Unit 1: Metabolic Processes Chapter 2: Cellular Respiration

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Unit 1 Metabolic ProcessesChapter 2 Cellular
Respiration
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Photoautrophheterotrophchemoautotroph
2.1 Cellular Respiration The Big Picture
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Overview of Cellular Respiration
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Process of Cellular Respiration

1. Glycolysis 10 steps breaking down glucose to
   pyruvate (in cytoplasm)
2. Pyruvate Oxidation 1 step occurring in the
   mitochondria matrix
3. Krebs Cycle (tricarboxylic acid cycle, the TCA
   cycle, or the citric acid cycle) 8 steps
   occuring in the mitochondria matrix
4. Electron transport and chemiosmosis (oxidative
   phosphorylation) many steps occurring in inner
   mitochondrial membrane

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Mitochondria convert the potential energy of
food molecules into ATP.
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• an outer mitochondrial membrane encloses the
  entire structure
• an inner mitochondrial membrane encloses a
  fluid-filled matrix
• between the two is the intermembrane space
• the inner membrane is elaborately folded with
  shelflike cristae projecting into the matrix.

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• The outer membrane contains many integral
  membrane proteins that form channels through
  which a variety of molecules and ions move in and
  out of the mitochondrion.
• The inner membrane contains complexes of 5
  integral membrane proteins that form the electron
  transport chain
• The matrix contains a mixture of soluble enzymes
  that catalyze the breakdown of pyruvate. This
  series of enzymatic reactions is the Kreb's cycle.

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OVERALL CHEMICAL EQUATION
1. Many enzymes, co-enzymes, and intermediate
chemicals are involved.
2. It is not a one-step process. Many reactions
occur to release energy in small amounts.
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• Oxidation-Reductions reactions
• Glucose is broken down in a series of chemical
  steps during cellular respiration. Each reaction
  requires a specific enzyme
• At several points in this biochemical pathway,
  oxidation-reduction reactions occur. One
  compound will be oxidized (lose
  electrons/hydrogens) and another will be reduced
  (gain electrons/hydrogens)
• Co-enzymes such as NAD and FAD acts as
  electron/hydrogen acceptors. They will shuttle
  the energy of the electrons to another part of
  the process.

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Nicotinamide Adenine Dinucleotide (NAD)
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In being reduced, NAD can accept two electrons,
but only one proton. The other proton goes into
solution as a hydrogen ion.
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Flavin Adenine Dinucleotide (FAD)
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• The coenzymes gain energy when they gain
  electrons (are reduced).
• This is a temporary state. In another series of
  reactions, the coenzymes give up the electrons
  (and thus the energy) and return to their
  oxidized state.
• The energy they transfer is used to make ATP.

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Methods of forming ATP

• Substrate-Level Phosphorylation - the direct
  transfer of a phosphate group from a substrate to
  ADP to make ATP
• Oxidative phosphorylation - the production of ATP
  using energy derived from the transfer of
  electrons in an electron transport system. This
  is an indirect method and occurs by chemiosmosis.
• Chemiosmosis - the production of ATP utilizing
  the kinetic energy released when H flow through
  the ATP synthase complex

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Substrate level phosphorylation-requires a
substrate-enzyme-direct transfer of a Pi
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GLYCOLYSIS

• IN CYTOSOL
• ONE OF THE OLDEST PATHWAYS all life on earth
  performs glycolysis
• DOES NOT REQUIRE OXYGEN (ANAEROBIC)

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Glucose Activation In the first step, a
phosphate group from ATP is attached to glucose.
This increase the energy level of glucose
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This step is an isomerization
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This is the second phosphorylation. At this
point, 2 ATP molecules have been USED.
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In this step, the glucose molecule is split into
two three carbon molecules. DHAP undergoes
isomerization to G3P. Why???
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In this reaction, G3P is phosphorylated by
inorganic phosphate groups in the cytosol. It is
also oxidized a hydrogen and 2 electrons are
used to reduce NAD to NADH.
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Substrate level phosphorylation!!! Formation of 2
ATP.
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2
Isomerization
2
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2
Phosphoenol pyruvate is also known as PEP
2
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Substrate level phosphorylation formation of two
ATPs Pyruvate is called Pyruvic acid when it is
written in the COOH form. The terms are used
interchangeably.
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• Glycolysis Balance sheet
• For each pyruvate molecule produced by
  glycolysis, 2 ATP are formed ? a total of 4 ATP
  from one glucose molecule.
• Since 2 ATP are used to energize the glucose in
  the first step, there is a net output of 2 ATP
  molecules.
• Some energy is bound in 2 molecules of NADH H
  and will be released in the electron transport
  chain to form ATP.

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What raw materials are necessary for a cell to
produce a molecule of ATP by substrate-level
phosphorylation?

• ADP
• Pi (or a phosphate-containing intermediate from
  glucose)
• A substrate enzyme

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A) In eukaryotic cells, where does glycolysis
occur?B) What does glycolysis mean?

1. In the cytoplasm.
2. The breaking of the glucose molecule into two
   pyruvate molecules

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• 4.
• List the final products of glycolysis.
• What two products of glycolysis may be
  transported into mitochondria for further
  processing?

1. 2 pyruvate, 4 ATP, 2 NADH, 2H, and 2 ADP
2. Pyruvate and NADH

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6. How do ATP and ADP differ in structure and
free energy content?

• ADP has 2 inorganic phosphate groups attached to
  an adenosine molecule, whereas, ATP has 3.
• ATP has 31 kJ/mol more potential energy than ADP

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PYRUVATE OXIDATION

• The PYRUVATE molecules produced by glycolysis
  enter the mitochondria by active transport.
• Pyruvate oxidation occurs in the matrix (inner
  membrane?) of the mitochondria.

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Pyruvate dehydrogenase complex

• Pyruvate oxidation is carried out by a very
  large enzyme complex, the pyruvate dehydrogenase
  complex, which is located in the mitochondrial
  matrix.
• The complex is comprised of three separate
  enzymes involved in the actual catalytic process,
  and uses a total of five different cofactors.
• This reaction is irreversible, and is tightly
  regulated

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PYRUVATE OXIDATION
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• The process of converting pyruvate to acetyl-CoA
  is an oxidative decarboxylation.
• First, the pyruvate is oxidized (it goes from 3C
  to 2C acetyl.) CO2 is released as a result).
• Secondly, NAD is reduced to NADH H
• Thirdly, the 2-carbon acetyl group combines with
  coenzyme A to form acetyl-CoA.
• This acetyl-CoA enters the Kreb's cycle.

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Krebs Cycle
Sir Hans Krebs, who won a Nobel Prize for its
discovery, preferred the term Tricarboxylic Acid
Cycle (TCA cycle)
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Stage 3 The Krebs Cycle

• A 2-carbon acetyl-CoA molecule is combined with a
  4-C compound called oxaloacetate to produce a 6-C
  citrate molecule.
• These citrate molecules are then oxidized to a
  5-C ?-ketoglutarate. Carbon dioxide and NADH are
  produced.
• ?-ketoglutarate molecules are then further
  oxidized to a 4-C succinyl Co-A compound. Carbon
  dioxide and NADH are produced.
• The 4-C succinyl Co-A is then modified to
  succinate. GTP is produced by substrate level
  phosphorylation. It is converted to ATP.

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• The 4 carbon succinate molecule is oxidized to
  fumarate. FADH2 is produced.
• Fumarate is hydrated to malate.
• Malate is oxidized to oxaloacetate. NADH is
  produced.
• And the cycle starts again.

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• Note
• Each of the 3 carbon atoms present in the
  pyruvate that entered the mitochondrion leaves as
  a molecule of carbon dioxide (CO2)
• At 3 steps in the cycle, a pair of electrons
  (2e-) is removed and transferred to NAD reducing
  it to NADH H
• At one step, a pair of electrons is removed from
  succinate and reduces FAD to FADH2

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Summary of Kreb's cycle

• 2 carbon dioxide molecules are released,
• 3 NADH are produced,
• 1 FADH2 is produced
• 1 molecule of ATP is formed
• 1 molecule of water is used
• molecule of oxaloacetate is left to start the
  cycle all over again.

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• Remember, there are 2 molecules of pyruvate
  formed from each molecule of glucose, therefore
  the cycle runs twice for each glucose molecule.
• Almost all the chemical energy extracted from the
  pyruvate is carried by the hydrogen and
  temporarily transferred to the reduced coenzymes.

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Describe the function of NAD and FAD in cellular
respiration.

• They act as coenzymes that harvest energy from
  the reactions of glycolysis, pyruvate oxidation,
  and the Krebs cycle and carry it to power ATP
  synthesis by oxidative phosphorylation.

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• NAD is used to shuttle electrons to the first
  component of the ETC.
• During oxidative phosphorylation, NAD removes 2
  hydrogen atoms from a part of the original
  glucose molecule.
• Two electrons and one proton attach to NAD,
  reducing it to NADH (NAD is the oxidized form of
  NADH).
• This reduction occurs during glycolysis, phruvate
  oxidation, and the Krebs cycle.

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• FAD functions in a similar manner to NAD.
• FAD is reduced by two hydrogen atoms from the
  original glucose molecule to FADH2.
• This is done during the Krebs cycle.
• These reductions are energy harvesting and will
  transfer their free energy to ATP molecules.
• Reduced NAD and FAD move free energy from one
  place to another and from one molecule to
  another.

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As a result of glycolysis, pyruvate oxidation,
and the Krebs cycle, only a small portion of the
energy of glucose has been converted to ATP. In
what form is the rest of the usable energy found
at this stage of the process?

• The rest of the usable energy is stored as FADH2,
  and NADH.
• 2 FADH2 are produced during the Krebs cycle.
• The free energy stored in these molecules is
  released during chemiosmosis and ETC.

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Electron Transport Chainand Chemiosmosis
Oxidative Phosphorylation
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ETC animation!

• http//www.biologycorner.com/bio3/notes-respiratio
  n.html

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The Electron Transport Chain
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The Electron Transport System

• The reactions of the electron transport chain
  take place within the inner membrane of the
  mitochondrion.
• This is the portion of respiration which yields
  the greatest amount of energy for the cell (32
  ATP).

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• So far only 4 molecules (net) of ATP are produced
  (by substrate-level phosphorylation).
• Most of the energy is still carried by the NADH
  H or the FADH2 .
• In the electron transport chain, this energy is
  used to form ATP.

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• Hydrogen atoms are carried into the chain by NADH
  H and FADH2 .
• At the membranes, the hydrogen atoms are
  separated into electrons (e-) and H.
• The electrons from the hydrogen atoms are passed
  along from one compound to another in a series of
  redox reactions.

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• At three sites along the chain, some of the free
  energy released from the transfer of the
  electrons is used to pump protons (H) against
  their concentration gradient from the matrix of
  the mitochondrion into the intermembrane space
  (an example of active transport).
• There are now more H ions in the intermembrane
  space than in the matrix.
• This results in a concentration gradient that is
  utilized in the synthesis of ATP.

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• NADH H enters at the first complex and
  contributes to the formation of 3 ATP.
• FADH2 enters at the second complex and
  contributes to the formation of 2 ATP.

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The integral membrane proteins (complexes)that
make up the respiratory chain accomplish the
following

• the stepwise transfer of electrons from NADH H
  (and FADH2) to oxygen atoms to form (with the aid
  of protons) water molecules (H2O)
• harnessing the energy released by this transfer
  to the pumping of protons (H) from the matrix to
  the intermembrane space
• protons are pumped at 2 - 3 complexes
• protons are pumped out at each complex as
  electrons pass through it.
• the gradient of protons formed across the inner
  membrane by this process of active transport
  forms a concentration gradient
• the protons can flow back down this gradient,
  re-entering the matrix, only through the ATP
  synthase complex.

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Chemiosmosis

• A high concentration of H develops on the outer
  side of the membrane.
• As their concentration increases, a strong
  diffusion gradient is set up.
• The only exit for these protons is through the
  ATP synthase complex.
• This special complex in the membrane permits H
  to pass through the membrane, down a
  concentration gradient.
• The energy released as these protons flow down
  their gradient is harnessed to the synthesis of
  ATP.
• As it does, enzymes use the kinetic energy of the
  moving H to join phosphate and ADP forming ATP.
• The process is called chemiosmosis and is an
  example of facilitated diffusion.

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• A total of 32 ATP molecules are formed from one
  molecule of glucose.
• For each pair of H atoms picked up by the NAD, 3
  molecules of ATP are produced and for each pair
  picked up by the FAD, 2 molecules of ATP are
  produced.
• At the end of the chain, most of the energy has
  been extracted from the electron pair - this
  electron pair is then transferred to an oxygen
  atom to form water.
• Since 2 ATP (net) come directly from glycolysis
  and 2 ATP from the cycle, a total of 36 ATP (net)
  are formed from each molecule of glucose.

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Sum up total production of NADH, FADH2, ATP from
a single glucose molecule
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Compare substrate-level phosphorylation and
oxidative phosphorylation.

• S.L.P. generates ATP directly from an enzyme
  catalyzed reaction, whereas O.P. generates ATP
  indirectly by the chemiosmotic potential created
• The process is oxidative because, it involves
  several sequential redox reactions, with oxygen
  being the final electron acceptor.
• It is more complex than S.L.P., and it produces
  more ATP.

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Why is aerobic respiration a more efficient
energy-extracting process than glycolysis alone?

• Glycolysis only transfers about 2.1 of the free
  energy available in 1 mol of glucose into ATP.
  Most of the energy is trapped in 2 pyruvate and 2
  NADH.
• Aerobic respiration further processes the
  pyruvate and NADH during pyruvate oxidation, the
  Krebs cycle, chemiosmosis, and ETC. By the end
  of aerobic respiration, all the energy available
  in glucose has been harnessed.

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14 a) What part of a glucose molecule provides
electrons in cellular respiration?

• Hydrogen atoms

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B) Describe how E.T.C. set up a proton gradient
in response to electron flow.

• The ETC passes protons from the mitochondrial
  matrix to the intermediate space.
• NADH gives up the two electrons it carries to
  NADH hydrogenase.
• Electron carriers, ubiquinone and cytochrome c,
  shuttle electrons from NADH hydrogenase to
  cytochrone b-c1 complex to cytochrome oxidase
  complex.
• Free energy is lost from the electrons during
  each step in this process, and this energy is
  used to pump H from the matrix into the
  intermembrane space.
• The final step in the electron transport chain
  sees oxygen accept 2 electrons from cytochrome
  oxidase complex, and it consumes protons to form
  water.

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c) How is the energy used to drive the synthesis
of ATP?

• The protons that accumulate in the intermembrane
  space create an electrochemical gradient.
• The gradient has 2 components electrical caused
  by a higher positive charge in the intermembrane
  space than in the matrix, and a chemical gradient
  created by a higher concentration of protons in
  the intermembrane space.
• The electrochemical gradient stores free energy
  the proton-motive force (PMF).
• The mitochondrial membrane is almost impermeable
  to protons, so the protons are forced to pass
  through ATP synthase, reducing the energy of the
  gradient.
• The energy is used by the enzyme ATP synthase to
  create the 3rd phosphate-ester bond forming ATP.

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d) What is the name of this process?

• Chemiosmosis (oxidative phosphorylation)

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e) Who discovered the mechanism?

• Chemiosmosis was discovered by Peter Mitchell in
  1961.

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A) Distinguish between an electron carrier and a
terminal electron acceptor.B) What is the final
electron acceptor in aerobic respiration?

1. An electron carrier is first oxidized and then
   reduced by a more electronegative molecule. A
   terminal electron acceptor is only reduced (it is
   at the end of the ETC)
2. oxygen

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Explain how the overall equation for cellular
respiration is misleading.

• It does not include the numerous enzymes,
  coenzymes, and intermediate chemicals involved in
  the process.
• It also shows the conversion of glucose and
  oxygen to carbon dioxide and water as a simple,
  one-step process, where it is actually much more
  involved than that.

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Difficulties and Misconceptions

• The following is a list of items students find
  deceiving.

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Sometimes 36 ATP are produced and sometimes 38
ATP are produced.

• Since the inner mitochondrial membrane is
  impermeable to NADH (from glycolysis), it has 2
  shuttle systems that pass electrons from
  cytosolic NADH in the inter-membrane space to the
  matrix.
• Glycerol-phosphate shuttle transfers the
  electrons from cystolic NADH to FAD to produce
  FADH2 (resulting in the synthesis of 2ATP)
• Aspartate shuttle (less common) transfers
  electrons to NAD instead of FAD, forming NADH
  (resulting in the synthesis of 3 ATP)

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DAY 14 2.3 Related Pathways p. 117-124
QUIZ ON CHAPTER 2 tomorrow
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Fermentation occurs in the ABSENCE OF OXYGEN.
LACTIC ACID FERMENTATION or ALCOHOLIC
FERMENTATION.
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• Aerobic respiration
• Yields 36 ATP/glucose
• Produces CO2 and water

• Fermentation
• Yields 2 ATP/gluocose
• Produces ethanol or lactic acid

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Protein Catabolism

• Proteins undergo deamination (removing an amino
  group from amino acids
• They are then converted into ammonia and excreted

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deamination
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Lipid Catabolism

• In beta-oxidation, fatty acids are sequentially
  degraded into 2-carbon acetyl portions that are
  converted into acetyl-CoA and respired through
  the Krebs cycle, ETC, and chemiosmosis.

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• Fat cannot be used directly to produce energy for
  a cell.
• First, fat must by hydrolyzed into glycerol and
  fatty acids. The glycerol can enter glycolysis
  after either being converted to glucose (via
  gluconeogenesis) or changed into
  dihydroxyacetonephosphate (DHAP).
• -The fatty acids are broken down to two-carbon
  units (acetyl-CoA) in a process called
  b-oxidation, which can be fed directly into Krebs
  cycle.

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Anaerobic Pathways

• When oxygen is not available
• Eukaryotes still carry out glycolysis by
  transferring the H atoms in NADH to pyruvate
• The NAD molecules formed allow glycolysis to
  continue

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Ethanol (Alcohol) Fermentation Occurs in
yeast cells and is used in wine, beer, and bread
making
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Ethanol (Alcohol) Fermentation

• A molecule of CO2 is removed from pyruvate,
  forming a molecule of acetaldehyde
• The acetaldehyde is converted to ethanol by
  attaching H from NADH
• FINAL PRODUCTS ATP, CO2, ethanol

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A particular organism releases carbon dioxide and
alcohol as its end products. The organism is most
likely which of the following?

• a. an animal
• b. an alga
• c. a green plant
• d. a yeast
• e. a virus

d. a yeast
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Anaerobic and aerobic respiration are similar in
all but one of the following ways. Which one is
the exception?

• A) NAD is reduced
• B) carbon dioxide is a product
• C) ADP is combined with inorganic phosphate to
  form ATP
• D) acetaldehyde is converted into ethanol
• E) both can release energy from glucose

D) acetaldehyde is converted into ethanol
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Lactate (lactic acid) fermentation

• Occurs in animal muscle cells during strenuous
  exercise
• FINAL PRODUCTS ATP, lactate

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What happens to lactic acid after it is formed in
a muscle cell?

• Lactic acid travels in the bloodstream to the
  liver, where it is oxidized back to pyruvate,
  which then goes through the Krebs cycle and
  oxidative phosphorylation.
• The presence of lactic acid in the muscle tissues
  leads to stiffness, soreness, and fatigue.

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Oxygen debt

• Oxygen debt refers to the extra oxygen required
  by the liver to oxidize lactic acid to CO2 and
  water (through the aerobic pathway)
• Panting pays for the oxygen debt

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During active exercise, the supply of oxygen
becomes inadequate for the level of activity you
are attempting to maintain. How do the catabolic
reactions of the cell continue?

• Glycolysis continues to supply small amount of
  ATP, and the pyruvate that normally would
  continue on the Krebs cycle as acetyl-CoA is
  instead converted to lactate to regenerate NAD
  to allow glycolysis to continue.

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VO2 max and the Lactate Threshold

• The maximum oxygen uptake (VO2 max) is the
  maximum volume of oxygen that the cells of the
  body can remove from the bloodstream in one
  minute per kg of body mass while the body
  experiences max. exertion.
• The lactate threshold (LT) is the value of
  exercise intensity at which blood lactate
  concentration begins to increase sharply.

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This course has placed an emphasis on
carbohydrates as an energy source, yet our diets
also contain fats and proteins. Explain the role
of fats and proteins in producing energy for an
organism.

• The emphasis on carbohydrates is justified, since
  they are the principle energy source for humans,
  both in terms of consumption and biochemical
  preference. However, there are a few other food
  sources that produce energy for us if the
  circumstances warrant.
• In the case of fat, the body usually turns to
  this as a source of energy once carbohydrate
  reserves are nearly depleted. Fat can be
  enzymatically broken down into glycerol and fatty
  acids. It is the fatty acids that contain most of
  the energy from the fat. In a process known as
  b-oxidation, the fatty acids are cleaved two
  carbon atoms at a time and joined to coenzyme-A
  to form acetyl-CoA. (Note Fatty acids must have
  an even number of carbons. Fatty acids with an
  odd number of carbons should produce acetyl-CoA
  also, but the last unit will be formyl-CoA, which
  is toxic!) This acetyl-CoA can then enter into
  the Krebs cycle and go on to produce energy in
  the same manner as carbohydrates.
• When most carbohydrate and fat has been
  exhausted, the body can turn to protein as an
  energy source. First, the protein has to be
  broken down into its component amino acids and
  deaminated. The deamination process leads to the
  production of ammonia, which is a waste product.
  Depending on what amino acid we are talking
  about, it can enter at either the level of
  pyruvate or a number of points in the Krebs cycle
  and produce energy in the same manner as
  carbohydrates.

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Overview of Cellular Respiration which occurs in
STAGE 1 GLYCOLYSIS STAGE 2 TWO MAIN
PATHWAYS, DEPENDING ON WHETHER THERE IS OXYGEN IN
THE CELL.
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Aerobic Respiration produces nearly 20 times as
much ATP as is produced by Glycolysis alone.
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The co-enzymes NADH H and FADH2 must now be
oxidized so they can continue to transfer the
hydrogen to the ETC. The components are arranged
in order of increasing electronegativity, with
the weakest at the beginning and the strongest
(oxygen) is at the end. As the NADH H and
FADH2 are oxidized, the electrons from the 2
hydrogen atoms are passed along the components in
a series of redox reactions. As the electrons
are passed along the complexes, energy is
stripped from them. This "downhill" series of
electron transfers gradually lowers the level of
energy in the electrons and when most of the
energy is spent, the electrons are accepted by
oxygen. The energy, that is stripped, is used to
pump the H across the membrane from the matrix
to the intermembrane compartment A high
concentration of H now exists in the
intermembrane compartment. The protons can flow
back down this gradient, re-entering the matrix,
only through another complex of integral proteins
in the inner membrane, the ATP synthase complex.
The energy released, as these electrons flow down
their gradient, is harnessed to the synthesis of
ATP. The process is called chemiosmosis and is an
example of facilitated diffusion.