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AP Biology Chapter 6: An Introduction to Energy and Enzymes

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Title: AP Biology Chapter 6: An Introduction to Energy and Enzymes


1
AP Biology Chapter 6 An Introduction to Energy
and Enzymes
2
Metabolism
  • Totality of an organisms reactions
  • (from Greek metabole, to change)
  • An emergent property from interactions between
    chemicals within the environment of the cell
  • Metabolism manages the material and energy
    resources of the cell

3
Bioenergetics
  • The study of how organisms manage their energy
    resources
  • Energy the capacity to do workability to
    rearrange a collection of matter
  • Kinetic energy of motion
  • Potential stored energy
  • Chemical energy form of potential energy stored
    in molecules as the result of the arrangement of
    atoms

4
Thermodynamics
  • First Law of Thermodynamics energy is
    constantenergy can be transferred and
    transformed, but it cannot be created nor
    destroyed
  • Second Law of Thermodynamics every energy
    transfer makes the universe more disordered or
    random, a.k.a. increases the entropy (measure of
    disorder)
  • .oh dear. Everything reaction a cell does makes
    it more chaotic? Thats not good better do
    something about that

5
Entropy
  • In most energy transformations, some of the
    energy stored is converted to heat (the most
    random - entropic - form of energy)
  • Organisms are open systems and exchange energy
    and materials with the surroundings
  • Take in and release organized and disorganized
    forms of matter and energy

6
Energy Loss
  • Depletion of energy in organisms is due to the
    loss as waste, and heat.

7
Entropy
  • Living organisms preserve their internal order
    by taking from their surroundings free energy, in
    the form of nutrients or sunlight, and returning
    to their surroundings an equal amount of energy
    as heat and entropy. - Albert Lehninger
  • What does it mean?

8
Maintaining Order
  • Cells maintain their orderliness by taking in
    orderly things like light photons or polymers,
    and discharging disorderly things like heat.
  • Life makes its environment more disorderly, in
    order to be orderly.

9
Free Energy
  • Free energy The portion of a systems energy
    that is available to perform work (when
    temperature is uniform throughout the system)
  • Not all of the energy in a system is free, i.e.
    available to be used.
  • G H T S
  • G Free Energy H Total Energy (of the
    system) T Temperature (in Kelvin) S Entropy

10
Discussion
  • ?G ?H - T ?S
  • ?G change in free energy, ?H change in total
    energy, T temperature, ?S change in entropy
  • Which part of the equation potential energy?
    Kinetic energy?
  • What happens to the amount of free energy
    available if we
  • Increase the total amount of energy in the
    system?
  • Increase the temperature of the system?
  • Increase the entropy of the system?
  • So, how can organisms use free energy to reduce
    their entropy?

11
Free Energy and Metabolism
  • Exergonic Reactions (energy outward) proceeds
    with a net release of free energy. ?G is
    negative. Reactions are spontaneous.
  • Endergonic Reactions (energy inward) absorbs
    free energy from its surroundings, stores free
    energy in molecules. ?G is positive. Reactions
    are nonspontaneous. Require energy to drive the
    reaction.

12
Discussion
Which one depicts an endergonic vs. exergonic
reaction?
13
Metabolism
  • Two types of reactions
  • Catabolic Pathways break down complex molecules
    into simpler ones (e.g. cellular respiration)
  • downhill reactions
  • Anabolic Pathways build complex molecules from
    simpler ones (e.g. synthesis of proteins from
    amino acids)
  • uphill reactions
  • These reactions are coupled together in cells,
    more on that later

(Cut)
(Add)
14
Discussion
  • Would catabolic reactions tend to be exergonic or
    endergonic? Why?
  • What about anabolic reactions? Why?

15
Catalysts
  • Catalyst chemical agent that changes the rate
    of a reaction without being converted or consumed
    by the reaction

16
Catalysts
  • Enzymes are biological catalysts, most often made
    of protein (there are a few ribozymes made of
    RNA)
  • Without enzymes, most bio reactions (even
    spontaneous, exothermic reactions) proceed VERY
    slowly.
  • Example Leave a cracker out on the counter. How
    long will it take for all the starch to turn to
    sugar?

17
Activation Energy Barrier
  • Chemical reactions involve forming and breaking
    of bonds. Existing bonds in reactants must be
    broken and new bonds of products formed, even in
    anabolism.
  • Breaking bonds requires an input of energy
  • The initial investment of energy for starting a
    reactionenergy required to break bonds is
    called the activation energy or free energy of
    activation (EA)

18
Enzymes and Activation Energy
  • Enzymes speed up reactions by lowering the
    activation energy, i.e. the EA barrier, so the
    transition state is within reach at moderate
    temperatures.
  • They do not change the ?G of the reaction
  • Analogy They dont help the high jumper up, they
    lower the bar

19
Enzymes are Substrate Specific
  • The reactant a specific enzyme works on is called
    a substrate
  • Enzymes bind to their substrate(s), allowing the
    catalytic action of the enzyme to create the
    products
  • Substrate Enzyme Product
  • Enzymes can distinguish their substrate by shape.
    The substrate must fit into the active site of
    the enzyme, a groove or pocket in the protein
  • http//highered.mcgraw-hill.com/sites/0072495855/s
    tudent_view0/chapter2/animation__how_enzymes_work.
    html

20
Enzyme-Substrate Cycle
21
Induced Fit
  • Active sites are not rigid like a lock-and-key
    but instead change shape slightly to fit snugly
    around the substratelike a handshake
  • Induced fit brings chemicals together into
    positions that enhance their ability to catalyze

http//highered.mcgraw-hill.com/sites/0072507470/s
tudent_view0/chapter25/animation__enzyme_action_an
d_the_hydrolysis_of_sucrose.html
22
Discussion
  • When making jello with fruit in it, you must be
    careful as it will not gel if fresh pineapple
    is used, but it will gel with canned pineapple.
    Fresh pineapple contains the enzyme bromelain
    which prevents proteins from arranging into
    tertiary and quaternary structures.
  • Explain!

23
Discussion
  • Papain is a hydrolytic enzyme that is present in
    papaya. It is sold as a component in powdered
    meat tenderizer available in most supermarkets.
  • How might such powders make meat more tender?

24
Environmental Effects on Enzymes
  • Enzymes have optimal conditions where they work
    best. These tend to match the environment
    (think evolution why would this be?)
  • http//www.kscience.co.uk/animations/model.swf

25
Environmental Effects on Enzymes
  • Temperature thermal agitation can disrupt
    polypeptide conformation. Optimal temp allows
    greatest number of molecular collisions without
    denaturing.
  • pH H concentration can also disrupt
    conformation.

26
Denaturation
  • Denaturation The loss of a proteins secondary
    (tertiary, quaternary) structure by the
    application of an external stress
  • Strong acids, strong bases, and high temperatures
    cause denaturation
  • Warped protein shape -gt Substrate cannot bind to
    active site -gt Function reduced or eliminated

http//highered.mcgraw-hill.com/sites/0072507470/s
tudent_view0/chapter2/animation__protein_denaturat
ion.html
27
Discussion
  • Pepsin is a digestive enzyme that functions in
    the stomach to break down proteins, while
    salivary amylase is an enzyme that functions in
    the mouth to break down carbohydrates. Using the
    following information, discuss the answers to
    these questions

28
Discussion
  • What is the optimal pH for pepsin? How does this
    relate to its environment?
  • What is the optimal pH for amylase? How does
    this relate to its environment?
  • (Note amylase breaks down starch starting in the
    mouth, continuing with the food bolus through the
    esophagus, stomach, and small intestine.)

29
Discussion
  • Would you expect carbohydrate breakdown to be
    ongoing in the stomach? Why/why not?
  • Would you expect pepsin to work in the intestine?
    Why/why not?

30
Discussion
  • When fruits veggies are frozen, the water in
    the vacuoles tends to expand and cause it to
    burst. This releases a number of hydrolytic
    enzymes and can cause the fruit to become mushy.
  • Fruits veggies are often blanched (placed in
    boiling water for a short time) before being
    frozen to prevent this.
  • Why does blanching help at all?

31
Discussion
  • When slicing fruit, an enzyme called catecholase
    causes a reaction between catechol and oxygen.
    The products formed by this reaction are
    benzoquinone and water since benzoquinone has a
    brown color, this results in the fruit browning.
  • Browning can be prevented by adding lemon juice
    to cut fruit. Why?

32
Cofactors
  • Many enzymes require non-protein helpers for
    catalytic activity, called cofactors, which are
    bound to the active site
  • They can be permanent or bind reversibly with the
    substrate
  • Cofactors are inorganic, such as iron, zinc, or
    copper
  • Coenzymes are organic cofactors

http//highered.mcgraw-hill.com/sites/0070960526/s
tudent_view0/chapter6/animations.html
33
Allosteric vs. Active Sites
  • Other molecules enable (or disable!) enzymes by
    binding not to the active site, but to the
  • Many enzymes have an allosteric site, a place
    where something can bond that is not the active
    site.
  • When something bonds to the allosteric site, it
    changes the enzymes shape.

Allosteric site
34
Enzyme Inhibitors
  • Inhibitors inhibit (reduce or turn off) the
    action of an enzyme by covalently bonding to the
    enzyme. Usually irreversibly.
  • Competitive Inhibition inhibitors bind with the
    active or allosteric site, competing with the
    substrate for access to the active site
  • Block access to active site
  • Can be overcome by increasing the concentration
    of the substrate

35
  • Competitive Allosteric site
  • Competitive Active site

36
Enzyme Inhibitors
  • Noncompetitive Inhibition bind with the
    allosteric site, changing the enzymes
    conformation and impeding the substrate binding

37
Enzyme Regulation
  • Inhibitors can be reversible or nonreversible.
  • There can also be allosteric activators (or
    allosteric effectors) which bind to the
    allosteric site and change enzyme conformation to
    expose or properly shape the active site
  • Activators enable enzyme activity. Inhibitors
    decrease enzyme activity.

38
Allosteric Regulation
  • Reversible noncompetitive inhibitors are in
    charge of most of the control of metabolism

39
Discussion
  • Like many poisons, as well as many antibiotics,
    the nerve gas DFP works by binding to the active
    site of an enzyme. In the case of DFP, it binds
    to the active site acetylcholine esterase(AChE).
  • AChE functions to break down the neurotransmitter
    acetylcholine, recycling its subcomponents into
    neurons for re-use. In essence, this hydrolytic
    function allows the neuron to fire again in the
    future.
  • A person affected by DFP experiences decreased
    neuronal function. What kind of molecule is DFP?

40
Feedback Inhibition
  • Products of a pathway can act as the allosteric
    inhibitors and switch off an enzyme in the
    catabolic process
  • Prevents excess product manufacture
  • Example ATP is the allosteric inhibitor for the
    ATP-generating catabolic pathway

http//highered.mcgraw-hill.com/sites/0072943696/s
tudent_view0/chapter2/animation__feedback_inhibiti
on_of_biochemical_pathways.html
41
Cooperativity
  • Substrate molecules can stimulate an enzyme.
    Binding a substrate can induce the enzyme to
    change into a shape which is more favorable for
    binding more substrates at other active sites
  • Amplifies the response of enzymes to substrates

42
Localization of Enzymes
  • Organisms are more efficient because they can
    keep all the enzymes required for a pathway in
    one place, organ or organelle.
  • Metabolic pathways can be assembled together into
    a multienzyme complex to keep everything
    organized and efficient

43
Discussion
  • Work together with a partner to invent an enzyme.
  • Determine what species its in
  • Determine its optimum environment
  • Determine what reaction it catalyzes, substrates
    and products
  • Determine how its regulated. How does the
    organism ensure that its only carrying out the
    reaction when needed, and that it does so
    efficiently?
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