Lecture 4: Building Blocks of Proteins: Amino Acids PDF

Lecture 4 Building blocks of proteins: amino acids. Learning Objectives At the end of your study relating to this topic you should be able to: Describe the properties of amino acids and how they relate to protein structure and function Recognize the types of side chains of amino acids an...

Lecture 4 Building blocks of proteins: amino acids. Learning Objectives At the end of your study relating to this topic you should be able to: Describe the properties of amino acids and how they relate to protein structure and function Recognize the types of side chains of amino acids and understand their chemical properties Know how amino acids join to form peptides and proteins Explain the importance of the peptide bond and describe its structure and key properties Textbook references: Chapter 4 “The structure of proteins” pages 51-55 in Biochemistry and Molecular Biology, 6th edition by D. Papachristodoulou, A Snape, W.H. Elliot and D.C. Elliot 9 Twenty different amino acids are the building blocks of proteins Amino acids, as the name implies, contain an amino (H2N–) group and a carboxyl (–COOH) group (these are termed the α-amino and α-carboxyl groups respectively). In a free amino acid these functional groups can ionise in solution to form carboxylate (-COO-) and ammonium (H3N+-) groups. Amino acids differ in their physical properties as a result of the structures of their side-chains (R-groups). All of these groups are linked to a central (α)-carbon atom in the amino acid. The functional groups linked to the α-carbon atom create a point of asymmetry in the amino acid and therefore stereoisomer (mirror image) D- and L- forms of amino acids exist. Living organisms make proteins that generally contain only L-amino acids. Bacteria, however, have the ability to chemically synthesise polymers that also contain D-amino acids. Figure 4-1. The general form of an amino acid Figure 4-2. Stereochemistry of an amino acid. L-configuration amino acids are found in gene- encoded proteins (Campbell, Farrell and McDougal p.61). 10 Amino acids are classified according to side chain structure The 20 amino acids commonly found in proteins differ from each other in their R-group side-chain chemical structure (see Figure 4-3). Several amino acids are classified as non-polar and have aliphatic carbon or aromatic ring side-chains which tend to be located away from aqueous environments. Other amino acids have polar side-chains and include those amino acids with ionisable acidic or basic groups. Note: the cysteine -SH is slightly polar, and could also be included with the uncharged polar group below (different texts classify it differently). Note: because in the structures above, the carboxyl group is Note: the Lys, Arg, and His side-chains are deprotonated (COO-, as would be expected at pH7), what you see shown in their protonated conjugate acid is the ionic form of the amino acids. These ionic forms are called form, as you would expect at pH 7. aspartate and glutamate. Figure 4-3. Structures of the 20 common amino acids found in proteins, shown in their form at pH 7. Some amino acids have ionisable groups that contribute to the net charge on a protein 11 Figure 4-4. Ionisation of amino acids (Campbell, Farrell and McDougal p.68). In addition to the α-amino and α-carboxyl groups, some amino acids have amino or carboxyl groups in the side-chain R-group, which can ionise and contribute to the net charge of the amino acid. The pKa value of the ionising group depends on both its location in the amino acid and on the nature of the group. In a protein, where the amino acids are covalently linked together, the net charge on the protein is derived principally from ionisation of side-chain amino and carboxyl groups. The isoelectric point (pI) of a protein is the pH at which the protein has a net charge of zero. From Table 4-1 you can see that almost all of the α-amino groups have a pKa between 9-10 and the α-carboxyl groups between 2-3. Additionally, seven other amino acids have side chains that are ionisable. Apart from Arg, these amino acids often appear in the active sites of enzymes. Remember from CHEM191: The pKa value for an ionisable group (on an amino acid in this case), is the pH at which 50% of the ionisable groups in the solution are ionised (and the other 50% are un- ionised), giving an overall net charge or zero (neutral). Table 4-1. pKa values of the ionisable functional groups of amino acids (Campbell, Farrell and McDougal p.69). 12 Amino acids are covalently linked by peptide bonds in proteins Figure 4-5. Formation of a peptide bond (Campbell and Farrell 4th ed. p.74). The C–N peptide bond linkage has partial double bond character due to electron resonance, resulting in the peptide bond being planar. The order of covalently linked amino acids in the polymer is known as the primary sequence. The amino acid with the unlinked α-amino group is known as the N-terminus of the protein (i.e. the first amino acid of the protein chain), the other end of the primary sequence containing the unlinked α-carboxyl group is known as the C-terminus (i.e. the last amino acid of the protein chain). By convention, the amino acid sequence is written N-terminus to C-terminus. This linear sequence of amino acids helps to define the structure and function of the mature protein. Individual amino acids in a protein may also be referred to as “residues”. In addition to being planar, the peptide bond is most often in a trans conformation (except for residues preceding a proline (about 10% cis)), and it has a fixed dipole. The prefixes ‘cis’ and ‘trans’ are from Latin, meaning ‘this side of’ and ‘the other side of’ respectively. In the context of (bio)chemistry, cis indicates that the functional groups (side chain R groups in the case of proteins), are on the same side of the carbon chain (the peptide bond in the case of proteins), while trans configuration means that the functional groups are on the opposing side of the carbon chain. Figure 4-6. Configuration of a peptide bond (Campbell, Farrell and McDougal p.72). Figure 4-7. Primary structure of a small peptide (Campbell, Farrell and McDougal p.71). 13 Proteins undergo post-translational modification Proteins transferred from the endoplasmic reticulum through the Golgi apparatus undergo a number of modifications, termed post-translational modifications, i.e. modifications that take place after the protein has been translated. These modifications are numerous and could include, for example, one or more of the following: proteolytic cleavage of a precursor form of the protein N-glycosylation addition of lipid formation of disulphide bridges (secreted proteins) hydroxylation (e.g. collagen) C-terminal amidation (bioactive peptides) phosphorylation (e.g. milk proteins) Modifications of this type are in most cases important for generating the correct active form of the protein. In addition to post-translational modification of newly synthesised proteins, proteins are subjected to a number of age-related modifications, for example glycation of haemoglobin, free radical damage to proteins, etc. The ultimate function of a protein is dictated by the amino acid sequence, the higher order structure of the protein, and the involvement of post-translational modifications. Protein function is quite diverse as illustrated by the following groupings: Enzymes Regulatory proteins Transport Storage Contractile & motile Structural Scaffold Protective 14