IB BIOLOGY: Respiration Notes Draw and annotate a molecule of ATP to show how it stores and releases energy.

Contrast oxidation and reduction from the perspectives of (a) the gain or loss of electrons from an element, and (b) gaining oxygen or losing hydrogen. Oxidation involves the loss of electrons from an element, whereas reduction involves the gain of electrons and that oxidation frequently involves gaining oxygen or losing hydrogen, whereas reduction frequently involves losing oxygen or gaining hydrogen. OIL RIG: Oxidation Involves Loss of Hydrogen, Reduction Involves Gain in Hydrogen.

Define cell respiration. • Respiration is the controlled release of energy from organic compounds in cells to

form ATP. Write the summary equation for cellular respiration.

Identify two components of the cell in which respiration takes place.

Glycolysis takes place in the cytoplasm (cytosol), while the citric acid (Krebs) cycle and oxidative phosphorylation take place within the mitochondria.

Distinguish between aerobic and anaerobic in terms of cell respiration. • Aerobic Cellular Respiration: A series of chemical reactions (biochemical

pathways) that produces ATP from glucose and oxygen. • Anaerobic Cellular Respiration: A series of chemical reactions where pyruvate

is converted in the cytoplasm to produces small amounts of ATP without oxygen. o Occurs in cytoplasm of cell o Two types

Alcohol fermentation: pyruvate is converted in the cytoplasm into ethanol, carbon dioxide and energy, with no further yield of ATP. Occurs in bacteria.

Lactic acid fermentation: Produces lactic acid and energy. Occurs in humans (or anything with muscles).

Diagram of anaerobic respiration

Phosphorylation: The process of joining a phosphate group to a molecule 1. Substrate-level phosphorylation

• Producing ATP by adding a phosphate molecule to ADP from a carbon (organic) substrate molecule

• This method doesn’t produce very much ATP (2-4) 2. Oxidative Phosphorylation

• Producing ATP in the electron transport chain by adding inorganic molecules to ADP

• This produces a lot of ATP (34-38)

Outline the process of glycolysis, including phosphorylation, lysis, oxidation and ATP formation (see diagram below). Step 1 - Glucose is phosphorylated. Two phosphate groups are added to glucose to form hexose biphosphate. These two phosphate groups are provided by two molecules of ATP. Step 2 - Lysis of hexose biphosphate: splits into two molecules of triose phosphate. Step 3 - Each triose phosphate molecules is oxidized. Two atoms of hydrogen are removed from each molecule. The energy released by the oxidation is used to add another phosphate group to each molecule. This will result in two 3-carbon compounds, each carrying two phosphate groups. NAD+ is the hydrogen carrier that accepts the hydrogen atoms lost from each triose phosphate molecule. Step 4 - Two pyruvate molecules are formed by removing two phosphate groups from each molecule. These phosphate groups are given to ADP molecules and form ATP.

Draw and label a diagram showing the structure on mitochondrion as seen in a TEM image. Include the inner and outer mitochondrial membranes, matrix, and ribosomes, as well as a scale bar.

Mitochondrion Size: 0.5 micrometers - 10 micrometers

KEY A: Matrix

• site for Krebs' cycle (contains necessary enzymes for reactions) • link reaction • ATP synthesis

B: Inner Membrane • site of oxidative phosphorylation • electron transport chain • increased surface area • ATP synthesis

C: Intermembrane Space • H+ / proton build up

Explain the relationship between the structure of the mitochondrion and its function. Having two membranes allows compartmentalization and accumulation of protons (hydrogen ions) during chemiosmosis Having a folded inner membrane (cristae) forms a large surface area and increases the length available to the electron transport chain, therefore maximizing ATP production during chemiosmosis The fluid matrix containing enzymes of the Krebs cycle. Explain oxidative phosphorylation in terms of chemiosmosis. Electrons are given to proton pumps that are embedded in the membrane between the matrix and inner membrane/cristae of the mitochondrion. The pumps are reduced, giving them energy to pump protons into the inner membrane space. The electrons are transferred along a chain of pumps, continuously losing energy. The proton pumps create a high concentration gradient of protons (H+) inside the inter membrane space. Thus, protons diffuse back into the matrix through facilitated diffusion of ATP synthase (channel protein and enzyme). As the protons pass along this protein channel, the kinetic energy of the protons causes the ATP synthase molecule to turn slightly, exposing active sites that create ATP by binding ADP with inorganic phosphate molecules. The result is 36 ATP produced by oxidative phosphorylation. Explain aerobic respiration including the link reaction, the Krebs cycle, the role of NADH +H+, the electron transport chain and the role of oxygen. In aerobic respiration (in mitochondria in eukaryotes), each pyruvate is decarboxylated (CO2 removed). The remaining two-carbon molecule (acetyl group) reacts with reduced coenzyme A, and, at the same time, one NADH + H+ is formed. This is known as the link reaction. Acetyl CoA then enters the Krebs Cycle where FAD / NAD+ accepts hydrogen and a high-energy electron to form NADH / FADH2. These electron carriers (FADH2 / NADH) donate electrons to electron transport chain. These electrons transfer their energy to member proteins (proton pumps) and actively pump protons (hydrogen ions) across inner membrane. Oxygen is the final electron acceptor and produces water as a “waste product”. In the final step, Chemiosmosis, protons build up (making a proton gradient) in the inter-membrane space of the mitochondrion. This gradient potential is then turned into ATP as protons flow into matrix of mitochondrion through ATPase / ATP synthase.

Describe the central role of acetyl CoA in carbohydrate and fat metabolism. Both carbohydrate and fat metabolism is accomplished by splitting the molecules into 2 carbon structures. These structures are then attached to Coenzyme A, creating Acetyl CoA and allowing the molecules to pass into the inner matrix of the mitochondrion in order to complete the Krebs Cycle and chemiosmosis. Draw the complete steps for the Krebs cycle. The krebs cycle is an example of a metabolic cycle. Each step in the cycle requires enzymes to reduce the activation energy. The reactions all take place in the matrix of the mitochondria and are usually represented as a circular diagram. Try to overcome the idea that the molecules are going in a circle but more that this reaction is taking place within the confined space of the matrix where each intermediate becomes the substrate for the next step.

Alternative Summary of Krebs Cycle

(a) Pyruvate (3C) (b) Link reaction (c) C4 + C2= C6 (d) Recycling of CoA (e) Decarboxylation C6 to C5 and the reduction of NAD (f) Decarboxylation C5 to C4 and the reduction of NAD (g) C4 to C4 with the reduction of coenzymes FAD and NAD. ATP is made directly. (h) C4 to C4 acceptor This cycle follows one acetyl group. Each glucose that enters glycolysis will produce 2 acetyl groups.

Annotate the diagram below with the stages of the electron transport chain and oxidative phosphorylation, including the generation of a H+ concentration gradient in the inter-membrane space, movement of electrons, oxidative phosphorylation by ATP synthase, use of O2 as the terminal electron acceptor.