TERMS YOU WANT TO KNOW for METABOLIC BIOCHEMISTRY Lecture 1 Proteins and Enzymes "metabolome" functional group metabolic pathway catabolism anabolism L-amino acid peptide bond C-terminus, N-terminus alpha helix beta sheet 1,2,3, 4 structure cofactor prosthetic group enzyme active site reaction coordinate diagram activation energy: ΔG "double dagger" transition state catalytic mechanisms entropy reduction acid-base catalysis metal ion catalysis covalent intermediate substrate product

Lecture 2 Enzymes II ligand Kd isotherm rectangular hyperbola enzyme-substrate complex saturable Michaelis-Menton equation Vmax Km kcat

turnover number Lineweaver-Burk plot inhibitor competitive inhibitor uncompetitive inhibitor catatlytic triad induced fit cooperativity allosteric enzyme sigmoidal isotherm allosteric inhibitor allosteric activator phosphorylation modification

Lecture 3 Bioenergetics heterotropic regulation homotropic regulation autotroph heterotroph Gibbs free energy enthalpy, DH entropy, DS delta G'o delta G' delta G Keq spontaneous ATP AMP leaving group

Lecture 4 Bioenergetics II committed step rate-limiting step flux redox reaction half-cell reaction E, 1/2 cell potential e donor

e acceptor NAD/NADH NADP/NADPH niacin FMN FAD riboflavin

Lecture 5 Glucose and Glycolysis preparatory phase payoff phase substrate level phosphorylation keto-enol form mutase isomerase kinase

Lecture 6 Glucose and Glycolysis II ethanol fermentation thiamine pyrophosphate (TPP) pyruvate decarboxylase alchohol dehydrogenase glycogen glycogen phosphorylase phosphoglycomutase fructose 2,6 bisphosphate pentose phosphate pathway NADPH ribose-5-P

Lecture 7 Krebs Cycle I TCA cycle Krebs cycle acetyl group CoA, CoA-SH, HS-CoA thioester bond iron sulfur cluster NAD/NADH FAD/FADH2

pyruvate dehydrogenase complex TPP cofactor lipoic acid cofactor FAD cofactor

Lecture 8 Krebs Cycle II prochiral amphibolic anapleurotic reactions pyruvate decarboxylase biotin glyoxylate cycle glyoxosome mitochondrion outer membrane porin inner membrane matrix

Lecture 9 Lipid Catabolism triglycerides diglycerides monoglycerides phopholipids fatty acids monounsaturated polyunsaturated chylomicrons lipoproteins apolipoproteins carnitine acyl-CoA beta-oxidation peroxisome ketone body HMG-CoA ketosis lipase

Lecture 10 Mitochondria and Respiration chemiosmotic hypothesis oxidative phosphorylation e- transport chain cofactors/carriers nucleotide-linked nicotinamide cofactors FAD/FMN cofactors ubiquinone semiquinone ubiquinol cytochromes heme iron-sulfer centers complexes 1-IV NADH dehydrogenase succinate dehydrogenase ubiquinone:cytochrome c oxidoreductase cytochrome oxidase proton gradient proton-motive force

Lecture 11 ETC and ATP synthesis proton gradient proton-motive force ΔpH Δ Ψ ATP synthase F1 subunit alpha, beta subunits gamma "cam" shaft Fo membrane region uncoupling agents O2 consumption ATP production brown adipose thermogenin coupling acceptor control flagellar motor

Lecture 12 Glucose Anabolism and Regulation gluconeogenesis bypass reaction coordinate regulation pyruvate carboxylase PEP-CK coordinate regulation gluconeogenic amino acids fructose 2,6 bisphosphate PFK2/FBP2 Glucagon Lecture 13 Lipid Anabolism acetyl CoA carboxylase fatty acid synthase E coli mammal ACP malic enzyme citrate lysase elongation desaturation cyclooxygenase (COX) arachidonic acid prostaglandins leukotrienes thromboxanes head group diacylglycerol CTP/CDP isoprene isoprenoid mevalonate mevalonate pathway squalene cholesterol HMG-CoA reductase

Lecture 14 Integrating Metabolism 101 glycogen glycogenin reducing end non-reducing end α1→4 bond α1→6 bond branch glycogen synthase branching enzyme glycogen phosphorylase debranching enzyme UDP-glucose glucagon insulin phosphorylation dephosphorylation Cori cycle Lecture 15 Amino Acids transamination pyridoxal phosphate (Vit B6) cognate amino acid/α keto acids a-ketoglutarate/glutamate glutamate/glutamine pyruvate/aspartate glutamate dehydrogenase glutamine synthetase urea urea cycle carbamoyl phosphate essential amino acids phenylketourea (PKU) ketogenic amino acids glucogenic amino acids N2 fixation nitrogenase legumes leghemoglobin glutamine synthetase

glutamine amidotransferase adenylylation uridylylation Lecture 16 Nucleotides PRPP purine pyrimidine nucleotide nucleoside glutamine PRPP amidotransferase PRPP synthetase aspartate transcarbamolyase inosine orotate de novo synthesis salvage pathway ribonucleotide reductase Lesch-Nayhan disease gout xanthine oxidase allopurinol thymidylate synthetase dihydrofolate reductase (DHFR) methotrexate Lecture 17 Cancer and Aging adipocyte hypoxia HIF-1alpha vascularization angiogenic factor proline hydroxylase apoptosis cytochrome c citrate lyase (also mentioned in lipid anabolism lecture) caloric restriction (CR) monkey C58

oxidative stress hypothesis ROS superoxide anion progeria daf2 daf 16 EAT genes (in C. elegans) SIR2 NAD-dependent protein deacetylase resveratrol STACs Lecture 18 Exercise adipocyte phosphocreatine creatine creatine kinase phosphocreatine, or creatinephosphate (CP) phosphagen system (Cori cycle (also mentioned in other lectures)) glucose-6-phosphatase respiratory exchange ratio (RER) FFA (free fatty acids) muscle fiber types I, IIa, IIb nuclear hormone receptors PPARdelta Lecture 19 Obesity and Diabetes glucagon pancreatic alpha-cell insulin pancreatic beta-cell diabetes type 1 type 2 glucokinase (liver-specific hexokinase) BMI ob/ob mouse

db/db mouse leptin leptin receptor PYY gherlin CB1 cannabinoid receptor rimonabant (Acomplia) nile red Pima Native Americans "thrifty gene" gastric bypass NEAT