3.3.13 Amino acids, proteins and DNA

• An amino acid has a basic amino group (NH2 and an acidic carboxyl group (COOH). This make them amphoteric. • They’re chiral molecules because the carbon has four different groups attached. So a solution of a single amino acid will rotate plane polarised light • They have an R group which is an organic side chain - (glycine is an exception as the R group is just an H)

When a molecule has both acidic and basic properties

E.g. glycine/ valine

• Find the longest protien chain that includes the carboxylic acid group and write down its name - e.g. for alanine the longest C chain containing a COOH group is 3C long… propanoic acid • Number the carbons in the chain starting with the carbon in the carboxylic acid group as No. 1 • Write down the positions of any NH2 groups and show that they are NH2 groups with the word “amino” - e.g. alanine has a NH2 group on carbon-2 • Include any other functional groups when naming the molecule Therefore the systematic name for alanine is 2-aminopropanoic acid

A dipolar molecule - it has both a postive and negative charge in different part of the molecule

Zwitterions only exist near an amino acids isoelectric point. This is the pH where the average overall charge on the amino acid is zero. It’s different for different amino acids depending on their R-group Isoelectric point - both the carbonyl group and the amino group are likely to be ionised: H3N+CRHCOO-

At low pH the COO- group is more likely to gain an H+ H3N+CRHCOOH

At high pH the NH3 group is likely to lose an H+ H2NCRHCOO-

Amino acids have different R groups, so they will have different solubilities in the same solvent. This means that you can easily separate and identify all of the different amino acids in a mixture using

1 - Draw a pencil line near the bottom of a thin layer chromatography plate and put a concentrated spot of the mixture of amino acids on it 2 - Dip the bottom of the plate (not the spot) into a solvent 3 - As the solvent spreads up the plate, the different amino acids move with it, but at different rates, so they separate out 4 - When the solvent’s nearly reached the top, take the plate out and mark the solvent front with a pencil. Then leave the plate to dry 5 - Amino acids aren’t coloured so they need to be amde visible by: ~ being sprayed with ninhydrin solution on the plate, turning the spots purple ~ by using a special plate with a fluorescent dye added to it. The dye will glow when UV light is shined on it, the spots of chemical (protein) will cover the plate making it appear dark, the spots can then be drawn around to show where they are without UV 6 - The Rf vaule can be calculated, and compared to a table of know Rf values to identify the amino acids

Rf = x/y = distance travelled by spot/distance travelled by solvent

Proteins are made up of lots of amino acids joined together by peptide links. The chain is put together by condensation reactions and broken apart by hydrolysis reactions Proteins are really polyamides

Peptide link/bond

H2NCRHCOOH + H2NCR’HCOOH <=> H2NCRHCONHCR’HCOOH + H2O

The dipeptide still has a NH2 group at one end and a COOH group at the other end, so can react in other condensation reactions with other amino acids to produce a polypeptide chain

Add hot aqueous 6 M hydrochloric acid and heat the mixture under reflux for 24 hours

Break each of the peptide links down the middle, then add either an H atom or an OH group to each of the broken ends to produce the original amino acids monomers

• Primary • Secondary • Tertiary • Quarternary - not required

The primary structure is the sequence of the amino acids in the long chain that makes up the protien (the poly peptide chain)

The peptide links can form hydrogen bonds with each other, meaning the chain isn’t a straight line. The shape of the protien is called it’s secondary structure. The most common secondary structure is a spiral called an alpha (α) helix. Another common type is a beta (β) pleated sheet. This is a layer of protein folded like a concertina

The chain of amino acids is itself often coiled and folded in a charecteristic way that identifies the protien. Extra bonds can form between different parts of the polypeptide chain, which give the protein a three dimensional shape. This is it’s tertairy structure.

• Hydrogen bonding • Disulfide bond

This effect the secondary and teritiary structure which effect how the protein folds or twists, this effects shape. The shape of the protein is vital to how it function - e.g. changing a shape of an enzyme may denature it

Hydrogens bonds exist between polar groups - e.g. -OH and -NH2. They stabalise both the secondary and tertiary structure of the protein