Lecture 4: Building blocks Flashcards
What is the backbone structure of an amino acid:
Amine group end, Carboxylic acid end group, hydrogen (central C) and R chain (central C)
The names of the amino acids can be abbreviated in both _____ letter and _____ letter codes.
Single letter or three letter codes
What do we mean by “amino acids are chiral”?
Have a asymmetric central carbon with four different groups attached
What are the 4 main groups of amino acid?
Non polar side chains - 9
Polar uncharged side chains - 6
Polar positively charged side chains (basic) - 3
Polar negatively charged side chains (acidic) - 2
What are the properties of non-polar amino acids?
These amino acids do not have a charge and are hydrophobic (water-fearing). The non-polarity arises due to the presence of nonpolar side chains or R-groups, such as methyl or ethyl groups.
Where in a protein would you expect to find non-polar amino acid residues?
In the inside or hydrophobic core of the protein.
Significance of Gly and Pro?
Glycine, G, R=H, nonchiral, flexible, almost in a group by itself, used in turns
Proline, R-group bonds back to main chain N, imino acid, rigid, almost in a group by itself, also used in turns
What chemical groups would we expect to find in the R-group of an ionizable amino acid?
Carboxylic acids, Amino groups, Thiolate group (sulfur) or Alcohol (OH)
Where in a protein would we often find ionizable amino acid residues?
In the outside of the protein structure (hydrophilic region)
What are the key properties of peptide bonds (covalent bond)?
- 40% double bond character, leads to planarity. Planar
conformation maximizes π bonding overlap - Rotational barrier of ~80 kJ/mol
- Note the dipole
- The peptide bond is predominately trans
- generally unreactive so make ideal backbone bond
Define pKa and pI, what can these values tell us about an amino acid side chain?
The pKa value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised
The pI, or isoelectric point is the pH at which the net charge on an amino acid (or protein) is zero
List some common examples of post-translational modifications:
- Phosphorylation
- Hydroxylation
- Carboxylation
- Metal Binding
- Iodination
- Glycosylation
What are some important functions of post-translational modifications?
Phosphorylation – often used to control enzyme activity –
like a chemical ON/OFF switch
Hydroxylation – needed to prevent connective tissues
diseases and scurvy, often proline & lysine involved
Carboxylation – needed for blood clotting, often glutamate
involved
In proteins, the ___ ____ of amino acids carry out the biochemical reactions.
side chains
The amino acid tryptophan contains a nitrogen in its side chain. However, it is considered non-polar. Explain why?
The nitrogen is involved in the aromatic system of the side chain. It’s lone pair of electrons are participating in the resonance of the ring, so it doesn’t have a lone pair to act as a base.
