TAMU BICH 411 - Final Exam Study Guide (6 pages)

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Final Exam Study Guide

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Final Exam Study Guide


Review of material that will be on the final exam.

Study Guide
Texas A&M University
Bich 411 - Comprehen Biochem Ii
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BICH 411 1st Edition Final Exam Study Guide Lectures 1 24 Study 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 waste Nitrogen 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 chloroplasts Nitrogen 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 ferrodoxins Amino 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 Lysine transamination 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 3 Alkaptonuria genetic defect in Phenylalanine degradation dark urine least severe of the 3 Phenylketonuria 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 metabolism Chapter 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 acid Purine nucleoside cycle deaminates AMP to IMP by AMP deaminase then resynthesizes AMP From 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 next reaction 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 Made from deoxyribonucleotides thymidylate synthase methylates dUMP to form dTMP reductive methylation know the atom sources for Purine and Pyrimidine Chapter 27 about 15 questions Anabolic pathways foods oxidized to carbon and water produce ATP and NADPH reductive with NADPH usually source of electrons

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