Unit 1: Metabolic Processes

Chapter 2: Cellular Respiration

Photoautrophheterotroph

chemoautotroph

2.1 Cellular Respiration: The Big Picture

Overview of Cellular Respiration

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

Mitochondria: convert the potential energy of food molecules into ATP.

• 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.

• 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.

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.

OVERALL CHEMICAL EQUATION:

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.

Nicotinamide Adenine Dinucleotide (NAD+)

In being reduced, NAD can accept two electrons, but only one proton. The other proton goes into solution as a hydrogen ion.

Flavin Adenine Dinucleotide (FAD)

• 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.

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

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

GLYCOLYSIS

• IN CYTOSOL• ONE OF THE

OLDEST PATHWAYS: all life on earth performs glycolysis

• DOES NOT REQUIRE OXYGEN (ANAEROBIC)

Glucose Activation:

In the first step, a phosphate group from ATP is attached to glucose. This increase the energy level of glucose

This step is an isomerization

This is the second phosphorylation.

At this point, 2 ATP molecules have been USED.

In this step, the glucose molecule is split into two three carbon molecules.

DHAP undergoes isomerization to G3P. Why???

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.

Substrate level phosphorylation!!!

Formation of 2 ATP.

Isomerization

2

2

Phosphoenol pyruvate is also known as PEP

2

2

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.

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.

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

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

A) In the cytoplasm.

B) The breaking of the glucose molecule into two pyruvate molecules

A) 2 pyruvate, 4 ATP, 2 NADH, 2H+, and 2 ADP

B) Pyruvate and NADH

4.

• List the final products of glycolysis.

• What two products of glycolysis may be transported into mitochondria for further processing?

#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

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.

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

PYRUVATE OXIDATION

• 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.

Krebs Cycle

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

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.

• 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.

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

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.

• 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.

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.

• 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.

• 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.

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.

Electron Transport Chainand Chemiosmosis

Oxidative Phosphorylation

ETC animation!

• http://www.biologycorner.com/bio3/notes-respiration.html

The Electron Transport Chain

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).

• 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.

• 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.

• 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.

• 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.

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.

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.

• 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.

Sum up total production of NADH, FADH2, ATP from a single glucose molecule

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.

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.

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

Hydrogen atoms

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.

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.

d) What is the name of this process?

• Chemiosmosis (oxidative phosphorylation)

e) Who discovered the mechanism?

• Chemiosmosis was discovered by Peter Mitchell in 1961.

A) Distinguish between an electron carrier and a terminal electron acceptor.

B) What is the final electron acceptor in aerobic respiration?

a) 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)

b) oxygen

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.

Difficulties and Misconceptions

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

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)

DAY 142.3 Related Pathways p. 117-124

QUIZ ON CHAPTER 2 tomorrow

Fermentation occurs in the ABSENCE OF

OXYGEN.

LACTIC ACID FERMENTATION

or

ALCOHOLIC FERMENTATION.

Aerobic respiration

• Yields 36 ATP/glucose

• Produces CO2 and water

Fermentation

• Yields 2 ATP/gluocose

• Produces ethanol or lactic acid

Protein Catabolism

• Proteins undergo deamination (removing an amino group from amino acids

• They are then converted into ammonia and excreted

deamination

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.

•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 -oxidation, which can be fed directly into Krebs cycle.

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

Ethanol (Alcohol) Fermentation

Occurs in yeast cells and is used in wine, beer, and bread making

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

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

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

Lactate (lactic acid) fermentation

• Occurs in animal muscle cells during strenuous exercise

• FINAL PRODUCTS: ATP, lactate

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.

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

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.

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.

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 -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.

Overview of Cellular Respiration which occurs in

STAGE 1: GLYCOLYSIS

STAGE 2: TWO MAIN PATHWAYS,

DEPENDING ON WHETHER THERE IS

OXYGEN IN THE CELL.

Aerobic Respiration produces nearly 20 times

as much ATP as is produced by Glycolysis

alone.

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.