I. Metabolism (Chapter 5) A. Overview 1. metabolism = all chemical processes performed by living systems a. two components, one of synthesis and one of degradation b. anabolism = synthesis of complex molecules from simpler ones with an input of energy c. catabolism = molecules broken down into simpler molecules with the release of energy (1) some energy conserved and made available for work (2) produces compounds for biosynthesis (3) generates reducing equivalents for energy or biosynthesis d. amphibolic pathways function catabolically and anabolically (1) glycolysis and Krebs cycle (2) most reactions are reversible or other enzymes exist to bypass irreversible catabolic steps 2. organisms can be classified based on carbon and energy sources a. carbon can be organic or inorganic (1) autotrophs use inorganic carbon (CO 2 ) to make all the organic molecules they need (2) heterotrophs use organic molecules to synthesize cell components b. energy can be from light or chemicals (1) phototrophs use light energy (a) light is the primary source of energy in the biosphere (b) photosynthesis converts light energy to chemical energy (2) chemotrophs use chemical energy (a) chemical energy is the most common form of energy in the biosphere (b) chemicals used can be organic or inorganic i) organotrophs ii) lithotrophs ( rock eaters ) B. Energetics 1. overview a. energy = ability to do work b. chemical energy resides in bonds between atoms, specifically in the electrons (1) reduction = gain electrons (2) oxidation = loss of electrons c. the ability to gain or lose electrons is measured as the oxidation/reduction (redox) potential (1) symbolized by E and measured in volts (2) good electron donors have negative redox values (top of the electron tower) (3) good electron acceptors have positive redox values (bottom of the electron tower) (4) the larger the difference in redox potentials, the greater the energy released in the reaction d. exergonic = reaction releases energy
e. endergonic = reaction requires input of energy 2. coupled reactions and the role of ATP a. ATP functions as an energy "storehouse" b. energy extraction in biological systems involves transfer of electrons, termed redox reactions c. electron carriers = coenzymes that shuttle electrons between molecules d. substrate level phosphorylation = energy released directly from substrate to phosphorylate ADP e. oxidative phosphorylation - ATP formed through a series of redox reactions through a respiratory pathway C. thermodynamics 1. the change in energy of a system depends only on the initial and final state and not on the path of the transformation 2. 1st law of thermodynamics a. energy neither created or destroyed b. cannot predict if reaction is spontaneous 3. 2nd law of thermodynamics a. entropy of a system proceeds towards a maximum b. process occurs spontaneously only if the sum of the entropies of the system and its surroundings increases: ( S system + S surroundings ) > 0 for a spontaneous reaction 4. entropy changes of chemical reactions difficult to measure; starting values difficult to determine a. instead of entropy, use free energy b. by combining the 1st and 2nd laws of thermodynamics: G = H -T S 5. So, the change in free energy of a reaction depends on changes in internal energy and entropy of the system 6. a reaction can occur spontaneously only if the G is negative a. the G of products must be less than the G of reactants b. G of a reaction is independent of the path or mechanism of the transformation c. G is unrelated to the reaction rate 7. for the reaction A + B C + D a. G = G o + RT ln ([C][D]/[A][B]) b. G o = standard free energy change, at ph 7, use G o ' c. G o ' = -RT ln ([C][D]/[A][B]) = -RT K' eq 8. the overall free energy change for a chemically coupled series of reactions is equal to the sum of the free-energy changes of the individual steps 9. a thermodynamically unfavorable reaction can be driven by a thermodynamically favorable reaction that is coupled to it D. energy required for work, active transport, synthesis 1. energy from external source a. chemotrophs use chemical energy b. phototrophs use light energy 2. ATP is the most common energy carrier in biological systems
3. several other biological compounds have high phosphate group transfer potential 4. To sum, cells use energy from oxidizable substrates or light to maintain high concentrations of ATP and an unfavorable reaction can be converted to a favorable one by coupling it to the hydrolysis of a sufficient number of ATP molecules E. Enzymes 1. protein catalysts with high specificity for the reaction catalyzed and molecules acted upon a. catalyst = increases rate of reaction without being permanently altered itself b. acts on reactants or substrates to form products 2. many enzymes are pure proteins but others have cofactors and/or coenzymes and are called holoenzymes a. apoenzyme = protein portion b. cofactor = cofactor firmly attached to apoenzyme c. coenzyme = loosely bound cofactor (e.g., NAD, many vitamins) 3. general mechanisms a. enzymes effect the rate, but not the energy yield or requirement b. in a reaction, reactants come together an form a transition-state complex that resembles both reactants and products (1) activation energy = energy required to bring reacting molecules together in the correct way to reach transition state (2) transition-state complex decomposes to yield products (3) enzymes accelerate reactions by lowering the activation energy c. active site or catalytic site = specific binding site for substrates on enzyme (1) enzyme may bring substrates together at active site (a) in effect, concentrates substrates (b) aligns substrates in correct orientation to form transition-state complex (2) effectively accelerate reaction 2-3 logs over uncatalyzed reaction rates (a) allows reactions to occur at lower temperatures (b) essential to life processes 4. inhibition and regulation a. enzyme activities strongly influenced by environmental factors (1) temperature can increase rate until protein denatures (2) ph effects charges on amino acids, altering 3-D enzyme structure b. substrate concentrations effect rate of reaction (active site is saturatable) c. competitive inhibition = enzyme reactions inhibited by chemicals that compete with the substrate for the active site (1) does not undergo reaction to form products (2) some can bind irreversibly (3) sulfanilamide, a sulfa drug (analog of PABA) d. noncompetitive inhibition = interact with enzyme but not at active site (1) allosteric inhibition (2) can alter the shape of enzyme active site (3) some inhibitors interact with metal ions, often permanently inactivating
enzymes e. end-product inhibition = allosteric inhibition of a key enzyme in a pathway by a product of the pathway (reversible) F. Catabolism (energy yielding reactions) 1. can be broken down to 3 stages a. stage 1 = large nutrient molecules are hydrolyzed to simpler molecules b. stage 2 = products of 1st stage degraded to simpler compounds that are key intermediates in amphibolic pathways (1) acetyl CoA, pyruvate, TCA intermediates (2) ATP, NADH, FADH 2 c. stage 3 = molecules completely oxidized to CO 2 in TCA cycle (1) high yield of energy (ATP, NADH, FADH 2 ) (2) can use oxygen or other electron acceptor 2. substrate level phosphorylation = phosphorylation of ADP coupled to exergonic breakdown of substrate molecule 3. glycolysis (Emden-Meyerhoff pathway) a. most common pathway for glucose degradation to pyruvate (1) stage 2 of catabolism (2) functions in presence or absence of O 2 (3) occurs in all major groups of microorganisms b. can be divided into 2 parts, 6-carbon and 3-carbon (1) 6-C, glucose phosphorylated twice to fructose-1,6-bisphosphate (2) no energy yield; 2 ATP consumed (3) 3-C stage starts with cleavage of F-1,6-P (4) 2 ATP/3-C compound (= 4/glucose) (5) also generates 2 NADH c. 9 steps from glucose to pyruvate (1) activation of glucose; phosphorylated by ATP to G-6-P (2) G-6-P converted to isomer F-6-P (3) ATP phosphorylates to F-1,6-diphosphate (a) so far 2 ATP consumed (b) no energy released (c) no oxidation-reduction (4) F-1,6-DP split into glycerol-3-phosphate (G-3-P) and dihydroxyacetone phosphate (DHAP) (a) isomers (b) DHAP converted into G-3-P (5) G-3-P oxidized and phosphorylated (P i ) to diphosphoglyceric acid (DPGA) (a) NAD reduced to NADH (b) single oxidation-reduction step of glycolysis (c) aerobes use NADH for energy; anaerobes reoxidize it, using an organic compound as the acceptor (6) DPGA becomes 3-phosphoglyceric acid; ADP phosphorylated to ATP (7) 3PG converted to 2PG
(8) 2PG dehydrated to phosphoenolpyruvate (9) PEP dephosphorylated (ADP ATP), pyruvate formed d. pentose phosphate or hexose monophosphate pathway = another pathway for sugar breakdown to pyruvate (1) can operate at same time as EMP pathway (2) produces high levels of NADPH (for synthetic reactions) e. Entner-Doudoroff pathway = another hexose to pyruvate pathway, substitutes for EMP pathway (1) generally in Pseudomonas, Rhizobium, Azotobacter, Agrobacterium, and a few other gram negative bugs (2) rare in gram positives; Streptococcus faecalis 4. fermentation = all metabolic processes that release energy from a sugar or other organic molecule, do not require oxygen or an electron transport system, and use an organic molecule as the final electron acceptor a. uses organic compounds (part of substrate) as terminal electron acceptors (1) substrate level phosphorylation (2) reducing equivalents recovered in organic endproducts b. yields small amount of ATP c. other definitions in use (1) any process that produces alcoholic beverages or acidic dairy products (general use) (2) any spoilage of food by microorganisms (general use) (3) any large-scale microbial process occurring with or without air (industrial definition) (4) any energy-releasing metabolic process that takes place only under anaerobic conditions (oversimplification) d. typical products of pyruvate fermentation (1) alcohol (beer, wine, whiskey) (2) solvents (acetone, butanol) (3) organic acids (lactic, acetic) (4) dairy products, soy sauce 5. tricarboxylic acid cycle a. stage 3 of catabolism b. pyruvate degraded to CO 2 (1) oxidized to CO 2 and acetyl-coa by pyruvate dehydrogenase complex (2) acetyl-coa = acetic acid and coenzyme A joined by high energy thiol ester bond (3) acetyl-coa arises from many other pathways c. tricarboxylic acid (TCA) cycle or citric acid cycle (1) substrate, acetyl CoA, condensed with 4 carbon intermediate, oxaloacetate, to form citrate (3 o alcohol) and begin the 6 carbon stage (2) citrate rearranged to give isocitrate, a more readily oxidized 2 o alcohol (3) isocitrate oxidized and decarboxylated to KG (4) KG oxidized and decarboxylated to succinyl-coa (a) cycle enters 4 carbon stage
(b) two oxidation steps yield FADH 2 and NADH for each acetyl-coa added originally (c) GTP produced from succinyl-coa by substrate level phosphorylation (5) eventually oxaloacetate is reformed, ready for next cycle d. overall, the TCA cycle generates 2 CO 2, 3 NADH, 1 FADH 2, and 1 GTP for each acetyl CoA oxidized e. TCA cycle enzymes widely distributed among microorganisms (1) even microorganisms that lack complete cycle (2) one major function is to provide compounds for biosynthesis 6. respiration = ATP-generating process in which molecules are oxidized and the final electron acceptor is (almost always) an inorganic molecule a. electron transport chain is an essential part of aerobic respiration (1) O 2 is final electron acceptor aerobically (2) anaerobically, final electron acceptor is an inorganic molecule other than O 2 or, rarely, an organic molecule (a) sulfate, nitrate, carbonate (b) fumarate b. electron transport chain = sequence of membrane associated electron carrier molecules that are capable of oxidation and reduction (1) ETS have two basic functions (a) accept electrons from a donor and pass them to an acceptor (b) conserve some of the energy released during electron transport for ATP synthesis (2) electrons passed through the chain, in direction of higher reducing potential, with stepwise release of energy (3) energy released drives the chemiosmotic generation of ATP (4) located in plasma membrane of prokaryotes, mitochondrial membrane of eucaryotes c. most information known about mitochondrial ETC (1) electrons transferred from NADH to FMN (2) FMNH 2 passes electrons to Q and two H + through the membrane (3) Q transports two H + from inside to outside, passes electrons to cytochromes (4) typical order is cyt b, cyt c 1, cyt c, cyt a, cyt a 3 (5) cyt a 3 reduces O 2 to H 2 O (6) FADH 2 can transfer electrons into the ETC at a lower level than NADH, so it produces only 2/3 as much energy for ATP generation (7) note that some carriers (cytochromes, iron-sulfur proteins) transport electrons only, while others (FMN, Q) transfer protons as well 7. anaerobic respiration = respiration in which electron acceptors other than O 2 are used 2-2- a. typically NO 3-, SO 4, CO 3, as well as some organics (e.g., fumarate) b. less energy generated than with O 2, due to lower potentials 8. chemolithotrophy = energy generation from inorganic molecules a. lithothroph = rock eating
b. typically H 2, H 2 S, NH 3 c. usually involves aerobic respiratory processes d. possess ETS components and generate a PMF e. most are autotrophs (use CO 2 as carbon source)(vs. heterotrophs, which use organic compounds as their source of C) 9. phototrophy a. photosynthesis = conversion of light energy into chemical energy (1) carbon fixation = synthesis of sugars from CO 2 (2) electrons come from hydrogens in water b. light reactions = light energy converts ADP to ATP (photophosphorylation) and NADP is reduced to NADPH c. dark reactions = electrons and energy used to reduce CO 2 to sugar d. light energy is absorbed by chlorophyll molecules (1) chlorophyll a used by green plants, algae, cyanotobacteria (a) membranous thylakoids in chloroplasts of plants, algae (b) thylakoids in cyanobacteria (2) bacteriochlorophylls used by other bacteria (3) bacteriorhodopsin = pigment in Halobacterium e. excited electrons jump from chlorophyll through an electron transport chain (1) similar to respiration (2) ADP converted to ATP by chemiosmosis f. green and purple bacteria are anoxygenic (1) use H 2, H 2 S, S o, reduced organics as electron source (2) can also grow chemotrophically in dark 10. catabolism of carbohydrates, lipids, and proteins a. carbohydrates are hydrolyzed and/or converted to glucose and fed into a glycolytic pathway b. lipids (1) glycerol moieties enter glycolytic pathway (2) fatty acids -oxidized to acetyl CoA, which is fed into TCA cycle or used for biosynthesis c. proteins are hydrolyzed external to plasma membrane; amino acids enter cell by specific transport mechanisms (1) amino acids are deaminated (2) resulting organic acid converted to pyruvate, acetyl CoA, or a TCA intermediate G. Anabolism (synthetic reactions) 1. general principles a. cells use free energy (ATP) to synthesize more complex molecules from smaller, simpler precursors b. macromolecules = polymers of smaller units; protein, nucleic acids, lipids, polysaccharides c. synthesis from simple precursors (monomers) that are common intermediates requires less genetic information, raw material, and energy d. many enzymes used for anabolism and catabolism
(1) amphibolic pathways often contain different enzymes at key steps for anabolism and catabolism (2) allows independent regulation (a) often by endproducts (b) concentrations of ATP, ADP, AMP, NAD + e. different cofactors (1) NADH catabolic (electron transport) (2) NADPH anabolic (electron donor) (3) fatty acid catabolism uses acyl CoA (4) fatty acid anabolism uses acyl carrier protein thioesters f. many macromolecules can form more complex structures by self assembly (1) flagella (2) ribosomes 2. Identification of anabolic pathways a. in vitro studies using cell free extracts to identify enzymes and intermediates b. nutritional mutants (1) prototroph = full synthetic pathway (2) auxotroph = mutant lacking key enzyme in synthetic pathway; requires addition of endproduct for normal growth (3) intermediate prior to missing enzyme step accumulates c. radioisotope labelling to identify intermediate compounds 3. photosynthetic CO 2 fixation 4. carbohydrate synthesis a. required for cell walls, nucleic acids b. gluconeogenesis very similar to reverse glycolysis (from non-glucose carbohydrate) (1) shares many enzymes with glycolysis (2) three non-reversible steps (a) PEP pyruvate (b) F-6-P F-1,6-BP (c) phosphorylation of glucose c. hexose biosynthesis key intermediate is uridine diphosphoglucose (UDPglucose) (1) also basis for RNA (2) polysaccharides and cell walls d. pentose sugars from pentose phosphate pathway 5. assimilation of inorganics (phosphorus, sulfur, nitrogen) 6. precursor molecules do not contain nitrogen or sulfur a. sulfur can be obtained from inorganic or organic sources (1) inorganic sulfur must be reduced to sulfide (2) cysteine (synthesized from inorganic sulfur) or methionine b. nitrogen can be used as N 2 (a few bacteria), ammonia, or nitrate (1) nitrate gets reduced to ammonia (2) ammonia gets incorporated into amino acids (3) N 2 gets "fixed" into ammonia
7. amino acids are synthesized from intermediates from glycolysis, TCA cycle, and pentose phosphate pathway a. 5 major pathways for aa synthesis b. key intermediates: (1) glucose (to erythrose-4-p): phe, tyr, trp (2) 3-phosphoglycerate: serine cysteine, glycine, histidine (purines) (3) oxaloacetate: aspartate asparagine, threonine, isoleucine, methionine, lysine (pyrimidines) (4) α-kg: glutamate, glutamine, proline, arginine (5) pyruvate, acetylcoa: alanine, lysine, isoleucine, valine, leucine. 8. lipid synthesis usually catalyzed by fatty acid synthetase complex a. acetyl CoA, malonyl CoA and NADPH as substrates b. triglycerides and phospholipids synthesized from dihydroxyacetone phosphate or glycerol phosphate