8.2.16 Lecture

Question 1

Describe the protein structure hierarchy.

Answer 1

Primary: amino acid sequence and disulfide bonds Secondary: local conformations of the backbone (no side chains) Tertiary: full 3D structure (includes side chains) Quaternary: non-covalent association of subunits in a multi-subunit protein

Question 2

Draw the peptide bond resonance structures.

Answer 2

Question 3

What are the characteristics of a peptide bond?

Answer 3

40% double bond character = no rotation

Planar

Trans

Polar

Can H-bond

Question 4

Describe and label the two angles that can rotate in a protein.

Answer 4

Question 5

Describe the bond angle exception created by Proline.

Answer 5

No rotation is possible at phi due to the reduced double bond character. Both cis and trans are possible. Proline breaks the alpha helix structure and leads to sharp turns. Note that the peptide bond can be rotated next to Proline.

Question 6

Regular secondary structures occur when…

Answer 6

…all amino acids in a chain have the same phi and same psi angles. These structures include alpha helices and beta sheets.

Question 7

How many amino acids make up a turn in an alpha helix?

Answer 7

3.6

Question 8

How are alpha helices stablized?

Answer 8

Via interchain hydrogen bonds (with O and with NH)

Question 9

What is an amphipathic structure?

Answer 9

One side of the structure is hydrophilic; the other side is hydrophobic.

Question 10

Describe a beta pleated sheet.

Answer 10

The backbone is stretched out and partially flattened. Proline can cause turns. Every other carbonyl O points in the opposite direction. Hydrogen bonding occurs to connect strands into sheets. Sheets can be parallel or antiparallel.

Question 11

Where are charged/polar amino acids located? Where are non-polar amino acids located?

Answer 11

Charged/polar amino acids are hydrophilic and are located on the outside of the protein. Non-polar amino acids are hydrophobic and are located on the inside of the protein.

Question 12

What are domains?

Answer 12

Domains are building blocks/modules used to construct larger proteins; small globular portion of a protein that folds independently of other domains. Domains typically have a hydrophobic core and a hydrophilic surface. They often carry a specific function, are often spatially isolated/connected by linking polypeptides, and involve covalent attachments.

Question 13

What is a fold?

Answer 13

A fold is a specific arrangment of the secondary structural elements of a domain.

Question 14

What is a superfold?

Answer 14

Folds that occur across proteins that are unrelated by evolution, sequence, or function.

Question 15

What are several examples of folds?

Answer 15

Alpha helix globin folds, alpha beta domain folds (central beta barrel, twisted beta sheet, beta barrel jelly roll)

Question 16

What is one method that helps to identify the fold of a protein based on its amino acid sequence?

Answer 16

Homology:

1. Search x-ray/NMR structure databases for a similar sequence; this serves as a template.
2. Perform a sequence alignment and look for identical or similar amino acids.
3. Utilize a computer program to “thread” the sequence through the x-ray structure of the template.

Question 17

What determines protein folding?

Answer 17

The amino acid sequence

Question 18

Some DNA mutations are ____ and have no effect on the proteins. Mutations of amino acids involved in enzyme activity or basic structure are ____.

Answer 18

Silent; deleterious.

Question 19

80% of the over 140,000 disease-associated mutations are found in ___, ___, and ___.

Answer 19

Regular secondary strecture, tight turns, and bends.

Question 20

Describe the forces stabilizing protein structures.

Answer 20

1. Covalent (strongest)
2. Noncovalent:
   a. H-bonds (common)
   b. Ionic bonds/salt bridges (infrequent within, impossible on surface)
   c. van der Waals (weak but prevalent)
   d. Hydorphobic interactions (hydrophobic effect)

Question 21

Define van der Waals forces.

Answer 21

van der Waals forces are attractive forces involving shifts in electron density such that one atom is ~ positive and the other is ~ negative. These forces are distant dependent.

Question 22

Define the hydrophobic effect.

Answer 22

When two hydrophobic side chains interact, they displace water around them. This increases entropy, decreases free energy, and increases stability.

Question 23

Describe simply the motions of proteins.

Answer 23

Proteins are jiggling due to the constant motion of the atoms. In addition, conformational changes can occur, such as in the reaction between hexokinase and glucose.

Question 24

What is an example of a fibrous protein?

Answer 24

Collagen

Question 25

Describe the structure of collagen.

Answer 25

Three polyproline type II helices, each ~1,000 amino acids long.

Question 26

What are the characteristics of a polyproline type type II helix?

Answer 26

3 amino acids/turn

Left-handed

Wrap in C –> N direction

Twice as extended as an alpha helix

Question 27

In Type I colagen, a Gly is found every ___ residues. The second and third residues are typically ___ and ___.

Answer 27

Three; Proline; Hydroxyproline