Protein Structure and Function
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Describe the basic structure of amino acids
Tetrahedral centre alpha carbon Carboxyl, amine, R, Hydrogen
What isomers does every amino acid have (Except glycine)
D and L - Handedness - Asymmetric/chiral (Based on COO- or NH3+)
How to distinguish between D and L forms of amino acids
D-form the groups read CORN in the anticlockwise direction (carboxyl, R group, amine) L-form reads CORN in a clockwise direction
Where are L-form aas found
All aas incorporated into proteins by living organisms are in the L-form
Where are D-form amino acids found
Cell walls in bacteria, used in some therapeutics
What do the amino and carboxyl terminals give the polypeptide
Structural orientation and polarity
What is a peptide residue
Each repeating unit of the polypeptide chain is termed a residue
What makes up each residue in a polypeptide chain
Alpha carbon, C’=O and NH3 group
How is the variable side chain R arranged in a polypeptide
Trans conformation (but 0.1% peptide bonds have a less energetically favourable cis arrangement)
Describe the secondary structure of a protein
E.g. beta sheet formed from the folding of the polypeptide chain. Beta sheet made up of beta strands. The bonds stabilise the overall sheet.
What two arrangements can Beta pleated sheets be in and which orientation is more stable
Antiparallel, parallel Hydrogen bonds Antiparallel is more stable
Describe four features of the alpha helix in the secondary structure
Right handed helix Stabilised by H-bonds H-bonds are 4 residues apart, between residue 1 and 5 3.6 residues/turn or 0.54 nm /turn
How do the proteins gain their properties for structure and function
Arrangement of side chain (in alpha helix and beta sheet, they protrude outwards)
How is the tertiary structure formed
Combining secondary structures E.g. seven helices of the transmembrane domain of the CXCR4 chemokine receptor
How is the quaternary structure formed
Two or more folded polypeptides combine to form the mature protein, same bonds stabilise the structure Haemoglobin - 2 Hbalpha and 2Hbbeta polypeptides
What do some proteins require for their function or folding and name some examples
Some proteins require cofactors for their function or folding. Heme - Haemoglobin - Hb and Fe Nicotinamide adenine diphosphate (NAD) Reduction/oxidation Flavin adenine dinucleotide (FAD) Reduction/oxdiation Organic cofactors - Coenzymes
Describe water soluble proteins
Globular in shape Hydrophilic residues mostly on the external surface Hydrophobic residues usually buried inside the protein Some may assemble into filaments (E.g. actin) or tubes (e.g. tubulin) or coiled-coils (cortexillin)
How are residues organised in membrane proteins
Membrane spanning regions have externally located hydrophobic residues that interact with the membrane lipids. They may have hydrophilic central channels
List some non-polar/hydrophobic amino acids
Alanine Valine Phenylalanine Proline Isoleucine Leucine Methionine
List some polar aliphatic amino acids
Serine Threonine Glutamine Asparagine Cysteine
List some polar aromatic amino acids
Tyrosine Histidine Tryptophan
How are glycine and histidine different to the other amino acids classified
Glycine is sometimes nonpolar or in a separate group Histidine is sometimes a charged basic amino acid.
What is the key difference between polar and charged amino acids
Polar amino acids contain oxygen atoms as part of carbonyl groups/nitrogens as secondary amine groups rather than carboxyl/amine groups (in charged amino acids)
If an amino acid has neither an amine/carboxyl group or a secondary amine/carbonyl group then what does it have and what is it classified as
Hydrocarbon Non-polar hydrophobic