Metabolism and Thermodynamics

Metabolism and Metabolic Pathways

• Metabolism refers to all the chemical reactions in an organism
• A metabolic pathway is a series of connected chemical reactions, often enzyme-catalyzed

Anabolic vs. Catabolic Pathways

• Anabolic pathways synthesize complex molecules from simpler ones, requiring energy input
• Catabolic pathways break down complex molecules into simpler ones, releasing energy

Forms of Energy

• Kinetic energy is the energy of motion
  • An example is thermal energy, which is the kinetic energy of molecules
• Potential energy is stored energy that can be released to do work
  • Chemical energy is potential energy stored in chemical bonds

Laws of Thermodynamics

• The first law states that energy cannot be created or destroyed, only transferred or transformed
• The second law states that every energy transfer or transformation increases the entropy (disorder) of the universe

Free Energy (ΔG) of Reactions

• A reaction with a positive ΔG is endergonic and requires energy input
• A reaction with a negative ΔG is exergonic and releases energy

Equations for Determining ΔG

• ΔG = ΔH - TΔS
  • ΔG is the change in free energy, ΔH is the change in enthalpy (total energy), T is the absolute temperature, and ΔS is the change in entropy
• ΔG = G(products) - G(reactants)

ATP (Adenosine Triphosphate)

• ATP is the primary energy currency of the cell, consisting of adenine, ribose, and three phosphate groups

ATP Production

• ATP is synthesized through cellular respiration and photosynthesis, where energy released from catabolic reactions or sunlight is used to add a phosphate group to ADP (adenosine diphosphate)

ATP Hydrolysis

• ATP hydrolysis is used to drive endergonic reactions by coupling them with the exergonic breakdown of ATP into ADP and inorganic phosphate
• This releases energy that can be used to perform cellular work

Activation Energy

• Activation energy is the initial energy needed to start a chemical reaction by contorting or breaking bonds
• Enzymes lower the activation energy barrier, making it easier for reactions to occur

Transition State

• A transition state is the unstable intermediate state during a chemical reaction when bonds are being broken and formed

Enzymes

• Enzymes are biological catalysts, typically proteins, that speed up reactions by lowering activation energy
• Enzymes bind to reactants (substrates) and stabilize the transition state, facilitating the reaction

Enzyme Active Sites

• The active site is where the substrate binds and the reaction occurs
• The allosteric site is a separate location where molecules can bind and affect enzyme activity

Factors Affecting Enzyme Function

• Temperature, pH, substrate concentration, enzyme concentration, and the presence of inhibitors or activators can all affect enzyme activity

Induced Fit

• Induced fit is the change in shape of the active site of an enzyme so that it binds more snugly to the substrate, enhancing catalysis

Enzyme Inhibition

• Competitive inhibition involves an inhibitor binding to the active site, blocking substrate binding
• Noncompetitive (allosteric) inhibition involves an inhibitor binding to an allosteric site, changing the enzyme's shape and reducing its activity

Enzyme Regulation

• Activators bind to enzymes and stabilize the active form, increasing activity
• Inhibitors bind to enzymes and stabilize the inactive form, decreasing activity

Allosteric Regulation

• Allosteric regulation is when a regulatory molecule binds to an enzyme at one site (allosteric site) and affects the protein's function at another site (active site)

Catabolic Pathways

• Three catabolic pathways release stored energy by breaking down organic molecules: fermentation, anaerobic respiration, and aerobic respiration
• Fermentation is a partial degradation of sugars that occurs without oxygen
• Anaerobic respiration is similar to aerobic respiration but uses other substances than oxygen to harvest chemical energy
• Aerobic respiration consumes organic molecules and oxygen to yield ATP

Cellular Respiration

• Reactants include glucose and oxygen
• Products include carbon dioxide, water, and ATP
• Glucose is oxidized, and oxygen is reduced
• Reduction yields water; oxidation yields carbon dioxide

Fuel for Cellular Respiration

• Glucose, fats, and proteins can be used as "fuel" for cellular respiration

Redox Reactions

• A redox reaction involves the transfer of electrons
• Oxidation is the loss of electrons from a substance
• Reduction is the gain of electrons to a substance

Oxidizing and Reducing Agents

• An oxidizing agent accepts electrons and becomes reduced
• A reducing agent donates electrons and becomes oxidized

Electron Acceptors in Aerobic Respiration

• NAD+ (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide) are the two major electron acceptors in aerobic respiration

Stages of Aerobic Respiration

• Glycolysis, citric acid cycle (Krebs cycle), and oxidative phosphorylation (electron transport chain and chemiosmosis) are the three stages

Glycolysis

• Input: Glucose, 2 ATP, 2 NAD+
• Output: 2 Pyruvate, 4 ATP (net 2 ATP), 2 NADH
• Occurs in the cytoplasm
• ATP is made by substrate-level phosphorylation

Pyruvate Oxidation

• Input: Pyruvate, CoA, NAD+
• Output: Acetyl CoA, CO2, NADH
• Occurs in the mitochondrial matrix
• No ATP is directly made

Citric Acid Cycle

• Input: Acetyl CoA, NAD+, FAD, ADP
• Output: CO2, NADH, FADH2, ATP
• Occurs in the mitochondrial matrix
• ATP is made by substrate-level phosphorylation

Oxidative Phosphorylation

• Input: NADH, FADH2, O2, ADP
• Output: H2O, ATP, NAD+, FAD
• Occurs in the inner mitochondrial membrane
• ATP is made by chemiosmosis using the H+ gradient generated by the electron transport chain

Substrate-Level Phosphorylation

• Substrate-level phosphorylation is the direct transfer of a phosphate group from an organic substrate to ADP, forming ATP

Glycolysis

• Glycolysis means "sugar splitting"

Phases of Glycolysis

• The energy investment phase consumes ATP
  • 2 ATP are invested
• The energy payoff phase produces ATP and NADH
  • 4 ATP and 2 NADH are gained

Pyruvate Entering Mitochondria

• Pyruvate enters the mitochondria if oxygen is present

Pyruvate Oxidation

• Pyruvate oxidation produces acetyl CoA, CO2, and NADH
• This is important because acetyl CoA enters the citric acid cycle

Citric Acid Cycle Products

• From one turn: 1 ATP, 3 NADH, 1 FADH2, and 2 CO2
• From two turns: 2 ATP, 6 NADH, 2 FADH2, and 4 CO2

Oxidative Phosphorylation

• Oxidative phosphorylation consists of the electron transport chain and chemiosmosis

Electron Transport Chain (ETC)

• The ETC is a series of protein complexes that transfer electrons from NADH and FADH2 to oxygen, releasing energy to pump protons (H+) across the inner mitochondrial membrane

Chemiosmosis

• Chemiosmosis is the movement of ions across a semipermeable membrane, down their electrochemical gradient
• ATP synthase is the enzyme that uses the proton gradient to synthesize ATP

Energy Flow During Cellular Respiration

• Glucose -> NADH/FADH2 -> electron transport chain -> proton-motive force -> ATP

Anaerobic vs. Aerobic Respiration

• Anaerobic respiration uses an electron transport chain with a final electron acceptor other than oxygen
• Aerobic respiration uses oxygen as the final electron acceptor

Fermentation

• Fermentation is similar to anaerobic respiration as it harvests chemical energy without oxygen
• Fermentation does not use an electron transport chain

Fermentation Steps

• Glycolysis to produce ATP, and reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate.

Fermentation Types

• Alcohol fermentation: Pyruvate is converted to ethanol, releasing CO2 and oxidizing NADH in the process to regenerate NAD+
  • The final electron acceptor is acetaldehyde
  • The product is ethanol
• Lactic acid fermentation: Pyruvate is reduced directly by NADH to form lactate as an end product, regenerating NAD+ with no release of CO2
  • The final electron acceptor is pyruvate
  • The product is lactate

Regulation of Catabolism

• Cells regulate catabolism through feedback inhibition and allosteric regulation of enzymes involved in metabolic pathways

Photosynthesis

• Photosynthesis is the process by which plants and other organisms convert light energy into chemical energy
• It occurs in chloroplasts within plant cells

Photosynthetic Organisms

• Plants, algae, and some bacteria are photosynthetic organisms

Autotrophs and Heterotrophs

• Autotrophs are self-feeders that produce their own organic molecules from CO2 and other inorganic raw materials
• Heterotrophs live on organic compounds produced by other organisms

Major Sites of Photosynthesis

• The major sites of photosynthesis are the leaves, specifically in the mesophyll tissue

Chloroplasts

• Chloroplasts contain thylakoids (membranous sacs) and stroma (fluid-filled space)
• Mesophyll tissue is the specialized ground tissue of leaves where photosynthesis occurs

Photosynthesis Equation

• 6CO2 + 6H2O + Light Energy -> C6H12O6 + 6O2, carbon dioxide + water + light energy yields glucose and oxygen

Stages of Photosynthesis

• The light reactions occur in the thylakoids and convert solar energy to chemical energy, producing ATP and NADPH
• The calvin cycle occurs in the stroma, using ATP and NADPH to convert CO2 to sugar

Sunlight

• Sunlight includes wavelengths from ultraviolet, visible, and infrared light

Absorption Spectra

• Absorption spectra show the wavelengths of light that a pigment absorbs

Visible Light Range

• The range of visible light is approximately 380 nm to 750 nm

Pigments

• Pigments are substances that absorb visible light
• Chlorophyll a is the main photosynthetic pigment
• Chlorophyll b and carotenoids are accessory pigments that broaden the spectrum of light that can be used in photosynthesis

Pigment Absorption of Photons

• When a pigment absorbs a photon, it becomes excited and its electrons jump to a higher energy level

Photosystems

• Photosystems consist of a reaction-center complex surrounded by light-harvesting complexes
• The light-harvesting complexes transfer energy of photons to the reaction center

Photosystems in Photosynthesis

• There are two photosystems in photosynthesis: Photosystem II (PSII) and Photosystem I (PSI)

Linear Electron Flow

• The source of electrons is water, which is split to produce oxygen, protons, and electrons
• Chlorophyll a molecules in the reaction center are special because they transfer an electron to the primary electron acceptor
• ATP, NADPH, and O2 are produced during the light reactions

Cyclic Electron Flow

• Photosystem I is involved in cyclic electron flow
• ATP is produced
• Only Photosystem I is used, and no NADPH or oxygen is produced
• One benefit is that it generates additional ATP to satisfy the high energy demands of the Calvin cycle

Chemiosmosis in Mitochondria vs. Chloroplasts

• In mitochondria, chemiosmosis transfers chemical energy from food molecules to ATP
• In chloroplasts, chemiosmosis transforms light energy into chemical energy in ATP

Calvin Cycle Phases

• Carbon fixation: CO2 is incorporated into organic molecules by Rubisco
• Reduction: ATP and NADPH are used to reduce the carbon compounds
• Regeneration: RuBP (the initial CO2 acceptor) is regenerated

Calvin Cycle End Product

• The end product of the Calvin cycle is glyceraldehyde-3-phosphate (G3P), a three-carbon sugar

Carbon Fixation

• During carbon fixation, CO2 reacts with RuBP
• The enzyme that catalyzes this reaction is Rubisco

Photorespiration

• Photorespiration occurs when Rubisco binds to O2 instead of CO2
• This process consumes ATP and releases CO2, reducing photosynthetic output