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					                     Energy in the Cell
•   Energy is in two basic forms:
•   1. potential energy, which is energy
    stored up, ready to use, like a coiled
    spring, the capacity to do work. 2.
    kinetic energy, which is energy of
    motion, actually doing work.
•   Food molecules contain potential
    energy in their chemical bonds.

•   ―calories‖ are a measure of energy.
    Some foods contain more energy per
    gram than others, because their
    chemical bonds store more energy.
    For instance, carbohydrates and
    proteins store 4 calories per gram,
    while fats store 9 calories per gram.
•   Cells convert the chemical bond
    energy in food molecules to chemical
    bond energy stored in ATP molecules.
•   ATP energy is used to run metabolism
    and all other bodily processes.
                     Thermodynamics
•   First Law: the total mount of energy in
    the Universe is constant. Energy is
    neither created not destroyed, it just
    changes form.
•   When energy is expended, part of it
    goes to do useful work, and the rest
    ends up as heat. None of it is lost, but
    it changes forms.
•   Second Law: disorder (entropy)
    increases. Energy goes from useful
    forms to useless heat.
•   Every energy transformation step is
    inefficient (as a consequence of the
    Second Law), meaning that some of
    the energy is converted to waste heat
    at every step, and the amount of
    useful work decreases with every step.
•   Life is very orderly compared to non-
    living things. Living things are able to
    locally reverse the overall direction of
    entropy by using a lot of energy.
•   The energy of living cells comes from
    the Sun, and it ends up as waste heat.
                             ATP
• In living cells, energy for
  immediate use is stored as
  molecules of ATP, adenosine
  triphosphate. When the
  energy is used, one of the
  phosphates attached to ATP is
  released, giving ADP,
  adenosine diphosphate.
• The 3 phosphates each have a
  negative charge, and so they
  repel each other. When the
  bond holding them together is
  broken, the phosphates fly
  apart, like a spring being
  released. The cell can use this
  energy in many different ways.
               Metabolic Reactions
•   A metabolic reaction is the
    conversion of one chemical
    compound into another one inside
    a living cell.
•   For every metabolic reaction, you
    start with reactants and convert
    them to products. An enzyme
    does the conversion. Each
    reaction uses a different enzyme.
•   The basic rule: reactions run
    downhill: more energetic reactants
    are converted to less energetic
    products.
•   If a reaction needs to run uphill,
    creating products that contain
    more energy than the reactants,
    energy in the form of ATP must be
    added.
•   Reactants are also called
    substrates.
                                 Enzymes
•   Enzymes are proteins that cause
    specific chemical reactions to occur.
•   Enzymes act as catalysts: they help
    the reaction occur, but they aren’t
    used up in the reaction.
•   All reactions require an input of energy
    to get them started: the activation
    energy. Think of touching a match to
    a piece of paper to start a fire: the
    match is supplying the activation
    energy.
•   Enzymes work by lowering the
    activation energy for a reaction. The
    reaction occurs thousands or millions
    of times faster than without the
    enzyme. The little bit of activation
    energy needed is supplied by the
    collision of the molecules involved.
•   Enzymes are very specific for their
    substrates: they work on only a very
    limited number of similar molecules.
    Enzyme-Substrate Interactions
•   Each enzyme has an active site, a special region
    that holds the substrates together and causes
    them to react
•   The active site promotes the reaction by orienting
    the substrates properly, straining their bonds so
    they break more easily, and by providing acidic or
    basic amino acids to help the reaction along.
•   Enzymes often use small accessory molecules
    called coenzymes to help carry out the reaction.
    Most vitamins are coenzymes. .

•   Enzymes often have small molecules that act as
    inhibitors or activators of their activity. These
    molecules alter the active site so the enzyme
    reacts differently to the substrate.
•   Enzyme activity is strongly influenced by
    temperature. They have an optimum
    temperature: to hot or too cold slows them down.
    Most of the enzymes in humans have an optimum
    temperature near body temperature.
•   pH and salt level also influence enzyme activity,
    with optimum values for each.
       Generating ATP from Food
•   ATP (adenosine triphosphate) is made
    from ADP (adenosine diphosphate)
    plus a phosphate ion (symbolized by
    Pi). Making ATP requires energy,
    which comes form the potential energy
    stored in food molecules.
•   More specifically, electrons from
    glucose or other food molecules are
    passed through a series of steps,
    releasing part of their energy in each
    step, and ultimately ending up
    attached to oxygen. The energy from
    the electrons going down the energy
    hill is used to create ATP from ADP
    and phosphate.
•   Similarly, high energy electrons are
    carried by the molecule NADH. When
    NADH uses its high energy electrons,
    it is converted to NAD+. Electrons in
    the cell are often accompanied by an
    H (hydrogen).
                                    Oxidation
•   Energy from chemical bonds is transferred in the form of electrons. Oxidation means removing
    electrons. Its opposite is reduction, which is gaining electrons. LEO = Lose Electrons Oxidation;
    GER = Gain Electrons Reduction.
•   Some common forms of oxidation: burning and rusting.
•   Cells oxidize glucose to form carbon dioxide and water. The cell removes electrons from glucose
    (in a series of steps), which converts it to carbon dioxide. The energy stored in the electrons is
    used to make ATP. Finally, the electrons are given to oxygen molecules, converting them to
    water.
•   By passing the electrons through a series of steps before their final destination in water, the cell
    can harvest the energy efficiently. In contrast, burning releases the energy all at once, so it can’t
    be captured easily.
•   The electrons are often accompanied by a hydrogen (H), and they are usually carried in the cell by
    the molecule NADH (or its close relative NADPH).
Aerobic and Anaerobic Respiration
• Respiration is generating energy by breaking down food molecules,
  converting the energy in their chemical bonds to ATP energy.
• Before oxygen was present in the atmosphere, all cells used
  anaerobic respiration, which means generating energy in the
  absence of oxygen.
• Many bacteria only have anaerobic respiration. Some are even
  poisoned by the presence of oxygen: the bacteria that cause
  gangrene, for example.
• Most eukaryotes use aerobic respiration, generating energy with the
  use of oxygen , in addition to anaerobic respiration. We use
  anaerobic respiration to start the process, but finish it with aerobic.
  Aerobic respiration is much more efficient than anaerobic.
• The anaerobic pathway is called glycolysis, which means ―breaking
  down glucose‖. It occurs in the cytoplasm.
• The aerobic pathway occurs in the mitochondria.
       Summary of Respiration
• 1. glycolysis (anaerobic) breaks glucose (a 6 carbon
  chain) into 2 molecules of pyruvate (3 carbons each).
  This require 2 ATPs as input, and yields 4 ATPs.
  Glycolysis thus nets 2 ATPs for each glucose.
   – intermediate step between glycolysis and the Krebs cycle:
     conversion of pyruvate to acetyl CoA.
• 2. Krebs cycle: acetyl CoA converted to carbon dioxide
  (aerobic).
• 3. electron transport: high energy electrons converted to
  ATP (aerobic).

• Aerobic respiration yields 34 more ATPs per glucose,
  giving a total of 36 ATPs generated from each glucose.
  All but 2 of them come from aerobic respiration.
                                 Glycolysis
•   Occurs in the cytoplasm, not in
    mitochondria
•   Does not use oxygen.
•   Almost all living things use this pathway.
•   Basic process: add phosphates (from ATP)
    to each end of the glucose, then split it in
    half, using that chemical bond energy to
    generate 4 ATPs. Final 3-carbon products
    = pyruvate.

•   Also releases 2 electrons, which are
    carried by NADH. These electrons can be
    converted to energy if oxygen is present,
    but they cause problems if not.
•   What to do with excess electrons? Need to
    regenerate NAD+ so it can take up more
    electrons, so give the electrons back to
    pyruvate in some way:
     –   In yeast, the pyruvate gets converted to
         ethanol when the electrons are added back.
     –   In humans and many bacteria, pyruvate
         gets converted to lactate (lactic acid).
         Causes muscle pain during intense exercise
         when not enough oxygen gets to the muscle
         cells.
                    Aerobic Pathway
•   Requires oxygen, occurs in the
    mitochondria
•   Conversion of pyruvate (from
    glycolysis) to carbon dioxide, with
    generation of high energy
    electrons and ATP.

•   Preliminary steps before starting
    the Krebs cycle: 3 carbon
    pyruvate to 2 carbon acetyl CoA;
    third carbon lost as carbon
    dioxide. Generates high energy
    electrons carried by NADH.
•   Krebs cycle: add 2 carbon acetyl
    CoA to 4 carbon sugar, remove
    the 2 extra carbons one at a time
    as carbon dioxide, generate
    several high energy electrons on
    NADH plus some ATP.
                     Electron Transport
•   The final stage in aerobic respiration
•   Krebs cycle generates many high energy
    electrons (carried by NADH). Also some
    from glycolysis. These need to be
    converted to ATP so the cell can use them.
•   Electron transport pumps electrons from the
    inner compartment to the outer compartment
    of the mitochondria.
•   Electrons are passed from NADH through 3
    proteins which use the electron energy to
    pump H+ ions through the membrane. Each
    protein pump drains energy from the
    electrons, so by the end of the process, the
    electrons are low energy.
•   The final protein pump adds the electrons
    (plus hydrogens) to oxygen, producing
    water.
•   The H+ level builds up between the
    membranes. It flows back into the inside
    through a special protein channel called
    ATP synthase, which uses the energy of
    their flow to combine ADP and Pi into ATP.
    This is the main way energy is generated in
    the cell.
•   Cyanide blocks electron transport chain—no
    more ATP is made
•   Brown fat runs electron transport chain
    without generating ATP, just to produce
    heat.
           Energy from Other Foods
•   Glucose is the primary food molecule
•   Carbohydrates are broken down into glucose in
    the stomach. It enters the blood through the small
    intestine.
•   Cells absorb glucose and trap it inside by adding a
    phosphate to it.
•   It is then either used directly or converted into
    starch, to be used later.
•   Fats are the primary energy storage molecules,
    containing more than twice as much energy per
    gram as carbohydrates or proteins. The fatty acids
    are converted to acetyl CoA (preliminary steps of
    aerobic metabolism). From there they enter the
    Krebs cycle. The glycerol molecules go into
    glycolysis.
•   The liver converts excess starch into fat.
•   Proteins are mostly broken down into amino acids
    which become parts of new proteins.
•   When proteins are used for energy, their carbon
    backbones enter glycolysis or Krebs cycle at
    various points. The amino group becomes
    ammonia, which is poisonous. Ammonia gets
    converted to urea, which is a lot less toxic, and
    then gets excreted in urine.
                        Photosynthesis
•   Photosynthesis means taking energy from
    sunlight and converting it to a form usable
    by living cells.
•   Green plants do photosynthesis; so do
    many bacteria and protists (which are single
    celled eukaryotes).
•   Two parts to photosynthesis:
•   1. the light-dependent reactions, in which
    sunlight is used to extract high energy
    electrons from water. These high energy
    electrons are then used to make ATP.
    Oxygen from the water is released into the
    atmosphere.
•   2. the light-independent reactions (or dark
    reactions, or Calvin cycle), in which that
    ATP energy is used to convert carbon
    dioxide into glucose.
•   In plants, all of these reactions occur in the
    chloroplast, an organelle that contains its
    own DNA and is thought to be derived from
    an ancient symbiosis between a free-living
    photosynthetic bacterium and a primitive
    eukaryote (just like the mitochondria).
•   All the food we animals eat comes from
    these reactions.
                  Light and Pigments
•   Visible light is a form of
    electromagnetic radiation, along with
    X-rays, ultraviolet, infrared,
    microwaves, radio waves, etc. The
    only difference between these forms of
    radiation is the wavelength.
•   Visible light is all frequencies between
    400 and 700 nanometers, with blue
    light at the 400 end and red at the 700
    end.
•   White light is a mixture of all these
    wavelengths; colors appear when only
    some wavelengths are present.
•   Chlorophyll is green because it
    absorbs the red and blue wavelengths,
    reflecting only the green wavelengths.
•   Other plant pigments absorb different
    wavelengths, so they have different
    colors.
•   Absorbing light puts chlorophyll into a
    high energy state. This energy is then
    harvested by a series of metabolic
    reactions.
       Light-Dependent Reactions
•   The chlorophyll molecules are
    arranged in groups of 200-300, called
    photosystems. Each photosystem
    acts like an antenna—any of the
    molecules can capture a photon of
    sunlight, but then that energy is
    transferred to a central ―reaction
    center‖ molecule, which passes the
    energy (excited electrons) out of the
    photosystem.
•   In green plants, there are 2 separate
    ways of extracting electrons. The
    more heavily used pathway needs 2
    photons to boost electrons up to a high
    enough energy to be bound to the
    plant cell’s energy carrying molecule,
    NADPH. The electrons on NADPH are
    then passed to the light-independent
    reactions to generate glucose.
•   The electrons are initially extracted
    from water, carried along with the
    hydrogens. The waste product is
    oxygen, which goes into the
    atmosphere. This is the source of all
    the oxygen in the atmosphere.
     Light-Independent Reactions
•   The energy from sunlight is captured
    in the form of excited electrons, which
    are bound to the electron-carrying
    molecule NADPH.
•   To form glucose, carbon dioxide
    (which has 1 carbon atom) is attached
    to a 5-carbon sugar, then processed
    through a series of intermediates
    called the ―Calvin cycle‖.
•   The Calvin cycle goes around 6 times
    to create the 6-carbon glucose from
    carbon dioxide. Each turn regenerates
    all the necessary intermediates. The
    cycle uses electrons from NADPH, and
    also energy from ATP.
•   After glucose is synthesized, it is
    converted to starch for storage, and
    then the starch is converted to sucrose
    (a disaccharide) for transport to other
    parts of the plant.

				
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