Chapter 4: Cellular Metabolism

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Chapter 4 Cellular Metabolism
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Bioenergetics

• Lets discuss some basic principles of energy
  distribution
• Energy is defined as the capacity to work
• Kinetic - energy of motion
• Potential - stored energy, objects not moving but
  have the potential to
• Energy can take the form of mechanical energy,
  heat, sound, electricity or light

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Potential Energy
Kinetic Energy
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Bioenergetics

• Common way to study is in heat thermodynamics
• Unit most used is kilocalorie (kcal)
• 1kcal1000 calories, 1 cal the amount of heat
  needed to raise 1 g of water 1oC
• Also use joules
• 1 joule 1.239 cal

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Bioenergetics

• Energy flows into ecosystems from sun
• (gt 13 x 1023 cal/year!)
• Energy often stored as potential in bonds
• Energy stored in bonds may transfer to new bonds
  - atoms pass from one molecule to another
• Molecule (or atom) loses electron -oxidation
• Molecule (or atom) gains electron -reduction

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Bioenergetics

• Oxidation reduction always occur together
  therefore such reactions are called redox
  reactions
• Red reduction
• Ox oxidation
• Energy is transferred and reduced molecule has
  more energy

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Bioenergetics

• Remember that energy is ruled by laws of
  thermodynamics
• Energy cannot be created nor destroyed but can
  only be transferred (balanced), potential to
  kinetic
• Entropy increases - that is disorder is
  continuously increasing
• Disorder is more likely than order
• example-a wall is much more likely to fall than
  rocks are going to spontaneously form a wall

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BioenergeticsEnergy in Chemical Bonds

• Energy is required to break bonds that hold atoms
  in molecule together
• The amount of energy that is available to break
  and form bonds called free energy
• Free energy (G) energy in chem. bonds (H)
  energy unavailable because of disorder (entropy)
  (S) times the absolute temperature (K C
  273)..

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BioenergeticsEnergy in Chemical Bonds

• G H TS
• If G is positive this means that products contain
  more free energy than reactants
• Dont proceed spontaneously, need energy
• This reaction is called endergonic
• If G is negative this means that products contain
  less free energy than reactants
• Occur spontaneously, called exergonic

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BioenergeticsActivation Energy

• If all chemical reactions that release free
  energy tend to occur spontaneously, why havent
  all such reactions already occurred?
• Energy required to break chemical bonds and
  initiate chemical reactions is called activation
  energy
• Activation energies are not a constant, they can
  be lowered by catalysts that stress particular
  chemical bonds
• These bonds become easier to break

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BioenergeticsActivation Energy

• For example.
• Imagine a bowling ball resting in a shallow
  depression on the side of a hill.
• Only narrow rim of dirt below the ball keeps it
  from rolling..
• If you remove that dirt it will roll downhill,
  never UP!
• Removing the lip allows the ball to move freely,
  you are the catalyst lowering the mound of dirt
  (activation energy)

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CatalystsEnzymes

• Chemical reactions within organisms are regulated
  by catalysts
• Most of the catalyst agents are enzymes
• Some catalysts are RNA
• Enzymes (type of protein) bind to a molecule
  (substrate) stressing bonds
• Brings reactants together correctly, or stresses
  chemical bonds
• Stresses break bonds easily decreasing activation
  energy

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Enzymes

• Lets look at an example of the effect of
  enzymes
• CO2 H2O H2CO3 (carbonic acid in vertebrate
  RBC)
• Without enzymes, a cell produces about 200
  molecules in an hour, not useful to cell.
• With an enzyme called carbonic anhydrase, a cell
  can produce 600,000 molecules every second!

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Enzymes

• In this example the enzyme increases the reaction
  10 million times!
• Almost all enzymes end with what three letters?
• ase
• A very important fact of enzymes are they are not
  consumed in the reaction

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Enzymes

• How do enzymes work?
• What type of question is this, proximate or
  ultimate?
• Enzymes bind to a molecule at the active site and
  form an enzyme-substrate complex
• Amino acid side groups of enzyme interact
  chemically w/ substrate stressing or distorting
  particular bond, lowering the activation energy.
• This interaction may facilitate the binding of
  other substrates

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Factors Affecting Enzymes

• The rate of an enzyme-catalyzed reaction is
  affected by
• Concentration of substrate
• Concentration of enzyme
• Temperature
• Salt
• pH
• Inhibitors/activators

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Enzymes

• Concentrations are easily understood
• Temperature
• increase in temperature increases reaction rate
  - more flexible
• Up to certain point, temperature optimum
• Above To, enzyme denatures
• pH
• most enzymes are optimized at a pH (optimum)
  between 6-8 (salt is similar)
• Inhibitor
• molecule binds to an enzyme decreasing its
  activity

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Enzymes

• Inhibitor
• Competitive compete w/ substrate
• Noncompetitive bind to allosteric site and turn
  off, change shape
• Activators - bind to allosteric sites but dont
  turn them off, actually increase enzyme activity
• Enzymes often assisted by cofactors

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Adenosine Triphosphate (ATP)

• Energy currency of all cells is ATP
• Cells use ATP to power nearly every energy
  powering process
• ATP is structured from 3 components
• Ribose 5 C sugar
• Adenine organic 2 C ring
• Triphosphate group chain of 3 phosphates

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Adenosine Triphosphate (ATP)

• How does ATP store energy?
• The key is in the triphosphate group
• Very unstable bonds (negative charges repel one
  another), low activation energy
• The outer bond is readily broken releasing 7.3
  kcal/mole
• ATP becomes adenosine diphosphate (ADP)
• Since ATP unstable, not good at storing energy,
  but carbs and lipids are

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Metabolism Biochemical Pathways

• The total of all chemical reactions in an
  organism are called metabolism
• Reactions that expend energy to form chemical
  bonds are called anabolic
• Reactions that harvest energy when chemical bonds
  are broken are called catabolic
• The products of one reaction become the substrate
  of another in biochemical pathways

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Metabolism Biochemical Pathways

• Biochemical Pathways are mediated by feedback
  inhibition
• The products of pathways often inhibits its
  ability to make more

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Metabolism Biochemical Pathways

• Metabolism has evolved a great deal as life has
  evolved
• This is especially true in organisms that capture
  energy from the sun to build organic molecules
  (anabolism) and ability to break down molecules
  to obtain energy (catabolism)

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Metabolism

• Processes involved in the evolution of metabolism
  are
• Degradation
• Glycolysis
• Anaerobic Photosynthesis
• Nitrogen Fixation
• Oxygen-forming photosynthesis
• Aerobic respiration

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Metabolism

• 1) Degradation the earliest life forms obtained
  energy by breaking down organic molecules that
  were abiotically
• Organisms then stored energy in ATP as do all
  organisms today
• 2) Glycolysis occurs in all organisms,
  breakdown of glucose yields to molecules of ATP
• 6 C ? 3 C in 10 easy steps
• Energy to make ATP comes from forming new ones w/
  less energy

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Metabolism

• 3) Anaerobic photosynthesis evolved in no O2
  environment, use light to pump protons produce
  ATP
• 4) Nitrogen fixation pros and nas need N cant
  get from photosynthesis but can from breaking
  down N2-occurs in bacteria

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Metabolism

• 5) Oxygen-forming photosynthesis substitution of
  H2O instead of H2S produced Oxygen from
  photosynthesis
• 6) Aerobic respiration- final event, cellular
  processes harvest energy from breaking energetic
  electrons from organic molecules, same proton
  pumps as photo.

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How Cells Harvest Energy
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How Cells Harvest Energy

• Every movement of organisms require energy
• Bacteria swimming
• Plant growth
• You reading this requires energy
• We discussed that cells spend energy via ATP, and
  ATP can be created from chemical energy or light
  energy (photosynthesis)

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How Cells Harvest Energy

• Organisms that harvest energy from sunlight are
  called what?
• Autotrophs (self-feeders)
• Organisms that rely on the energy produced from
  plants are called what?
• Heterotrophs (fed by others)
• 95 of organisms are heterotrophs, so we will
  focus on creating ATP with this system.

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How Cells Harvest Energy

• Most foods contain carbs, proteins and fats,
  carbs fats contain many C-H bonds and C-O bonds
  (energy in bonds)
• Enzymes break down large molecules to small ones
  (digestion)
• Other enzymes break bonds and harvest energy
  called catabolism

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How Cells Harvest Energy

• Cellular respiration - cells harvest energy from
  transferring electrons used to make ATP
• Aerobic respiration O2 accepts depleted H atom
• Anaerobic respiration inorganic accepts H atom
• Fermentation organic accepts H atom
• Catabolism of carbohydrates in your cells is very
  similar to burning wood
• C6H12O6 6CO2 6H2O energy (heat or ATP)

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How Cells Harvest Energy

• Key for cells to harvest useful energy from
  catabolism is to transfer energy to useful ATP
• Each Phosphate (-) charged which repel each other
• Phosphate groups push against the bond and store
  energy there (like a cocked mousetrap)
• ATP is used for all movement and processes but
  also used to drive endergonic reactions

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Glucose Catabolism

• Cells synthesize ATP from catabolism of organic
  molecules in 2 different ways
• Substrate-level phosphorylation
• Phosphate group transferred to ADP from phosphate
  bearing intermediate
• Aerobic respiration
• ATP forms from harvesting electrons along the
  electron transport chain - eventually donated to
  oxygen
• Eukaryotes produce majority of ATP this way (from
  glucose)

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Glucose Catabolism

• In most organisms, both of these processes are
  used together
• To harvest energy to make ATP from the sugar
  glucose in the presence of oxygen, cell carries
  out series of 4 (enzyme-catalyzed) reactions

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Glucose Catabolism

• These 4 stages of reactions are
• Glycolysis (phosphorylation)
• Pyruvate Oxidation (aerobic respiration)
• The Krebs Cycle (aerobic respiration)
• Electron Chain Transport (aerobic respiration)

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Stage 1 GlycolysisA Substrate Level
Phosphorylation

• Glycolysis
• The first step is to first extract energy from
  glucose which requires a 10-reaction biochemical
  pathway (glycolysis) that produces ATP by
  substrate-level phosphorylation and 2 pyruvate.
• Enzymes used in cytoplasm of cell
• 4 ATP molecules are produced -2 ATP molecules are
  used net of 2 ATP
• 4 electrons harvested as NADH (can be used to
  make ATP in aerobic respiration)

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Glycolysis

• 1st 5 reactions demand energy from ATP
• The first 3 reactions are considered the priming
  reactions
• 1) phosphorylation of glucose by ATP
• 2-3) rearrange, another phosphorylation
• 4-5) molecule split into 2 molecules (G3P)
• Each G3P molecule will yield 2 ATP

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Glycolysis

• The second half of glycolysis converts our G3P
  into pyruvate yielding ATP
• 6) Oxidation and phosphorylation from NAD
  produce 2 NADH molecules
• 7-10) converts G3P into pyruvate produce ATP
• 2 ATP in, 4 ATP out (gain 2)
• 2 NADH
• 2 Pyruvate

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Glycolysis

• Glycolysis is believed to be one of the earliest
  biochemical reactions to evolve
• It occurs in all cells, happens in the cytoplasm
  and is not associated with any organelles
• Can readily occur in anaerobic environments
  (lacking oxygen)
• Metabolism has evolved one layer of reactions
  added to another.
• What happens to pyruvate?

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Pyruvate OxidationStage 2

• Pyruvate Oxidation
• Pyruvate (the end product of glycolysis) is
  converted into CO2 and Acetyl-CoA
• For each molecule of pyruvate converted, one
  molecule of NAD is reduced to NADH
• This will become important for later stages of
  aerobic respiration

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Oxidation of Pyruvate

• Picks up where glycolysis left off
• This process takes place in mitochondria
• Provides a lot of energy, occurs in 2 steps
• Oxidizes pyruvate to form acetyl-CoA
• Oxidizes Acetyl-CoA in the Krebs cycle

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Oxidation of Pyruvate

• Oxidation of Pyruvate
• Pyruvate has 3 carbons
• one is cleaved and leaves as CO2
• 2 Carbon called acetyl group
• H (and pair of e-) which reduce NAD to NADH
• Pyruvate NAD CoA Acetyl-Coa NADH
  (produces ATP) CO2
• Acetyl-CoA is important b/c metabolic breakdown
  of pros, fats etc. all produce it
• It is then channeled for fat synthesis or ATP
  production

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Oxidation of Pyruvate

• Using Acetyl-CoA
• So what determines whether acetyl-CoA is used for
  ATP synthesis or fat storage?
• Guess
• Depends on the level of ATP in the cell!
• If ATP is not being used, Acetyl-CoA is used for
  fat synthesis (develop fat reserves)
• If ATP low, Acetyl-CoA ATP

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The Krebs CycleStage 3

• The Krebs Cycle
• Acetyl-CoA is used in 9 reactions (Krebs Cycle)
  which is sometimes called Citric Acid Cycle
• In Krebs Cycle, 2 more ATP are produced from
  substrate-level phosphorylation
• A lot of electrons are removed by reduction of
  NAD to NADH

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The Krebs Cycle

• After glycolysis catabolizes glucose to produce
  pyruvate
• Pyruvate is oxidized to form acetyl-CoA
• Acetyl-CoA is oxidized in a series of 9 reactions
  called The Krebs Cycle
• 9 reactions broken into 2 steps
• Priming-prep molecule for energy extraction
• Energy extraction-remove e-/generate ATP

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The Krebs Cycle

• The Krebs Cycle uses these 9 reactions to extract
  energetic electrons to synthesize ATP
• Acetyl-CoA enters the cycle and two CO2 molecules
  and several electrons are the products of this
  cycle

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The Krebs Cycle

• The Krebs Cycle
• Reaction 1 Condensation
• acetyl-CoA joins with oxaloacetate to form
  citrate
• Reaction is inhibited when cell has ample ATP
• Acetyl-CoA is channeled to fat synthesis
• Reaction 2 3 Isomerization
• H group and OH group must reposition-product is
  called isocitrate

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The Krebs Cycle

• The Krebs Cycle
• Reaction 4 First oxidation
• isocitrate undergoes oxidative reaction yielding
  a pair of electrons that reduce NAD to NADH
• End product is CO2, NADH and a-ketoglutarate
• Reaction 5 Second oxidation
• a-ketoglutarate is oxidized yielding a pair of
  electrons reduce NAD, CO2 leaves and succinyl
  group that joins w/CoA to make succinyl-CoA

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The Krebs Cycle

• The Krebs Cycle
• Reaction 6 Substrate-level phosphorylation
• Succinyl and CoA have unstable bond (high energy)
• Bond is cleaved (like glycolysis) and energy
  drives phosphorylation of GDP to GTP to ATP
• Reaction 7 Third oxidation
• Succinate oxidized to fumarate however free
  energy change cant convert NAD, so FAD accepts
  electron for electron transport chain

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The Krebs Cycle

• The Krebs Cycle
• Reaction 8 9 Regeneration of oxaloacetate
• Water is added to fumarate to form malate
• Malate is oxidized to release two electrons to
  reduce NAD to NADH and form oxalacetate
• Oxalacetate can again combine with acetyl-CoA to
  start the cycle all over again!
• Remember, 2 pyruvate enter the Krebs Cycle, so
  we have made an additional 2 ATP.
• What happens to NADH and FADH, and wheres all
  the energy?

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Electron Transport ChainFinal Step in Aerobic
Respiration

• In Electron Transport Chain, electrons carried by
  NADH are used to drive the synthesis of a large
  amount of ATP
• Most ATP used for reactions in our cells are
  acquired from this step

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How we get energy

• C-H bonds share electrons equally
• Electrons want to move to a more electronegative
  atom (i.e. Oxygen), releasing energy as it shifts
• Glucose energy-rich food is abundant with C-H
  bonds
• Energy produced not only from release of e- from
  C-H bonds but from a shift in position

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Electron Transport Chain (ETC)

• Two e- and one H transferred to NAD to form
  NADH
• NADH carries e- to ETC, series of molecules
  (proteins) embedded w/in inner membrane of
  mitochondria
• NADH delivers to top, Oxygen accepts at bottom
• Each step, e- moves slightly more
  electronegative, moving down an energy gradient

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Electron Transport Chain

• NADH FADH2 molecules formed during the first 3
  stages of aerobic respiration each contain a pair
  of electrons
• These molecules carry their electrons to
  mitochondria where they transfer the electrons to
  a series of proteins collectively called electron
  chain transport

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Electron Transport Chain

• The first protein to receive the es is called
  the NADH dehydrogenase
• A carrier passes the es from the NADH
  dehydrogenase to a protein called bc1
  complex-drives protons across membranes
• e- carried to another protein called cytochrome
  oxidase complex
• O2 4H 4e- ? 2H2O

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Electron Transport Chain

• Cytochrome complex uses 4 electrons to reduce a
  molecule of oxygen
• Each oxygen then combines with 2 hydrogen ions to
  form water
• It is the availability of a plentiful acceptor
  (oxygen) that makes oxidative respiration
  possible
• ETC used in aerobic respiration

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Electron Transport Chain

• Building of an Electrochemical Gradient
• As electrons are harvested by oxidative
  respiration by passing along the electron
  transport chain, the energy they release
  transports protons out of the matrix
• Electrons from NADH activate all three of these
  proton pumps while FADH2 activates only two

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Electron Transport Chain

• Producing ATPChemiosis
• As the concentration gradient on the outside
  increases, the internal mitochondria attracts
  protons and they pass through ion channels
• When protons pass through, channels synthesize
  ATP from ADP P, which is then transported into
  cytoplasm
• This process is called chemiosis
• Works by diffusion, similar to osmosis

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Summarizing Aerobic Respiration

• How much metabolic energy is actually gained?
• Theoretical Yield
• 4 ATP from substrate-level phosphorylation
• 30 ATP from NADH (3 from each of 10 molecules)
• 4 ATP from FADH2 (2 from each of 2 molecules)
• This equals 38 gross however subtract 2 ATP that
  initiated NADH in glycolysis for 36 ATP NET

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Summarizing Aerobic Respiration

• Why theoretical?
• Is somewhat lower because mitochondrial membrane
  is leaky and protons can enter without going
  through ion channels
• Also protons generated by mitochondria are often
  used for other things besides ATP synthesis
• Total net gain is usually closer to 30 ATP

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Summarizing Aerobic Respiration

• How is ATP synthesis initiated or stopped?
• 2 control points
• Phosphofructokinase (in glycolysis)
• Levels of a ATP control inhibition
• Citrate synthesis (in Krebs cycle)
• Levels of a ATP control inhibition

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Tidying Up Respiration

• Glucose is not the only source of energy
• Both proteins and lipids can be used for cellular
  respiration
• Essentially same steps involved
• Fats produce more energy than glucose
• The break down of one triglyceride 462 ATP!
• By weight, you get 2.5 X the ATP from fats as
  from sugar
• Cells can metabolize w/out O2
• Fermentation - only glycolysis
• Lactic acid only glycolysis
• Transfer H from NADH to Pyruvate ? Lactic Acid

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Waste Products

• Carbohydrates
• Lipids
• Proteins
• Amino acids used for rebuilding tissues
• Waste nitrogen compounds
• NH3 (ammonia) released by fish thru gills
• Urea released by amphibians and mammals in urine
• Uric acid released by insects, birds, and
  reptiles in urine/feces

CO2 and H20
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Anaerobic Respiration

• In the absence of oxygen, some organisms are
  capable of using inorganic molecules to accept
  electrons producing ATP
• Methanogens use CO2 as electron acceptor
  reducing CO2 to CH4 (methane) from which H is
  from other organisms
• Sulfur Bacteria bacteria that live in rocks use
  SO4 (sulfate) as electron acceptors and reduce it
  to H2S