Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, descriptions in middle, figures on right)

Term | Definition | Relevant Figures | 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 6.3a | Keratins | Major fibrous proteins of hair and fingernails. They also compose a major fraction of animal skin | Figure 6.11 | Axis | A site of symmetry in a symmetric molecule |  | Keratins | A fibrous protein containing much sheet structure and are found mostly in birds and reptiles, in structures like feathers and scales. | Figure 6.11 | sheet | A fundamental protein secondary structure discovered by Linus Pauling. It contains two residues per turn and forms hydrogen bonds with residues on adjacent chains. | Figure 6.3b, Figure 6.7 | 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 | Bovine pancreatic trypsin inhibitor (BPTI) | An enzyme of58 amino acids that is one of the smallest and simplest globular proteins. Its sole function is to bind to and inhibit proteolytic enzymes like trypsin. |  | C2 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 | C3 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 | C4 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 |  | Chou-Fasman rules | Algorithm for predicting secondary structure on the basis of amino acid sequence of a protein | Table 6.6 | Class 1 protein motion | Vibrations and oscillations of individual atoms and molecules in a protein |  | Class 2 protein motion | Concerted motions of structural elements, like helices and groups of residues in a protein |  | Class 3 protein motion | Motions of whole domains of a protein - opening and closing of clefts |  | Collagen | The most abundant single protein of most vertebrates. Fibers of this protein form the matrix or cement material in bond on which the mineral constituents precipitate. The fibers are a major portion of tendons and a network of the fibers is an important constituent of skin. |  | Collagen hydroxylation | A process that occurs after collagen is synthesized. The process involves vitamin C (ascorbic acid) and modifies prolines and lysines in the protein. |  | Conformational entropy | A protein folding process, which involves going from a multitude of random-coil conformations to a single, folded structure involves a decrease in randomness and thus a decrease in entropy. Conformational entropy works against folding by adding to positive G |  | D2 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 |  | Desmosine | A cross linking structure found in elastin |  | 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. |  | Elastin | An elastic fibrous protein found in ligaments and arterial blood vessels |  | Fibroin | The fibrous protein of silk. |  | Fibrous proteins | A type of protein 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 subunit interactions | Interactions between protein subunits in which the interacting regions of the subunits are different from each other | 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 |  | Internal Hydrogen Bonds | Forces stabilizing a protein's secondary structure on the basis of partial charge. These occur between amino acid side chains, such as hydroxyls of serine or threonine, amino groups and carbonyl oxygens of asparagine or glutamine, ring nitrogens in histidine | Figure 6.21 | 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 interanal side chains are still free to move about |  | - angles | In a peptide bond the atoms of the amine, 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 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 in proteins | 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. |  | Repeat distance | The distance along the axis it takes for a helix to exactly repeat itself. |  | Rise | The distance a helix "rises" between adjacent polymer units. | Figure 6.5 | Salt bridges | Formed when a pair of positively and negatively charged side chains form a kind of salt within a protein molecule |  | 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, it 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 6.13a | van der Waals Interactions | Weak interactions between uncharged molecular groups that help stabilize a protein's structure. |

Category - Lists

Query - What items are in the list described below?

Reversal - there is no reversal of Lists

Six thermodynamic factors described in the text affecting protein folding | Conformational entropy |  | Charge-Charge interactions |  | Salt bridges |  | Internal Hydrogen Bonds |  | van der Waals Interactions |  | Hydrophobic effect |

Three primary effects on entropy and enthalpy upon which the folded structure of globular proteins depends | 1. Unfavorable conformational entropy change |  | 2. Favorable enthalpy arising from intramolecular side group interactions |  | 3. Favorable entropy change arising from burying of hydrophobic groups within the molecule |

Category - General

Query - In the "Pathway" model of protein folding, what description applies to the pathway intermediate below?

Reversal - none

(pathway intermediates on left, descriptions on right)

Name | Description | US | Intermediate conformation in protein folding - Completely unfolded | II | Intermediate conformation in protein folding - partially folded - some amide protons protected from exchange, some secondary structure present, but no enzymatic activity | IN | Intermediate conformation in protein folding - Almost completely folded - has enzymatic activity, but some incorrect alignments are retained

Category - Lists

Query - The process of making collagen was described in the text as requiring seven steps. What step occurs before/after (randomize) the following step?

[[Program should pick a step and whether a student is to give the preceding or following step - note here that the second term (after query) is actually the step from below that the computer randomly picks]].

1. Translation (synthesizing the primary structure) | 2. Hydroxylation of the lysine and proline side chains | 3. Attachment of lysines to sugars to create procollagen | 4. Assembly of central regions into triple helices/folding of N-terminal and C-terminal ends to globular structures | 5. Export of procollagen complexes to the extracellular space | 6. Cleavage of N-terminal and C-terminal regions, yielding the tropocollagen triple helix | 7. Cross linking between strands to solidify fiber