Download Amino Acids - The Exam Formula

Amino Acids An amino acid is a molecule that contains both amine and carboxylic acid groups. The general structure looks like that shown below. The only thing that changes is the ‘R’ group for different amino acids: Amino acids are usually chiral i.e. have 4 different groups attached to the central carbon but not always, for example, glycine has R= H, which is not chiral. The chiral amino acids can then of course form optical isomers (mirror images). OCR: general formula is RCH(NH2)COOH. They also refer to these amino acids as α-­‐amino acids, which means the NH2 group is on the ‘2 position’ (see naming amino acids below). Naming amino acids Depending on the R group, amino acids change their name, for example when R = CH3, we have alanine, when R= H we have glycine. You don’t need to know these names but you may have to name amino acids as you would any other molecule. If we look at alanine: We would name this as you did for alkanes, alkenes, alcohols etc. at AS chemistry. • longest chain is 3 carbons, therefore must be ‘prop’. • these names always end in ‘oic’ acid, so we can say we have propanoic acid here. • always number from the acid group, and we can see that the amine is on carbon number 2. • the amine part comes at the start of the name and you call it ‘amino’, therefore we would say 2-­‐
amino in this case. • put it all together à 2-­‐aminopropanoic acid. Addition of acid and base Amino acids can react as amines or carboxylic acids. There is nothing special about the amine or acid groups in these molecules, they just react as normal amines and acids. Amines are basic and therefore will react with acids i.e. pick up an H+ to give NH3+ Carboxylic acids are obviously acidic and therefore will react with base i.e. lose an H+ to give COO-­‐ This leads us to very common exam questions. What happens to the structure at a low pH or if you add acid? (both mean the same thing). This just means the amine picks up an H+. Low pH (add something like HCl) High pH (add something like NaOH) And vice versa, what happens at high pH or if you add base? This just means the acid loses an H+ to form COO-­‐: The number of times they ask questions like these is ridiculous, so make sure you can do this! Zwitterions Amino acids exist as zwitterions. You can view zwitterions as a combination of the low and high pH reactions above i.e. the + on the amine and the – on the acid are both present: Due to the + and – charges there is a strong electrostatic attraction (ionic bond) which means that amino acids exist as crystalline solids and have high melting points. When do zwitterions form? Zwitterions form at very specific pHs, which varies depending upon the amino acid. The pH where a zwitterion forms is called the isoelectric point. Different amino acids have different isoelectric points. So in a question they would have to give you some information, you wouldn’t be expected to guess just by looking at the amino acid to know when the zwitterion forms. OCR: they often give you the isoelectric point in questions and ask what is the structure at various pHs. If the pH they ask is the same as the pH of the isoelectric point, then you draw the zwitterion. Edexcel: the zwitterion forms due a ‘proton transfer’ from the acid to the amine. Amide/peptide bond formation The main reaction that you need to know about is amide/polyamide formation. This goes back to the nucleophilic reactions we looked at previously. But you don’t need to know the mechanism, just how to get to the product. They are all condensation reactions i.e. removal of water. In the example below we are joining together alanine and serine. The only product you ever get is an amide, which is highlighted in the red circle on the right. They often refer to the amide as a peptide bond (they are the same thing). Rule: remove one ‘H’ from the NH2 and the ‘OH’ from the acid à H2O. Then join the two units together: This should be very easy. You don’t need a mechanism. Just do the same thing every single time, the only thing that changes is the amino acids. Note: you could of course just use one amino acid in these reactions over and over. We have only added two amino acid units together here (the product above is a dipeptide) but you could keep doing it to form longer polyamide/peptide chains and by adding thousands together you get to a protein. Breaking the amides (hydrolysis) Another exam favourite is going backwards from the amide to the amino acids, which is known as hydrolysis i.e. adding water to the amide to split it up. This is just the reverse of the above reaction but causes problems for students: The diagram above shows how to break the amide. The red line indicates the bond that was formed to make the amide bond so this is the bond that is broken to go back to the starting amino acids. Rule: split the molecule between the C-­‐N bond then add an ‘H’ to the NH and add an ‘OH’ to the C=O. Note: you are adding water but the reaction has to be done under acidic or basic conditions. So you need to be careful with the products that you write out after hydrolysis. As you now know from the earlier reactions, under acidic conditions we get NH3+ and under basic conditions we get COO-­‐. So you need to be careful depending on the question as you will have to write out the amino acid products accordingly. The products I have written out above are not technically correct as I didn’t specify acidic or basic conditions. It was just to demonstrate how to get back to the amino acids. AQA: we mentioned that proteins are made up of many amino acid units. They write out these protein chains to show which amino acids make up the protein using abbreviations for the amino acids, such as: -­‐Gly-­‐Ala-­‐Iso-­‐Ser-­‐ These chains could go on for a long time! It’s just lots of amino acids. Different proteins have different orders of these amino acids. The long polymer chains that are formed tend to coil and are hydrogen bonding between C=O and NH2 groups result, which gives the protein its structure. TLC If you break up a polyamide or peptide to form many amino acid molecules, you can roughly identify which amino acids you have by using thin-­‐layer chromatography (TLC) (see chromatography tutorial). When doing this technique you will end up with a TLC ‘plate’ with several or many spots on it, each corresponding to an amino acid. They use the Rf value to try to identify which amino acids are present as each should have a slightly different Rf value. The problem with this is of course that many things could have very similar Rf values so it is not a perfect method and can still be difficult to identify the amino acids. Edexcel: amino acids are colourless and cannot be seen on the TLC plate. To get round this they stain the plate with ninhydrin, to give a purple colour where the amino acids are.