Chapter 2 Terms

Question 1

The distinctive R group that is a part of an amino acid.

Answer 1

Side Chain (R group)

Question 2

Almost all have an S absolute configuration; only these amino acids are found in proteins.

Answer 2

L amino acid

Question 3

Amino acids in solution at neutral pH exist predominantly in this form.

Answer 3

Dipolar ion (zwitterion)

Question 4

The linkage between the alpha-carboxyl group of one amino acid to the alpha-amino group of another amino acid.

Answer 4

Peptide bond (amide bond)

Question 5

The most common cross link of linear polypeptide chains is known as this. It is formed by the oxidation of a pair of cysteine residues, resulting in a cystine.

Answer 5

Disulfide bond

Question 6

The amino acid sequence of a protein is referred to as its _________ structure.

Answer 6

Primary structure

Question 7

The free rotations about two bonds of each amino acid that allow proteins to fold in many different ways can be specified by ________ angles.

Answer 7

Torsion angle

Question 8

The angle of rotation about the bond between the nitrogen and the alpha-carbon atoms is called _____.

Answer 8

phi angle

Question 9

The angle of rotation about the bond between the alpha-carbon and the carbonyl carbon atoms is called ______.

Answer 9

psi angle

Question 10

The visual that illustrates the allowed values of phi and psi combinations. Values that are forbidden are due to steric clashes.

Answer 10

Ramachandran diagram

Question 11

Folded segments formed by a regular pattern of hydrogen bonds between the peptide N-H and C=O groups of amino acids that are near one another in the linear sequence are called _______ structures.

Answer 11

Secondary structure

Question 12

A rodlike structure; A tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array. The structures is stabilized by hydrogen bonds between the NH and CO groups of the main chain (backbone).

Answer 12

alpha helix

Question 13

Each residue is related to the next one by a ____, of 1.5 angstroms along the helix axis and a rotation of 100 degrees, which gives 3.6 amino acid residues per turn of helix.

Answer 13

Rise (translation)

Question 14

It’s composed of two or more polypeptide chains called beta strands. The structure can run antiparallel or parallel.

Answer 14

beta pleated sheet

Question 15

It is almost fully extended rather than being tightly coled as in the alpha helix; adjacent chains of this structure linked together form beta sheets.

Answer 15

beta strand

Question 16

The structural element responsible for reversals in the direction of protein polypeptide chains.

Answer 16

Reverse turn (beta turn; hairpin turn)

Question 17

A superfamily of proteins where two or more alpha helices can entwine to form a very stable structure.

Answer 17

Coiled coil

Question 18

A central region of 300 amino acids that contains imperfect repeats of a sequence of 7 amino acids.

Answer 18

Heptad repeat

Question 19

The overall course of the polypeptide chain of a protein is referred to as its _______ structure. The compact, asymmetric structure that individual polypeptides attain.

Answer 19

Tertiary structure

Question 20

Combinations of secondary structure that are present in many proteins and frequently exhibit similar functions. For example, a helix-turn-helix unit is found in many proteins that bind DNA.

Answer 20

Motif (supersecondary structure)

Question 21

Some polypeptide chains fold into two or more compact regions that may be connected by a flexible segment of polypeptide chain. These compact globular units are called ______.

Answer 21

Domains

Question 22

Each polypeptide chain in a Quaternary structure is called a _______.

Answer 22

Subunit

Question 23

Proteins consisting of more than one polypeptide chain display ______ structure.

Answer 23

Quaternary structure

Question 24

Gives rise to protein folding as a all or none process.

Answer 24

Cooperative transition

Question 25

These proteins, completely or in part, do not have a discrete 3D structure under physiological conditions. These are rich in charged and polar amino acids with few hydrophobic residues.

Answer 25

Intrinsically unstructured protein (IUP)

Question 26

These proteins appear to exist in an ensemble of structures of approximately equal energy that are in equilibrium. Small molecules or other proteins may bind to a particular member of the ensemble, resulting in a complex having a biochemical function that differs from that of another complex formed by the same metamorphic protein bound to a different partner.

Answer 26

Metamorphic protein

Question 27

Agents that, when in aggregates and primarily consist of beta sheets, cause infectious neurological diseases. They are primarily composed of the protein PrP.

Answer 27

Prion