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Mol.CellBio Ch3

Protein Structure and Function

Term or ConceptExplanation
Amino acid sequence is deduced by... DNA and mRNA sequences control Amino Acid sequences.
Primary Structures Linear, a single peptide or a polymer of peptides (polypeptides)
Alpha Helix in Secondary Structures Carboxyl oxygen atom of each peptide bond is hydrogen bonded to the amide hydrogen atom of the amino acid residues toward the C-terminus.
Beta Helix in Secondary Structures Pleated sheet, can be parallel or antiparallel. Has Type I and Type II turns.
Motifs Combinations of secondary structures.
Domains Stable, folded protein units.
Quaternary Structures Combinations of protomers.
Symmetry Two, three, four, five fold.
SDS-PAGE Denatures proteins by binding to them with a ratio of about 1 SDS for every 2 amino acids. This gives proteins a constant charge-to-mass ratio, allowing seperation based on mass.
Immunoblot Based on the high specifity of antibody-antigen interactions.
Cofactors Inorganic compounds that are required by enxymes
Coenzymes Organic compounds that are required by enzymes
Prosthetic Group A coenzyme or cofactor which is tightly bound to the enzyme
Holoenzyme A catalytically active enzyme with its cofactor or coenzyme
Apoenzyme or Apoprotein The protein part of the holoenzyme
Active Site The distinguishing feature of an enzyme-catalyzed reaction is that it takes place within the confines of a pocket.
Substrate The molecule that is bound and acted upon by the enzyme
Sources of Binding Energy Increase in entropy, and/or energy stored as torsional stress resulting from a change in conformation.
Binding Energy is Used For... Entropy reduction and/or desolvation, positioning the substrate in order to favor the formation of the transition state, removing catalytic amino acids from the vicinity of the products and expulsion of the products.
Allosteric Enzymes Enzymes regulated by reversible non-covalent binding of regulatory compounds called allosteric modulators.
Homotropic When normal ligand and modulator are the same.
Heterotropic When normal and modulator are different.
Chaperone Collective term for two types of proteins that prevent misfolding of a target protein or actively facilitate its proper folding.
Cooperativity Property exhibited by some proteins with multiple ligand-binding sites whereby binding of one ligand molecule increases or decreases the binding affinity for successive ligand molecules.
Ligand Any molecule other than a substrate that binds tightly and specifically to a macromolecule.
Proteasome Large multifunctional protease complex in the cytosol that degrades intracellular proteins marked for destruction by attachment of multiple ubiquitin molecules.
Proteome The entire complement of proteins produced by a cell.
Ubiquitin 76 residue polypeptide that adds to lysine.
Step 1 Ubiquitination Activation of ubiquitin-activating enzyme.
Step 2 Ubiquitination Transfer of this molecule to a cysteine residue in ubiquitin-conjugating enzyme.
Step 3 Ubiquitination Formation of a peptide bond between the ubiquitin molecule bound to UCE and a lysine residue in the target protein, a reaction catalyzed by ubiquitin ligase.
Endoproteases Attack selected peptide bonds within a polypeptide chain.
Exopeptidases Remove residue from terminus sites.
Peptidases Split oligopeptides into di and tripeptides.
Cyclic AMP Activates protein kinase A by inducing conformational change.
Phosphorylation The addition of phosphate groups, which changes a protein's charge and induces conformational change.
Created by: WisemanLeo
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