AP Bio Unit 3: Cellular Energetics

• AP Bio unit 3 covers cellular energetics, which can be challenging due to topics like cellular respiration and photosynthesis.
• The goal is to provide the information needed to succeed on unit exams or the AP Bio test.
• The topics covered are:
  • Enzymes
  • Cellular energy and ATP
  • Photosynthesis (big picture, light reactions, Calvin cycle)
  • Cellular respiration (big picture, glycolysis, link reaction, Krebs cycle)
  • Electron transport chain.
• Glenn woken Feld, also known as Mr. W, is a retired AP biology teacher.
• A study checklist is available for download at AP bios.

Enzymes

• Enzymes catalyze reactions in cells, typically being proteins, though some RNAs can also act as enzymes.
• They function by lowering the activation energy of reactions they catalyze, thereby increasing the rate of these reactions.
• Enzymes exhibit high specificity due to their active site complementing the shape and charge of their substrate.
• The substrate is the substance upon which an enzyme acts.
• Environmental conditions, such as pH, temperature, or ion concentration, affect enzyme function due to the disruption of hydrogen, ionic, and hydrophobic bonds within the enzyme's structure.
• Enzymes have optimal pH, ionic, and temperature conditions where their active site best fits their substrate.
• Changes in the shape of the active site can prevent the enzyme from binding with its substrate.
• Denaturation, a change in the enzyme's shape, results from environmental changes and can lower or negate enzyme function.

Enzyme Activity & pH

• Most enzymes operate at peak efficiency within a specific pH optimum.
• Enzyme performance decreases as pH moves above or below the optimum.
• Altering pH disrupts the bonds holding a protein in its specific shape, leading to denaturation and a poor fit between the enzyme and its substrate.

Enzyme Activity & Temperature

• Enzyme activity increases with temperature up to a certain point due to increased kinetic energy and molecular motion.
• Above a certain temperature, enzymes denature, reducing their catalytic ability.
• This denaturation occurs because the enzyme can no longer bind with its substrate.

Reversible vs Irreversible Denaturation

• Reversible denaturation is when optimal conditions can be restored to regain the enzyme's optimal shape and function.
• Irreversible denaturation permanently changes the enzyme's shape, destroying its catalytic ability.
• Cooking an egg is an example of irreversible denaturation of a protein, where the change is permanent.

Enzyme Activity & Substrate Concentration

• At low substrate concentrations, the probability of enzyme-substrate interaction is low, resulting in a low production rate.
• As substrate concentration increases, the collision and reaction rate also increase.
• A saturation point is reached when all enzymes have their active sites interacting with substrate, leading to a peak in the reaction rate.

Competitive vs Non-competitive Inhibition

• Competitive inhibition involves a foreign molecule blocking the enzyme's active site, preventing the substrate from binding and thus inhibiting the reaction rate.
• Non-competitive inhibition occurs when a foreign molecule binds to the allosteric site, causing a change in the shape of the active site, preventing substrate binding and diminishing or blocking enzyme activity.

Metabolic Pathways

• A metabolic pathway is a linked series of enzyme-catalyzed chemical reactions occurring within a cell.
• These pathways can be linear, such as glycolysis, or cyclical, such as the Kreb cycle and the Calvin cycle.

Autotrophs

• Autotrophs are organisms that can produce their own food.
• Photoautotrophs, including plants and cyanobacteria, use light energy to create organic compounds through photosynthesis.
• Chemoautotrophs, including some bacteria and archaea, derive energy from chemosynthesis that involves oxidizing inorganic substances.

Heterotrophs

• Heterotrophs obtain energy and matter by capturing the energy present in organic compounds produced by other organisms.
• They can be consumers, decomposers, or parasites, metabolizing organic compounds from other organisms or their remains.

Exergonic vs Endergonic Reactions

• Exergonic reactions release energy and increase entropy (disorder).
• Endergonic reactions require energy and decrease entropy (increase organization).

ATP Structure and Function

• The structure of ATP includes a five-carbon sugar (ribose), a nitrogenous base (adenine), and three phosphate groups.
• ATP powers work within cells, with each cell making its own ATP.
• Cells store energy by combining ADP and a phosphate group into ATP during cellular respiration or photosynthesis.
• Cells release energy for work by removing a phosphate group from ATP, which creates ADP and phosphate.

Energy Coupling

• Energy coupling involves linking an exergonic reaction to an endergonic reaction to drive the endergonic reaction forward.
• An example includes cellular respiration driving ATP formation or ATP breakdown powering muscle contraction.

Photosynthesis Overview

• Photosynthesis is the process where photoautotrophs combine carbon dioxide and water using light energy to create carbohydrates, releasing oxygen as a waste product.
• The formula of photosynthesis is 6CO2 + 6H2O + light energy → C6H12O6 + 6O2.
• Photosynthesis is an endergonic reaction because it converts low-energy inputs into a high-energy product and reduces entropy.

Photosynthesis Evolution

• Photosynthesis evolved approximately 3.5 billion years ago, relatively soon after the emergence of life.
• It led to the creation of an oxygen-rich atmosphere, enabling aerobic metabolism and the formation of an ozone layer.

Photosynthesis Phases

• The two phases of photosynthesis include the light reactions and the Calvin cycle.
• The light reactions convert light energy into the chemical energy of ATP and NADPH.
• The Calvin cycle converts the chemical energy in NADPH and ATP into carbohydrate by fixing carbon dioxide.

Chlorophyll

• Chlorophyll is the pigment that absorbs light energy in photosynthesis
• Absorption Spectrum shows the amount of light absorbed at different light wavelengths by a pigment.
• Chlorophyll absorbs most energy in the blue and red parts of the spectrum but very little in the green part.
• Carotenoids are other pigments involved, absorbing other wavelengths.

Action Spectrum of Photosynthesis

• The action spectrum shows how various light wavelengths drive photosynthesis, with blue and red driving the most, and green driving very little.

Chloroplast Structure and Photosynthesis

• Chloroplasts, found within cells in the top part of a leaf, have an outer and inner membrane, DNA, ribosomes, and thylakoids.
• Thylakoids are membrane-bound sacs containing membrane-bound photosystems and chlorophyll for the light reactions.
• Grana are stacks of thylakoids; the stroma surrounds them and contains DNA, ribosomes, and is where the Calvin cycle occurs.

Light Reactions

• The light reactions convert light energy into the chemical energy of NADPH and ATP in the thylakoids, with oxygen as a waste product.
• The inputs of light reactions are light and water; the outputs are ATP and NADPH. NADP+ and ADP are the inputs to light reactions.
• Key structures include photosystems (complex assemblies of proteins) with embedded chlorophyll molecules that convert light energy into a flow of electrons.
• Photosystem 2 comes before photosystem 1 in the electron pathway.

Light Reactions & ATP Creation

• Photo excitation of chlorophyll in photosystem 2 leads to a flow of electrons along an electron transport chain in the thylakoid membrane.
• This electron transport chain powers a proton pumpthat moves protons from the stroma into the thylakoid space, creating a chemiosmotic gradient.
• Protons diffuse through ATP synthase, generating ATP from ADP and phosphate.
• Water-splitting complex splits water molecules to create oxygen and protons that accumulate in the thylakoid space, enhancing the gradient.

Light Reactions & NADPH creation

• Photo excitation of chlorophylls in photosystem 1 starts the process.
• Electrons flow to NADP+ reductase, which reduces NADP+ into NADPH.

The Z Scheme

• A graphical representation of everything that happens in the light reactions
• Describes electron energy, flow, and reduction/oxidization of compounds.

Calvin Cycle

• The Calvin cycle takes the products of the light reactions (ATP and NADPH) and carbon dioxide to create sugars in three phases: carbon fixation, energy investment and harvest, and regeneration of the starting C compound.

Carbon Fixation Phase

• Carbon dioxide is combined with RuBP, a reaction catalyzed by the enzyme rubisco.
• This is the most abundant protein on Earth.
• This reaction creates a six-carbon product that dissociates almost immediately into two three-carbon molecules.

Energy Investment and Harvest Phase

• The three-carbon product is reduced and phosphorylated.
• ATP contributes a phosphate to the molecule and NADPH donates an electron, resulting in G3P or glyceraldehyde 3-phosphate, also called PGAL.

Phase 3 of the Calvin Cycle

• 3 RuBPs, which are a total of 15 carbon atoms, are combined with 3 Carbon dioxides for a total of 18 carbon atoms
• The product is six three carbon molecules.
• One of those g3ps is pulled out leaving 5 g3ps. With 3 carbons each there are 15 carbons left
• Next a variety of enzymes rearrange the molecules into 3 five carbon RuBPs.
• This is followed by phosphorylation.

Cellular Respiration big picture

• Equation: C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + energy (ATP)
• It is an exergonic reaction
• Phases
  • Glycolysis = cytoplasm
  • Link Reaction = brings product of glycolysis into the mitochondrian
  • Kreb Cycle = mitochondrian matrix
  • Oxidative Phosphorylation = mitochondrial membrane

Briefly describe what happens in each phase of cellular respiration

• Glycolysis in cytoplasm generate ATP and NADH
• Link Reaction in the mitochondrial matrix converts the product of glycolysis to Acetyl CoA
• In the Kreb Cycle enzymes oxidize the two carbon in a cetyl COA and that powers the production of NADH and FADH2
• Electron Transport Chain takes reduced products and oxidizes them, which created electron low and in turn chemiosmosis.

Parts 2 and 3 of Cellular Respiration: Glycolysis, Link Reaction, and Krebs Cycle

• Glycolysis occurs in the cytoplasm and does not require oxygen.
• it has 3 parts (investment, cleavage, and energy harvest)
  • Investment: enzymes phosphorate glucose until it becomes fructose 1,6, bisphosphate
  • Cleavage: enzymes take the compound above and cleave it into 2 three carbon molecules of G3P -Harvest Phase: take G3P and they oxidize it, those electrons are transferred to NAD, it reduces to NADH. Additionally, enzymes take ADP and phosphate to create ATP.
• Net yield = 2 ATP . 2 NADH
• What happens between glycolysis and the kreb cycle - the link reaction
  • pyruvic acid is transported across the inner and outer mitochondrial membranes, enters matrix
  • An enzyme removes CO2 (one third of our CO2).
  • Enzymes oxidize the two carbon molecules called the ACITAL group, electrons are donated to NAD which becomes NADH
• Finally the acetyl group is attached to a molecule called co-enzyme and the result is acel COA (the start point of Kreb cycle)
• Kreb Cycle = occurs in the mitochondrial matrix. Cyclical series of reactions that generate NADH, FADH2 and ATP. Enzymes take ACITAL to citric acid (another name is cycle). Then more enzymes oxidize citric acid where electrons are lost and used to create NADH, FADH2
• sub level phosphorylation occurs of ADP and phosphate unto ADP 1 ATP molecule, 3 NADH, one FADH2 are generated. CO2 is produces as a byproduct/ waste.

Cellular Respiration Part 4: The Electron Transport Chain and Oxidative Phosphorylation

• In the previous phases, NADH and FADH2 were created, they are now in the mitochondrial Matrix. Mobile electron carriers that diffuses to the inner membrane to get oxidized.
• The electrons now flow through electron transport chain
• Some proteins in Chain are proton pumps
• Electrons flow in a series like an electrical current.
• Active transport needs energy, it transports the protons into the intermembrane
• This all creates an electrochemical and a pH gradient. More protons in the intermembrane than in the matric.
• O2 acts as the final electron acceptor
• The final step is the protons who can only reach the intermembreane throght only one channel (ATP synthase).
• Protons that diffuse through is is used to create ATP as the ADP and phosphate are phosphorylated

Cellular Respiration and Heat

• Cell wals called brown fat cells are dense with mitochondria that generate heat
• Hormonse use a uncoupling channel called thermogenin
• Protons can diffuse back to matric without passing through ATP synthase

ATP Generation in Mitochondria and Chloroplast

• Both processes use an electron transport chain to pump protons to an enclosed space, creating a proton gradient.
• Photosynthesis pumps protons from the stroma to the thylakoid space.
• Cellular respiration pumps protons from the matrix to the intermembrane space.
• Both processes use chemiosmosis (diffusion of protons through an ATP synthase channel) to generate ATP.

Cellular Resiration Part 5: Anorobic Respiration and Fermentation

• Aerobic Respiration needs O2 and uses glycolysis plus the link reaction and cycle plus ETC

• Anorobic Respiration occurs only when O2 is absent, it involves glycolysis and fermentation

• With aerobic there are approximately 32 ATP molecules

• What is fermentation and why does it occur

• Fermentation is glycolysis followed by reactions that regenerate NAD , so in turn Glycolysis can only create twom molecules of ATP is NAD is available.

Compare and contrast alcohol and lactic acid fermentation

• Alcohol : enzymes removes CO2 from pyruvic acid which generates acid atldhy, next, other enzymes reduce the acid atldhy into thanol

• lactic acid fermentation happens only when under pressure or not enough O2 can be created; the pyruvate is reduced to lactic acid and in turn allows glycolysis to continue but only creating 2 extra ATP molecules