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40 Cards in this Set
- Front
- Back
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How do different peptide conformations occur |
Rotation around the single bond |
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Why are most rotations of the alpha carbon bonded to carbon or nitrogen not allowed |
Steric clashes and the Ramachandran plot |
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Small polypeptides can have a large number of allowed conformations but why aren't these found |
Only thermodynamically most stable are found in nature |
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Why do proteins 3d fold |
Maximises non covalent and hydrophobic bonding for stability |
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A linear polymer will probably end up as what |
A linear fold |
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How is protein folding illustrated |
With protein funnels |
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What occurs as you go down the funnel |
Free energy decreases do native structure is more stable Can roll any way down the funnel to form intermediates sacastic manner |
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What is the top coil of a funnel |
The random coil, primary structure and interactions make it energetically favourable to form the secondary and tertiary intermediates |
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What is the depth of the funnel denoted by |
Delta g, the progressive stabilisation of intermediates as deepens |
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Is there just one pathway to the final structure |
No, many pathways down the funnel |
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What are the five forces that stabilise proteins |
Covalent bonds inc. disulphide bonds Non covalent bonds H bonds Electrostatic interactions bondsElectrostatic interactionsHydrophobic effect Hydrophobic effect |
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How do van Der Waals increase and then why do they decrease |
Increase between two atoms electrostatic attraction then decrease due to large repulsion |
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What is the point of maximum electrostatic attraction In vdws called |
Vdws contact distance Electrostatically most stable |
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How are van Der Waals represented in diagrams |
2 Partly merging Spheres |
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What is hydrophobic effect Example of when nonpolar molecules enter water |
High h bonding occurs in water Non polar molecules don't h bond with water Disrupts water to make it more ordered around it, forming a cage An increase in order decrease entropy Thermodynamically unfavorable |
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Why do non polar molecules associate in water |
To reduce the amount of order introduced |
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Hydrophobic side chains cluster where in the protein and why |
Interior of the protein Drive protein folding as the density of water in the protein interior is much lower than outside so is thermodynamically favourable to be inside Increase entropy |
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What are h bonds |
Mainly electrostatic, slightly covalent Has a weakly acidic donor and an acceptor with a lone pair of electrons |
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What is the order of strength for the four bonds |
Covalent is strongest Salt bridge Hydrogen Vdws are weakest |
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What is the stronger h bond, linear or kinked |
Linear |
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What is a salt bridge |
Attractions between oppositely charged amino acids e.g. arg and glu |
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Salt bridges can be long range, how ar distance and energy association related |
Energy association is inversely proportional to distance between r chains As side chains get further away, energy increases |
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Why do salt bridges have a different energy of association in water compared to the protein interior |
Waters partial ionic character interferes with the reactions between oppositely charged side chains |
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What are dipole dipole interactions causes by |
Asymmetric electron distribution between two atoms |
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What are the three types of dipole dipole interactions |
Between 2 permanent dipoles e.g. 2 carbonyls Much smaller charge so lower energy association Permanent and induced dipole e.g.ch3 and carbonyl Vdws- instantaneous dipoles and subsequent induced dipole- v weak but so many that it has a major impact on stability |
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What does the helical wheel represent |
The alpha helix, looking at it down axis to plot where the different residues are placed in therms of side chains |
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Where are hydrophilic and hydrophobic clusters positioned on the alpha helix |
Hydrophobic inwards, hydrophilic outwards, asymmetric distribution Ampipathic behaviour |
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Hey is glycine underrepresented in alpha helices |
Only has h as r group so least steric clashes, has most phi and psi angled so other stable structures can form Conformationally flexible |
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Where is proline forums in the alpha helix and why |
Terminals as is conformationally inflexible N and alpha carbon bond cannot rotate so helical geometry cannot be adopted |
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What is the net dipole movement of the alpha helix |
N terminus at the top is positive, c terminus at bottom is negative due to resonance of small dipoles in each peptide bond |
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Where are positive and negative amino acids positioned |
Positive at bottom Negative at top, n terminus |
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Why is a beta sheet different to an alpha helix |
Much more extended with parallel and antiparallel strands Side chains alternate above and below the sheet plane Amino acids separated by 3.5A but only 1.5A in a helix |
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What direction do flat arrows pointing in |
C terminal |
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What do the shape of beta pleated sheets |
Slightly twisted B barrels can also form |
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How are the turns between. Secondary structures in globular proteins, loose or tight What else can turns be |
Tight "reverse turns" Rigid or dynamic ,no repeating phi and psi but are not random coils Can delineate different secondary structures in a protein |
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Define a reverse turn |
Beta turn C of I bonds with NH of I+3 to stabilise the turn |
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What two amino acids are often found in beta turns |
Glycine has high conformational flexibility many allows phi and psi angles Proline induces a sharp angle so links the chain |
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What handed are alpha helices How to tell |
Right handed Turn right hand towards body, if helix curves this way it's RH |
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What is the turn and the pitch of the alpha helix and why does side chains point outwards |
3.6 residues 5.4A Would cause steric clashes if pointed inwards |
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What do two bulky side chains next to one another cause for the alpha helix |
Steric clashes so destabilises helix |
