These side chains are weak bases, fully protonated (Lys, Arg) or partly protonated (His) in normal biological conditions, pH 7.0-7.4.Īlthough the side chain has a hydrocarbon segment, the positive charge dominates over any hydrophobic effect. Positively charged amino acids: Arg, Lys, His Hence, it is important to understand how various biochemical molecules will interact with H 2O.

This makes water a liquid rather than a gas like methane, CH 4, whose molecules do not form H-bonds.īiochemistry is concerned with how molecules function in living cells, which is an aqueous environment. H-bonding attracts H 2O molecules to each other. Therefore, polar amino acids interact well with H 2O. Water molecules are excellent H-bond donors and acceptors. Instead, they result in temporary attractive forces that help hold molecules together. Typical hydrogen bonds (or H-bonds) are about 5-10% as strong as a normal covalent bond, but they are not permanent bonds like covalent bonds. Hydrogen bonds are electrostatic interactions between a donor consisting of the dipole of a polar O-H or N-H bond and an acceptor, consisting of an available lone pair of electrons on a nearby N or O atom (which may be on different molecule) (Figure 2.5).įigure 2.5 Typical hydrogen bond donors and acceptors Ser and Thr both have an -OH group on the side chain.Īsn and Gln both have amide side chains -CONH 2 derived from the corresponding carboxylates Asp and Glu.Īll four are good hydrogen bond formers, with little hydrocarbon. Therefore, in overall, these two amino acids are only somewhat non-polar.Īmino acids with polar, uncharged side chain: Ser, Thr, Asn, Gln However, the hydrophobicity is partly offset by the presence of a polar OH group in Tyr (Figure 2.4), or slightly polar NH group in Trp. Tyrosine and tryptophan are the most hydrophobic amino acids, based on their total surface area of CH atoms. Proline is unique because the side chain links back to the -N, forming a 5-member ring (Figure 2.3).įigure 2.4 The structure of Tyrosine, highlighting the polar OH group in its side chain. Glycine is the only non-chiral structure, since it has two identical H substituents on the α-carbon.Ĭysteine has the side chain -CH 2-SH, which is not very polar, because S is much less electronegative than O. Figure 2.3 The cyclical structure of Proline Note: The α-carbon of all other natural amino acids is chiral, with L- configuration. Glycine has a side chain that is simply H linked directly to the α-carbon: +NH 3CH 2CO 2 –Īlthough it’s a non-polar bond, it’s not large enough to make the whole molecule very non-polar. However, S is much less electronegative than O, so methionine fits in the very non-polar class.Īmino acids with moderately non polar side chains: Gly, Cys, Pro, Trp, Tyr Note: methionine has one S atom in its hydrocarbon chain. The hydrophobicity of a side chain is simply related to the number of CH, CH 2 or CH 3 groups. Hydrocarbon side chains tend to cluster together, so as to minimize the area of direct contact between hydrocarbon and H 2O, a property known as the hydrophobic effect. Hydrocarbon side chains are described as hydrophobic, i.e. Hydrocarbon regions of a molecule are also generally chemically unreactive. Non-polar groups interact well with each other and poorly with polar groups. Figure 2.2 The relative electronegativity of atoms participating in a chemical bond determines if that bond is non-polar or polar. Therefore, we say that C=O and O-H are polar, while C-C and C-H are non-polar. In bonds such as O-H or C=O, electrons shift towards the electronegative O atom, creating a dipole (Figure 2.2). In contrast, O and N are more electronegative. Since C and H have similar electronegativity, bonding electrons are evenly distributed in hydrocarbon regions. Very electronegative O > N > S > C ≈ H moderately electronegative Electronegativity refers to the tendency of a nucleus to hold electrons (it does NOT mean possession of negative charge). Polarity is a property that occurs when atoms in a molecule have very different electronegativity.

Polar peptide backbone of amino acids