Amino acids

How different amino acids are there?

20

How many sub-groups of amino acids are there?

6

Name all sub-groups of amino acids

Aliphatic, Aromatic, Basic, Acidic, Other, Polar

Properties of aliphatic amino acids

• hydrophobic/non-polar 

• Variable length and carbon branching

• Exception is methionine which includes a sulphur

Name all amino acids in aliphatic group

Alanine, Valine, Leucine, Isoleucine, Methionine

Properties of aromatic group

• larger

• mostly hydrophobic

• tyrosine has hydroxyl group - forms hydrogen bonds

• tryptophan has an indole ring - forms hydrogen bonds

• pi stacking occurs (benzene rings stack)

Name the amino acids in the aromatic group 

Phenylalanine, Tyrosine, Tryptophan

Properties of charged amino acids

• Ionisable sidechains - charged in cellular environment

• basic have +ve charge

• acidic have -ve charge

• histidine is partially charged

Name amino acids in basic group

Histidine, Lysine, Arginine

Name amino acids in acidic group

Aspartic acid, Glutamic acid

Properties of polar group

• hydrophillic (interact with water outside the protein or each other through H bonds)

• histidine cam also be polar

• cysteine can form disulphide bonds

Properties of other group

• glycine R-group is a H atom so is has conformational flexibility

• proline R-group is also bonded to amine group to create 5-membered ring so rigid

How can protein concentration be determined using aromatic amino acids?

Use Beer-Lambert law where:

Absorbance = extinction coefficient x concentration x path length

 

If an acid is strong will it have a low or high pKa?

Low - higher degree of ionisation so donates protons more readily than a weaker acid

What is the henderson-hasselbach equation?

Looking at the amine group, which way will the equilibrium shift when the pH is 7.4?

To the left, protonation will take place, +ve charge

Looking at the carbonyl group, which way will the equilibrium shift at pH 10?

To the right, deprotonation will take place, -ve charge

At pH 7.4 what is the net charge of the molecule? What is the name of this ion?

Net charge is 0, but there is both a +ve and -ve charge so it is called a Zwitterion

What is the isoelectric point (pl)?

The pH at which a particular molecule carries no net charge, unique to each.

Is this an L or D amino acid?

D (Lysine)

Is this L or D alanine?

L-alanine

Is L-alanine R or S?

S

Are all L-amino acids S?

L-cysteine is the only natural amino acid that is R, this is due to the Sulphur group