Biochemistry Final Study Guide with Figures
Biochemistry Final Study Guide with Figures BIO 311
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This 29 page Bundle was uploaded by Brianna Lisi on Thursday February 11, 2016. The Bundle belongs to BIO 311 at Drexel University taught by Professor Louden in Winter 2016. Since its upload, it has received 45 views. For similar materials see Biochemistry in Biology at Drexel University.
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Date Created: 02/11/16
Gluconeogenesis: The synthesis of glucose from noncarbohydrate precursors Glucose stores are depleted during periods of starvation or fasting beyond a day Brain relies on glucose as source of energy, glucose must be synthesized from molecules other than carbohydrates Reverse of glycolysis o Pyruvate Glucose + 2 Pyruvate + 2NADH + 4ATP + 2 GTP + 6 H O + 2H2 glucose + 2NAD + 4ADP + 2 GDP + 6P DP i It takes 6 nucleotide triphosphate molecules to synthesis glucose, only 2 are generated from glycolysis: takes 4 EXTRA molecules to drive unfavorable gluconeogenesis Any molecule that can be converted to pyruvate is considered glucogenic o Lactate and Glycerol are glucogenic o The enzymes of glycolysis: Hexokinase, Phosphofructokinase, Pyruvate kinase o The enzymes of gluconeogenesis: o Pyruvate carboxylase (ATP), phosphoenolpyruvate (PEP) carboxykinase, Fructose 1,6 bisphosphatase, Glucose 6 phosphatase o Pyruvate carboxylase: metabolically irreversible, uses biotin as a cofactor, allosterically activated by acetylCoA, anaplerotic for the TCA cycle (replemishes OAA), takes place in mitochondria o Phosphoenolpyruvate carboxykinase: (PEPCK) Synthesis of PEPCK increases in fasting Takes place in cytosol Pyruvate is carboxylated in the mitochondria by pyruvate carboxylase Oxaloacetate cant pass out of the mitochondria ( no transporter exists), so it is converted to malate which is then converted to OAA in cytosol o Oxaloacetate (OAA) decarboxylated and phosphorylated in the cytosol by phosphoenolpyruvate carboxykinase (PEPCK) o Fructose 1,6 bisphosphatase (F1,6BPase): o Metabolically irreversible reaction o F1,6BPase is allosterically inhibited by AMP and fructose 2,6-bisphosphate (F2,6BP) o Glucose 6- Phosphatase: o Irreversible hydrolysis reaction o Glucose 6- phosphatase found only in liver and kidney (pancreas and small intestine) o Only those tissues can serve as source of glucose from gluconeogenesis o Glucose 6 Phosphate o Precursor for Glycogen synthesis Glucose synthesis o Starting point for the Pentose Phosphate Pathway o Glucose 6 phosphatase is present only in tissues responsible for maintaining blood glucose levels, liver and kidney o In liver, glucose 6 phosphatase is highly regulated REGULATION OF GLUCONEOGENESIS/GLYCOLYSIS Flux through a pathway is controlled at rate limiting steps Flux through the rate determining steps may be altered by several mechanisms: o Allosteric control, covalent modifications, substrate cycles (futile cycles) and genetic control (enzyme concentrations) Glycolysis and gluconeogenesis are reciprocally regulated in the liver This prevents both pathways form operating at the same time high AMP indicates that the energy charge is low and signals the need for ATP High ATP and citrate indicate the energy charge is high and intermediates are abundant Glucagon stimulates gluconeogenesis Insulin stimulates glycolysis Substrate (“futile”) cycles and Reciprocal regulation of glycolysis and gluconeogenesis in the liver: PFK-2, FBPase-2 Glucagon: through the activation of PKA, phosphorylate FBPase2 and PFK2 o Activate FBPase2, inactivate PFK2: favor dephosphorylation of fructose 2,6 phosphate to fructose 6-P , favor gluconeogenesis The Cori Cycle: Interaction of glycolysis and gluconeogenesis Lactate from peripheral tissues (muscles) goes to liver and is made into glucose The glucose can go back to the peripheral tissues Liver uses lipid for energy Placement of the liver in the circulation : First pass at removing nutrients absorbed from the intestine Can make nutrients available to other major tissues The liver participates in interconnections of all types of metabolic fuels o Carbs, amino acids, fatty acids The liver regulates distribution of dietary fuels and supplies fuel from its own reserves PENTOSE PHOSPHATE PATHWAY (HEXOSE PHOSPHATE SHUNT) Overview 2 stages : oxidative stage and non-oxidative stage o Important products are as follows: Production of NADPH – the pyridine nucleotide used for reductive biosynthesis Fatty acids, cholesterol, nucleic acids NADPH also important in elimination of oxygen radicals Formation of ribose 5- phosphate for ribonucleotides RNA, DNA, coenzymes Mammary glands, liver, adrenal glands, adipose Not in brain and muscle Enzymes of pathway are cytosolic Oxidative Stage: Produces a 5 carbon sugar phosphate, ribulose 5- phoaphate with production of NADPH (with redox reactions) NADPH produced by Glucose 6-phosphatase st dehydrogenase in 1 step of oxidative stage ANDrdy 6- phosphogluconate dehydrogenase in 3 step of oxidative stage Releases 3 molecules of CO2 Non-oxidative Stage: Produces glyceraldehyde 3- phosphate and fructose 6-phosphate Oxidative Phase: Production of 2 NADPH and ribulose 5-phosphate from glucose 6-phosphate Functional roles of NADPH F -Fatty acid synthesis: liver, adipose, mammary -Cholesterol synthesis: liver -Steroid hormone synthesis: adrenal, ovaries, testes -Detoxification:liver Reduced glutathione as an antioxidant: RBC -Generation of superoxide radicals (neutrophils): microbial activity Role of NADPH in RBC: Oxygen species cause cellular damage - production of superoxide (Hb-Fe2+-O2HbFe3+ +O2- - O2+ 2H2O 2H2O2 both O2 and H2O2 can produce reactive free radical species, damage cell membranes, and cause hemolysis Non-oxidative phase: Disposes excess pentose phosphates by converting to glycolytic intermediates Series of C-C bond cleavage and formation reactions o Ribulose 5-P Ribose 5-P or Xylulose 5-P o 2Xylulose 5-P + Ribose 5-P 2 Fructose 6-P +GAP Trans-ketolase and trans-aldolase have broad substrate specificities o They catalyze the exchange of 2 or 3 carbon fragments between sugar phosphates o For both enzymes, one substrate is an aldose, one substrate is a ketose Denitrification of Superoxide Anion and Hydrogen Perioxide : Antioxidant enzymes: o Superoxide dismutase o Glutatione peroxidase o Glutatione reductase Detoxify reactive oxygen species, generate reducing power, feed into PPP LECTURE 10: AMINO ACID METABOLISM: Nitrogen Fixation: Fixation of atmospheric N2 Performed only by certain prokaryotes o Certain free living soil bacteria o Symbiotic bacteria that live in root nodules in plants Enzymatic process (nitrogenase complex ), highly conserved N 2 10H + + 8e + 16ATP à 2NH 4 + 16ADP + H 2 o 1e/2ATP per cycle o 2ATP binding shifts reduction potential o Fe-S clusters o Iron o Molybdenum o 8 electrons (6 for N2, 2 for H2) o Electrons are transferred from pyruvate to dinitrogenase via ferredoxin and dinitrogenase reductase o Dinitrogenase reductase reduces dinitrogenase one electron at a time with 6 electrons to fix N2 and 2 electrons to reduce H2 8 total needed Oxygen toxicity to bacterial nitrogenase: plant derived leghemoglobin Glutamine Synthetase: o Catalyzes assimilation of NH4 into glutamate to yield glutamine o Subunit structure of glutamine synthetase (12 identical subunits) o Primary regulatory point in nitrogen metabolism. Regulation occurs in at least 2 ways: 1) Allosteric regulation: Ala, Gly, etc are allosteric inhibitors of enzyme. All 8 molecules needed to effectively block enzyme activity. Adjusts glutamine levels according to immediate metabolism requirements 2) Covalent modification: adenylation of enzyme tyrosine residue adenylation, covalent, inhibitory by Adenylyltransferase (AT) Covalent modification: adenylylation and deadelylylation are promoted by adenylyltransferase o responds to levels of glutamine, a-ketoglutarate, ATP, Pi a-ketoglutarate and ATP stimulate uridylylation Glutamine and Pi inhibit uridylylation anelylyltransferase activity is modulaatedf by bingding to regulatory protein PII o PII is regulated by covalent modification (uridylylation) at tyrosine residue Adenylyltrasferase with uridylated PII (PII-UMP) stimulates deadenylylation of glutamine synthetase ( activating it ) Adenylyltrasferase with deuridylated PII stimulates adenylylation of glutamine synthetase ( deactivates it ) o Uridylylation/deurylylation of PII stimulated by uridylyl- transferase OVERVIEW OF AMINO ACID BIOSYNTHESIS: Amino acid carbon skeletons are derived form 3 general sources: o Glycolysis, TCA cycle, Pentose phosphate pathway Precursor: a Keotglutarate Makes glutamate glutamine, proline, arginine biosynthesis for proline and arginine o major source of arginine produced in urea cycle in mammals o Ornithine L-CitrullineArgininosuccinate Arginine Precursor: 3-Phosphoglycerate Makes serine glycine, cysteine Biosynthesis of cysteine from serine in bacteria and plants o Origin of sulfur used for Cysteine synthesis o Adenosine 5’-phsphosulfate (APS) o 3’ Phosphoadenosine 5’phosphosulfate (PAPS) APS and PAPS are the sulfur sources Biosynthesis of cysteine from homocystein (intermediate- orig. derived from methionine) and serine in mammals o Homocysteine+serine cysteine Precursor: Oxaloacetate Makes aspartate asparagine, methionine, lysine, threonine Aspartate to lysine ( 10 steps ): common intermediate (in Lys, Met, Thr) is aspartate B-semialdehyde Precursor: Pyruvate Makes isoleucine, valine, leucine Precursor: Phsphoenolpyruvate and Erythrose 4-phosphate Makes phenylalanine, tyrosine, tryptophan o Chorismate: intermediate in aromatic amino acid biosynthesis in bacteria, fungi, and plants- derived carbon from PEP and carbon from erythrose 4-P Biosynthesis of Tryptophan from chorismate in bacteria and plants intermediate= 5 phosphoribosyl-1-pyrophosphate (PRPP) Biosynthesis of Phenylalanine and Tyrosine from chorismate in bacteria and plants intermediate = prephenate Animals can produce Tyrosine directly from Phenylalanine via hydroxylation Precursor: Ribose 5 Phosphate o Makes histidine Biosynthesis of histidine in bacteria and plants derived from PRPP, ATP, glutamine, and glutamate Sequential Feedback Inhibition: Coordinated regulatory mechanisms in E.coli (asparatate as precursor) Isoenzymes are allosterically regulated MAJOR POINT: this type of regulation prevents one end product from shutting down key steps in a pathway when other products are required Molecules Derived from Amino Acids: many examples (hormones, coenzymes, nucleotides, antibiotics) o d-Aminolevulinate Mammals: glycine precursor Bacteria & plants: glutamate precursor Heme synthesis from d-aminolevulinate Porphyrias: Most affected people are heterozygotes (usually asymptomatic) “acute intermittent porphyria”: build up of d-aminolevulinate and porphobilinogen can result in abdominal pain and neurological dysfunction many porphyrias ( homozygous state) can cause anemia due to insufficient heme synthesis o treatment: diet, IV administration of heme/derivatives Creatine: In humans, typically half of stored creatine originates from food ( mainly from meat and fish) Endogenous synthesis of creatine in the liver is sufficient for normal activities Made from arginine and glycine Hydrolysis of phosphocreatine important source of metabolic energy Glutathione: Leads to reducing intracellular environment Glutamate, cysteine, & glycine are precursors Few disulfide bonds in intracellular proteins vs many in extracellular (antibodies, growth hormone, etc) Important in keeping SH groups (cysteines) and Fe2+ (ferrous) Amino acid decarboxylation leads to amines, often highly bioactive (e.g. neurotransmitters, vasodilation) Treatment of ulcers; inhibits secretion of gastric acid: Tagamet/cimetidine histamine receptor antagonist -Polyamines, DNA packaging ( like histones ) come from ornithine and methionine Biosynthesis of nitric oxide o Gaseous biological messenger o Works by diffusion through cell membrane o Arginine is the precursor o Diffusion at short distance.. neurotransmission, blood clotting, pressure control DEGRADATION OF PROTEINS AND AMINO ACIDS: CHAPTER 18 Overview of amino acid catabolism in mammals Fates of amino group and carbon skeleton take separate but interconnected paths What happens to amino acids once cleaved from larger proteins? Fate of amino group nitrogen of AA: o Removed from AA by aminotransferases to yield ammonia (nitrogen not used in energy-producing pathway) Aminotransferases In many aminotransferase reactions, a- ketoglutarate is the amino group acceptor All amino transferases have pyridoxal phosphate (PLP) as a cofactor Fate of rest of carbon skeleton of AA: o Enter metabolic pathways as precursors of glucose or Krebs cycle intermediates Fates of ammonium ions o Some used in synthesis of nitrogen compounds (amino acids, nucleotides) o Excess ammonium ions converted into ammonia, urea, or uric acid (depends on organism) and then excreted Metabolic Fates of Amino Groups: We derive a small amount of oxidative energy from catabolism of amino acids Amino acids derived from breakdown of cellular proteins, ingested proteins, and body proteins (when other forms of fuel aren’t available) Proteases degrade ingested proteins in stomach and small intestine o Early step in catabolism: separation of amino group from carbon skeleton Most cases: amino group transferred to a- ketoglutarate to form glutamate ( requires ryridoxal phosphate) Glutamate: transported to liver mitochondria where glutamate DH releases amino group (as NH4+) Ammonia from other tissues transported to liver as 1) amide nitrogen of glutamine or 2) amino group of alanine (from skeletal muscle) o Pyruvate produced by deamination of alanine (liver) is converted to glucose (transported back to muscle): glucose-alanine cycle Amino Group Catabolism: Depending on the organism, NH4+ is excreted in different forms o Most terrestrial organisms ammonia is converted to urea and excreted: Urea Cycle The “Krebs Bicycle” “ links between urea and TCA cycle Aspartate-agininosuccinate shunt: link the two cycles o Connections more complex than shown: TCA enzymes, fumarase and malate DH, exist in cytosolic and mitochondrial forms The glucose-alanine cycle: Alanine serves as a carrier of ammonia & a carbon skeleton of pyruvate from skeletal muscle to the liver Pyruvate produced by deamination of alanine (liver) is converted to glucose (transported back to muscle) Ammonia is excreted INBORN ERRORS OF METABOLSIM: Albinism: (lack of pigmentation in skin and hair) - enzyme = Tyrosine 3 monooxygenase (tyrosinase) Alkaptonuria: (dark pigment in urine, arthritis)- enzyme= homogentisate 1,2 dioxygenase Aegininemia: (mental retardation)- enzyme: arginase Argininosuccinic academia: (vomiting, convusions) – enzyme= argininosuccinase Phenylketonuria: (neonatal vomiting, mental retardation)- enzyme= phenylalanine hydrolase NUCLEIC ACID METABOLISM: LECTURE 11, CHAPTER 22 Biosynthesis and degradation of nucleotides: Two biosynthesis pathways: o 1) De novo synthesis: “new” synthesis Metabolic precursors: amino acids, ribose 5-P, CO2, and NH3 o 2) Salvage pathway: end products made from “scavenged” components Recycling of free base and nucleosides produced from nucleic acid breakdown 2 kinds of nucleotides classified by ring structure : origins of components of ring structure of purines Uracil DE NOVO SYNTHESIS BEGINS WITH PRPP AND ENDS WITH FORMATION OF INOSINATE (IMP) multistep pathway that produces important common intermediate to the synthesis of AMP/GMP- inosinate (IMP) Biosynthesis of AMP & GMP: IMP is an important precursor AMP& GMP are parent compounds of ATP and GTP Energy and NH3 group source from ATP and Gln Regulation of adenine and guanine nucleotide biosynthesis in Ecoli. 3 major feedback mechanism: PRPP synthetase and glutamine- PRPP amidotransferae, adenylosuccinate synthetase, IMP dehydrogenase – three points of control I. De novo synthesis of pyrimidine nucelotides involves asparate, PRPP, and carbamoyl phosphate 6 member pyrimidine ring made first, then attached to ribose 5 phosphate… differs from de novo purine nucleotide synthesis pathway o carbamoyl phosphate first enzyme to start the reaction, PRPP comes in later Bacterial carbamoyl phosphate synthetase: Has 3 separate active sites “substrate channeling”: important in limiting substrate/intermediates diffusion- multiple steps carried out by the same enzyme critical especially if intermediates are unstable Bacterial pyrimidine biosynthesis through aspartate transcarbamolyase (ATCase) another example of feedback inhibition ATCase is first enzyme in pyrimidine de novo synthesis pathway In the presence of CTP it gets larger which tells you that you need more substrate to reach max velocity Negative allosteric control of the enzyme Ribonucleotides are precursors of deoxribonucleotides Ecoli ribonucleotide reductase o Enzyme acts on ribonucleotide diphosphates o Reduction involves replacement of 2’ OH group with H o Regulation of ribonucleotide reductase by dNTPs: Primary regulatory site (left) and substrate specificity (effector bound to second regulatory site (right)): idea is to provide a balanced pool of precursors for DNA synthesis Both activity & substrate specificity regulated by effector binding Enzyme activity: o ATP activates o dATP inactivates Substrate specificity: o When ATP or dATP is bound: favors reduction of UDP & CDP o When dTTP or dGTP is bound: favors reduction of GDP or ADP, respectively Thymidylate is derived from dCDP and dUMP important mechanism of action for drugs- biosynthetic pathway Degradationof purines and pyrimidines produces uric acid and urea Catabolism of pyrimidines: methylmalonyl semialdehyde eventually degraded to succinyl- CoA (TCA Cycle) SALVAGE PATHWAY Free purine & pyrimidine bases constantly released via metabolic degradation of NTs Free purines are salvaged and reused to make NTs: one of the major pathways… o Adenine + PRPP ----> AMP + PPi A similar pathway exists for pyrimidines in bacteria and, possibly, mammals Defect in salvage pathway enzyme (hypoxanthine-guanine phosphoribosyltransferase: HGPRT) results in Lesch-Nyhan syndrome o Almost exclusive to male children o Defective HGPRT results in elevated de novo purine synthesis & increases in uric acid o Symptoms: mental retardation, self-mutilation Excess urea causes gout, treated with allopurinol, inhibitor of xanthine oxidase (XO) o The oxypurinol generated acts as strong competitive inhibitor of XO o Chemotherapeutic agens often target enzymes in the nucleotide biosynthetic pathway o Glutamine, azaserine, acivicin
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