Matter by qingyunliuliu

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									The Working Cell
       Chapter 5
Cool “Fires” Attract Mates and Meals

   Fireflies use light, instead of
    chemical signals, to send signals
    to potential mates
   Females can also use light
    flashes to attract males of other
    firefly species — as meals, not
    mates
   The light comes from a set of
    chemical reactions, the luciferin-
    luciferase system (from Lucifer,
    meaning light-bearer)
   Fireflies make light energy from
    chemical energy
   Life is dependent on energy
    conversions
Energy And The Cell
    Living cells are compartmentalized by membranes
    Membranes are sites where chemical reactions
     can occur in an orderly manner
    Living cells process energy by means of enzyme-
     controlled chemical reactions
5.1 Energy is the capacity to perform
   work
   Energy is defined as the capacity to do work
    A   somewhat circular definition of work is used also
   All organisms require energy to stay alive
   Energy makes change possible
   Energy is the capacity to rearrange matter
   Moving objects can do work by TRANSFERRING
    MOTION to other matter
     E.g.,   pushing a cart up a hill
Two main categories…
(but many forms!)
   Kinetic energy is energy that is actually doing work
      Associated with movement of molecules and
       atoms in a body
            Also, light is a form of KE
   Potential energy is stored energy (ability to do
    work) as a result of its LOCATION or STRUCTURE
      Negatively charged electrons of an atom have
       PE owing to their positions in electron shells at a
       certain distance from the positive nucleus
       (farther it is, the more PE it has)
      Chemical Energy is the PE of molecules and
       can be released to power the work of the cell
       (these are all manipulations of electromagnetic
       forces and the Electric Field)
      Organic molecules have PE as a result of the
       arrangement of their atoms and bonds; this PE
       is the energy that is available to do the work of
       the cell
5.2 Two laws govern energy conversion

   First law of thermodynamics
     Conservation   of energy: DU = dQ + dW
   Energy can be changed from one form to another
   However, energy cannot be created or destroyed
     Not   so true at the quantum level…
Second law of thermodynamics
   Energy changes are not 100% efficient
   Energy conversions increase disorder, or entropy
       Entropy is more properly related to the energy distribution of
        energy states of a collection of molecules, and this aspect is
        usually discussed in statistical mechanics.
        (http://www.science.uwaterloo.ca/~cchieh/cact/applychem/entropy.html)

   Some energy is always lost as heat
     This  energy becomes unusable (unavailable to do
        work)
5.3 Chemical reactions either store
   or release energy
   Cells carry out thousands of chemical reactions per second
   The sum of these reactions constitutes cellular metabolism
   A cell is a chemical factory that transforms energy from one
    form to another
There are two types of chemical
reactions:
   Endergonic reactions absorb energy and yield
    products rich in potential energy
     Energy is stored in the covalent bonds of the
      product molecules


                            Potential energy of molecules
                                                                        Products



                                                                                   Amount of
                                                                                    energy
                                                                                    INPUT

                                                            Reactants
Exergonic…
   Exergonic reactions release energy and yield products
    that contain less potential energy than their reactants
   Reactants’ covalent bonds contain more energy than
    those in the products
   E.g., burning of wood releases the PE of glucose (which
    constitutes the carbohydrate, cellulose) as heat and light
    (and the products CO2 and H2O)

                              Potential energy of molecules   Reactants



                                                                                     Amount of
                                                                                       energy
                                                                                      OUTPUT

                                                                          Products
5.4 ATP shuttles chemical energy within
   the cell
   In cellular respiration, some energy is stored in
    ATP molecules
   ATP powers nearly all forms of cellular work
   ATP molecules are the key to energy coupling
Hydrolysis cleaves a high-energy
phosphate bond!
      When the bond joining a phosphate group to the
       rest of an ATP molecule is broken by hydrolysis,
       the reaction supplies energy for cellular work
         Allthree phosphate groups are negatively charged
         These like charges are crowded together
         This mutual repulsion contributes to the PE stored in
          ATP (much like a compressed spring)
                Adenine
Phosphate
 groups
                               Hydrolysis
                                                                    Energy
                   Ribose
      Adenosine triphosphate
                                            Adenosine diphosphate
                                                    (ADP)
Pi is like a ball on a spring…

    The phosphate bonds of an ATP are like
     coiled springs, barely held together by
     strings
    When the string breaks, the spring
     uncoils and releases all the energy it had
     stored
    The released energy pushes the ball
     towoards a wall, causing it to stick to the
     wall
        This is equivalent to the Pi being attached
         to a target protein when the phosphate
         bond is broken/unravelled
ATP powers cellular work
by phosphorylation…
     How ATP powers cellular work
     The transfer of a phosphate group to a molecule is
      called phosphorylation.
     Most cellular work depends on ATP energizing
      other molecules by phosphorylating them
                   Potential energy of molecules




Phosphorylation:                                   Reactants   Products
   Endergonic



ATP -> ADP:                                         Protein               Work
  Exergonic
How does ATP transfer energy from exergonic to
endergonic processes in the cell?
 By phosphorylation: the addition of phosphate groups.
 Energy released in exergonic processes (like glucose
  breakdown during cellular respiration) is used to
  phosphorylate ADP to form ATP
   This is an endergonic (energy-storing) reaction
 ATP transfers energy to endergonic processes by
  phosphorylating other molecules
   Working cell may consume and regenerate 10 million
   ATP molecules/second!!!
The ATP Cycle…




                             Dehydration synthesis




                                                             Hydrolysis
               Energy from                                                Energy for
               exergonic                                                  endergonic
               reactions                                                  reactions



 Figure 5.4C

                                                        The ATP cycle
HOW ENZYMES WORK
5.5 Enzymes speed up the cell’s chemical
    reactions by lowering energy barriers
   For a chemical reaction to begin, reactants must absorb
    some energy
   This energy is called the energy of activation (EA) or
    activation energy
   This represents the energy barrier that prevents molecules
    from breaking down spontaneously
   So how can specific reactions required by a cell get over
    the energy barrier?
   One way might be to add heat
       But this would speed up ALL reactions and too much heat
        would even denature proteins and so kill the cell
Solution: Catalyst…                                                EA
                                                                   withou
    A protein molecule that                             EA        t
                                                         with      enzym
     functions as a biological            Reactants      enzym     e
                                                                   Net
     catalyst is called an                               e         change
                                                                   in
     enzyme & can decrease                                         energy
                                                        Products
     the energy barrier
       EA




                                 Enzyme
       barrier
                                                       Increases
                                                        rate of
                                                        reaction
     Reactants                                          without itself
                                                        being
                                                        transformed
 1               Products   2
Recap…
    ATP breaks down easily and could spontaneously
     decompose if not blocked by an “energy barrier”
    The energy barrier is the amount of energy that
     reactants must absorb to start a chemical reaction
    The amount of energy required is called the Energy
     of Activation/Activation Energy (EA)
    In ATP, EA is the amount of energy required to break
     the bond between the second and third phosphate
     group
    Enzymes can lower activation energy by holding
     reactant molecules in specific positions.
        As the substrates bind to the enzyme's active site,
         they are held in a position that facilitates the
         reaction. This takes less activation energy than the
         unaided reaction.
5.6 A specific enzyme catalyzes
   each cellular reaction
   Enzymes are selective
     This selectivity determines which chemical reactions
      occur in a cell
     An enzyme protein has a unique 3-d shape which
      determines which chemical reactions it catalyzes
     A single enzyme molecule may act on thousands
      (or even millions) of substrate molecules per
      second!
How enzymes work…                        Enzyme
                                         (sucrase)
                                                          Active
                                                           site          Substrate
                                                                         (sucrose)



                     Glucose       Fructose                 1
                         4
                                                     Enzyme available
                    Products are                     with empty active
                      released                       site




                                     3

                             Substrate is                                     2
                             converted to
                              products                                     Substrate
                                                                            binds to
                                                                         enzyme with
                                                                          induced fit
                                               Hydrolysis of
                                               sucrase substrate
    The enzyme
     is unchanged and can repeat the process
                    Induced Fit Analogy…
   The protein enzyme has an induced fit because the binding
    of the substrate changes the electrical attractions and
    weak bonds (van der waals, hydrogen, etc.) between the
    two molecules and between the atoms of the protein itself
   An analogy is as if the protein is a structure made out of
    magnets and the substrate is another magnet that comes
    along…
   As it comes along, it exerts various attractive (or repulsive)
    forces which distort the protein structure; when the
    substrate magnet sticks to the protein magnet structure, it
    changes the protein magnet structure and distorts it; etc.
5.7 The cellular environment
   affects enzyme activity
   Enzyme activity (which depends on its shape & structure) is
    influenced by
       temperature
          affects molecular motion
          enzyme’s optimal temperature produces highest rate of contact
           between reactant molecules and the enzymes active site
          higher temperatures denature enzyme, changing its 3-d shape

       salt concentration
            salt ions interfere with some of the chemical bonds that maintain
             protein structure
       pH
            Extra hydrogen ions (at low pH) also interfere with some of the
             chemical bonds that maintain protein structure
   Some enzymes require nonprotein co-factors
   Some cofactors are organic molecules called co-enzymes
5.8 Enzyme inhibitors block enzyme
   action
   Inhibitors interfere with
    enzymes
       If inhibitor attaches to
        enzyme by covalent bonds,                Substrate                  Active
                                                                            site
        inhibition is irreversible; if
        weak bonds (e.g., hydrogen                Enzyme
        bonds), then it’s reversible
   A competitive inhibitor                            NORMAL BINDING OF SUBSTRATE

    takes the place of a substrate
                                         Competitive               Noncompetitive
    in the active site                   inhibitor                 inhibitor

   A noncompetitive inhibitor
    alters an enzyme’s function
    by changing its shape                                    ENZYME INHIBITION
                                                                                     Figure 5.8
5.9 Connection: Some pesticides and
   antibiotics inhibit enzymes
   Certain pesticides are toxic to insects because they inhibit key enzymes
    in the nervous system
      Cyanide inhibits an enzyme involved in the production of ATP during
        cellular respiration
      Nerve gases (like Sarin) bind covalently to an amino acid in the
        active site of acetylcholinesterase (vital to transmission of nerve
        impulses; inhibition leads to paralysis and death)
      Malathion (pesticide) irreversibly inhibits acetylcholinesterase, too
   Many antibiotics inhibit enzymes that are essential to the survival of
    disease-causing bacteria
      E.g., penicillin inhibits an enzyme that bacteria use in making cell
        walls
   Many antibiotics have different effects and can be broad- or narrow-
    spectrum:
    http://helios.bto.ed.ac.uk/bto/microbes/penicill.htm#Other%20antibiotics
   Analgesics, like Ibuprofen and aspirin, inhibit enzymes involved in
    inducing pain (Substance P)
   Protease inhibitors (HIV drug) target a key viral enzyme
Membranes are fluid mosaics
MEMBRANE STRUCTURE AND FUNCTION
5.10 Membranes organize the chemical activities of
     cells
   Membranes organize the chemical reactions making up
    metabolism
       Provide the structural basis or metabolic order
                        
                        




                  Cytoplasm

                                                    Figure 5.10
Membranes are
selectively permeable…

   Membranes control the flow of substances into and
    out of a cell
   This is what makes them selectively permeable
   Membranes can also hold teams of enzymes that
    function in metabolism
5.11 Membrane phospholipids form a bilayer
                                 Head
   Phospholipids are
    the main structural
    components of
    membranes
   They each have a
    hydrophilic head
    and two
    hydrophobic tails                            Symbol

    (amphipathic)
   In water,
    phospholipids form
                                         Tails
    a stable bilayer      Figure 5.11A
In water…
    In water, phospholipids form a stable bilayer
      The      heads face outward and the tails face inward


                                        Water
        Hydrophilic
        heads


       Hydrophobic
       tails




                                        Water


        Figure 5.11B
5.12 The membrane is a fluid mosaic of
     phospholipids and proteins

   Phospholipid molecules form a flexible bilayer
   Cholesterol and protein molecules are embedded in
    it
   Carbohydrates (on glycoproteins and glycolipids)
    and proteins act as cell identification tags
   ID tags allow cells in an embryo to sort themselves
    into tissues and organs
   ID tags also allow immune system cells to recognize
    and reject foreign cells (e.g., infectious bacteria, etc.)
Animal cells…
     The plasma membrane of an animal cell
                 Glycoprotein       Carbohydrate
                                    (of
                                    glycoprotein)
 Fibers of the
 extracellular
 matrix
                                                            Glycolipid




                      Phospholipid
                         Cholesterol
          Microfilaments        Proteins
          of the
          cytoskeleton                          CYTOPLASM


 Figure 5.12
5.13 Proteins make the membrane a
    mosaic of function
   Some membrane proteins form cell junctions
   Some attach the membrane to the cytoskeleton and external fibers
   Others transport substances across the membrane
      Although small, nonpolar molecules (like O2 and CO2) pass freely
         through the membrane, other essential molecules (like glucose and
         water) need assistance from proteins to enter or leave the cell
   Still others act as ID tags
   Many membrane proteins are enzymes
      And may function in catalytic teams for molecular assembly lines




                                                       Transport
Many membrane
proteins are enzymes
    Some proteins function as receptors for chemical
     messages from other cells
        The binding of a messenger to a receptor may trigger signal
         transduction
             A chain reaction involving other proteins which relay the
              message to a molecule that performs a specific activity inside
              the cell
                                                               Messenger molecule

                                                                     Receptor




                                                         Activated
                                                         molecule

                         Figure 5.13   Enzyme activity        Signal transduction
5.14 Passive transport is diffusion across
    a membrane
   In passive transport,
    substances diffuse through
                                             Molecule
    membranes without work by the            of dye        Membrane   EQUILIBRIUM
    cell
   They spread from areas of high
    concentration to areas of lower
    concentration
   NET movement as the
    molecules move down their
    respective concentration
    gradients
   At equlibrium, molecules                                          EQUILIBRIUM
    continue to move back and foth,
    but there is no significant NET
    change in concentration on
    either side of the membrane
   Small, non-polar molecules
    diffuse easily across the
    phopholipid bilayer (like O2 into
    RBC and CO2 out of RBC)             Figure 5.14A & B
5.16 Osmosis is the passive transport of water
                    Solute concentration lower                    Higher concentration of solute
                       than that of cell
                                                        Hypotonic      Hypertonic
    In osmosis, water travels from an area             solution       solution
     of lower solute concentration to an area
     of higher solute concentration
    Water (the solvent) can cross this
     membrane but the solute cannot
    Water crosses the membrane until the
     solute concentrations (molecules of
     solute/mL of solution) are equal on both
     sides
                                                Selectively                 Solute
    Clusters of polar water molecules form     permeable                   molecule
     weak bonds with solute molecules, so       membrane
     that fewer water molecules are free to
     diffuse across the membrane                   HYPOTONIC SOLUTION         HYPERTONIC SOLUTION
    Less concentrated solution on the left        Water
     (with fewer solute molecules) has more        molecule
     free water molecules
    Net movement of water down its
     concentration gradient
    Direction of osmosis determined by the
     difference in TOTAL solute
     concentration, not by the nature of the
     solutes                                                  Selectively
                                                              permeable         Solute molecule with
                                                              membrane       cluster of water molecules

                                                                NET FLOW OF WATER                  Figure 5.15
5.17 Water balance between cells and their
     surroundings is crucial to organisms
   Osmosis causes cells to shrink in a hypertonic solution and
    swell in a hypotonic solution      solution with solute concentration
       The control of water balance         higher than that of the cell
        (osmoregulation) is essential for organisms


                               ISOTONIC      HYPOTONIC       HYPERTONIC
                               SOLUTION       SOLUTION        SOLUTION




                      ANIMAL
                        CELL

                               (1) Normal    (2) Lysing      (3) Shriveled
                                                           Plasma
                                                          membrane

                      PLANT
                       CELL


        Figure 5.16            (4) Flaccid   (5) Turgid      (6) Shriveled
5.15 Transport proteins facilitate diffusion
    across membranes
   Small nonpolar molecules diffuse freely through the phospholipid bilayer
        Many other kinds of molecules pass through selective protein pores by
         facilitated diffusion because of their size, polarity, or charge
        Here, proteins make it possible for a substance to move down its concentration
         gradient
        Facilitated diffusion is a type of passive transport because it does not require
         energy
        The driving force is the concentration gradient
        Several different kinds of transport proteins:
             Channel/pore/tunnel
             Another type of protein binds its passenger, changes shape, and releases its
              passenger on the other side
             Rate of facilitated diffusion depends on the number of transport protein molecules
              for a particular substance present in the membrane                     Solute
                                                                                   molecule




                                                               Transport
                                                               protein
5.18 Cells expend energy for active
    transport
   Transport proteins can move solutes across a
    membrane against a concentration gradient
   This is called active transport
   Active transport requires ATP
                              FLUID                                             Phosphorylated

Active Transport…             OUTSIDE
                              CELL
                                          Transport
                                             protein
                                                                               transport protein




Phosphorylation of protein:
   Endergonic
ATP -> ADP: Exergonic
                                           First
                                           solute

                              1   First solute,        2   ATP transfers   3   Protein releases
                                  inside cell,             phosphate to        solute outside
                                  binds to protein         protein             cell
    Active
                              Second
     transport in             solute

     two solutes
     across a
     membrane

Because of change of shape    4   Second solute        5   Phosphate       6   Protein releases
                                  binds to protein         detaches from       second solute
   (i.e., bond strengths)
                                                           protein             into cell
5.19 Exocytosis and endocytosis
    transport large molecules
   To move large molecules or particles through a membrane
     a vesicle may fuse with the membrane and expel its contents
      (exocytosis: exo (outside) and kytos (cell))
     Tear glands use exocytosis to export a salty solution
      containing proteins
     Pancreatic cells manugfacture the hormone insulin and
      secrete it into the bloodstream by exocytosis

                    FLUID OUTSIDE CELL




                    CYTOPLASM
     Figure 5.19A
Endocytosis!
   Or the membrane may fold inward, trapping
    material from the outside (endocytosis)
     Inphagocytes, invagination produces a vacuole,
      which usually fuses with one or more lysosomes
      containing hydrolytic enzymes. Materials in the
      vacuole are broken down by these enzymes and
      degraded.
Three kinds…

   Three kinds of endocytosis
Pseudopod of   Food being                        Plasma             Material bound to
amoeba         ingested                         membrane            receptor proteins




                                                                      PIT
                                                  Cytoplasm




―Cellular Eating‖           ―Cellular                      Receptor-mediated
                                                             endocytosis is
                              Drinking‖: not                 highly specific and
                              specific: takes                picks up particular
                              in any and all                 molecules –
                                                             TASTE!
                              solutes
5.20 Connection: Faulty membranes can
     overload the blood with cholesterol
    Cholesterol is a component of membranes as well as starting material
     for other steroids, like the sex steroids (estrogens, androgens, and
     progesterones)
    LDLs can deposit cholesterol in the lining of blood vessels, causing the
     lining to bulge inward and reduce blood flow
    Harmful levels of cholesterol can accumulate in the blood if membranes
     lack cholesterol receptors
                               Phospholipid
    LDL PARTICLE
                               outer layer


                                               Receptor protein




       Protein

                 Cholesterol


    Plasma membrane                                     Vesicle
                               CYTOPLASM

Figure 5.20
5.21 Chloroplasts and mitochondria make
     energy available for cellular work
   Enzymes and membranes are central to the processes that
    make energy available to the cell
   Chloroplasts carry out photosynthesis, using solar energy to
    produce glucose and oxygen from carbon dioxide and water
    (Calvin Cycle)
   Mitochondria consume oxygen in cellular respiration, using
    the energy stored in glucose to make ATP
     Glycolysis -> Krebs (Citric Acid) Cycle -> Oxidative
      Phosphorylation
     Glycolysis ->Lactic Acid Fermentation
     Glycolysis ->Alcohol Fermentation
The Solar Furnace!
                                           Sunlight energy




    Nearly all the chemical                 Chloroplasts,
                                        site of photosynthesis
     energy that organisms        CO2                            Glucose
                                   +                                +
     use comes ultimately from    H2O       Mitochondria            O2
                                           sites of cellular
     sunlight                                 respiration

    Chemicals recycle among
     living organisms and their
     environment
    In each transfer, some
                                           (for cellular work)
     energy is lost to the
     disorganizing energy of
     heat (entropy increases!)                Heat energy

								
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