Flashcards
BIOC222: Mod1
Cards in this deck (23)
- 1The peptide bond is ____ & ____. Describe other characteristics of primary protein structureRigid & planar. There is a slight dipole due to partial charges on CO & NH
- 2What forces stabilise secondary protein structure? Assign energy values to eachCovalent bonds: V strong, 340-460 kJ/mol
Ionic interactions: 80-90 kJ/mol
H bonds: 20 kJ/mol (these are directional)
Van Der Waals: 0.3-9 kJ/mol - 3Provide details of the two common secondary formationsALPHA HELICES:
- 3.6 residues per turn
- CO directed at NH, 2.8Å per turn
- Sidechains down & out = no steric hindrance
BETA SHEETS:
- Parallel or antiparallel
- Fully extended to end-up bent - 4What are the 3 bond angles in the amino acid, & what does each represent?Omega: carbon to nitrogen (always 0 or 180)
Psi: alpha carbon to carbon
Phi: nitrogen to alpha carbon - 5Detail the differences between glycine, proline, & cysteineGlycine: no side chain = very flexible.
Proline: cyclic side chain = steric hindrance, locked at phi angle of 60.
Cysteine: very nucleophilic, forms disulphide bridges. - 6Combining what 2 topology visualisations provides good active site understanding?Ribbon + ball & stick
- 7What is a surface topology view of a protein good for?Identifying conserved surface residues that may relate to protein function
- 8What are the 3 methods of solving protein structure? Briefly discuss eachNMR: small proteins, good for atomic distance + dynamics in soln
X-Ray Crystallography: crystallised (challenge). Static snapshot @ high res, most common
Cryo-electron Microscopy: big proteins in thin layer of buffer - 9What may be more conserved than primary sequence in a protein?Folds in the secondary/tertiary structure
- 10What are 3 determinants of protein stability?Residue interactions (VDW, ionic)
Metal ion coordination (cysteine does so)
Disulphide bridges - 11What was Anfinsen trying to show with his experimentsAll information required for correct protein folding exists in the primary sequence
- 12How did Anfinsen denature ribonuclease A in his experiments?Urea (chaotropic salt) to denature, & beta-mercaptoethanol to alter disulphide bridges
- 13Describe how chaotropic salts workAlter hydrogen-bonding networks in water. This affects stabilities of molecules dissolved in water, e.g. proteins
- 14How did Anfinsen track enzymatic activity during his experiments?Assays
General structural properties
Environment of certain residues - 15How were assays used?Directly track enzyme's activity. Fallback in fact not all proteins in soln are enzymes. Requires very robust assay
- 16How were general structural properties used?Circular dichroism (secondary structure), heat capacity, light scattering
- 17How were certain residues environments used?Such as Trp absence or fluorescence. Biochemical properties that require certain residues to be present
- 18What did Anfinsen discover?If you allow the disulphide bonds to form first (βME oxidation) before folding, protein doesn't work. If other folding interactions occur first, then βME oxidation w/ trace amounts, protein works.
- 19Describe how circular dichroism worksCertain amino acids change polarised light, esp characteristic of secondary structures. If light changes a certain way, it is characteristic of a particular secondary structure component
- 20Describe Levinthal's ParadoxIf a 101 residue peptide has residues each with 2 potential stable conformations, the protein has 2^100 possible conformations. If each 10^12 conformations sampled per second, would still take 10^10 years to trial all.
- 21What 2 peptide arrangements have notably lower free energy than the functional conformation, making them particularly problematic?Amyloid fibrils & amorphous aggregates
- 22How do ultra-stable misconformations of proteins arise?When a protein misfolds, it either converts back to its functional state (chaperones), or moves into unproductive aggregates (amyloid fibrils, etc.).
- 23How does the cell make sure the proper disulphide bonds form (recall the importance from Anfinsen's)Foldases, specifically protein disulphide deisomerase. This exists in the endoplasmic reticulum, and ensures disulphide bridges form between the correct residues, allowing functionality
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- Flashcards on BIOC222: Mod1, created by Guy Turner on 13/01/2019.
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- Guy Turner
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