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Protein Structure

Proteins have a very complex structure. They are made up of chains of amino acids in a specific sequence, which is determined by segments of the genetic code in a cell’s DNA. The number of amino acids in the chain can vary from as little as ten to many thousands.

Up to 20 different amino acids can be built into the protein directly from the DNA sequence via messenger RNA. These amino acids are called the proteinogenic amino acids.

They include the nine essential amino acids, which must be supplied in the food. They are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine.

The remaining 11 non-essential amino acids, which can be made in the body from other molecules are: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine.

Primary structure

The primary structure of proteins refers to the sequence of the amino acids in the amino acids chain or ‘polypeptide’ chain.

The primary structure is held together by chemical bonds made during the synthetic process of the protein taking place in the cells’ cytoplasma at the ribosomes, which is where the amino acid chain is made using the messenger RNA as a template for the formation.

Thus the sequence of bases in messenger RNA (mRNA) - being a copy of the DNA base sequence in the gene for the protein - is translated into the specific amino acid sequence, which determines the special characteristics of the protein in question. In this process transfer RNA (tRNA) is an important intermediary bringing the amino acids in the correct position at the ribosome enabling formation of the peptide chain (se figure).

In our body there are over 10,000 different proteins. Each protein has its own unique number and sequence of amino acids.

Protein folding is the process by which a protein assumes its functional shape or conformation. It is the physical process by which a polypeptide chain folds into its characteristic and functional three-dimensional structure.

As mentioned above each protein starts as an unfolded polypeptide chain when translated from the sequence of messenger RNA to the linear chain of amino acids.

In this chain the amino acids interact with each other to produce a well-defined three-dimensional structure, which is the final functional form of the protein. This form is determined by the amino acid sequence (Anfinsen's dogma).

The final three-dimensional structure of the protein is obtained through the following additional conformations.

Secondary structure

The secondary structure of proteins refers to regular local sub-structures, which are formed in certain areas of the amino acid chain. There are two main types of secondary structure, the alpha helix and the beta sheet. They arise due to weak (hydrogen) bonding between certain groups in the amino acid chain. These secondary structures give rise to a regular geometry in certain parts of the protein molecule. Several sequential secondary structures may form a "supersecondary unit".

Tertiary Structure

The tertiary structure of proteins refers to the three-dimensional structure of the whole single protein molecule. The alpha-helices and beta-sheets are folded into a compact globule. The folding is driven by the non-specific hydrophobic interactions, but the structure is stable only when the parts of a protein domain are locked into place by specific tertiary interactions, such as salt bridges, hydrogen bonds, and the tight packing of side chains and disulfide bonds.

Quaternary structure

The quaternary structure of proteins is the three-dimensional structure of a multi-subunit protein. The final 3D structure is determined by how the subunits fit together. In this context, the quaternary structure is stabilized by the same non-covalent interactions and disulfide bonds as the tertiary structure. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, and a tetramer if it contains four subunits.

Proteins consist frequently of several structural subunits.

Structural domains

A structural domain is a part of the protein's overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the proteins of one gene or one gene family but instead appear in a variety of proteins. Domains often are named after their biological function in the protein they belong to; for example, the "calcium-binding domain of calmodulin". Because structural domains are independently stable, they can be "swapped" by genetic engineering between different proteins.

The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded. Failure to fold into the normal structure generally produces inactive proteins, but in some instances misfolded proteins have a modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins.

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