AP BIO MR W

🧪 Enzymes

Key Properties of Enzymes

• Enzymes are typically proteins, though some RNAs can act as enzymes.

• Enzymes catalyze reactions in cells by lowering the activation energy, thereby increasing the reaction rate.

  Activation energy with enzyme<Activation energy without enzymeActivation energy with enzyme<Activation energy without enzyme

• Enzymes are highly specific due to their active site complementing the shape and charge of their substrate, the substance on which the enzyme acts.

Factors Affecting Enzyme Activity

pH Levels

• Enzymes function optimally within a narrow pH range.

• Moving above or below the optimum pH disrupts hydrogen bonds, ionic bonds, and hydrophobic clustering, which alters the shape of the active site and hinders substrate binding.

• This disruption can lead to denaturation, which impairs or negates enzyme function.

Temperature

• Enzyme activity increases with temperature up to a certain point due to increased kinetic energy, which enhances the likelihood of enzyme-substrate binding.

• Beyond an optimal temperature, the enzyme denatures, reducing its ability to bind with the substrate and catalyze reactions.

Denaturation: Reversible vs. Irreversible

Substrate Concentration

• At low substrate concentrations, the rate of product formation is low due to infrequent enzyme-substrate interactions.

• As substrate concentration increases, so does the reaction rate, until a saturation point is reached where all enzymes are bound to substrates, resulting in a peak reaction rate.

Enzyme Inhibition

Competitive Inhibition

Non-Competitive Inhibition

⚡ Cell Energy

Metabolic Pathways

Autotrophs vs. Heterotrophs

Autotrophs

• Photoautotrophs: Utilize light energy to create organic compounds via photosynthesis (e.g., plants, cyanobacteria).

• Chemoautotrophs: Derive energy from oxidizing inorganic substances through chemosynthesis (e.g., certain bacteria and archaea).

Heterotrophs

• Obtain energy and matter by metabolizing organic compounds through consumption, absorption, or decomposition.

• Include ecological consumers, decomposers, and parasites.

Exergonic vs. Endergonic Reactions

ATP (Adenosine Triphosphate)

• ATP consists of a five-carbon sugar (ribose), adenine, and three phosphate groups.

• ATP stores and releases energy by breaking or forming bonds with its phosphate groups.

⚡️ Energy Coupling and ATP

ATP: The Cellular Powerhouse

ATP (adenosine triphosphate) is a crucial molecule within cells, consisting of:

• A ribose sugar

• A nitrogenous base called adenine

• Three phosphate groups

The primary functions of ATP are to:

• Power cellular work

• Store energy

Each cell synthesizes its own ATP, with no sharing between cells. ATP is created when cells use energy from food (during cellular respiration) or light (during photosynthesis) to combine ADP (adenosine diphosphate) and a phosphate group.

To release energy for work, cells remove a phosphate group from ATP, breaking the terminal phosphate group and creating ADP and phosphate.

Energy Coupling Defined

Examples of Energy Coupling:

1. Cellular Respiration: The exergonic process of cellular respiration drives the formation of ATP from ADP and phosphate.

2. Active Transport and Muscle Contraction: The exergonic conversion of ATP to ADP and phosphate is coupled to endergonic processes like active transport and muscle contraction.

☀ Photosynthesis: Harnessing Light Energy

The Big Picture

Photosynthesis is a process in which photoautotrophs (like plants) use light energy to combine carbon dioxide and water to produce carbohydrates (glucose), with oxygen released as a waste product.

Chemical Equation: 6CO2+6H2O+Light Energy→C6H12O6+6O26CO2​+6H2​O+Light Energy→C6​H12​O6​+6O2​

Endergonic Nature of Photosynthesis

Photosynthesis is an endergonic reaction because:

• It converts low-energy inputs (carbon dioxide and water) into a high-energy product (glucose).

• It reduces entropy, increasing organization (e.g., converting diffuse carbon dioxide gas into solid matter).

  • There are 12 molecules on the reactants side of the equation.

  • There are 7 molecules on the products side of the equation.

Evolutionary Significance

Photosynthesis first evolved approximately 3.5 billion years ago, relatively soon after the emergence of life (3.8 billion years ago).

Consequences of Photosynthesis:

• Creation of an oxygen-rich atmosphere by splitting water molecules, enabling aerobic metabolism.

• Formation of the ozone layer, which shields life from ultraviolet radiation, making life on land possible.

Two Phases of Photosynthesis

1. Light Reactions:

   • Convert light energy into chemical energy in the form of ATP and NADPH (an electron carrier similar to NADH).

2. Calvin Cycle:

   • Converts the chemical energy in NADPH and ATP into carbohydrate by fixing carbon dioxide into sugars.

chlorophyll and Light Absorption

Role of chlorophyll

chlorophyll is the pigment that absorbs light energy in photosynthesis. Its structure includes a hydrocarbon tail (for fitting into the thylakoid phospholipid bilayer) and a nitrogen ring with magnesium in the center.

Absorption Spectrum

An absorption spectrum illustrates the amount of light absorbed at different wavelengths by a pigment. Chlorophyll has two forms (chlorophyll a and chlorophyll b) that:

• Absorb most energy in the blue and red parts of the spectrum.

• Absorb very little in the green part of the spectrum, which is why leaves appear green (reflecting green light).

Carotenoids are other pigments involved in photosynthesis that absorb different wavelengths.

Action Spectrum

The action spectrum demonstrates how various light wavelengths drive photosynthesis.

• Blue and red light drive the most photosynthesis.

• Green light drives very little photosynthesis.

Engelmann's Experiment: In the 1800s, Thomas Engelmann used a prism to separate light into different wavelengths on a filament of algae. Aerobic bacteria clustered around the algae in the blue and red light, indicating higher oxygen production and thus more photosynthesis in those areas.

🍃 chloroplast Structure and Function

chloroplast Location

chloroplasts are found in cells within the top part of the leaf.

chloroplast Structure

Key structures of the chloroplast include:

⚙ Light Reactions: Converting Light to Chemical Energy

Overview

The light reactions convert the energy in light into the chemical energy of NADPH and ATP.

• NADPH: An electron carrier.

• ATP: The molecule cells use to build things.

Location: Thylakoids

Inputs: Light and water

Outputs: Oxygen (waste product), NADPH, and ATP

The outputs of the Calvin cycle are the inputs of the light reactions: NADP+, ADP, and P.

Key Structures

• chloroplast: The organelle where photosynthesis takes place.

• Grana: Stacks of thylakoids.

• Thylakoid Membrane: A single thylakoid membrane containing photosystems.

• Photosystems: Complex assemblies of proteins with embedded chlorophyll molecules that convert light energy into a flow of electrons.

Process

Photosystems in the thylakoid membrane act like a solar panel, converting light energy into electricity. They also split water molecules in photosystem II.

Electrons flow along an electron transport chain. At one point, the electrons flow through proton pumps, which pump protons from the stroma into the thylakoid space.

ATP synthase is an enzyme that generates ATP as protons diffuse through it. NADPH is also created during this process.

Creating ATP

Photoexcitation of chlorophyll in photosystem II leads to a flow of electrons along an electron transport chain in the thylakoid membrane.

⚡️ Light Reactions: Powering the Calvin Cycle

Chemiosmotic Gradient

The electron transport chain generates an electrical current, powering a proton pump in the thylakoid membrane.

This gradient is both a diffusion and an electrical gradient, driving protons back into the stroma through ATP synthase. As protons diffuse through ATP synthase, their kinetic energy drives the endergonic reaction that synthesizes ATP from ADP and phosphate.

A water splitting complex, part of photosystem II, splits water molecules into oxygen (a waste product) and protons, further enhancing the proton gradient and ATP production.

Reducing Power: NADPH

Photoexcitation of chlorophylls in photosystem I initiates electron flow through its electron transport chain. These electrons reduce NADP+ into NADPH via the enzyme NADP+ reductase.

NADPH provides electrons and hydrogens to reduce carbon dioxide into carbohydrates during the Calvin cycle.

The Z Scheme

The Z scheme is a graphical representation of the light reactions:

• Y-axis: Electron energy level.

• Light excites electrons in photosystem II, boosting them to a higher energy level.

• Water is split into protons and oxygen.

• Electrons flow through the electron transport chain of photosystem II, powering ATP synthesis via proton pumps.

• Electrons arrive at photosystem I at a lower energy level.

• Light re-excites these electrons to a higher energy level, passing them to the primary electron acceptor.

• Electrons flow through the electron transport chain of photosystem I to NADP+ reductase.

• NADP+ reductase generates NADPH from NADP+ and a proton.

• Products: ATP and NADPH.

🔄 The Calvin Cycle: From CO2 to Sugars

The Calvin cycle uses the products of the light reactions (ATP and NADPH) and carbon dioxide to create sugars. It occurs in three phases:

1. Carbon Fixation

2. Energy Investment and Harvest

3. Regeneration of the Starting Compound

1. Carbon Fixation Phase

Carbon dioxide is combined with ribulose-1,5-bisphosphate (RuBP), catalyzed by the enzyme RuBisCO.

The resulting six-carbon product immediately breaks down into two three-carbon molecules.

2. Energy Investment and Harvest Phase

The three-carbon product from the carbon fixation phase is reduced and phosphorylated:

• Phosphorylation: ATP donates a phosphate group to the molecule.

• Reduction: NADPH donates an electron to the molecule.

This yields glyceraldehyde-3-phosphate (G3P), also known as phosphoglyceraldehyde (PGAL), which is a high-energy molecule. G3P can be harvested and used to build plant biomass and, ultimately, the biomass of other organisms that consume the plant.

3. Regeneration Phase

To understand the carbon flow in the Calvin cycle, consider the number of carbon atoms at each stage:

1. Carbon Fixation: Three RuBPs (15 carbons) + three CO2 (3 carbons) → six three-carbon molecules (18 carbons total)

2. Energy Investment: Six G3P molecules (18 carbons)

3. Harvest: One G3P is removed (3 carbons), leaving five G3P molecules (15 carbons)

4. Regeneration: The remaining five G3Ps (15 carbons) are rearranged into three five-carbon RuBPs (15 carbons), requiring phosphorylation.

Cellular Respiration: The Big Picture 🖼

• Cellular respiration's chemical equation:

  C6H12O6+6O2→6CO2+6H2O+Energy (ATP)C6​H12​O6​+6O2​→6CO2​+6H2​O+Energy (ATP)

• Is it endergonic or exergonic?

  Exergonic Reaction: Cellular respiration is exergonic because it releases energy and creates disorder, transforming organized glucose into less organized molecules.

• Where in eukaryotic cells does it occur?

  • Glycolysis: Cytoplasm

  • Link Reaction: Brings product of glycolysis into the mitochondrion

  • Kreb Cycle: Matrix

  • Oxidative Phosphorylation: Mitochondrial membrane

Phases of Cellular Respiration ⚙

1. Glycolysis

   • Energy in glucose generates ATP and NADH.

   • End product: A three-carbon molecule called pyruvic acid or pyruvate.

   • One glucose (six-carbon molecule) becomes two pyruvates (three-carbon molecules each).

2. Link Reaction

   • Pyruvate enters the mitochondrial matrix.

   • Enzymes convert pyruvate to acetyl CoA (two carbons), releasing CO2CO2​ (1/3 of exhaled CO2CO2​).

   • The conversion powers the reduction of NAD+NAD+ to NADH.

3. Kreb Cycle

   • Enzymes oxidize the two carbons in acetyl CoA.

   • Powers the production of three NADH, one FADH2FADH2​, and one ATP.

   • Releases two carbon dioxides (2/3 of exhaled CO2CO2​).

   • For every glucose, the Krebs cycle runs twice, as does the link reaction.

4. Electron Transport Chain (ETC)

   • Oxidizes reduced mobile electron carriers, creating electron flow.

   • Powers the production of ATP from ADP and phosphate through chemiosmosis.

Glycolysis, Link Reaction, and the Krebs Cycle 🔄

Glycolysis Breakdown 🍬

• Occurs in the cytoplasm and is anaerobic.

• Three phases: Investment, Cleavage, and Energy Harvest.

  1. Investment

     • Enzymes phosphorylate glucose, using ATP to add phosphate groups to intermediate compounds, resulting in fructose 1,6-bisphosphate.

  2. Cleavage

     • Enzymes cleave fructose 1,6-bisphosphate into two molecules of G3P (glyceraldehyde-3-phosphate).

  3. Energy Harvest

     • Enzymes oxidize G3P, transferring electrons to NAD+NAD+, reducing it to NADH.

     • Other enzymes phosphorylate ADP to ATP, yielding a gross energy of 4 ATPs.

• Net yield of glycolysis: 2 ATPs, 2 NADHs, and two molecules of pyruvate.

The Link Reaction 🤝

• Pyruvic acid is transported across the mitochondrial membranes into the mitochondrial matrix.

• Enzymes remove CO2CO2​ from pyruvic acid.

• Remaining two-carbon molecule (acetyl group) is oxidized, and electrons are transferred to NAD+NAD+, reducing it to NADH.

• Acetyl group attaches to coenzyme A, forming acetyl CoA.

Krebs Cycle Details 📝

• Occurs in the mitochondrial matrix.

• Cyclical series of reactions generating NADH, FADH2FADH2​, and ATP.

• Alternative names: citric acid cycle or tricarboxylic acid cycle (TCA cycle).

• Starting point: Enzymes transfer the two-carbon acetyl group from acetyl CoA to oxaloacetate, forming citric acid.

• Enzymes oxidize citric acid, transferring electrons to NAD+NAD+ and FAD, reducing them to NADH and FADH2FADH2​, respectively.

• Substrate-level phosphorylation of ADP and phosphate yields ATP.

• For each acetyl CoA entering the cycle, one ATP, three NADH, and one FADH2FADH2​ are generated, with CO2CO2​ released as a byproduct.

• Oxaloacetate is the starting and ending compound.

Electron Transport Chain and Oxidative Phosphorylation ⚡

Generating ATP 🔋

• NADH and FADH2FADH2​ (mobile electron carriers) accumulate in the mitochondrial matrix.

• They diffuse to the inner membrane and are oxidized, releasing electrons that flow through the electron transport chain (ETC).

• Electron transport chain: A series of membrane-embedded proteins in the mitochondrial inner membrane.

• NADH enters the chain earlier, with more energy in its electrons compared to FADH2FADH2​.

• Some electron transport proteins act as proton pumps, actively transporting protons from the matrix to the intermembrane space, creating an electrochemical gradient.

• Oxygen acts as the final electron acceptor, pulling electrons down the chain, absorbing electrons and protons from the matrix, and increasing the gradient.

🌡 Thermogenesis via Brown Fat Cells

In newborn humans, hibernating mammals, and other mammals, brown fat cells, densely packed with mitochondria, generate heat when body warmth is needed.

Hormones induce thermogenin (also known as UCP or uncoupling channel) protein channels to form in the inner mitochondrial membrane. Instead of protons being forced to diffuse through ATP synthase to generate ATP, these channels allow protons to diffuse back to the matrix from the intermembrane space without passing through ATP synthase. The electron transport chain still operates, generating heat as electrons move.

🔄 Aerobic vs. Anaerobic Respiration

🍺 Fermentation: Regenerating NAD+

Fermentation is a process involving glycolysis, followed by reactions that regenerate $NAD^+$.

Alcohol Fermentation (Ethanol Fermentation)

Occurs in yeast:

1. Enzymes remove $CO_2$ from pyruvic acid (pyruvate).

2. Acetaldehyde is produced.

3. Acetaldehyde is reduced to ethanol by other enzymes.

4. $NADH$ is oxidized to $NAD^+$, allowing glycolysis to continue.

$CO_2$ produced makes bubbles in beer and gives bread its spongy texture.

Lactic Acid Fermentation

Occurs in muscle tissue under anaerobic conditions:

1. Pyruvate is reduced to lactic acid.

2. $NADH$ is oxidized to $NAD^+$, allowing glycolysis to continue.

Lactic acid fermentation occurs during intense anaerobic exercise.

🤝 Similarities Between ATP Generation in Mitochondria and Chloroplasts

• Both use an electron transport chain to pump protons into an enclosed space, creating a proton gradient.

  • In photosynthesis, protons are pumped from the stroma to the thylakoid space.

  • In cellular respiration, protons are pumped from the matrix to the intermembrane space.

• Both use chemiosmosis, where protons diffuse through an ATP synthase channel to generate ATP.

The similarities suggest a common ancestor in ancient history for mitochondria and chloroplasts. ATP synthase evolved once and was then shared by the ancestors of chloroplasts and mitochondria.