Term
| Native State/Native Conformation |
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Definition
| Final folded most stable state of the protein |
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Term
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Definition
| the constant vacillation from the absolute most stable form to forms slightly less favorable and back to the most favored form |
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Term
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Definition
| the precise arrangement of groups around a central atom, can only be changed by breaking and reforming chemical bonds |
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Term
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Definition
| spatial arrangement of atoms that depends upon rotation around a single bond or bonds |
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Term
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Definition
| regular repeating structures that occur over short localized regions. involve folding of the peptide backbone. stabilized by hydrogen bonds between the carbonyl oxygens and amid hydrogens of the peptide bond. |
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Term
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Definition
| long range interactions within the protein molecule. Fold the molecule into a compact shape. Involve folding of a.a. side chains of the molecule. stabilized by hydrophobic interactions between hydrophobic side chains, polar interactions between polar side chains, interactions between polar groups of peptide bond and polar side chains, and electrostatic interactions |
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Term
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Definition
| association of two or more polypeptide chains (subunits) into a functional molecule. involves formation of a multimeric protein. |
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Term
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Definition
| most prevalent and stable form of helical structure in naturally occurring proteins. spiral that turns in the right handed direction. 3.6 a.a. per turn of the helix. amid group and carbonyl group are parallel along axis of the helix with the carbonyl groups pointing towards the carboxyl end and amido groups toward the amino end. Hydrogen bonds between the carbonyl oxygen and the amido hydrogen four a.a. upstream, toward the C-Terminus of the helix, stabilize the helical structure. (a.a. 1 is hydrogen bonded to a.a. 5) |
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Term
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Definition
| Pro and Gly. Cyclic nature of Pro puts a kink in the helix and the conformational flexibility of Gly destabilizes the helix |
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Term
| the first ___ amido hydrogens and the last ____ carbonyl oxygens do not have hydrogen bonding partners within the helix |
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Definition
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Term
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Definition
| Polypeptide chain folds to prevent "fraying at the ends" to provide appropriate hydrogen bonding partners for the end groups. |
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Term
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Definition
| two or more strands of polypeptide chain run adjacent to each other. the carbonyl oxygen and the amido hydrogen of the peptide bond lie in the plane of the Beta structure. the R groups of the amino acids alternate above and below the plane of the Beta sheet. sometimes called a Beta Pleated Sheet. |
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Term
| Polypeptide strands that make up the Beta sheet can run in the ____ direction or ____ direction |
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Definition
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Term
| At least ___ strands of antiparallel Beta sheet is required to form a stable structure and between ___ and __ strands are required to form a stable parallel structure |
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Definition
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Term
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Definition
| small piece of non-repetitive structure that occurs by itself, but most often it occurs as an irregularity in antiparallel Beta structures. two strands of multi stranded antiparallel Beta sheet in which one strand, the long on, contains one more a.a. than the other stand, the short one. the extra a.a. is accommodate in the long strand by creating a bulge in the long stand and slightly bending the short strand. gently bending the polypeptide back bone. |
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Term
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Definition
| direction of polypeptide strand changes 180 degrees. |
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Term
| In a Beta turn the 180 degree change occurs over the span of ____ a.a. |
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Definition
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Term
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Definition
| greater than 90%. contains Pro at position 2. Position 3 can be any a.a. |
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Term
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Definition
| does not contain Pro, but always contains a Gly at position 3 |
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Term
| Tertiary Structures are stabilized by these 4 weak intermolecular interactions and 1 covalent interaction |
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Definition
| hydrophobic (london forces), Hydrogen Bonds, salt bridges, hydration, and disulfide bonds |
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Term
| Hydrophobic Interactions Occur between |
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Definition
| side chains of the non polar a.a. |
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Term
| Hydrogen Bonds can form between |
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Definition
| side chains of uncharged polar a.a., uncharged polar a.a. side chains and the carbonyl oxygen and/or the amido hydrogen of peptide bonds not involved in secondary structures (helix capping), and between uncharged polar a.a. side chains and acidic and/or basic a.a. side chains |
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Term
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Definition
| electrostatic interactions between the negative charge on acidic a.a. side chains and the positive charge on basic a.a. side chains |
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Term
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Definition
| structured water interacting with the polar groups on the surface of the protein. weakens the interactions between polar groups on the protein surface increasing flexibility |
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Term
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Definition
| Covalent interaction that occurs between appropriately positioned Cys residues. form only after the protein has correctly folded and they stabilize the final folded structure |
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Term
| Suprersecondary Structures/Structural Motifs |
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Definition
| combinations of secondary structures that have been found to commonly occur in proteins. regions of secondary structure that interact with each other locally rather than globally. Often not structurally stable by themselves. Ex: Helix-Loop-Helix, Beta-Alpha-Beta Unit, Hairpin, Greek Key, Beta Meander, Alpha/Beta Barrel |
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Term
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Definition
| discrete independently folded units within tertiary structure. usually combinations of several structural motifs. independently stable and usually perform specific function within the protein |
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Term
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Definition
| plays a role in protein-protein binding |
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Term
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Definition
| plays a role in protein-ligan and/or protein-protein binding |
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Term
| Epidermal Growth Factor Domain |
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Definition
| involved in interactions between extracellular proteins and the cell surface |
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Term
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Definition
| Individual polypeptide chains that make up a multimeric protein |
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Term
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Definition
| Composed of two Alpha-subunits and two Beta-chains |
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Term
| Non-Regular Non-Repeating Structures |
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Definition
| The remaining regions of the molecule that assume no definite repeating structure when a protein folds into its higher order structures. held together into a specific conformation in the final structure by weak non covalent forces and/or disulfide bonds. |
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Term
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Definition
| The entire complement of preteens that is or can be expressed by a cell, tissue, or organism |
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Term
| Intrinsically Unstructured Proteins (IUP)/Natively Unfolded Proteins |
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Definition
| Low molecular weight proteins that are fully unfolded in their native state. Regions (>30<100 a.a.) of natively unfolded structure have also been identified in large proteins |
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Term
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Definition
| low sequence complexity, low proportion of bulky hydrophobic a.a., high proportion of certain polar and charge a.a. (Gln, Ser, Glu, and Lys), and a high proportion of a.a. with a high degree of conformational flexibility (Gly, Ala, and Pro) |
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Term
| Three Major Classes of Proteins based upon their final folded shape |
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Definition
| Fibrous Proteins, Globular Proteins, and Membran Proteins |
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Term
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Definition
| long rod like molecules that are insoluble or only slightly soluble in water. physically tough and are components of structures such as skin, cartilage, tendons, bones, hair, ligaments, hooves, and claws |
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Term
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Definition
| spherical in shape and usually very water soluble. have a hydrophobic interior surrounded by a hydrophilic exterior |
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Term
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Definition
| embedded in or pass through cellular membranes. fold so that there are at least two distinct domains: hydrophobic region that interacts with the hydrophobic membrane lipids and one or more polar regions that interact with intracellular and/or extracellular water |
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Term
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Definition
| contain a prosthetic group that is integral to their structure and necessary for their function |
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Term
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Definition
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Term
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Definition
| Part of conjugated protein without prosthetic group |
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Term
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Definition
| Intact functional protein, the apoprotein with its required prosthetic group |
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Term
| Conjugated Proteins Include |
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Definition
| Glycoproteins (prosthetic groups are carbohydrates), Lipoproteins (prosthetic groups are lipids), Nucleoproteins (prosthetic groups are nucleotides or nucleic acids), Phosphorproteins (prosthetic groups have phosphoric groups in ester linkage to hydroxyl groups on the protein), and Metalloproteins (contain either metal ions attached either by ionic interaction for by coordinate covalent bonds) |
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Term
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Definition
| Carbohydrate Moiety linked to the protein by covalent bonds involving the hydroxyl group of Ser or Thr |
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Term
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Definition
| Carbohydrate linked to the protein by covalent bonds involving the amide bond of Asn |
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Term
| Hydrophobic Interactions/Hydrophobic Effect |
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Definition
| The main driving force in the folding process |
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Term
| Stability of a tertiary and/or quaternary folded protein depends upon interplay of these three factors |
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Definition
| unfavorable entropy change of the protein molecule as it folds, favorable enthalpy change arising from intramolecular side chain interactions, and the favorable entropy change arising from burying the hydrophobic groups within the molecule and the concomitant release of structured water |
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Term
| Hierarchy of Folding Process |
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Definition
1. Secondary structures form first, driven by sequences of a.a. in the primary structure that favor certain secondary structures
2. protein collapses into a Molten Globule mediated by hydrophobic interactions between the non polar a.a. side chains. May have some secondary structures at this point, but many of the a.a. are not yet fixed in the native state.
3. Supersecondary structures form as the molten globule rearranges
4. Domains form from collections of super secondary structures as the molten globule continues to rearrange and the side chains of the a.a. become fixed in their native location.
5. the polypeptide assumes its correctly folded tertiary structure
6. If necessary, correctly folded polypeptides interact to form multimeric proteins. |
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Term
| ___ to __ % of cellular proteins require the aid of a group of specialized proteins called________ |
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Definition
| 10,30, Molecular Chaperones. They are present in all living organisms and are quite often required for the correct folding and subunit association in multimeric proteins. Some also escort selected proteins to their specific cellular location |
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Term
| Alpha Hemoglobin Stabilizing Protein (AHSP) |
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Definition
| Molecular Chaperone the prevents the alpha chain from aggregating and precipitating while Beta chains are being synthesized in hemoglobin |
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Term
| Heat Shock Proteins (Hsp) |
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Definition
| Molecular Chaperons. Hsp 70 and Hsp 40. Hsp 40 binds to the unfolded polypeptide, followed by Hsp 70 and ATP. Hsp 70 binds to the hydrophobic regions of unfolded polypeptides preventing inappropriate aggregation. ATP is hydrolyzed to ADP and PO4^-3,a dn the energy released is used to fold the protein. ADP is then exchanged for ATP and the folded protein is released. |
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Term
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Definition
| 14 Hsp 60 polypeptides associated to form 2 rings, each contains 7 Hsp 60 subunits |
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Term
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Definition
| heptamer lid structure comprised of Hsp 10 polypeptides that closes one end of the GroEL rings. |
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Term
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Definition
| the unfolded protein enters GroEL at its open end. ATP binds to GroEL and is hydrolyzed to ADP and PO4^-3, which leads to conformational changes in the GroEL that causes the release of GroES. More ATP binds and GroES binds to the GroEL ring containing the protein. The energy formed from the formation of ADP is used to (re)fold the protein, release GroES (again), and release the protein. It is repeated 3 times before it gives up and the protein is signaled for destruction. |
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Term
| Protein-Disulfide isomerase |
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Definition
| associated with chaperones that catalyzes the formation/rearrangement of disulfide bonds within proteins |
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Term
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Definition
| when native conformation, higher level structures, are destroy. primary structure is unchanged. |
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Term
| Things that denature proteins |
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Definition
| Heat, Physical Agitation, pH, Detergents, Nonpolar Organinc Solvents, Chaotic Agents, and Heavy Metals |
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Term
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Definition
| Denatures Proteins by increasing the kinetic energy within a protein molecule which disrupts the weak interactions that stabilize the higher levels of protein structure |
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Term
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Definition
| Denatures Proteins by increasing kinetic energy by shear force |
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Term
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Definition
| Denatures Proteins by altering the ionization state of side chains and disrupting salt bridges that stabilize the protein |
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Term
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Definition
| Denatures Proteins by increasing solubility of hydrophobic side chains in water, turns protein inside out |
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Term
| Nonpolar Organic Solvents |
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Definition
| Denatures Proteins by increasing the solubility of hydrophobic side chains, turns protein inside out. Ex: alcohol, ether, benzene |
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Term
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Definition
| Denatures Proteins by by disrupting hydrogen bonds within the protein and decreasing the polarity of water which increases the solubility of the hydrophobic side chains in water. Ex: urea or guanidinium chloride. |
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Term
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Definition
| high charge density on metal ions disrupt salt bridges. Fe3+ and Cu2+ can oxidize sulfur containing groups to sulfuric acids and/or sulfones. mercury binds to the sulfur of Cys side chains: disrupting hydrogen bond formation, causing abnormal disulfide bond formation, and prevent normal disulfide bond formation. |
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Term
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Definition
| most abundant protein in vertebrates. part of bone, teeth, ligaments, tendons, and skin. at least 20 different types. all rich in Gly, Pro, and Lys but DO NOT contain Cys |
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Term
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Definition
| monomoer unit of collagen. folds into a left handed helix containg 3.3 a.a. per turn. Three protropocollagen molecules combine to form a triple helix- The Collagen Triple Helix or Tropocollagen. these triple helices associate with each other i a staggered overlapping fashion involving 75% of the molecule |
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Term
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Definition
| protein of hair, wool, hooves, and horns. primary structure is rich with Cys (up to 15%) and every 4th a.a. is a hydrophobic a.a. folds into a 100% right handed alpha helix. 4 molecules of alpha-Keratin coil around each other in a left handed manner to form a Protofibril |
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Term
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Definition
| Stabilized by hydrophobic interactions. 11 protofibrils interact with each other in a 9 + 2 configuration to form a Microfibril. |
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Term
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Definition
| numerous microfibirals associate together |
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Term
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Definition
| reversibly binds and stores oxygen in muscle tissue |
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Term
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Definition
| transport protein. primary structures of alpha subunits are different than the primary structures of the Beta subunits. show a high degree of structural homology with myoglobin. a1b1 act as a pair as well as a2b2. each subunits contain a molecule of heme between the E and F helix and bind one oxygen molecule reversibly |
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Term
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Definition
| insoluble, not easily denatured, and resistant to protease digestion. contains 50% Beta sheet and only 20% alpha helix. appears to arise from a.a. change in primary structure. has the ability to replicate itself at the expense of PrPc. |
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Term
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Definition
| Alpha-helical content is 40%, with little or no Beta Sheet |
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