CHAPTERS 9-10

METABOLISM

Prescott, 8th ed.

Chapter 9 is a review chapter: key terms and concepts you should know!
METABOLIC PATHWAYS CATABOLIC REACTIONS - to? 1. release energy which is used to generate ATP from ADP and phosphate. 2. release electrons which serve as _reducing power" for more energy production and also for biosynthesis. 3. provide some of the "building blocks" for biosynthesis. ANABOLIC REACTIONS - for growth, reproduction, and repair

RELATIONSHIP OF ENERGY TO METABOLISM

relationship to energy - endergonic vs. exergonic reactions ADENOSINE TRIPHOSPHATE ELECTRONS ACTIVATION ENERGY required to drive the reaction

OXIDATION-REDUCTION REACTIONS
coupled reactions 2 H protons and 2 electrons are transferred 1 H atom = 1 proton and 1 electron OXIDATION donation of electrons and hydrogen ions (H+) REDUCTION accepting electrons or H+ ELECTRON DONAR (initially glucose, or another organic compound) ELECTRON ACCEPTOR ELECTRON CARRIERS (intermediary, transient carriers) job is to trap a pair of electrons 1. Nicotinamide adenine dinucleotide (nicotinic acid derivative) 2. Flavoproteins (riboflavin derivatives): Flavin adenine dinucleotide (FAD)and flavin mononucleotide (FMN) 3. Cytochromes (iron-bearing compounds) the more reduced a compound, the more likely it will give up e- s and the more energy it contains the ability of compound to give up e s can be measured by electromotive force (in volts) the more - the EF, the stronger the compd's reducing power when these are in a series, the e s will travel from one compound to another

ENZYMES
PROTEIN COMPOSITION STRUCTURE Amino acids Helical chain Globular tertiary protein structure FUNCTION/FEATURES lowers activation energy needed to drive a chemical reaction specificity microbial types of enzymes: exoenzymes and endoenzymes destroyed by denaturation MECHANISM OF ACTION

substrate(s) bind to enzyme, contacting each other more frequently variables: temperature pH substrate concentration inhibitors OTHER FEATURES SUBSTRATE COENZYMES importance of cofactors or coenzymes carrying H ions or electrons INHIBITION Competitive inhibitor competes for active site of enzyme w/ substrate noncompetitive inhibitors bind at ALLOSTERIC SITE -------------------------------------------------------------------------------------------------------------------------------------

SKIP section 9.9

9.10 REGULATION OF METABOLISM

Allosteric enzyme 1A. Allosteric activity of an enzyme (2 binding sites, binding changes conformation of enzyme) 1. Active site for substrate 2. Allosteric site for end product B. Feedback inhibition 1. Final end product of metabolic pathway 2. Inhibition of first enzyme e.g. threonine intermediate a b c d isoleucine (shuts off enzyme 1 in path) for pathways of amino acids, purines, pyrimidines No formation effect on successive substrates No effect on synthesis of enzymes, just ACTIVITY Transientchange in EP concentration alters the feedback inhibition

CHAPTER 10

METABOLISM: Catabolic Pathways/Energy Release

Much of this chapter is review also!

10.1 ENERGY PATHWAYS FOR CHEMOORGANOTROPHS

OVERVIEW
eucaryotic cells - in cytoplasm and mitochondrial membranes procaryotic cells - along cell membranes (CH2O)X + O2 CO2 + H2O +ATP (CH2O)X = glucose, fructose, sucrose, etc.

PHOSPHORYLATION MECHANISMS =

oxidative vs. substrate-level phosphoyrlation

10.2-10.5 AEROBIC RESPIRATION GLYCOLYSIS

breakdown/oxidation of glucose to pyruvate/pyruvic acid EMBDEN-MEYERHOF PATHWAY in cytoplasm
**carbs, organic and fatty acids, and amino acids may be used 1. SUBSTRATE-LEVEL PHOSPORYLATION phosphorylation = addition of phosphate group originally from an ATP

i.e. phosphate group serves as energy carrier requires a high energy molecule (molecule + PO4 attached by a special bond) bond is broken, releasing the energized PO4 which then combines with ADP 2. INITIAL ELECTRON DONAR GLUCOSE broken down into two 3C molecules 2 e-s given to NAD

3. ALTERNATIVE MECHANISMS OF GLUCOSE BREAKDOWN to pyruvate not important other than in passing (Entner-Doudoroff/pentose phosphate pathway) TRANSITION STEP TO ACETYL-COENZYME A to enter TCA cycle pyruvate loses a CO2 and is converted to a 2 carbon compd coenzyme A is a derivative of vitamin B, used to carry the 2 carbon fragment acetyl coA enters TCA cycle THIS HAPPENS TWICE, B/C 2 PURUVIC A. ARE PRODUCED FROM 1 GLUCOSE

KREBS CYCLE (TCA cycle, citric acid cycle)

Hans Krebs Nobel prize in 1953 in aerobic respiration, organic compds are e- donars (e.g. glucose) oxidized inorg. compds are e- acceptors (NAD, FAD) complete oxidation of organic compounds (from glucose to carbon dioxide) importance? energy is contained in the bonds of the organic compounds intermediate products serve as C skeleton chains for synthesis conduit b/t anabolic and catabolic pathways THIS HAPPENS TWICE, B/C 2 ACETYLCOA ARE PRODUCED FROM 1 GLUCOSE 2 pyruvic a. + 8NAD+ + 2FAD + 2ADP + PO4 6CO2 + 8NADH + 2FADH2 + 2ATP What is produced? 1. REDUCED ELECTRON CARRIERS _ 8 NADH + 2 FAD (flavoprotein) 2. INTERMEDIATE ORGANIC COMPOUNDS UTILIZED IN BIOSYNTHESIS liberation of carbon dioxide when COOHs are cut off the molecules 3. SUBSTRATE-LEVEL PHOSPHORYLATION 4 GDP 4 GTP (GTP acts like ATP in synthesis reactions and is converted to it)

ELECTRON TRANSPORT & OXIDATIVE PHOSPHOYRLATION

ETC = various carriers in the chains of different organisms ELECTRON CARRIERS located in cell membrane of procaryotes or mitochondria of eucaryotes NADH or FAD passes electrons to FLAVOPROTEINS - flavin mononucleotide (FMN) passes electrons to QUINONES (vitamin K derivative) passes electrons to CYTOCHROMES passes electrons to FINAL ELECTRON CARRIER = O2 oxidizes cytochrome a forms water + hydrogen peroxide + superoxide 02O2 + e- 02superoxide dismutase converts superoxide to H2O2 O2 + 2e H2O2 catalase converts peroxide to water OXIDATIVE PHOSPHORYLATION

chemiosmosis = proton motive force BASED ON H+ (comes from FAD or from water) protons (H+) are pumped across cell membranes during e- transport a proton concentration is set up - a charge separation across the membrane a pH potential is set up between inner surface and outer surface of membrane the protons flow (proton-motive force) into the cytoplasm across membrane at specific locations where ATP synthase is located (ADP +PO4 ATP) TOTAL ENERGY YIELD PER GLUCOSE MOLECULE in procaryotes - 38 ATP - 19X more energy than fermentation in eucaryotes - 36 because of energy req'd to pump e-s across mitochondrial membrane other advantages? most efficient utilization of org. compds intermediate products used in biosynthesis

10.6 ANAEROBIC RESPIRATION

facultative anaerobes and some strict aerobes - but under anaerobic conditions i.e. swamps, sewage digesters, poorly aerated soils ORGANIC COMPOUNDS AS INITIAL ELECTRON DONARS

use glycolysis and Kreb cycle as aerobes do REDUCTION OF INORGANIC COMPOUNDS IN ETC - but NOT oxygen 1. FINAL ELECTRON ACCEPTORS are oxidized N or S compounds most often are reduced, just like oxygen is reduce to water in aerobic resp. 2. EXAMPLE ORGANISMS SULFUR REDUCERS SO4 H2SO4 - Desulfovibrio DENITRIFIERS NO3 NO2 NH3 N2 MISCELLANEOUS: methane producers C03 CH4 C. ATP YIELD AS COMPARED TO AEROBIC RESPIRATION less ATP (30-34/glucose) due to lack of final transfer of electrons in ETC to oxygen

10.7 FERMENTATION
anaerobic metabolic pathways, but NOT THE SAME as anaerobic respiration---WHY? NO ELECTRON TRANSPORT CHAIN various definitions a process producing alcoholic beverages or acidic dairy products spoilage of a food by m/o large-scale industrial microbial process occurring without air an energy-releasing metabolic pathway taking place under anaerobic conditions a metabolic process releasing energy from a sugar or other organic compd, no O2 required, no ETC required, and organic compd is final e- acceptor GLYCOLYSIS precedes the fermentation reaction. SUBSTRATE-LEVEL PHOSPHORYLATION (see above in aerobic resp.) ORGANIC COMPOUNDS BOTH INITIAL E- DONAR & E- ACCEPTOR e- donar = NADH e- acceptor = pyruvic acid or derivative

needed to recycle NADH NAD so that glycolysis can continue so NADH donates e-s to an organic compound, like pyruvic acid, to reduce it most of the energy remains in the end product

MAJOR FERMENTATION ROUTES LACTIC ACID BACTERIA make LACTIC ACID (food production)
1. HOMOLACTIC FERMENTERS = 80% of product is lactic acid prevalant in fermented milk food production - yogurt Lactobacillus, Streptococcus, and mammalian cells 2. HETEROLACTIC FERMENTERS = 50% of product is lactic acid lactic acid, CO2, ethanol lactobacilli and Leuconostoc used to make pickles, sauerkraut

OTHER BACTERIA
TO MIXED ACIDS - Enterobacteriaceae, e.g. E. coli ethanol, acetate, hydrogen, formic acid, CO2

YEASTS
TO ALCOHOL yeast, Saccharomyces cerevesiae pyruvate to acetaldehyde +2CO2 + 2NADH to 2 alcohol * mutant strains of Candida causing drunkenness TO MISCELLANEOUS CHEMICALS

ALTERNATIVE NON-GLUCOSE, ORGANIC COMPDS for ATP generation

other carbs, lipids, proteins, amino acids, etc. converted into intermdiate compds that can enter at various spots in glycolysis, Krebs, etc.

SKIP SPECIFICS OF 10.8-10.10

10.11 CHEMOLITHOTROPHY

OXIDATION OF INORGANIC COMPOUNDS IN PRODUCING ENERGY

use Calvin cyle (C3 pathway) to convert CO2 to reduced organic compd (some can use org. compds) CHEMO(LITHO)AUTOTROPHS e.g. the ATP comes from reduced sulfur compds released from the thermal vents OXYGEN required reduced INORGANIC COMPOUND AS ELECTRON DONAR (S, H2S, NH3, etc.) END PRODUCTS are oxidized inorganic compds (NO3, NO2, SO4, etc.) EXAMPLE ORGANISMS SULFUR OXIDIZERS S or H2S + 02 SO4 NITROGEN OXIDIZERS NH3 + O2 NO2 Or NO2 + O2 NO3 Nitrifiers/nitrifying bacteria are important in soil fertility - Nitrosomonas, Nitrobacter of environmental importance others: methane oxidizers CH4 CO2 hydrogen bacteria H H2O iron bacteria ferrous Fe+2 ferric Fe+3 Thiobacillus ferrooxidans 4FeSO 4 + O2 2Fe2(SO4)3 +2H2O 4Fe(OH)3 + 6H2S04

10.12 PHOTOSYNTHESIS
photoautotrophs (use CO2 for carbon) or photoheterotrophs (use org. compds for carbon)

LIGHT REACTION (LIGHT-DEPENDANT)

1. Light-trapping chlorophyll/bacteriochlorophyll pigments 2. Photophosphorylation (similar to ETC, with e- carriers in a chain)

NADPH supplies reducing power for Calvin cycle Oxygenic (oxygen by-product) VS. anoxygenic (no oxygen made) Electron donors --WATER (PHOTOAUTOTROPHS) when e-s donated O2 (cyanobacteria) --OTHER electron donor may be H2S S (sulfur bacteria) Different light reactions in photosynthetic organisms a. PLANTS AND CYANOBACTERIA (aerobic organisms) oxygenic photosystem I and II electron donor = water chlorophylls (in chloroplasts in the eucaryotic cells) b. GREEN/PURPLE SULFUR &NONSULFUR BACTERIA (anaerobic organisms) anoxygenic photosystem I only (not as efficient) bacteriochlorophylls (NOT in chloroplasts) electron donor = reduced S compounds, H2, or organic compounds

SKIP DETAILS ON PHOTOSYSTEMS/PHOTOPHOSPHORYLATION

CHAPTER 11 METABOLISM: Anabolic Pathways/Biosynthesis

THE ONLY TOPICS WE ARE COVERING IN THIS CHAPTER. 11-3 DARK REACTION of photosynthesis (Fixation of carbon dioxide)
use Calvin cycle (C3 pathway) to convert CO2 to reduced organic compd requires much 18ATP and reducing power 12NADH takes 6 turns of cycle to convert into 1 6-C compd like glucose

11-5 NITROGEN (N2) FIXATION

N2 2NH3 (ammonia) occurs naturally in some plants like rice, also lightening produces it for production of nitrates in the soil, fertilizer for plant roots Examples of nitrogen-fixing bacteria: free-living cyanobacteria in soil and water B Anabaena bacteria: free-living Clostridium in soil symbiotic Rhizobium in roots of legumes (peas, beans, alfalfa, clover) NH3 converted to NO3 via nitrifying bacteria (nitrifiers) see above Oxidation of Inorganic Compounds (ammonia to nitrites and nitrates)