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25 Cards in this Set
- Front
- Back
- 3rd side (hint)
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Regarding secondary structure formation in a protein, the fact that atoms of the peptide bond lie in a plane contributes what influential factors?
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The resonance stabilization energy of the planar structure is 88 kJ/mol;
A twist about the C-N bond involves a twist energy of 88 kJ/mol times the square of the twist angle; ***Twists can occur about either of the bonds linking the alpha carbon to the other atoms of the peptide backbone |
don't memorize energies; just know they are known
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What is the main consequence of the amide plane?
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Double bond nature of peptide bond causes planar geometry
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What type of interactions dictate and stabilize protein structure?
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Noncovalent interactions
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What are the noncovalent interactions that dictate protein structure and their energies?
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van der Waals: 0.4 - 4 kJ/mol
hydrogen bonds: 12-30 kJ/mol ionic bonds: 20 kJ/mol hydrophobic interactions: <40 kJ/mol |
VHIH
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Where is the information necessary for folding the peptide chain into its "native” structure contained?
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in the primary amino acid structure of the peptide
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Angle about the C(alpha)-N bond is denoted _________.
Angle about the C(alpha)-C bond is denoted _________. |
phi
psi |
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The entire path of the peptide backbone is known if...
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all phi and psi angles are specified
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Peptide bond planes are joined by __________________________. The rotation parameters are φ and ψ.
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the tetrahedral bonds of the alpha-carbon.
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Many possible conformations about an alpha-carbon between two peptide planes are forbidden because of STERIC CROWDING.
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Ramachandran determined that the _________________ combinations are the basis for ___________ secondary structures
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sterically favorable;
preferred |
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Unfavorable orbital overlap precludes some combinations of phi and psi. What are some unfavorable angles?
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phi = 0°, psi = 180° is unfavorable;
phi = 180°, psi = 0° is unfavorable; phi = 0°, psi = 0° is unfavorable |
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What two things does this plot tell you?
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1) Describes acceptable ψ/φ angles for individual AA’s in a polypeptide chain.
2) Helps determine what types of 2o structure are present |
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All secondary structures are ________ structures that are stabilized by __________ bonds.
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local;
hydrogen |
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________ is a ubiquitous component of protiens and was used to identify alpha helices.
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Keratin
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There may be several alpha-helical structures in a single polypeptide chain: true or false?
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true
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All H-bonds in the alpha-helix are oriented in the same direction, giving the helix a dipole with the N-terminus being ___________ and the C-terminus being ____________.
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positive; negative
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Arrangement of N–H and C=O groups (each with an individual dipole moment) along the helix axis creates a large net dipole for the helix.
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Which AAs destabilize an alpha helix?
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glycine and proline
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Two amphipathic helices can associate through __________ interactions
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hydrophobic
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Beta-pleated sheet strands may be
a. parallel b. antiparallel c. either d. neither |
c. either
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There are how many residues per turn in a beta pleated sheet?
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Two
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What does this image illustrate?
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That anti-parallel beta sheets are more stable than parallel
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Loops connect alpha-helices and beta-sheets. Loops usually contain ___________ residues.
Loops are found on ______________. |
hydrophillic ;
surfaces of proteins |
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Turns are loops with:
a. different charges b. more than 5 AAs c. more than 7 AAs d. are often found to have proline and glycine e. are often found to have proline and glutamine f. c and d g. b and d |
g. b and d
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How Do Polypeptides Fold into Three-Dimensional Protein Structures?
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Secondary structures form wherever possible (due to formation of large numbers of H bonds)
Helices and sheets often pack close together |
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Protein folding makes ________ bonds and minimizes ___________ contact.
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H; solvent
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Fibrous proteins are usually:
a. synthesized b. soluble c. insolube d. made of beta sheets e. made of alpha helices |
c. insoluble
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