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Flashcards in Chapter 2 Terms Deck (27):

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

Side Chain (R group)


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

L amino acid


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

Dipolar ion (zwitterion)


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

Peptide bond (amide bond)


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.

Disulfide bond


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

Primary structure


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

Torsion angle


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

phi angle


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

psi angle


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

Ramachandran diagram


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.

Secondary structure


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).

alpha helix


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.

Rise (translation)


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

beta pleated sheet


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.

beta strand


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

Reverse turn (beta turn; hairpin turn)


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

Coiled coil


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

Heptad repeat


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

Tertiary structure


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.

Motif (supersecondary structure)


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 ______.



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



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

Quaternary structure


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

Cooperative transition


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.

Intrinsically unstructured protein (IUP)


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.

Metamorphic protein


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