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BIOCHEM 320 > 3D, primary and secondary > Flashcards

3D, primary and secondary Flashcards

1
Q

what kind of double bond do peptide bonds feature and why

A

partial double bond due to resonance

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2
Q

describe the length of the C=O bond in a peptide bond

A

longer than usual

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3
Q

describe the length of the C-N bond in a peptide bond

A

shorter than usual

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4
Q

what configuration are most peptide bonds in in proteins

A

trans

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5
Q

which bonds can rotate in an polypeptide

A

the ones attached to alpha carbons only, phi and psi

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6
Q

which atoms define torsion

A

central 2 and the 2 on either side

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7
Q

draw trans 180 newman conformations for phi and psi

A

see slide 13

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8
Q

why is L-proline restricted in rotation? which bond is this around?

A

phi bond restricted because cyclic side chain

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9
Q

what kind of bonds are found in regular secondary structure?

A

repeating phi and psi angles for sequential amino acids

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10
Q

what kind of H-bonding patterns do stable forms of secondary structures feature?

A

repeating

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11
Q

what are 3 examples of regular secondary structure

A

alpha helix, beta sheets, collagen helixes

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12
Q

what kind of bonds are found in irregular secondary structures

A

non repeating phi and psi angles

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13
Q

what are 3 types of irregular secondary structure

A

beta turns, coils, loops

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14
Q

what kind of twist is in the alpha helix

A

right handed

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15
Q

where are the H-bonds in an alpha helix

A

c=o of i and NH of i+4

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16
Q

where do the sidechains project in an alpha helix

A

away from core

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17
Q

what is the bond angle for phi and psi in an alpha helix

A

(-57,-47)

18
Q

how many residues per turn of alpha helix

A

3.6

19
Q

which R-groups from the primary sequence interact favourable in alpha helix

A

3-4 residues apart

20
Q

what are atoms in the alpha helix backbone stabilized by

A

van der waals and H-bonding

21
Q

which terminus in the alpha helix is negatively charged

A

C-terminus

22
Q

which terminus in the alpha helix is positively charged

A

N-terminus

23
Q

which direction is the C=O bonds pointing towards in an alpha helix

A

C-terminus

24
Q

what is found at each end of the alpha helix

A

4 unpaired amino acids not involved in H-bonds

25
Q

which amino acids are usually found ar the N-terminus of an alpha helix?
what about the C-terminus

A

glu and asp
lys and arg

26
Q

which end of an amino acid would interact with phosphates or nucleotides

A

the N terminus

27
Q

what are the 3 kind of beta sheets

A

parallel antiparallel mixed

28
Q

what is phi and psi for parallel beta sheets
what is phi and psi for antiparallel beta sheets

A

(-120, +120)
(-140, +140)

29
Q

what are beta sheets formed by

A

H-bonds between strands

30
Q

what are the 2 types of situations involving strands for beta sheets

A

separated within primary structure or coming from different peptides

31
Q

compare the repeat period for parallel vs antiparallel beta sheets

A

shorter for parallel

32
Q

T or F: the hydrogen bonding pattern for antiparallel vs parallel beta sheets is the same

A

false

33
Q

T or F: individuals strands in a beta-sheet always follow each other in the primary sequence

A

false

34
Q

are beta sheets planar

A

no they are not planar

35
Q

what can beta sheets twist into

A

saddle shapes or barrels

36
Q

where are the H-bonds between in beta turns

A

C=O of residue 1 to NH of residue 4

37
Q

what is the degree change in the direction of the polypeptide in a beta turn

A

180 degrees

38
Q

how are the types of beta turns characterized

A

combinations of phi and psi angles

39
Q

which amino acids are often found in beta turns

A

proline and glycine

40
Q

what is always the third residue in a type II beta-turn?
why is this?
what is the name/ designation for this third residue?

A

glycine
geometry (80,0)
i+2

41
Q

which amino acids have the highest propensity for alpha helix formation

A

ala glu and met

BIOCHEM 320 (6 decks)

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