Chapter 2. Protein Composition and Structure

Question 1

Proteins that 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 another ensemble structure bound to a different partner.

Answer 1

Metamorphic protein

Question 2

in a protein, the spatial arrangement of amino acid residues that are relatively close to one another in the linear sequence; the alpha helix and the Beta strand are both elements of secondary structure.

Answer 2

Secondary structure

Question 3

Only L amino acids are constituents of proteins. Most L amino acids have an S absolute configuraton.

Answer 3

L amino acid

Question 4

a covalent bond formed by the oxidation of two sulfhydryl groups; oxidation of cysteine residues in a polypeptide yields a disulfide bond linking the two residues.

Answer 4

Disulfide bond

Question 5

a covalent linkage formed between the alpha-carboxyl group of one amino acid and the alpha-amino group of another; also known as an amide bond.

Answer 5

Peptide bond (amide bond)

Question 6

In proteins, a structural element composed of four amino acids, in which the CO and NH groups of residue 1 are hydrogen bonded to the NH and CO groups of residue 4, respectively; such a structure forms a hairpin turn, allowing polypeptide chains to reverse their direction.

Answer 6

Reverse turn (β turn; hairpin turn)

Question 7

Proteins that, completely or in part, do not have a discrete three-dimensional structure under physiological conditions, but assume a defined structure upon interaction with other proteins.

Answer 7

Intrinsically unstructured protein (IUP)

Question 8

in proteins containing more than one polypeptide chain, the spatial arrangements of those chains (subunits) and the nature of contacts among them.

Answer 8

Quaternary structure

Question 9

usually refers to the linear sequence of amino acids in a protein; more generally, the linear sequence of units that form a polymer.

Answer 9

Primary structure

Question 10

A dipolar ion (from the German zwitter, “between”); at neutral pH, amino acids have a protonated amino group and a dissociated carboxyl group and are therefore zwitterions.

Answer 10

Dipolar ion (zwitterion)

Question 11

The angle of rotation about the bond between the nitrogen and the α-carbon atoms.

Answer 11

Phi φ Angle

Question 12

Imperfect repeats of a sequence of seven amino acids that facilitate the formation of a left-handed superhelix, called an α-coiled-coil, by two right-handed a-helices.

Answer 12

Heptad repeat

Question 13

an independently folded unit in the tertiary structure of a polypeptide chain; may contain a number of supersecondary structures. In multienzyme complexes, each domain may carry out one or more catalytic reactions. Also, in proteins, a compact globular unit of 100 to 400 residues, possibly joined to other domains by a flexible polypeptide segment; often encoded by a specific exon in the gene encoding the protein.

Answer 13

Domain

Question 14

The measure of relation between residues, 1.5 Å; along the helix axis and a rotation of 100 degrees, which gives 3.6 amino acid residues per turn of helix.

Answer 14

rise (translation)

Question 15

In these proteins, two α helices can entwine to form a very stable structure, which can have a length of (100 nm, or 0.1 μm) or more.

Answer 15

Coiled coil

Question 16

a steric contour plot that depicts allowed ranges of the angles phi and psi for amino acid residues in polypeptide chains. For each residue, its conformation in the main chain of a polypeptide can be completely defined by phi the degree of rotation at the bond between the nitrogen and the alpha carbon atoms) and psi (the degree of rotation at the bond between the alpha carbon and the carbonyl carbon atoms).

Answer 16

Ramachandran plot

Question 17

The angle of rotation about the bond between the α-carbon and the carbonyl carbon atoms.

Answer 17

Psi ψ Angle

Question 18

The sharp transition from the folded to the unfolded state of proteins observed with increasing concentration of denaturants.

Answer 18

Cooperative Transition

Question 19

Combinations of secondary structure present in many proteins that frequently exhibit similar functions.

Answer 19

Motif (Supersecondary Structure)

Question 20

A cellular protein called PrP. Infectious prions are aggregated forms of the PrP protein termed PrP SC.

Answer 20

Prion

Question 21

a common structural motif in proteins, in which a polypeptide main chain forms the inner portion of a right-handed helix, with the side chains extending outward; the helix is stabilized by intrachain hydrogen bonds between NH and CO groups of the main chain.

Answer 21

α helix

Question 22

in proteins, the spatial arrangement of amino acid residues that are far from each other in the linear sequence, as well as the pattern of disulfide bonds.

Answer 22

Tertiary structure

Question 23

the distinctive R group bonded to the alpha-carbon of an amino acid.

Answer 23

Side chain (R group)

Question 24

any of the polypeptide chains in a protein that contains more than one of such chains.

Answer 24

Subunit

Question 25

an extended polypeptide chain, with an axial distance of 3.5 angstrom between adjacent amino acids, often found in a beta pleated sheet.

Answer 25

β strand

Question 26

a common structural motif in proteins, in which two or more beta strands are associated as stacks of chains, stabilized by interchain hydrogen bonds; a number of beta strands running in the same direction form a beta pleated sheet, while such strands running in opposite directions form an antiparallel pleated sheet.

Answer 26

β pleated sheet

Question 27

A measure of the rotation about a bond, usually taken to lie between -180 and +180 degrees.

Answer 27

Torsion angle