Cellular Energetics

AP Biology

Unit 3

Cellular Energetics

Energy

  • Kinetic Energy
    • Energy from movement
  • Heat Energy
    • Higher temperature means higher energy
  • Chemical Energy
    • Sorta potential energy

Thermodynamics

  • The First Law
    • Conservation of Energy
      • You cannot make or destroy energy, however you can transport it
  • The Second Law
    • The entropy of the universe is always increasing
  • Delta G = Delta H - T Delta S
    • Delta S is entropy
    • T is temperature
    • Delta G is how much energy can be used to work
    • Delta H is total energy or potential energy
    • Delta G > 0 = Not Spontaneous
    • Delta G < 0 = Spontaneous
    • Delta H > 0 = Endergonic - Taking in energy
    • Delta H < 0 = Exergonic - Releasing energy

ATP and Reaction Coupling

  • Adenosine Triphosphate
  • The breaking of a phosphate from the triphosphate is an exergonic reaction and releases energy and becomes:
  • Adenosine Diphosphate

Enzyme Structure

  • Enzymes are macromolecules
    • Biological catalysts that speed up biochemical reactions
    • Most enzymes are proteins
      • Tertiary shape must be maintained for functionality
      • Have a region called the active site
  • The active site interacts with the substrate
    • Enzymes have an active site that specifically interacts with substrates
      • Has a unique shape and size
      • Can have chemical charges or not
      • Physical and chemical properties of substrate must be compatible
      • Slight changes can occur to align with substrate
      • Enzymes names often end in -ase, ex. kinase
    • Enzymes are reusable
      • Not chemically changed by reactions
      • Cells typically maintain a specific enzyme concentration
      • Enzymes can facilitate synthesis or digestion reactions

Enzyme Catalysis

  • Enzymes are biological catalysts
  • Enzyme structure is very specific and each enzyme only facilitating one type of reaction
  • All biochemical reactions require initial starting energy called activation energy
  • Some reactions result in a net release of energy and some an absorption of energy
  • Typically reactions resulting in a net release require less energy and vice versa
  • Enzymes lower the activation energy requirement of all enzyme-mediated reactions, accelerating the rate of reaction

Environmental Impacts on Enzyme Function

  • A change to the molecular structure of an enzyme may result in loss of enzyme function
    • Enzymes have a unique functional 3D shape known as tertiary structure
    • Changes in shape of enzyme = denaturation
    • Changes in temperature and pH can lead to denaturation, which is irreversible and function is losses or decreased
    • Optimum Temperature
      • Range in which enzyme mediated reactions occur the fastest
      • Reaction rates change when optimum temperatures aren’t maintained
    • Environmental increase in temperature
      • Initially increases reaction rate
        • Increased speed of molecular movement
        • Increased frequency of enzyme-substrate collisions
      • Temperature increases outside of optimum range results in denaturation
    • Environmental decrease in temperature
      • Generally slows down reaction rate
      • However, does not disrupt enzyme structure
  • Environmental pH can alter efficiency
    • pH measures concentration of hydrogen ions in solution
    • Small changes in pH values result in large shifts of hydrogen ion concentration
    • Optimum pH
      • Range in which reactions occur fastest
      • Increases and decreases outside range can result in denaturation
  • Inhibitors
    • Competitive inhibitors - Compete with normal substrate for the normal enzyme’s active site
      • CAN BE OVERCOME W/ MORE SUBSTRATE
      • If inhibitor concentrations exceed substrate concentration, reactions are slowed, and vice versa. If binding is irreversible, enzyme function is prevented.
    • Noncompetitive inhibitors
      • Enzymes have regions other than active site to which molecules can bind, called ALLOSTERIC site
      • Noncompetitive inhibitors DO NOT bind to active site, they bind to allosteric site
      • Binding causes conformational shape change
      • Binding prevents enzyme function because active site is no longer available
      • Reaction rate decreases
      • CANT BE OVERCOME W/ MORE SUBSTRATE

Cellular Respiration

  • Using Oxygen and Glucose to make ATP
  • C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP
  • Glycolysis → Pyruvate Oxidation → Krebs Cycle →ETC
  • The Mitochondria
    • Cristae - The folds inside the mitochondria
    • Inner Membrane
    • Outer Membrane
    • Mitochondrial Matrix
  • Glycolysis
    • Inside the cytoplasm
    • Does not require oxygen
    • 6 Carbon Ring Glucose → 2 3-Carbon-Ring Pyruvates
    • Requires 2 ATPs to happen and generates 4 ATPs and 2 NADH (a coenzyme) in the end
  • Fermentation
    • Anaerobic
    • Since NADH can’t be used it converted back to NAD+
    • Frees up NAD+
    • Byproducts can include alcohol or lactic acid, etc
  • Pyruvate Oxidation
    • Pyruvate diffuses into mitochondria
    • Pyruvate dehydrogenase complex
    • One of the pyruvates is oxidized
    • One of the carbons with the linked oxygen molecule leaves the chain as CO2 and leaves behind a two-carbon compound called Acetyl CoA
    • Gives off Carbon
  • Krebs Cycle
    • Happens across the mitochondrial matrix
    • Acetyl CoA goes to the Krebs Cycle and is broken down further which gives off more CO2
    • NAD+ comes along and picks up a hydrogen to become NADH
    • Oxaloacetic acid combines with the Acetyl CoA to form citric acid
    • Every time a carbon comes off of citrate, ATP is released
    • NAD+ and FAD are both coenzymes related to Vitamin B and are good at holding onto high energy electrons
    • Each Pyruvate yields 3 NADH and 1 FADH per cycle
    • In total produces 6 NADH and 2 FADH
    • 2 ATPs produced
    • Produces FADH2 and NADH
  • The Electron Transport Chain
    • NADH and FADH2 will put their electrons through the transport chain
    • Electrons will move through a series of proteins and the energy of those proteins will be used to pump protons (H+ ions) to the outside which is the intermembrane space
    • Protons will want to come back to the other side of the inner membrane seeking equilibrium, and will be allowed back in through certain proteins (ATP SYNTHASE)
    • The energy of the proton flow drives a spinning mechanism which puts ADP and phosphates together to form ATP
    • The electrons from the 10 NADH (2 glycolysis, 2 pyruvate dehydrogenase, and 6 krebs) can produce up to 3 ATPs each
    • Each FADH has enough energy to create 2 ATPs
    • 32-34 ATP created, plus 2 from glycolysis and krebs = roughly 38 ATPs total

Photosynthesis

  • Autotrophs
    • Make food for themselves (autonomous)
    • 6CO2 + 6H2O +Light → C6H12O6 + 6O2
  • Chloroplast
    • Stroma - Dense fluid which fills chloroplast (basically like he cytoplasm)
    • Thylakoid - Sacs in the stroma in which processes take place
    • Granum - A stack of thylakoids is called a granum
    • There’s more than just chlorophyll working to absorb light
    • Reflect green light, typically absorb more blue and red
  • Photosynthesis
    • Photo = Light reactions
      • Water and light go into the thylakoid membrane and produce oxygen as a waste product and NADPH and ATP
    • Synthesis = Calvin’s Cycle
      • After the light reactions, the energy transfers to the Calvin’s cycle where CO2 comes in and glucose comes out
    • Light Reactions
      • Photosystem II and I
        • Proteins with chlorophyll on the inside of it is called a photosystem
        • Photosystem 2 is the FIRST PHOTOSYSTEM BECAUSE IT WAS DISCOVERED SECOND
        • Light is used to move electrons through an electron transport chain
        • Water is split and gives off Oxygen (O2), and diffuses out of the cell
        • Every time the electrons from the transport chain move through proteins they pump protons into the inside of the thylakoids
        • Opposite of cellular respiration, the protons go from inside to outside through the ATP SYNTHASE rotor and create ATP
        • The ATP is now in the stroma and ready to go for the Calvin Cycle
        • This also creates NADPH at the end of the transport chain
      • The Calvin Cycle
        • RUBP (5 carbon molecule) is put together with Carbon (1 carbon molecule) by an enzyme called RuBisCo
        • This new molecule is broken down into 3-carbon molecules called PGA
        • The cycle will receive energy from ATP and NADPH
        • It’ll now create a chemical called G3P by the NADPH adding H’s to the PGA’s
        • G3P can be assembled into sucrose or glucose
        • Some is used and some is recycled to make RUBP

Photosynthesis (again)

  • Organisms capture and store energy for use in biological processes
    • Photosynthesis is the biological process that captures energy from the sun and produces sugars
    • Evidence supports to claim that prokaryotic photosynthesis by organisms such as cyanobacteria was responsible for the production of oxygen in the atmosphere
    • Photosynthetic pathways are the foundation of eukaryotic photosynthesis
  • Light dependent reactions of photosynthesis in eukaryotes involve a series of pathways
    • Light dependent reactions capture light by using pigments
    • Pigments help transform light energy into chemical energy
    • Chemical energy is temporarily stored in the chemical bonds of carrier molecules called NADPH
    • Light dependent reactions help facilitate ATP synthesis
    • ATP and NADPH transfer stored chemical energy to power the production of organic molecules in another pathway called the Calvin cycle
    • Oxygen is produced as result of water hydrolysis
  • During photosynthesis, chlorophylls absorb energy from light
    • Capture of energy from sunlight and converting it to high energy electrons
    • Electrons are energized and the electrons are used to establish a proton gradient and reduce NADP+ to NADPH
  • Photosystems 2 and 1 are embedded in the internal membranes of thylakoid membranes
    • A photosystem is a light capturing unit in a thylakoid membrane
    • The hydrogen molecules from the splitting of water in PS2 are released into the thylakoid space and used to create a proton gradient
    • PS2 and 1 pass high energy electrons through the ETC
    • Opposite of cellular respiration, H+ ions want to go from inside to outside into the stroma through the ATP synthase
  • The energy captured in light powers the production of carbohydrates in the Calvin cycle
    • Calvin cycle uses ATP, NADPH, and CO2 to produce carbohydrates
    • Making organic products that plants need using the products from light reactions
    • They get CO2 from environment

Photorespiration

  • Occurs when there isn’t abundant CO2
  • Oxygen can jump into the Calvin cycle and use rubisco to form another chemical
  • This chemical has no use and the cell has to break it down
  • This may happen when it’s really hot and the stomata are closed because the plant doesn't want to lose water
  • CAM PLANTS
    • Only open stomata at night
    • In very hot areas
    • Storage of CO2 as malic acid and then using malic acid during the day and reverting it back to CO2
    • CO2 can then be introduced into the calvin cycle
  • C4 PLANTS
    • Take CO2 molecules in and use enzymes to make a 4 carbon molecule
    • The 4 carbon molecule will move to some cells on the inside of the leaf called the bundle sheath cells
    • Introduce CO2 to the Calvin Cycle