Bio Test 2 - PP 11 Cellular Respiration (TCA)

The Citric Acid Cycle

- A two-carbon acetyl group is transferred from acetyl CoA to oxaloacetate (4 carbon molecule), forming citrate (6 carbon molecule). - Two carbons of citrate are then oxidized to CO2 during 8 steps and oxaloacetate is regenerated. - There is no net gain of carbon in this Cycle. - Cycle intermediates must be maintained.

Define TCA

- Aerobic, energy producing pathway, in mitochondria - TCA cycle is regulated by the state of cellular energetics and O2 availability - The function of the TCA cycle is to fully oxidize carbon atoms derived from carbohydrates, fats and proteins to produce energy

Understand the role of oxygen as final acceptor of electrons

- And to oxygen electrons ultimately falls as it's the most electronegative of them all - After Complex IV, electrons flow to oxygen which is very electronegative so it pulls electrons down the chain, keeping them moving like the cars of a train - As O2 does this electron grabbing trick, it also grabs protons from the matrix - They all combine to form H2O - Oxygen accepts the final electrons in ETC to become molecule of water - Oxygen that we inhale is picked up by bloodstream and delivered to our cells; ends up in inner mitochondrial membrane; accepts final electrons in ETC; becomes part of molecule of water - Thus, oxidation-reduction reactions in mitochondria generate water as final end product (sometimes called metabolic water) - Acting as final electron acceptor might seem to be such a small task, but if oxygen doesn't do this job for about four minutes, we can't sustain life - Depriving cell of oxygen is like hitting "off" switch of ETC; shuts off vast majority of cell's ATP production - We must take in enough oxygen to act as final electron acceptor so we can produce enough ATP to meet body's needs

loses

- Before pyruvate enters citric acid cycle, it ___ one of its carbons as molecule of carbon dioxide

When glucose and lipid reserves are inadequate, liver cells

- Break down internal proteins - Absorb additional amino acids from blood - Amino acids are deaminated - Nitrogen is not used for energy so amino group is removed by remaining carbon skeleton can be oxidized for fuel - Carbon chains broken down to pyruvate, acetyl coA, etc to provide ATP - Mitochondria generate ATP by breaking down amino acids in citric acid cycle - Not all amino acids enter cycle at same point, so ATP benefits vary

Citric Acid Cycle

- Completes the breakdown of glucose by oxidizing a derivative of pyruvate to carbon dioxide - Aerobic, energy producing pathway, in mitochondria. - Regulated by the state of cellular energetics and O2 availability -

Proton gradient

- Drives the mechanical energy for the production of ATP by the ATPase Synthase - The product of the electron transport chain. A higher concentration of protons outside the inner membrane of the mitochondria than inside the membrane is the driving force behind ATP synthesis.

ETC Process

- ETC: How cells make ATP, occurs in the mitochondria (energy factory) - Mitochondria: double membraned organelles, inner and outer membrane - Mitochondrial matrix is the fluid inside where reactions like Krebs cycle reside - Glycolysis and Krebs make NADH and FADH2 from food; these electron carriers make their way from the matrix to the inner membrane - This is where you find the ETC, a series of enzymes embedded in the membrane which take the electron carrier's electrons and use their energy for pumping protons - The mitochondrial ETC uses electron energy for pumping protons from the mitochondrial matrix to the intermembrane space increasing proton concentration in that place - The only way the protons can escape is through a channel and an enzyme, ATP synthase - ATP synthase uses diffusing protons' kinetic energy to make ATP from ADP and P - The chain is a series of enzymes in a row where each accepts electrons then lets them go to the next carrier in the transport chain (organized like a bucket brigade) - What drives electrons down this enzymatic series is the growing level of each carrier's electronegativity - And to oxygen electrons ultimately falls as it's the most electronegative of them all - NADH starts the ETC as it donates electrons to Complex Number I; this powers active transport as protons are displaced and get pumped from the matrix to the intermembrane space - From Complex I electrons flow to Ubiquinone, also known as "Q", which floats through the inner membrane happily and brings its electrons to Complex III - Complex III is another proton pump using electron energy - Protons jam up in that intermembrane compartment like a hundred people in a one-bedroom apartment - Complex II is for FADH2, which donates electrons, which then get passed to Q; Q once again passes them to Complex III which pumps protons using electron energy - From Complex III, the electrons proceed to another mobile carrier, Cytochrome C, which donates the electrons to Complex IV, another proton pump - After Complex IV, electrons flow to oxygen which is very electronegative, so it pulls electrons down the chain, keeping them moving like the cars of a train - As O2 does this electron grabbing trick, it also grabs protons from the matrix - They all combine to form H2O - Now all these protons in the intermembrane space are trapped as they can't get out of that place because protons are charged and could never get through a phospholipid bilayer as they can't diffuse - But like all particles, they're dying to go from where their concentration's high to where it's low - Stuck in the intermembrane space they're frustrated to diffuse to the matrix, they're highly motivated - And this gradient's been made steeper by O2 which absorbs protons from the matrix stew - So, from proton pumping, and oxygen's actions, add another force: electrochemical attraction - Think of all those trapped protons, each one's positive, the matrix in comparison is negative - Opposites attract so the protons are dying to get to the matrix, oh how they're trying - There's only one channel that let's protons pass, and they use it like high school students busting out of class - It's a channel and an enzyme, ATP synthase, the closer in this game, an energy ace - ATP synthase is embedded in the inner membrane, it's got channels for diffusing protons right through it. When cells make ATP, we'll watch how they do it. - The matrix side of ATP synthase has binding sites for ADP and P which come in and bind and as ATP synthase lets protons barge through, their kinetic energy gets put to use - Like water through a turbine proton movement generates rotation, changing synthase's binding conformation which catalyzes chemical bond formation. ADP and P make ATP that energy sensation!

Glucose oxidation

- Glucose is broken down to 2 glyceraldehyde 3 phosphate and then 2 pyruvate, with the net formation of two molecules each of ATP and NADH. - Mg+ needed as coenzymes

Understand how energy is transformed from reduced NADH to H+ gradient

- Glycolysis and Krebs make NADH and FADH2 from food; these electron carriers make their way from the matrix to the inner membrane - This is where you find the ETC, a series of enzymes embedded in the membrane which take the electron carrier's electrons and use their energy for pumping protons - The mitochondrial ETC uses electron energy for pumping protons from the mitochondrial matrix to the intermembrane space increasing proton concentration in that place

TCA cycle

- Input is Acetyl-CoA with two carbons - The carbons get removed releasing CO2 - The cycle's function's energy transformation 3 NADH, 1 FADH2 creation and also the synthesis of one ATP which cells use for energy - For every glucose cell absorbed the cycle runs two times - It precedes ETC, it follows glycolysis - It occurs in the mitochondrial matrix

ATP synthase

- Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP - As the H+ ions diffuse through the enzyme, they attach P groups to ADP to produce ATP

Identify the role of the TCA cycle in producing reduced cofactors (activated carriers).

- Molecules, called electron shuttles, accept the energy released by stepwise rearrangements and the subtraction of carbons in the form of electrons. Electron shuttles are small organic molecules, such as NAD+ and FADH, that transport high energy electrons to where they need to be by gaining electrons (through "reduction") and losing electrons (through "oxidation"). The electrons transported by electron shuttles will later be used to generate ATP - Energy shuttles: - NADH: An energy shuttle which delivers high energy electrons to the electron transport chain where they will eventually power the production of 2 to 3 ATP molecules. When this electron shuttle is not carrying high energy electrons, meaning it has been oxidized (lost its electrons), it is left with a positive charge and is called NAD+. - FADH2: Another energy shuttle that carries high energy electrons to the electron transport chain, where they will ultimately drive production of 1 to 2 ATP molecules. The oxidized form of FADH2 is FAD and happens just like in NADH. - NADH and FADH2 later bring electrons to the ETC - Each turn of the cycle forms one molecule of GTP, three NADH molecules and one FADH2 molecule. These carriers will connect with the last portion of aerobic respiration to produce ATP molecules. - The cycle is amphibolic (both catabolic and anabolic)

Oxygen role in ETC

- Oxygen that we inhale is picked up by bloodstream and delivered to our cells; ends up in inner mitochondrial membrane; accepts final electrons in ETC; becomes part of molecule of water - Thus, oxidation-reduction reactions in mitochondria generate water as final end product (sometimes called metabolic water)

Understand the concept of coupling H+ gradient with ATP formation

- Proton gradient drives the mechanical energy for the production of ATP by the ATPase Synthase - Chemiosmosis is the movement of hydrogen ions across a membrane, down their electrochemical gradient - The passage of protons through the carrier causes the carrier and its stalk (orange) to spin rapidly like a tiny motor. - This motion alters the conformation of proteins in the stationary head (green), prompting them to produce ATP. - Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers

Substrates of citric acid cycle

- Pyruvate - Acetyl-CoA - Citrate - Isocitrate - α-Ketoglutarate - Succinyl-CoA - Succinate - Fumarate - Malate - Oxaloacetate

Understand the conversion of pyruvate to acetyl-CoA

- Step 1. A carboxyl group is snipped off of pyruvate and released as a molecule of carbon dioxide, leaving behind a two-carbon molecule - Step 2. The two-carbon molecule from step 1 is oxidized, and the electrons lost in the oxidation are picked up by NAD+ to form NADH - Step 3. The oxidized two-carbon molecule—an acetyl group, highlighted in green—is attached to Coenzyme A (CoA), an organic molecule derived from vitamin B5, to form acetyl CoA. Acetyl CoA is sometimes called a carrier molecule, and its job here is to carry the acetyl group to the citric acid cycle. - These steps produce one CO2 and NADH - The steps above are carried out by a large enzyme complex called the pyruvate dehydrogenase complex, which consists of three interconnected enzymes and includes over 60 subunits. At a couple of stages, the reaction intermediates actually form covalent bonds to the enzyme complex—or, more specifically, to its cofactors. - The pyruvate dehydrogenase complex is an important target for regulation, as it controls the amount of acetyl CoA fed into the citric acid cycle. - If we consider the two pyruvates that enter from glycolysis (for each glucose molecule), we can summarize pyruvate oxidation as follows: - (Step 1) Two molecules of pyruvate are converted into two molecules of acetyl CoA. - (Step 2) Two carbons are released as carbon dioxide—out of the six originally present in glucose. - (Step 3) 2 NADH are generated from NAD+ - Why make acetyl CoA? Acetyl CoA serves as fuel for the citric acid cycle in the next stage of cellular respiration. The addition of CoA helps activate the acetyl group, preparing it to undergo the necessary reactions to enter the citric acid cycle.

Understand the flow of electrons in respiratory chain

- The chain is a series of enzymes in a row where each accepts electrons then lets them go to the next carrier in the transport chain (organized like a bucket brigade) - What drives electrons down this enzymatic series is the growing level of each carrier's electronegativity

Understand the balance sheet of energy production and carbon oxidation in the TCA cycle

- The citric acid cycle goes around twice for each molecule of glucose that enters cellular respiration because there are two pyruvates—and thus, two acetyl CoAstart text, C, o, A, end texts—made per glucose. - In a single turn of the cycle, - two carbons enter from acetyl CoA, and two molecules of carbon dioxide are released; - three molecules of NADH and one molecule of FADH2 are generated; and - one molecule of ATP or GTP is produced. - These figures are for one turn of the cycle, corresponding to one molecule of acetyl CoA. Each glucose produces two acetyl CoA molecules, so we need to multiply these numbers by 2 if we want the per-glucose yield. - Two carbons—from acetyl CoA—enter the citric acid cycle in each turn, and two carbon dioxide molecules are released. However, the carbon dioxide molecules don't actually contain carbon atoms from the acetyl CoA that just entered the cycle. Instead, the carbons from acetyl are initially incorporated into the intermediates of the cycle and are released as carbon dioxide only during later turns. After enough turns, all the carbon atoms from the acetyl group of acetyl CoA will be released as carbon dioxide.

inner membrane of mitochondria

- The electrochemical H+ gradient across the ___ ___ of mitochondria includes a large force due to the membrane potential and smaller force due to H+ concentration - where the electron transport chain take place

O2

- The final acceptor of electrons

Chemiosmosis

- The movement of hydrogen ions across a membrane, down their electrochemical gradient - The passage of protons through the carrier causes the carrier and its stalk (orange) to spin rapidly like a tiny motor. - This motion alters the conformation of proteins in the stationary head (green), prompting them to produce ATP. - A process for synthesizing ATP using the energy of an electrochemical gradient and the ATP synthase enzyme.

Understand the function of ATP synthase (ATPase)

- The only way the protons can escape is through a channel and an enzyme, ATP synthase - ATP synthase uses diffusing protons' kinetic energy to make ATP from ADP and P - Only channel that let's protons pass - ATP synthase is embedded in the inner membrane, it's got channels for diffusing protons right through it. When cells make ATP, we'll watch how they do it. - The matrix side of ATP synthase has binding sites for ADP and P which come in and bind and as ATP synthase lets protons barge through, their kinetic energy gets put to use - Like water through a turbine proton movement generates rotation, changing synthase's binding conformation which catalyzes chemical bond formation. ADP and P make ATP that energy sensation! - ATP synthase has binding sites for ADP and Pi (inorganic phosphate). When protons diffuse through ATP synthase, their kinetic energy (energy of motion) causes these binding sites to change shape. This catalyzes formation of a bond between ADP and Pi, transforming them into ATP

Oxidative phosphorylation

- The process through which ATP is synthesized by the respiratory apparatus - The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.

Mitochondrial intermembrane space

- The space between the inner and outer membranes of the mitochondria that has a high H+ concentration - Pyruvate is imported here where it is oxidized to Acetyl-CoA

passively diffused

- This creates a large concentration gradient of H+ ions that are ___ ___ back into the matrix through the ATP synthase

Citric Acid Cycle Function

- To fully oxidize carbon atoms derived from carbohydrates, fats and proteins to produce energy

Electron transport chain

- a series of enzymes, coenzymes, and electron transport proteins that are embedded in the inner mitochondrial membrane (transmembrane proteins). - the apparatus is organized spatially to facilitate electron transfer and ATP synthesis

fatty acid structure

- contain three long hydrocarbon chains (fatty acids) linked to modified sugar, glycerol

Pyruvate

- end product of glycolysis - Pyruvate is a 3-C molecule, produced by glycolysis in the cytosol - Pyruvate is imported into the matrix of mitochondria where all the reactions of the tricarboxylic acid cycle (TCA cycle) will take place

Lipolysis

- enzyme-catalyzed process that liberates fatty acids and glycerol - breakdown of fat

fatty acid beta oxidation

- occurs in mitochondria and works in in cell respiration (enters in krebs cycle) - Glycerol is converted to glyceraldehyde-3-phosphate and enters glycolysis - Fatty acids are are imported into the Mitochondria after they have been activated for oxidation in the cytosol. - catabolized to acetyl-CoA by β-oxidation

Fatty acid oxidation

- provides a source of Acetyl-CoA - generates a FADH2, a NADH and a Acetyl-CoA per cycle, until the fatty acid chain has been fully oxidized

Ubiquinone

- soluble electron transporter in the electron transport chain that connects the first or second complex to the third - the electrons lost by NADH (or FADH2) are transferred to coenzyme Q (___), then to cytochromes and finally to O2 to generate H2O

intermembrane space

- the fluid filled space between the inner and outer mitochondrial membranes - When electrons pass between the proteins and coenzymes, the released energy is used to move hydrogen ions out of the matrix into the ___ ___

ATP

-We must take in enough oxygen to act as final electron acceptor so we can produce enough ___ to meet body's needs

Each turn of the citric acid cycle produces

1 GTP, 3 NADH, and 1 FADH2

Cellular respiration steps

1. Glycolysis 2. Krebs Cycle 3. Electron Transport Chain

Acetyl-CoA

Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.

Oxygen

At the end of the chain, the electrons are picked up by the terminal electron acceptor, which is ___, to produce water

fatty; amino

Cells are capable of breaking down ___ acids and ___ acids in addition to glucose; many of same metabolic pathways and products are utilized

CO2

Diffuse through cytosol, exit cell, and enter bloodstream; when they reach lungs, they are exhale

Remember what is produced during glycolysis

During glycolysis, 2 pyruvate, 2 NADH, 2 ADP, 4 ATP (Net Gain of 2) is produced

Identify the production of GTP from the TCA cycle

Each turn of the cycle forms one molecule of GTP

132 pounds

Human body generates huge amount of ATP per day—about ___ pounds

acidic

If carbon dioxide accumulates in blood, it affects blood pH, making it more ___

respiratory chain

NADH (FADH2) oxidation occurs through the ___ ___ which carry reducing potential to O2

ETC

NADH and FADH2 donate electrons to generate proton motive force, E from electrons is used to create lots of ATP

water

Oxygen accepts the final electrons in ETC to become molecule of ___

Cyanide

Poison that binds to the key enzyme of ETC and inactivates it; makes cells unable to produce adequate ATP, even when blood oxygen level is normal or elevated

Fermentation

Process by which cells release energy in the absence of oxygen

Used to generate ATP

Reduced NADH and FADH2

antidotes

Several agents can be given as ___ to cyanide poisoning, most of which either reverse its actions or bind to it and render it less harmful

Steps of TCA cycle

Step 1. In the first step of the citric acid cycle, acetyl CoA joins with a four-carbon molecule, oxaloacetate, releasing the CoA group and forming a six-carbon molecule called citrate. Step 2. In the second step, citrate is converted into its isomer, isocitrate. This is actually a two-step process, involving first the removal and then the addition of a water molecule, which is why the citric acid cycle is sometimes described as having nine steps—rather than the eight listed here. Step 3. In the third step, isocitrate is oxidized and releases a molecule of carbon dioxide, leaving behind a five-carbon molecule—α-ketoglutarate. During this step, NAD+ is reduced to form NADH. The enzyme catalyzing this step, isocitrate dehydrogenase, is important in regulating the speed of the citric acid cycle. Step 4. The fourth step is similar to the third. In this case, it's α-ketoglutarate that's oxidized, reducing NAD+ to NADH and releasing a molecule of carbon dioxide in the process. The remaining four-carbon molecule picks up Coenzyme A, forming the unstable compound succinyl CoA. The enzyme catalyzing this step, α-ketoglutarate dehydrogenase, is also important in regulation of the citric acid cycle. Step 5. In step five, the CoA of succinyl CoA is replaced by a phosphate group, which is then transferred to ADP to make ATP. In some cells, GDP—guanosine diphosphate—is used instead of ADP, forming GTP—guanosine triphosphate—as a product. The four-carbon molecule produced in this step is called succinate. Step 6. In step six, succinate is oxidized, forming another four-carbon molecule called fumarate. In this reaction, two hydrogen atoms—with their electrons—are transferred to FAD, producing FADH2. The enzyme that carries out this step is embedded in the inner membrane of the mitochondrion, so FADH2 can transfer its electrons directly into the electron transport chain. Step 7. In step seven, water is added to the four-carbon molecule fumarate, converting it into another four-carbon molecule called malate. Step 8. In the last step of the citric acid cycle, oxaloacetate—the starting four-carbon compound—is regenerated by oxidation of malate. Another molecule of NAD+ is reduced to NADH in the process.

Identify the fate of carbons from glucose in the TCA cycle

Step 1: GlycolysisA 6-carbon glucose molecule is split into two 3-carbon molecules called pyruvates. Pyruvate is needed in order to create acetyl CoA. Step 2: The transformation of pyruvate to acetyl CoAThis is a very short step in between glycolysis and the citric acid cycle. The 3-carbon pyruvate molecule made in glycolysis loses a carbon to produce a new, 2-carbon molecule called acetyl CoA. The carbon that is removed takes two oxygens from pyruvate with it and exits the body as carbon dioxide (CO2). CO2 is the waste product that you release when you exhale. - Acetyl-CoA carries 2 carbons and is a highly reduced molecule with energized electrons. It fuels up the Krebs cycle as it cycles on. - At the start of Krebs cycle, the acetyl CoA has its two carbons ripped away and enzymes combine oxaloacetate (with 4 carbons) with them which makes 6-carbon Citric Acid - Enzymes work on citric acid and remove a CO2 and other enzymes modify and oxidize it too which results in the five-carbon alpha-Ketoglutarate - Every oxidation can power the reduction of NAD+ which gains electron-carrying function becoming NADH which later on powers ATP creation in respiration - Another oxidation follows, another CO2 removed, leaving us with a 4-carbon molecule. Another NADH results from this oxidation - This four-carbon molecule Succinyl-CoA has lots of energy enzymes can take away. A series of reactions yields one ATP. This leaves enough energy for cells to reduce an FADH to an FADH2. One last NAD+ will also get reduces as the final electron carrier NADH gets produced - We've harvested what energy came in at Krebs's start. Now we have Oxaloacetate at this final part. Oxaloacetate is the finale ready to meet Acetyl-CoA and here at the final tally - Krebs goes around and around spinning like bicycle wheel - Krebs is like the axle of aerobic respiration - Breathe out its CO2 with every exhalation

reversible oxidation and reduction

The individual components of the electron transport chain undergo ___ ___ and ___ while passing electrons down the chain

free energy

Transfer of electrons is accompanied by changes in the ___ ___ of the system

Electrons

___ removed from both fatty acids and amino acids are sent to ETC for oxidative phosphorylation; final common pathway for each nutrient

Citric Acid Cycle Equation

acetyl CoA + 3 NAD + FAD + GDP + HPO4-2 —————> 2 CO2 + CoA + 3 NADH + FADH + GTP

Breathe out

carbon dioxide

removed

carbons are ___ during citric acid cycle and are also lost as carbon dioxide

Carbon dioxide comes from

carbons lost during carbohydrate catabolism

TCA

catalyzes the complete oxidation of acetyl groups derived from food

Pyruvate dehydrogenase

converts pyruvate to acetyl-CoA

Where does Glycolysis occur?

cytosol/cytoplasm

Voltage gradient

drives ADP-ATP exchange across the inner mitochondrial membrane

pH gradient

drives pyruvate and inorganic phosphate import

Reduction

gain of electrons

Oxidizing agent

gains electrons and is reduced in a chemical reaction. AKA electron acceptor

Where does the ETC occur?

inner membrane of mitochondria

Reducing agent

loses electrons and is oxidized in a chemical reaction AKA electron donor

Oxidation

loss of electrons

Where does the TCA cycle occur?

mitochondrial matrix

Triglycerides

most fats exist as

Glycolysis and the citric acid cycle

provide the precursors needed for cells to synthesize many important molecules such as amino acids, cholesterol, fatty acids, nucleotides, glycolipids, glycoproteins

Under aerobic conditions

pyruvate is further metabolized by the citric acid cycle