Nucleo'de Metabolism - Complete Lecture Note | Kansas State University

University:
Kansas State University
Course:
BIOCH 765 | Biochemistry II
Academic year:

2014
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67

Pages:

37
Author:

Jackdams

BIOCH 765: Biochemistry II Spring 2014 Nucleo'de Metabolism (Chapter 23) INTRODUCTION TO NUCLEIC ACIDS 2 Eukaryo'c cell 3 Genome is believed to deﬁne a species 4 Nucleic Acids ¥ Polymer of nucleotides: highly ﬂexible (compared to peptides) ¥ Nucleic acids are universal in living things, as they are found in all cells and viruses. ¥ Nucleic acids were ﬁrst discovered by Friedrich Miescher in 1871. 5 Building Blocks of Nucleo'des ¥ Phosphate group + pentose carbohydrate + base (nitrogenGcontaining heterocyclic ring) ¥ Deoxyribonucleic acid (DNA): A/G/C/T ¥ Ribonuclei acid (RNA): A/G/C/U Nucleotide nucleobase 6 Nucleo'des have many roles ¥ Building blocks of the nucleic acid polymers RNA and DNA. ¥ Energy transfer or energy coupling to drive biosynthesis and other processes (muscle contraction, transport, etc). ¥ Oxidation reduction reactions. ¥ Intracellular signaling. ATP 7 Base Pentose sugars Phosphate sugar ¥ The pentose sugar in the nucloetide is either ribose or deoxyribose. Ð The base is added at the 1 position and phosphates are added at the 5 position. Ð Most nucleotides, including those incorporated into RNA, contain ribose. Ð 2’GOH reduced to –H in deoxynucleotides Ð 3’GOH participates in forming phosphodiester linkage Ð Deoxynucleotides are exclusively used for DNA synthesis. 8 Nucleo'de forma'on O H ║ N 6 2 N H2O Ñ O ═ P Ñ OH O¯ N H 5 H―OCH2 OH O 4 3 OH NH2 H2O 1 O 2 H ║ O¯ OH N 5 Ñ Ñ O¯ The base is added at the 1 position and phosphates are added at the 5 position N Ñ O ═ P ―OCH2 4 O¯ N O 3 OH 6 N 2 N NH2 1 2 OH 9 NitrogenBContaining Heterocyclic Bases ¥ There are two classes of aromatic amine structures used for the bases: purines and pyrimidines. Ð There are two purine bases and three pyrimidine bases Ð Why are they (weak) bases? H + + H+ 10 Nomenclature of nucleo'des ¥ Suﬃx: osine for purine bases; idine for pyrimidine bases ¥ preﬁx deoxy for DNA 11 Forma'on of nucleic acids ¥ Nucleotides are linked through phosphate groups and 3 position of the sugar (3G5Gphosphodiester linkage) 5 end 3-5-phosphodiester linkage 3 end12 Primary structure of nucleic acid ¥ SoGcalled (genome) sequence: order of nucleotides ¥ Always from 5 to 3 (top to bottom or left to right) ¥ Nucleotides and nucleic acids are acidic because of the presence of PGOH groups Ð At pH 7, all of these groups are ionized: PGOG, although they are usually drawn in their protonated forms for the purposes of structure illustration. 13 Secondary structure of DNA ¥ Double helix (ﬁrst deﬁned by Watson and Crick, 1953)  RightGhand helix  Antiparallel pair of strands  The deoxyGsugars and phosphate groups are on the outside and the heterocyclic bases are stacked on top of each other on the inside  Stabilized by hydrogenGbonds major groove minor groove 14 WatsonBCrick Base Pairs (Uridine) ¥ GGC and AGT(U) ¥ DNA almost exclusively exist as duplex held together by forming WatsonGCrick base pairs ¥ A robust mechanism for faithful replication and translation ¥ Other pairings possible but mostly in RNA to give rise to nonGtrivial structures 15 BaseBpair stacking While the phosphodiester bonds form the backbone, the H-bonds of the base pairing interactions contribute to holding the DNA strands together. The planar aromatic bases form a stack that runs parallel to the fiber axis. The stacked bases have interbase hydrophobic and dipole interactions. These interactions contributes to the stability of DNA structure. Therefore, a combination of the H-bonding between complementary base pairs and the stacking interactions act cooperatively to stabilize the folded double helix structure of DNA. 16 Ribonucleic acids (RNA) ¥ RNAs exist as single stranded molecules. ¥ Several types: transfer RNA (tRNA), messenger RNA (mRNA), ribosomal RNA (rRNA) ¥ Much shorter than DNAs ¥ More ﬂexible and often lack stable secondary structures like doubleGhelix of DNA ¥ Less stable with shorter lifeGtime (DNA is stable throughout cell life cycle, while RNAs are typically not) ¥ Some RNAs (tRNA and rRNA) can have tertiary structures (like proteins). 17 Ter'ary Structure of RNA ¥ Some RNA fold into tertiary structures CCA tail (to amino acids) T arm Acceptor stem D arm Anticodon stem tRNA LBstructure Anticodon loop 18 Nucleo'des do not provide a signiﬁcant source of metabolic energy 19 Quick Summary ¥ Nucleotides: compositions and types (sugar and base vary) ¥ Nucleic acids: polymer of nucleotides Ð Ð Ð Ð DNA (w/ deoxyribose): A, G, C, T RNA (w/ ribose): A, G, C, U DNA structures: sequence, double helix, base pairing RNA structures: singleGstranded, tertiary structures 20 Chapter 23.1 SYNTHESIS OF PURINE RIBONUCLEOTIDES Key Concepts 23.1 • IMP is synthesized through the assembly of a purine base on riboseB5Bphosphate. • Kinases convert IMPBderived AMP and GMP to ATP and GTP. • Purine nucleo'de synthesis is regulated by feedback inhibi'on & feedforward ac'va'on. • Salvage reac'ons convert purines to their nucleo'de forms. 21 Atomic Origins of Purine ¥ ¥ ¥ ¥ Isotope labeling analysis of excreted uric acid N: from aspartate/glycine/glutamine C: from formate/glycine/HCO3B Glycine likely incorporated as a whole 22 Inosine Monophosphate (IMP) ¥ Ini'ally synthesized purine deriva've ¥ Precursor to both AMP and GMP ¥ Key “surprise”: purines not synthesized as free base, but as ribonucleo'des! ¥ Pathways highly conserved in diﬀerent organisms spanning from E. Coli to human! 23 de novo Biosynthesis of IMP ¥ 11 reac'ons ¥ Star'ng from ac'va'on of riboseB5Bphosphate ¥ Imidozole ring forms ﬁrst (steps 1B6), followed by pyrimidine ring (steps 7B11) ¥ Consumes several ATPs along the way ¥ Several enzymes are mul'Bfunc'onal and rely on channeling for eﬃciency de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP de novo Biosynthesis of IMP IMP to AMP/GMP Oxidation followed by ÒtransaminationÓ ÒtransaminationÓ 36 AMP/GMP to ATP/GTP ¥ Nucleoside triphosphates required for NA synthesis ¥ Kinases convert AMP/GMP to ADP/GDP and ATP/GTP ¥ Adenylate kinase: AMP + ATP 2 ADP ¥ Guanylate kinase: GMP + ATP GDP + ADP ¥ Nucleoside diphosphate kinase: GDP + ATP GTP + ADP ¥ ATP synthesized by various energyBgenera'ng reac'ons such as glycolysis and oxida've phosphoryla'on Ð ATP genera'on ul'mately drive all above kinase reac'ons! 37 Regula'on of Purine Nucleo'de Synthesis ¥ Levels of nucleo'des in cell are cri'cal Ð Energy balance Ð Too low: impede transcrip'on and replica'on and others! Ð Too high: muta'on elevated! ¥ IMP pathway: regulated at ﬁrst two steps Ð Feedback inhibi'on Ð Feedforward ac'va'on! 38 Purine Salvaging ¥ Free purines released in nucleic acid degrada'on ¥ Can be converted into corresponding nucleo'des through salvage pathways Ð Diverged in diﬀerent species ¥ Two enzymes in human Ð Adenine phosphoribosyltransferase (APRT): Adenine + PRPP AMP + Ppi Ð HypoxanthineBguanine phosphoribosyltransferase (HGPRT) Hypoxanthine + PRPP IMP + PPi Guanine + PRPP IMP + PPi Ð HGPRT Deﬁciency: LeschBNyhan synthdrome ¥ Aﬀects mostly males ¥ Neurological abnormali'es: retarda'on, selfBinjuring and others ¥ Increase uric acid excre'on: why? 39 Quick Summary ¥ List the star'ng materials and cofactors required for IMP biosynthesis. Ð the importance of mul'func'onal enzymes in nucleo'de biosynthesis. ¥ Describe the reac'ons that convert IMP to ATP and GTP. ¥ How do guanine and adenine nucleo'des inhibit their own synthesis? How do they promote synthesis of each other? ¥ Describe how free purines are converted back to nucleo'des. 40 Chapter 23.2 SYNTHESIS OF PYRIMIDINE RIBONUCLEOTIDES Key Concepts 23.2 • UMP is synthesized as a pyrimidine base to which riboseB5Bphosphate is added. • CTP and UTP are derived from UMP. • The early steps of pyrimidine nucleo'de synthesis are the major control points. 41 Atomic Origins of Pyrimidines ¥ ¥ ¥ ¥ Isotope labeling analysis of excreted uric acid Aspartate + Glutamine (amide) + HCO3B Ini'ally synthesized as uridine monophosphate (UMP) Simpler and quite diﬀerent from IMP: prymidine ring synthesized ﬁrst before coupled to riboseB5Bphosphate (from PRPP) 42 On a single polypeptide chain De novo Synthesis of UMP 43 UMP to UTP/CTP ¥ UMP + ATP B> UDP + ATP B> UTP ¥ CTP synthetase aminates UTP to produce CTP Ð GLN provides the amino group 44 Regula'on of UMP Synthesis ¥ Mainly regulated at step 2 (ATCase reac'on) in bacteria ¥ In animals: controlled by regula'on of CPS II 45 Quick Summary ¥ Compare the pathways of purine and pyrimidine nucleo'de synthesis with respect to (a) precursors, (b) energy cost, (c) acquisi'on of the ribose moiety, and (d) number of enzyma'c steps. ¥ How are CTP and UTP derived from UMP? ¥ How does regula'on of pyrimidine synthesis diﬀer in bacteria and animals? 46 What general pathway(s) can eukaryo'c cells use to produce nucleo'des? A. Anabolic and amphibolic pathways. B. Salvage and de novo pathways. C. Catabolic and de novo pathways. D. Salvage pathways only. E. Anabolic pathways. The N7 in the purine ring is contributed by which of the following molecules? A. Aspartate B. Glycine C. Glutamate D. Glutamine E. Arginine The N3 in the pyrimidine ring is contributed by which of the following molecules? A. Aspartate B. Glycine C. Glutamate D. Glutamine E. Arginine Which enzyme catalyzes the reac'on shown below? A. B. C. D. Carbamoyl phosphate synthetase I Carbamoyl phosphate synthetase II Glutamine transcarbamoylase Glutamate synthase Which of the following statements is true regarding regula'on of purine nucleo'de biosynthesis? A. GlutamineBPRPP amidotransferase is inhibited by purine monophosphates. B. IMP dehydrogenase is inhibited by AMP. C. Adenylosuccinate synthetase is inhibited by ATP. D. A and C are correct. E. All the above statements are correct. Chapter 23.3 FORMATION OF DEOXYRIBONUCLEOTIDES Key Concepts 23.3 • Ribonucleo'de reductase uses a free radical mechanism to convert ribonucleo'des to deoxyribonucleo'des. • Thymidylate synthase transfers a methyl group to dUMP to form thymine. 52 Ribonucleo'de Reductase (RNR) ¥ No de novo synthesis ¥ Three classes of RNRs: replace 2’– OH of NDP with H via a free radical mechanism ¥ Class I RNR: heterotetramer with a Fe/Mn prosthe'c group 53 R22 (PDB: 1R1B) Class I RNRs ¥ R1 subunit contains several redoxBac've thiol groups ¥ Novel binuclear Fe(III) prosthe'c group ¥ Coordinated by a Tyr radical! 54 Proposed)RNR)Reac'on)Mechanism) 1. RNR extracts a H from 3Õ (rate limiting step) 2 & 3: Acid catalyzed cleavage of 2Õ-OH to yield a radical-cation intermediate 4 & 5. Reduction by sulfhydryl pair and extraction of an H atom from RNR to restore its radical state Unshared 3Õ electron pair stabilizes the radical (c))Jianhan)Chen) RNR is oxidized at the end! 55) Oxida'on)and)Reduc'on)of)RNRs) ¥ Oxidized)RNRs)do)not)bind)NDPs!) Ð Conforma'onal)switch) Ð Conserved)the)free)radicals) Ð Would)otherwise)damage)the)substrate)and)enzyme)itself) ¥ Thioredoxin)reduces)RNR)to)return)RNR)to)the)original)state) ¥ Thioredoxin)reductase)recover)reduced)form)of)thioredoxin) ) ) (c))Jianhan)Chen) 56) Electron Transfer Pathway of RNRs ¥ Thioredoxin reduces RNR to return RNR to the original state ¥ Thioredoxin reductase recover reduced form of thioredoxin Ð NADPHBmediated reduc'on with FAD as coBenzyme 57 Regula'on of RNRs ¥ Kinases convert dNDPs to dNTPs dNDP + ATP dNTP + ADP ¥ Complex feedback network that is remarkable sensi've to dNTP levels Ð Deﬁciency of and dNTPs is lethal Ð Excess of dNTPs is mutagen'c Complex regulation of R1 oligermization and conformational states 58 dUMP to dTMP via Methylation • Catalyzed by thymidylate synthase H, 䨀⠀ O N s 61 Regeneration of THF: two reactions H H O�N I dRib-® dUMP FdUMP : thymidylate synthase dTMP - NS, N10.Methylene-THF dUMP + Glycine + 2 NH3-CH2-Cooserine hydroxymethyltransferase DHF THF NH3-cH-coo- NAoP + NADPH +H+ ihydrofolate eductase Methotrexate Aminopterin Trimethoprim CH20H Serine 謀言JMt 59 Thvmidvlate Svnthase: Mechanism Proposed mechanism 1. Cys 146 attacks CG 2. CS of enolate ion attacks the CH2 of the iminium cation 3. Enzyme abstracts the proton at CG position (which is released into solvent) 4. Redox exchange: transfer of methyl group and release of DHF; product released 㘀　 dTTP Generation • dTMP generated from dUMP, which is generated by hydrolysis of dUTP dUTP diphosphohydrolase {dUTPase) dUTP + H2 0 ------> dUMP + Ppi • dTMP, once generated, is converted back to dTTP. • Apparently wasteful process. Why? dUMP binding site of dUTPase DNA polymerases do not discriminate dUTP and dTTP too well; need to suppress dUTP concentration to prevent incorrect incorporation of uracil. ⤀氀 NH1 ¢Ⰰ㨀0 䌀䨀儀开N:t H Cytosine C Pyrimidine In DNA ✓" Uracil u In RNA 61 Inhibition of dTMP Synthesis in Cancer Therapy • dTMP production critical for rapid cell proliferation, such as in cancers: sensitive to dTMP synthesis interruption • Normal cells slow growing if at all: less sensitive • Nonreactive dUMP analogs as inhibitors of dTMP synthase • 5-Fluodeoxyuridylate (5-Fluo dUMP) (suicide substrate) - One of the early cancer drugs (approved before 1984) - Treat several types of cancer including colon, rectum, and head and neck cancers. It is also used for other types of cancer, and the skin cream is used for other condi琀椀ons as well. - Trade Names: 5-FU, Adrucil, Efudex (topical), 5-fluorouracil • Inhibition of DHFR blocks THF regeneration: also inhibits dTMP synthesis Uracil 5-Fluorouracil 62 Quick Summary ¥ Describe the produc'on of dNTPs from their corresponding NDPs. ¥ What is the role of thioredoxin and NADPH in the forma'on of deoxyribonucleo'des? ¥ Describe the roles of dUTPase, thymidylate synthase, and dihydrofolate reductase in the synthesis of dTMP. ¥ What is the role of NADPH in the forma'on of thymidylate? 63 Chapter 23.4 NUCLEOTIDE DEGRADATION Key Concepts 23.4 • Purines are broken down to uric acid. • Uric acid may be further catabolized for excre'on. • Pyrimidines are converted to CoA deriva'ves for catabolism. 64 Overview of Nucleo琀椀de Metabolism Hco3- i / Aspartate / ⴀ唀 ⸀ⴀ-N -N' 6 c amine sC - Formate 1 7\ Formate -c2- 3 /4c -⸀开9 7 ' N , I 5 一嘀H I Glutamine- N3 4묀5c-Aspartate amide 6 HC03- - c2 '- 1 C 蠀褀言c ATP I , ⸀ⴀ � � � IAspartatel I Purine nucleotides Uric acid II I N � ,Glutammel� utamine amide Gl I 昀㨀 Ribose-5-phosphate Glycine Pyrimidine nucleotides I A II I Ribose-1-phosphate Malonyl-CoA 65 Purine Catabolic Pathways H -N , \ ( ) o騀褀N氀준N I HI H2 0 Rib-® XMP Pi � Adenosine ⠀✀ H20 -------∀欀 Purine salvage pathways 1. ✀尀 NH: lnosine Pi ��::::side (PNP) Hypoxanth1ne 02 Pi� ( purine nuceloside phosphorylase (PNP) 3. Ribose-1-P can be conve爀琀ed to PRPP nucleotidase Guanosine Pi Pi � ��:\:!side ��::::side Ribose+P . phosphorylase Ribose-1- � phosphorylase P (PNP) xant✀㄀ine oxidase + H20 吀眀o key enzymes: Nucleotidase and 2. Adenosine not processed by PNP! nucleotidase Xanthosine Ribose-1-P � phosphorylase . GMP H20 \ H202 02 guanine deaminase . Xanth1ne ( 0 H 㸀㴀 o騀褀N氀준N 7�� I H Uric acid • Guanine H20 NH: + H20 -.⸀⸀ xant✀㄀1ne oxidase H2 02 Ⰰ謀 H , \ (PNP) \ 0 H 66 Adenosine Deaminase (ADA) 8-stranded beta-barrel with its ac琀椀ve side in a pocket at the C-terminal end Contains a catalytically ac琀椀ve Zn2+ Defects in ADA active site selectively kill lymphocytes and lead to severe combined immunodeficiency disease (SCID) Invariably fatal; 昀椀rst disease treated successfully by gene therapy (w/ caveats!) Inactive ADA leads to accumulation of dATP (SO-fold higher), which in turn inhibits RN Rs and prevents synthesis of other dNTPs. Lymphocytes particularly active in dAMP phosopholyla琀椀on 67 Purine Nucleo琀椀de Cycle N H, 樀倀 ) Aspartate N + GTP Ribose-5-ph< i IMP adenylosuccinate GDP+ P1 � synthetase NH ooc -CH, -CH -coo· I AMP IMP + GTP 㬀尀 adenylosuccinate lyase adenylosuccinate synthetase Adenylosuccinate GDP+ P; Net: H2O + Aspartate + GTP - NH! + GDP+ P; + NAOH; ⠀堀) Aspartate Fumarate + NAO +I Ribose-5-phosphate I Adenylosucdnate J adenylosuccinate Fumarate - lyase ! fumarate ,;娀尀1�11 Increase skeletal muscle activity increases CTA and replenishes CTA intermediates via puri漀漀i渀椀漀漀l攀攀tide cycle! Go N AMP Glutamh Glutama N Ribo,e-5-pho,phate I 㘀㠀 Xanthine Oxidase: mini-electron transport system N HN 㨀猀 N HN 䨀㨀 o N l o iypoxanthine N "'�!r 䰀준 I N)- � I N)- I � I :N�0-H O 0騀褀 N N H H H H Hypoxanthine j 1""' HN o xanthine oxidase ( 02 + H20 ✀尀 H202 Xanthine H202 H � xanthine oxidase 0 H O�N氀준N ,7�� 0 㸀㴀 \ I H H Uric acid H 1ipK=S.4 0騀蜀N䰀꤀N H H Urate Occurs exclusively in liver and small intestine H202 converted to 02 by catalase Excreted or degraded to various levels depending on the species - Marine invertebrates can break down uric acid all the way down to ammonia • H O H �N 7 � o- + H+ 69 Excreted by Degrada琀椀on of Uric Acid • N Uric acid (keto tautomer) Uric acid (enol tautomer) ) irnri guani deamin • Xanth1ne � NH� 02 + H20 H O开꤀ N Organisms that do not excrete urea can remove excess nitrogen through uric acid - Complicated reac琀椀ons but conserved water (uric acid barely soluble) Primates {Birds Reptiles Insects Uric acid >H,o •O, � urate oxidase C02 +H㨀㈀02 1 x�⤀㴀o {Other mammals 0 H f 0 � H � Allantoln H,O nase lallantoi 开蠀 Ⰰ頀 A H⸀稀N COOH NH2 0 N H N H H 0 Allantoic acid {Teleost fish o allantoicase H, CO伀䠀 � CHO Glyoxylic acid 䤀䤀 0 2 H2N-�-NH㨀稀 2H20 Urea � urease 2(02 . { Cartilaginous fish Amphibia Marine { invertebrates Gout: caused by excess of uric acid ¥ ¥ ¥ ¥ Very painful arthri'c joint inﬂamma'on Caused by deposi'on of insoluble sodium urate crystal Kidney stones, renal damage and urinary tract obstruc'on 3 per 1000 persons 71 Major Pyrimidine Catabolism Pathways 72 Quick Summary ¥ What compounds are produced by the degrada'on of purines and pyrimidines? ¥ Describe the reac'ons catalyzed by nucleoside phosphorylase, adenosine deaminase, and xanthine oxidase. ¥ What is the func'on of the purine nucleo'de cycle? ¥ What are the physiological implica'ons of excre'ng waste nitrogen in the form or urate, urea, or ammonia? ¥ Describe how purine catabolism is related to SCID, muscle func'on, and gout. 73

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