Ch. 3 Cliff's Biology: Cellular Respiration

Gluconeogenesis

Remember that we don't just breakdown Glc, we can also produce it!! Occurs in liver and kidney (liver responsible for maintaining Glc levels in blood)

Pyruvate Decarboxylation (mito matrix)

-Pyr to acetyl CoA, producing 1 NADH and 1 CO2 (2 Pyr, net=2 NADH, 2 CO2) -catalyzed by PDC (pyruvate dehydrogenase complex)

Alternate Energy Source: Carbs

-Glycogen=Glc polymer, storage molecule, 2/3 stored in liver and 1/3 in muscles **insulin after large meals stores Glc as glycogen, glucagon has opposite effect and turns on glycogen degradation (insulin activates PFK enzymes, glucagon inhibits) -Disaccharides hydrolyzed into monosaccharides, most of which can be converted into Glc or glycolytic intermeds **all cells capable of producing/storing glycogen, but only muscle cells and esp liver cells have large amts

ATP (adenosine triphosphate)

-RNA nucleotide (due to its ribose sugar) -unstable molecule b/c 3 phosphates in ATP are negatively charged and repel one another -when one PO3 removed via hydrolysis, more stable ADP results **change from less stable to more stable molecule always releases energy!! -provides energy for all cells by transferring phosphate from ATP to another molecule

Electron Transport Chain (ETC, inner mito membrane/cristae)

-cristae=folds in inner mito membrane, increase SA for more ETC action! -oxidative phosphorylation: process of ADP→ATP from NADH and FADH2 via passing of e⁻ thru various carrier proteins; energy doesn't accompany phosphate grp but comes from e⁻ in ETC establishing H⁺ gradient that supplies energy to ATP synthase! -NADH makes more energy than FADH2, more H pumped across per NADH (both coenzymes)--3:2 yield -final electron acceptor=oxygen, combines w/native H to form water **oxidizing agent causes something ELSE to get oxidized, itself becomes reduced (VV for reducing agent) -carriers extract energy from NADH, FADH2 while pumping protons into IMS; ATP synthase uses pH/electrical gradient to make ATP as it shuttles H+ back into inner matrix -CoQ (coenzyme Q)/ubiquinone=soluble carrier dissolved in membrane, can be fully reduced/oxidized, passes e- -cytC=protein carrier in ETF, common in many living orgs, used for genetic relation *cytochromes have nonprotein parts i.e. Fe (donate/accept electrons, for redox!) -couples exergonic flow of electrons w/endergonic pumping of protons across cristae membrane -total energy from 1 Glc=~36 ATP, but in proks 38 (not actual yield, mito efficacy varies) **proks have no mito so unlike euks they don't need to tx Pyr into mito matrix (done via active tx, costs ATP), they use cell membrane for respiration

Glycolysis (cytosol)

-decomp of Glc into Pyr -2 ATP input, 2 NADH, 4 ATP, 2 Pyr output (net=2 ATP via substrate level phosphorylation) -hexokinase phosphorylates Glc, imp b/c then it can't diffuse out and tricks gradient -PFK adds 2nd phosphate, makes Frc-1,6-BP (irreversible, commits to glycolysis, MAJOR REGULATORY POINT!)

Cellular Respiration

-exergonic, oxidative process (-686 kcal/mol) -external resp=entry of air into lungs, gas exch b/w alveoli and blood -internal resp=gas exch b/w blood, cells and intracellular resp processes -during respiration, high-E H atoms removed from organic molecules (dehydrogenation) -aerobic respiration: in presence of O₂ (glycolysis, pyr decarb, krebs, ox phos), H₂O=final product [C₆H₁₂O₆+6O₂→6CO₂+6H₂O+energy]

Facultative vs. Obligate Anaerobes

-facultative can use O2 when present (more efficient), but switch to fermentation/anaerobic if it isn't -obligate cannot live in presence of O2

Krebs Cycle/CAC/Tricarboxylic Acid Cycle (mito matrix)

-fate of Pyr produced in glycolysis -acetyl coA merges w/OAA to form citrate, 7 intermediates in cycle -3 NADH, 1 FADH2, 1 ATP (via sub-level phos), 2 CO2/cycle (2 cycles since 2 Pyr/Glc in glycolysis) -net=6 NADH, 2 FADH2, 2 ATP (tech. GTP), 4 CO2 -CO2 produced here is that which animals exhale when they breathe

Anaerobic Respiration (cytosol)

-glycolysis and fermentation -AEROBIC regenerates NAD+ via O2, which is req'd for continuation of glycolysis (w/o O2, no replenishing, NADH accumulates, cell would die w/no new ATP, so fermentation occurs... -alcohol and lactic acid fermentation

Lactic Acid Fermentation

-human muscle cells, other microorgs -Pyr→lactate (AND NADH→NAD⁺) -lactate tx'd to liver, converted back to Glc once surplus ATP

Alternate Energy Source: Protein

-least desirable energy, only when carbs and fats unavailable -most AAs deaminated in liver, then converted to Pyr or acetyl CoA or other CAC intermediates, enter cell resp at these varies points (varies by AA) -ox deamination removes ammonia molecule directly from AA, ammonia is toxic to vertebrates: fish excrete, insects/birds convert to uric acid, mammals convert to urea for excretion

Chemiosmosis in Mitochondria

-mechanism of ATP generation that occurs when energy stored in form of H+ conc gradient across membrane -Krebs produces NADH/FADH2, which are oxidized (lose e-), H+ tx from matrix to IMS, pH/electric gradient created -ATP synthase uses energy from gradient to create ATP by letting protons flow through channel **[H+] up=pH down!!

Mitochondria (structure, relation to cell respiration)

-outer membrane -intermembrane space (H+) -inner membrane (oxidative phosphorylation) -mitochondrial matrix (krebs)

Alcohol Fermentation

-plants, fungi (yeasts), bacteria (botulinum) -Pyr→acetaldehyde+CO₂, then acetaldehyde→ethanol (AND NADH→NAD⁺) **acetaldehyde=final e- acceptor, thus forming ethanol!! final molecule is NOT final e- acceptor. same w/O2 being final e- acceptor in cell respiration, forming H2O

Alternate Energy Source: Fats

-store more energy than carbs per C (C in more reduced state, hence why fats are 10 cal/g, whereas carbs/protein are 4) -triglycerides in SI lumen (tube itself) broken down via lipases into monoacylglycerides and FAs, absorbed into enterocytes (SI cell lining), where reassembled into triglycerides and (along w/cholesterol/proteins/phospholipids) packed into chylomicrons which move on to lymph capillary for tx to rest of body and stored as adipose tissue -lipases in adipose tissue are hormone-sensitive (i.e. to glucagon) -glycerol→PGAL, enters glycolysis -every 2C of FA chain→1 acetyl CoA **FAs in blood carried by albumin -FAs broken down for energy via B-oxidation (mito matrix): 2 ATP spent to activate entire chain -saturated FAs produce 1 NADH, 1 FADH2 for EVERY CUT into 2 C (vs. every 2 carbons, i.e. 18C chain is 9-2C pieces but only cut 8 times, each cut=B-oxidation step) -unsaturated FAs produce 1 less FADH2 for every DB (can't use DB forming step) -results in BIG ATP yield--more per C than carbs/sugars

Alternate Energy Sources

-when Glc supply low, body uses other energy sources: other carbs, fats, proteins (priority order)→first converted to Glc or its intermediates→then degraded in glycolysis or CAC

What is the purpose of oxygen in aerobic respiration? A. Oxygen accepts electrons at the end of an electron transport chain. B. Oxygen is necessary to carry away the waste CO2. C. Oxygen is used in the formation of sugar molecules. D. The oxygen molecule becomes part of the ATP molecule. E. Oxygen donates H+ used in the formation of NADH.

A. At the end of the electron transport chain in oxidative phosphorylation, 1⁄2 O2 combines with 2 electrons and 2 H+ to form water.

Discuss the Krebs cycle and oxidative phosphorylation. Specifically address ATP and coenzyme production, the location where these biosynthetic pathways occur, and chemiosmotic theory.

A. The Krebs cycle and oxidative phosphorylation are the oxygen-requiring processes involved in obtaining ATP from pyruvate. Pyruvate is derived from glucose through glycolysis, a process that does not require oxygen. Before pyruvate enters the Krebs cycle, it combines with coenzyme A. During this initial reaction with coenzyme A, 2 electrons and 2 H+ removed from pyruvate combine with NAD+ to form 1 NADH + H+. NADH is a coenzyme storing enough energy to generate 3 ATP in oxidative phosphorylation. A CO2 molecule is also released. The end product of this reaction is acetyl CoA. To begin the Krebs cycle, acetyl CoA combines with oxaloacetate (OAA) to form citrate, releasing the coenzyme A component. A series of reactions then occurs that generates 3 molecules of the coenzyme NADH (from NAD+), 1 molecule of the coenzyme FADH2 (from FAD), and 1 ATP (from ADP + Pi) for each molecule of acetyl CoA that enters the Krebs cycle. The last product in the series of reactions, OAA, is the substance that reacts with acetyl CoA; thus, the Krebs reactions sustain a cycle. Energy from the coenzymes NADH and FADH2 is extracted to make ATP in oxidative phosphorylation. For each of these coenzymes, 2 electrons pass through an electron transport chain, passing through a series of protein carriers (some are cytochromes, such as cytochrome c). During this passage, 3 ATP are generated for each NADH originating in the Krebs cycle. FADH2 generates 2 ATP. At the end of the electron transport chain, O2 accepts the electrons (and 2 H+) to form water. NAD+ and FAD can be used again to receive electrons in the Krebs cycle. The total number of ATP generated from a single pyruvate is 15 ATP. B. The Krebs cycle and oxidative phosphorylation occur in the mitochondria. The Krebs cycle occurs in the matrix of the mitochondria. The protein carriers for the electron transport chain are embedded in the inner mitochondrial membranes, called the cristae. Thus, oxidative phosphorylation occurs in these cristae membranes. C. Chemiosmosis describes how ATP is generated from ADP + Pi. During oxidative phosphorylation, H+ (protons) are deposited on the outside of the cristae, between the cristae and the outer membrane. The excess number of protons in this intermembrane space creates a pH and electric gradient. The gradient provides the energy to generate ATP as protons pass back into the matrix through ATP synthase, a channel protein in the cristae.

Which of the following sequences correctly indicates the potential ATP yield of the indicated molecules from greatest ATP yield to least ATP yield? A. Pyruvate, ethanol, glucose, acetyl CoA B. Glucose, pyruvate, acetyl CoA, NADH C. Glucose, pyruvate, NADH, acetyl CoA D. Glucose, FADH2, acetyl CoA, pyruvate E. Glucose, FADH2, NADH, pyruvate

B. These molecules each have the potential to produce the following amounts of ATP: glucose, 36 ATP; pyruvate,15 ATP; acetyl CoA, 12 ATP; NADH, 3 ATP (or 2 ATP if they originate in glycolysis); FADH2, 2 ATP. The metabolic pathway that breaks down ethanol to H2O and CO2 in the human liver is variable. However, answer A can be eliminated without knowing how many ATP molecules ethanol can yield because glucose produces more ATP than does pyruvate.

As levels of atmospheric O2 increase beyond 5%, the amounts of CO2 released increase. This is probably a direct result of A. an increase in glycolytic activity B. a greater availability of appropriate enzymes C. an increase in Krebs cycle activity D. an increase in atmospheric temperature E. a decrease in the pH of the cytoplasm

C. CO2 is produced in the Krebs cycle. As in the previous question, the production of CO2, rather than its consumption, indicates that photosynthesis is not occurring, and that the plant activity is taking place at night.

All of the following processes produce ATP EXCEPT: A. glycolysis B. the Krebs cycle C. lactic acid fermentation D. oxidative phosphorylation of NADH E. oxidative phosphorylation of FADH2

C. Lactic acid fermentation, the conversion of pyruvate to lactate, removes electrons from NADH to make NAD+. No ATP is generated by this step.

All of the following processes release CO2 EXCEPT: A. the Krebs cycle B. alcohol fermentation C. oxidative phosphorylation D. the conversion of pyruvate to ethanol E. the conversion of pyruvate to acetyl CoA

C. Oxidative phosphorylation describes the transfer of electrons from NADH and FADH2 to electron acceptors that pump H+ across the inner mitochondrial membrane. Oxygen is required as the final electron acceptor of these electrons. However, no CO2 is involved. In contrast, all the remaining answer choices describe processes that release CO2. Note that answer choices B and D describe the same process.

At levels of atmospheric O2 below 1%, the amount of CO2 released is relatively high. This is probably because A. The Krebs cycle is very active. B. O2 is being converted to H2O. C. Alcohol fermentation is occurring. D. There are insufficient amounts of coenzyme A. E. Photosynthesis cannot function at night.

C. When O2 is absent (or very low), anaerobic respiration (alcohol fermentation) is initiated. Alcohol fermentation releases CO2. Photosynthesis, which would consume CO2 to produce glucose, is obviously not occurring. This indicates that the plant activity illustrated by the graph is occurring at night (or during a heavily clouded day).

After strenuous exercise, a muscle cell would contain increased amounts of all of the following EXCEPT: A. ADP B. CO2 C. lactate (or lactic acid) D. glucose E. Pi

D. During strenuous exercise, glucose is broken down to pyruvate. Aerobic respiration produces CO2. Anaerobic respiration, which would occur during strenuous exercise, would increase lactate formation. Exercise would also consume ATP, producing ADP and Pi.

All of the following statements about cellular respiration are true EXCEPT: A. Some of the products from the breakdown of proteins enter the Krebs cycle. B. Some of the products from the breakdown of lipids enter the Krebs cycle. C. If oxygen is present, water is produced. D. The purpose of oxygen in aerobic respiration is to donate the electrons that transform NAD+ + H+ to NADH. E. Lactate or ethanol is produced when oxygen is unavailable.

D. The purpose of O2 is to accept the electrons at the end of the electron transport chain in oxidative phosphorylation. The electrons, O2, and H+ form water. Products from the breakdown of lipids and proteins are converted to pyruvate, acetyl CoA, or intermediate carbon compounds used in the Krebs cycle.

What is the value of the alcohol fermentation pathway? A. It produces ATP. B. It produces lactate (or lactic acid). C. It produces ADP for the electron transport chain. D. It replenishes CO2 for the dark reaction. E. It replenishes NAD+ so that glycolysis can produce ATP.

E. In the absence of oxygen, all of the NAD+ gets converted to NADH. With no NAD+ to accept electrons from the glycolytic steps, glycolysis stops. By replenishing NAD+, alcohol fermentation allows glycolysis to continue.

Chemiosmosis describes how ATP is generated from ADP. All of the following statements conform to the process as it occurs in mitochondria EXCEPT: A. H+ accumulates in the area between the membrane of the cristae and the outer membrane of the mitochondrion. B. A pH gradient is created across the cristae membranes. C. A voltage gradient is created across the cristae membranes. D. A proton gradient is created across the cristae membranes. E. Electrons flowing through the ATP synthase channel protein provide the energy to phosphorylate ADP to ATP.

E. Protons, not electrons, pass through ATP synthase as they move down the proton gradient. A proton gradient is the same as a pH gradient, and an electrical gradient or voltage is produced by the greater number of positive charges (from the protons) in the intermembrane space relative to the number of positive charges inside the crista membrane.

Biothermodynamics: Coupled Chemical Reactions

Gibbs Free Energy (G=H-TS) tells us whether a given chemical reaction can occur spontaneously. If ∆G is negative, the rxn can occur spontaneously, but if it is positive then the reaction is nonspontaneous. This applies to biology when chemical reactions with common intermediates are coupled. In this case, the overall Gibbs Free energy change is the SUM of the ∆G values for each rxn. Therefore, an unfavorable rxn (pos ∆G1) can be driven by a second, highly favorable rxn (neg ∆G2 where magnitude of ∆G2>∆G1). i.e. rxn of Glc w/Frc to form Sucrose has a ∆G=+5.5 kcal/mol (doesn't occur spontaneously). The breakdown of ATP to form ADP and Pi has a ∆G=-7.3 kcal/mol. These two reactions can be coupled together, so that Glc binds w/ATP to form Glc-1-P and ADP. The Glc-1-P is then able to bond w/Frc yielding sucrose and Pi. The ∆G value of the coupled rxn is -1.8 kcal/mol (rxn occurs spontaneously). This principle of coupling rxns to alter the ∆G is the basic principle behind all enzymatic action in biological organisms.

Describe, at the molecular level, how cells extract energy from starches, proteins, and lipids by the process of aerobic respiration.

Starches are polymers of glucose. Various enzymes break down starches to glucose, which in turn enter the glycolytic pathway. Disaccharides like sucrose are catalyzed to glucose and fructose. The glucose enters the glycolytic pathway at the beginning, but the fructose undergoes some intermediate steps and enters the glycolytic pathway after a couple of steps. Lipids are broken down to glycerol and fatty acids. Both of these components undergo enzymatic reactions that eventually produce acetyl CoA. Proteins are broken down to amino acids. Each of the various amino acids produces different products when broken down. Some of these products are converted to acetyl CoA; others are converted to OAA or other Krebs cycle intermediates. NH3 is a toxic waste product from amino acid breakdown and is exported from the cell.

Substrate-Level Phosphorylation vs. Oxidative Phosphorylation

substrate level: direct enzymatic transfer of phosphate to ADP, no extraneous carriers needed oxidative: phosphate group added to ADP to form ATP, BUT energy for bond does NOT accompany PO3, instead e- from ETC supply energy used to form H+ gradient which supplies energy to ATP synthase to generate ATP from ADP and PO3