Protein section 1

FOUR MAJOR FUNCTIONAL GROUPS:

How is amide bond formed

The acidity of the carboxylic acid is due to....

when the charge of the carboxylate resides two equivalent electronegative oxygens the structure is called

pKa values vary somewhat depending on

The corresponding carboxylate anion is more stable in the presence of the adjacent, positively charged, ammonium ion, therefore

The effect of environment on pKa is particularly important in non-polar conditions such as..

What stereoisomers predominate in nature

Into which groups can amino acids be divided

Which amino acid imparts unusual structural flexibility

What amino acid has two chiral centres due to the both of its α and β- carbons being asymmetric, and therefore has four possible stereoisomers.

Confer negative charge on proteins because their side chains are ionised at pH 7, under physiological conditions acidic side chains exist as the conjugate base

The most basic of the 20 amino acids.

The pKa of this protein is around pH 7 and thus at physiological pH it can act as either an acid or a base. This makes it especially important in acid-base catalysis and it has an important role to play in many enzymes. It also forms complexes with zinc in proteins which has importance for both structure and mechanism.

Fill in the blanks

Contains a non-polar methyl thioether group. This makes it one of the more hydrophobic amino acids

The hydroxymethyl group of this amino acid does not appreciably ionise at physiological pH. Essentially hydrophilic.

The side chain is somewhat hydrophobic, but also extremely reactive. It is polarisable and can lose its proton to bercome the thiolate anion. Can form disulphide bridges in proteins.

Has two chiral centres and thus can have four stereoisomers

The formation of disulphide bonds in proteins is an important [blank_start]secondary[blank_end] structural feature. This helps to impart [blank_start]stability[blank_end] and conformational rigidity to some proteins

This amino acid is unique in that its three carbon side chain is bonded to both the α carbon and the α amino group. The heterocyclic pyrrolidine ring created restricts the geometry of polypeptides.

This amino acid has a hydroxyl function associated with the phenol ring. Acid base chemistry is facilitated as the ring enhances the stability of the conjugate base. It can sometimes act as an acid.

[blank_start]Phe, Tyr and Trp[blank_end] are all highly aromatic and can absorb UV light at 280nm. Proteins have an optical density at 280nm because of these side chains

drag the appropriate amino acid to the blank space

The more [blank_start]hydrophobic[blank_end] amino acids have a tendency to be sequestered away from the solvent towards the [blank_start]centre[blank_end] of protein molecules. This provides one of the major driving forces for protein [blank_start]folding[blank_end]

[blank_start]Hydrophilic[blank_end] residues tend to interact with the solvent more easily via [blank_start]hydrogen[blank_end] bonding and thus can be on the [blank_start]outside[blank_end] of proteins.

Under [blank_start]physiological[blank_end] conditions this effectively restricts the [blank_start]peptide[blank_end] bond to one of two configurations: cis or trans To minimise steric crowding due to close proximity of bulky groups on th carbonyl carbon and the nitrogen the [blank_start]trans[blank_end] form is favoursed, except where [blank_start]PROLINE[blank_end] is involved.

Proline has an [blank_start]alkyl[blank_end] chain rather than a [blank_start]hydrogen[blank_end] atom as the [blank_start]second[blank_end] substituent on nitrogen In amides containing proline the [blank_start]cis[blank_end] form is not dramatically disadvantaged In proteins about [blank_start]10%[blank_end] of all peptide bonds involving proline are cis.

THE SHAPE OF POLYPEPTIDES IS DEFINED BY [blank_start]ROTATION[blank_end] ABOUT THE C-N AND C-C BONDS

All atoms around the peptide bond lie in a [blank_start]planar[blank_end] conformation. This rotation is described by the torsion angles φ Phi between [blank_start]C-N[blank_end] and ψ Psi between [blank_start]C-C.[blank_end] If all psi and phi angles are the same the peptide assumes a [blank_start]repeated[blank_end] structure. For certain combinations of angles this can take the form of a [blank_start]helical stucture (the alpha helix)[blank_end] or a beta-sheet structure. Clearly the peptide structure exhibits [blank_start]flexibility[blank_end] and this is important for the complex [blank_start]structure[blank_end] of proteins.

What characteristic of atoms and groups of atoms limits the possible psi and phi torsion angles that the backbone of the polypeptide chain can adopt without causing protruding R groups to bump into each other.

The Ramachandran plot shows the allowed

Label the chemical structure

Amino acids with basic R groups