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34 Cards in this Set
- Front
- Back
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What kind of reaction forms a peptide bond?
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Condensation. We lose water
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What two atoms are involved in Phi angle?
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N-C-alpha
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WHat two atoms are involved in psi angle?
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C-Calpha
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How many angles are allowed? Why?
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Not many because of steric hindrance
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What is the exception of Ramachandran plots?
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glycine, because it is very rotational
proline, basically no roteation |
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how are alpha helices stabilized?
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favorable interactions between side chains 3-4 amino acids apart
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what kind of amino acids are contained in beta strands?
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alanine, glycine
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what do turns and loops do?
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link secondary structure elements together
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What kind of residues are in turns/loops usually? what can they do with solvent?
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usually contained charged and polar residues, can hydrogen bond to the solvent
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What are B-turns/hairpin loops made out of?
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glycine, proline, also h#1 bonds to h#4
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2 major groups of tertiary structure?
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globular and fibrous
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motifs/supersecondary structure
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recurring structural patterns, formed by different combinations of alpha and beta
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domain
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distinct structural unit of a polypeptide
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alpha helix stability is affected by:
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electrostatic repulsion or attraction between charged side chains, repulsion between bulky side chains, interactions between residues 3-4 amin acids apart,no glycine or proline
each end is dipole stabilized |
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what can fibrous proteins do?why?
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strength, structural support, shape, flexibility, external protection, because of their length
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what are a few types of fibrous proteins?
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coiled coil alpha helicies (keratin, mysin)-tough, insoluble
triple helix collagin (not alpha helix)- has high tensile strength w/o stretching, b-sheets(silks,amyoloids)-soft flexible |
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a few things about alpha keratin:
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found in hair, wool, nails, claws
intermediate filaments family 2 alpha helices form 2 chain coil 2 chain colied coils form a protofilament, when then form protofibrils |
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what characterizes collagen triple helices?
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found in connective tissue,tendons, bone, 3 single helices twisted to make a superhelix, each individual helix has 3 residues/turn, repeats of Gly-X-Y- where X is proline, y is modified proline
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What characterizes b-sheets?
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rich in glycine and alanine, extremely hydrophobic, multiple layers of antiparallel B-pleated sheets
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Ways to denature protein
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heat, pH extremes, organic solvents, detergents, denaturants
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2 models for protein folding
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hierarchical folding, molten globular
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What happens when a protein folds?
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Free energy goes down, water entropy goes up, protein order goes up
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What problems do you encounter in protein folding?
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sulfide bond, isomers of proline- fixed by peptide prolyl isomerase, aggregation of intermediates through exposed hydrophobic groups: they clump together usually
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What do chaperones do?
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catalyze off-pathway proteins back on path
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What is required for chaperones to function?
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ATP
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what does hsp70 do?
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binds to unfolded or partially folded proteins to prevent aggregation, reverses denaturing/aggregation of incorrectly folded protein, requires ATP
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What is GroEL/ES made of?
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14 subunits in 2 rings, 7 per
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How does Groel/es bind the proteins?
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by exposed hydrophobic surfaces, atp drivin
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What are the steps of the Groel/es process?
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protein binds via exposed hydrophobic surfaces w/ ATP
groES binds, causes conformational change and protein is transported to the hydrophilic microenvironment ATP is hydrolyzed 2nd unfolded protein binds to other ring |
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How many atp is required for groel folding?
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7
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amyloid
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disease where deposition of insoluble aggregates of previously soluble proteins
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what are amyloids formed from?
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b-fibrils, b-cross
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What characterizes beta crosses?
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helical arrangement of b-strands perpendicular to fiber axis,
often have aromatic residues, |
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which form of prion is active and inactive?
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prp^c is normal, prp^sc is abnormal
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