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BIOCH 320 > 3 - 3D structure - 2ary structure > Flashcards

3 - 3D structure - 2ary structure Flashcards

1
Q

why do peptide bonds have partial double bond character

A

resonance

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2
Q

what kind of rotation do amide bonds have

A

limited

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3
Q

what is the C=O distance in amide like relative to in typical carbonyl

A

LONGER

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4
Q

what is the C-N distance in amide like relative to typically

A

SHORTER

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5
Q

do peptide bonds have an electric dipole

A

yes but small

towards C=O from NH

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6
Q

what are the 2 main configurations of peptide bonds and what is most common

A

trans or cis (with respect to alpha carbon) - mostly trans

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7
Q

which aroms are all in a plane

A

6 atoms around the C-N peptide bond

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8
Q

how many m in an A

A

10^-10m

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9
Q

what are Phi (φ) and psy(ψ)

A

torsions describing rotation around alpha carbon bonds

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10
Q

what is Phi (φ)

A

bond from N to alpha carbon

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11
Q

what is psy(ψ)

A

bond from alpha carbon to C=O carbon

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12
Q

how many atoms define a torsion

A

4 - central 2 + 2 on other side

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13
Q

when are Phi (φ) and psy(ψ) defined as 0

A

when the two peptide bonds are flanking the alpha carbon when in same plane (atoms 1 and 4 are cis)

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14
Q

is 0,0 allowed conformation

A

no (steric hindrance)

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15
Q

which coordinates of phi (φ) and psy(ψ) are in the extended chaine

A

around 180 each

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16
Q

is it - or + if its a CW rotation of bond in back relative to bond in front

A

+

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17
Q

is it - or + if its a CCW rotation of bond in back relative to bond in front

A

-

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18
Q

which area of the ramachandran plot is beta sheet

A

top left

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19
Q

what is the x axis for ramachandran plot

A

Phi (φ)

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20
Q

what is the Y axis for ramachandran plot

A

psy(ψ)

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21
Q

what does blue mean on ramachandran plot

A

fully allowed conformation

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22
Q

what does green mean on ramachandran plot

A

at limit of unfavorable interaction

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23
Q

what is glycines ramachandran plot like and why

A

lots of allowable areas because there is no beta carbon so lots of flexibility

also asymmetrical because it is achrial

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24
Q

is phi or psy(ψ) more restricted in proline

A

Phi (φ) more restricted than psy(ψ) (Phi (φ) is between N-C which is in the cyclic side chain)

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25
Q

what are the phi (φ) and psy(ψ) in regular secondary structure

A

repeating angles for sequential amino acids, often similar angles

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26
Q

what are the phi (φ) and psy(ψ) in irregular secondary structure

A

non repeating angles

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27
Q

what are the H bonds like in regular secondary structure

A

stable forms have repeating H bonding patterns

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28
Q

what are the main types of regular secondary structures and another type

A

common: alpha helix beta sheet

also there are collagen helices

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29
Q

what are the types of irregular secondary structures

A

beta turns, coils, loops

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30
Q

where are alpha sheets usually in the ramachandran plot

A

more on the lower left

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31
Q

is alpha helix left or right handed

A

right

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32
Q

where are the H bonds in alpha helix

A

C=O of residue (i) to NH of residue (1+4)

33
Q

which NH and C=O residues do not H bond

A

first 4 NH and last 4 C=O

34
Q

where are the side chains in alpha helices

A

projecting away from core

35
Q

how many residues per turn in alpha helix

A

3.6

36
Q

how many A per turn in alpha helix

A

5.4

37
Q

where is phi (φ) and psy(ψ) in alpha helix

A

near (-57, -47)

38
Q

what stabilizes the atoms in the helix backbone (they are packed densely in the core)

A

van der waals and hydrogen bonding

39
Q

how many residues apart in the alpha helix interact favourably (like close by in helix)

A

r groups 3-4 residues apart

40
Q

what direction is the helix dipole

A

negative C terminal and positive N terminal

41
Q

which a.a. are often found at the N terminus and why

A

negative ones (Asp, Glu) because of charge complementarity

42
Q

which a.a. are often found at the C terminus and why

A

positive ones (Arg, Lys) because of charge complementarity

43
Q

which direction is the dipole in the NH bond

A

H towards N (N is more negative)

44
Q

which direction is the dipole in the C=O bond

A

C towards O (O is more negative)

45
Q

what are the types of beta sheets

A

parallel, antiparallel, mixed

46
Q

where is phi (φ) and psy(ψ) in parallel beta sheets

is it more or less extended

A

near (-120, +120) (less extended)

47
Q

where is phi (φ) and psy(ψ) in antiparallel beta sheets

is it more or less extended

A

near (-140, +140) (extended)

48
Q

what causes the formation of beta sheets (allows them to stay too)

A

H bonds between strands

49
Q

are beta strands only from the same 1ary structure

A

yes but also can also come from different peptides

50
Q

what does the H bonding pattern look like in antiparallel beta sheets

A

parallel couplets (2 then space, 2 then space…)

51
Q

what does the N to C pattern look like in antiparallel beta sheets

A

they are oriented opposite to eachother

52
Q

how can you determine N-C directionality

A

NRO is N-C

53
Q

what does the N to C pattern look like in parallel beta sheets

A

they are oriented in same direction (N to C in both . directions)

54
Q

what does the H bonding pattern look like in parallel beta sheets

A

they are not parallel, they are more diagonal looking

55
Q

does antiparallel or parallel have more pronounced pleats

A

parallel (-120, +120) (not as extended)

56
Q

does antiparallel or parallel have less pronounced pleats

A

anti parallel (-140, +140) (extended)

57
Q

does antiparallel or parallel travel more distance

A

anti parallel (-140, +140) (extended)

58
Q

does antiparallel or parallel travel less distance

A

parallel (-120, +120) (not as extended)

59
Q

and beta sheets form between two subunits in a quaternary structure

A

yes-they dont need to have to follow eachother within primary sequence

60
Q

are beta sheets planar

why or why not

A

no, they typically twist into saddle shapes or barrels

61
Q

where are irregular 2 structures on the ramachandran plot

A

all different, not concentrated to a single location

62
Q

what kind of structure are beta turns

A

irregular 2ary

63
Q

what characterizes beta turns

A

backbone H bond

64
Q

when are beta turns used

A

to change direction in polypeptide (180 turns), like connecting antiparallelbeta strands

65
Q

what are types of beta turns

A

type 1 and type 2

66
Q

what amino acids are most common in beta turns and why

A

proline (good for turning)

glycine (good for flexibility)

67
Q

what are the phi (φ) and psy(ψ) in beta turns

A

they vary

68
Q

what is the difference with type 1 and 2 beta turns (general and specific)

A

diff geometry

type 2 always have glycine as 3rd residue

69
Q

what is always constant in beta turns

A

type 2 always have glycine as 3rd residue

70
Q

why does type 2 beta turns always have glycine as 3rd residue

A

it is the only thing that can adopt a (80, 0) geometry

71
Q

where is the (80,0) in the ramachandran plot (glycine(

A

right and middle

72
Q

which amino acids are most found in alpha helices

A

ala
glu
met

73
Q

which amino acids are least found in regular structures

A

glycine and proline

74
Q

what kind of structure is ala found in most

A

alpha helix

75
Q

what kind of structure is glu found in most

A

alpha helix

76
Q

what kind of structure is met found in most

A

alpha helix

77
Q

what kind of structure is glycine found in most

A

irregular + collagen helix

78
Q

what kind of structure is proline found in most

A

irregular + collagen helix

BIOCH 320 (16 decks)

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