Terminology

3/10 helix - A protein secondary structure containing 3 amino acid residues per turn and hydrogen bonds in 10 atom rings (Figure 6.4).

Helix - A fundamental helical, secondary structure of protein molecules discovered by Linus Pauling. It contains 3.6 residues per turn and forms hydrogen bonds in 13 atom rings (Figure 6.3).

Keratins - Major fibrous proteins of hair and fingernails. They also compose a major fraction of animal skin (Figure 6.11)
Keratin - A fibrous protein containing much sheet structure - found mostly in birds and reptiles, in structures like feathers and scales (Figure 6.11).
Sheet - A fundamental protein secondary structure (ribbon-like) discovered by Linus Pauling. It contains two amino acid residues per turn and forms hydrogen bonds with residues on adjacent chains (Figure 6.12).
Turn - Amino acids which completely reverse the direction of the polypeptide chain in only four amino acid residues of a protein sequence. This occurs via hydrogen bonding between resides 1 and 4 (Figure 6.18).
C 2 Symmetry - A type of two-fold symmetry in which the units are related to one another by a two-fold axis (called a dyad axis). The two subunits are rotated 180 from each other (Figure 6.30).
C 3 Symmetry - A type of three-fold symmetry in which the units are related to one another by a three-fold axis. The subunits are rotated 120 from each other (Figure 6.30).
C 4 Symmetry - A type of four-fold symmetry in which the units are related to one another by a four-fold axis. The subunits are rotated 90 from each other (Figure 6.30).
Chaperonins - Proteins which help in the proper assembly of protein structure. They include heat-shock proteins and GroEL of E. coli.
Charge-Charge Interactions - Interactions between positively and negatively charged side chain groups.
Conformational Entropy - A protein folding process, which involves going from a multitude of random-coil conformations to a single, folded structure. It involves a decrease in randomness and thus a decrease in entropy.
D 2 symmetry - A type of symmetry in which the units are related to one another by a four-fold axis in one plane and units in another plane have two-fold symmetry with the first plane (Figure 6.30).
Denaturation - Loss of tertiary and secondary structure of a biopolymer, such as protein or nucleic acid, so that the polymer becomes a random coil.
Dihedral Symmetry - Symmetric interactions involving multiple pairs of isologous interactions - D2 symmetry, for example (Figure 6.30).
Domain - A compact, locally folded region of tertiary structure in a protein.
Fibrous proteins - A class of proteins distinguished by a filamentous or elongated form. Most play structural roles in animal cells and tissues, holding things together.
turn - Amino acids in a polypeptide which completely reverse the direction of the polypeptide chain in only three amino acid residues. This occurs via hydrogen bonding between resides 1 and 3. The sequence of amino acids in the turn includes a proline (Figure 6.19).
Globular Proteins - Proteins containing polypeptide chains folded into compact structures that are not extended or filamentous.
Helical symmetry - A type of rotational symmetry in which the axis of symmetry is at the center of a helix (Figure 6.30).
Heterologous Interactions - Interactions between identical subunits that are not symmetrical (Figure 6.33)
Heterotypic Protein-Protein Interactions - Protein-protein interactions between entirely different protein molecules.
Hydrophobic Effect - Stabilization of protein structure resulting from association of hydrophobic groups with each other, away from water.
Isologous Interactions - A symmetric interaction in which two identical interactions occur, symmetrically placed about a dyad axis. Isologous interactions are present whenever 2-fold axes are present (Figure 6.30).
Levinthal's Folding Paradox - States that there are approximately 1050 theoretical conformations a protein could assume. If one new conformation could be attempted every 10-13 seconds, it would still take over 1030 years to randomly try all of the possibilities, yet ribonuclease can completely fold in about a minute.
Molten Globule State - Intermediate structures of a protein in which the overall tertiary framework of the protein is established, but the internal side chains are still free to move about.
- Angles - In a peptide bond the atoms of the amine, alpha carbon, and carbonyl carbon for each amino acid are contained within separate amide planes. Orientation of the planes with respect to each other and to the joining alpha carbon are defined by these angles (Figure 6.2).
Helix - A theoretical protein secondary structure with 4.4 residues per turn and a 16 atom hydrogen bonded ring that is sterically possible, but has not yet been observed (Figure 6.4).
Pitch - The spacing distance between individual adjacent coils of a helix (Figure 6.5).
Point Group Symmetry - A type of symmetry that involves a defined number of subunits arranged about one or more axes of symmetry. An n-fold axis of symmetry corresponds to rotation of each subunit by 360/n with respect to its neighbor.
Prions - An unsual class of proteins that can transmit disease independently of nucleic acids
Procollagen - A newly translated form of collagen in which hydroxylation and addition of sugar residues has occurred, but the triple helix has not formed (Figure 6.14).
Prosthetic Group - A metal ion or small molecule (other than an amino acid) that forms part of a protein in the protein's native state and is essential to the protein's functioning. Its attachment to the protein may be either covalent or noncovalent.
Protein Disulfide Bonds - Covalent bond between non-adjacent cysteines in a protein, creating cystine (an oxidation). Helps to stabilize tertiary structures (Figure 6.24).
PrP - The protein believed to be responsible for transmitting the disease of prions. The protein is encoded by the host's genome and exists in two forms, only one of which causes the disease (Figure 6.27).
Quaternary Structure - For a protein, the level of structure that results when separate, folded polypeptide chains (subunits) associate in a specific way to produce a complete protein (Figure 6.29).
Ramachandran Plots - A map of - angles (plotted graphically as versus ) that can be used to describe the backbone conformation of any polypeptide residue as well as simple secondary structures of proteins (Figure 6.9).

Random Coil - Refers to a linear polymer that has no secondary or tertiary structure but instead is wholly flexible with a randomly varying geometry. This is the state of a denatured protein or nucleic acid.
Rise - The distance a helix rises between adjacent polymer units (Figure 6.5).
Scurvy - A condition that occurs in vitamin C deficiency in which lysine and proline residues in collagen cannot be modified.
Secondary Structure - Local folding of the backbone of a linear polymer to form a regular, repeating structure. The B- and Z-forms of the DNA helix and the -helix and -sheet structures of polypeptides are examples (Figure 6.27).
Site-directed Mutagenesis - Technique for altering the sequence of a DNA molecule. If the alteration occurs in a region coding for protein, the amino acid sequence of the protein may be altered as a consequence.
Tertiary Structure - Large-scale folding structure in a linear polymer that is at a higher order than secondary structure. For proteins and RNA molecules, the tertiary structure is the specific three-dimensional shape into which the entire chain is folded (Figure 6.27).
Tropocollagen - The basic unit of the collagen fiber. It is a triple helix of three polypeptide chains, each about 1000 residues in length (Figure 6.13).
van der Waals Interactions - Weak interactions between uncharged molecular groups that help stabilize a protein's structure.