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Amino acids can form short chains called peptides or longer chains called polypeptides, which include proteins. The order of amino acids in a polypeptide chain determines the three-dimensional structure of the molecule, which is crucial for protein function. Amino acids have a general structure consisting of a carbon atom, an amino group, a carboxyl group, and an R group. Peptide bonds form between the amino and carboxyl groups of adjacent amino acids, releasing a water molecule. The sequence of amino acids in a protein is its primary structure, while bonds between side chains contribute to its secondary, tertiary, and quaternary structures. An organism’s DNA encodes the amino acid sequence for each protein, which is assembled during translation of mRNA in ribosomes.
Amino acids can be linked together to form chains containing anywhere from two to many thousands of units. The short chains are known as peptides, while the longer chains are called polypeptides, which include proteins. An amino acid sequence is simply the order of these units in a polypeptide chain. In the case of proteins, the sequence determines the three-dimensional structure of the molecule, which in turn is crucial for the function of the protein. The amino acid sequences in proteins found in a living organism are encoded in that organism’s DNA.
Structure of amino acids
Amino acids all have a general structure consisting of a carbon atom with an amino group (NH2) on one side, a carboxyl group (COOH) on the other, and what is called an R group, or side chain. “R” stands for radical, which in this context simply means a part of a molecule. It is the side chain composition that distinguishes the different amino acids from each other. In the simplest, glycine, it consists of only one hydrogen atom, but in others the side chain is more complex. For example, in tyrosine it has a ring structure and in lysine it consists of a long chain of hydrocarbons, a molecule made up of a carbon skeleton with hydrogen atoms attached.
How sequences are formed
The amino group is basic and carries a positive charge, while the carboxyl group is acidic and carries a negative charge. Since acids and bases react with each other, this makes it possible for the amino group of one amino acid to bond with the carboxyl group of another. This is known as a peptide bond and it releases a water molecule as a byproduct. Chemical processes like this are known as condensation reactions, because some of each molecule is lost in the process: the H from NH2 and the OH from the COOH group combine to form water (H2O). Strictly speaking, the amino acid units that form peptides and proteins should be called amino acid residues, but are usually simply referred to as amino acids.
Sequence descriptions
A chain of these units will typically have an amino group at one end and a carboxyl group at the other. For consistency, the sequences are described from left to right, with the amino terminus, known as the N-terminus, on the left, and the carboxyl terminus, or C-terminus, on the right. It is also possible, however, for opposite ends of a polypeptide chain to form a peptide bond, resulting in a cyclic molecule.
Proteins and other polypeptides can therefore be described by the sequence of amino acid units. For brevity, unit names are usually abbreviated to three letters or a single letter. For example, in the three-letter system, arginine is Arg, leucine is Leu, and proline is Pro. In the one-letter system, the letters for these units are R, L, and P, respectively. Therefore, a particular sequence of amino acids could be represented as Leu-Arg-Leu-Pro-Arg-Pro, or as LRLPRP.
Form and function of proteins
The sequence of units in a protein is known as its primary structure. However, bonds can also form between the side chains of a polypeptide chain, causing them to fold in various ways, and between the side chains of adjacent polypeptide chains. These types of bonds contribute to the so-called secondary, tertiary and quaternary structures of proteins, which determine the overall three-dimensional shapes of molecules. The bonds between side chains are usually weaker than peptide bonds and factors such as heat and various chemicals can break them, causing a protein to lose its shape, but preserving the primary structure. This is known as denaturation.
Although there are over 100 known amino acids, only about 20 are found in the proteins that make up living organisms. However, these 20 can form many thousands of different sequences, of varying lengths. Many proteins consist of more than one polypeptide chain and can form huge molecules of enormous complexity.
Proteins, genes and DNA
An organism’s DNA can be thought of as a set of instructions for putting together all the proteins it needs. The amino acid sequence required for each protein is encoded in DNA in the form of groups of three nucleotides known as codons, each representing a particular amino acid unit. The processes of transcription of DNA and translation of RNA allow these units to be assembled in the correct sequences to form the proteins needed when cells divide.
First, DNA is transcribed to form a strand of messenger RNA or mRNA. The mRNA travels out of the nucleus and into the cytoplasm of the cell into a ribosome, where translation occurs. mRNA serves as a template for amino acids, allowing them to join together. For each codon, the transfer RNA, or tRNA, carries the appropriate free amino acid from the cytoplasm to the ribosome where they join the existing chain. When mRNA is translated, the units are joined to form the specific sequence for that protein.
