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22 Cards in this Set
- Front
- Back
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Characteristics of a Peptide Bond |
Planar, trans, dipole |
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pKa is... |
the pH at which a given group is 50% ionised |
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pI is... |
the pH at which a molecule has no net charge ie. positive and negative charges are equal |
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Bond Angles |
Phi - angle between Ca-N Psi - angle between Ca-C Omega - dihedral angle (almost always trans) Chi - side chain angle (a molecule can have more than one chi angle) |
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Types of interactions involved in holding together a protein at the 3D level |
-Disulfide bonds -Metal ion coordination -Hydrophobic interactions -Electrostatic attraction -Side chain H bonding |
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Methods of looking at proteins |
-NMR spectroscopy -Electron microscopy -Crystallography |
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Quaternary structure |
Refers to the arrangement of subunits Contains more than one chain of amino acids. |
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Primary structure |
the amino acid sequence. The primary structure determines the higher structure of the protein and thus its properties. |
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Types of protein folding mechanisms |
Chaperone independent, Chaperone mediated, Chaperonin assisted. |
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The final folded protein tertiary structure consists of one ore more functional units known as... |
Domains |
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Areas on a Ramachandran plot |
Top left beta, Bottom left alpha (r), top right alpha (l) |
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Alpha helix |
-the most common secondrary structure -3.6 residues/turn -side chains point out - so they are able to react -Right and left handed - R handed much more common |
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Beta sheet |
-quite flat pleated sheets -side chains above or below -can be parellel or antiparellel - approx. 15 amino acids per stand |
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Turns |
-really short, allow for changes in direction - Proline and Glycine common |
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Domains |
Characterised by the fact they hve specific functions eg EF hand protein - binds Ca 2+ ions |
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Catalytic Mechanisms |
1. Acid-base catalysis 2. Covalent catalysis 3. Metal ion catalysis 4. Electrostatic catalysis 5. Proximity and orientation effects 6. Preferential binding of the transition state complex |
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Acid-base catalysis |
-Involves H+ transfer -Histidine is particularly suitable to these reactions as pKa is -6.5 which is close to physiological pH and depending on environment of the active site His can donate or accept a proton therefore acting as either and acid or a base. |
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Covalent Catalysis |
-Involves formation of a highly reactive, short lived intermediate which is covalently attatched to the enzyme. -Enzyme normally contains a nucleophilic group -Cleavage of the covalent bond often occurs through hydrolysis -Typical protease mechanism |
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Metal Ion Catalysis |
About one third of known enzymes require metal ions for catalytic activity These metals provide : -substrate orientation - binding energy - sites for oxidation-reduction reactions eg Hexokinase uses Mg2+ as a cofactor |
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Cofactors |
Sometimes enzymes require other 'factors' to help them catalyse reactionsthese may be: - Metal ions -Small organic molecules (coenzymes) |
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Coenzymes |
-Are a subset of cofactors -function as carriers (electrons, atoms, molecules) -often derived from vitamins |
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Enzyme Nomenclature |
-naming system for enzymes EC number - 1st # - class - 2nd # - sub class - 3rd # - sub sub class - 4th # - serial number |
