Chapter 6

Question 1

What is conformation?

Answer 1

Every functional 3D structure from the same organism is exactly the same.

Question 2

Why do proteins assume a certain conformation?

Answer 2

Because it’s thermodynamically favorable (lowest Gibbs free energy).

Question 3

What are the four levels of protein organization?

Answer 3

A protein’s primary structure is defined as the amino acid sequence of its polypeptide chain; the secondary structure is the local spatial arrangement of a polypeptide’s backbone (main chain) atoms; tertiary structure refers to the three-dimensional structure of an entire polypeptide chain; and quaternary structure is the three-dimensional arrangement of the subunits in a multisubunit protein.

Question 4

What are the two principles to remember?

Answer 4

1)Hydrophobic residues are buried within a protein’s core.
2)The number of hydrogen bonds and ionic interactions within a protein is maximized.

Question 5

The stability of a protein’s structure is maintained through what?

Answer 5

Weak interactions (hydrogen bonds, hydrophobic/hydrophilic interactions, ionic interactions, van der Waals interactions, disulfide bonds).

Question 6

What is the primary structure of proteins?

Answer 6

Amino acids joined together in a linear way by peptide bond; with no folding.
The primary covalent bond in proteins is the peptide bond, which constrains the conformation of the polypeptide.

Question 7

What configuration do almost all peptide bonds in proteins occur in?

Answer 7

Trans configuration.

Question 8

What are the three dihedral angles peptide conformations are defined by?

Answer 8

phi, psi, omega

Question 9

What bonds does phi involve?

Answer 9

C-N-C(alpha)-C bonds, with rotation occurring about the N-C(alpha) bond.

Question 10

What bonds does psi involve?

Answer 10

The N-C(alpha)-C-N bonds

Question 11

What bonds does omega involve?

Answer 11

The peptide bond C(alpha)-C-N-C(alpha), where rotation is constrained.

Question 12

Which dihedral angle is not often considered? Also, think about what happens to it regarding trans and cis configurations.

Answer 12

The omega angle, because peptide bonds are almost always trans, which constrains omega to be + or - 180 degrees. When the peptide bond is cis, omega = 0 degrees.

Question 13

What degree are phi and psi when the first and fourth atoms are furthest apart and the peptide is fully extended and all the peptide groups are in the same plane?

Answer 13

180 or -180 degrees

Question 14

When omega is 0 degrees, what configuration is it? What about 180 degrees?

Answer 14

0- cis
180- trans

Question 15

What is the secondary structure of proteins?

Answer 15

The simplest secondary structure that a peptide can assume is the alpha helix. With the “R” group protruding from the helical structure of the peptide.

Question 16

How many protein structures are alpha helices?

Answer 16

1/4th of all protein structures.

Question 17

Why is there a predominance of alpha helices as secondary structures?

Answer 17

Due to their stability from extensive internal hydrogen bonding.

Question 18

What conformation do alpha helices have in nature?

Answer 18

The right-handed conformation. The left-handed conformation has never been observed in nature.

Question 19

What types of amino acids can form right-handed alpha helices, and how do they have to do it?

Answer 19

D-amino acids and L-amino acids. In order to do so, the alpha helix must be a homogenous mix of either stereoisomer.

Question 20

Because of the shape of an alpha helix, the R group of amino acids 3 or 4 residues apart must be what?

Answer 20

Compatible.

Question 21

What does Proline cause in alpha helices?

Answer 21

A kink

Question 22

What is flexible, and a major component of alpha helices, though by themselves, don’t form an alpha helices?

Answer 22

Glycine

Question 23

Every alpha helix has what on the N and C - terminals?

Answer 23

A dipole.

Question 24

In beta-pleated sheets, what conformation are the peptide bonds in and what amino acid do they involve?

Answer 24

Cis conformation and proline.

Question 25

What are fibrous proteins?

Answer 25

Linear proteins with polypeptide chains arranged in long sheets or strands. Insoluble proteins, that give strength and flexibility to the biological structures they make up.

Question 26

What are globular proteins?

Answer 26

Spherical proteins with polypeptide chains arranged in a spherical or globular shape.

Question 27

What is scurvy?

Answer 27

A disease caused by the lack of Vitamin C (L - ascorbic acid), which causes a degeneration of connective tissue.

Question 28

What is Vitamine C inadvertently necessary for?

Answer 28

The hydroxylation of proline makes 4-hydroxyproline because it restores prolyl 4- 4-hydroxylase.

Question 29

What are some symptoms of scurvy?

Answer 29

Loss of teeth, pale skin, sunken eyes

Question 30

What is fibroin the main component of?

Answer 30

Silk. Produced by spiders and insects, the polypeptide chains are made up of layers of antiparallel beta-sheets.

Question 31

What is a motif?

Answer 31

A recognizable folding pattern involving 2 or more elements of secondary structure and the connections between them.

Question 32

What is a supersecondary structure and a fold?

Answer 32

The same as a motif.

Question 33

What is a domain?

Answer 33

Part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein.

Question 34

What is X-ray crystallography?

Answer 34

X-ray diffraction patterns are generated from a crystal of a protein, and the diffraction pattern is used to calculate the 3D electron-density map. The electron density map shows the atomic nuclei, so a structure can be pieced together. The diffraction pattern is for the heme in myoglobin.

Question 35

When molecules get complicated, what can resolve their structure and how?

Answer 35

2D NMR can resolve their structure by overlapping two different NMR frequencies.

Question 36

What are the different types of structural motifs?

Answer 36

Beta-alpha-beta loop, Beta - barrel, alpha/beta barrel

Question 37

What is denaturation?

Answer 37

The loss of 3D structure sufficient enough to cause a loss in function.

Question 38

What can proteins be denatured by?

Answer 38

heat, pH, organic solvents (alcohol or acetone), solutes (urea, guanidine, hydrochloride), and detergents (SDS).

Question 39

What is Tm (melting temp)?

Answer 39

The point at which half of the
protein is denatured.