Metabolism: Fueling Cell Growth

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Metabolism Fueling Cell Growth

• Chapter 6

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6.1 Principles of Metabolism

• Metabolism is the process of chemical reactions
  that produce biomolecules and energy
• Some metabolic processes are common to all
  bacteria, while others are unique

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• Metabolism has two components
• Catabolism
• The break-down of macromolecules into subunits
  (e.g., polypeptides to amino acids)
• Generates energy (ATP) for use by the cell
• Generates waste products
• Anabolism
• Synthesis of macromolecules and cellular products
• Consumes energy

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Harvesting Energy

• Energy is the capacity to do work
• Potential energy is stored energy
• Kinetic energy is energy of motion

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Harvesting Energy (cont.)

• First Law of Thermodynamics
• Energy cannot be created nor destroyed
• However, it can be converted from one form to
  another
• Photosynthetic organisms convert radiant energy
  (sunlight) into chemical energy (ATP)
• Chemoorganotrophic organisms convert one form of
  chemical energy (glucose) into another form (ATP)

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Harvesting Energy (cont.)

• Some molecules release energy when they break
  down
• This energy is termed free energy and is
  available to the cell for other chemical
  reactions
• If the reactants (starting compounds) have more
  stored energy than the products (ending
  compounds), then free energy is released
• These reactions are termed exergonic
• If the reactants have less stored energy than is
  needed to produce the products, then free energy
  must be applied to the reaction for it to proceed
• These reactions are termed endergonic

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Components of Metabolic Pathways C

• In biological systems, a series of connected
  chemical reactions is termed a metabolic pathway
• These reactions usually have several
  intermediates, often weak acids, leading to an
  end product
• Metabolic pathways can be
• Linear
• Branching
• Circular

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The Role of Enzymes C

• Some chemical reactions occur very slowly
• Enzymes accelerate the rate of a reaction, often
  by using energy (e.g., ATP)
• Enzymes bind to a substrate (molecule) and
  convert it to a product

1 Time required for a reaction to occur
spontaneously 2 Number of reactions that occur
per second if enzyme is included
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The Role of ATP C

• Adenosine triphosphate (ATP) is the principal
  chemical energy of cells
• Triphosphates have potential energy
• The release of the gamma phosphate of ATP is a
  spontaneous event that releases free energy that
  can be used in other reactions

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The Role of the Chemical Energy Source C

• The compound that releases energy when broken
  down is the energy source
• Many bacteria use sugars, such as glucose, as an
  energy source
• Others use sulfur- and ammonia-based compounds as
  energy sources
• Regardless of source, electrons (e-) must be
  transferred between electron carrier molecules
• The movement of electrons between such molecules
  are referred to as redox (reduction-oxidation)
  reactions
• Molecules that lose e- (and often H) are
  oxidized
• Molecules that gain e- (and often H) are reduced

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• An oxidation reaction that results in the removal
  of a H (and its accompanying e-) is a
  dehydrogenation reaction
• A reduction reaction that results in the addition
  of a H (and its accompanying e-) is a
  hydrogenation reaction
• Three principal molecules are involved in
  reduction reactions
• FADH2
• NADH
• NADPH

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The Role of the Electron Carriers C

• While H can exist in water, e- must be bound to
  carrier molecules
• The electron carrier molecules control the flow
  of electrons from one molecule to another, thus
  control redox reactions
• Electron carriers are commonly used in regulating
  energy-using and energy-producing reactions
• Glycolysis (production of ATP and pyruvate)
• Pentose phosphate pathway (production of NADPH)
• TCA cycle (production of ATP, NADH, FADH2)
• Aerobic respiration (production of ATP)

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6.2 Enzymes

• Enzymes are proteins that facilitate the
  conversion of a substrate into a product
• Each enzyme has an active site where it acts upon
  the substrate
• Enzymes are not consumed during the reaction and,
  thus, are reusable
• The enzyme engages the substrate in a specific
  orientation, termed induced fit, to catalyze a
  reaction

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Enzymes (cont.)

• Cofactors and Coenzymes
• Some enzymes require the assistance of
  non-protein components (cofactors) to function
• Some cofactors are inorganic (e.g., Zn2)
• Others are organic, termed coenzymes, and most
  are derived from vitamins
• Some cofactors bind to the enzyme, while others
  bind to the substrate

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Enzymes (cont.)

• Environmental factors that influence enzyme
  activity
• Temperature
• pH
• Salt concentration

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Enzymes (cont.)

• Allosteric regulation
• Regulatory molecules can bind to enzymes outside
  of the active site to regulate the enzymes
  activity
• These molecules affect the 3D structure of the
  enzyme, which alters its active site
• This regulation provides an on/off switch for
  enzymes

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Enzymes (cont.)

• Enzyme inhibitors
• Competitive - molecules that bind to the enzymes
  active site and out-compete the substrate
• Higher molar concentration
• Higher affinity for active site
• Noncompetitive - molecules that bind outside of
  the active site, but alter the enzymes ability to
  bind to the substrate

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6.3 The Central Metabolic Pathways
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Glycolysis

• Glucose hydrolysis
• Input
• 1 Glucose
• 2 ATP
• Output
• 4 ATP
• NADH (reducing agent)
• 2 pyruvate

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Pentose Phosphate Pathway

• Alternative glucose hydrolysis
• Output
• 5- and 7-carbon sugars
• NADPH (biosynthesis)
• Glyceraldehyde-3-phosphate, which can enter
  glycolysis

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Tricarboxylic Acid Pathway(aka Citric acid
cycle Krebs cycle)

• Input pyruvate (from glycolysis)
• Output
• 2 ATP
• 6 NADH (reducing agent)
• 2 FADH2 (reducing agent)

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6.4 Respiration

• Aerobic respiration uses reducing agents produced
  by glycolysis and TCA cycle to produce ATP
• NADH
• FADH2
• A phosphate group is covalently linked to ADP to
  form ATP, termed oxidative phosphorylation
• A two-step mechanism is used to generate ATP
• Electron transport chain that builds a proton
  (H) gradient across a membrane
• Proton motive force (PMF) that powers an enzyme,
  ATP synthase, to link phosphate to ADP

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Respiration (cont.)

• In prokaryotes, the membrane is the cytoplasmic
  membrane surrounding the cell
• In eukaryotes, the membrane is the inner membrane
  of the mitochondrian
• Both systems are nearly identical

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Respiration (cont.)

• Electron Transport Chain generates the PMF
• NADH and FADH2 are electron donors
• They give up their electrons to a series of
  protein complexes that use the energy to
  translocate H across the membrane
• The accumulation of H on one side of a membrane
  forms an electrochemical gradient

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Respiration (cont.)
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Respiration (cont.)

• ATP Synthase
• Enzyme composed of more than a dozen polypeptides
• Produces ATP by rotational catalysis
• Operates by the proton motive force

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Respiration (cont.)
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Putting it all together...
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Respiration (cont.)

• Net production from 1 glucose molecule is 38 ATP
  molecules
• 2 ATP from glycolysis
• 2 ATP from TCA cycle
• 34 ATP from aerobic respiration

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6.5 Fermentation

• In respiration, a terminal electron acceptor is
  used to consume donated electrons
• Oxygen is commonly used as the acceptor by
  aerobic microorganisms
• Fermentation is used by organisms that cannot
  perform respiration to consume electrons
• Oxygen is not available
• Obligate anaerobe (lacks genes for the proteins
  of the electron transport chain)
• Fermentation products are particularly useful for
  identifying enteric bacteria

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6.6 Catabolism of Organic Compounds Other Than
Glucose

• Polysaccharides and disaccharides
• Broken down into simple sugars
• These simple sugars can enter glycolysis
• Lipids are broken down by lipases
• Glycerol can enter glycolysis
• Fatty acids can enter the TCA cycle
• Proteins are broken down by proteases
• Amino acids can be recycled

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6.7 Chemolithotrophs

• Use reduced inorganic compounds as a source of
  energy
• Hydrogen sulfide (H2S)
• Ammonia (NH3)
• These compounds are electron sources that are
  used in oxidative phosphorylation to produce ATP

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6.8 Photosynthesis

• Photosynthetic bacteria capture photons from
  radiant energy for ATP synthesis
• Pigments, such as chlorophyl, capture light
  energy and funnels it to an electron transport
  chain

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• The ETC is used to generate a proton gradient
  that produces ATP and converts inorganic carbon
  into organic carbon (carbon fixation)

6CO2 6H2O ? C6H12O6 6O2
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6.9 Carbon Fixation

• The Calvin cycle is used to convert inorganic
  carbon (CO2) to organic carbon
• CO2 enters the cycle and an enzyme, RUBISCO,
  covalently-links it to a 5-carbon molecule,
  forming a 6-carbon molecule
• The process is energetically-expensive, consuming
  18 ATP and 12 NADPH