Free Unit Notes

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I. Enzymes (Topic 3.1)

  A. Enzyme action

1. Enzymes are biological catalysts, usually proteins, that speed reactions by lowering activation energy, the energy needed to start a reaction.

2. A substrate is a reactant that binds to an enzyme’s active site. Its shape and charge must be compatible with that site.

3. Induced fit occurs when substrate binding changes the enzyme’s shape slightly, helping the reaction occur.

4. Enzymes position substrates, strain bonds, or stabilize the transition state. Products are released, and the enzyme can be reused.

5. Enzymes do not change the reaction’s overall free-energy change, equilibrium, or final products.

  B. Helpers and reaction-energy graphs

1. Some enzymes require a cofactor, a nonprotein helper such as a metal ion. An organic helper is called a coenzyme.

2. On a reaction-energy graph, an enzyme lowers the peak above the reactants. The starting and ending energy levels remain unchanged.

II. Environmental Impacts on Enzyme Function (Topic 3.2)

  A. Temperature, pH, and structure

1. Moderate warming usually increases reaction rate because enzymes and substrates move faster and collide more often.

2. Above an enzyme’s optimal temperature, disrupted interactions can change its structure and reduce activity.

3. Low temperatures usually slow reactions without permanently damaging the enzyme.

4. Changes in pH alter charges and interactions within an enzyme. This can affect substrate binding and catalysis.

5. Denaturation is the loss of an enzyme’s functional structure. Extreme heat, pH, or chemical conditions can cause it.

   a. Some enzymes regain their shape and activity when suitable conditions return; others remain denatured.

6. Each enzyme has its own optimal conditions. Salt concentration and other chemicals can also affect its activity.

  B. Enzyme, substrate, and product concentrations

1. Adding substrate usually increases reaction rate until the enzymes become saturated, meaning most active sites are occupied.

2. At saturation, adding more substrate has little effect. Adding enzyme can increase the rate if enough substrate is available.

3. As substrate is used up, the reaction may slow. Product buildup can favor the reverse reaction or inhibit enzymes.

  C. Inhibition and regulation

1. A competitive inhibitor competes with the substrate for the active site. Increasing substrate concentration can reduce reversible competitive inhibition.

2. A noncompetitive inhibitor binds away from the active site and reduces enzyme activity. More substrate does not restore the original maximum rate.

3. Allosteric regulation occurs when a molecule binds at a regulatory site and changes enzyme activity. It can inhibit or activate the enzyme.

4. In feedback inhibition, a pathway’s end product inhibits an earlier enzyme, reducing unnecessary production.

  D. Measuring enzyme activity

1. Reaction rate equals the change in product amount divided by elapsed time. Substrate disappearance can also measure rate.

2. A steeper product-versus-time slope means a faster reaction. Compare the same time interval and include units, such as μmol/min.

3. Change one independent variable and measure reaction rate as the dependent variable. Keep other conditions constant and use an appropriate control.

   a. A treatment without enzyme tests whether the reaction occurs without the catalyst.

III. Cellular Energy (Topic 3.3)

  A. Energy and living systems

1. Cells need a continuous energy supply to maintain organization, grow, reproduce, and perform work. Major loss of energy supply can cause death.

2. The first law of thermodynamics states that energy is conserved. Cells transform energy rather than create it.

3. The second law of thermodynamics states that energy transfers increase total entropy, or energy dispersal. Some usable energy becomes heat.

4. Cells maintain internal order by taking in energy and increasing entropy in their surroundings.

5. Metabolic pathways transfer energy through a series of controlled reactions. One reaction’s product often becomes the next reaction’s substrate.

  B. Free energy and ATP coupling

1. Exergonic reactions release free energy and have a negative ΔG. Endergonic reactions require energy and have a positive ΔG.

2. A favorable reaction can still be slow if it has a high activation-energy barrier.

3. Energy coupling uses an energy-releasing reaction to drive an energy-requiring process.

4. ATP, adenosine triphosphate, contains adenine, ribose, and three phosphate groups. It transfers energy for short-term cellular work.

5. ATP hydrolysis produces ADP and inorganic phosphate. Cells couple this energy-releasing reaction to transport, movement, and molecule synthesis.

6. Making ATP from ADP and inorganic phosphate requires energy from processes such as respiration or photosynthesis.

  C. Electron carriers and shared pathways

1. Oxidation is the loss of electrons. Reduction is the gain of electrons. These processes occur together.

2. NAD⁺, FAD, and NADP⁺ accept electrons to form NADH, FADH₂, and NADPH. These reduced carriers transfer electrons to other reactions.

3. Shared core pathways, including glycolysis and membrane-based ATP production, support common ancestry among Bacteria, Archaea, and Eukarya.

IV. Photosynthesis (Topic 3.4)

  A. Purpose, origins, and chloroplast structure

1. Photosynthesis converts light energy into chemical energy stored in organic molecules. Oxygen-producing photosynthesis uses CO₂ and water to make carbohydrates and O₂.

2. Photosynthesis began in prokaryotes. Cyanobacteria helped oxygenate Earth’s atmosphere, and prokaryotic pathways preceded those in eukaryotes.

3. In plants and algae, chloroplasts contain membrane sacs called thylakoids, often stacked into grana.

4. The thylakoid membrane contains photosystems, electron carriers, and ATP synthase. The stroma is the fluid outside the thylakoids.

  B. Light reactions

1. Light reactions occur in thylakoid membranes. They use light, water, ADP, inorganic phosphate, and NADP⁺ to produce ATP, NADPH, and O₂.

2. Chlorophyll absorbs light and excites electrons in photosystem II. Water splits to replace these electrons, releasing H⁺ and O₂.

3. Electrons pass through an electron transport chain, a series of electron carriers. Their energy helps move H⁺ from the stroma into the thylakoid interior, or lumen.

4. Light excites the electrons again in photosystem I. They ultimately reduce NADP⁺ to NADPH.

5. H⁺ accumulates in the lumen, creating an electrochemical gradient, a difference in concentration and charge across the membrane.

6. H⁺ flows back into the stroma through ATP synthase, which makes ATP from ADP and inorganic phosphate.

   a. Chemiosmosis uses proton flow down an electrochemical gradient to drive ATP synthesis.
   b. ATP synthesis powered by light-driven electron transport is photophosphorylation.

7. The O₂ released during photosynthesis comes from water, not CO₂.

  C. Calvin cycle and carbon storage

1. The Calvin cycle occurs in the stroma. It uses CO₂, ATP, and NADPH to produce G3P, a three-carbon molecule used to build carbohydrates.

2. During carbon fixation, CO₂ becomes part of an organic molecule. ATP supplies energy, and NADPH supplies electrons for carbohydrate production.

3. Most of the carbon stays in the cycle to regenerate its CO₂ acceptor. Some G3P leaves to support sugar synthesis.

4. For three CO₂ fixed, the cycle uses nine ATP and six NADPH to produce one net G3P.

5. The cycle returns ADP, inorganic phosphate, and NADP⁺ to the light reactions. It does not use light directly but depends on their products.

  D. Factors affecting photosynthesis

1. Light intensity, wavelength, CO₂ availability, temperature, and water supply can limit photosynthetic rate.

2. Increasing light raises the rate only until another factor becomes limiting. Chlorophyll absorbs some wavelengths more effectively than others.

3. Closing stomata, the pores in leaves, reduces water loss but also limits CO₂ entry and can slow carbon fixation.

4. Oxygen production or CO₂ uptake can indicate photosynthetic rate. Measurements in living tissue reflect respiration occurring at the same time.

V. Cellular Respiration (Topic 3.5)

  A. Purpose and locations

1. Cellular respiration transfers energy from organic molecules to ATP. Plants, animals, fungi, and many microorganisms carry it out.

2. In eukaryotes, glycolysis occurs in the cytosol. Pyruvate oxidation and the citric acid cycle occur in the mitochondrial matrix.

3. The inner mitochondrial membrane contains the electron transport chain and ATP synthase. Its folds, or cristae, increase surface area for ATP production.

4. Prokaryotes lack mitochondria and use their plasma membrane for respiratory electron transport. Some use oxygen; others use different final electron acceptors.

  B. Glycolysis

1. Glycolysis splits one six-carbon glucose into two three-carbon pyruvate molecules. It does not directly require oxygen.

2. Per glucose, glycolysis uses two ATP and makes four ATP, giving a net gain of two ATP. It also produces two NADH.

3. ATP is made by substrate-level phosphorylation, the direct transfer of phosphate from an organic molecule to ADP.

  C. Pyruvate oxidation and the citric acid cycle

1. Pyruvate oxidation converts two pyruvate into two acetyl-CoA per glucose. It releases two CO₂ and produces two NADH, with no ATP made directly.

2. The citric acid cycle, also called the Krebs cycle, oxidizes the acetyl groups and regenerates the molecule that accepts them.

3. Across two turns per glucose, the cycle produces four CO₂, six NADH, two FADH₂, and two ATP equivalents by substrate-level phosphorylation.

4. CO₂ is released during pyruvate oxidation and the citric acid cycle, not during glycolysis or electron transport.

  D. Oxidative phosphorylation

1. NADH and FADH₂ donate electrons to the electron transport chain in the inner mitochondrial membrane.

2. Electron transfer releases energy that pumps H⁺ from the matrix into the intermembrane space.

3. The intermembrane space has a higher H⁺ concentration and lower pH than the matrix.

4. H⁺ flows back into the matrix through ATP synthase. Chemiosmosis drives ATP production by oxidative phosphorylation.

5. Oxygen is the final electron acceptor in aerobic respiration. It combines with electrons and H⁺ to form water.

6. Oxidative phosphorylation typically produces about 26–28 ATP per glucose. Together with earlier stages, this gives roughly 30–32 ATP in many eukaryotic cells.

   a. These yields vary with transport costs and cell conditions; they are estimates rather than fixed values.

  E. Fermentation and pathway disruptions

1. Without oxygen, aerobic electron transport stops. NADH cannot be efficiently oxidized, and the citric acid cycle slows as NAD⁺ becomes scarce.

2. Fermentation regenerates NAD⁺ from NADH so glycolysis can continue. It adds no ATP beyond glycolysis’s net two ATP per glucose.

3. In lactic acid fermentation, pyruvate is reduced to lactate. In alcohol fermentation, pyruvate-derived acetaldehyde is reduced to ethanol, and CO₂ is released.

4. An electron transport inhibitor reduces proton pumping and ATP production. An uncoupler lets H⁺ bypass ATP synthase, reducing ATP yield and releasing more energy as heat.

   a. Controlled uncoupling can help endothermic animals produce heat to maintain body temperature.

  F. Connections and experimental evidence

1. Photosynthesis stores energy in carbon compounds; respiration transfers some of that energy to ATP. Matter cycles between these processes, while energy ultimately disperses as heat.

2. Both processes use electron transport, proton gradients, and ATP synthase. Membranes must maintain the gradients for efficient ATP production.

3. Oxygen consumption or CO₂ production can indicate respiratory rate. Compare equal tissue amounts and control temperature and measurement time.

4. Graph results with labeled axes, units, an appropriate scale, and error bars when supplied. Use the data and pathway mechanism together to explain a treatment’s effect.

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