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CHE 541 > 5 - Protein Folds and Quaternary Structure > Flashcards

5 - Protein Folds and Quaternary Structure Flashcards

1
Q

What two forces are “fighting” each other in an alpha helix?

A

Enthalpy (H-bonds, favorable) vs entropy (order, unfavorable)

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2
Q

How many turns are needed to form a stable alpha helix?

A

3-4 turns

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3
Q

When are beta sheets stable?

A

When they are packed together (H-bonds)

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4
Q

What is a common phi/psi angle for a beta sheet?

A

Phi = -140, psi = 130

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5
Q

What is the most common type of beta sheet?

A

Antiparallel (C and N terminus run in opposite directions in neighboring strands)

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6
Q

Why are antiparallel beta sheets common?

A

The carbonyl and amide hydrogens line up perfectly to H bond

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7
Q

What types of gaps are found in antiparallel beta sheets?

A

A large gap and a small gap (alternating)

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8
Q

How come beta sheets are pleated?

A

The phi and psi angles

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9
Q

What type of twist is seen in an antiparallel beta sheet?

A

Right handed twist

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10
Q

What is a parallel beta sheet?

A

C and N terminus run in parallel directions in neighboring strands

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11
Q

Why are parallel beta sheets less common?

A

The geometry of the H-bonds is not as effective, so it is not as stable

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12
Q

What types of gaps are found in parallel beta sheets?

A

Even gaps throughout

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13
Q

How come parallel beta sheets are less pleated?

A

There is a change in side chain orientation, making them less pleated

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14
Q

True or false: a structure can have both parallel and antiparallel beta sheets

A

True: this is a mixed beta sheet

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15
Q

True or false: all beta sheets are twisted

A

True: this is important for tertiary structure

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16
Q

What is a beta turn?

A

Amino acids that facilitate the turn between two beta sheets

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17
Q

What is the most common amino acid for a beta turn and why?

A

Gly, because a positive phi angle is needed for the beta sheet twist

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18
Q

What is a beta hairpin?

A

A 2 H-bond anti-parallel adjacent strand connected by a short (2 amino acid) turn

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19
Q

What is the importance of turns in a beta sheet?

A

There is lots of activity there (glycosylation, etc.)

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20
Q

True or false: a beta sheet can be ampipathic

A

True: each face could have different properties

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21
Q

How can you determine if a beta sheet is ampipathic?

A

Every other amino acid defines one face, look for polarity

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22
Q

What is tertiary structure?

A

A folded protein composed of a collection of secondary structure components

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23
Q

What are some common motifs in tertiary structure?

A

EF hand, coiled coil, four helix bundle, beta-barrel, TIM barrel, beta-solenoid

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24
Q

In terms of tertiary structure, where are active sites located?

A

They tend to be located at intersections (loops)

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25
Q

What is a helix loop helix?

A

Two alpha helices connected by a loop

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26
Q

What do helix interactions usually lead to in tertiary structure?

A

Align ridges and grooves made by side chains

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27
Q

What does the coiled coil motif use?

A

Amphipathic alpha helices

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28
Q

What does the beta barrel motif use?

A

A barrel with beta sheets

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29
Q

What is the structure of a coiled coil motif?

A

2 alpha helices form an interface together

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30
Q

How do the alpha helices of a coiled coil interact?

A

They have hydrophobic interactions with one face from each alpha helix

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31
Q

How does the structure of an alpha helix in a coiled coil differ from an alpha helix by itself?

A
  1. Coiled coil has 3.5 amino acids per tern (as opposed to 3.6)
  2. Coiled coil has a heptad repeat
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32
Q

What is a heptad repeat?

A

A repeating pattern of 7 amino acid residues

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33
Q

What is the advantage of having 3.5 amino acids per turn?

A

It allows for better registry between repeating groups for good a-d overlap

34
Q

What is an a-d overlap?

A

The interactions between the “a” residue on one strand and the “d” residue (4 amino acids away) on another strand in a coiled coil

35
Q

What is the disadvantage of having 3.5 amino acids per turn?

A

Lose optimal H-bonding due to changes in geometry (angles)

36
Q

Why is a coiled coil coiled?

A

The i+7 residue (8th residue) is tilted for good interface

37
Q

What is an example of a coiled coil?

A

Fos Jun

38
Q

How is a coiled coil used in Fos Jun?

A

Lock helices together for transcription factor

39
Q

What is a 4 helix bundle?

A

4 alpha helices that associate together through hydrophobic interfaces

40
Q

What types of alpha helices are in 4 helix bundles?

A

Normal (3.6 amino acids per turn)

41
Q

What is a helix turn helix?

A

Two alpha helices connected by a turn

42
Q

Where are helix turn helix motifs used?

A

To bind to major groove of DNA

43
Q

What is an EF hand?

A

A helix loop helix motif for calcium binding

44
Q

Where does calcium bind in an EF hand?

A

In the loop

45
Q

What is an example of a protein with an EF hand?

A

Calmodulin

46
Q

Why does calcium bind in the loop of an EF hand?

A

Need conformation flexibility to satisfy the rigid metal coordination requirements (specific geometry)

47
Q

What is a ridge in an alpha helix?

A

The orientation of the side chains

48
Q

What is a groove in an alpha helix?

A

An absence of side chains between two ridges

49
Q

What is the importance of a ridge and a groove?

A

Can insert a ridge into a groove for a good packing surface

50
Q

How does an i, i+4 / i, i+4 ridge packing work?

A

One helix is tilted 25 degrees, the second starts at 25 degrees and is flipped 180 degrees and then rotated 50 degrees

51
Q

What is the advantage of fitting a ridge in a groove?

A

Can screen out water

52
Q

How does an i, i+3 / i, i+4 ridge packing work?

A

One helix is tilted 25 degrees, the second starts at -45 degrees, is flipped 180 degrees, and then rotated -20 degrees

53
Q

What is an i, i+4 ridge?

A

25 degrees

54
Q

What is an i, i+3 ridge?

A

-45 degrees

55
Q

What is an alpha/beta motif?

A

A motif with both alpha helices and beta sheets

56
Q

What is an example of an alpha/beta motif?

A

A TIM barrel

57
Q

What is the structure of a TIM barrel?

A

A beta sheet pore surrounded by alpha helices

58
Q

What forms the pore in a TIM barrel?

A

The beta sheets

59
Q

What forms the core in a TIM barrel?

A

The alpha helices

60
Q

What is the schematic of an alpha helix?

A

A cylinder

61
Q

What is the schematic of a beta sheet?

A

An arrow ( N –> C)

62
Q

What is the TIM barrel motif?

A

8 pairs of alternating alpha helices and beta sheets (N terminus alpha helix, C terminus beta sheet, 16 elements all together)

63
Q

What is an example of an enzyme with a TIM barrel?

A

Triose phosphate isomerase

64
Q

What is a Rossman fold?

A

A structure with alternating alpha helices and beta sheets, but with a different topology than a TIM barrel

65
Q

What is the structure of a Rossman fold?

A

An open beta sheet structure

66
Q

What is an example of an enzyme with a Rossman fold?

A

Lactate dehydrogenase

67
Q

What is the Rossman fold motif?

A

6 beta sheets and 4 alpha helices that alternate (N terminus beta sheet, C terminus beta sheet, 2 sets with a crossing loop)

68
Q

Where is the active site found in a TIM barrel?

A

On the pore loops (connected helices and sheets)

69
Q

How come loops are often active sites?

A

They have great flexibility for chemistry without disrupting the energetics

70
Q

Where is the active site in a Rossman fold?

A

At the crevice formed at the switch point

71
Q

What is a crevice in a Rossman fold?

A

The place where lots of loops are close together (connecting helices and sheets)

72
Q

What is a switch point in a Rossman fold?

A

Goes from one side of the beta sheet to the other

73
Q

What is an example of a motif with only beta sheets?

A

A greek key motif

74
Q

What is the structure of a greek key motif?

A

Antiparallel beta sheets forming a “stand”

75
Q

Where is the active site in a greek key?

A

At the loops at the top of the “stand”

76
Q

What is the greek key motif?

A

6 sets of 4 antiparallel beta sheets (last set has both N terminus and C terminus)

77
Q

What is an example of an enzyme that has a greek key motif?

A

Neurarimadase in influenza

78
Q

What is a protein domain?

A

A portion of a protein that can exist independelty

79
Q

Where do binding sites frequently occur at?

A

Domain intersections

80
Q

What are some characteristics of protein domain intersections?

A

They are more highly variable, so they can be disrupted without changing the overall structure

CHE 541 (20 decks)

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