Chapter 22 – Biosynthesis of Amino Acids, Nucleotides, and Related Molecules22.1 Overview of Nitrogen MetabolismThe Nitrogen Cycle Maintains a Pool of Biologically Available Nitrogen- The most important source of nitrogen is airo Relatively few species can convert atmospheric nitrogen into a useful form- Nitrogen cycle – a vast set of processes that salvage and reuse biologically available nitrogeno Fixation – reduction of atmospheric nitrogen by nitrogen-fixing bacteria to yield ammoniao Nitrification - most ammonia that reaches the soil is oxidized to nitrateo Plants and bacteria reduce the nitrate and nitrite through nitrate and nitrite reductases, forming ammoniao Animals use plants as a source of amino acidso When organisms die, microbial degradation of their proteins returns ammonia to the soilo Denitrification – conversion of nitrate to N2 under anaerobic conditions by bacteria These bacteria use this process to generate ATP- Anammox – anaerobic ammonia oxidationo Converting ammonia and nitrite to N2Nitrogen Is Fixed by Enzymes of the Nitrogenase Complex- Only certain bacteria and archaea can fix atmospheric nitrogeno Cyanobacteria of soils and fresh and salt waterso Methanogenic archaea, strict anaerobes that obtain energy and carbon by converting H2 and CO2 to methaneo Other kinds of free-living soil bacteriao Symbionts in the root nodules of leguminous plants- The first important product of nitrogen fixation is ammonia, produced in an exergonic reaction- Nitrogen fixation has a really high activation energy due to the triple bond in N2o Overcome by the binding and hydrolysis of ATP- Nitrogenase complex – a highly conserved complex of proteins that carries out biological nitrogen fixationo Dinitrogenase reductase – a dimer of two identical subunits that contains a single 4Fe-4S redox center bound between the subunits and can be oxidized and reduced by one electron 2 binding sites for ATP/ADPo Dinitrogenase – a tetramer with two copies of two different subunits that contains iron and molybdenum Redox centers have 2 Mo, 32 Fe, and 30 S per tetramer P clusters- Nitrogen fixation is carried out by a highly reduced form of dinitrogenase andrequires eight electionso Six electrons to reduce N2o Two electrons to produce H2o Dinitrogenase is reduced by the transfer of electrons from dinitrogenase reductase one at a timeo Each turn of the cycle requires 2 ATPo Ferredoxin , reduced flavodoxin, and other sources reduce dinitrogenase reductase- Dinitrogenase reductase is inactivated in airo Some nitrogen-fixing bacteria live anaerobically or repress nitrogenase synthesis when in airo Some aerobic species uncouple electron transfer from ATP synthesiso Symbionts in root nodules of leguminous plants have both energy requirements and oxygen lability taken care of Leghemoglobin – an oxygen-binding heme protein that bathes bacteria in root nodules to protect them from oxygenAmmonia Is Incorporated into Biomolecules through Glutamate and Glutamine- Glutamate and glutamine provide the entry point for ammonia into amino acids and other nitrogen-containing biomoleculeso Glutamate is the source of amino groups for most other amino acidso Glutamine is the source of amino groups in a wide range of biosynthetic processes- The most important pathway for the assimilation of NH4+ into glutamate requires two reactionso Glutamine synthetase catalyzes the reaction of glutamate and NH4+ to yield glutamine Two stepso Glutamate synthetase – catalyzes a reaction that produces glutamate from glutamine in plants and bacteria- Glutamate can also be formed by reaction of -ketoglutarate and NH4+, catalyzed by L-glutamate dehydrogenaseo Uses NADPHo L-glutamate dehydrogenase is located in the mitochondrial matrix in eukaryotesGlutamine Synthetase Is a Primary Regulatory Point in Nitrogen Metabolism- Glutamine synthetase is regulated allosterically and by covalent modificationo Alanine, glycine, and at least six end products of glutamine metabolism are allosteric inhibitorso Covalent modification by adenylation (addition of AMP), which increases the sensitivity to allosteric inhibitors- Adenylyltransferase – promotes adenylylation and deadenylylationo Activity is modulated by binding to a regulatory protein called PII, which is regulated by covalent modification (uridylylation) Uridylylated PII stimulates deadenylylation Deuridylylatd PII stimulates adenylylation Uridylyltransferase – uridylylates and deuridylylates PII- Inhibited by binding of glutamine and Pi to uridylyltransferase- Stimulated by binding of -ketoglutarate and ATP to PIIo PII also regulates the activation of transcription of the gene encoding glutamine synthetase Deuridylylated PII decreases transcription- When glutamine levels are high, glutamine synthetase activity decreases- When glutamine levels are low and -ketoglutarate and ATP are available, glutamine synthesis increases- Multiple layers of regulation increase sensitivitySeveral Classes of Reactions Play Special Roles in the Biosynthesis of Amino Acids and Nucleotides- Chemical rearrangements:o Transamination reactions and other rearrangements promoted by enzymes containing pyridoxal phosphateo Transfer of one-carbon groups, with either tetrahydrofolate or S-adenosylmethionine as cofactoro Transfer of amino groups derived from the amide nitrogen of glutamine- Glutamine amidotransferases – the enzymes catalyzing amino group transferso All have two structural domains: One binding glutamine One binding the second substrate, which serves as amino group acceptor22.2 Biosynthesis of Amino Acids- Nonessential amino acids – amino acids that are not needed in the diet- Essential amino acids – amino acids that must be obtained from food- 5-phosphoribosyl-1-pyrophosphate (PRPP) – an intermediate in several pathways of amino acid and nucleotide synthesiso Synthesized from ribose 5-posphate Catalyzed by ribose phosphate pyrophosphokinase-Ketoglutarate Gives Rise to Glutamate, Glutamine, Proline, and Arginine- Proline – a cyclized derivative of glutamate- Arginine – synthesized from glutamate via ornithine and the urea cycle in animals- Arginase converts arginine to ornithine and urea and the ornithine is converted to glutamate -semialdehyde by ornithine -aminotransferase Serine, Glycine, and Cysteine Are Derived from 3-Phosphoglycerate-
View Full Document
Unlocking...