13.9 Amino Acids and Proteins

First things first… A BASIC AMINO ACID STRUCTURE Now lets split this amino acid into its 3 main component parts..

The NH 2 Group..

The COOH group

The Mysterious “R” group Okay, so I half lied, this is called an R group, but the actual chemical name isn’t R, in fact R is only representative for an other group.. Any other group that can attach to the CH already on the amino acid. It is still very important!, it is the R group that is unique to every amino acid, It is the R group that gives the amino acids different names No two structurally different amino acids will have the same R group. So with out different R groups, we wouldn’t be able to have different amino acids. This group remains unchanged when a zwitter ion is formed. Otherwise known as.. Well.. Anything really

Okay so we know that: a)Amino acids are compounds which contain two different functional groups. b)When in an aqueous solution, they contain both positively and negatively charged groups. This means amino acids, are called bifunctional compounds, bi meaning two. They also form Zwitterions when in an aqueous solution. These properties make Amino Acids very useful. This is because amino acids in a solution, can act as buffers, they have both a positively and negatively charged side meaning they can act as either an acid or a base to neutralise a reaction. A buffer solution is one which resists changes in pH when small quantities of an acid or an alkali are added to it. The formula of a zwitter ion is H 3 N + -CHR-COO - In the zwitter ion form, the H 3 N + acts as an acid, it has a positive charge and will Donate a H+ ion, when placed in an alkali solution. This makes the overall zwitter molecule Negative as the NH3 group has lost a H+ ion. The COO - group in a zwitter ion acts as a base an will accept H+ ions when in an acidic solution, again working to neutralise the solution. This agrees with the Brønsted– Lowry theory.

Therefore amino acids exist as ions in 3 different forms.. H 3 N + -CHR-COO - In Neutral solution H 2 N-CHR-COO - In Acidic Solution In Alkaline solution Zwitter ion works to neutralise via the COO- acting as a base and accepting H+ ions from the acid in the solution. Has equally charged negative and positive groups. Zwitterion works to neutralize via the H 3 N +, which acts as an acid and donates a H+ ion to the alkali solution.

Amino Acid solubility in water  We have just learnt that in an aqueous solution, amino acids form zwitter ions, which are bifunctional compounds meaning they have both positive and negative parts  They're buffers as they can act as either a base or acid in order to neutralise a solution/compound.  Because amino acids easily form zwitterions in aqueous solutions, which are polar, they should be soluble in water. So lets test it out.  Go back to AS when we said that for something to be soluble in water it needs to be Polar, or at the very least have polar parts.  Our zwitter ion has positively charged and negatively charged parts, just like water. So that’s a tick on our list for solubility in water  Now lets see how the molecules interact..

So how does Water interact with a zwitter ion in order to dissolve? Remember: Oxygen is very electronegative, this means its got a stronger pull over the electrons it shares with hydrogen, thus creating partial charges. This allows zwitter ions which also have polar charges to form ionic bonds with the water molecule. H+ COO- The H+ part of the water molecules will be attracted to the COO- part of the zwitter ion The O- part of the water molecules will be attracted to the NH 3 part of the zwitter ion

Making peptides Our body is made of many different proteins, these make up things in our body that are vital, for example cell membranes, enzymes ect.. Proteins are made up of polypeptides and polypeptides? They’re made up of amino acids! This means that someway, somehow amino acids need to link together to form dipeptides and poly peptides? Lets find out how..

Because of this repelling of electrons, it is important to show this in the diagram as the H and O not being next to each other. So how DO two amino acids join together? With the removal of a H20 molecule, an OH from the COOH group of amino acid (A) and a H from the NH2 group of amino acid (B) After the removal of a H2O molecule, a bond reforms between the carbon and nitrogen atoms. The Oxygen atom attached to the Carbon and the Hydrogen attached to the Nitrogen in theory would be next to each other in space, however, as the oxygen double bond has a high density of electrons, it naturally wants to repel as far away from any near groups of electrons as it can get. This means that ultimately, hydrogen is pushed further away. The peptide link that is formed is a secondary amide group A B Remember: when labelling the peptide bond it is important o label the whole secondary amide, NOT just the – between the C from one amino acid and N from the next. This is an R group

 TWO AMINO ACIDS JOINT LIKE THIS ARE CALLED A DIPEPTIDE.  MORE THAN TWO JOINED LIKE THIS IS A POLYPEPTIDE.

Naming polypeptides  So we could use their full structural names to name amino acids and polypeptides. However as they’re all identical apart from their R group, this would be pretty pointless.  We learnt earlier that each amino acid has a unique R group, this means that they can be named according to their R group. Here is an example : This two glycine molecules, glycine has the R group ‘H’. Therefore when we name it we use the first 3 letters of both amino acids that have been used. Here it would be “GlyGly” A polypeptide an contain up to 40 residues

Proteins  Proteins are naturally occurring condensation polymers made from amino acid monomers, joint together by peptide bonds.  A protein contains more than about 40 amino acid residues.  All proteins in our body are made up of only 20 different monomers (amino acid types)  What makes each protein different is the order in which the amino acids are joined to one another, for instance valalagly could code for a part of a cell membrane. But glyglycyst could code for something else entirely. A residue is used for an α- amino acid which has lost the elements of water in forming a dipeptide/polypeptide.

Structures of proteins  Okay so, just as shapes can be classified as 2d or 3d, different parts /stages of protein structure can also be classified. 1. Like we said earlier, the first stage for making a protein is the order of the amino acids that are linked together. This is called the primary structure. Other structures then happen as a result of interactions, between amino acid chains such as  Instantaneous dipole – induced dipole bonds between non-polar side chains  Hydrogen bonds between polar side chains  Ionic bonds between ionisable side chains  Covalent bonds All these different intermolecular bonds account towards different structures of amino acids.

Proteins continued.. The chains in a protein can be twisted or folded, as a result of hydrogen bonding, there are two arrangements of folding which are most common, these are:  Tightly coiled into a helix, where the C=O group of one peptide forms a hydrogen bond to an N-H group four peptide links along the chain.  Stretched out in a long chain, these lie alongside each other, hydrogen bond to each other to form a beta pleated sheet. THIS IS SECONDARY STRUCTURE Once this initial folding has happened, further folding can happen, overall shape is stabilised by intermolecular interactions. THIS IS TERTIARY STRUCTURE