RNA (Ribonucleic Acid): a "nucleic acid" molecule related to DNA. (Kandel, 448) Large linear molecule made up of a single chain of ribonucleotide subunits. (Lawrence) A direct copy of DNA. (Micklos, 45)
Unlike DNA, RNA is single-stranded. An RNA strand has a backbone made of alternating sugar ("ribose") and "phosphate groups." Attached to each sugar is one of four bases - adenine, uracil, cytosine, or guanine. (NHGRI) Ribonucleic acid contains information that has been copied from DNA. Cells make several different forms of RNA, and each form has a specific job in the cell. Many forms of ribonucleic acid have functions related to making proteins. RNA is also the “genetic material” of some “viruses” instead of DNA. Ribonucleic acid can be made in the laboratory and used in research studies. (NCIt) There are a number of different forms of RNA and two of these are very important in "protein synthesis" - "messenger RNA" and "transfer RNA." (Indge, 237) Unique among “macromolecules” in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses "catalytic" activity. (MeSH)
Complementary RNA (cRNA): synthetic RNA transcribed from a single-stranded DNA template. (Lawrence) RNA whose base sequence is complementary to specific "DNA sequences." (GHR) Synthetic "transcripts" of a specific DNA molecule or fragment made by an "in vitro" transcription system. (HGPIA)
Messenger RNA (mRNA): a form of RNA that is “transcribed” from one of the two "strands" of DNA that carries the gene’s instructions for protein synthesis from the “nucleus” of the cell to the “cytoplasm.” (Kandel, 258). The true template for protein synthesis. (Watson, 73) Carries genetic information to protein synthesis machinery. (Norman, 6/17/09) Made by “RNA polymerase II.” (Micklos, 47) The mRNA is an RNA version of the gene that leaves the cell “nucleus” and moves to the “cytoplasm” where proteins are made. During protein synthesis, an organelle called a “ribosome” moves along the mRNA, reads its “base sequence,” and uses the “genetic code” to translate each three-base triplet, or “codon,” into its corresponding “amino acid.” (NHGRI) Also referred to as 'transcript.'
Pre-mRNA: the RNA transcript prior to any processing. (Brooker, G-29) Contains all the information in an individual’s genome. Stays inside the nucleus. Must be processed to remove sequences of genetic code that will not be used. (Norman, 7/21/09) In (animals), transcription produces a longer RNA which undergoes certain processing events before it exists the nucleus. (Brooker, G-22)
Mature mRNA: the final functional product. (Brooker, G-22)
MicroRNA (miRNA): small molecules found in plants and animals that may regulate the activity of genes. (GNN) Small double-stranded, non-protein coding RNAs generated from single-stranded microRNA gene transcripts. They become part of the RNA-induced 'silencing complex' and repress the translation of target RNA by "binding" (to mRNA). (MeSH) Noncoding RNA. Small, just 21 or 22 bases long. The human genome has close to 1,000 distinct microRNAs that regulate at least one-third of the protein-encoding genes. A typical human cell has 1,000 to 200,000 microRNAs. When a microRNA binds a target mRNA, it prevents translation. (Lewis, 204)
Ribosomal RNA (rRNA): synthesizes proteins. (Norman, 6/17/09) Forms part of "ribosomes," which provide the arena in which “translation” occurs. (Brooker, 236) Made by “RNA Polymerase I.” (Micklos, 47) Experiments done in my lab at Harvard and at both Caltech and Cambridge showed that ribosomes were, in effect, molecular factories. Messenger RNA passed between the two ribosomal subunits, like ticker tape being fed into an old-fashioned computer. (Watson, 73) 243 types of rRNA are grouped on chromosomes (in clusters), each cluster harboring 150 to 200 copies of a 44,000-base repeat sequence. Once transcribed from these clustered genes, the rRNAs go to the "nucleolus," where the are cut into their final forms. (Lewis, 208) Editor’s note - in 1967 Fred Sanger determined the first rRNA nucleotide sequence - ‘5S ribosomal RNA.’ It included 120 nucleotides from the “E. coli” bacteria.
Large Subunit: binds to "tRNA." tRNA retrieves amino acids from the "cytoplasm" that match base pairing sequence of mRNA. (Norman, 7/22/09)
Small Subunit: location of the site for mRNA binding. Attached to mRNA strand at a specific site ‘upstream’ from the 'start sequence'. The positioning of the small subunit is aided by ‘initiation factors.' (Norman, 7/22/09)
RNA Polymerase: assists in the construction of the RNA molecules. (Lewis, 180) An enzyme important in the process of RNA transcription. Helps join nucleotides together to produce the mRNA molecule. (Indge, 238) Contains a cavity that allows it to slide along the DNA. The DNA strands enter at the side of the protein and are separated. Nucleotides can enter this region through a small pore. (Brooker, 236) In (animals), cannot bind to the “promoter" by itself; a group of other proteins must bind with it. (Micklos, 74)
RNA Polymerase I: makes ribosomal RNA. (Micklos, 47)
RNA Polymerase II: synthesizes messenger RNA. (Micklos, 47)
RNA Polymerase III: synthesizes small RNA molecules including transfer RNA. (Micklos, 47)
Transfer RNA (tRNA): a type of RNA responsible for converting the information contained in DNA into the formation of a new ”polypeptide.” Transfer RNA molecules, which carry amino acids, bind to the mature messenger RNA so that a polypeptide can be made, one amino acid at a time. (Brooker, 69) Important in assembling amino acids in the correct order during protein synthesis. A tRNA molecule with a particular “anticodon” will always attach to the same amino acid. (Indge, 276) Carries amino acids to rRNA. (Norman, 6/17/09) Translates the language of mature mRNA into that of amino acids. (Brooker, 236) Transfer RNA’s, each with its amino acids, were appropriately ordered before being chemically linked to form polypeptide chains. (Watson, 73) Dispersed among the chromosomes in clusters. Altogether, our 500 or so types of tRNA genes account for 0.1% of the genome. (Lewis, 207) Made by RNA polymerase III. (Micklos, 47) Editor’s note - in 1965 Robert Holley published the first tRNA sequence which included the seventy-seven ribonucleotides of ‘alanine’ transfer RNA.
Anticodon: a three-nucleotide sequence in tRNA that is complementary to a codon in mRNA. (Brooker, G-3) The sequential set of three nucleotides in transfer RNA. Interacts with its complement in messenger RNA, the codon, during "translation." (MeSH) During translation, a ribosome becomes attached to a molecule of mRNA. The ribosome is just the right size to hold two codons of mRNA. Suppose one of these codons has the sequence of “bases” ‘G-C-U’ which codes for the amino acid ‘alanine.’ Only a "tRNA" molecule with the complementary anticodon ‘CGA,’ will be able to bind to this codon. A tRNA molecule with this anticodon will always carry alanine. (Indge, 19)