2. Protein Structure Flashcards
Describe the general structure of amino acids.
H2N-alphaC(H)(R)-COOH
NH3+ & COOH (high pH)
NH3+ & COO- (zwitterion)
NH2 & COO- (low pH)
HA (Protonated) <–KA–> A- + H+ (Deprotonated)
Ka = acid dissocation constant.
pKa = -logKa
Ka = 10-pKa
Explain the different properties of amino acids.
Polar/Non-Polar
Hydrophillic: if polar
Hydrophobic: if non-polar
Acidic: Negatively charged side chain.
Basic: Positively charged side chain.
Aliphatic: Straight chained only.
Aromatic: Phenyl groups etc.
Describe the key features of peptide bonds and explain how they contribute to protein structure.
Amino acids are covalently bonded together with peptide bonds.
No longer amino acids, referred to as residues.
Molecule of water released when a peptide bond forms.
Properties
- Planar
- Rigid (C-N bond has partial double bond characteristics)
- Trans conformation (O=C-C-H, O/H on opposite sides)
- Bonds either side of the peptide bond are free to rotate, making the proteins flexible.
Outline the different levels of protein structure and identify the key intermolecular forces involved in stabilising these structures.
Primary: Amino acid sequence.
Secondary: Local spatial arrangement, a-helix (hydrogen bonds between N-H and C=O) & beta-sheets (hydrogen bonds between strands).
Tertiary: 3D configuration of protein.
- globular with several types of secondary structure.
- fibrous with single type of secondary structure repeating.
Quaternary: Association of different polypeptides to form a protein.
Explain why protein structure is important for protein function.
Size
- number of amino acid residues.
- molecular weight in kilodaltons (kDa)
Isoeletric Point (PI)
- pH at which a protein has no overall charge.
Active sites/allosteric sites must be specific for the enzyme to function.
Provide an outline of how proteins fold and why it is important for function.
Localised folding with the most stable conformations maintained.
Driven by the need to find the most stable conformation.
Explain why protein misfolding can cause disease.
Unknown why misfolding occurs.
Leads to formation of amyloid fibres (misfolded, insoluble version of a normally folded protein).
Aggregate together and are not destroyed by cells.
What is the henderson-hasselbalch equation?
pH = pKa + log[deprotonated form]/[protonated form]
pH < pKa = protonated
pH > pKa = deprotonated
