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85 Cards in this Set
- Front
- Back
amino acid residues
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amino acids making up a protein
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polypeptides
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amino acid polymer
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peptides
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amino acid polymer with less than 50 amino acids
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proteins
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amino acid polymer with more than 50 amino acids
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amphoteric
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a molecule being able to behave as an acid or a base
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zwitterions
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molecules that bear both positive and negative charges on different atoms
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nonpolar amino acids
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glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, cysteine, proline
hydrophobic R groups, important in maintaining 3D protein structure |
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aromatic
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a class of hydrocarbons that contain cyclic structures with unique properties, unsaturated, hydrophobic
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aliphatic
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nonaromatic hydrocarbons, hydrophobic
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polar amino acids
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serine, threonine, tyrosine, asparagine, glutamine
hydrophilic R groups hydroxyl or amide |
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acidic amino acids
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aspartate, glutamate
carboxylate group on R, negative at physiological pH |
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basic amino acids
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lysine, arginine, histidine
positive charge at physiological pH, all have nitrogen-related R groups |
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other roles of amino acids
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1. chemical messengers
2. precursors to a variety of complex N-containing molecules 3. metabolic intermediates |
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neurotransmitters
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substances released from one nerve cell that influence the function of a second nerve cell or a muscle cell
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hormones
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chemical signal molecules produced in one cell that regulate the function of other cells
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asymmetric/ chiral carbons
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carbons with four different groups bonded to it
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stereoisomers
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molecules that differ only in the spatial arrangement of their atoms
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enantiomers
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two molecules that are mirror images of each other due to different spatial arrangement
have identical properties except for rotating polarized light in opposite directions |
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optical isomers
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molecules that are otherwise identical except for rotating polarized light in opposite directions
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dextrorotatory
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+, rotates polarized light in the clockwise direction
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levorotatory
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-, rotates polarized light in the counterclockwise direction
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primary stereoisometric form found in living things
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primarily L
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icoelectric point
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the pH at which a molecule has no net charge
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peptide bonds
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amide linkages formed when the unshared electron pair of the alpha-amino nitrogen atom of one amino acid attacks the alpha-carboxyl carbon of another in a nucleophilic acyl substitution reaction
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N-terminal
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amino acid in a polypeptide that has the free amino group. written on the left
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C-terminal
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amino acid in a polypeptide that has the free carboxyl group. written on the right
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disulfide bridge
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bond between two sulfide groups on two cysceines
help stabilize many polypeptides |
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Schiff bases
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imine product of the reaction when amine groups react reversibly with carbonyl groups
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aldimines
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Schiff bases formed from reactions between amino groups and aldehyde groups
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functions of proteins
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catalysis, structure, movement, defense, regulation, transport, storage, stress response
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heat shock proteins
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proteins that promote the correct refolding of damaged proteins
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multifunction proteins
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proteins that can perform multiple, often unrelated, functions
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protein families
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classification of proteins based on amino acid sequence and similarities in 3D structure. Proteins are thought to share a common ancestry
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superfamilies
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classification of proteins that are more distantly related
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fibrous proteins
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shape classification with long, rod-shaped molecules that are insoluble in water and physically tough
often function as structural or protective proteins |
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globular proteins
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shape classification with compact, spherical molecules that are usually water-soluble
dynamic functions |
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simple protein
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proteins that contain only amino acids
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conjugated protein
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simple proteins combined with a nonprotein component
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prosthetic group
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nonprotein component of a conjugated protein
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apoprotein
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a conjugated protein without its prosthetic group
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holoprotein
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a conjugated protein with its prosthetic group
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glycoproteins
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conjugated proteins with a carbohydrate prosthetic group
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lipoproteins
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conjugated proteins that contain lipid molecules
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metalloproteins
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conjugate proteins that contain metal ions
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phosphoproteins
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conjugate proteins that contain phosphate groups
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hemoproteins
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conjugate proteins that contain heme groups
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primary structure
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amino acid sequence of a protein
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secondary structure
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partial folding of a polypeptide showing certain localized arrangements of adjacent amino acids
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tertiary structure
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overall 3D shape of a polypeptide
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quaternary structure
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proteins that consist of two or more polypeptide chains
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homologous
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describes proteins with similar amino acid sequences that have arisen from the same ancestral gene
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molecular diseases
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diseases caused by mutations in protein folding
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alpha-helix
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common secondary structure formed when a polypeptide chain twists into a right-handed helical conformation. H bonds occur between the N-H of each amino acid and the carbonyl carbon four amino acids away. R groups stick out form the helix.
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beta-pleated sheet
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common secondary structure formed when two or more polypeptide chain segments line up side by side. Stabilized by hydrogen bonds that form between polypeptide backbone N-H and carbonyal groups of adjacent chains. May be parallel or antiparallel.
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supersecondary structures/ motifs
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patterns of alpha-helix and beta-pleated sheet structures within a protein
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protein folding
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a process in which an unorganized, nascent molecule acquires a highly organized structure
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fold
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the core 3D structure of a domain of a large globular protein
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domain
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typically structurally independent segments that have specific functions in large globular proteins
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modular proteins
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eukaryotic proteins that contain numerous duplicate or imperfect copies of one or more domains that are linked in series
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hydrophobic interactions
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stabilizes tertiary structure as hydrophobic R groups are forced together away from water as well as expelling water from inside the protein, increasing entropy, making the action favorable
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electrostatic interactions
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stabilizes tertiary structure via interactions between groups of opposite charge. Strongest are between ionic groups. Can only occur in absence of water.
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salt bridges
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noncovalent bonds in protein folding
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ligands
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signal molecule
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subunit
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one polypeptide chain within a protein that contains more than one
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hydrogen bonds
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stabilizes tertiary structure by forming hydrogen bonds within a protein or on the surface.
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covalent bonds
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stabilizes tertiary structure by chemically linking structures. Disulfide bride most prominent. Important for protecting the protein from changes in pH or salt concentration.
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hydration
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stabilizes tertiary structure formed from structured water around the protein.
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oligomers
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multisubunit proteins in which some or all subunits are identical
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protomers
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a component of an oligomer; may consist of one or more subunits
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allostery
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the control of protein function through ligand binding
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allosteric transitions
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ligand-induced conformational changes so that the protein's affinity for other ligands is altered
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effectors/modulators
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ligands that trigger allosteric transitions
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intrinsically unstructured proteins (IUPs)
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unstructured proteins
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natively unfolded proteins
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proteins with a complete lack of ordered structure
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denaturation
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the process of structure disruption, which may or may not involve protein unfolding
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causes of denaturation
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changes in pH via strong acids or bases, alters H bonds
organic solvents disrupt hydrophobic interactions detergents disrupt hydrophobic interactions reducing agents break disulfide bridges and disrupt H-bonds and hydrophobic interactions increased salt concentration disrupts the solvation sphere heavy metal ions disrupt salt bridges and bind with sulfhydryl groups temperature increase disrupts weaker interactions mechanical stress disrupts interactions |
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amphipathic
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molecules containing both hydrophobic and hydrophillic components
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site-directed mutagenesis
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a recombinant DNA technique in which specific sequence changes can be introduced into a predetermined position in cloned genes
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circular dichromism
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a type of spectroscopy in which the relationship between molecular motion and structure is probed with electromagnetic radiation
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molten globule
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a partially organized globular state of a folding polypeptide that resembles the molecule's native state
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molecular chaperones
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molecules that aid in the folding of polypeptides by protecting primary structure from inappropriate interactions and ensuring quick precise folding
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hsp70s
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a family of molecular chaperones that bind to and stabilize proteins during the early stages of folding
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hsp60s or chaperonins
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a family of molecular chaperones which mediate protein folding by forming a hollow protein complex with a hydrophobic interior
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aldol condensation
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a reaction in which two aldehydes form an alpha, beta-unsaturated aldehyde linkage
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cooperative binding
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a mechanism in which binding of one ligand to a target molecule promotes the binding of other ligands.
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