Unit 3 Cellular Energetics AP BIO

Reactions

• Transfer of energy

Exergonic

• Releases energy (transfers energy out)

• ΔG < 0

• When energy is released it is typically heat

• -ΔH < 0

Endergonic

• Takes in energy (transfers energy in)

• -ΔG > 0

• -ΔH > 0

Gibbs Free Energy

• Energy available to do work

  • Work - amount of force within a distance

Entropy

• Measure of disorder within the universe

Enthalpy

• Total amount of energy within the system

Activation Energy

• Amount of energy needed to begin a Rxn

Enyzmes

• Lowers the activation energy of a reaction without putting anything into them

• They are specific PROTEINS!!

• Modifies the transition state to make is easier to complete the reaction

  • Provides an alternative pathways for reaction to occur

Protein Structure (Review)

• Primary - Chain of amino acids

• Secondary - Beta pleated sheets & Alpha helix

• Tertiary - Folding by additional bonds (disulfide, hydrogen bonding, etc.)

• Quartenary - Multiple polypetides

Enzyme Substrates

• A “lock & key mechanism”

• Very specific to their enzyme

  • e.g. catalyse ONLY bonds to hydrogen peroxide

• Undergoes confirmational change

  • Inactive - Same folding

  • Active - Folding changes

Allosteric Bonding Site

• Controls the activity of an enzyme

  • Can inhibit activity OR

  • Promote activity

Allosteric/Non-Competitive Inhibitor

• Binds to the allosteric bonding site

• Changes the proteins shape so it CANNOT bind to the substrate (rids of activity)

Cofactors/Inorganic Partners

• Can promote reactivity through the allosteric bonding site

• Activates an enzyme and helps them to function as a catalyst

Enzyme Endings

• Oftentimes Substrate + Ase

Positive Control

• A similar product known to work is used to compare results

Negative Control

• A product known to have no effect is used to decipher a cause

Anabolic Pathway

• Builds molecules/synthesizes them

• Requires more energy than it produces

• Does NOT happen spontaneously

Catabolic Pathway

• Breaks down molecules/decomposes them

• Requires little energy to proceed and uses less than it produces

• Does NOT happen spontaneously

Catalyst

• Something that speeds up the rate of reactions

• Best example —> Enzymes

Active Sites

• Pockets on enzymes used to attach to certain molecules

Substrate

• The molecule an enzyme binds to

• Synonym for reactants in a biochemical reaction

Coenyzmes/Organic Partners

• Small molecules that can separate from the protein component of the enzyme and participate directly in the reaction.

• They can transfer electrons, atoms, or molecules from one enzyme to another.

Feedback Inhibition

• Occurs when product concentration becomes too high

• Product binds to the initial enzyme, stopping the entire pathway, effectively stopping production

• This is reversible as the bonding is NOT permanent

Environmental Conditions That Affect Enzyme Function

• Substrate Concentration

• Enzyme Concentration

• Temperature

• pH

• Inhibitors

  • Allosteric

  • Competitive

• Cofactors & Coenzymes

  • Organic & Inorganic

Competitive Inhibitors

• Binds to the ACTIVE site

• Competes with the substrate

1st Law of Thermodynamics

• In an isolated system, the amount of energy stays constant but can change forms, meaning energy cannot be created or destroyed

2nd Law of Thermodynamics

• Energy transfers are inherently inefficient because the entropy of a closed system ALWAYS increases

• As energy transfers occur, not all energy is converted to usable energy, some is lost as heat

Oxidizing Agent

• A compound that oxidizes another

Oxidized Compounds

• They have been REMOVED an electron

• Results in a decrease in potential energy

Reducing Agent

• A compound that reduces another

Reduced Compounds

• They have been GIVEN an electron

• Results in an increase in potential energy

Electron Shuttles

• These compounds bind and carry high-energy electrons between compounds through biochemical pathways

Oxidized Form of Compounds

• Compound ⁽⁺⁾

Reduced Form of Compounds

• Compound (H)

Electron Carriers

• NAD⁺ → NADH

• FAD → FADH

Glycolysis

• 4 ATP - 2 ATP = 2 ATP

• Produces 2 NADH Electron Carriers

• Breaks down into 2 Pyruvate

• Contains Energy Investment Phase & Energy Payoff Phase

  • EIP - 2 ATP → 2ADP + P_i

  • EPP - 4ADP + P_i → 4ATP AND 2NAD⁺ + 4e^- + 4H⁺ → 2NADH + 2H⁺

• In every cell (points to common ancestry)

• Occurs in cytosol

ATP → ADP

• Generates 1 ATP

• Adenosine TRIphosphate → Adenosine DIphosphate

ADP → ATP

• Uses 1 ATP

• Adenosine DIphosphate → Adenosine TRIphosphate

NAD⁺ → NADH

• Reduction Rxn

• Electron Carrier

• Created through glycolysis

FADH→ FAD

• Oxidation Rxn

• Electron Carrier

• Used in photosynthesis

Hydrolysis of ATP

• Creates ADP, inorganic Phosphate ion (P_i), & free energy

• Water is broken down into Hydrogen and Hydroxide ions & is regenerated when ADP is reformed into ATP

Intermediate Complex

• The enzyme binds to several substrates that react with each other

  • This allows substrates like ATP to break off a phosphate ion and transfer it to ADP (Substrate-level Phosphorylation)

Dephosphorylation

• The release of 1 or 2 phosphate groups from ATP, forming ADP and RELEASING energy

Phosphorylation

• The addition of phosphate groups, REQUIRING energy

• Typically for storage of energy

Substrate-level Phosphorylation

• A covalently bonded phosphate group is removed from an intermediate reactant and transfers onto an available ADP compound, producing ATP

• Uses free energy

Chemiosmosis

• Takes place in the mitochondria

• Produces ATP in cellular metabolism, generating 90% of the ATP created during glucose catabolism and is used in photosynthesis

Oxidative Phosphorylation

• The production of ATP using the process of chemiosmosis

• Contains the involvement of oxygen within the process

• Uses electron transport chain with electron carriers NADH & FADH₂

• Levels concentration gradient of H⁺ ions to synthesize ATP by using necessity to transfer to lower concentration gradient to synthesize ADP & P_i (With the presence of oxygen)

Cell Domains (Intro to Cells Review)

• Prokaryote

  • Bacteria

  • Archaea

• Eukaryote

  • Eukarya

Anoxygenic Photosynthesis

• Photographs that use compounds other than water as electron donors

• Does NOT release oxygen as a byproduct

Oxygenic Photosynthesis

• Phototrophs that use water as electron donors

• Creates oxygen as a byproduct

Bacteriochloropylls

• Used by anoxygenic organisms

• Absorbs light at longer wavelengths than chlorophyll

• Used in areas where light is scarce

Great Oxidation Event

• A period when free oxygen accumulated in the atmosphere

• Resulted in the extinction of many anaerobic lifeforms (oxygen was toxic)

• Jumpstarted the evolution of aerobic respiration

Endosymbiosis

• The process of a cell engulfing another cell, resulting in the engulfed cell becoming an organelle

• Resulted in the creation of Chloroplasts as the engulfed cyanobacterium transferred its genes to the host cell’s nucleus, integrating its functions into the new cellular structure.

• Explains the appearance of photosynthesis within several distinct lineages

Secondary Endosymbiosis

• A eukaryotic cells engulfs another eukaryotic cell that was already photosynthetic

• Some eukaryotic groups acquired chloroplasts through engulfing red or green algal in this process

  • These are characterized by having more than two membranes

Tertiary Endosymbiosis

• The engulfment of a secondary endosymbiotic organism

• Further distributed photosynthetic capabilities

Stroma

• Where the Calvin Cycle takes place and contains enzymes for glucose production

  • CO₂ → C₆H₁₂O₆

• Within chloroplasts

Calvin Cycle

• Cyclic electron flow

• Utilizes ATP & NADPH to reduce CO₂ to sugar (G3P)

• Goes through 3 phases

  • Carbon Fixation

  • Reduction

  • Regeneration of RuBP

• Occurs in the Stroma

Carbon Fixation (Phase 1)

• CO₂ is incorporated into the Calvin Cycle one at a time (3 times total to produce 1 net G3P)

  • Each CO₂ attaches to a molecule of RuBP, being catalyzed by the Rubisco enzyme to form 3-phosphoglycerate (3-PGA)

Reduction (Phase 2)

• Each molecule of 3-phosphoglycerate is phosphorylated by ATP (uses 6 total)

  • 6 NADPH molecules donate electron to 1, 3-biphosphoglycerate

    • Reduces to G3P

    • 6 molecules of G3P are formed but only ONE is counted as a net gain

    • The other 5 G3P molecules are used to regenerated RuBP

Regeneration of RuBP (Phase 3)

• 5 G3P molecules are used to regenerate 3 molecules of RuBP

  • 3 ATP used for regeneration

• Cycle becomes ready to take in CO₂ again

Calvin Cycle (Inputs/Outputs)

• Inputs

  • 3 CO₂ → From environment

  • 9 ATP → From light reactions

  • 6 NADPH → From light reactions

• Outputs

  • 1 G3P → Sugar for mitochondria

  • 9 ADP → To light reactions

  • 6 NADPH⁺→ To light reactions

Light Reactions

• Occurs in the Thylakoid & Thylakoid Membrane

• Convert light energy into chemical energy through the production of ATP and NADPH.

• Water is split, releasing oxygen as a byproduct.

G3P

• Three carbon sugar produced by Calvin Cycle

• 2 are used to synthesize 1 glucose

C₃ Plants → Basic

3 Carbon (G3P)

• On hot days, they close their stomata to stop water less

• Results in less CO₂ & more O₂ present

• Rubisco binds to O₂ & uses ATP

  • Produces O₂ & uses ATP

  • NO sugar produced

  • Bad for the plant

C₄ Plants → Change location

4 Carbon molecule

• Spatial separation of steps

• Stomata PARTIALLY closes to conserve water

• Mesophyll cells fix CO₂ into 4-C molecule

CAM Plants → Changes time of day

Carbon AM

• Light dependent reactions occur during the day

• Carbon fixation occurs at night (sugar)

Aerobic Cellular Respiration

• The breakdown of sugars to get ATP (energy!)

• C₆H₁₂O₆ + O₂ → 6CO₂ + 6H₂O (+ ATP)

• Produces 30-32 ATP per glucose molecule

• Evolutionary Conserved!

• Prokaryotes do NOT partake b/c they have no mitochondria! 😙

Stage 1 Aerobic Cellular Respiration

Glycolysis

• Yields 2 pyruvate, 2 NADH, & 2 ATP per glucose molecule

• Outside of Mitochondria (cytosol)

• Anaerobic respiration

Stage 2 Aerobic Cellular Respiration

Pyruvate Oxidation + Citric Acid Cycle (If oxygen is present, pyruvate enters the mitochondria!)

• Pyruvate Oxidation

  • Pyruvate → Acetyl CoA (1st Molecule in Citric Acid Cycle)

  • Produces NADH + CO₂

Stage 3 Aerobic Cellular Respiration

Electron Transport Chain & then Oxidative Phosphorylation

• Electron Transport Chain

  • ATP Synthase synthesizes ADP & P_i into ATP

    • Energy from H⁺ ion transferred to synthesize ADP & P_i

    • Chemiosmosis

• Oxidative Phosphorylation

  • Occurs in the inner folds of mitochondria (Cristae)

  • Final stage of aerobic respiration that generates the majority of ATP

  • Uses electrons from NADH and FADH₂ to create a proton gradient (H⁺) for ATP production

Red Blood Cells

• DON’T have mitochondria

• Relies on glycolysis to produce ATP

• Lifespan of ~120 days

Citric Acid Cycle/Krebs Cycle

• Uses 2 Acetyl CoA

• Produces 2 ATP, 6 NADH, 2 FADH₂ & 4 CO₂

• Occurs in the Mitochondrial Matrix

• H⁺ produced is also used in Oxidative Phosphorylation

Anaerobic Cellular Respiration

• Pyruvate from Glycolysis is turned into 2 lactic acid

• Does not go through Pyruvate Oxidation or the Citric Acid Cycle. It produces a net gain of 2 ATP through substrate-level phosphorylation.

• Less efficient compared to other forms as it produces very little ATP

Fermentation

• Pathway of anaerobic respiration!

  • Pyruvate from Glycolysis is turned into 2 Acetyl Aldehyde

  • Acetyl Aldehyde is turned into 2 Ethanol (Alcahawlll 😛)

    • Is turned into lactic acid within the muscle cells of most animals

  • Produces 2 ATP

Photorespiration

• Occurs in Calvin Cycle step 1

  • RuBP is oxygenated instead of carboxylated

• Bad for plants since carbon is used to create sugar!

Earth’s Early Formation

• Chemosynthetic bacteria evolved first because earth’s early atmosphere had no oxygen! (Mainly hydrogen and helium)

  • The atmosphere couldn’t protect bacteria from outside radiation

• Photosynthetic bacteria evolved next as there was still not free oxygen

• Heterotrophs & cellular respiration evolved after photosynthetic bacteria dude to the presence of oxygen

Chemosynthetic Bacteria

• Microorganisms that obtain energy by oxidizing inorganic molecules, typically in an environment devoid of sunlight.

• They play a crucial role in early Earth conditions by sustaining life through chemical reactions.

Photosynthetic Bacteria

• Utilized carbon from ash in the air to produce energy through photosynthesis, converting sunlight into chemical energy and releasing oxygen as a byproduct.

• They played a significant role in altering Earth's atmosphere and enabling aerobic life.

Heterotrophs

• Utilized aerobic cellular respiration once oxygen was produce by photosynthetic respiration