chapter 6 section 3

Question 1

Why is the peptide bond planar?

Answer 1

Partial double-bond character restricts rotation.

Question 2

Around which bonds can rotation occur?

Answer 2

φ (Cα–N) and ψ (Cα–C).

Question 3

What do φ and ψ angles describe?

Answer 3

Orientation of the peptide backbone around Cα.

Question 4

What is the amide plane?

Answer 4

The flat peptide bond unit that defines φ and ψ flexibility.

Question 5

How is “handedness” of a helix determined?

Answer 5

By viewing twist direction along the backbone (right- or left-handed).

Question 6

What stabilizes an α-helix?

Answer 6

Hydrogen bonds between C=O and N-H four residues apart.

Question 7

How are side chains oriented in an α-helix?

Answer 7

They project outward from the helix

Question 8

Why does an α-helix have a dipole?

Answer 8

Alignment of peptide bond dipoles → partial + at N-terminus, – at C-terminus.

Question 9

What is helix capping?

Answer 9

Extra stabilization at helix ends via H-bonds or hydrophobic contacts.

Question 10

Which amino acid breaks helices?

Answer 10

Proline, due to restricted φ rotation.

Question 11

What stabilizes β-sheets?

Answer 11

Hydrogen bonds between backbone strands.

Question 12

Difference between parallel and antiparallel β-sheets?

Answer 12

Parallel strands run same direction; antiparallel run opposite.

Question 13

How do hydrogen bonds differ in parallel vs antiparallel sheets?

Answer 13

Parallel = bent/weaker; antiparallel = straighter/stronger.

Question 14

How are side chains arranged in β-sheets

Answer 14

Alternate above and below the sheet plane.

Question 15

What is a β-turn?

Answer 15

A tight loop reversing chain direction, stabilized by H-bonding.

Question 16

What determines 3D protein structure?

Answer 16

Its amino acid sequence (primary structure).

Question 17

Main stabilizing interactions in proteins?

Answer 17

H-bonds, hydrophobic effect, ionic bonds, van der Waals, disulfides.

Question 18

Where are hydrophobic residues found?

Answer 18

Protein interior.

Question 19

Where are charged residues usually found?

Answer 19

On the protein surface.

Question 20

Why are van der Waals forces important?

Answer 20

ndividually weak, but collectively stabilize packing.

Question 21

What is a structural protein?

Answer 21

Provides shape/support, often forming multimeric assemblies.

Question 22

What is the proteome?

Answer 22

The complete protein set in a cell at a given time.

Question 23

Why is the proteome larger than the genome?

Answer 23

lternative splicing + post-translational modifications.

Question 24

What is a post-translational modification?

Answer 24

A chemical change after synthesis (e.g., phosphorylation).

Question 25

What is molecular recognition based on?

Answer 25

Structural complementarity.

Question 26

Main method for determining protein structures?

Answer 26

X-ray crystallography.

Question 27

What does resolution measure in crystallography?

Answer 27

Smallest distance resolved in diffraction

Question 28

What does R-value measure?

Answer 28

Fit of the model to experimental data.

Question 29

What is an XFEL used for?

Answer 29

Studying ultrafast protein dynamics with microcrystals.

Question 30

What is solid-phase peptide synthesis?

Answer 30

Sequential amino acid addition to a resin-anchored chain.

Question 31

What is the φ (phi) angle?

Answer 31

Rotation around the Cα–N bond.

Question 32

Why is φ rotation limited?

Answer 32

Steric clashes between atoms restrict allowed values.

Question 33

What does a φ = 0° conformation represent?

Answer 33

he amide plane bisects the H–Cα–R bond in a cis-like arrangement.

Question 34

How does φ differ from ψ?

Answer 34

φ is Cα–N rotation; ψ is Cα–C rotation.

Question 35

Why is φ important in protein folding?

Answer 35

Along with ψ, it defines backbone conformations and secondary structures.