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A2 CHEMISTRY NOTES – AMINO ACIDS Amino Acids What are amino acids? Amino acids are are compounds containing an amino group, -NH2, and a carboxylic acid group, -COOH. The biologically important amino acids have the amino group attached to the carbon atom next door to the -COOH group. They are known as ________ ______. The two simplest of these amino acids are 2-aminoethanoic acid and 2-aminopropanoic acid. Because of the biological importance of molecules like these, they are normally known by their traditional biochemical names. 2-aminoethanoic acid, for example, is usually called _______, and 2-aminopropanoic acid is usually known as ___________. The general formula for a 2-amino acid is: . . . where "R" can be -OH, -SH, other amine or carboxylic acid groups. Physical properties Melting points The amino acids are crystalline solids with surprisingly _____ melting points. It is difficult to pin the melting points down exactly because the amino acids tend to decompose before they melt. Decomposition and melting tend to be in the 200 - 300°C range. Because it has both a basic _______ group and an acidic _________ acid group there is an internal transfer of a __________ ion from the -COOH group to the -NH2 group to leave an ____ with both a negative charge and a positive charge. This is called a ______________. This is the form that amino acids exist in even in the solid state. Instead of the weaker _________ bonds and other intermolecular forces that you might have expected, you actually have much stronger ______ attractions between one ion and its neighbors. These ionic attractions take more energy to break and so the amino acids have ______ melting points for the size of the molecules. 1 A2 CHEMISTRY NOTES – AMINO ACIDS Optical activity Apart from glycine, 2-aminoethanoic acid, the carbon at the centre of the structure of the general formula for amino acids has _______ different groups attached. This is equally true of the __________ instead of this simpler structure. Because of these ______ different groups attached to the same carbon atom, amino acids (apart from glycine) are _______. The lack of a plane of symmetry means that there will be two stereoisomers of an amino acid (apart from glycine) - one the non-superimposable mirror image of the other. For a general 2-amino acid, the isomers are: All the naturally occurring amino acids have the right-hand structure in this diagram. This is known as the "L-" configuration. The other one is known as the "D-" configuration. Adding an alkali to an amino acid solution If you increase the pH of a solution of an amino acid by adding ________ ions, the hydrogen ion is removed from the ____ group. Adding an acid to an amino acid solution If you decrease the pH by adding an ____ ions to a solution of an amino acid, the _______ part of the zwitterion picks up a ____ ion. 2 A2 CHEMISTRY NOTES – AMINO ACIDS Peptides and polypeptides Glycine and alanine can combine together with the elimination of a molecule of ______ to produce a dipeptide. Either: Or: In each case, the linkage shown in the structure of the dipeptide is known as a _________ link. In chemistry, this would also be known as an ______ link. If you joined lots and lots together (as in a protein chain), you get a ______________. A protein chain will have somewhere in the range of __ to ______ amino acid residues. Hydrolysis of polypeptides H 3 A2 CHEMISTRY NOTES – AMINO ACIDS The Structure of Proteins The primary structure of proteins This is the term is used to describe the order of the ______ acids joined together to make the protein. This primary structure is usually shown using abbreviations for the amino acid residues. These abbreviations commonly consist of three letters or one letter, for example: Amino acids join together to make polypeptides which in turn make up proteins. Enzymes and many structues within cells are made up of proteins. The chemical bonds in the _______ link hold the primary structure together __________ bonds hold the secondary, tertiary and quaternary structures together 4 A2 CHEMISTRY NOTES – AMINO ACIDS Chromatography of amino acids Amino acids have no ________. Therefore all of these procedures are carried out "blind", and the results will be seen when a revealing agent (____________) is sprayed on the resulting chromatogram. 1. Chromatography paper is cut and marked with a __________ line and labeled as shown. 2. Different pipette are used to place a drop of each amino acid on the paper. 3. A small amount of chromatography solvent (butanol/ethanoic acid) is poured into the glass chamber (to about 1 cm depth) and a lid is used to allow the atmosphere to become saturated with vapour. 4. The solvent gradually rises up the paper, passing the line and heading upwards. After about 3 hours, the liquid should have risen about three-quarters of the height of the paper. 5. The paper is removed from the apparatus, and a pencil is used to mark the position of the solvent front. 6. The chromatograms is placed into an oven at about 45 C to dry. 7. In a fume cupboard __________ is sprayed evenly over the paper. 8. The chromatograms is returned to the oven to develop the _______. Spots should be visible as _______ smears on the paper. Calculation of Rf values The distance from the start line to the solvent front and to the front of each spotis measured. An Rf value for each spot is calculated (Rf means relative to front): distance moved by spot distance moved by solvent front The values obtained can be with reference Rf values. Different solvents and different types or makes of chromatogaphy papers will give slightly different results. Amino Acid alanine arginine asparagine glutamic acid glycine histidine serine threonine tryptophan Rf Value 0.38 0.20 0.5 0.30 0.26 0.11 0.27 0.35 0.66 Amino Acid aspartic acid cysteine glutamine isoleucine leucine lysine methionine phenylalanine Praline not a true amino acid 5 Rf Value 0.24 0.4 0.13 0.72 0.73 0.14 0.55 0.68 0.43