5. Protein structure

Question 1

what determines 3D protein structure

Answer 1

the amino acid sequence (primary structure)

Question 2

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

Answer 2

true

Question 3

how many conformations do most proteins exist in

Answer 3

1 or 2

Question 4

what type of forces stabilize protein structures

Answer 4

non-covalent forces

Question 5

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

Answer 5

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

Question 6

define configuration in regards to protein structure

Answer 6

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

Question 7

define conformation in regards to protein structure

Answer 7

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

Question 8

what does it mean for a protein to be stable

Answer 8

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

Question 9

describe gibbs free energy (G) for a stable protein

Answer 9

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

Question 10

why does a stable protein conformation have the lowest G value

Answer 10

due to many weak interactions

Question 11

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

Answer 11

• 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

Question 12

how does folding occur (ie what needs to happen)

Answer 12

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

Question 13

describe the enthalpy difference between folded and unfolded

Answer 13

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

Question 14

what are the weak interactions of a folded protein

Answer 14

• 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

Question 15

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

Answer 15

true

Question 16

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

Answer 16

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

Question 17

why do proteins have lots of hydrophobic residues

Answer 17

• promotes folding

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

Question 18

define salt bridge

Answer 18

an ionic interaction of oppositely fully charged groups

Question 19

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

Answer 19

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

Question 20

T or F: salt bridges help drive folding

Answer 20

true

Question 21

how do salt bridges help drive folding

Answer 21

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

Question 22

what properties do peptide bonds help with for the polypeptide chain

Answer 22

length, resonance, and rigidity

Question 23

where is the peptide bond located

Answer 23

between the carboxyl C and the amino N of two residues

Question 24

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

Answer 24

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

Question 25

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

Answer 25

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

Question 26

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

Answer 26

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

Question 27

what are the two possible positions of an alpha carbon

Answer 27

cis or trans

Question 28

which position of the alpha carbon is least favorable? why

Answer 28

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

Question 29

in which position are nearly all peptide bonds in

Answer 29

trans

Question 30

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

Answer 30

true

Question 31

what is a Phi bond?

Answer 31

N-C(a)

Question 32

what is a Psi bond?

Answer 32

C(a)-C

Question 33

what are phi and psi bonds often referred to as

Answer 33

dihedral angles

Question 34

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

Answer 34

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

Question 35

what are the angles of the cis and trans positions

Answer 35

cis=0 | trans=+/- 180

Question 36

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

Answer 36

true

Question 37

how might phi and psi angles be limited

Answer 37

steric hindrance of the groups

Question 38

what does a Ramachadran plot show

Answer 38

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

Question 39

what does each color represent on a ramachandran plot

Answer 39

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

Question 40

on a ramachandran plot, what does each dot represent

Answer 40

1 amino acid

Question 41

which axis shows the phi bond

Answer 41

x axis

Question 42

which axis shows the psi bond

Answer 42

y axis

Question 43

how might glycine look on a ramachadran plot

Answer 43

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

Question 44

how might proline look on a ramachadran plot

Answer 44

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

Question 45

which region of a ramachandran plot shows beta sheets

Answer 45

upper left quadrant

Question 46

which region of a ramachandran plot shows alpha helixes

Answer 46

bottom left quadrant

Question 47

what is the secondary structure of a polypeptide

Answer 47

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

Question 48

how might a secondary structure become regular

Answer 48

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

Question 49

what are the common regular secondary structures

Answer 49

alpha helix, beta conformation, beta turn

Question 50

describe the shape of an alpha helix

Answer 50

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

Question 51

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

Answer 51

true

Question 52

T or F: the alpha helix is hollow

Answer 52

false

Question 53

describe the direction of the R groups of an alpha helix

Answer 53

they protrude outwards from the helical backbone

Question 54

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

Answer 54

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

Question 55

are most alpha helices right or left

Answer 55

right

Question 56

what is the length of one turn of the helix

Answer 56

5.4 Å

Question 57

what is the length of one residue of the helix

Answer 57

1.5Å

Question 58

how many amino acids are there per one helical turn

Answer 58

3.6

Question 59

what is the degree of rotation per amino acid R group

Answer 59

100 degrees

Question 60

what are the phi angles of the helix

Answer 60

-57

Question 61

what are the psi angles of the helix

Answer 61

-47

Question 62

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

Answer 62

4

Question 63

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

Answer 63

true

Question 64

which amino acids have the greatest tendency to form alpha helices

Answer 64

those with numbers close to zero (ie alanine)

Question 65

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

Answer 65

true

Question 66

describe how dipole moments relate to alpha helices

Answer 66

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

Question 67

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

Answer 67

the longer the helix=the longer the dipole

Question 68

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

Answer 68

false

Question 69

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

Answer 69

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

Question 70

what percentage of alpha helices do proteins contain on average

Answer 70

26%

Question 71

what is the average length of a helix

Answer 71

12 amino acids in length (3-4 turns)

Question 72

describe the structure of an amphipathic alpha helix

Answer 72

hydrophobic amino acids on one face, hydrophilic on the other

Question 73

describe amphipathic helices on the surface of proteins

Answer 73

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

Question 74

what are the 3 types of beta conformations

Answer 74

strands, sheets, and turns

Question 75

describe beta strands

Answer 75

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

Question 76

describe beta sheets

Answer 76

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

Question 77

describe beta turns

Answer 77

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

Question 78

what are the two types of beta sheets

Answer 78

antiparallel and parallel

Question 79

describe antiparallel beta sheets

Answer 79

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

Question 80

describe parallel beta sheets

Answer 80

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

Question 81

which type of beta sheet is stronger + why

Answer 81

antiparallel, hydrogen bonds are straight

Question 82

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

Answer 82

true

Question 83

what is the purpose of beta turns

Answer 83

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

Question 84

how many amino acids does a beta turn require

Answer 84

4

Question 85

T or F: hydrogen bonds form in beta turns

Answer 85

true

Question 86

where do beta turns form hydrogen bonds

Answer 86

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

Question 87

how many types of beta turns are there? why

Answer 87

2, they have different phi and psi angles

Question 88

which type of beta turn is more common

Answer 88

type 1 (the hydrogen bond is more straight)

Question 89

which residues are common in beta turns

Answer 89

glycine and proline

Question 90

why do beta turns commonly involve gly and pro residues

Answer 90

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

Question 91

what is the purpose of circular dichroism

Answer 91

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

Question 92

what does circular dichroism show

Answer 92

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

Question 93

how do you interpret circular dichroism

Answer 93

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

Question 94

what is tertiary structure

Answer 94

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

Question 95

how are tertiary structures held together

Answer 95

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

Question 96

what is quaternary structure

Answer 96

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

Question 97

can monomers have quaternary structure

Answer 97

no

Question 98

define homodimer

Answer 98

when the polypeptide chains of quaternary structure are identical

Question 99

define heterodimer

Answer 99

when the polypeptide chains of quaternary structure are not identical