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How Proteins are Made

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Proteins are the molecular machines at the heart of life. Capable of moving muscles, digesting food, and informing the brain about stimuli as diverse as the light bouncing off of a beautiful painting or the chemicals wafting up from a rotting corpse, proteins are essential to nearly every action performed by a modern day cell. According to the basic dogma of molecular biology, DNA1 can be transcribed into RNA which is then translated into amino acid chains. These chains can then fold into the functional proteins used by the cell.


The blueprints, or genes, for a cell's proteins are contained in its DNA2. Each double-helical DNA molecule consists of two long sugar-phosphate backbones to which are attached, like charms on a charm bracelet, four different types of nitrogenous bases: guanidine (G), cytosine (C), adenosine (A), and thymidine (T). Through hydrogen bonds, the bases on one strand of a DNA molecule are able to form specific pairs with the bases on the other strand, G pairing with C and A pairing with T. Because of this specific pairing, the sequence of the bases on any strand reflects the sequence of its complementary strand.

For example, if one strand contains the sequence TCAGACGAGGAGGTC, the other strand must contain the sequence GACCTCCTCGTCTGA. This complementariness allows the blueprint for each protein to be reproduced on new strands of DNA each time the cell divides. Some of these blueprints are constantly being read by the cell (constitutively expressed), while others are read only at specific times, by specific cell types, or in response to specific signals.

When a gene is in an active, 'readable' state, a protein complex called RNA polymerase can make single stranded RNA copies of the original DNA sequence of the gene. Like DNA, a strand of RNA contains a sugar-phosphate backbone to which four different types of nitrogenous bases are attached. RNA contains the base uracil (U) instead of thymidine; however, since U is very similar to T, lacking only one methyl group, RNA is able to form U-A base pairs analogous to the T-A base pairs in DNA. RNA polymerase makes use of RNA's ability to form specific base pairs with DNA to make its messenger RNA copies.

For example, if the original gene for a protein contains the sequence TCAGACGAGGAGGTC, its complementary strand will contain the sequence GACCTCCTCGTCTGA and its initial RNA transcript will contain the sequence GACCUCCUCGUCUGA3.


Finally, an RNA/protein complex called the ribosome builds a protein, a chain of amino acids, based on the blueprint in the messenger RNA. In most organisms, the blueprint is translated based on the 'universal' genetic code. The molecular basis for this code lies in transfer RNA. These are RNA molecules that are transcribed in the same manner as messenger RNA but which, instead of being read as messages, can fold independently into L-shaped structures. One arm of the L contains an anticodon loop which displays three bases specific to the transfer RNA. Since there are four different types of bases that can occur in the anticodon (U, A, G, and C), there are 4x4x4=64 possible anticodons. Sixty-one of these possible anticodons are found in transfer RNAs. Proteins called aminoacyl-tRNA syntheses can recognise specific transfer RNAs and attach one of 20 amino-acids to the other arm of the L. Because of the specificity of the aminoacyl-tRNA syntheses, each anticodon will always be associated with the same amino acid. Therefore, by allowing three-base codons in the messenger RNA to pair in a specific fashion with their corresponding anticodons in transfer RNA, ribosomes are able to translate a specific RNA sequence into a specific amino acid sequence.

For example, the RNA sequence GACCUCCUCGUCUGA is translated into the amino acid sequence serine-aspartate-glutamate-glutamate-valine in the nuclei of most cells.

As each transfer RNA arrives at the ribosome, its amino acid is removed and added to the growing amino-acid chain that will become the protein. This process is terminated when the ribosome arrives at a stop codon in the messenger RNA, one of the three codons for which there is no transfer RNA containing the corresponding anticodon. These stop codons are recognised by release factors, which cause the ribosome to release the newly synthesized protein4.

Each of the 205 amino acids encoded by the 'universal' code has unique structural and chemical properties, distinct preferences for certain three-dimensional conformations, for certain interactions with other amino acids. Based on the particular combination of properties the protein derives from its component amino acids, a given protein will be able to adopt certain three-dimensional folded shapes6, to catalyze specific chemical reactions, and to interact with other proteins - in effect, to become one of many microscopic machines carrying out the tasks vital to this thing we call life.

1It is necessary to point out that we are referring to Deoxyribonucleic Acid and not Douglas Noel Adams.2Therefore, by modifying an organism's DNA, one can introduce new protein blueprints into that organism. For a perspective on this sort of genetic engineering, see Frankenstein (Genetically Modified) Foods.3The messenger RNA can then be processed in a number of ways.4The protein can then be post-translationally modified in a number of ways.5In addition to the canonical 20 amino acids, proteins can contain post-translationally modified amino acids as well amino acids such as seleno-methianine which are incorporated during translation in certain contexts.6These folded shapes are most easily adopted at a protein's native temperature. Heating up a protein solution can result in tangling up all of the protein chains, resulting in an amorphous colloid, which is bad if you're a cell but quite nice if you're trying to make scrambled eggs.

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