translate the genetic information encoded in messenger RNA (mRNA) and synthesize proteins, the building blocks of life. But what are ribosomes made of? And where do they come from? Let's uncover these questions in this topic.
Structure and functions
A ribosome is a complex cellular structure present in all living organisms. It is responsible for the synthesis of proteins within the cell. The process begins with the transcription of DNA into mRNA in the nucleus. The mRNA then exits the nucleus and binds to a ribosome. The ribosome moves along the mRNA, reading each codon (a sequence of three nucleotides) and recruiting the appropriate amino acid (which is bound by tRNA) to add to the growing chain. Thus, the ribosome translates a specific sequence of nucleotides in the mRNA into a specific sequence of amino acids, which form a protein.
Ribosomes are very ancient and conservative structures: they exist in both prokaryotic and eukaryotic cells. Ribosomes are also present in both chloroplasts and mitochondria. These organelle-specific ribosomes are slightly different from the ones found in the cytoplasm, and their presence is essential for the proper functioning of these organelles. In fact, these ribosomes are similar to the ones found in bacteria, which supports the theory that chloroplasts and mitochondria were once free-living bacteria that were engulfed by ancestral eukaryotic cells. Chloroplastic ribosomes are more similar to bacterial ones, as many pieces of ribosomal RNA in mitochondria are shortened or replaced by other structures.
Prokaryotic ribosomes are smaller (70S) and consist of two subunits – 30S and 50S. They are found in the cytoplasm and are often attached to the cell membrane.
Eukaryotic ribosomes are larger in size (80S) and consist of two subunits – 40S and 60S. They are present in the cytoplasm and also in the endoplasmic reticulum.
Subunits have functional differences. The large subunit of eukaryotic ribosomes is involved in the catalysis of peptide bond formation during protein synthesis. In contrast, the small subunit is involved in binding to the mRNA and initiating protein synthesis.
Ribosomal RNA and proteins
In prokaryotes, ribosomes are made up of about 60% ribosomal RNA (rRNA) and 40% ribosomal proteins by weight and are about half protein and half rRNA in eukaryotes. Both types of molecules are needed for the proper functioning of the ribosome.
Although it is never translated into proteins, ribosomal RNA is the most common type of RNA in cells, comprising roughly 80% of cellular RNA. The catalytic functions of ribosomes are covered by ribosomal RNAs.
There are some differences in the RNA composition of ribosomes in prokaryotes and eukaryotes. Prokaryotic ribosomes have 16S rRNA, while eukaryotic ribosomes have 18S rRNA in their small subunit. In the large subunit, prokaryotes have 23S rRNA and 5S rRNA, whereas eukaryotes have 28S rRNA, 5.8S rRNA, and 5S rRNA.
rRNA is a popular field of scientific interest. Ribosomal RNA genes resist mutations and alterations due to their crucial role in protein synthesis. rRNA is also one of the few gene products present in all cells. Therefore, genes that encode rRNA (rDNA) are often sequenced to identify an organism's taxonomic group, calculate related groups, estimate rates of species divergence, and investigate microbial diversity. For example, the primary method used to distinguish between similar prokaryotic species is by analyzing the nucleotide similarity derived from 16s rRNA. As a result, there are specialized databases containing many thousands of rRNA sequences.
Ribosomal proteins are essential for the proper assembly and function of the ribosome. They play a crucial role in stabilizing the structure of the ribosome and facilitating the interactions between its different components such as the ribosomal RNA and other ribosomal proteins. There are over 50 ribosomal proteins in prokaryotic ribosomes and approximately 80 different ones in eukaryotic cells.
Ribosomal proteins are structurally and functionally conserved across species.18 proteins among the large ribosomal subunits and 15 proteins found in various small ribosomal subunits are universal for all lifeforms. And archaea don't have unique ribosomal proteins at all!
Mutations in ribosomal proteins can have serious consequences, with some genetic disorders being linked to mutations in specific ribosomal proteins. For example, Diamond-Blackfan anemia is a rare genetic disorder that is caused by mutations in genes encoding for ribosomal proteins, leading to abnormal development of red blood cells and other developmental abnormalities.
Making of ribosomes
Cell spends about 60% of its own energy on making and maintenance of ribosomes. The genes coding for ribosomal RNAs (rRNAs) are usually transcribed together as a single unit. In prokaryotes, the 16S, 23S, and 5S rRNA genes are transcribed together with sequences of transport RNAs as a single unit. Before the transcription is complete, the cell starts to process this long transcript and, as a result, releases RNAs as separate molecules.
Eukaryotes transcribe 3 of their 4 rRNAs in the nucleolus, a special structure in the nucleus. There, RNA polymerase I uses special genes, which are present in multiple copies throughout the genome. These genes contain sequences of 18S, 28S, and 5.8S rRNAs, which are separated by internal transcribed spacers (ITS). After transcription, the large precursor rRNA (pre-rRNA) undergoes a series of processing and maturation steps in order to become functional ribosomal RNA. During these steps, a series of small nucleolar ribonucleoprotein (snoRNP) complexes add chemical modifications to specific nucleotides in the pre-rRNA molecule. These modifications are important for the proper folding and functioning of the mature rRNA. The cleavage of the pre-rRNA transcript removes spacer sequences and releases rRNAs as individual molecules.
The 5S rRNA is transcribed outside the nucleolus by RNA polymerase III. The pre-5S rRNA then moves to the nucleolus, where it also undergoes the processing step.
Finally, the mature rRNA molecules assemble together with ribosomal proteins into ribosomal subunits. Synthesis of ribosomal proteins occurs in the cytoplasm, and they enter the nucleus through nuclear pores. Once both subunits are assembled, they move out of the nucleus into the cytoplasm, where they form a functioning ribosome.
Conclusion
The ribosome is a complex molecular machine found within cells that serves as the site of biological protein synthesis. Ribosomes are composed of the small subunit and the large subunit and are made up of RNA (ribosomal RNA or rRNA) and protein molecules. The small subunit of the ribosome binds messenger RNA and participates in the initiation of translation. In contrast, the large subunit catalyzes the formation of peptide bonds between amino acids to form the final protein product. Prokaryotic and eukaryotic ribosomes differ in size and structural components.