AP Biology Cellular Respiration Notes

AP Biology Cellular Respiration – Part 1
(Associated Learning Objectives: 1.15, 1.16, 2.2, 2.4, 2.5, 2.13, 2.14, 2.22, 4.1, 4.4, 4.17)

Important Content from previous topics:
1) The electron transport chain is a series of redox reactions, occurring on a membrane, intended to create a concentration gradient and there in a source of potential energy.
2) Redox reactions are just the transferring of electrons from one molecule to another molecule.
3) Carbohydrates, sugar, are primary energy molecules made in photosynthesis. G3P is half of a sugar glucose molecule.

I. Cellular Respiration
A. This is the process of releasing energy contained in organic molecules (mainly sugar) to do work. (This is an example of catabolism.)
1. The process is for making ATP using oxygen, if available.
2. The process releases heat (Remember, heat is low quality energy) and free electrons. (Remember that electrons are a source of Kinetic Energy.)
B. With O2 present in the cell – Cellular Respiration can occur in the mitochondria.
C. Without O2 present in the cell – Fermentation will occur in the cytoplasm of the cell.
D. 6 H20 + C6H12O6  6 CO2 + 6 H2O + Free E + Heat E
1. ∆G = -686 k/cal per mol Glucose (A negative ∆ G means Free E is available, from breaking down glucose, to do work. In this case, the work is making ATP by phosphorylation.)
a. The Free E is used to make ATP from ADP by phosphorylation.

II. Redox Reactions (This is the transfer of electrons.) Electron can be represented by the symbol e-.
A. Oxidation (loss of electrons)
B. Reduction (gaining of electrons) These two are processes. “tion” means “process”
C. Reducing Agent (electron seller)
D. Oxidation Agent (Buyer for electrons) These two refer to actual molecules or elements. *Always together (The Law of Conservation of Matter)

III. Electronegativity
A. Think of this as the desire to acquire electrons. Look at a molecules valence shell.
B. Oxygen—Has the most desire; Hydrogen—Has the least desire. (It wants to get rid of its one electron.)
C. Electron Transport Chain is a series of “transferring of electrons” or Redox reactions. Just look at the name. We are moving electrons from one molecule to the next. So one is receiving electrons (called reduction) and one is losing them (called oxidation) all the way down the line.
1. Free E is released from each transfer between the molecules in the chain.
2. NAD+ and FAD+ (These are electron carriers. They take the released electrons, from the breakdown of organic molecules, to the chain for release into the chain.)
a. Oxidizing Agents (These carriers are accepting 2 e-, so they are Oxidizing agents.)
b. NADH or FADH2 (The 2 negative electrons combine with the carrier. The first negative electron cancels the carriers positive charge. The second negative electron makes the carrier negative. This causes a positive H+ ion to attach to become NADH or FADH2.)
i. 2 e – are carried at a time to the chain.
3. The Electron Transport Chain is ALWAYS in a membrane.
a. For Bacteria- It is the plasma membrane.
b. For Eukaryotes – It is the Mitochondrial inner membrane or Thylakoid membrane.
4. The WHOLE process is a controlled release of energy.
5. Oxygen is at end of the chain to receive the two electrons. (Remember Oxygen is the most Electronegative element in living organsisms. The Oxygen takes the 2 negative electrons from the chain. This gives it a negative 2 charge, so two positive H+ ions attach to make water. a. Forming water keeps the chain open so that we can keep feeding it electrons at the top. If the chain stops, we lose the ability to make energy. (This is what Cyanide does! It prevents oxygen from taking the electrons out of the chain, so it backs up and quits working.)

IV. Cellular Respiration is a Three Step Process:
A. Step 1: Glycolysis - This is the breaking of Glucose into 2 molecules of G3P. All organisms can do this process as it occurs in the cytoplasm of a cell.)
B. Step 2: Kreb’s Cycle (This is all about making electron carriers in the continued breakdown.)
C. Step 3: e- Transport Chain - This is where the Free E of the electrons is used to help make ATP.)
1. This is referred to as Oxidative Phosphorylation (makes 90% of ATP) because it will need oxygen to be present.
D. Substrate-Level Phosphorylation (makes 10% of ATP) uses another SUBSTance to help make
ATP.
E. The whole process yields a maximum of 38 ATP/ 95% of time only 36 produced though.

V. The Process of Glycolysis (Breaking of Glucose)
A. In this process, Glucose (C6 H12 O6 ) will be broken apart into 2 molecules of G3P. Each molecule of G3P will then be converted to a molecule of Pyruvate. At the end of the process, the cell will have 2 molecules of Pyruvate that can be put into the mitochondria, if oxygen is present and it is a Eukaryotic Cell. 1. Glucose is said to be oxidized, as it is losing electrons in the breakdown.
B. There are two parts to Glycolysis: 1. E Investment Phase a. Glucose is broken into 2 molecules of G3P. b. To break it in half requires 2 ATP be used. (One phosphate is put on EACH side of the Glucose molecule. This makes it unstable and Glucose breaks in half to make 2 G3P molecules.) (The enzyme, Phosphofructokinase, puts the SECOND phosphate on the Glucose molecule; it is the “ON/OFF Switch” for the WHOLE process. If it does NOT put the second phosphate on the Glucose molecule, the Glucose WILL NOT break in half.) 2. E Payoff Phase a. The 2 molecules of G3P will then be converted to 2 molecules of Pyruvate. b. This phase will yield 4 ATP + 2 NADH total.(2 ATP and 1 NADH per molecule.) The cell pays back the two it used for the first part. This leaves the cell with a payoff of two ATP. (What we refer to as NET Gain.)
C. Remember this process occurs with or without O2 present in the cell. D. ALL organisms can do it as it occurs in the cytoplasm of a cell. Therefore, this process must have been one of the earliest processes to evolve within organisms to harvest energy from molecules present within the earth’s earliest environments. Even before free oxygen was present in the atmosphere.

AP Biology
Cellular Respiration – Part 2
(Associated Learning Objectives: 1.15, 1.16, 2.2, 2.4, 2.5, 2.13, 2.14, 2.22, 4.1, 4.4, 4.17)

Important concepts from previous topics:
1) Surface area of membranes is important to all cells, prokaryotic or eukaryotic.
2) An existing concentration gradient is also a source of potential energy.
3) The amount of energy in a molecule is directly related to the amount of Hydrogen atoms in the molecule

I. If Oxygen is present within the Eukaryotic cell (“Aerobic” means “with Oxygen”), the cell can perform the other two parts of Cellular Respiration – Kreb’s Cycle and Electron Transport Chain.
A. In order to enter the inner mitochondrial space, where the Kreb’s cycle occurs, Pyruvate must be converted to Acetyl Coenzyme A. This is referred to as the Pyruvate conversion. It occurs in the space between the outer membrane and the inner membrane of the mitochondria. 1. This Pyruvate Conversion involves three steps: a. Step 1: Removal of CO2from each molecule of Pyruvate. (Remember there are 2.) b. Step 2: NAD+ or FAD+ (Both can perform this act as they are both electron carriers.) becomes reduced by accepting the 2 e- from the broken bond. This allows for a H+ ion to attach and make NADH or FADH2. (Remember these are Oxidizing Agents because they are receiving electrons.) c. Step 3: To the open bond, Coenzyme A is attached using sulfur as the connecting link. 2. The final product is Acetyl Coenzyme A. (EACH molecule is now located in the inner mitochondrial space.)
B. Kreb’s cycle (This occurs in the inner mitochondrial space where there is room to work.) Remember, the main purpose of the Kreb’s cycle is to make electron carriers. See how many it makes per Acetyl Coenzyme A put into the cycle. 1. EACH Acetyl Coenzyme A that goes through the cycle will produce: a. 3 NADH (electron carrier) So 2 molecules X 3 = 6 NADH electron carriers b. 1 FADH2(electron carrier)  So 2 molecules X 1 = 2 FADH2 electron carriers c. 1 ATP  So 2 molecules X 1 = 2 ATP d. 2 CO2 (A waste product.)  So 2 molecules X 2 = 4 CO2 that diffuse out of the cell. C. Electron Transport Chain a. This occurs on the inner mitochondrial membrane. i. This membrane is folded (THE FOLDS INCREASES SURFACE AREA; MORE ATP CAN BE PRODUCED AS THERE IS ROOM FOR MORE ELECTRON TRANSPORT CHAINS.) b. Electrons move by a series of Redox reactions using increasing electronegativity. i. Move 2 at a time DOWN the chain toward OXYGEN, making H2O at end. c. NADH drops its two electrons off at FMN “first molecule at top of chain”. (In doing so, the pair of electrons will pass through 3 protein Proton Pumps. If three protons, H+ ions, are pumped into the space BETWEEN the membranes 3 ATP will be able to be produced.)
d. FADH2 drops its two electrons off at Q, which is a lipid.
(These pairs of electrons will only pass through two Proton pumps; therefore only 2 protons, H+, will be pumped into the space between the membranes and thereby only 2 ATP will be able to be produced.) e. Remember the Cytochromes indicated common ancestory for ALL organisms, as ALL electron transport chains will possess these proteins. f. Cynanide kills by replacing Oxygen at the chain and stopping the flow of electrons. g. Free Energy, from the electrons, fuels the active transport of H+ ions into the inner mitochondrial space between the membranes .
i. H+ (ions/protons) are pumped into the confined space between the membranes using the Free E released from electrons as they go down the chain. ii. The concentration of H+ ions builds inside the space(like blowing up a balloon) to create a concentration gradient. High[ ] in between and low [ ] in the center. iii. The H+ ions are released using ATP Synthesizing Complex. (It would be like pulling the cork in the sink.)

iv. The H+ ions rush out (going from High [ ]–>Low [ ]) allowing the ATP Synthesizing Complex to use the Kinetic E to turn ADP  ATP in large amounts by phosphorylation.
v. This is another example of Energy Coupling – two processes working together and involving energy. (Same as it was in Photosynthesis.) One process is active transport and the other is diffusion. vi. This type of energy coupling, for making ATP, is referred to as Chemiosmosis. vii. The Electron Transport Chain can makes 34 or 32 ATP. It depends on which electron carrier showed up in the Pyruvate conversion. If it was NAD+, the process makes 34. If it was FAD+, the process makes 32. FAD+ usually shows up because NAD+ is too busy in the Kreb’s cycle.)
D. ADD IT ALL UP NOW: 2 Net ATP From Glycolysis 2 Net ATP from the Kreb’s cycle 34 OR 32 Net ATP from the Electron Transport Chain using all the NADH andFADH2. 38 Maximum OR 36 Normal

AP Biology
Cellular Respiration – Part 3
(Associated Learning Objectives: 1.15, 1.16, 2.2, 2.4, 2.5, 2.14, 2.16, 2.18, 2.22, 4.1, 4.4, 4.17)

Important concepts from previous topics:
1) All cells, prokaryotic and eukaryotic, can perform Glycolysis in the cells cytoplasm.
2) Since all organisms can perform Glycolysis, they must have unity by common ancestry.
3) Enzymes control most processes within cells; therefore the must be regulated (controlled). Most are controlled at the allosteric site using inhibitors and activators.

I. If NO OXYGEN is present within the cell (“Anaerobic” means “without oxygen”): A. Fermentation will occur to free up the electron carriers to keep at least Glycolysis going making ATP. 1. Two types of fermentation can occur. It depends on the organism doing it. a. Alcohol Fermentation (This occurs in bacteria and Yeast –a fungus.) i. They convert the two Pyruvate molecules to 2 molecules of Ethanol by cutting off CO2 and filling the open bond with H from the electron carriers. This frees up the electron carrier to keep Glycolysis going and thereby making some ATP which is needed to stay alive. ii. Beer, wine, and bread are made by this type of fermentation. b. Lactic Acid fermentation (This occurs in animals mainly.) i. Converts Pyruvate into Lactic Acid by breaking the ketone, the double bonded Oxygen in the middle, and adding H. The H comes from the electron carrier. Here again keeping the process of Glycolysis going to make a little amount of ATP to keep the cells alive in the absence of Oxygen. ii. Cheese, yogurt, and muscle cramps (These force you STOP exercising.) are all created by this type of fermentation.

II. Facultative Anaerobes
A. These organisms can perform both Aerobic and Anaerobic Respiration, but prefer to use oxygen – because it produces more ATP than by using fermentation.

III. Evolutionary Significance of Glycolysis
A. Early Earth had no free Oxygen – Since Glycolysis doesn’t need Oxygen to occur it and all organisms can perform the process; it most likely would have been the first energy making process to evolve. 1. Remember, there was no free Oxygen gas in the Miller/Urey experiment. B. Common Ancestory – All living organisms continue to use the process because it works effectively! C. Endosymbiant Hypothesis – mitochondria are found in all eukaryotic cells because they are effective at getting more energy from the pyruvate by breaking in down further!

IV. Versatility of Respiration A. Amino Acid Utilization (These must undergo Deamination to be used in the Kreb’s cycle.) 1. Cut off the Amine group (Hence DE amination) and put on Coenzyme A using a sulfur molecule to the remaining 2 carbon skeleton from the Amino Acid. Then Feed into the Kreb’s cycle to make energy. The resulting NH3 (Ammonia) is put into the blood stream for disposal by the kidneys using water in the form of urea (mammals) or uric acid (birds and reptiles). Fish release the NH3 directly into the water. B. Lipid Utilization (These undergo Beta Oxidation.)(Beta is second letter of Greek Alphabet.) 1. Cut the Fatty acid tails of the lipid molecules up into 2 carbon skeletons and attach Coenzyme A using a sulfur molecule to each 2 Carbon skeleton. Then feed them into the Kreb’s cycle to make energy.

V. Biosynthesis – This is using food building blocks to make self. (Basically it is Anabolism.) (It requires ATP.)

VI. Feedback Inhibition – The enzyme Phosphofructokinase acts as the “on/off switch” for whole process – in Glycolysis. When there is plenty of ATP in a cell, the excess ATP and Citrate, from the Kreb’s cycle, work together as co-inhibitors, attaching at the allosteric site, to shut down the whole process until energy is needed again by the cell.