Biochemistry Flashcards
Oxidation reactions
gain of O atoms
loss of H atoms
loss of e-
Reduction reactions
loss of O atoms
gain of H atoms
gain of e-
Catabolism
breaking down molecules
e.g., extract energy from glucose - oxidative catabolism
Anabolism
building up molecules
generally reductive
Bronsted-Lowry Acid
proton (H+) donor
Bronsted-Lowry Base
proton (H+) acceptor
often OH- ions
any substance that can accept H+
any anion or neutral species w/ lone pair of e-
Lewis Acid
e- pair acceptor
Lewis Base
e- pair donor
Acidic AAs
aspartic acid (Asp) - D glutamic acid (Glu) - E
Basic AAs
lysine (Lys) - K
arginine (Arg) - R
histidine (His) - H
Hydrophobic/Nonpolar AAs
glycine (Gly) - G alanine (Ala) - A valine (Val) - V leucine (Leu) - L isoleucine (Ile) - I phenylalanine (Phe) - F tryptophan (Trp) - W *methionine (Met) - M *proline (Pro) - P
Polar AAs
serine (Ser) - S threonine (Thr) - T tyrosine (Tyr) - Y asparagine (Asn) - N glutamine (Gln) - Q cysteine (Cys) - C
Enzymes
Induced-fit model
substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme
Enzymes
Active site model
lock and key hypothesis
substrate and active site are perfectly complementary
Enzyme function
accelerate rate of reaction by stabilizing transition state
Enzyme active sites
highly specific in its substrate recognition, including stereospecificity
found in humans: L AAs and D sugars
enzymes that act on hydrophobic substrates have hydrophobic AAs in their active sites, while hydrophilic/polar substrates will have hydrophilic AAs in their active sites
small alterations in active site structure can drastically alter enzymatic activity
both temp and pH have role in enzymatic function
Proteases (protein-cleaving enzymes)
have active site with serine residue whose OH group can act as a nucleophile, attacking the carbonyl C of an AA residue in a polypeptide chain
e.g., trypsin, chymotrypsin, elastase
these enzymes usually have a recognition pocket near the active site - this is a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides
Cofactors
metal ions or small molecules (not themselves a protein) - required for activity in many enzymes
majority of vitamins in diet are precursors for cofactors
Coenzymes
when a cofactor is an organic molecule
often bind to the substrate during a catalyzed reaction
e.g., coenzyme A (CoA)
Regulation of Enzyme Activity
1: covalent modification - proteins can have several different groups covalently attached to them, and this can regulate their activity, lifespan in the cell, and/or cellular location.
e.g., addition of a phosphoryl group from ATP by a protein kinase to hydroxyl (OH) of serine, threonine, or tyrosine residues.
phosphorylation of different sites on an enzyme can activate or inactivate the enzyme. protein phosphorylases also phosphorylate proteins, but use free-floating inorganic phosphate (Pi) in the cell instead of ATP. protein phosphorylation can be reversed by protein phosphatases.
2: proteolytic cleavage - many enzymes (and other proteins) are synthesized in inactive forms (zymogens) that are activated by cleavage by a protease.
3: association with other polypeptides - some enzymes have catalytic activity in 1 polypeptide subunit that is regulated by association with a separate regulatory subunit.
e.g., some proteins demonstrate continuous rapid catalysis if their regulatory subunit is removed - constitutive activity (continuous/unregulated).
e.g., other proteins that require association with another peptide in order to function.
4: allosteric regulation - modification of active-site activity through interactions of molecules with other specific sites on the enzyme (allosteric sites)
Allosteric regulation
biochemical switch - turn if on/off
binding of allosteric regulator to allosteric site generally noncovalent and reversible
when bound can alter conformation of enzyme to increase or decrease catalysis
Feedback inhibition/Negative feedback
enzymes act as part of pathways - usually only around 2 key enzymes regulated, such as enzyme that catalyzes first irreversible step in pathway
e.g., A->B->C->D, if enough D can shut off enzyme early in pathway
Feedforward stimulation
stimulation of an enzyme by its substrate or by a molecule used in the synthesis of the substrate
e.g., A might stimulate E3 (enzyme later in pathway)
Reaction rate
V = velocity
amount of product formed per unit time, in moles per second (mol/s)
depends on:
- [S]
- [E]
if little S, rate V is directly proportional to amount of S added: double S and rxn rate doubles
if adding more S doesn’t increase V, enzyme is saturated - Vmax
Km = [S] at which rxn velocity if half its maximum (mark Vmax on y-axis, divide distance by 1/2 to find 1/2Vmax, Km found by drawing horizontal line to curve and vertical line down to x-axis)
low Km –> not much S required to get rxn rate to 1/2Vmax, so E has high affinity for S
