Metabolism, Energy, and Thermodynamics

Metabolism, Energy, and Thermodynamics

• Metabolism is the sum of all chemical reactions in an organism, requiring enzymes to speed up reactions
• Anabolism synthesizes molecules and requires energy, for example, protein synthesis
• Catabolism breaks down molecules and releases energy, such as cellular respiration
• Energy is the capacity to cause change
• Kinetic energy is the energy of motion, like thermal energy
• Potential energy is stored energy due to structure or location, such as chemical energy in bonds
• The first law of thermodynamics states that energy cannot be created or destroyed, only transformed
• The second law of thermodynamics states that energy transformations increase entropy (disorder), with some energy lost as heat
• Entropy is a measure of disorder; maintaining order requires energy, for example, plants use sunlight to build glucose

Endergonic and Exergonic Reactions

• Endergonic reactions require energy input; energy is stored in products
• Exergonic reactions release energy by breaking bonds
• Spontaneous reactions move towards equilibrium and release free energy that can do work
• Coupled reactions involve exergonic reactions driving endergonic reactions
• ATP hydrolysis is often the exergonic reaction

ATP – Cellular Energy Currency

• ATP consists of adenine, ribose (sugar), and three phosphates
• Phosphate groups have high-energy bonds; breaking them releases energy
• ATP hydrolysis provides energy due to repelling phosphate groups
• ATP powers mechanical work (moves motor proteins), transport work (pumps substances across membranes), and chemical work (drives endergonic reactions)
• Substrate-level phosphorylation involves energy from catabolism adding phosphate to ADP
• Oxidative phosphorylation and chemiosmosis use a proton/electron gradient to generate ATP

Enzyme-Catalyzed Reactions

• Activation energy is the energy needed to start a reaction
• Enzymes lower activation energy, making reactions faster
• Enzymes are biological catalysts that speed up reactions without being consumed
• A substrate is a reactant that binds to the enzyme
• The active site is the location where the reaction occurs
• An enzyme-substrate complex involves temporary binding before product formation
• The induced fit model is when an enzyme changes shape slightly to fit the substrate
• Increased substrate concentration increases activity until saturation
• High temperature can denature enzymes
• Enzymes work best within specific pH ranges
• Competitive inhibition is when an inhibitor binds to the active site
• Noncompetitive inhibition is when an inhibitor binds elsewhere, changing enzyme shape
• Cofactors are nonprotein helpers (e.g., metal ions)
• Coenzymes are organic cofactors (e.g., NAD, FAD, NADP)

Metabolic Pathways & Feedback Inhibition

• Metabolic pathways are a series of enzyme-catalyzed reactions where the product of one step is the substrate for the next
• Feedback inhibition is when the end product of a pathway inhibits an earlier enzyme
• Feedback inhibition prevents waste by stopping production when enough product is made

Energy Flow & Redox Reactions

• Energy flows into an ecosystem as sunlight and leaves as heat
• Photosynthesis converts sunlight into chemical energy (glucose, O₂)
• Cellular respiration breaks down glucose to produce ATP
• Oxidation is the loss of electrons
• Reduction is the gain of electrons
• NAD⁺ becomes NADH (reduced)
• FAD becomes FADH₂ (reduced)
• NADP⁺ becomes NADPH (used in photosynthesis)
• Oxidative phosphorylation produces ~90% of ATP
• Substrate-level phosphorylation is direct enzyme-driven ATP production (e.g., glycolysis & citric acid cycle)

Overview of Cellular Respiration

• Cellular respiration converts glucose into ATP
• The four stages of cellular respiration are glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation
• Glycolysis occurs in the Cytoplasm
• Pyruvate Oxidation occurs in the Mitochondrial Matrix
• Citric Acid Cycle occurs in the Mitochondrial Matrix
• Oxidative Phosphorylation (ETC & Chemiosmosis) occurs in the Inner Mitochondrial Membrane
• Equation: C6H12O6+6O2→6CO2+6H2O+ATPC_6H_{12}O_6 + 6O_2 → 6CO_2 + 6H_2O + ATPC6 H12 O6 +6O2 →6CO2 +6H2 O+ATP

Glycolysis (Anaerobic)

• Glycolysis occurs in the cytoplasm
• Reactants: Glucose (6C), 2 ATP, 2 NAD⁺
• Products: 2 Pyruvate (3C), 2 NADH, 4 ATP (Net gain: 2 ATP)
• Energy Investment uses 2 ATP to break glucose into two 3-carbon molecules
• Energy Payoff produces 4 ATP & 2 NADH
• Glycolysis is anaerobic and does not require oxygen

Pyruvate Oxidation & Citric Acid Cycle

• Pyruvate oxidation occurs in the mitochondrial matrix
• Reactants: 2 Pyruvate, 2 NAD⁺
• Products: 2 Acetyl-CoA, 2 NADH, 2 CO₂
• The citric acid cycle occurs in the mitochondrial matrix
• Reactants: 2 Acetyl-CoA, 6 NAD⁺, 2 FAD
• Products: 4 CO₂, 2 ATP, 6 NADH, 2 FADH₂
• Acetyl-CoA (2C) combines with oxaloacetate (4C) to form citrate (6C)
• High-energy electrons are stored in NADH & FADH₂
• The citric acid cycle produces 2 ATP per glucose

Oxidative Phosphorylation (Electron Transport Chain & Chemiosmosis)

• The electron transport chain (ETC) is located in the inner mitochondrial membrane
• Reactants: NADH, FADH₂, O₂
• Products: H₂O, ~26-28 ATP
• NADH & FADH₂ donate electrons to the ETC
• Electrons move through protein complexes, releasing energy
• Oxygen is the final electron acceptor, forming water
• An H⁺ gradient (Proton-Motive Force) is generated
• H⁺ ions pass through ATP synthase, driving ATP production
• Oxidative phosphorylation produces the most ATP (~26-28 ATP per glucose)
• The electron transport chain (ETC) produces water

Anaerobic Respiration & Fermentation

• When oxygen is absent, anaerobic respiration or fermentation occurs
• Anaerobic respiration uses a different final electron acceptor (e.g., nitrate, sulfate)
• Fermentation uses no ETC; relies only on glycolysis
• Reactants: Glucose, 2 NAD⁺
• Products: 2 ATP and either lactic acid (animals, bacteria) or ethanol + CO₂ (yeast, some bacteria)
• Cellular respiration produces ~30-32 ATP per glucose
• Fermentation produces only 2 ATP per glucose
• Fermentation is anaerobic and does not require oxygen

Metabolism Beyond Glucose

• Carbohydrates enter Glycolysis
• Proteins are converted into intermediates
• Fats: glycerol enters glycolysis, fatty acids undergo beta-oxidation, forming Acetyl-CoA
• Fats store more energy than carbs or proteins and provide the most ATP

Trophic Levels & Energy Flow

• Autotrophs make organic molecules from inorganic sources using light (photosynthesis). Examples: Green plants, algae, cyanobacteria
• Heterotrophs obtain organic molecules from other organisms. Examples: Animals, fungi
• Photosynthesis converts solar energy into chemical energy (carbohydrates)
• Photosynthesis endergonic redox reaction: CO2 is reduced and H2O is oxidized

Photosynthetic Organisms

• Photosynthetic organisms include euglena (protist), sunflowers (plant), moss (plant), gloeocapsa (cyanobacterium), trees, kelp (protist), and diatoms (protist)

Structure of Photosynthetic Cells

• Chloroplast Anatomy: Outer & Inner Membrane
• Thylakoid Membrane contains pigments that absorb light
• Granum is a stack of thylakoids
• Stroma is a fluid-filled region between the thylakoid and inner membrane
• Leaf Anatomy: Mesophyll is the site of most photosynthesis
• Stomata are microscopic pores for gas exchange (CO2 entry, O2 & H2O exit)

Solar Energy & Pigments

• Light is energy (photons) with different wavelengths
• Violet has shorter wavelength, higher energy
• Red has longer wavelength, lower energy
• Pigments absorb & reflect light: Chlorophyll a, Chlorophyll b, β-carotene
• Leaves appear green because they absorb red & violet, reflecting green

Stages of Photosynthesis

• The two main stages are light reactions and the Calvin cycle

Light Reactions

• Occurs in the thylakoid membrane
• Pigments absorb light, exciting electrons
• Photosystem II (PSII) uses an electron transport chain to produce ATP
• Photosystem I (PSI) reduces NADP+ to NADPH
• Reactants: H2O, ADP, NADP+
• Products: O2, ATP, NADPH
• ATP synthase uses an H+ gradient to produce ATP

Calvin Cycle (Light-Independent Reactions)

• Occurs in the stroma
• Uses ATP & NADPH from light reactions
• Carbon Fixation: CO2 is incorporated into RuBP using rubisco
• Reduction Phase: 3-PGA is converted into G3P using ATP & NADPH
• Regeneration of RuBP: 5 G3P molecules regenerate RuBP, requiring ATP
• Reactants: CO2, ATP, NADPH
• Products: G3P (used to form glucose & other organic molecules)
• For one G3P, the cycle must run 3 times, for one glucose, the cycle runs 6 times

Photorespiration & Alternative Pathways

• Photorespiration occurs when rubisco binds O2 instead of CO2, reducing efficiency
• Photorespiration is more common in hot, dry environments

C3 Plants

• In C3 Plants, the first detectable molecule is a 3-carbon compound (3-PGA)
• The stomata of C3 Plants are open during the day
• C3 Plants are efficient in cool, moist environments

C4 Plants

• In C4 Plants, the first detectable molecule is a 4-carbon compound (oxaloacetate)
• Spatial separation of processes
  • CO2 fixation occurs in mesophyll cells
  • The Calvin cycle occurs in bundle sheath cells
• C4 Plants are best in high light & temperature conditions

CAM Plants

• Temporal separation
  • Night: Stomata open, CO2 fixed into a 4-C molecule (malate)
  • Day: Stomata close, CO2 is released for the Calvin cycle
• CAM Plants are best for water conservation (deserts)

Cell Division & Chromosomes

• Cell division is the process by which cells reproduce
• Functions of cell division include growth, repair, and reproduction
• Mitosis produces two identical daughter cells (growth & repair)
• Meiosis produces gametes with half the chromosome number (reproduction)
• A genome is all the DNA in a cell
• Prokaryotic DNA consists of a single circular chromosome
• Eukaryotic DNA consists of multiple linear chromosomes packaged in chromatin
• Chromatin is uncondensed DNA in the nucleus
• A chromosome is condensed DNA visible during cell division
• Sister chromatids are two identical copies of a replicated chromosome
• The centromere is the region where sister chromatids are attached
• Diploid (2n) is two sets of chromosomes (e.g., somatic/body cells)
• Haploid (n) is one set of chromosomes (e.g., gametes: sperm & egg)
• Humans have 46 chromosomes (23 pairs)
• A karyotype is an image showing the number, size, and shape of chromosomes in a cell

Cell Cycle & Mitosis

• The cell cycle consists of interphase and the M-phase
• Interphase comprises 90% of the cycle
• During the G₁ phase (first gap), the cell grows and prepares for DNA replication
• During the S phase (synthesis), DNA is replicated
• During the G₂ phase (second gap), the cell produces proteins needed for mitosis
• G₀ phase is when cells exit the cycle (e.g., nerve cells)
• M-Phase (Mitosis & Cytokinesis)
• Mitosis: Division of the nucleus into two identical nuclei
• Cytokinesis: Division of the cytoplasm

Mitosis Phases

• Prophase
  • Chromatin condenses into chromosomes
  • The nuclear envelope breaks down
  • Spindle fibers form
• Prometaphase
  • The nuclear envelope fully dissolves
  • Spindle fibers attach to kinetochores on chromatids
• Metaphase
  • Chromosomes align at the metaphase plate
• Anaphase
  • Sister chromatids separate and move to opposite poles
• Telophase
  • Chromosomes decondense
  • Nuclear envelopes reform around new nuclei
• Cytokinesis
  • In animals, a cleavage furrow pinches the cell in two
  • In plants, a cell plate forms a new cell wall between daughter cells

Cell Cycle Control & Cancer

• G₁ Checkpoint (Restriction Point)
  • Ensures DNA is undamaged before replication
  • If the signal is not received, the cell enters G₀ (non-dividing state)
• G₂ Checkpoint
  • Checks for DNA replication completion & damage
  • Ensures necessary proteins for mitosis are present
• Metaphase Checkpoint
  • Ensures all chromosomes are properly attached to spindle fibers
• Checkpoint proteins detect issues; if unfixable, cells undergo apoptosis (programmed cell death)
• Loss of checkpoints leads to uncontrolled cell division which leads to cancer

External Cell Cycle Control

• Growth factors are proteins that stimulate cell division (e.g., PDGF)
• Density-dependent inhibition is when cells stop dividing when crowded
• Anchorage dependence is when cells must be attached to a surface to divide

Cancer & Tumors

• Cancer cells do not follow normal growth controls
• Characteristics of cancer cells are that they ignore density-dependent inhibition, divide uncontrollably, and do not require growth factors
• Tumors:
  • Benign tumors remain localized and are non-invasive
  • Malignant tumors invade tissues and undergo metastasis (spread)