Protein structure

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Proteins are made up of polymers of amino acids. The amino acids are joined together by peptide bonds in a condensation reaction. This series of peptide bonds is also known as the polypeptide backbone, off which are side chains made up of amino acids. This type of reaction is catalysed by the ribosome in the cytoplasm and releases a water molecule. There are four levels of protein structure, which determine the proteins overall structures and functions.

Contents

Primary Structure

The primary structure is the specific linear sequence of amino acids joined by covalent peptide bonds in a polypeptide chain[1]. The primary structure is determined by DNA base sequence via triplet base coding. The R group of an amino acid determines the function and properties of the protein, which is reflected in the proteins tertiary structure.

Secondary Structure

The secondary structures of proteins is formed by the way the protein coils, the main ones are the alpha helix and the beta pleated sheet[2]. The secondary protein structure is stabilised by hydrogen bonds which are 1/10 the strength of covalent bonds[3]. These hydrogen bonds are provided by the peptide bonds. For example, the bond is formed between the carbonyl oxygen on amino acid residue 'N' and the amide nitrogen on amino acid 'N + 4'.

Tertiary Structure

The protein then continues to fold from the secondary structure to form a three-dimensional structure. This is known as the tertiary structure, or commonly reffered to as the 3D conformation of the protein. There are many bonds which maintain the tertiary structure including: ionic bonds (between NH3+ and COO-), hydrogen bonds, hydrophobic interactions (i.e. some amino acids have hydrophobic 'R' groups which position themselves furthest away from water) and disulphide bridges. Disulphide bridges are formed in the tertiary structure. They are formed between amino acids which contain a thiol group (SH). The H+ is lost very easily in an oxidation reaction with another SH group and the two join with a disulphide bond. Proteins that have to work outside of the cell use disulphide bonds to increase their stability.

Quaternary Structure

If two or more tertiary structures form a single structure then it is a quaternary structure. An example of a quaternary structure are haemoglobin molecules, which are made up of four globin molecules which contain 2 alpha and 2 beta subunits. These are also known as red blood cells and are found in blood[4].

Proteins can come in all different shapes and sizes[5] due to the fact that there is any possible sequence of amino acids and that a protein can be made of an alpha helix, a beta-pleated sheet or both. The amino acids which tend to be conserved in proteins are those which make up the active site, as this is the part of the protein which has most functional significace[6].

Polypeptide Backbone

The polypeptide backbone is made up of rigid peptide bonds and some flexible links which allow protein molecules to fold. The backbone also consists of a repeated sequence of three atoms of each residue in the chain-the amide N, the alpha carbon and the carbonyl carbon, the highest distance between corresponding atoms of adjacent residues is 3.80A when the peptide bond is trans but, when the chain is fully extended, the residues are staggered, so the maximum linear dimension of a polypeptide with n residues is n x 3.63A. Energetically, the trans form is highly favoured probably because of the fewer repulsion between non-bonded atoms. The intrinsic stability of the cis isomer is comparable to that of the trans isomer.

References

  1. http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html
  2. Alberts et al. (2008). The Biology of the Cell. 5th ed. New York: Garland Science. 154
  3. Khan Academy. Hydrogen Bonds in Water. 2015 [cited 04/12/17]; Available from: https://www.khanacademy.org/science/biology/water-acids-and-bases/hydrogen-bonding-in-water/a/hydrogen-bonding-in-water
  4. Alberts et al., (2008) Molecular Biology of the Cell, 5th Edition, Garland Science, Chapter 3, Page 136
  5. Alberts et al.(2008) Molecular Biology of the Cell, 5th Edition, Garland Science Chapter 3 Page 144
  6. Thomas E. Creighton(1993) Proteins, 2nd edition, USA: W.H. Freeman and Company.
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