L3 - Amino Acids & Proteins Flashcards
How do proteins contribute to the cell?
- enzymes to catalyse reactions
- structural proteins (e.g. in connective tissue, muscle and bones)
- proteins interact with RNA & DNA to control nucleic acids (e.g. transcription factors)
- lipid bound proteins act as transport systems (e.g.
membranes for gradient maintenance) - many are glycosylated (interact with sugars)
- providing recognition of other molecules (e.g. antibodies, growth factors and receptors)
How are proteins studied?
- In isolation
- Or in a mixture - to study pathways and interactions in a cellular environment
What happens to lactoferrin when it binds to iron?
- undergoes a substantial change in conformation
- which allows other molecules to distinguish between iron-free and iron bound forms
What happens to lactoferrin when it binds to iron?
- undergoes a substantial change in conformation
- which allows other molecules to distinguish between iron-free and iron bound forms
What determines the identity and properties of the amino acid?
the nature of the R group
Why are amino acids considered chiral molecules?
- The a-carbon atom has 4 different substituents
- all amino acids except glycine have non superimposable mirror images (2 H groups)
Mirror images of amino acids and bacteria
Amino acids = L form (laevus, left)
Bacterial cell walls = D form (dexter, right)
4 main groups of amino acids
- Hydrophobic acids with non polar Groups
- Polar amino acids with neutral R groups (charge not evenly distributed)
- Positively charged amino acids with R groups that have a positive charge at physiological pH
- Negatively charged amino acids with R groups that have a negative charge at physiological pH
Features of glycine
- shows no chirality (R group is H)
- flexible amino acid due to H side chain - provides flexibility to proteins where other side chains would be too bulky
Features of proline
- side chain bonds to the amine
- imposes tight restraints on the conformation of the protein
- the peptide bond forms both cis and trans conformations
- found in proteins that need to be rigid
e.g. collagen, polyproline helices, turns of globular proteins
Features of histidine
- Found in the active site of many enzymes (involved in catalysis, binds metal tightly
- Has imidazole ring that can bind and release protons during enzymatic reactions
- Only amino acid with a pKa of the side chain of near neutral pH (6.7)
- Side chain can alter its charge at physiological pH - can protonated or deprotonated
- The charge on this residue can be modulated by other amino acids surrounding it in the 3D structure of the protein
Features of cysteine
- Contains a free thiol (SH) group
- Can form a covalent bond with another cysteine on the protein chain when they approach each other
- This gives rise to stability and structure
- The disulphide bond is the only covalent bond found to hold the protein chain in its correct fold
- Side chain has pKa of 8.4 so is found in active sites
Oxidation & reduction of cysteine
- Cysteine residues form a covalent bond in some proteins to form cystine
Oxidation = forms disulphide bridge, cystine, 2 H+, 2e-
Reduction = forms cysteine
At the midpoint of a titration curve, what is the pKa equivalent to?
pH of weak acid
Why are amino acids considered Zwitterionic ?
- Exist predominantly as dipolar ions in solution at neutral pH (7.0)
- The amino group is protonated (NH3+)
- The carboxyl group is deprotonated (COO-)
