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55 Cards in this Set
- Front
- Back
What type of reaction occurs to make a peptide bond?
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dehydration
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Which atoms in a polypeptide are immovable?
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OCNH
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What conformation is favored for most amino acids and why?
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Trans-, the cis-conformation possesses unfavorable steric interactions.
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Why do proteins consist of "propeller blades"? |
Rotation can occur between units, but there's no free rotation about the amide bond.
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What limit the range of values for phi and psi?
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steric interactions
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True or false: chiral center (alpha-carbon) has a fixed conformation. |
False, configuration
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regularities in local conformations maintained by networks of hydrogen bonds
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secondary structure
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What are four examples of secondary structure? |
alpha helix beta strand or beta sheet loop and turn random coil |
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deliberate disordered regions
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random coil
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arises when a number of consecutive amino acids have similar phi and psi values
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secondary structure
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What does hydrogen bonding occur between in alpha helices?
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carbonyl oxygen of the Nth amino acid and the hydrogen of the amide on the N+4th amino acid
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How many amino acids are required to complete a turn of an alpha helix?
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3.6
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What is the net dipole of an alpha helix? |
positive N-terminus, negative C-terminus
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Why do alpha helices have a net dipole?
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all hydrogen bonds point in the same direction
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What is the pitch of an alpha helix?
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0.54 nm or 5.4 Å
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What is the rise of an alpha helix? |
0.15 nm or 1.5 Å
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How many degrees does each amino acid rotate? |
100
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What are the phi, psi coordinates of alpha helices? |
120, -60
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Where are side chains located in alpha helices?
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They project outward.
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What amino acids destabilize alpha helices? |
G P |
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How does G destabilize alpha helices? |
absence of side chain results in greater freedom of rotation
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How does P destabilized alpha helices?
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produces kink because cyclic structure occupies space that neighboring amino acid would otherwise occupy
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What amino acid has phi and psi values that vary over a considerable range? |
G
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What can be said about amphipathic alpha helices?
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All hydrophobic residues are on one side.
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one turn (360 degrees) of an alpha helix
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pitch
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What stabilizes beta sheets?
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long range cross-sheet hydrogen bonds
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Where do side chains project in beta sheets? |
alternately above and below the plane
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Why do beta sheets with multiple strands have a slight right-handed twist? |
Because amino acids are constructed from L-amino acids.
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What are the phi, psi coordinates for beta sheets?
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-120, 120
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What is slightly more stable: parallel or antiparallel beta sheets?
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antiparallel
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Describe the "pleated" topology of beta sheets.
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R groups up R groups down R groups up R groups down |
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What are loops?
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regions of proteins that cause directional changes
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Where do loops appear?
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on the surface of proteins
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Are loops hydrophilic or hydrophobic? |
hydrophilic
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How many amino aid residues do loops typically possess?
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more than five
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What are turns or beta turns? |
subclass of loops with five or fewer amino acids connecting two secondary structural features
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What amino acids do turns often contain? |
P G
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For which amino acid is the cis-conformation not as disfavored as it is for others?
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P
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What is the trans-to-cis ratio in most amino acids? |
1000:1
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What is the trans-to-cis ratio in proline? |
3:1
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What amino acid has the greatest percentage of cis-conformation? |
P
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portion of a protein that adopts many possible conformations |
random coil
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often sites that control regulation or signaling, undergo covalent modification, bind drugs, and are modified in alternative splicing |
random coil
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What percentage of myoglobin is random coil? |
30%
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regions that do not have a major single conformation |
molten globules
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True or false: beta sheets have a net dipole moment. |
false
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produce directional change |
loops and turns
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provide important flexibility |
random coils
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Why is the peptide bond planar?
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partial double-bond character, limits rotation
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Due to the side group steric clash, what are almost all peptide bonds? |
trans
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What is the trans-cis ratio if cis-Ala-Trp is 4 kcal/mol less stable than trans-Ala-Trp? |
1000:1
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What is every factor of ten in an equilibrium? |
1.36 kcal/mol
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What sequence exploits the structural properties of an alpha helix to make a stable, side-by-side, two-helix fold?
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Place a hydrophobic residue at every 4th position in the sequence.
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What secondary structure is stabilized by CO and NH hydrogen bonding within the peptide chain?
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alpha helix
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What amino acid residue disrupts the alpha helix because its side chain contains a unique ring structure that restricts bond rotations? |
P
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