Protein Structure Flashcards
Concept of primary protein structure
Linear sequence of amino acids that make up the protein
Concept of secondary protein structure
Local structural motifs within a protein, dictated by primary structure
Concept of tertiary protein structure
The arrangement of secondary structure motifs into domains
Concept of quaternary protein structure
The 3D structure of multimeric proteins composed of several subunits
The type of reaction by which Amino Acids are joined together
Condensation
Trimeric peptide sketch with amino terminus, carboxyl terminus and side chains
3 amino acids joined together, NH2 = amino terminus, COOH = carboxyl terminus, R1/R2/R3 side chains
A-helix distinguishing features
Helical shape
N-H from one residue forming H bond with C=O 4 residues later.
Side chains project outwards
Proline will cause a kink - loses NH2 so no H bond formed.
B-pleated sheet distinguishing features
Sheet shape made of beta strands
N-H, C=O point out at right angles to the backbone
H bonds form between N-H and C=O of differing strands
Alternate strands running parallel = parallel sheet
Alternate strands running anti-parallel =
Anti-parallel sheet
Bonds responsible for holding together secondary structure?
H-bonds
Bonds responsible for tertiary structure
Covalent bonds Hydrogen bonds Ionic interactions Van der Waals forces Hydrophobic interactions
Covalent bond features
Strongest bonds
Exist in backbone
Exist between cysteine side chains - disulphide bridges.
Hydrogen bond features
Occur between electronegative species and hydrogen atoms
Occur between sidechains, sidechains and water, or sidechains and the backbone itself
Ionic interactions features
Electrostatic attraction between charged side chains. Mostly on surface of proteins, hydrophilic
Van der waals forces features
Weak
Electrostatic forces
Based on fluctuating electron clouds
Hydrophobic interactions features
Hydrophobic side chains placed next to each other in the hydrophobic core of the protein. Creates hydrophobic core and hydrophilic surface.
Principle of electrophoresis
AAs have charged side chains, electrophoresis can separate proteins on basic of overall charge and/or molecular weight
Why can proteins with single mutations be separated by electrophoresis?
Single amino acid change
Weight and/or charge changes.
Change detectable as a difference in the distance the two proteins travel under electrophoresis.
What is an example of N-linked glycosylation?
Addition of sugar groups to asparagine (N) residues of Luteinizing Hormone Receptor
Why does N-linked glycosylation have an effect on electrophoresis distance?
Mutation of two asparagine to glutamine can be picked up by electrophoresis as a reduction in the overall molecular weight of LHR.
