Progress Test Flashcards
Bonds that stabilise the tertiary structure
- Ionic Bond
- Hydrogen Bond
- Hydrophobic Interactions
- Disulphide Bridges
Protein subunits
Proteins are polymers of amino acids which are linked my peptide bonds (covalent bonds) to form polypeptide chains.
The unique sequence of amino acids determines the proteins structure and thus function.
Main techniques to determine protein structure
- Protein crystallography
- Electron cryo-microscopy
- NMR spectroscopy
Examples of Proteins involved in…
DNA Replication - DNA Polymerase RNA Replication - RNA Polymerase Oxygen Transport - Haemoglobin Immune Protection - Antibodies Digestion - Trypsin (protease), Amylase (starch -> sugar) Metabolism - Alcohol Dehydrogenase.
General Amino Acid Properties
- Basic Backbone Structure 2HN - HCR - C’OOH
- Chiral (Mostly L form)
- Most amino acids exist as zwitterion form (NH3+, COO-)
- 4 main groups of amino acids
- Non-Polar Amino Acids
Lots of ‘aliphatic’ chains (C+H), which are oily.
Or Aromatic side chains (gives ability to be fluroescence)
Or Cys (R chain = CH2 - SH)
Often packed together deep inside protein to form hydrophobic core, which gives stability.
Gly R chain = H, it is not chiral and thus more flexible.
Pro R chain bonds back with the amino acid main chain forming a 5 membered ring making it rigid. As r group bonds to amine group, Pro = imino acid.
- Uncharged Polar
R chains have OH or ONH2 group
Can be involved in polar, uncharged hydrogen bonds.
- Positively charged Polar
R chains have NH+ (NH2+ or NH3+) group
They’re basic polar amino acids (shown as conjugate acid)
Usually found on the surface of the protein and will interact with water. Sometimes can be buried if it’s in the active site or an electrostatic link. (Lys and His often found in the active site).
Negatively charged Polar
R chains have COO- groups (additional carboxyl group).
They’re acidic polar amino acids (shown as conjugate base).
Usually found on the surface of the protein and will interact with water. Sometimes can be buried if it’s in the active site or an electrostatic link
pKa
pKa for the ionisable group on an amino acid or protein, is the pH at which the group is 50% ionised.
COOH group pKa around 2
NH3+ group pKa around 9-10
R group pKa can range from 4 -12
pH > pKa = side chain will be deprotonated
pH < pKa = side chain will be protonated
pI
pI (isoelectric point) is the pH at which the net charge of the molecule / protein is 0.
Post-translational modification
Oxidation = loss of electrons
Phosphorylation = add phosphate group (often used as an on / off switch in signalling pathways.
Hydroxylation = add hydroxide group (needed to prevent connective tissue disease)
Carboxylation = add carboxylic acid group (needed for blood clotting, often involves Glu).
Metal binding
Iodination = add iodine (eg thyroid hormone)
Glycosylation = add carbohydrate (increase solubility)
Peptide bond
Ribosome active site environment catalyses the removal of H20 and the formation of a peptide bond between 2 amino acids.
Properties:
- Peptide bond has 40% double bond character. Thus you cannot rotate around the bond freely and it becomes planar.
- Partial dipole forms between +ve and -ve partial charges.
- Is mainly Trans
Amino Acid Residues
Amino acids in a peptide / protein = amino acid residues
Peptide = Short stretch of amino acids (<50)
Protein = Larger chain of amino aicds (>50) usually with defined biological function.
Levels of Protein Structure
Primary = Sequence of amino acids Secondary = The local 3D structure of a protein chain over a short stretch of adjacent amino acid residues (a helices, B sheets). Tertiary = 3D stricture of a complete protein chain, Quaternary = The interchain packing and structure for a protein that contains multiple protein chains.
