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Ch. 8 & 9 (Metabolism (Biological Order & Disorder (Complex…

- - - - Downhill reactions
      - Cellular respiration
        
        Breakdown of glucose, in the presence of O2, to CO2 & H2O
        
        Stored energy is released to do work
      - Releases energy
    - - Consumes energy to build molecules
      - Uphill reactions
      - Biosynthetic Pathways
      - EX: Synthesis of proteins from amino acids
  - - - Does not violate 2nd law of thermodynamics
  - - - Proceeds w/a net release of free energy (output)
      - Because it loses free energy (G decreases), ΔG is negative (more energy was released than needed for endergonic reaction
      - occur spontaneously (energetically favorable)
      - Magnitude of ΔG = the maximum amount of work a reaction can perform
        the greater the decrease in free energy , the greater amount of work that can be done
      - Catabolic
      - Downhill
    - - For every exergonic reaction there is an endergonic reaction
        
        These reactions happen at the same time & are integrated together
      - Non spontaneous
      - Anabolic
      - Forms bonds
      - Input energy
      - ΔG >0 (ΔG is positive) (not enough energy was released from exergonic reaction
      - Picks up the energy from the exergonic reaction
      - Uphill
  - - - Living cell is not in equilibrium
      - Constant flow of materials in/out keeps the metabolic pathways from reaching equilibrium
        (open system)
      - A catabolic pathway in a cell releases free energy in a series of reactions
- - - - Respiration - gas exchange between organism & its environment, happens @ level of the cell
        
        Cellular respiration
        
        Aerobic - w/O2
        
        Jogging
        
        Swimming
        
        Running
        
        Walking
        
        C6H12O6 -> 6CO2 + 6H2O + ENERGY
        
        Anaerobic - w/out O2
        
        Kicking a ball
        
        The swing of a golf club
      - Breathing - The alternation of inhalation & exhalation
        
        Inhale O2 -> lungs -> blood -> organs -> CO2 -> organs -> blood -> lungs -> CO2 out (exhale)
      - Cell breathes, ultimate exchange of O2 to CO2 happens in & near Mitochondria
  - - - ATP = Energy for the Cell
        
        Glucose – energy storage molecule C6H12O6
  - - - Eat + Breathe -> Exhale + H2O +Energy
        Glucose + O2 -> CO2 + H2O + ATP
      - Cell sends glucose to mitochondria
      - Reactant A->B->C->D->E Product
  - - - Occurs in CYTOPLASM
      - Does NOT require O2
      - Step 1-3 A fuel molecule is energized using ATP - Pairing an exergonic & endergonic reaction
        Exergonic - ATP->ATP
        
        Glucose forms a bond with Phosphate ( by released energy)
        
        Fructose bonds w/phosphate
        
        Fructose -1, 6-diphosphate
        
        6 Carbon splits into tow 3 Carbons
        Glyceraldehyde-3, phosphate
      - Steps 1-4: PREPARATORY PHASE (energy investment)
      - Net production of 2 ATP
        -2 were used 4 were made (4-2=2)
      - Steps 5-9: ENERGY PAYOFF PHASE
      - A redox reaction generates NADH
        6-9. ATP & Pyruvic Acid are produced
      - Glycolysis Reactants:
        
        1 glucose
        
        2NAD+ from ETS
        
        2ADP+ 2P
      - Glycolysis Products:
        
        2 ATP
        
        2 Pyruvic acid
        
        2 NADH got to ETS
        
        2H+
      - Substrate-level Phosphorylation- Enzyme transfers a phosphate group from a substrate molecule directly to ADP to make ATP (The one adding the phosphate group)
        
        ADP must become ATP
        added phosphate
        formed bond
        ENDERGONIC
    - - Starts in Cytoplasm -> mitochondria
      - No O2 required
      - Transitions reaction reactants:
        
        2 pyruvic acid
        
        2 NAD+ from ETS
        
        2 Coenzyme A
      - Transition reaction products:
        
        2 CO2
        -2NADH - go to ETS
        
        2 Acetyl CoA
      - Aerobic Respiration
      - Gives CO2 (NOT ATP)
      - Pyruvic acid becomes reactant after glycosis
      - Each glucose gives 2 pyruvic molecules
    - - Happens in the mitochondria matrix
      - Does not require O2
      - Circular Metabolic Pathway
      - Krebs Cycle Reactants:
        
        2 Acetly CoA
        
        6 NAD+ from ETS
        
        2 ADP + 2P
        
        2 FAD from ETS
      - Krebs Cycle Products:
        
        4 CO2
        
        6 NADH go to ETS
        
        2 FADH2 got to ETS
        
        2 ATP
      - Occurs 2 times per glucose molecule (circle turns twice)
    - - Happens in inner mitochondrial membrane
      - Requires O2- aerobic
      - Reactants:
        
        10 NADH
        
        2 FADH2
        
        O2
        
        H+
        
        ADP, P
      - Products:
        
        H2O
        
        32 or 34 ATP
        
        NAD+
        
        FAD
      - Makes the most ATP
      - Located in the outer membrane (bigger membrane = more room to fit molecules)
  - - - Ethyl alcohol fermentation
        Yeast --> Wine
        Yeast---> Bread
        
        Pyruvic acid is converted to CO2 & ethanol
        
        THis recycles NAD+ to keep glycolysis working
      - Lactic acid fermentation:
        Produces muscle fatigue
        bacteria ---> cheese
        bacteria---> yogurt
        
        Pyruvic acid is converted to lactic acid
        
        NAD+ is recycled
- - - - Cells apply energy to perform work
        EX: Transporting solutes across a plasma membrane
  - - - Dinoflagellates (oceans)
      - Fireflies (land)
  - - - Exists in various forms, & some forms are used to do work,
      - Ability to rearrange a collection of matter
      - Move matter against opposing forces
        
        Gravity
        
        Friction
      - The walk of life depends on the ability of the cells to transform energy from one form to another
      - Can be converted from one form to another
        
        Organism are energy transformers
        Food -> Chemical Energy -> Kinetic or Potential Energy
        
        Small amount of energy is lost as heat
    - - Associated with motion
      - Moving objs. perform work by transmitting movement to other matter
    - - Associated w/random movement of atoms or molecules
      - Heat - Thermal energy in transfer between objs.
    - - Energy matter processes because of its location or structure
      - EX: Water behind a dam
    - - potential energy available for release in chemical reactions (forming or breaking bonds)
      - Glucose is high in chemical energy (food broken down)
  - - - The study of energy transformation
      - Surroundings - Everything outside of the system
      - System - Matter under study
    - - Organisms
        
        Absorb energy
        
        Release heat
        
        Release metabolic waste products to surroundings; O2
    - - Energy of the universe is constant
        
        Can be transferred
        
        Can be transformed
        
        Can not be created or destroyed
    - - Every energy transfer or transformation increases the entropy of the universe
        
        Entropy - Measure of molecular disorder or randomness
        
        The more random the greater the entropy
        
        Physical disintegration of a system's organized structure
        
        The concept of entropy
        
        Helps us understand why certain processes are energetically favorable occur on their own
        
        If a given process, by itself, leads to an increase in entropy, it can proceed w/out input energy
      - Some energy becomes unavailable to do work
      - Living cells unavoidably convert organized forms of energy to heat (disordered energy)
    - - Occur w/out input energy
      - Can happen quickly or slowly
      - For it to occur, it must increase entropy in the universe
    - - Decrease in entropy
      - Energy is required
- - - - Once ΔG is known, it can be used to predict spontaneous processes
        
        It is ONLY spontaneous if the ΔG is negative
        
        For ΔG to be negative the ΔH must be negative, or TΔS must be positive or both
        
        Negative ΔG (ΔG <0)
        
        Spontaneous process decreases system's free energy
    - - Very important in the study of metabolism
        
        Goal: to determine which reactions can supply energy for cellular work
  - - - ΔG= G final state – G initial state
      - ΔG can only be negative when the process loses free energy during the change from initial state to final state
      - Less free energy , final state is less likely to change (more stable now)
    - - Unstable system's (higher G) change in such a way they become stable
    - - Chemical Reactions are reversible
      - Forward and backward reaction occur at the same rate
      - No further net change in concentration of products & reactants
      - Free energy valley
      - System's never spontaneously move away from equilibrium
        
        Because system's at equilibrium cannot spontaneously change, it can do no work
    - - Free energy increases when a reaction is somehow pushed away from equilibrium
      - A process is spontaneous and can perform work only when it it moving toward equilibrium
- - - - Substrate - The reactant an enzyme acts on
      - Active site - Open spot on structure, has specific shape, formed by a few of the enzymes amino acids (shape decided by protein molecules)
        
        Enzyme molds to substrate
        
        Held in active site by weak interactions
        
        Active site lowers EA
        
        Substrate converts to products
        
        Products release
        
        Active site available for new substrate
        
        Catalysis in the Enzyme's Active Site
        
        in enzymatic reaction, substrate binds to the active site of the enzyme
        
        Enzymes are fast actin, emerge from reactions in their original form
        
        Very small amounts of enzymes can have huge metabolic effects, used repeatedly in catalytic cycles
        
        Most metabolic reactions are reversible, enzyme can catalyze either forward or reverse reaction
        
        The rate of enzyme catalyzed by reaction can be sped up by increasing substrate concentration
        
        When all active sites are engaged the enzyme is saturated
        
        if saturated the reaction rate can only be sped up by adding more enzyme
        
        The active site can lower an EA barrier by:
        
        Orienting substrates correctly
        
        Straining substrate bonds
        
        Providing a favorable microenvironment
        
        Covalently bonding to the substrate
      - Substrate binds to an enzymes active site (forming enzyme-substrate complex)
        
        While bound, enzyme converts substrate to product
        
        Reaction catalyzed by each enzyme is very specific
        
        Induced fit - of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze reaction
  - - - Often supplied in the form of thermal energy that reactant molecules absorb from their surroundings
  - - - Under environmental conditions where the new function is beneficial, natural selection would favor the mutated allele
- - - - The pumping of substances across membranes against the direction of spontaneous movement
    - - The contraction of muscle cells
    - - The pushing of endergonic reactions that would not occur spontaneously
      - Energy coupling using ATP Hydrolysis drives chemical work
    - - The use of an exergonic process to drive an endergonic one
      - ATP is responsible for mediating most energy coupling in cells
      - Most of the time it acts as an immediate source of energy that powers cellular work
  - - - When the terminal phosphate bond is broken, energy is released
        
        release comes from the chemical change to a state of lower free energy
        
        Inorganic phosphate leaves ATP, then because ADP
        
        Reaction is exergonic
  - - - In an organism the same generation of heat can be beneficial
        
        Shivering uses ATP hydrolysis during muscle contractions to warm the body
      - In most cases however, the generation of heat alone would be inefficient, and possibly dangerous
        
        Instead, the cell's proteins harness the energy released during ATP hydrolysis to perform the 3 types of work
        
        If ΔG of an endergonic reaction is < energy release by ATP hydrolysis, then the 2 reactions can be coupled. Coupled reactions are exergonic
        
        Involves phosphorylation - transfer of a phosphate group from ATP to some other molecule; like a reactant
        
        Phosphorylated Intermediate- recipient molecule w/phosphate group covalently bonded to it
        
        Key to coupling exergonic & endergonic reaction
    - - An organism at work uses ATP continuously
      - ATP is a renewable resource that can be regenerated by adding a phosphate to ADP
        
        The energy to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in cell
      - ATP Cycle - The shuttling of inorganic phosphate & energy
        
        Couples the cell's energy energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones.
        
        Revolving door through which energy passes during its transfer from catabolic to anabolic pathways