Biochemistry Flashcards
Amphoteric
a molecule can act as an acid or base because it can either accept or donate a proton
Zwitter ion
a overall neutral molecule, but has positive and negative groups . They are called dipolar ions
Isoelectric point (pI)
The pH at which the molecule is electrically neutral
pI = (pKa(amino) + pKa(carboxy)) / 2
pI (acidic AA) = (pKa(carboxyl)+pKa(side chain)) / 2
pI (basic AA) = (pKa(amino)+pKa(side chain)) / 2
Peptide
Composed of amino acid subunits (residues). There can be dipeptides, tripeptides, oligopeptides (up to 20), or polypeptides.
Peptide bonds
Links residues between the -COO of 1 AA and the N of another AA. It is hard to denature them with heat, unlike secondary, tertiary, and quaternary structure. Their formation is a condensation or dehydration reaction because its results in the removal of a water molecule
Chymotrypsin
Hydrolytic enzyme that cleaves peptide bonds next to large hydrophobic amino acids
Antiparallel
When strands are running in opposite directions. It is more stable
Common beta turns
Proline and Glycine, in position 2 and 3
Tertiary structure
Overall spatial arrangement of atoms in a polypeptide chain or in a protein, the arrangement of secondary structure. Makes up the active site! Ex/ disulfide bridges
Solvation layer
Formed when solvent molecules form around a solute when a solute dissolves in the solvent. If hydrophobic side chains are placed in aqueous solution, water molecules can not interact with the side chain and are forced to arrange themselves in organized fashion to maximize H bonds. This decreases entropy (non-spontaneous process)
Quarternary structure
Aggregate of subunits (smaller globular proteins). Ex/ hemoglobin and immunoglobulin
Conjugated proteins
Proteins with covalently attached prosthetic groups
Ex/ carbohydrate, nucleic acid, lipid, vitamins, metal ions
Lipoproteins
lipid prosthetic groups
Glycoproteins
carbohydrate prosthetic groups
Nucleoproteins
nucleic acid prosthetic groups
Association rule
Groups of similar polarity tend to group together. This interaction between side chains is what influences the tertiary structure of a protein
Competitive inhibition
Inhibitors that bind the active site and prevent substrate access. Increase Km (cause the [S] to be higher in order to reach Km) and do no effect Vmax. Can only be overcome with the addition of more [S]
Noncompetitive inhibition
Allosteric inhibitors that induce a conformation change in the enzyme when binding. Do not alter Km (any copies of the enzyme that are active maintain the same affinity) and decrease Vmax (less [E] available to react). Adding more [S] has no effect. Only adding more [E] overcomes the inhibitor
Mixed inhibition
Allosteric inhibitors that can either increase Km if bound to free enzyme or decrease Km if bound to the ES complex, depending on the affinity for each. They decrease Vmax. They cause less [E] to be available to react
Uncompetitive inhibition
Allosteric inhibitors that decrease the Km and decrease Vmax. They lock the ES complex and dont allow the formation of P
Irreversible inhibition
When the active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered
Zymogens
Enzymes that are secreted in inactive forms
Binding proteins
They have the ability to transport substances that are otherwise insoluble. They can regulate gene transciption but do not have enzymatic activity @ active site
Enzyme
Lower activation energy, increase reaction rate, do not alter Keq, are not consumed in the reaction, are pH and temperature sensitive, and do not effect ΔG