Lecture Seven - Amino acids and proteins I Flashcards
Define amino acid, and alpha amino acids.
Amino acid - a compound that contains both an amino group (NH2) and a carboxyl group (COOH).
Alpha amino acid - an amino acid in which the amino group is ont he carbon adjacent to the carboxyl group.
What are the R groups in amino acids?
They are the side chains on amino acids, and determine the name of the amino acid.
They can cause the amino acid to be polar, non-polar, acidic or basic.
And these determine the behaviour in water (more importantly - how the peptide folds (shape)).
Describe the chirality of amino acids.
With the exception fo glycine, all protein-derived amino acids have at least one stereocentre (the alpha carbon) and are chiral.
Chirality - asymmetric in such a way that the structure and its mirror image are notsuperimposable.
Describe fischer projection.
When alpha amino acids are drawn in teh fischer projection, they can be designated as having either a D- or L- configuration.
The vast majority of alpha amino acids have the L-configuration at the alpha carbon.
Rules of fischer projection:
1) Most oxidised end of the molecule is placed at the top.
2) The longest carbon chain is placed vertically.
L-amino acid = NH2 is placed on the left.
D-amino acid = NH2 is placed on the right.
Any bond which is verticle projects away from you.
Any bond which is horisontal projects towards you.
NOTE: D and L projections have nothing to do with R and S confugurations.
What is a zwitterion?
The ionised form of an amino acid - internal salt form.
How do acid base titrations work with amino acids?
Titration of the neutral amino acid glycine with sodium ydroxide.
Note the relationship between pH, pKa and the various species.
H from the OH in COOH is liberated first.
H from the NH3+ is liberated second.
Low pH has a net positive charge.
High pH has a net negitive charge.
Changes in pH change the charge of the solution.
What is the isoelectric point?
The isoelectric point, pI, of an amino acid is the pH at which the majority of its molecules in solution have no net charge.
The pI for glycine, for example, falls between the pKa values for the carboxyl and amino groups.
Describe electrophoresis.
A mixture of amino acids (and proteins) can be separated using this technique.
A sample of amino acids is applied as a spot on the paper strip.
An electric potential is applied to the electrode vessels and amino acids migrate toward the electrode with charge opposite to their own.
Molecules with a high charge density move faster than those with low charge density.
Molecules at their isoelectric point remain at the origin.
After separation is complete, the strip is dried and developed to make the separated amino acids visible.
Ninhydrin is used as a reagent which can detect amino acids by staining them.
The purple anion formed with nunhydrin can be used for amino acid analysis.
- Qualitative - where the spot is on the strip.
- Quantitative - the intensity of the colour is related to the concentration.
What are piptides?
Peptide - The name given to a short polymer of amino acids joined by peptide bonds, they are classified by the number of amino aids in the chain. Macromolecule containing many peptide bonds (amide bonds).
Dipeptide - A molecule containing two amino acids joined by a peptide bond.
Tripeptide - A molecule containing three amino acids joined by peptide bonds.
Define a protein.
A biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains.
What is the short hand naming convention for polypeptides.
The short hand naming convention is to add ‘H’ to the N-terminal end of the peptide and the ‘OH’ to the C-terminal end.
C-terminal = carboxylic acid end.
N-terminal = amine end.
By convention, peptides are weitten from the left, beggingin with the free NH3+ group and ending with the free COO group.
What is a disulfide bond (cystine)?
As well as amide (or peptide) links, proteins often contain a disulfide line -S-S- between two -SH groups in the same or adjacent protein strands.
These links are easily oxidised and reduced (weaker than peptide bonds - transient links).
