Biology: Chap. 6/7

ATP Production from Inorganic Phosphates

• Inorganic phosphates are combined to form ATP.
• ATP is typically used immediately after it is produced.

Glycolysis

• Occurs in two steps.
• Net production: 2 ATP and 2 NADH.

Pyruvate Oxidation

• Produces 2 NADH.
• Liberates 2 carbon dioxide molecules.

Citric Acid Cycle

• Produces 2 ATP.
• Produces 6 NADH and 2 FADH2 (reducing power).
• Liberates 4 carbon dioxide molecules.
• Glucose is completely oxidized to CO_2.
• Six carbon dioxide molecules are produced from one glucose molecule.

Energy Distribution

• A small amount of energy is produced as ATP (4 units per glucose).
• Most potential energy is stored in reducing agents (NADH and FADH2).

Oxidative Phosphorylation

• The reducing power of NADH and FADH2 is used to produce ATP.
• Occurs in the inner membrane of the mitochondria.
• Mitochondria have an outer and inner phospholipid bilayer.
• The process takes place in the inner membrane.

Oxidative Phosphorylation in Detail

• Takes place in the inner mitochondrial membrane, a phospholipid bilayer.
• Mitochondrial Matrix: The middle of the mitochondria.
• Intermembrane Space: The space between the two mitochondrial membranes.
• Ions and carbohydrates cannot diffuse across the phospholipid bilayer without protein channels.

Protein Clusters

• Protein clusters act as oxidation-reduction factors within the inner mitochondrial membrane.
• Protein Cluster 1
• Protein Cluster 2: Situated on top of the membrane.
• Protein Cluster 3
• Protein Cluster 4
• As you move from protein 1 to protein 4, they become stronger oxidizing agents.
• Each protein has a stronger pull for electrons than the last.

Electron Transport Chain

• Electrons are pushed into the protein clusters and travel down the chain.
• As electrons move, the proteins perform work and use energy.
• Reactions become less energetic along the chain.

NADH and Protein Complex 1

• NADH donates electrons to protein complex one, reducing it.
• NADH is oxidized back to NAD+ and reused in the citric acid cycle and glycolysis.

Coenzyme Q

• Coenzyme Q is a mobile, hydrophobic factor within the membrane.
• It oxidizes protein complex one and moves within the membrane.
• Coenzyme Q then reduces protein complex three.

Active Transport by Protein Complex 1

• Energy is liberated during the reduction of protein complex one.
• Protein complex one pumps hydrogen ions from low to high concentration (active transport).

FADH2 and Protein Complex 2

• FADH2 typically resides on protein complex two.
• Protein complex two is reduced by FADH2, which turns back into FAD.
• Electrons are liberated and find their way to protein complex three via choline.

Cytochrome C

• Cytochrome C oxidizes protein complex three and reduces protein complex four.
• Energy is liberated, and protein complex three actively transports hydrogen ions into the intermembrane space.

Increasing Oxidizing Strength

• Proteins must be stronger oxidizing agents at each step because electrons lose energy.

Oxygen's Role

• Oxygen acts as a strong oxidizing agent at protein complex four.
• Oxygen combines with hydrogen ions to oxidize protein complex four and is reduced to water.
• Protein complex four pumps hydrogen ions into the intermembrane space.
• Oxygen pulls electrons through the chain to drive the reactions, including generating NADH.

Hydrogen Ion Gradient

• High concentration of hydrogen ions in the intermembrane space creates a gradient.
• Ions cannot diffuse back across the hydrophobic phospholipid bilayer.
• The intermembrane space becomes positively charged relative to the mitochondrial matrix.

ATP Synthase

• ATP synthase allows hydrogen ions to diffuse down their concentration gradient.
• This process liberates energy used by ATP synthase to combine ADP and inorganic phosphates to generate ATP.
• This is the primary method of ATP generation.

Color Coding

• Proteins are colored blue.
• ATP related components are colored red.
• Non-protein helpers (coenzymes) are colored green.

Anabolic vs. Catabolic Reactions

• Anabolic reactions build up (e.g., running, breathing, thinking) and use energy.
• Catabolic reactions break down (e.g., aerobic respiration).
• ATP couples anabolic and catabolic reactions.
• Catabolic reactions take ADP and phosphate and combine them to make ATP.
• ATP donates its energy via phosphorylation in anabolic reactions.

ATP Usage

• ATP is generated and immediately used.
• Muscles get energy when ATP phosphorylates muscle proteins.

Metabolic Rate

• The rate of ATP cycling increases with energy usage.
• Faster cycling requires more oxygen and produces more carbon dioxide.

Diagram Expectations

• Be prepared to diagram the oxidative phosphorylation process.
• Note where electrons enter (NADH, FADH2) and leave (oxygen).

Common Student Error

• Electrons leave through oxygen, not ATP synthase.
• ATP synthase uses the hydrogen ion gradient, not the electrons directly.

Purpose of Hydrogen Ion Gradient

• The hydrogen ion gradient provides energy for ATP synthase.
• The gradient is like a spring; pushing hydrogen ions down the gradient stores energy.

Inefficiencies and Heat Generation

• Energy transfer is not perfectly efficient; some energy is released as heat.
• Special mitochondria have proteins that allow hydrogen ions to diffuse out without making ATP, generating heat.

Thermoregulation

• Inefficient mitochondria generate heat to maintain body temperature.
• This requires high energy needs and frequent meals.
• Lizards have lower energy needs because they don't waste energy on thermoregulation.

Overworking the Metabolic System

• Cell needs for ATP can exceed the ability to produce it, especially in muscle cells.
• Cells have safety mechanisms to stop functioning and focus on maintaining themselves if ATP levels get too low.

Evolutionary Efficiency

• Evolution does not necessarily produce perfect efficiencies.
• The goal is to make more copies in the next generation.
• Random mutations are tested, and successful ones propagate.

Oxygen Deprivation

• If cells cannot get enough oxygen, the oxidative phosphorylation system shuts down.
• No more citric acid cycle or pyruvate oxidation.
• Glycolysis can still occur.
• However, glycolysis requires NAD+, which is typically regenerated in oxidative phosphorylation.

Fermentation

• Fermentation takes pyruvate and uses it to oxidize NADH, replenishing NAD+.
• Two main types of fermentation:

Lactic Acid Fermentation

• Performed by many organisms, including humans.
• Pyruvate is reduced to lactate.
• NADH is oxidized to NAD+.
• The replenished NAD+ allows glycolysis to continue.
• Lactate is either metabolized, converted back to pyruvate, or removed from the cell.
• Lactic acid bacteria produce lactic acid, which sours fermented foods like cheese, yogurt, sauerkraut, and kimchi.

Ethanol Fermentation

• Performed by domestic yeasts.
• Pyruvate is reduced to ethanol and carbon dioxide.
• NADH is oxidized to NAD+.
• Ethanol fermentation is used in the production of bread and alcoholic beverages.
• Carbon dioxide causes bread to rise, and ethanol is the alcohol in beer and wine.

Fermentation Purpose

• Organisms undergo fermentation to make NAD+ so that glycolysis can continue.

Metabolism of Other Molecules

• Cells prefer to consume glucose, but can metabolize other molecules

Starch

• Is a polymer of glucose. When consumed the starch turns into glucose through glycolysis

Fats

• Fats are glycerol with three fatty acids.
• Lipase enzymes split fats into glycerol and fatty acids.
• Glycerol enters glycolysis.

Beta Oxidation

• Only happens in the mitochondria and requires oxygen.
• Occurs in the mitochondria.
• Fatty acids are split and combined with coenzyme A to produce acetyl coenzyme A.
• Also produces NADH and FADH2, which donate electrons to oxidative phosphorylation.

Proteins

• Proteases hydrolyze proteins into amino acids.
• Amino acids undergo deamination to remove the nitrogen group.
• Deamination produces an organic acid and ammonia.

Ammonia Disposal

• Fish ammonia diffuses out of the skill
• Mammals transform ammonia into urea, which is excreted in urine.
• Birds and reptiles transform ammonia into uric acid, which is excreted as a white paste.

Versatility of Metabolism

• Glucose, lipids, and proteins can all be metabolized for energy.
• Biosynthesis allows the process to run backwards.
• Acetyl coenzyme A cannot be directly converted back into pyruvate.

Gluconeogenesis

• Liver uses oxaloacetate to make glucose.
• Acetyl groups are converted into ketone bodies, which are exported into the bloodstream, to be burned by glycosis, where other tissues can in turn burn Ketone bodies.

Photosynthesis: Overview

• Carbon dioxide combines with water and is provided energy from the light to create food (glucose) and air (oxygen).
• Water is oxidized and carbon dioxide is reduced.

Traditionally Photosynthesis has two groups of reactions:

• Light Dependent Reactions
• Light Independent Reactions

Light Dependent Reactions

- Absorb light energy.
- Oxidizes water into Oxygen.
- NADP(anabolic reaction) is reduced to NADPH.
-Some energy is captured to take some ADP + Inorganic Phosphate and convert it to ATP.

Light Independent Reactions

• Carbon Dioxide Fixation step(taking carbon dioxide to the atmosphere and reducing it.)
• Carbon Dioxide is reduced into glyceraldehyde free phosphate.
• NADPH is oxidized back into NADP.