Genes control the synthesis of proteins, the most important molecules making up all life. Life is not just protein, for example, an oak tree is made up mostly of polysaccharides. But it is genes and proteins that determine what makes an oak tree a tree and not a fish or a bird or a bacterium.
Genes are stored, replicated and passed on in DNA. DNA is transcribed into messenger RNA (mRNA). When a mRNA molecule reaches a ribosome, it is translated into polypeptide chains, which fold into proteins. DNA, RNA and polypeptide chains are all linear polymers – long molecules composed of smaller repeating subunits.
RNA is an abbreviation for RiboNucleic Acid, as it is a long chain of repeating ribose subunits, each ribose has a nucleotide attached. These nucleotides can be guanine (G) , uracil (U) , adenine (A) , or cytosine (T) . Hydrogen bonds form nucleotides, most commonly 3 bounds between G and C and 2 bonds between U and T, referred to as complementary nucleotides. These bonds shape the RNA molecule and RNA can fold into many different useful structures and shapes. The ribosome itself is mostly composed of RNA. Some scientists speculate that early life came from an RNA World, as RNA could theoretically contain and copy genetic information as well as serve as the structure of organisms before DNA or proteins. Since ribose is not symmetrical, neither is RNA. Scientists refer to a 3 Prime (3’) and 5 prime (5’) end of RNA. These terms came from the convention of numbering Carbon atoms in a ribose molecule from 1’ to 5’.
DNA is an abbreviation for DeoxyriboNucleic Acid, and is similar to RNA. Deoxyribose is similar to ribose, but lacks an −OH, called a hydroxyl group, giving us the terms deoxy sugar and Deoxyribose. This difference in structure leads to DNA forming the well-known double-helix structure – a deoxyribose backbone with nucleotides is paired with another deoxyribose backbone with complementary nucleotides. This arrangement facilitates copying DNA or transcription, since when separating both strands, either strand contains all the genetic information stored in both pairs, and either a new pair or messenger RNA can be created. This structural difference from RNA, however, limits the number of structures DNA can fold into, making an organism built entirely of DNA implausible. Similar to RNA, we can use the 3’ and 5’ convention to refer to direction, but can also use positive and negative strands, or coding and template strands. In DNA, uracil is replaced by thymine (T).
During translation, the hydrogen bonds on RNA are broken so the ribosome can read RNA as a sequence of nucleotides, this process is referred to as elongation. The mRNA is read from the 3’ end. The first section of the mRNA typically doesn’t encode for a protein, and since it is towards the 5’ end, it is referred to as the 5 prime untranslated region(5’ UTR). Similarly, RNA after the end of the coding region is referred to as the 3 prime untranslated region(3’UTR). Both the 5' UTR and 3' UTR were once thought of as unimportant, but play a role in regulating how much protein is made. A single mRNA is read in parallel by several ribosomes at once, with each ribosome reading a different portion of the mRNA at the same time. The translation process is remarkably similar between all known forms of life.
Nucleotides are translated in sequences of codons, 3 nucleotides identifying the specific amino acid that should be added to a polypeptide chain to create the protein. The mRNA is read until the first start codon, typically AUG. Having 3 possible combinations of 4 possible nucleotides gives 64 possible codons. With only 20 amino acids coded for in unexceptional circumstances, there is redundancy in this code, for example, ‘CUU, CUC, CUA and CUG all typically encode the amino acid Leucine. Each codon is associated with a transfer RNA(tRNA), a molecule of RNA specific to the codon that carries the amino acid. Normally each tRNAs must be available, if CUU is read and that tRNA is unavailable, it doesn’t matter if CUC CUA or CUG codons are available, translation will stop. A codon for a tRNA that doesn’t arrive in time typically aborts the translation and the partial protein product is recycled. Life has exceptions to rules, and there are some cases, known as wobble-pairs, where a different tRNA can be used that encodes the same animo acid. Nucleotides are read until a stop codon (typically UAG, UAA, or UGA) is reached.
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