Metabolism: Fueling Cell Growth

1
MetabolismFueling Cell Growth

• Chapter 6

2
Metabolism

• Cells must accomplish two fundamental tasks to
  grow
• Synthesize new components
• Biosynthesis
• Harvest energy
• The sum total of chemical reactions of
  biosynthesis and energy-harvesting is termed
  metabolism

3
Principles of Metabolism

• Metabolism is broken down into two components
• Anabolism
• Catabolism
• Catabolism
• Degradative reactions
• Reactions produce energy from the break down of
  larger molecules
• Anabolism
• Reactions involved in the synthesis of cell
  components
• Anabolic reactions require energy
• Anabolic reactions utilize the energy produced
  from catabolic reactions

4
Principles of Metabolism

• Harvesting energy
• Energy defined as capacity to do work
• Exists as
• Potential energy
• Stored energy
• Kinetic energy
• Energy in motion
• Doing work
• Energy can be converted from one form to another
• Potential ? kinetic
• Kinetic ? potential

5
Principles of Metabolism

• Harvesting energy
• Amount of energy available released from bonds is
  free energy
• Energy available to do work
• If reactants have more free energy than products,
  energy is released
• Exergonic reaction
• If products have more energy that reactants,
  energy is consumed
• Endergonic reaction

6
Principles of Metabolism

• Components of metabolic pathways
• Process occurs in sequence of chemical reactions
• Starting compound is converted to intermediate
  molecules and end products
• Intermediates and end products can be used as
  precursor metabolites
• Metabolic pathways employ critical components to
  complete processes
• Enzymes
• ATP
• Chemical energy source
• Electron carriers
• Precursor metabolites

7
Principles of Metabolism

• Role of enzymes
• Enzymes facilitate each step of metabolic pathway
• They are proteins acting as chemical catalysts
• Accelerate conversion of substrate to product
• Catalyze reactions by lowering activation energy
• Energy required to initiate a chemical reaction

8
Principles of Metabolism

• Role of ATP
• Adenosine triphosphate (ATP)
• Energy currency of cell
• Negatively charged phosphate groups attached to
  adenosine molecule
• Negative charges of phosphate repel
• Create unstable bond that is easily broken
  releasing energy
• ATP created by three mechanism
• Substrate phosphorylation
• Oxidative phosphorylation
• Photophosphorylation

9
Principles of Metabolism

• Substrate phosphorylation
• Uses chemical energy to add phosphate ion to
  molecule of ADP
• Oxidative phosphorylation
• Uses energy from proton motive force to add
  phosphate ion to ADP
• Photophosphorylation
• Utilizes radiant energy from sun the
  phosphorylate ADP to ATP

10
Principles of Metabolism

• Role of chemical energy source
• Energy source
• Compound broken down to release energy
• Variety of compounds available
• Glucose most common organic molecule
• Harvesting energy requires series of coupled
  reactions
• Oxidation-reduction reactions

11
Principles of Metabolism

• Oxidation-reduction reactions
• Reactions in which one or more electrons is
  transferred from one substance to another
• Compounds that LOSE electrons are oxidized
• Termed electron donor
• Compounds that GAIN electrons are reduced
• Termed electron carrier
• In reactions electrons are removed
• Protons often follow generally in the form of H
  ion
• H ion has one proton and no electron

12
Principles of Metabolism

• Role of electron carriers
• Three different types of electron carriers
• Nicotinamide adenine dinucleotide
• NAD
• Flavin adenine dinucleotide
• FAD
• Nicotinamide adenine dinucleotide phosphate
• NADP
• Reduced forms represent reducing power
• Due to usable energy in bonds
• Reduced forms
• NADH
• FADH2
• NADPH

13
Principles of Metabolism

• Precursor metabolites
• Intermediate products produced in catabolic
  pathways
• Used in anabolic pathways
• Serve as raw materials for construction of
  macromolecules

14
Principles of Metabolism

• Scheme of metabolism
• Three key pathways
• Central metabolic pathways
• Glycolysis
• Pentose phosphate pathway
• Tricarboxcylic acid cycle
• Central pathways are catabolic and provide
• Energy
• Reducing power
• Precursor metabolites

15
Principles of Metabolism

• Glycolysis
• Oxidizes glucose to two molecules of pyruvate
• Pentose phosphate pathway (PPP)
• Breaks down glucose
• Produces molecules for biosynthesis
• Works in conjunction with glucose degrading
  pathways
• Tricarboxylic acid cycle (TCA) Krebs Cycle
• Before entering cycle pyruvate enters transition
  step
• Pyruvate formed in glycolysis and PPP
• Cycle turns twice to complete oxidation of one
  glucose molecule

16
Principles of Metabolism

• Respiration vs. fermentation
• Respiration uses reducing power to generate ATP
• NADH and FADH2 transfer electrons to produce
  proton motive force
• Allows for recycling of electron carriers
• Electrons join with terminal electron acceptor
• Oxygen in aerobic respiration
• Anaerobic respiration uses another inorganic
  molecule
• Fermentation is partial oxidation of glucose
• Produces very little ATP
• Uses pyruvate or derivative as terminal electron
  acceptor
• Other organisms may use other organic molecules
  as terminal electron acceptor

17
Enzymes

• Act as biological catalysts
• Very specific
• A particular enzyme will only act with one or a
  limited number of substrates
• Enzymes do not alter the reactants or products of
  a chemical reaction
• Enzymes are not altered by the chemical reaction
  they catalyze
• Enzymes are usually named for the substrate they
  act on and end in the suffix ase
• Protease

18
Enzymes

• Enzyme action
• Enzymes act in two steps
• Substrate binds to the active site of the enzyme
  to form an enzyme/substrate complex
• A substrate is the specific substance on which
  the enzyme acts
• Products are formed

• E S ? ES ? E P
• Enzyme is released to bind new substrate
• Enzymes are regulated to prevent over production
  of product

19
Enzymes

• Cofactors and coenzymes
• Cofactors
• Non-protein component reacting with enzyme
• Coenzymes
• Organic cofactors
• Act as carriers for molecules or electrons
• NAD, FAD and NADP are coenzymes
• Not as specific as enzymes
• May act with numerous enzymes

20
Enzymes

• Environmental factors of enzyme activity
• Enzymes function in narrow range of environmental
  factors
• Factors affecting enzyme activity are
• Temperature
• Increases temperature increases speed of reaction
• Extremely high temperature makes enzyme non
  functional
• pH
• Enzymes function best at pH just above 7
• Salt concentration
• Low salt concentration are most desired

21
Enzymes

• Allosteric regulation
• Regulation regulates production of product
• Regulatory molecule binds to allosteric site of
  enzyme
• Alters affinity of enzyme to substrate
• Allosteric enzymes initiates activity of give
  pathway
• Regulation controls metabolic activity
• Feedback inhibition
• End product of pathway acts on allotter site of
  enzyme
• Shuts pathway down

22
Enzymes

• Enzyme inhibition
• Non-competitive inhibition
• Inhibitor and substrate act on different enzyme
  sites
• Allosteric inhibition
• Feedback inhibition
• Competitive inhibition
• Inhibitor competes for active site with substrate
• Inhibitor structurally similar to substrate
• Sulfa drugs compete with PABA for active site on
  enzyme that produces folic acid

23
Central Metabolic Pathways

• Pathways modify organic molecules to form
• High energy intermediates to synthesize ATP
• Intermediates to generate reducing power
• Intermediate and end products as precursor
  metabolites
• Pathways
• Glycolysis
• Pentose Phosphate Pathway
• Tricarboxylic Acid Cycle

24
Central Metabolic Pathways

• Glycolysis
• Primary pathway to convert one glucose to two
  pyruvate
• 10 step process
• Pathway generates
• Two 3-C pyruvate molecules
• Net gain of two ATP
• 2 ATP expended to break glucose
• 4 ATP harvested
• Two molecules reducing power
• NADH
• Six different precursor metabolites
• 5 intermediates and pyruvate

25
Glycolysis
26
Central Metabolic Pathways

• Pentose phosphate pathway
• Generates 5 and 7 carbon sugars
• Also produces glyceraldehyde 3-phosphate
• Can go into glycolysis for further breakdown
• Pathway major contributor to biosynthesis
• Produces reducing power in NADPH
• Two vital precursor metabolites

27
Central Metabolic Pathways

• Transition step
• Links glycolysis to Tricarboxylic Acid Cycle
• Modifies 3-C pyruvate from glycolysis to 2-C
  acetyl CoA
• CO2 is removed through decarboxylation
• Remaining 2-C acetyl group joined to coenzyme A
• Forms Acetyl CoA
• NAD is reduced to NADH
• Each pyruvate enters transition step
• Reaction occurs twice for one glucose
• Yield from transition step
• Reducing power
• NADH
• Precursor metabolites
• Acetyl CoA

28
Central Metabolic Pathways

• Tricarboxylic acid cycle
• Completes the oxidation of glucose
• Incorporates acetyl CoA from transition step
• Releases CO2 in net reaction
• Cycle turns once for each acetyl CoA
• Two turns for each glucose molecule
• Cycle produces
• 2 ATP
• 6 NADH
• 2 FADH2
• 2 precursor metabolites

29
Tricarboxylic Acid Cycle
30
Respiration

• Uses NADH and FADH2 to synthesize ATP
• Oxidative phosphorylation
• Occurs in electron transport chain
• Generates proton motive force
• Combined with ATP synthase
• Uses energy in proton motive force to synthesize
  ATP

31
Respiration

• Electron transport chain
• Group of membrane-embedded electron carriers
• Arrangement of carriers aids in production of
  proton motive force
• Four types of electron carriers
• Flavoproteins
• Iron-sulfur proteins
• Quinones
• Cytochromes

32
Respiration

• Mechanism of proton motive force
• Certain carriers accept protons and electrons,
  some accept only electrons
• Pump protons across membrane
• Creates a proton gradient (proton motive force
• Arrangement of carriers causes protons to be
  shuttled across membrane

33
Respiration

• Electron transport chain of mitochondria
• Chain consists of following components
• Complex I
• A.k.a NADH dehydrogenase complex
• Complex II
• A.k.a succinate dehydrogenase complex
• Coenzyme Q
• A.k.a cyrochiome bc, complex
• Complex III
• Cytochrome C
• A.k.a. Cyrochiome c oxidate complex
• Complex IV
• Each carrier accepts electrons from previous
  carrier
• In process protons are pumped across membrane

34
Electron Transport Chainof Mitochondria
35
Respiration

• Electron transport chain of prokaryotes
• Respiration is either aerobic or anaerobic
• In aerobic respiration some prokaryotes have
  enzymes equivalent to complex I and II of
  mitochondria
• Do not have enzyme equivalents of complex III or
  cytochrome c
• Use quinones instead (ubiquinone)
• Shuttles electrons directly to terminal electron
  acceptor
• Oxygen acts as acceptor when available

36
Electron Transport Chainof Prokaryotes (Aerobic)
37
Respiration

• Electron transport chain in prokaryotes
• Anaerobic respiration is less efficient
• Alternative electron carriers used
• Oxygen does not act as terminal electron acceptor
• Some bacteria use nitrate
• Nitrate converted to nitrite
• Nitrite converted to ammonia
• Sulfur-reduce bacteria use sulfate as terminal
  electron acceptor
• Quinone carrier (menaquinone) produces vitamin K

38
Respiration

• ATP synthase
• Harvest energy from proton motive force to
  synthesize ATP
• Permits protons to flow back into cell
• Produces enough energy to phosphorylate ADP ? ATP
• 1 ATP is formed from entry of 3 protons
• 10 protons pumped out per NADH
• One NADH produces 3 molecules ATP
• 6 protons pumped out per FADH
• One FADH2 produces 2 molecules of ATP

39
Respiration

• ATP from oxidative phosphorylation
• ATP produced through re-oxidation of NADH and
  FADH2
• Maximum theoretical yield
• From glycolysis
• 2 NADH ? 6 ATP
• From transition step
• 2 NADH ? 6 ATP
• From TCA
• 6 NADH ? 18 ATP
• 2 FADH2 ? 4 ATP

40
Respiration

• Total ATP yield from prokaryotic aerobic
  respiration
• Substrate phosphorylation
• 4 ATP
• Net 2 from glycolysis
• 2 ATP from TCA
• Oxidative phosphorylation
• 34 ATP
• 6 ATP from glycolysis
• Re-oxidation of 2 NADH
• 6 from transition step
• Re-oxidation of NADH
• 22 from TCA cycle
• Re-oxidation of NADH and FADH2
• Total yield
• 4 34 38 (theoretical maximum)
• Eukaryotic cells have theoretical maximum of 36
• 2 ATP spent crossing mitochondrial membrane

41
Fermentation

• Used by organisms that cannot respire
• Due to lack of suitable inorganic electron
  acceptor or lack of electron transport chain
• ATP produced only in glycolysis
• Other steps for consuming excess reducing power
• Recycles NADH
• Fermentation pathways use pyruvate or derivative
  as terminal electron acceptor

42
Fermentation

• End products of fermentation include
• Lactic acid
• Ethanol
• Butyric acid
• Propionic acid
• 2,3-Butanediol
• Mixed acids
• All are produced in a series of reaction to
  produce appropriate terminal electron acceptors

43
Catabolism of Other Organic Compounds

• Cells use variety of organic molecules as energy
  sources
• Use hydrolytic enzymes to break bonds
• Hydrolytic reactions add water to break bonds

44
Catabolism of Other Organic Compounds

• Polysaccharides and disaccharides
• Starch and cellulose polymers of glucose
• Amylases breaks down starch to glucose subunits
• Cellulases breaks down cellulose to glucose
  subunits
• Glucose enters glycolysis for metabolism
• Disaccharides are hydrolyzed by specific
  disaccharidases
• Disaccharides are formed between glucose and
  other monosaccharides
• Glucose liberated through hydrolysis enters
  glycolysis
• Other monosaccharide modified before metabolism

45
Catabolism of Other Organic Compounds

• Lipids
• Simple lipids are combination of fatty acids and
  glycerol
• Hydrolyzed by lipases
• Glycerol is converted to dihydroxyacetone
  phosphate
• Molecule enters glycolysis
• Fatty acids degraded by ß-oxidation
• Transfers 2-C fatty acid units to coenzyme A
• Forms acetyl CoA that enters TCA cycle

46
Catabolism of Other Organic Compounds

• Proteins
• Hydrolyzed by proteases
• Amino group removed through deamination
• Remaining carbon skeleton converted to precursor
  metabolite

47
Chemolithotrophs

• Chemolithotrophs able to reduce inorganic
  chemicals as source of energy
• Organisms fall into four groups
• Hydrogen bacteria
• Oxidize hydrogen gas
• Sulfur bacteria
• Oxidize hydrogen sulfide
• Iron bacteria
• Oxidized reduced iron
• Nitrifying bacteria
• Two groups
• One oxidizes ammonia to nitrite
• One oxidizes nitrite to nitrate

48
Chemolithotrophs

• Chemolithotrophs generate ATP through oxidative
  phosphorylation
• Amount of energy gained depends on energy source
  and terminal electron acceptor
• Organisms thrive in specific environments
• Particularly where reduced inorganic compounds
  are found
• Do not require external carbon source
• Produce organic carbon from inorganic source
  through carbon fixation

49
Photosynthesis

• Photosynthetic organisms harvest energy from
  sunlight
• Use energy to power synthesis of organic
  compounds from CO2
• Photosynthesis has two distinct stages
• Light dependent reactions
• A.k.a light reactions
• Converts light energy to chemical energy
• Light independent reactions
• a.k.a dark reactions
• Uses energy from light reactions to produce
  organic compounds

50
Photosynthesis

• Capturing radiant energy
• Photosynthetic organisms highly visible due to
  light capturing pigments
• Pigments include
• Chlorophyll
• Found in plants, algae and cyanobacteria
• Bacteriochlorophylls
• Found in purple and green photosynthetic bacteria
• Accessory pigments
• Includes carotenoids and phycobilins
• Carotenoids found in eukaryotes and prokaryotes
• Phycobilins found only in cyanobacteria
• Reaction center pigments
• Function as electron donors
• Antennae pigments
• Funnels light energy to reaction center pigments

51
Photosynthesis

• Converting radiant energy to chemical energy
• Light reactions accomplish two tasks
• Synthesize ATP through photophosphorylation
• Generate reducing power to fix carbon dioxide
• Reducing power may be NADH or NADPH

52
Light Dependant Reactions
53
Carbon Fixation

• Carbon dioxide converted to organic carbon
  through carbon fixation
• Occurs in dark reactions in photosynthesis
• Consumes great deal of energy
• Calvin cycle most common pathway of carbon
  fixation

54
Carbon fixation

• Calvin Cycle
• A.k.a Calvin-Benson cycle
• Has three essential stages
• Incorporation of CO2 into organic compound
• Reduction of resulting molecules
• Regeneration of starting compound
• One molecule of fructose produces from 6 turns of
  cycle
• 6 turns consumes 18 ATP and 12 NADPH
• Process has three sages

55
Anabolic Pathways

• Synthesis of subunits from precursor metabolites
• Pathways consume ATP, reducing power and
  precursor metabolites
• Macromolecules produces once subunits are
  synthesized

56
Anabolic Pathways

• Lipid synthesis
• Synthesis begins with transfer of acetyl group
  from acetyl CoA to acyl carrier protein
• Carrier hold fatty acid during elongation
• Fatty acid released when reaches required length
• 14, 16 or 18 carbons long
• Glycerol is synthesized from dihydroxyacetone
  phosphate

57
Anabolic Pathways

• Amino acid synthesis
• Some precursors are formed in glycolysis other in
  TCA cycle
• Glutamate synthesis essential for formation of
  other amino acids
• Synthesis incorporates ammonia with
  a-ketoglutarate produce in TCA cycle
• Amino group from glutamate can be transferred to
  produced other amino acids
• Precursors for aromatic amino acids produced in
  pentose phosphate pathway and glycolysis

58
Anabolic Pathways

• Nucleotide synthesis
• Nucleotides synthesized as ribonucleotides and
  modified to deoxribonucleotides
• Replace OH group on 2 carbon of ribose and
  replace with hydrogen atom
• Remove oxygen