APBIO: Unit 3: Cellular Energetics

Energy in Living Systems: Bioenergetics, Thermodynamics, ATP, Redox, and Gradients

• The study of how cells obtain, transform, and use energy is called bioenergetics.

• Life consists of an organized set of chemical reactions that continuously transform energy.

• Cells do not create energy; they transform it from one form to another while obeying the laws of thermodynamics.

The Laws of Thermodynamics (What they mean in biology)

1. First Law of Thermodynamics:

   • Energy cannot be created or destroyed, only transferred or transformed.

   • Example: In cells, chemical energy stored in glucose is transformed into chemical energy of ATP, with some energy released as heat.

2. Second Law of Thermodynamics:

   • Every energy transfer increases the entropy (disorder) of the universe.

   • Cells maintain internal order (lower entropy) by increasing disorder elsewhere, often releasing heat and producing many small, random molecules from fewer large ones.

   • Key point: energy must be inputted to maintain order in a cell; thus, energy loss must be less than energy input.

   • Misconception: Cells do not violate the second law by building complex structures; they are open systems that take in energy and matter and release heat and waste.

Free Energy and Reaction Favorability

• Gibbs Free Energy (Delta G) describes reaction favorability:

  • Exergonic Reactions (release free energy):

  • Occur when ext{ΔG} < 0 (products have less free energy than reactants).

  • Endergonic Reactions (require free energy):

  • Occur when ext{ΔG} > 0 (products have more free energy than reactants).

  • Energy diagrams visualize the energy changes; exergonic reactions end lower than they start, while endergonic reactions end higher.

  • Important distinction for AP Biology: spontaneous does not mean fast.

Example: Using the Sign of Delta G

• A reaction has:

  • ext{ΔG} < 0: exergonic, can proceed without net energy input.

  • ext{ΔG} > 0: endergonic, requires an energy source or coupling to an exergonic reaction.

Reaction (Energy) Coupling and ATP

• Cells perform endergonic work (e.g., synthesizing macromolecules, transporting ions) through energy coupling:

  • Linking an exergonic process to an endergonic one ensures the overall process is exergonic.

• ATP (adenosine triphosphate) is the primary coupling molecule:

  • Structure: Adenosine is bonded to three phosphate groups.

  • ATP is often described as storing energy in phosphate bonds; however, it’s more accurate to say ATP hydrolysis results in a favorable free energy change.

  • Breaking off the terminal phosphate releases energy for cellular work.

  • ATP hydrolysis:

  • $ATP+H2^{}O\to ADP+Pi+Energy$

  • ATP hydrolysis is often coupled with phosphorylation of another molecule, changing its structure and making an unfavorable reaction favorable.

Sources of ATP

• Major sources include:

  • Cellular Respiration: Breaks down sugars to produce ATP.

  • In autotrophs, sugars are generated during photosynthesis.

  • In heterotrophs, glucose is derived from consumed food.

  • Analogy: ATP is like a currency—cells earn ATP through fuel breakdown or capturing light energy and spend it on work.

Redox Reactions: The Core of Respiration and Photosynthesis

• Redox reactions (reduction-oxidation) involve electron transfer:

  • Oxidation: loss of electrons (often loss of hydrogen).

  • Reduction: gain of electrons (often gain of hydrogen).

  • Mnemonic: OIL RIG (Oxidation Is Loss, Reduction Is Gain).

• Important electron carriers include:

  • NADH, NADPH, and FADH2.

  • NAD+ accepts electrons to become NADH; FAD accepts electrons to become FADH2.

• In respiration, electrons flow from energy-rich molecules (like glucose) to oxygen, releasing energy in controlled steps.

• In photosynthesis, light energy elevates electrons to higher energy states, primarily assisted by NADPH for sugar synthesis.

Gradients as Potential Energy

• A concentration gradient stores potential energy; cells convert energy into electrochemical gradients across membranes and utilize it to produce ATP.

• This process is a fundamental aspect of chemiosmosis used in both mitochondria and chloroplasts.

Exam Focus

• Common exam patterns include:

  • Predicting process favorability (exergonic/endogonic) using Delta G.

  • Explaining ATP hydrolysis and its coupling to drive unfavorable reactions.

  • Identifying oxidation vs. reduction in electron transfer scenarios.

• Common errors include:

  • Mistaking spontaneous for fast (thermodynamics vs. kinetics).

  • Oversimplifying ATP storage in phosphate bonds.

  • Confusing NADH (used for ATP production in respiration) with NADPH (used primarily for biosynthesis).

Enzymes: Biological Catalysts That Control Reaction Rates

• Enzymes act as biological catalysts that increase the speed of reactions necessary for life.

  • Without enzymes, many vital reactions would be too slow.

What Enzymes Are and What They Do

• Catalyst: speeds up a reaction without being consumed.

  • Enzymes increase the reaction rate by lowering activation energy and facilitating transition states.

  • They do not alter the free energy of reactants or products, thereby not changing overall Delta G.

  • Remember:

  • Enzymes lower activation energy, do not change overall energetics, and accelerate thermodynamically favorable reactions.

Activation Energy and the Transition State

• Even exergonic reactions require an initial energy input to reach a high-energy transition state known as activation energy.

• Enzymes primarily lower activation energy by stabilizing this transition state.

Enzyme Specificity, Naming, and the Enzyme-Substrate Complex

• Enzymes are specific to particular reactions.

  • Target molecules are substrates; they bind in the active site forming an enzyme-substrate complex.

  • Active site organizes substrates and creates an environment conducive to the reaction.

Induced Fit Model

• Instead of the lock-and-key model, the induced fit model explains how enzymes change shape to better accommodate substrates.

Mechanisms of Enzyme Action

• Methods include:

  • Orienting substrates.

  • Creating favorable microenvironments (acidic/basic).

  • Straining substrate bonds.

  • Occasionally forming temporary covalent bonds.

Cofactors and Coenzymes

• Some enzymes require additional helpers called cofactors:

  • Inorganic cofactors include metal ions (e.g., Fe²⁺, Mg²⁺).

  • Organic cofactors are called coenzymes; examples include vitamins, often acting as electron carriers (e.g., NAD+).

Factors Affecting Enzyme Activity and Reaction Rates

Temperature

• Reaction rates usually increase with temperature (as molecules collide more vigorously), until an optimum is reached and denaturation occurs.

  • Denaturation: can sometimes be reversible but is often irreversible at high heat.

pH

• Enzymes work best at an optimal pH. Incorrect pH levels can disrupt hydrogen bonds and alter the enzyme's structure, reducing function.

Salinity

• High salt concentrations can interfere with ionic interactions and protein folding, reducing enzyme activity.

Substrate Concentration and Saturation Point

• As substrate concentration increases, rates initially rise until the enzyme reaches saturation (all active sites occupied).

• Example: A saturation curve shows quick rises at low substrate concentrations followed by a plateau as saturation occurs.

Enzyme Regulation

• Regulating enzymes conserves resources and prevents overproduction.

Inhibition Types

1. Competitive Inhibition:

   • An inhibitor competes for the active site; excess substrate reduces its effect.

2. Noncompetitive Inhibition:

   • An inhibitor binds at an allosteric site, altering enzyme shape; substrate can still bind but catalysis is reduced.

   • Feedback inhibition prevents overproduction by using the final product to inhibit early enzymes in the pathway.

Exam Focus on Enzymes

• Typical patterns include interpreting enzyme activity graphs against temperature or pH, understanding why enzymes affect rates but not Delta G, and predicting impacts of inhibitors.

Cellular Respiration: Converting Fuel Into ATP

• Cellular respiration converts organic molecules into ATP through redox reactions and electron transport.

Overall Equation

1. Common summary for aerobic respiration:
   $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + ATP$

   • If ATP is produced with oxygen present, it is aerobic respiration.

2. Anaerobic respiration occurs without oxygen, shifting to fermentation to continue glycolysis.

Four Stages of Aerobic Respiration

1. Glycolysis (cytoplasm/cytosol)

2. Formation of Acetyl-CoA (pyruvate oxidation, occurs in eukaryotic mitochondria)

3. Krebs cycle (citric acid cycle, occurs in mitochondrial matrix)

4. Oxidative Phosphorylation (electron transport chain + chemiosmosis, in the inner mitochondrial membrane)

Stage 1: Glycolysis

• Glycolysis breaks down one glucose into two pyruvic acid molecules (3C).

• Key features:

  • Occurs in the cytoplasm.

  • Produces a net of 2 ATP and 2 NADH:
    $C_6H_{12}O_6 + 2 NAD^+ + 2 ATP \rightarrow 2 Pyruvate + 4 ATP + 2 NADH$

Stage 2: Formation of Acetyl-CoA

• Each pyruvic acid enters the mitochondrion and is converted to Acetyl-CoA (2C), releasing CO2 and producing NADH.

• Catalyzed by the pyruvate dehydrogenase complex (PDC).

Stage 3: The Krebs Cycle (Citric Acid Cycle)

• Occurs in the mitochondrial matrix.

• Each Acetyl-CoA combines with oxaloacetate (4C) to form citrate (6C), returning to oxaloacetate in a series of reactions.

• Outputs per cycle:

  • 1 ATP (GTP in some organisms)

  • 3 NADH

  • 1 FADH2

• Since one glucose yields 2 Acetyl-CoA, double the outputs per glucose.

Stage 4: Oxidative Phosphorylation (ETC)

• Major reduced carriers are NADH and FADH2:

  • Accounting per glucose:

  • Glycolysis: 2 NADH

  • Acetyl-CoA Formation: 2 NADH

  • Krebs Cycle: 6 NADH, 2 FADH2 (total of 12 electron carriers)

• Electron transport occurs in the inner mitochondrial membrane, facilitated by NADH dehydrogenase and cytochrome c.

• Electrons flow down the chain, releasing energy and ultimately combining with oxygen to form water:
  
  $O_2 + 4e^- + 4H^+ \rightarrow 2H_2O$

Chemiosmosis and Proton Motive Force

• The energy released during ETC activities pumps protons into the intermembrane space, creating a proton gradient.

• Protons diffuse back through ATP synthase, generating ATP.

• This process is referred to as chemiosmosis.

ATP Yield

• Exact ATP yield varies, but typically:

  • Eukaryotic aerobic respiration yields about 30 to 32 ATP per glucose.

• Estimated yields:

  • Each NADH from glycolysis yields about 1.5 ATP.

  • Most other NADH yield 2.5 ATP.

  • Each FADH2 yields 1.5 ATP.

• Example: NADH typically yields more ATP than FADH2 because of earlier donation in the ETC.

Exam Focus on Respiration

• Trace carbon and electrons through glycolysis and Krebs cycle.

• Explain substrate-level vs. oxidative phosphorylation.

• Common errors include incorrectly stating glycolysis uses oxygen and misunderstanding ETC function.

Fermentation and Metabolic Flexibility

• Without oxygen, cells must still regenerate NAD+ to continue glycolysis.

• Fermentation allows NADH oxidation back to NAD+ by transferring electrons to organic molecules.

Types of Fermentation

1. Lactic Acid Fermentation:

   • Involves the reduction of pyruvate by NADH to form lactate, regenerating NAD+.

   • Occurs in some bacteria and animal muscle cells under low-oxygen conditions, causing muscle fatigue.

2. Alcohol Fermentation:

   • Pyruvate converts to ethanol and CO2, regenerating NAD+ (prominent in yeast).

• Fermentation yields significantly lower ATP compared to aerobic respiration, as it does not utilize the ETC.

Comparing Fermentation vs Aerobic Respiration

Photosynthesis: Capturing Light Energy to Build Sugars

• Photosynthesis captures light energy to store it in organic molecules and contrasts with respiration.

Overall Equation

• A common photosynthesis equation:
  

• Key note: Oxygen produced comes from water, not carbon dioxide.

Two Stages of Photosynthesis

1. Light Reactions (light-dependent)

   • Capture photons, excite electrons, release oxygen, and produce ATP and NADPH.

2. Light-Independent Reactions (Calvin cycle)

   • Use ATP and NADPH to convert CO2 into carbohydrates.

Chloroplast Structure

• Parts:

  • Stroma: Site of the Calvin cycle.

  • Grana: Stacks of thylakoids (where light reactions and electron transport occur).

  • Thylakoid lumen: Accumulates protons.

  • Analogy: Chloroplasts act as solar-powered gradient generators.

Exam Focus on Photosynthesis

• Common patterns include where light reactions vs Calvin cycle occur and tracing oxygen source (water).

The Light Reactions

• Begin with photons striking pigments, exciting electrons to capture energy effectively.

• Major Pigments include chlorophyll a, b, and carotenoids clustered into antenna complexes to maximize light capture.

Photosystems and Reaction Centers (PSII and PSI)

• Two major photosystems function in thylakoid membranes:

  • PSII: Reaction center P680

  • PSI: Electrons are re-excited and passed to electron acceptors.

Photolysis (Water Splitting)

• To replace lost electrons in PSII, water is split, producing oxygen, protons, and electrons.

• This provides strong evidence that oxygen is a byproduct of water, not CO2, in photosynthesis.

Electron Transport and ATP Production

• As electrons travel through complexes, their energy pumps protons into the thylakoid lumen, creating a proton gradient used for ATP production called photophosphorylation:

  • In mitochondria, protons accumulate in the intermembrane space; ATP is synthesized in the matrix.

• NADPH Formation:

  • Electrons from PSI generate NADPH from NADP+.

Linear vs. Cyclic Electron Flow

• Linear Flow:

  • Electrons flow from water to PSII to ETC to PSI to NADPH (produces ATP and NADPH).

• Cyclic Flow:

  • Electrons cycle back through the ETC without reducing NADP+, boosting ATP without producing NADPH or oxygen.

The Calvin Cycle (Calvin-Benson Cycle)

• Uses ATP and NADPH to fix carbon from CO2, producing organic molecules.

Phases of the Calvin Cycle

1. Carbon Fixation:

   • RuBisCO attaches CO2 to RuBP (5C), creating a 6C intermediate that splits to form two 3C molecules.

2. Reduction:

   • ATP provides energy; NADPH reduces 3C molecules to higher energy sugars (e.g., G3P).

3. Regeneration:

   • Some G3P exits to aid in sugar formation; the remaining is rearranged using ATP to regenerate RuBP.

Limiting Factors and Adaptations

• Photosynthesis can be limited by:

  • Light intensity.

  • Carbon dioxide concentration.

  • Temperature (enzymes like RuBisCO are sensitive to temperature).

• Plants in hot climates use adaptations (e.g., CAM, C4) to optimize photosynthesis while minimizing water loss and photorespiration.

CAM and C4 Pathways

• CAM plants: Stomata open at night, storing CO2 in organic acids for daytime use.

• C4 plants: Separate initial carbon fixation spatially using different leaf structures to minimize photorespiration.

Connecting Respiration and Photosynthesis

• Photosynthesis and respiration are complementary processes:

  • E.g., Krebs cycle oxidizes carbohydrates to CO2, while the Calvin cycle reduces CO2 to carbohydrates.

• Chemiosmosis is a shared mechanism in both processes, with ATP production driven by electron transport chains creating proton gradients.

• Common experimental inquiries involve interpreting graphs/data related to both processes and understanding the regulatory mechanisms controlling metabolism.