stability of the carboxylate anion relative to the acid
the charge of the carboxylate residue
when the charge of the carboxylate resides two equivalent electronegative oxygens the structure is called
pKa values vary somewhat depending on
the temperature of the solution
the precise molecular structure
the environment in which the acid-base chemistry is taking place.
how homogenous is the solution
The corresponding carboxylate anion is more stable in the presence of the adjacent, positively charged, ammonium ion, therefore
the carboxylic acid group of glycine is more acidic than a simple carboxylic acid since
the simple carboxylic acid is more acidic than the carboxylic acid group of glycine
The effect of environment on pKa is particularly important in non-polar conditions such as..
the interior of a protein
the outer part of the protein
the acidic part of the protein
the basic part of the protein
What stereoisomers predominate in nature
Into which groups can amino acids be divided
amino acids with hydrocarbon side chains
carboxylic acid side chains
amide side chains
acyclic with basic N containing side chains
hydroxyl functional groups
suphur containing side chains
nitrogen heterocycles and proline
hydrophilic side chains
hydrophobic side chain
phosphorus containing side chains
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.
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
Phe, Tyr and Trp
Ser, Thr and Cys
Val, Leu, Ile
Lys, Arg, His
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.
helical stucture (the alpha helix)
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.