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Ch 8-9 (metabolism (An organism’s metabolism transforms matter and energy,…

- - - - Thermal energy
        
        Heat is thermal energy in transfer between objects
      - Potential energy
      - Kinetic energy
      - Chemical energy
    - - Anabolic pathways
      - Catabolic pathways
      - Bioenergetics
    - - Thermodynamics is the study of energy transformations
        
        The Second Law of Thermodynamics
        
        Every energy transfer or transformation increases the entropy of the universe
        
        Entropy is a measure of molecular disorder, or randomness
        
        Spontaneous processes occur without energy input; they can happen quickly or slowly
        
        According to the first law of thermodynamics, the energy of the universe is constant
    - - Organisms create ordered structures from less organized forms of energy and matter
        
        Organisms also replace ordered forms of matter and energy in their surroundings with less ordered forms
        
        For example, animals consume complex molecules in their food and release smaller, lower energy molecules and heat into the surroundings
        
        Entropy (disorder) may decrease in a particular system, such as an organism, as long as the total entropy of the system and surroundings increases
  - - - Free-Energy Change, G
        
        ΔG = ΔH − TΔS
        
        ΔG is negative for all spontaneous processes; processes with zero or positive ΔG are never spontaneous
      - A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell
      - Free energy is a measure of a system’s instability, its tendency to change to a more stable state
      - Equilibrium is a state of maximum stability
      - Exergonic and Endergonic Reactions in Metabolism
        
        An exergonic reaction proceeds with a net release of free energy and is spontaneous
        
        An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous
        
        Equilibrium and Metabolism
        
        Cells are not in equilibrium; they are open systems experiencing a constant flow of materials
        
        A defining feature of life is that metabolism is never at equilibrium
        
        A catabolic pathway in a cell releases free energy in a series of reactions
  - - - the use of an exergonic process to drive an endergonic one
    - - Structure
        
        ATP is composed of ribose (a sugar), adenine(a nitrogenous base), and three phosphate groups
        
        The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis
        
        Energy is released from ATP when the terminal phosphate bond is broken
        
        This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
      - hydrolysis
        
        The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP
        
        In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction
        
        Overall, the coupled reactions are exergonic
        
        ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)
        
        ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
        The recipient molecule is now called a phosphorylated intermediate
  - - - catalysis
        
        A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction
        
        Enzymes are extremely fast acting and emerge from reactions in their original form
        Very small amounts of enzyme can have huge metabolic effects because they are used repeatedly in catalytic cycles
        
        An enzyme is a catalytic protein
        For example, sucrase is an enzyme that catalyzes the hydrolysis of sucrose
      - Substrate Specificity
        
        The reactant that an enzyme acts on is called the enzyme’s substrate
        
        The enzyme binds to its substrate, forming an enzyme-substrate complex
        
        While bound, the activity of the enzyme converts substrate to product
        
        The active site is the region on the enzyme where the substrate binds
        
        The active site can lower an EA barrier by
        
        orienting substrates correctly
        
        straining substrate bonds
        
        providing a favorable microenvironment
        
        covalently bonding to the substrate
      - Activation Energy Barrier
        
        The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA)
        Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings
        
        In catalysis, enzymes or other catalysts speed up specific reactions by lowering the EA barrier
      - Effects of Temperature and pH
      - Enzyme Inhibitors
        
        Noncompetitive inhibitors
        
        bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective
        
        Competitive inhibitors
        
        bind to the active siteof an enzyme, competing with the substrate
    - - nonprotein enzyme helpers
        
        Cofactors may be inorganic (such as a metal in ionic form) or organic
        
        An organic cofactor is called a coenzyme
        
        Coenzymes include vitamins
  - - - Localization of Enzymes Within the Cell
        
        In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria
        
        Some enzymes act as structural components of membranes
        
        Structures within the cell help bring order to metabolic pathways
    - - may either inhibit or stimulate an enzyme’s activity
      - occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site
      - Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site
      - Cooperativity
        
        amplify enzyme activity
        
        allosteric because binding by a substrate to one active site affects catalysis in a different active site
    - - the end product of a metabolic pathway shuts down the pathway
      - prevents a cell from wasting chemical resources by synthesizing more product than is needed
- - - - At the completion of glycolysis and the Krebs cycle, glucose has broken down into carbon dioxide which is released from the mitochondrian.
  - - - Transition Reaction
        
        Location-cytoplasm->mitochondria
        
        no oxgen
        
        reactants: 2 pyruvic acid
        2 NAD+ from ETS
        2 Coenzyme A
        
        products:2CO2
        2NADH-go to ETS
        2 Acetyl CoA
      - location: in cytoplasm of cell near mitochondria
      - no need oxygen
      - reactants:1 glucose
        2NAD+ from ETS
        2ADP + 2P
        
        products:2 ATP
        2 pyruvic acid
        2 NADH go to ETS
        2H +
      - Substrate-level Phosphorylation
        
        Enzyme transfers a phosphate group from a substrate molecule directly to ADP to make ATP
    - - Location-mitochondrial matrix
      - no oxygen
      - reactants:
        
        2 Acetyl CoA
        
        6 NAD+ from ETS
        
        2 ADP + 2P
        
        2 FAD from ETS
      - products:
        
        4 CO2
        
        6 NADH go to ETS
        
        2 FADH2 go to ETS
        
        2 ATP
    - - Location-inner mitochondrial membrane
      - need oxygen
      - reactants:
        
        10 NADH
        
        2 FADH2
        
        O2
        
        H+
        
        ADP, P
      - products
        
        H2O
        
        32 or 34 ATP
        
        NAD+
        
        FAD
      - Oxidative Phosphorylation
        
        Occurs in cristae of mitochondrian
        
        responsible for greatest production of ATP
        
        oxidative comes from use of oxygen as terminal electron acceptor
        
        phosphorylation comes from a molecule of ATP being phosphorylated to ATP
        
        aerobic
        
        electron carriers bring the electrons to a group of coenzymes(the electron transport chain)
        
        as electrons being transported down, energy released
        
        final acceptor of electron is oxygen
  - - - pyruvic acid to carbon dioxide and either ethyl alcohol or lactic acid