Lecture 5 Primary And Secondary Structures Of Proteins

Front 1

What type of reaction occurs to make a peptide bond?

Back 1

dehydration

Front 2

Which atoms in a polypeptide are immovable?

Back 2

OCNH

Front 3

What conformation is favored for most amino acids and why?

Back 3

Trans-, the cis-conformation possesses unfavorable steric interactions.

Front 4

Why do proteins consist of "propeller blades"?

Back 4

Rotation can occur between units, but there's no free rotation about the amide bond.

Front 5

What limit the range of values for phi and psi?

Back 5

steric interactions

Front 6

True or false: chiral center (alpha-carbon) has a fixed conformation.

Back 6

False, configuration

Front 7

regularities in local conformations maintained by networks of hydrogen bonds

Back 7

secondary structure

Front 8

What are four examples of secondary structure?

Back 8

alpha helix

beta strand or beta sheet

loop and turn

random coil

Front 9

deliberate disordered regions

Back 9

random coil

Front 10

arises when a number of consecutive amino acids have similar phi and psi values

Back 10

secondary structure

Front 11

What does hydrogen bonding occur between in alpha helices?

Back 11

carbonyl oxygen of the Nth amino acid and the hydrogen of the amide on the N+4th amino acid

Front 12

How many amino acids are required to complete a turn of an alpha helix?

Back 12

3.6

Front 13

What is the net dipole of an alpha helix?

Back 13

positive N-terminus, negative C-terminus

Front 14

Why do alpha helices have a net dipole?

Back 14

all hydrogen bonds point in the same direction

Front 15

What is the pitch of an alpha helix?

Back 15

0.54 nm or 5.4 Å

Front 16

What is the rise of an alpha helix?

Back 16

0.15 nm or 1.5 Å

Front 17

How many degrees does each amino acid rotate?

Back 17

100

Front 18

What are the phi, psi coordinates of alpha helices?

Back 18

120, -60

Front 19

Where are side chains located in alpha helices?

Back 19

They project outward.

Front 20

What amino acids destabilize alpha helices?

Back 20

G P

Front 21

How does G destabilize alpha helices?

Back 21

absence of side chain results in greater freedom of rotation

Front 22

How does P destabilized alpha helices?

Back 22

produces kink because cyclic structure occupies space that neighboring amino acid would otherwise occupy

Front 23

What amino acid has phi and psi values that vary over a considerable range?

Back 23

G

Front 24

What can be said about amphipathic alpha helices?

Back 24

All hydrophobic residues are on one side.

Front 25

one turn (360 degrees) of an alpha helix

Back 25

pitch

Front 26

What stabilizes beta sheets?

Back 26

long range cross-sheet hydrogen bonds

Front 27

Where do side chains project in beta sheets?

Back 27

alternately above and below the plane

Front 28

Why do beta sheets with multiple strands have a slight right-handed twist?

Back 28

Because amino acids are constructed from L-amino acids.

Front 29

What are the phi, psi coordinates for beta sheets?

Back 29

-120, 120

Front 30

What is slightly more stable: parallel or antiparallel beta sheets?

Back 30

antiparallel

Front 31

Describe the "pleated" topology of beta sheets.

Back 31

R groups up

R groups down

R groups up

R groups down

Front 32

What are loops?

Back 32

regions of proteins that cause directional changes

Front 33

Where do loops appear?

Back 33

on the surface of proteins

Front 34

Are loops hydrophilic or hydrophobic?

Back 34

hydrophilic

Front 35

How many amino aid residues do loops typically possess?

Back 35

more than five

Front 36

What are turns or beta turns?

Back 36

subclass of loops with five or fewer amino acids connecting two secondary structural features

Front 37

What amino acids do turns often contain?

Back 37

P G

Front 38

For which amino acid is the cis-conformation not as disfavored as it is for others?

Back 38

P

Front 39

What is the trans-to-cis ratio in most amino acids?

Back 39

1000:1

Front 40

What is the trans-to-cis ratio in proline?

Back 40

3:1

Front 41

What amino acid has the greatest percentage of cis-conformation?

Back 41

P

Front 42

portion of a protein that adopts many possible conformations

Back 42

random coil

Front 43

often sites that control regulation or signaling, undergo covalent modification, bind drugs, and are modified in alternative splicing

Back 43

random coil

Front 44

What percentage of myoglobin is random coil?

Back 44

30%

Front 45

regions that do not have a major single conformation

Back 45

molten globules

Front 46

True or false: beta sheets have a net dipole moment.

Back 46

false

Front 47

produce directional change

Back 47

loops and turns

Front 48

provide important flexibility

Back 48

random coils

Front 49

Why is the peptide bond planar?

Back 49

partial double-bond character, limits rotation

Front 50

Due to the side group steric clash, what are almost all peptide bonds?

Back 50

trans

Front 51

What is the trans-cis ratio if cis-Ala-Trp is 4 kcal/mol less stable than trans-Ala-Trp?

Back 51

1000:1

Front 52

What is every factor of ten in an equilibrium?

Back 52

1.36 kcal/mol

Front 53

What sequence exploits the structural properties of an alpha helix to make a stable, side-by-side, two-helix fold?

Back 53

Place a hydrophobic residue at every 4th position in the sequence.

Front 54

What secondary structure is stabilized by CO and NH hydrogen bonding within the peptide chain?

Back 54

alpha helix

Front 55

What amino acid residue disrupts the alpha helix because its side chain contains a unique ring structure that restricts bond rotations?

Back 55

P