A. METABOLISM refers to all the chemical reactions which occur
in life. These reactions are: 1.CATABOLIC - degradative reactions
which: a.Convert food into twelve, key, low molecular weight
intermediates (which can be converted in anabolic reactions into
low molecular weight precursors of proteins, polysaccharides,
lipids, and polynucleotides). b.Oxidize food, generating NADH + H+,
which transfers electrons to the electron transport chain, with
resulting ATP generation. c.Convert food into low molecular weight
compounds which can serve to generate ATP by substrate level
phosphorylation. 2.ANABOLIC - biosynthetic reactions which generate
amino acids, fatty acids, monosaccharides, and mononucleotides and
polymerize them into proteins, lipids, polysaccharides, and
polynucleotides. B.PATHWAYS. Sets of reactions in which the product
of one reaction serves as the substrate for the next reaction are
called PATHWAYS. For example, compound A might be converted into
compound E by four, successive reactions. C.ENZYMES are necessary
to catalyze most biochemical reactions so that the reaction reaches
equilibrium within a time scale useful for life. Enzymes usually
are proteins; they usually catalyze one, specific reaction; usually
every reaction requires catalysis by one specific enzyme. Although
a given reaction, such as A + B = C + D, might come to equilibrium,
in the test tube, with only slightly more C + D formed than the
amount of A + B remaining, in living organisms, this reaction
usually goes to completion. This is possible because C or D is
removed by, for example, conversion to some other product -if C or
D is not removed, the reaction comes to equilibrium. D. GLYCOLYSIS
is the oxidation/conversion of glucose to pyruvate (also called the
Embden-Meyerhoff Pathway): NAD+ is converted into NADH+ H+ ATP is
generated by substrate level phosphorylation E.RESPIRATION converts
pyruvate to CO 2 (Krebs cycle, citric acid cycle, Tricarboxylic
acid cycle) and in the process: NADH + H+ are formed, FAD is
converted into FADH2, GDP is converted into GTP. The reducing
compound pool reduces the electron transport chain, generating a pH
gradient across the Cytoplasmic membrane, the resulting proton
motive force is used by ATP synthase to convert ADP + Pi into ATP
(Oxidative Phosphorylation) A terminal electron acceptor is
required to accept electrons from the electron transport chain. In
aerobic respiration O 2 accepts electrons and is converted to H 2
O. F.FERMENTATION is a process by which glucose oxidation
(glycolysis) can+ be sustained in the absence of a terminal
electron acceptor. That is the oxidation/reduction reactions are
internally balanced. Pyruvate is reduced to lactate or ethanol by
NADH H+, regenerating NAD+. G.Microbes have evolved to occupy many
niches. Four modes of respiration include aerobic, anaerobic,
chemolithotrophic, and photosynthetic. 2
Slide 3
OVERVIEW - ANABOLISM, CATABOLISM ENERGY Free Energy Change,
Exergonic, Endergonic ENZYMESEnzymes - Catalysts, Lower Activation
Energy Bind substrates Strain specific bonds in substrates; help
form bonds COENZMES Low molecular weight compounds, Function with
enzymes Apoenzyme plus coenzyme = holoenzyme OXIDATION/REDUCTION
REACTIONS - REDOX Oxidation - loss of electron - electron donor
Reduction - gain of electron - electron acceptor Coupled
Oxidation/Reduction reactions ELECTRON CARRIERS Nicotinamide
adenine dinucleotide [NAD] - coenzyme involved in
oxidation/reduction NAD+ plus 2e- plus 2H+ NADH plus H+
OxidizedReduced [Reducing Power] HIGH AND LOW ENERGY BONDS Esters -
low energy glucose-6-phosphate Anhydrides -high energy ATP,
adenosine triphosphate - Universal source of high energy
1,3-diphospho glyceric acid - (1,3-diphospho glycerate) 3
Slide 4
CARBON/ENERGY GLUCOSE BYPRODUCTS H 2 O; CO 2 CHEMICAL
SYNTHESIS; FOOD TRANSPORT [MOTILITY] G-6-PO 4 ATP LOW MOLECULAR
WEIGHT BUILDING BLOCKS MACROMOLECULES AMINO ACIDS FATTY ACIDS
MONOSACCHARIDES MONONUCLEOTIDES PROTEINS-ENZYMES; FLAGELLIN;
RIBOSOMES ETC. PHOSPHOLIPIDS POLYSACCHARIDE [PEPTIDOGLYCAN] DNA/RNA
[t,r,m] 4
Slide 5
G -FREE ENERGY - ENERGY RELEASED IN FORM ABLE TO DO WORK G'
CHANGE IN FREE ENERGY UNDER STANDARD CONDITIONS AND pH NEGATIVE G -
EXERGONIC FREE ENERGY RELEASED REACTION OCCURS SPONTANEOUSLY
EQUILIBRIUM FAVORS RIGHT A + B C + D LARGE - G SMALL- G 5
Slide 6
POSITIVE G - ENDERGONIC FREE ENERGY REQUIRED REACTION WILL NOT
OCCUR SPONTANEOUSLY EQUILIBRIUM FAVORS LEFT G VALUE -DOES NOT
PREDICT HOW LONG WILL BE REQUIRED TO REACH EQUILIBRIUM 1 / 2 O 2 +
H 2 H 2 O G = -237 kj/mole [4.2 KILOJOULES = 1 KILOCALORIE] 6
Slide 7
G GG NO ENZYME PLUS ENZYME ACTIVATION ENERGY + ENZYME NO ENZYME
SUBSTRATEPRODUCT ENZYMES 10 8 - 10 20 x RATE 1. BIND SUBSTRATE(S)
2. HOLD SUBSTRATE IN ENZYME CATALYTIC SITE- STRAIN BONDS OR HELP
FORM BONDS 3. REDUCE ACTIVATION ENERGY ENZYME DOES NOT CHANGE: FREE
ENERGY OF SUBSTRATE/PRODUCT EQUILIBRIUM; G IS THE SAME +/- ENZYME
(Not a time scale) 7
Slide 8
ENZYME - TURN OVER NUMBER - NUMBER OF MOLECULES OF REACTANT
(SUBSTRATE) CONVERTED TO PRODUCT PER MOLECULE OF ENZYME PER UNIT OF
TIME (e.g., SECOND) TYPICAL: 2,000 / SECOND = 120,000 / MINUTE
8
ENZYME - ALDOLASE ENZYME - SUBSTRATE COMPLEX + + FRUCTOSE-1,6-
BISPHOSPHATE DI-HYDROXY ACETONE PHOSPHATE GLYCERALDEHYDE
-3-PHOSPHATE ALDOLASE 359 a.a.; MW = 39,147 + ALDOLASE SPLITS HERE
BREAKS TWO BONDS FORMS TWO MOLECULES APPRECIATE !10
Slide 11
OXIDATION - LOSS OF ELECTRON REDUCTION - GAIN OF ELECTRON H 2 +
1 / 2 O 2 H 2 O H 2 - ELECTRON DONOR H 2 2e - + 2H + 1 / 2 O 2 -
ELECTRON ACCEPTOR 1 / 2 O 2 + 2e - O - - NET CHANGE : 2H + + O - -
H 2 O REDUCING AGENT OXIDIZING AGENT H 2 - REDUCING AGENT - DONATES
ELECTRONS - BECOMES OXIDIZED 1/2 O 2 - OXIDIZING AGENT - ACCEPTS
ELECTRONS - BECOMES REDUCED SUMMARY: 11
Slide 12
COENZYMES LOW MOLECULAR WEIGHT, NON-PROTEIN MOLECULES WHICH
PARTICIPATE WITH ENZYMES IN METABOLIC REACTIONS. ESSENTIAL FOR
THOSE REACTIONS. LESS SPECIFICITY THAN ENZYMES. RECYCLE. 12
Slide 13
NICOTINAMIDE ADENINE DINUCLEOTIDE NAD + 2e + 2H NADH + H
OXIDIZED STATE; OXIDIZES FOOD PICKS UP 2e - and 2H + FROM FOOD;
REDUCING AGENT IS REDUCED REDUCED STATE NADH + H NAD + 2e + 2H
TRANSFERS e - TO OTHER E.T.C. TO GENERATE ATP IS OXIDIZED REDUCED
STATE; REDUCES ELECTRON TRANSPORT CHAIN OXIDIZED STATE 13
Slide 14
+2e +2H REDUCED OXIDIZED +H NAD + NADH + H + NICOTINAMIDE
ADENINE DINUCLEOTIDE APPRECIATE ! 14
Slide 15
HIGH AND LOW ENERGY BONDS FOOD OXIDATION MAIN EVENT - ENERGIZES
THE CYTOPLASMIC MEMBRANE; PERMITS FORMATION OF HIGH ENERGY BONDS -
ANHYDRIDES HYDROLYSIS OF HIGH ENERGY BONDS RELEASES LOTS OF ENERGY
WHICH CAN BE USED TO DRIVE WORK: ANABOLISM (CHEMICAL SYNTHESIS)
FOOD TRANSPORT 15
Slide 16
-D-GLUCOSE-6-PHOSPHATE ESTER LOW ENERGY 1,3 DIPHOSPHO GLYCERIC
ACID ANHYDRIDE HIGH ENERGY ADENOSINE TRIPHOSPHATE ANHYDRIDE HIGH
ENERGY 16
Slide 17
METABOLISM B - ENERGY FROM FOOD OXIDATION GLYCOLYSIS - glucose
conversion to pyruvate [Embden-Meyerhoff Pathway] NADH plus H+
generated Substrate level phosphorylation RESPIRATION -pyruvate
conversion to carbon dioxide plus water [in aerobic respiration]
Tricarboxylic acid cycle generates NADH plus H+, FADH2, GTP Flow of
electrons to Electron Transport Chain ELECTRON TRANSPORT CHAIN
(SYSTEM) ENERGIZED MEMBRANE CHEMIOSMOSIS PROTON MOTIVE FORCE pH
Gradient; H+ and OH- ATP Synthase - Oxidative Phosphorylation
Terminal Electron Acceptor (Oxygen in aerobic respiration)
REDUCTION; DELTA E o ; DELTA G FERMENTATION - Pyruvate> Lactic
Acid (lactate) Pyruvate> Ethanol plus CO 2 GLYCOLYSIS PLUS
FERMENTATION: Allow glucose conversion to lactate or ethanol with
internally balanced redox reactions. Do not require terminal
electron acceptor. Result in only partial oxidation of glucose
carbons. Yield only small amount of potential energy of glucose.
Allow ATP generation by substrate level phosphorylation. Permit
growth in absence of oxygen. 1
Slide 18
CITRIC ACID CYCLE NAD + NADH + H + FAD FADH 2 GDP GTP
GLYCOLYSIS NAD + NADH + H + ADP ATP SUBSTRATE LEVEL PHOSPHORYLATION
ELECTRON TRANSPORT CHAIN NADH + H + NAD + ADP ATP [OXIDATIVE
PHOSPHORYLATION] 6O 2 6H 2 O TERMINAL ELECTRON ACCEPTOR GLUCOSE 2
PYRUVATES 6CO 2 RESPIRATION (AEROBIC) 2
Slide 19
FERMENTATION NOTE: NAD RECYCLES 2 LACTATES OR 2 ETHANOLS +2 CO
2 NADH + H + NAD + GLUCOSE NADH + H + NAD + PYRUVATE 3
Slide 20
SUBSTRATE LEVEL PHOSPHORYLATION OXIDATIVE PHOSPHORYLATION LOW
MOLECULAR WEIGHT - PO 4 CONTAINING COMPOUND + ADP ATP (PLUS LOW
MOLECULAR WEIGHT COMPOUND) NADH + H + TRANSFER ELECTRONS TO
ELECTRON TRANSPORT CHAIN ELECTRON FLOW IS COUPLED TO ATP SYNTHESIS
ADP + Pi ATP REQUIRES TERMINAL ELECTRON ACCEPTOR e.g., O 2 WAYS TO
GENERATE ATP 4
GLUCOSE GLUCOSE-6-PO 4 FRUCTOSE-6-PO 4
FRUCTOSE-1,6-BISPHOSPHATE CH 2 O PO 3 H 2 CH 2 OH C O HC O HC OH CH
2 O PO 3 H 2 45 DIHYDROXY ACETONE PHOSPHATE GLYCERALDEHYDE
-3-PHOSPHATE GLYCOLYSIS ATP ADP 6
Slide 23
6 GLYCERALDEHYDE -3-PHOSPHATE GLYCOLYSIS ADP ATP H C O H C OH H
C O PO 3 H 2 H C O P OH H C OH H C O PO 3 H 2 H OO OH C OH H C OH H
C O PO 3 H 2 H O 1,3 BISPHOSPHO- GLYCERATE 3-PHOSPHO- GLYCERATE 7
Pi e-e- NAD + NADH + H + REDUCING POWER SUBSTRATE LEVEL
PHOSPHORYLATION 7
Slide 24
GLYCOLYSIS ADP ATP 2-PHOSPHO GLYCERATE PHOSPHOENOL PYRUVATE 8
SUBSTRATE LEVEL PHOSPHORY- LATION C OH H C O PO 3 H 2 H C OH H O C
O P C OH H C O H O CH 3 C OH C O O OH 10 9 PYRUVATE C O P OH OC OH
HIGHER ENERGY THAN ANHYDRIDE OH 8
Slide 25
AEROBIC RESPIRATION PYRUVATE NADH + H + NAD + CoA CO 2 CoA
CITRIC ACID (C 6 ) OXALO- ACETATE Q 9
Slide 26
10
Slide 27
ENERGY YIELD FROM PYRUVATE OXIDATION 1 PYRUVATE3 CO 2 1 NAD + 4
NADH & H + 12 ATP 1 FAD1 FADH 2 2 ATP 1 GDP + 1 Pi1 GTP 1 ATP
15 ATP EQUIVALENT TO 11 APPRECIATE !!!
Slide 28
ELECTRON TRANSPORT CHAIN (SYSTEM) 1.ACCEPTS e - FROM DONORS
NADH & FADH 2 2.USES ENERGY RELEASED IN OXIDATION/ REDUCTION
REACTIONS TO ENERGIZE MEMBRANE AND SYNTHESIZE ATP 1. NADH
DEHYDROGENASES 2. FLAVO PROTEINS 3. IRON-SULFUR PROTEINS 4.
QUINONES (NON - PROTEINS) 5. CYTOCHROMES RE-DOX ENZYMES 12
Slide 29
REDUCTION POTENTIAL E' O -0.4SUBSTRATES, AS
GLYCERALDEHYDE-3-PHOSPHATE -0.3NADH, NADH DEHYDROGENASE
-0.2FLAVOPROTEIN -0.1IRON SULFUR PROTEINS QUINONES 0 CYTOCHROMES
+0.4NO 3 - NO 2 - +0.8OXYGEN O 2 ENERGY POOR 13 ENERGY RICH
H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ H+H+ OH - ADP + Pi ATP ATP
SYNTHASE ENERGIZED MEMBRANE - SYNTHESIZES ATP [ROTATES FLAGELLA]
OUTSIDE THE MEMBRANE INSIDE THE MEMBRANE 15
Slide 32
ATP SYNTHASE TINIEST BIOMOLE- CULAR MOTOR IN WHOLE UNIVERSE
10NANO METERS 9-12 SUBUNITS ATOMIC FORCE MICROSCOPY CYTOPLASMIC
MEMBRANE SHAFT CYTOPLASM
Slide 33
STATOR THE MOTOR ROTOR INCLUDES SHAFT PREVENT F1 SUBUNITS FROM
ROTATING PROTON GRADIENT ALLOWS MOTOR TO ROTATE ROTOR WITH SHAFT
ROTATING SHAFT CHANGES CONFORMATION OF F1 SUBUNITS CHANGES ALLOW:
ADP + Pi TO ENTER; BIND BETA CATALYTIC SITE; ATP TO BE SYNTHESIZED;
ATP TO BE RELEASED H+ TRANSPORTED INSIDE
Slide 34
ATP SYNTHASE ADP + Pi + H + ATP + H 2 O ANHYDRIDE 16
Slide 35
E o - REDUCTION POTENTIAL - TENDENCY TO DONATE ELECTRONS; i.e.,
TO OXIDIZE SOMETHING UNDER STANDARD CONDITIONS (I MOLAR) MEASURED
IN VOLTS MUST BE MEASURED RELATIVE TO STANDARD STANDARD IS
HYDROGEN: H + + e- > 1/2H 2 E o = 0 VOLTS (BY CONVENTION)
CONSIDER: MATERIAL X + e- > X- WHAT IS REDUCTION POTENTIAL?
CHAMBER ACHAMBER B X + e- > X- BRIDGE H + + e- > 1/2H 2
ELECTRONS FLOW TO H+, E o IS NEGATIVE X HAS LOWER AFFINITY FOR e-
THAN H+ ELECTRONS FLOW TO X, E o IS POSITIVE X HAS HIGHER AFFINITY
FOR e- THAN H+ VOLTMETER MEASURES VOLTAGE
Slide 36
E o BIOLOGY pH = 7.0 H+ + e- > 1/2H2 -0.42 NAD + + 2e- + 2H+
> NADH + H + -0.32 STRONG REDUCER 1/2O 2 + 2e- + 2H+ > H 2 0
+0.82 STRONG OXIDIZER
Slide 37
DELTA G OF REACTION DETERMINED BY DELTA E o OXIDANT + e- >
REDUCTANT (a) 1/2O 2 + 2e- + 2H+ > H 2 0 +0.82 (b)NAD + + 2e- +
2H+ > NADH + H + -0.32 DELTA Eo = (a) - (b) = +0.82 - (-0.32) =
1.14 DELTA G = - n x F x DELTA E n = NUMBER OF e- [2 IN THIS
EXAMPLE] F = FARADAY CONSTANT IN CALORIES 23.062 Kcal/volt.mol
DELTA G IS NEGATIVE AND = - 53 Kcal/MOLE THIS PATHWAY IS EXERGONIC
SUPPOSE FINAL ELECTRON ACCEPTOR IS NITRATE?
Slide 38
YIELD - GLYCOLYSIS + RESPIRATION GLYCOLYSIS 1 GLUCOSE2
PYRUVATES AEROBIC RESPIRATION 2 PYRUVATES + 6O 2 6CO 2 + 6H 2 O
INPUT: 2ATPYIELD SUBSTRATE LEVEL PHOSPHORYLATION4 ATP 2 NADH ETC6
ATP 8 NADH24 ATP 2 FADH 2 4 ATP 2 GTP [EQUIVALENT]2 ATP GROSS40 ATP
NET38 ATP 17 APPRECIATE !!
Slide 39
PROTON MOTIVE FORCE (ENERGIZED MEMBRANE) ADP + Pi ATP REDUCING
POWER (FROM FOOD OXIDATION) LIGHT ENERGY (PHOTOSYNTHESIS) FLAGELLA
ROTATION ACTIVE TRANSPORT (FOOD) 18
Slide 40
LACTIC ACID FERMENTATION CH 3 C OH C O O PYRUVATE CH 3 C OH H C
OH O LACTATE REDUCED e-e- NADH + H + NAD + NET: GLUCOSE 2 LACTATE 2
ADP + 2 Pi 2 ATP 19
Slide 41
ETHANOL FERMENTATION NET: GLUCOSE 2CO 2 + 2 ETHANOL 2 ADP + 2
Pi 2 ATP CH 3 C OH C O O PYRUVATE REDUCED TO e-e- NADH + H + NAD +
CH 3 H C O CH 3 H H C OH ACETALDEHYDE ETHANOL + CO 2 20
Slide 42
METABOLISM - PART C MODES OF NUTRITION AND RESPIRATION -
BIODIVERSITY Aerobic respiration, Anaerobic respiration
Chemolithotrophic metabolism Phototrophic metabolism NITROGEN
FIXATION CATABOLISM ANABOLISM INTERACTIONS ANABOLISM - BIOSYNTHESIS
Low Molecular Weight Building Blocks (Precursors of Macromolecules)
Twelve key, central metabolites Pentoses Amino Acids - Alanine
(from Pyruvate) Tryptophan (from Phosphoenolpyruvate and
erythrose-4-phosphate) 1
Slide 43
MODE AEROBIC ANAEROBIC CHEMO- LITHOTROPHIC PHOTO- TROPHIC
CARBON ORGANIC COMPOUNDS ANABOLISM ORGANIC COMPOUNDS CO 2 ALL
ORGANIC COMPOUNDS ENERGY ORGANIC COMPOUNDS OXIDATION TO CO 2
ORGANIC COMPOUNDS H 2 H 2 S NH 3 LIGHT PROVIDES ENERGY ELECTRON
ACCEPTOR O 2 H 2 O NO 3 - NO 2 - NO 2 - N 2 SO 4 - - SO 3 - - SO 3
- - H 2 S O 2 H 2 O NO TERMINAL e - ACCEPTOR e - FLOW IS CYCLIC
FOOD NUTRITION AND RESPIRATION MODES 2
Slide 44
PHOTOTROPHIC NUTRITION AND RESPIRATION [PLANTS AND
CYANOBACTERIA - OXYGENIC, EVOLVE OXYGEN FROM H 2 O] ANOXYGENIC
PHOTOSYNTHETIC BACTERIA - DO NOT GENERATE O 2 - HAVE
BACTERIOCHLOROPHYLL PROTON DONORS [H 2 S; SUCCINATE] PROTON
GRADIENT- PROTON MOTIVE FORCE ATP SYNTHESIS EXCITED B Ch P
BACTERIO- CHLOROPHYLL [B Ch P] LIGHT 3
Slide 45
NITROGEN FIXATION N 2 ATMOSPHERIC NH 3 AMMONIA ORGANIC NITROGEN
RHIZOBIUM - LEGUMES AZOTOBACTER - FREE LIVING 4
Slide 46
ORGANIC COMPOUNDS (GLUCOSE) CATABOLISM BY-PRODUCTS (WASTE) ATP
SIMPLE COMPOUNDS [12 KEY, CENTRAL METABOLITES] LOW MOLECULAR WEIGHT
PRECURSORS OF MACROMOLECULES CELLULAR CONSTITUENTS ANABOLISM 5
Slide 47
GLUCOSE-6-PHOSPHATE FRUCTOSE-6-PHOSPHATE RIBOSE-5-PHOSPHATE
ERYTHROSE-4-PHOSPHATE DIHYDROXY-ACETONE PHOSPHATE
3-PHOSPHOGLYCERATE PHOSPHOENOL PYRUVATE PYRUVATE ACETYL-CoA
KETOGLUTARATE SUCCINYL-CoA OXALOACETATE MONO AND DISACCHARIDES
POLY- SACCHARIDES FATTY ACIDS LIPIDS AMINO ACIDS PROTEIN MONO-
NUCLEOTIDES RNA, DNA VITAMINS CO 2 ORGANIC COMPOUNDS HETEROTROPHS
AUTOTROPHS LIST IS NOT ASSIGNED 6
Slide 48
PENTOSE BIOSYNTHESIS GLUCOSE-6-PRIBULOSE-5-P RIBOSE-5-P RING
STRUCTURE - RIBOSE-5-P GLUCOSE-6-PHOSPHATE CO 2 7
INDOLE GLYCEROL PO 4 L-TRYPTOPHAN SERINE GLYCERALDEHYDE- 3-
PHOSPHATE 11
Slide 53
TAKE AWAY: FREE ENERGY; ENZYME PROPERTIES & FUNCTION;
OXIDATION/REDUCTION; COENZYME PROPERTIES & FUNCTIONS; NAD+
& NADH PLUS H+; HIGH & LOW ENERGY BONDS. GLYCOLYSIS,
RESPIRATION, FERMENTATION WHAT GOES IN/COMES OUT; HOW CELLS BENEFIT
FROM EACH. SUBSTRATE LEVEL PHOSPHORYLATION & OXIDATIVE
PHOSPHORYLATION. ELECTRON TRANS- PORT CHAIN; CHEMIOSMOSIS, PROTON
MOTIVE FORCE; ATP SYNTHASE. MODES OF MICROBIAL
NUTRITION/RESPIRATION; PHOTOSYNTHESIS/NITROGEN FIXATION. ANABOLISM
PATHWAYS; WHAT IS INVOLVED IN TRYPTOPHAN BIOSYNTHESIS? FUNCTIONAL
GROUPS, GENETIC INFORMATION AND ITS USE.