Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOL 2421 - Cellular Biochem > 5. Protein structure > Flashcards

5. Protein structure Flashcards

1
Q

what determines 3D protein structure

A

the amino acid sequence (primary structure)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

T or F: the function of a protein is dependent on its structure

A

true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

how many conformations do most proteins exist in

A

1 or 2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what type of forces stabilize protein structures

A

non-covalent forces

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

T or F: a proteins shape is different each time it folds

A

false; each protein has (at most) a few unique and consistent 3D structures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

define configuration in regards to protein structure

A

requires the breaking of bonds (ie switching a protein from cis to trans)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

define conformation in regards to protein structure

A

rotations about bonds don’t require breaking of bonds (ie binding to another molecule)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what does it mean for a protein to be stable

A

it maintains a functional, folded, native conformation under biological conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

describe gibbs free energy (G) for a stable protein

A

a stable conformation has the lowest G compared to other conformations (this comes from many weak interacts)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

why does a stable protein conformation have the lowest G value

A

due to many weak interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what features of an unfolded protein promote low G values (this discourages folding btw)

A
  • unfolded state=high entropy
  • polar residues in the unfolded state can form lots of hydrogen bonds with water (=many weak interactions)
  • charged residues in the unfolded state can interact with salts
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

how does folding occur (ie what needs to happen)

A

a hydrogen bond that already existed in the folded state must be broken with water (so enthalpy doesn’t change much)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

describe the enthalpy difference between folded and unfolded

A

since hydrogen bonds needed for folding come from pre-existing hydrogen bonds, the enthalpy (# of bonds) doesn’t change much

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what are the weak interactions of a folded protein

A
  • hydrophobic effect on the interior
  • Van der Waals in the interior
  • stabilizing ionic bonds between residues
  • hydrogen bonds between residues
  • disulfide bridges if the protein is to be secreted
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

T or F: the hydrophobic effect plays the biggest role in promoting the folded state

A

true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

how does the hydrophobic effect plays the biggest role in promoting the folded state

A

it reduces the highly ordered solvation shell of water as residues clump together, which increases the entropy of the folded state. Without the large increase upon folding, the conformational entropy of the folded state wouldn’t be overcome. Proteins usually have a large number of hydrophobic residues because of this

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

why do proteins have lots of hydrophobic residues

A
  • promotes folding

- entropy is increased as the highly ordered water shell is depleted when residues clump

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

define salt bridge

A

an ionic interaction of oppositely fully charged groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

T or F: salt bridges can form in the unfolded state

A

true; they can form between a polypeptide with salts in the aqueous solution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

T or F: salt bridges help drive folding

A

true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

how do salt bridges help drive folding

A

the strength of a salt bridge is higher as it moves from the aqueous cytoplasm to the protein’s hydrophobic interior

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what properties do peptide bonds help with for the polypeptide chain

A

length, resonance, and rigidity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

where is the peptide bond located

A

between the carboxyl C and the amino N of two residues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

compare the peptide C-N bond with a simple amide C-N bond

A

the peptide C-N bond is a bit shorter than a simple amide C-N bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

what is the result of the peptide C-N bond being shorter than a simple amide C-N bond

A

it suggests partial sharing (resonance) or two electron pairs between the C and the N, and a formation of a small electric dipole

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

T or F: the peptide C-N bond can rotate freely

A

false; there is a slight double bond character, so the bond cannot rotate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

what are the two possible positions of an alpha carbon

A

cis or trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

which position of the alpha carbon is least favorable? why

A

cis is less favorable because if steric hindrance between the R groups off the alpha carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

in which position are nearly all peptide bonds in

A

trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

T or F: besides the C-N peptide bond, rotation occurs around other bonds in the backbone

A

true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

what is a Phi bond?

A

N-C(a)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

what is a Psi bond?

A

C(a)-C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

what are phi and psi bonds often referred to as

A

dihedral angles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

how do you determine the angle of a phi or psi bond

A

the atoms around the bond of interest are labelled 2 and 3. Place 1 at the bottom and 4 can then rotate with respect to 1. Look down atom 2, then look where 4 is and we can determine the angle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

what are the angles of the cis and trans positions

A

cis=0

trans=+/- 180

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

T or F: even with the free rotation of phi/psi bonds, a rigid peptide bond greatly restricts the possible number of conformations that a polypeptide chain can adapt

A

true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

how might phi and psi angles be limited

A

steric hindrance of the groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

what does a Ramachadran plot show

A

the likeliness of different conformations with respect to the phi and psi angles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

what does each color represent on a ramachandran plot

A

dark blue=no steric hindrance (fully allowed)
light blue=conformations with slight clashes
white=non-permitted conformations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

on a ramachandran plot, what does each dot represent

A

1 amino acid

41
Q

which axis shows the phi bond

A

x axis

42
Q

which axis shows the psi bond

A

y axis

43
Q

how might glycine look on a ramachadran plot

A

it’s R group is only H, so there’s many options available (small R group=less steric hindrance). Glycine will have many dots in the white areas

44
Q

how might proline look on a ramachadran plot

A

it’s R group is cyclic and very rigid, so it will be very limited in the types of angles it can make. It will only be in dark blue areas, but will be more constricted

45
Q

which region of a ramachandran plot shows beta sheets

A

upper left quadrant

46
Q

which region of a ramachandran plot shows alpha helixes

A

bottom left quadrant

47
Q

what is the secondary structure of a polypeptide

A

can refer to any chosen segment of a polypeptide and describes the local spatial arrangement of its main-chain atoms (not side chains)

48
Q

how might a secondary structure become regular

A

if the phi and psi angles remain very similar across the entire segment

49
Q

what are the common regular secondary structures

A

alpha helix, beta conformation, beta turn

50
Q

describe the shape of an alpha helix

A

the backbone is tightly wound around an imaginary longitudinal axis through the center

51
Q

T or F: the alpha helix maximizes the number of hydrogen bonds for the segment

A

true

52
Q

T or F: the alpha helix is hollow

A

false

53
Q

describe the direction of the R groups of an alpha helix

A

they protrude outwards from the helical backbone

54
Q

what are the two directions of alpha helices, and how do you determine this

A

left and right. Put your thumb in the direction of the helix, then see how your hand curls

55
Q

are most alpha helices right or left

A

right

56
Q

what is the length of one turn of the helix

A

5.4 Å

57
Q

what is the length of one residue of the helix

A

1.5Å

58
Q

how many amino acids are there per one helical turn

A

3.6

59
Q

what is the degree of rotation per amino acid R group

A

100 degrees

60
Q

what are the phi angles of the helix

A

-57

61
Q

what are the psi angles of the helix

A

-47

62
Q

how many residues apart do hydrogen bonds form (between carbonyl C and amide N)

A

4

63
Q

T or F: each amino acid in a polypeptide has an intrinsic propensity to form an alpha helix

A

true

64
Q

which amino acids have the greatest tendency to form alpha helices

A

those with numbers close to zero (ie alanine)

65
Q

T or F: the neighbors of a residue influence its propensity to form an alpha helix

A

true

66
Q

describe how dipole moments relate to alpha helices

A

each peptide bond has a small dipole, so these dipoles are aligned in the helix, resulting in a net dipole for the entire helix

67
Q

how does the net dipole of an alpha helix relate to the length of the helix

A

the longer the helix=the longer the dipole

68
Q

T or F: the ends of a helix have hydrogen bonding pairs

A

false

69
Q

how might the unsatisfied ends of a helix find a hydrogen bonding pair

A

the partial charges may bond with the R groups to form caps of the helix

70
Q

what percentage of alpha helices do proteins contain on average

A

26%

71
Q

what is the average length of a helix

A

12 amino acids in length (3-4 turns)

72
Q

describe the structure of an amphipathic alpha helix

A

hydrophobic amino acids on one face, hydrophilic on the other

73
Q

describe amphipathic helices on the surface of proteins

A

the hydrophilic surface faces the aqueous solvent, and the hydrophobic surface faces the protein interior

74
Q

what are the 3 types of beta conformations

A

strands, sheets, and turns

75
Q

describe beta strands

A

single segment of backbone atoms into a zigzag pattern. The R groups alternate extending above and below the backbone

76
Q

describe beta sheets

A

several beta strands side by side: zigzag causes a pleated appearance

77
Q

describe beta turns

A

instances in globular proteins where the polypeptide chain reverses direction by 180 degrees

78
Q

what are the two types of beta sheets

A

antiparallel and parallel

79
Q

describe antiparallel beta sheets

A

stands have opposing amino-to-carboxyl orientations (more strength due to straight hydrogen bonds)

80
Q

describe parallel beta sheets

A

strands have the same amino-to-carboxyl orientations (weaker due to angled hydrogen bonds)

81
Q

which type of beta sheet is stronger + why

A

antiparallel, hydrogen bonds are straight

82
Q

T or F: it’s common for beta sheets to have a hydrophobic side and a hydrophilic side

A

true

83
Q

what is the purpose of beta turns

A

they tend to connect the ends of two adjacent antiparallel beta sheets

84
Q

how many amino acids does a beta turn require

A

4

85
Q

T or F: hydrogen bonds form in beta turns

A

true

86
Q

where do beta turns form hydrogen bonds

A

the carbonyl oxygen of residue 1 forms a hydrogen bond with the amino group hydrogen of residue 4

87
Q

how many types of beta turns are there? why

A

2, they have different phi and psi angles

88
Q

which type of beta turn is more common

A

type 1 (the hydrogen bond is more straight)

89
Q

which residues are common in beta turns

A

glycine and proline

90
Q

why do beta turns commonly involve gly and pro residues

A

gly: extra flexibility due to smallest R group
pro: can uniquely form cis peptide bonds 6% of the time, which works great for a tight turn

91
Q

what is the purpose of circular dichroism

A

it’s often used to determine the secondary structures present in a protein, and to monitor conformational changes or denaturation in proteins

92
Q

what does circular dichroism show

A

shows the percentage of alpha helices and beta sheets in a protein

93
Q

how do you interpret circular dichroism

A

on the graph, there’s light absorbance depending on the structure of the protein

94
Q

what is tertiary structure

A

overall 3D arrangement of all the atoms in a polypeptide. Residues far apart may interact

95
Q

how are tertiary structures held together

A

via several types of non-covalent interactions (ie disulfide bonds, hydrogen bonds, ionic bonds)

96
Q

what is quaternary structure

A

the arrangement of multiple polypeptides into a 3D shape to form a functional protein

97
Q

can monomers have quaternary structure

A

no

98
Q

define homodimer

A

when the polypeptide chains of quaternary structure are identical

99
Q

define heterodimer

A

when the polypeptide chains of quaternary structure are not identical

BIOL 2421 - Cellular Biochem (21 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions