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

AP Biology Chapter 6:
An Introduction to Energy and
Enzymes
Metabolism
 Totality of an organism’s
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
BIOENERGETICS
The study of how organisms manage their
energy resources
 Energy: the capacity to do work—ability 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
THERMODYNAMICS


First Law of Thermodynamics:
energy is constant—energy 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?
That’s not good… better do
something about that…
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
ENERGY LOSS

Depletion of energy in organisms is due
to the loss as waste, and heat.
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?
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.
FREE ENERGY
Free
energy: The portion of a system’s
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
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?
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.

DISCUSSION
Which one depicts an endergonic vs. exergonic reaction?
METABOLISM

Two types of reactions:
(“Cut”) 

(“Add”)

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
DISCUSSION


Would catabolic reactions tend to be
exergonic or endergonic? Why?
What about anabolic reactions? Why?
Catalysts
 Catalyst = chemical agent that changes the
rate of a reaction without being converted
or consumed by the reaction
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?
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
reaction—energy required
to break bonds– is called
the activation energy or
free energy of activation
(EA)
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 ΔG of the reaction
Analogy: They don’t help the high jumper up,
they lower the bar
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/student_view0/chapter2/animation__how_enzymes_work.html
Enzyme-Substrate Cycle
Induced Fit
 Active sites are not rigid like a “lock-and-key”
but instead change shape slightly to fit snugly
around the substrate—like a handshake
 Induced fit brings chemicals together into
positions that enhance their ability to
catalyze
http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.html
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!
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?
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
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.
Denaturation
 Denaturation = The loss of a protein’s
secondary (tertiary, quaternary) structure by
the application of an external stress
Strong acids, strong bases, and high
temperatures cause denaturation
Warped protein shape -> Substrate cannot bind
to active site -> Function reduced or eliminated
http://highered.mcgrawhill.com/sites/0072507470/student_view0/chapt
er2/animation__protein_denaturation.html
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…
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.)
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?
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?
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?
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.mcgrawhill.com/sites/0070960526/student_view0/chapter
6/animations.html
Allosteric vs. Active Sites
• Other molecules enable (or disable!)
enzymes by binding not to the active site,
but to the:
Allosteric site
• 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 enzyme’s shape.
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
• Competitive –
Allosteric site
• Competitive –
Active site
Enzyme Inhibitors
 Noncompetitive Inhibition:
bind with the allosteric site,
changing the enzyme’s
conformation and impeding
the substrate binding
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.
Allosteric Regulation
 Reversible noncompetitive inhibitors are in
charge of most of the control of metabolism
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?
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
http://highered.mcgrawpathway
hill.com/sites/0072943696/student_view0/chapter2/animation__feedba
ck_inhibition_of_biochemical_pathways.html
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
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
Discussion
 Work together with a partner to invent an
enzyme.
Determine what species it’s in
Determine its optimum environment
Determine what reaction it catalyzes, substrates
and products
Determine how it’s regulated. How does the
organism ensure that it’s only carrying out the
reaction when needed, and that it does so
efficiently?