Biochemistry - Ch 06 - Lecture 8 Thru 13 - Protein Structure And Folding (Vocab)

Front 1

Define:

αα motif

Back 1

A protein motif consisting of two α helices packed against each other with their axes inclined.

Front 2

Define:

α helix

Back 2

a regular secondary structure of polypeptides, with 3.6 residues per right-handed turn, a pitch of 5.4 Å, and hydrogen bonds between each backbone N-H group and the backbone C=O group that is four residues earlier.

Front 3

Define:

α/β barrel

Back 3

A β barrel in which successive parallel β strands are connected by α helices such that a barrel of α helices surrounds the β barrel.

Front 4

Define:

βαβ motif

Back 4

A protein motif consisting of an α helix connecting two parallel strands of a β sheet.

Front 5

Define:

β barrel

Back 5

A protein motif consisting of a β sheet rolled into a cylinder

Front 6

Define:

β hairpin

Back 6

A protein motif in which two antiparallel β strands are connected by a reverse turn.

Front 7

Define:

Breathing

Back 7

The small conformational fluctuations of a protein molecule

Front 8

Define:

Chaotropic agent

Back 8

A substance that increases the solubility of nonpolar substances in water and thereby tends to denature proteins.

Front 9

Define:

Coiled coil

Back 9

An arrangement of polypeptide chains in which two α helices wind around each other, as in α keratin.

Front 10

Define:

Cyclic symmetry

Back 10

A type of symmetry in which the asymmetric units of a symmetric object are related by a single axis of rotation.

Front 11

Define:

β bulge

Back 11

An irregularity in a β sheet resulting from an extra residue that is not hydrogen bonded to a neighboring chain.

Front 12

Define:

Diffraction Pattern

Back 12

The record of the destructive and constructive interferences of radiation scattered from an object. In X-Ray crystallography , this takes the form of a series of discrete spots resulting from a collimated beam of X-rays scattering from a single crystal.

Front 13

Define:

Dihedral Symmetry

Back 13

A type of symmetry in which the asymmetric units are related by a twofold rotational axis that intersects another rotation axis at a right angle.

Front 14

Define:

Domain

Back 14

A group of one or a few polypeptide segments of about 40-200 residues that folds into a globular unit.

Front 15

Define:

Electron density

Back 15

The arrangement of electrons that gives rise to a diffraction pattern in X-ray crystallography.

Front 16

Define:

Fibrous Protein

Back 16

A protein characterized by a stiff, elongated conformation, that tends to form fibers.

Front 17

Define:

Globular Protein

Back 17

A water-soluble protein characterized by a compact, highly folded structure.

Front 18

Define:

Helix Cap

Back 18

A protein structural element in which the side chain of a residue preceding or succeeding a helix folds back to form a hydrogen bond with the backbone of one of the helix's four terminal residues.

Front 19

Define:

Hydropathy

Back 19

A measure of the combined hydrophobicity and hydrophiliciry of an amino acid residue; it is indicative of the likelihood of finding that residue in a protein interior.

Front 20

Define:

Ion Pair

Back 20

An electrostatic interaction between two ionic groups of opposite charge. In protein, it is also called a salt bridge.

Front 21

Define:

NMR

Back 21

Nuclear magnetic resonance (NMR)

A spectroscopic method for characterizing atomic and molecular properties based on the signal emitted by radiofrequency-excited atomic nuclei in a magnetic field. It can be used to determine the three-dimensional molecular structure of a protein or nucleic acid.

Front 22

Define:

Oligomer

Back 22

(1) A short polymer consisting of a few linked monomer units.

(2) A protein consisting of a few protomers (subunits)

Front 23

Define:

Peptide Group

Back 23

The planar -CO-NH- group that encompasses the peptide bond between amino acid residues in a polypeptide.

Front 24

Define:

Pitch

Back 24

The distance a helix rises along its axis per turn.

5.4 Å for an α-helix.
34 Å for B-DNA

Front 25

Define:

Protomer

Back 25

One of two or more identical units of an oligomeric protein. A protomer may consist of one or more polypeptide chains.

Front 26

Define:

Quartenary Structure

Back 26

The spatial arrangement of a macromolecule's individual subunits.

Front 27

Define:

Ramachandran Diagram

Back 27

A plot of Φ versus Ψ that indicates the sterically allowed conformations of a polypeptide.

Front 28

Define:

Regular Secondary Structure

Back 28

A segment of a polymer in which the backbone adopts a regularly repeating conformation.

Front 29

Define:

Rotational Symmetry

Back 29

A type of symmetry in which the asymmetric units of a symmetric object can be brought into coincidence through rotation.

Front 30

Define:

Secondary Structure

Back 30

The local spatial arrangement of a polymer's backbone atoms without regard to the conformations of its substituent side chains.

α helices and β sheets are common secondary structural elements of proteins.

Front 31

Define:

Supersecondary Structure

Back 31

A common grouping of secondary structural elements.

Also called a motif.

Front 32

Define:

Tertiary Structure

Back 32

The entire three-dimensional structure of a single-chain polymer, including that of its side chains.

Front 33

Define:

Torsion (dihedral) Angle

Back 33

The dihedral angle described by the bonds between four successive atoms. The torsion angles Φ and Ψ indicate the backbone conformation of a polypeptide

Front 34

Define:

X-Ray Crystallography

Back 34

A method for determining three-dimensional molecular structures from the diffraction pattern produced by exposing a crystal of a molecule to a beam of X-Rays.

Front 35

Define:

Zinc Finger

Back 35

A protein structure moif, often involved in DNA binding, that consist of 25 to 60 residues that include HIS and/or CYS residues to which one or two Zn²+ ions are tetrahedrally coordinated.