Biochem Chapter 4

Dalton

A _______ is a unit of mass very nearly equal to that of a hydrogen atom (used to measure protein mass).

Alpha Helix

A coiled secondary structure stabilized by intrachain hydrogen bonds.

Urea

A colorless crystalline compound that is the main nitrogenous breakdown product of protein metabolism in mammals and is excreted in urine.

Domain

A conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.

Conformation

A general central principle of biochemistry: sequence specifies ______________.

Dimer

A molecule complex consisting of two identical molecules linked together.

Tetramer

A polymer comprising four monomer units.

Side Chains

A polypeptide chain consists of a regularly repeating part, called the main chain or backbone, and a variable part, comprising the distinctive ____ ______.

Directionality

A polypeptide chain has ____________, because its ends are different: an alpha-amino group is at one end, and an alpha-carboxyl group is at the other.

Intrinsically Unstructured Proteins

A protein that, completely or in part, do not have a discrete three-dimensional structure under physiological conditions.

Residue

A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a polypeptide is called a ________.

Subunit

A single protein molecule that assembles (or "coassembles") with other protein molecules to form a protein complex.

Folding Funnel

A specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells.

Motif

A supersecondary structure that is present in many proteins and frequently exhibits similar functions.

Ramachandran Plot

A way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure.

Trans

Almost all peptide bonds in proteins are in the ____ configuration.

Coiled Coil

Alpha-Keratin, which is the primary component of wool and hair, consists of two right-handed alpha helices intertwined to form a type of left-handed superhelix called a _______ ____.

Molten Globule

Compact, partially folded conformations of proteins that have near-native compactness, substantial secondary structure, little detectable tertiary structure and increased solvent-exposed hydrophobic surface area relative to the native state.

Right

Essentially all alpha helices found in proteins are (right/left) _____-handed.

Translation

In an alpha-helix, each residue is related to the next one by a rise, also called 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.

Disulfide Bonds

In some proteins, the linear polypeptide chain is covalently cross-linked. The most common cross-links are ________ _____, formed by the oxidation of a pair of cysteine residues.

Same

In the cis configuration, these groups are on the ____ side of the peptide bond.

Opposite

In the trans configuration, the two alpha-carbon atoms are on __________ sides of the peptide bond.

Compact

Myoglobin is an extremely (compact/loose) molecule.

Oligopeptides

Peptides made of small numbers of amino acids are called _______________.

Chaperones

Proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures.

Quaternary Structure

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

Tertiary Structure

Refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds.

Screw Sense

The _____ _____ of a helix can be right-handed (clockwise) or left-handed (counterclockwise).

Pitch

The _____ of the alpha helix is the length of one complete turn along the helix axis and is equal to the product of the translation (1.5 angstroms) and the number of residues per turn (3.6), or 5.4 angstroms.

Psi

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

Phi

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

3.5

The distance between adjacent amino acids along a beta strand is approximately ____ angstroms, in contrast with a distance of 1.5 angstroms along an alpha helix.

Intermediates

The essence of protein folding is the tendency to retain partly correct __________ because they are slightly more stable than unfolded regions.

Water Molecule

The formation of a dipeptide from two amino acids is accompanied by the loss of a _____ ________.

Proline

The helices present in collagen are stabilized by steric repulsion of the pyrrolidine rings of the _______ residues.

Amino Acid

The information needed to specify the catalytically active three-dimensional structure of ribonuclease is contained in its _____ _____ sequence.

Glycine

The inside of the triple-stranded helical cable is very crowded and explains why ________ has to be present at every third position on each strand: the only residue that can fit in an interior position is ________. (Same word in both blanks)

Titin

The largest protein known is the muscle protein _____, which serves as a scaffold for the assembly of the contractile proteins of muscle.

Peptide Bond

The linkage joining amino acids in a protein is called a ________ ____.

Thermodynamically

The native protein is the most ________________ stable structure.

Quaternary Structure

The number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.

Double-Bond

The peptide bond has considerable ______-____ character owing to resonance structures: the electrons resonate between a pure single-bond and a pure double-bond.

Uncharged

The peptide bond is __________, allowing polymers of amino acids linked by peptide bonds to form tightly packed globular structures that would otherwise be inhibited by charge repulsion.

Planar

The peptide bond is essentially _______.

Cystine

The resulting unit of two linked cysteines is called _________.

Primary Structure

The sequence of amino acids in the polypeptide chain is reffered to as the _________ _________.

Nonpolar

The striking fact about myoglobin is the interior consists almost entirely of ________ residues.

Levinthal's Paradox

The theory of protein folding that noted because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations.

Tertiary Structure

The three-dimensional structure where the R groups of amino acids that are far apart in the primary structure bond with one another.

Torsion Angles

The two adjacent rigid peptide units may rotate about their single bonds, taking on various orientations, which allows the proteins to fold in many different ways. The rotations about these bonds can be specified by _______ ______.

Metamorphic Proteins

These proteins appear to exist in an ensemble of structures of approximately equal energy that are in equilibrium.

Secondary Structure

Three-dimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain.

Glycine

What is the amino terminus of the tripeptide Gly-Ala-Asp?

Antiparallel

What type of Beta sheets have Beta strands that run in opposite directions?

Parallel

What type of Beta sheets have Beta strands that run in the same direction?

Denatured

When a protein is converted into randomly coiled peptide without its normal activity, it is said to be ___________.

Steric Exclusion

______ ________, the fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle.

Myoglobin

_________, a single polypeptide chain of 153 amino acids, is an oxygen-binding protein found predominantly in heart and skeletal muscle; it appears to facilitate the diffusion of oxygen from the blood to the mitochondria, the primary site of oxygen utilization in the cell.