CH 306 Chapter 3

Question 1

Proteins are quite stable. The life- time of a peptide bond in aqueous solution is nearly 1000 years. However, the free energy of hydrolysis of proteins is negative and quite large. How can you account for the stability of the peptide bond in light of the fact that hydrolysis releases considerable energy?

Answer 1

The energy barrier that must be crossed to go from the polymerized state to the hydrolyzed state is large even though the reaction is thermodynamically favorable.

Question 2

Table 3.1 gives the typical pKa values for ionizable groups in proteins. However, more than 500 pKa values have been determined for individual groups in folded proteins. Account for this discrepancy.

Answer 2

This observation demonstrates that pKa values are affected by the environment. A given amino acid can have a variety of pKa values, depending on the chemical environment inside the protein.

Question 3

Why is rotation about the peptide bond prohibited, and what are the consequences of the lack of rotation?

Answer 3

The peptide bond has partial double-bond character, which prevents rotation. This lack of rotation constrains the conformation of the peptide backbone and limits possible structures.

Question 4

Forms between two cysteine amino acids

Answer 4

Disulfide bond

Question 5

A rodlike structure with a tightly coiled backone

Answer 5

a-helix

Question 6

Angle of rotation about the bond between the N atom and the a-carbon atom

Answer 6

phi-angle

Question 7

Fully extended poly- peptide chain

Answer 7

B-strand

Question 8

Formed by hydrogen bonds between parallel or antiparallel chains

Answer 8

B-pleated sheet

Question 9

Regular repeating three-dimensional structures

Answer 9

Secondary structure

Question 10

The bond responsible for primary structure

Answer 10

Peptide (amide) bond

Question 11

Sequence of amino acids in a protein

Answer 11

Primary structure

Question 12

Angle of rotation between the a-carbon atom and the carbonyl carbon atom

Answer 12

psi-angle

Question 13

A plot of phi and psi angles

Answer 13

Ramachandran plot

Question 14

What is meant by the term polypeptide backbone?

Answer 14

The (nitrogen–a carbon–carbonyl carbon) repeating unit

Question 15

Define the term side chain in the context of amino acid or protein structure.

Answer 15

Side chain is the functional group attached to the a-carbon atom of an amino acid.

Question 16

Differentiate between amino acid composition and amino acid sequence.

Answer 16

Amino acid composition refers simply to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as the primary structure—the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein. Different proteins may have the same amino
acid composition, but amino acid sequence identifies a unique protein.

Question 17

List some of the benefits of knowing the primary structure of a protein.

Answer 17

The primary structure determines the tertiary structure. Knowing the primary structure helps to elucidate the function of the protein. Knowledge of the primary structure of mutated proteins enables an understanding of the biochemical basis of some diseases. Primary structure can reveal the evolutionary history of the protein.

Question 18

Differentiate between amino acid composition and amino acid sequence.

Answer 18

Amino acid composition refers simply to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as the primary structure—the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein. Different proteins may have the same amino acid composition, but amino acid sequence identifies a unique protein.

Question 19

What are the levels of protein structure? Describe the type of bonds characteristic of each level.

Answer 19

Primary structure—peptide bond; secondary structure—local hydrogen bonds between components of the polypeptide backbone; tertiary structure—various types of noncovalent bonds between R groups that are far apart in the primary structure; quaternary structure—various noncovalent bonds between R groups on the surface of subunits.

Question 20

List some of the differences between an a helix and a b strand.

Answer 20

The helix is a condensed, coiled structure, with the R groups bristling outward from the axis of the helix. The distance between two adjacent amino acids is 1.5 Å. The strand is a fully extended polypeptide chain, and the side chains of adjacent amino acids point in opposite directions. The distance between adjacent amino acids is 4.5 Å. Both structures are stabilized by hydrogen bonding between components of the polypeptide backbone.

Question 21

Basic component of quaternary structure

Answer 21

Subunit

Question 22

Proteins that in whole or in part lack discrete three-dimensional structure under physiological conditions

Answer 22

Intrinsically unstructured protein

Question 23

Refers to the spatial arrangement of amino acid residues that are far apart in the sequence

Answer 23

Tertiary structure

Question 24

Proteins that exist in an ensemble of structures of approximately equal energy that are in equilibrium

Answer 24

Metamorphic protein

Question 25

An energy landscape

Answer 25

Folding funnel

Question 26

Compact regions that may be connected by a flexible segment of polypeptide chain

Answer 26

Domain

Question 27

Refers to the arrangement of subunits and the nature of their interactions

Answer 27

Quaternary structure

Question 28

Cause of spongiform encephalopathies

Answer 28

Prion

Question 29

Combinations of secondary structure are present in many proteins

Answer 29

Supersecondary structure