Figure 4b shows only two amino acids joined together, but a complete polypeptide molecule would contain C=O and N-H groups at regular intervals along the chain. A hydrogen bond is normally represented by a dashed (or dotted) line, as follows:Īll of these are possible. A hydrogen bond can occur between a hydrogen atom with a partial positive charge (by virtue of its attachment to an oxygen or a nitrogen atom) in one part of the molecule, and a different oxygen atom or nitrogen atom (which has a partial negative charge), elsewhere in the same molecule, or in another molecule. Hydrogen bonding depends on partial positive and negative charges (much smaller than those mentioned above) which are present in some molecules. Although hydrogen bonds are weaker than the bonds that hold the atoms together to make up the amino acids in the protein chain, hydrogen bonding nevertheless plays a very important role, not only in protein folding, but elsewhere in chemistry too, particularly in conferring on water its unique properties. The third type of interaction is called hydrogen bonding. Similarly, two aspartates, each with a negative charge, will also repel one another. On the other hand, two lysines, both with a positive charge, will repel one another, pushing the two parts of the protein chain apart where they occur. If these amino acids occur in a protein, they can attract one another and bend the protein chain so that they lie close together. The amino acid lysine has a positive charge, whereas aspartate has a negative charge. Since the inside of the body provides a watery (aqueous) environment, the protein chain folds up with these hydrophobic groups clustered together on the inside, and the hydrophilic groups on the outside, as shown in Figure 7. The side chain of phenylalanine, containing the benzene ring, is one example. Four of the most important ones will be considered here.įirstly, some of the side chains of the amino acids – the R groups – a few of which were listed in Table 5 are hydrophobic, that is, they tend to associate with one another and to repel (or exclude) water molecules. The way in which each particular protein molecule folds is determined by a range of different interactions between the amino acids that make it up. Tri-means ‘three’ (the Latin and Greek roots are similar), as in tripod (podos is ‘foot’ in Greek), and poly- (as in polypeptide) means ‘many’ (polys is ‘much’ in Greek). Sometimes the Latin prefix bi- is used as an alternative for ‘two’ as in bicycle, binoculars, etc. You have already met carbon dioxide (a gas made up of one carbon and two oxygen atoms) and dipeptide, two amino acid molecules joined together. As you read on, you will meet disulfide – where di-means ‘two’ (from the Greek dis meaning twice) and -sulfide means related to the element sulfur. The second half of the words, -phobic and -philic, mean ‘hating’ and ‘beloved’, respectively, from the Greek words phobos which means ‘fear’ and philos,‘friend’. Even the element hydrogen was named because it was originally generated (genos in Greek means ‘descent’) from water. You probably recognise hydro- as being related to ‘water’ (it is from the Greek word for water), since it occurs in words like hydroelectric, hydrothermal, hydroponics, hydrostatic, etc. Coming up very soon are the words ‘hydrophobic’ and ‘hydrophilic’. During your studies you will meet a number of words which have Latin or Greek roots and whose meaning you may be able to work out.