BICH 411 1st EditionFinal Exam Study Guide Lectures: 1 - 24Study Old Test Questions for lectures 1-18! She will reuse them for the old material on the exam (chapters 18-24, about 25 questions)Chapter 25-about 20 questions-Definitions:-Nitrogen cycle – nitrogen movement between the soil and the atmosphere, including:-nitrogen assimilation: Nitrate (NO3-) being reduced to ammonium (NH4+)-about 99% of the nitrogen cycle – 2-step metabolic pathway-nitrogen fixation: forming NH4+ from N2 gas-once ammonium is formed, it’s used in organic molecules or goes through the Urea cycle to be excreted as wasteNitrogen assimilation – nitratenitriteammonium-takes 8 electrons total! (2 for nitrate reductase, 6 for nitrite reductase)-involves thiol (-SH group) of enzyme, FAD, cytochrome b, and MoCofactor-Nitrate reductase reduces the nitrate to nitrite (using 2 electrons)electrons are from NADH -in the cytosol-Nitrite reductase reduces nitrite to ammonium (using 6 electrons)electrons are from reduced ferrodoxins (via 4Fe-4S and siroheme)-in the chloroplastsNitrogen Fixation – Nitrogen gasammonium-only in certain prokaryotes-requires:-reduced ferrodoxin (for a reductant)-ATP-Anaerobic conditions-Nitrogenase complex (4 ATP required per electron pair – 16 ATP total for each N2)**reducing nitrogen is so expensive due to the VERY high activation energy (from the triple bond)**Ammonium has 3 possible fates:-Carbamoyl-Phosphate Synthase I (CPS I) – transformed to carbamoyl-P-Glutamate Dehydrogenase – ammonium reduces alpha-ketoglutarate to form glutamate-Glutamine synthetase - ammonium is used to amidate glutamate to form glutamine-has feedback inhibitors: Gly, Ala, Ser, His, Trp, CTP, AMP, carbamoyl-P, glucosamine-6-phosphate-adenylation inactivates this enzyme!Carbamoyl-Phosphate Synthetase I (CPS I)NH4+ + HCO3- + 2 ATP  H2N-COO-PO32- + 2 ADP + Pi + 2 H+ **this is a good reaction to know**-early part of Urea Cycle-requires 2 ATP!  one activates bicarbonate and the other phosphorylates carbamate**This is the committed step of the Urea Cycle!2 pathways for Ammonium Assimilation to lead to Glutamine Synthesis-the main way uses glutamate dehydrogenase and glutamine synthetase-occurs in organisms with plenty of nitrogen (high ammonium)-uses 1 NADPH, 2 NH4+, and 1 ATP per alpha-ketoglutarate-For Nitrogen-deficient environments:-Glutamate synthase (aka glutamate:oxo-glutarate amino transferase (GOGAT))-regenerates glutamate -for each alpha-ketoglutarate, uses 2 NH4+, 2 ATP, and 1 NADPH-reductant + alpha-ketoglutarate + glutamine 2 glutamate + oxidized reductant-Reductant can be NADH, NADPH, or reduced ferrodoxinsAmino acid Families (grouped by metabolic intermediate precursors)-alpha-ketoglutarate family:-glutamate-glutamine-proline-arginine-lysine-oxaloacetate family-aspartate-methionine-threonine-isoleucine-lysine-pyruvate family-alanine-valine-leucine-3-phosphoglycerate family-serine-glycine-cysteine-phosphoenolpyruvate and erythrose-4-P family the aromatic amino acids-phenylalanine-tyrosine-tryptophan**histidine comes from PRPP and ATP-the purely ketogenic amino acids are: Leucine and Lysinetransamination – transfers alpha-amino group from an amino acid to an alpha-keto acid-glutamate-dependent-requires pyridoxal phosphate (PLP)***Urea Cycle (don’t need to know enzymes)-breaks down Arginine (derived mostly from alpha-ketoglutarate) to release 2 nitrogens and 1 carbon as Urea the 2 nitrogens and 1 carbon in Urea come from the Guanidino group of Arginine**produces fumarate which goes to the TCA cycle**  anapleurotic benefit-regulation occurs at the committed step CPS I-N-acetylglutamate is the allosteric activator-Farmers target plant enzymes that synthesize essential amino acids – they inhibit weed growth,but don’t affect animals or people since we can’t synthesize these amino acids (we don’t have these enzymes)Maple Syrup Urine Disease – defect in metabolism of branched amino acids – build up of Ketoacids (concentrated in urine and ear wax)-urine smells like maple syrup-now tested for on newborns**the worst of the 3Alkaptonuria – genetic defect in Phenylalanine degradation-dark urine*least severe of the 3Phenylketonuria – genetic defect in Phenylalanine degradation-can suffer mental retardation of consume Phe during development-not much of a problem when older-Glutamate is the most central amino acid for metabolismChapter 26 -about 15 questions-the longest stage is the DNA synthesis stage, so nucleic acids are a target for anticancer and antibacterial agents**remember nucleotides are used for energy too (CTP, UDP priming)-THF is used two different ways-purine synthesis: donates C2 and C8 (one carbon units)(carry one carbon units except CO2 – biotin carries CO2)-purines and pyrimidines are made from precursor – look at biosynthesis-purine precursor is IMP, formed from ribobose-5-P-pyrimidine precursors are carbamoyl-P and aspartate**review the intermediates and enzymes**-purine synthesis requires 6 ATP equivalents-GTP is the energy for AMP synthesis-ATP is the energy for GMP synthesis-bases can be salvaged and put onto a new ribose -purine salvage involves HGPRT enzyme (a purine phosphoribosyltransferase)-energetically advantageous-Lesch-Nyhan syndrome involves a HGPRT deficiency (x-linked so in males)-experience buildup of uric acid  arthritis, retardation-Purine catabolism produces Uric Acid – normally animals oxidize it to urea, allantoic acid or ammonia-Dalmatians excrete uric acidPurine nucleoside cycle – deaminates AMP to IMP by AMP deaminase, then resynthesizes AMPFrom IMP-converts aspartate to fumarate in the process anapleurotic!-Fumarate replenishes the citric acid intermediates lost in side reactions(skeletal muscle lacks the usual anapleurotic enzymes, relies on AMP deaminase for this)Carbamoyl-Phosphate Synthetase II  in the cytosol(CPS I was in the mitochondria)-forms carbamoyl-phosphate for pyrimidine synthesis -uses HCO3-, glutamine, and 2 ATP-gets its nitrogen from Glutamine!!-Metabolic Channeling  transferring metabolites between different enzyme sites on a -polypeptide-advantageous** - the product for the first reaction is the substrate for the nextreaction  more efficient!-ribonucleotide reductase  gets electrons from NADPH, thioredoxin reductase moves electrons to thioredoxin-thioredoxin provides reducing power for ribonucleotide reductase-Why is thymine special? 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