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
Cooperativity
type of allosteric interaction - 1 active site acts like allosteric regulatory site for other active sites
positive and negative
positive: binding of S to 1 subunit increases the affinity of other subunits for S (tense to relaxed)
sigmoidal curve results from positive cooperative binding:
- at low [S], E complex has low affinity for S, adding more S increses rate a little
- steep at [S]s where adding S greatly increases rxn rate, E complex in relaxed state
- levelling off where E saturated
cooperative enzymes must have more than 1 active site, usually multisubunit complexes, may be single-subunit enzyme
cooperativity not just applied to catalytic enzymes: hemoglobin (Hb) is protein complex of 4 polypeptide subunits, each contain heme prosthetic group w/ single O2 binding site, Hb is carrier (of O), not catalyst of reaction (not enzyme), exhibits positive cooperative O2 binding. Hb-O2 dissociation curve is sigmoidal.
Competitive inhibition
compete with S for binding at active site
inhibition can be overcome by adding more S –> if [S] high enough, can outcompete inhibitor
Vmax not affected (can get same Vmax but takes more S)
Km increased
Noncompetitive inhibition
bind at allosteric site, not active site
no matter how much S added, inhibitor not displaced from its site - Vmax decreases
Km same - S can still bind active site, but inhibitor prevents catalytic activity of E
Uncompetitive inhibition
only able to bind to E-S complex (cannot bind before the S has bound)
binds allosteric sites - Vmax decreases (by limiting amount of available E-S complex which can be converted to product)
by sequestering E bound to S, this increases apparent affinity of E for S as it cannot readily dissociate - Km decreases
Mixed-type inhibition
inhibitor can bind to either unoccupied E OR E-S complex
if E has greater affinity for inhibitor in free form, E will have lower affinity for S (similar to competitive inhibition) - Km increases
if E-S complex has greater affinity for inhibitor, E will have greater affinity for S (similar to uncompetitive inhibition) - Km decreases
if equal affinity = uncompetitive inhibitor
in each, inhibitor binds to allosteric site and additional S cannot overcome inhibition - Vmax decreases
Inhibition summary
Competitive:
Vmax same, Km inc
Noncompetitive:
Vmax dec, Km same
Uncompetitive:
Vmax dec, Km dec
Mixed:
Vmax dec, Km varies
Lineweaver-Burk plot
x-axis = 1/[S] y-axis = 1/V
slope = Km/Vmax y-int = 1/Vmax x-int = -1/Km
inc in [S] = dec in 1/[S] - dec in value on x-axis
inc in rxn rate (V) = dec in 1/V - as V inc, value on y-axis dec
Inhibitors and L-B plot
Competitive:
y-int same, x-int dec (b/c Km inc)
Noncompetitive:
y-int inc (Vmax decreases so slope inc), x-int same
Uncompetitive:
y-int inc, x-int inc
Cellular respiration
glucose oxidized to produce CO2 and ATP - 4 step process
2,3 - require O in cell, but neither use O directly
1: glycolysis - glucose partially oxidized while its split in half into 2 identical pyruvate molecules (pyruvic acid), produces small amount ATP and NADH
- occurs in cytoplasm
- O not required
2: pyruvate dehydrogenase complex (PDC) - pyruvate produced in glycolysis is dearboxylated to form acetyl group, acteyl group then attached to coenzyme A (carrier that can transfer acetyl group into Krebs cycle), small amount NADH produced
3: Krebs cycle (tricarboxylic acid cycle [TCA cycle] or citric acid cycle) - acetyl group from the PDC is added to oxaloacetate to form citric acid. citric acid decarboxylated and isomerized to regenerate original oxaloacetate. modest amount of ATP, large amount of NADPH, and small amount FADH2 produced.
4: e- transport/oxidative phosphorylation - high-energy e- carried by NADH and FADH2 are oxidized by the ETC in inner mito membrane. the reduced e- carriers dump e- at beginning of chain, and O is reduced to H2O at end. e- energy libertated by the ETC is used to pump protons out of innermost compartment of mito. H+ allowed to flow back into mito, and energy of this proton flow used to produce the high-energy triphophate group in ATP.
- oxidative –> refers to use of O to oxidize the reduced e- carriers NADH and FADH2)
Glycolysis
universal 1st step in glucose metabolism, all cells from all domains possess enzymes in this pathway
2 net ATP produced
PDC
2 3C pyruvates oxidized to 2 2C
pyruvate –> acetyl-CoA
2NADH produced
1 CO2 released (oxidized)
Krebs cycle
2C from acetyl-CoA + oxaloacetate = citrate (6C)
2 CO2 released
NADH, FADH2 produced
oxaloacetate regenerated
ETC
oxidation of the high-energy e- carriers NADH and FADH2 coupled to the phophorylation of ADP to produce ATP
5 e- carriers
proton gradient used to drive phosphorylation of ADP to ATP
Gluconeogenesis
when dietary sources of glucose are unavailable and when liver had depleted its stores of glycogen and glucose
occurs primarily in liver (and a bit in kidneys)
converts non-carb precursor moleculess into intermediates where they eventually become glucose
glycolysis-in-reverse
requires 4 ATP, 2 GTP, 2 NADH
made thermodynamically stable by coupling rxns to the hydrolysis of high-energy phosphate bonds of GTP and ATP
Pentose Phosphate Pathway
G6PDH = primary point of regulation
6-phosphogluconate –> ribulose-5-P
2x NADPH generated
FA Metabolism
FA oxidation
free FAs can undergo B-oxidation
begins at outer mito membrane with activation of the FA
rxn catalyzed by acyl-CoA sythetase
requires 2 ATP to generate fatty acyl-CoA, then transported into mito, undergoes 4 rxns to liberate acetyl-CoA, also produce FADH2 and NADH
acetyl-CoA can go to Krebs cycle
unsat FA: less energy produced, skip step of generating FADH2 (b/c don’t need to create double bond)
