Dietary Fiber, Atherosclerosis, and Cardiovascular Disease
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Pentose PO4 Pathway, Fructose, Galactose Metabolism.Pptx
Pentose PO4 pathway, Fructose, galactose metabolism The Entner Doudoroff pathway begins with hexokinase producing Glucose 6 PO4 , but produce only one ATP. This pathway prevalent in anaerobes such as Pseudomonas, they doe not have a Phosphofructokinase. The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose monophosphate shunt) is a biochemical pathway parallel to glycolysis that generates NADPH and pentoses. While it does involve oxidation of glucose, its primary role is anabolic rather than catabolic. There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon sugars. For most organisms, the pentose phosphate pathway takes place in the cytosol. For each mole of glucose 6 PO4 metabolized to ribulose 5 PO4, 2 moles of NADPH are produced. 6-Phosphogluconate dh is not only an oxidation step but it’s also a decarboxylation reaction. The primary results of the pathway are: The generation of reducing equivalents, in the form of NADPH, used in reductive biosynthesis reactions within cells (e.g. fatty acid synthesis). Production of ribose-5-phosphate (R5P), used in the synthesis of nucleotides and nucleic acids. Production of erythrose-4-phosphate (E4P), used in the synthesis of aromatic amino acids. Transketolase and transaldolase reactions are similar in that they transfer between carbon chains, transketolases 2 carbon units or transaldolases 3 carbon units. Regulation; Glucose-6-phosphate dehydrogenase is the rate- controlling enzyme of this pathway. It is allosterically stimulated by NADP+. The ratio of NADPH:NADP+ is normally about 100:1 in liver cytosol. -
Lecture 7 - the Calvin Cycle and the Pentose Phosphate Pathway
Lecture 7 - The Calvin Cycle and the Pentose Phosphate Pathway Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire 1 Introduction The Calvin cycle Text The dark reactions of photosynthesis in green plants Reduces carbon from CO2 to hexose (C6H12O6) Requires ATP for free energy and NADPH as a reducing agent. 2 2 Introduction NADH versus Text NADPH 3 3 Introduction The Pentose Phosphate Pathway Used in all organisms Glucose is oxidized and decarboxylated to produce reduced NADPH Used for the synthesis and degradation of pentoses Shares reactions with the Calvin cycle 4 4 1. The Calvin Cycle Source of carbon is CO2 Text Takes place in the stroma of the chloroplasts Comprises three stages Fixation of CO2 by ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules Reduction of 3-phosphoglycerate to produce hexose sugars Regeneration of ribulose 1,5-bisphosphate 5 5 1. Calvin Cycle Three stages 6 6 1.1 Stage I: Fixation Incorporation of CO2 into 3-phosphoglycerate 7 7 1.1 Stage I: Fixation Rubisco: Ribulose 1,5- bisphosphate carboxylase/ oxygenase 8 8 1.1 Stage I: Fixation Active site contains a divalent metal ion 9 9 1.2 Rubisco Oxygenase Activity Rubisco also catalyzes a wasteful oxygenase reaction: 10 10 1.3 State II: Formation of Hexoses Reactions similar to those of gluconeogenesis But they take place in the chloroplasts And use NADPH instead of NADH 11 11 1.3 State III: Regeneration of Ribulose 1,5-Bisphosphosphate Involves a sequence of transketolase and aldolase reactions. 12 12 1.3 State III: -
The Pentose Phosphate Pathway and Its Involvement in Cisplatin Resistance
International Journal of Molecular Sciences Review The Pentose Phosphate Pathway and Its Involvement in Cisplatin Resistance Isabella Giacomini 1, Eugenio Ragazzi 1 , Gianfranco Pasut 2 and Monica Montopoli 1,3,* 1 Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Egidio Meneghetti 2, 35131 Padova, Italy; [email protected] (I.G.); [email protected] (E.R.) 2 Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via Marzolo 5, 35131 Padova, Italy; [email protected] 3 Veneto Institute of Molecular Medicine, Via Giuseppe Orus 2, 35129 Padova, Italy * Correspondence: [email protected]; Tel.: +39-049-827-5090 Received: 30 December 2019; Accepted: 29 January 2020; Published: 31 January 2020 Abstract: Cisplatin is the first-line treatment for different types of solid tumors, such as ovarian, testicular, bladder, cervical, head and neck, lung, and esophageal cancers. The main problem related to its clinical use is the onset of drug resistance. In the last decades, among the studied molecular mechanisms of cisplatin resistance, metabolic reprogramming has emerged as a possible one. This review focuses on the pentose phosphate pathway (PPP) playing a pivotal role in maintaining the high cell proliferation rate and representing an advantage for cancer cells. In particular, the oxidative branch of PPP plays a role in oxidative stress and seems to be involved in cisplatin resistance. In light of these considerations, it has been demonstrated that overexpression and higher enzymatic activity of different enzymes of both oxidative and non-oxidative branches (such as glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and transketolase) increase cisplatin resistance, and their silencing or combined treatment with cisplatin could restore cisplatin sensitivity. -
Carbohydrates: Structure and Function
CARBOHYDRATES: STRUCTURE AND FUNCTION Color index: . Very important . Extra Information. “ STOP SAYING I WISH, START SAYING I WILL” 435 Biochemistry Team *هذا العمل ﻻ يغني عن المصدر المذاكرة الرئيسي • The structure of carbohydrates of physiological significance. • The main role of carbohydrates in providing and storing of energy. • The structure and function of glycosaminoglycans. OBJECTIVES: 435 Biochemistry Team extra information that might help you 1-synovial fluid: - It is a viscous, non-Newtonian fluid found in the cavities of synovial joints. - the principal role of synovial fluid is to reduce friction between the articular cartilage of synovial joints during movement O 2- aldehyde = terminal carbonyl group (RCHO) R H 3- ketone = carbonyl group within (inside) the compound (RCOR’) 435 Biochemistry Team the most abundant organic molecules in nature (CH2O)n Carbohydrates Formula *hydrate of carbon* Function 1-provides important part of energy Diseases caused by disorders of in diet . 2-Acts as the storage form of energy carbohydrate metabolism in the body 3-structural component of cell membrane. 1-Diabetesmellitus. 2-Galactosemia. 3-Glycogen storage disease. 4-Lactoseintolerance. 435 Biochemistry Team Classification of carbohydrates monosaccharides disaccharides oligosaccharides polysaccharides simple sugar Two monosaccharides 3-10 sugar units units more than 10 sugar units Joining of 2 monosaccharides No. of carbon atoms Type of carbonyl by O-glycosidic bond: they contain group they contain - Maltose (α-1, 4)= glucose + glucose -Sucrose (α-1,2)= glucose + fructose - Lactose (β-1,4)= glucose+ galactose Homopolysaccharides Heteropolysaccharides Ketone or aldehyde Homo= same type of sugars Hetero= different types Ketose aldose of sugars branched unBranched -Example: - Contains: - Contains: Examples: aldehyde group glycosaminoglycans ketone group. -
1. Nucleotides A. Pentose Sugars – 5-Carbon Sugar 1) Deoxyribose – in DNA 2) Ribose – in RNA B. Phosphate Group C. Nitroge
1. Nucleotides a. Pentose sugars – 5-Carbon sugar 1) Deoxyribose – in DNA 2) Ribose – in RNA b. Phosphate group c. Nitrogenous bases 1) Purines a) Adenine b) Guanine 2) Pyrimidines a) Cytosine b) Thymine 2. Types of Nucleic Acids a. DNA 1) Locations 2) Functions b. RNA 1) Locations 2) Functions E. High Energy Biomolecules 1. Adenosine triphosphate a. Uses 1) Active transport 2) Movement 3) Biosynthesis reactions b. Regeneration 1) ADP + Pi + Energy → ATP 4. Classes of proteins a. Structural – ex. Collagen, keratin b. Transport – Hemoglobin, many β-globulins c. Contractile – Actin and Myosin of muscle tissue d. Regulatory - Hormones e. Immunologic - Antibodies f. Clotting – Thrombin and Fibrin g. Osmotic - Albumin h. Catalytic – Enzymes 1) Characteristics of enzymes • Proteins (most); ribonucleoproteins (few/ribozymes) • Act as organic catalysts • Lower the activation energy of reactions • Not changed by the reaction • Bind to their substrates o Lock-and-key model of enzyme activity o Induced-fit model • Highly specific • Named by adding -ase to substrate name; e.g., maltose/maltase • May require cofactors which may be: o Nonprotein metal ions such as copper, manganese, potassium, sodium o Small organic molecules known as coenzymes. The B vitamins like thiamine (B1) riboflavin (B2) and nicotinamide are precursors of coenzymes. • May require activation; e.g., pepsinogen pepsin in stomach chief cells 4. Factors Affecting Enzyme Action • pH o pepsin (stomach) @ pH = 2; trypsin (small int.) @ pH = 8 • Temperature o Denatured by high temp’s. • Enzyme inhibitors o Competitive inhibitors o Noncompetitive inhibitors • Effect of substrate concentration and reversible reactions and the Law of Mass D. -
PENTOSE PHOSPHATE PATHWAY — Restricted for Students Enrolled in MCB102, UC Berkeley, Spring 2008 ONLY
Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Bryan Krantz: University of California, Berkeley MCB 102, Spring 2008, Metabolism Lecture 5 Reading: Ch. 14 of Principles of Biochemistry, “Glycolysis, Gluconeogenesis, & Pentose Phosphate Pathway.” PENTOSE PHOSPHATE PATHWAY This pathway produces ribose from glucose, and it also generates 2 NADPH. Two Phases: [1] Oxidative Phase & [2] Non-oxidative Phase + + Glucose 6-Phosphate + 2 NADP + H2O Ribose 5-Phosphate + 2 NADPH + CO2 + 2H ● What are pentoses? Why do we need them? ◦ DNA & RNA ◦ Cofactors in enzymes ● Where do we get them? Diet and from glucose (and other sugars) via the Pentose Phosphate Pathway. ● Is the Pentose Phosphate Pathway just about making ribose sugars from glucose? (1) Important for biosynthetic pathways using NADPH, and (2) a high cytosolic reducing potential from NADPH is sometimes required to advert oxidative damage by radicals, e.g., ● - ● O2 and H—O Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Two Phases of the Pentose Pathway Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY NADPH vs. NADH Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Oxidative Phase: Glucose-6-P Ribose-5-P Glucose 6-phosphate dehydrogenase. First enzymatic step in oxidative phase, converting NADP+ to NADPH. Glucose 6-phosphate + NADP+ 6-Phosphoglucono-δ-lactone + NADPH + H+ Mechanism. Oxidation reaction of C1 position. Hydride transfer to the NADP+, forming a lactone, which is an intra-molecular ester. -
Questions with Answers- Nucleotides & Nucleic Acids A. the Components
Questions with Answers- Nucleotides & Nucleic Acids A. The components and structures of common nucleotides are compared. (Questions 1-5) 1._____ Which structural feature is shared by both uracil and thymine? a) Both contain two keto groups. b) Both contain one methyl group. c) Both contain a five-membered ring. d) Both contain three nitrogen atoms. 2._____ Which component is found in both adenosine and deoxycytidine? a) Both contain a pyranose. b) Both contain a 1,1’-N-glycosidic bond. c) Both contain a pyrimidine. d) Both contain a 3’-OH group. 3._____ Which property is shared by both GDP and AMP? a) Both contain the same charge at neutral pH. b) Both contain the same number of phosphate groups. c) Both contain the same purine. d) Both contain the same furanose. 4._____ Which characteristic is shared by purines and pyrimidines? a) Both contain two heterocyclic rings with aromatic character. b) Both can form multiple non-covalent hydrogen bonds. c) Both exist in planar configurations with a hemiacetal linkage. d) Both exist as neutral zwitterions under cellular conditions. 5._____ Which property is found in nucleosides and nucleotides? a) Both contain a nitrogenous base, a pentose, and at least one phosphate group. b) Both contain a covalent phosphodister bond that is broken in strong acid. c) Both contain an anomeric carbon atom that is part of a β-N-glycosidic bond. d) Both contain an aldose with hydroxyl groups that can tautomerize. ___________________________________________________________________________ B. The structures of nucleotides and their components are studied. (Questions 6-10) 6._____ Which characteristic is shared by both adenine and cytosine? a) Both contain one methyl group. -
8| Nucleotides and Nucleic Acids
8| Nucleotides and Nucleic Acids © 2013 W. H. Freeman and Company CHAPTER 8 Nucleotides and Nucleic Acids Key topics: – Biological function of nucleotides and nucleic acids – Structures of common nucleotides – Structure of double‐stranded DNA – Structures of ribonucleic acids – Denaturation and annealing of DNA – Chemistry of nucleic acids; mutagenesis Functions of Nucleotides and Nucleic Acids • Nucleotide Functions: – Energy for metabolism (ATP) – Enzyme cofactors (NAD+) –Signal transduction (cAMP) • Nucleic Acid Functions: – Storage of genetic info (DNA) – Transmission of genetic info (mRNA) –Processing of genetic information (ribozymes) –Protein synthesis (tRNA and rRNA) Nucleotides and Nucleosides • Nucleotide = – Nitrogeneous base –Pentose – Phosphate • Nucleoside = – Nitrogeneous base –Pentose • Nucleobase = – Nitrogeneous base Phosphate Group •Negatively charged at neutral pH • Typically attached to 5’ position – Nucleic acids are built using 5’‐triphosphates •ATP, GTP, TTP, CTP – Nucleic acids contain one phosphate moiety per nucleotide •May be attached to other positions Other Nucleotides: Monophosphate Group in Different Positions Pentose in Nucleotides • ‐D‐ribofuranose in RNA • ‐2’‐deoxy‐D‐ribofuranose in DNA •Different puckered conformations of the sugar ring are possible Nucleobases •Derivatives of pyrimidine or purine • Nitrogen‐containing heteroaromatic molecules •Planar or almost planar structures •Absorb UV light around 250–270 nm Pyrimidine Bases • Cytosine is found in both DNA and RNA •Thymineis found only in DNA -
De Novo Nucleic Acids: a Review of Synthetic Alternatives to DNA and RNA That Could Act As † Bio-Information Storage Molecules
life Review De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as y Bio-Information Storage Molecules Kevin G Devine 1 and Sohan Jheeta 2,* 1 School of Human Sciences, London Metropolitan University, 166-220 Holloway Rd, London N7 8BD, UK; [email protected] 2 Network of Researchers on the Chemical Evolution of Life (NoR CEL), Leeds LS7 3RB, UK * Correspondence: [email protected] This paper is dedicated to Professor Colin B Reese, Daniell Professor of Chemistry, Kings College London, y on the occasion of his 90th Birthday. Received: 17 November 2020; Accepted: 9 December 2020; Published: 11 December 2020 Abstract: Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. -
Nucleotides and Nucleic Acids
CHAPTER 8 Nucleotides and Nucleic Acids Functions of Nucleotides and Nucleic Acids • Nucleotide Functions: – Energy for metabolism (ATP) – Enzyme cofactors (NAD+) – Signal transduction (cAMP) • Nucleic Acid Functions: – Storage of genetic info (DNA) – Transmission of genetic info (mRNA) – Processing of genetic information (ribozymes) – Protein synthesis (tRNA and rRNA) Nucleotides and Nucleosides • Nucleotide = – Nitrogeneous base – Pentose – Phosphate • Nucleoside = – Nitrogeneous base – Pentose • Nucleobase = – Nitrogeneous base Phosphate Group • Negatively charged at neutral pH • Typically attached to 5’ position – Nucleic acids are built using 5’- triphosphates • ATP, GTP, TTP, CTP – Nucleic acids contain one phosphate moiety per nucleotide • May be attached to other positions Other Nucleotides: Monophosphate Group in Different Positions Pentose in Nucleotides • -D-ribofuranose in RNA • -2’-deoxy-D-ribofuranose in DNA • Different puckered conformations of the sugar ring are possible Purine Bases • Adenine and guanine are found in both RNA and DNA • Also good H-bond donors and acceptors • Adenine pKa at N1 is 3.8 • Guanine pKa at N7 is 2.4 • Neutral molecules at pH 7 • Derivatives of pyrimidine or purine • Nitrogen-containing heteroaromatic molecules • Planar or almost planar structures • Absorb UV light around 250–270 nm Pyrimidine Bases • Cytosine is found in both DNA and RNA • Thymine is found only in DNA • Uracil is found only in RNA • All are good H-bond donors and acceptors • Cytosine pKa at N3 is 4.5 • Thymine pKa at N3 is 9.5 -
Positron Emission Tomography Probe Demonstrates a Striking Concentration of Ribose Salvage in the Liver
Positron emission tomography probe demonstrates a striking concentration of ribose salvage in the liver Peter M. Clarka,1, Graciela Floresb,c, Nikolai M. Evdokimovb,d, Melissa N. McCrackenb, Timothy Chaia, Evan Nair-Gillb, Fiona O’Mahonye, Simon W. Beavene, Kym F. Faullf,g, Michael E. Phelpsb,c,1, Michael E. Jungd, and Owen N. Wittea,b,h,i,1 Departments of aMicrobiology, Immunology, and Molecular Genetics, bMolecular and Medical Pharmacology, dChemistry and Biochemistry, and gPsychiatry and Biobehavioral Sciences, cCrump Institute for Molecular Imaging, eDivision of Digestive Diseases, fPasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, hEli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and iHoward Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 Contributed by Michael E. Phelps, June 5, 2014 (sent for review March 10, 2014) PET is a powerful technique for quantifying and visualizing bio- zyme extracts (2, 7). Additionally, fasting serum ribose concen- chemical pathways in vivo. Here, we develop and validate a trations (∼100 μM) in humans are similar to plasma and serum novel PET probe, [18F]-2-deoxy-2-fluoroarabinose ([18F]DFA), for concentrations of other gluconeogenic substrates, including pyru- in vivo imaging of ribose salvage. DFA mimics ribose in vivo and vate (∼50 μM) and glycerol (∼100 μM) (8, 9). Finally, the con- accumulates in cells following phosphorylation by ribokinase and 18 version of ribose to glucose requires less energy and reducing further metabolism by transketolase. We use [ F]DFA to show power than either pyruvate or glycerol (1). that ribose preferentially accumulates in the liver, suggesting a Other data suggest that ribose may have alternative and dis- striking tissue specificity for ribose metabolism. -
Glucose Hemi-Acetal & Acetal (Glyoside) Formation: Some
GLUCOSE HEMI-ACETAL & ACETAL (GLYOSIDE) FORMATION: SOME COMMON CONCEPTS IN CARBOHYDRATE (“SUGAR”) CHEMISTRY Carbohydrates • (carbon + hydrate) are molecules with three or more carbons and a general formula that approximates CnH2nOn Saccharides • are carbohydrates or sugars • monosaccharides have one sugar moiety • disaccharides have two sugars linked together • trisaccharides have three sugars linked together • tetrasaccharides have four sugars linked together, etc... • polysaccharides have an indeterminate number which can be hundreds of thousands or more Prefixes and Suffixes • the suffix (ending) for sugar names is: -ose • the prefix defines the number of carbons: o triose (3 carbons) o tetrose (4 carbons) o pentose (5 carbons) o hexose (6 carbons), etc… • a further prefix defines the types of carbonyl group in the sugar: o aldo- (aldehyde) or o keto- (ketone) o for example glucose (shown below) is an "aldohexose" whereas fructose is a "ketohexose" • the term pyranose means a six-membered sugar ring (hemiacetal or acetal - see below) • the term furanose means a five-membered ring • These terms are often prefixed as in "glucopyranose" which means glucose cyclized to its six-membered ring form (see below) Intro Chem Handouts Carbohydrate Chemistry Page 1 of 4 D- and L- Sugars • This is a naming convention • Using standard nomenclature numbering, determine the configuration (R or S) of the highest numbered stereogenic center ("chiral center" or "asymmetric center"): o if it has R-configuration, the sugar is a D-sugar o if it has S-configuration, the sugar is an L-sugar Glucose Hemi-Acetal Formation • The open form of D-glucose (and many other sugars) can cyclize to form hemiacetals.