Metabolism

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Metabolism

• The sum total of all the chemical conversions in
  a cell.
• The chemical breakdown and buildup of substances
  requires energy transformations mediated by
  enzymes.

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Energy

• Definitions of energy
• Capacity to do work (physicists definition)
• Capacity for change (biochemists definition)
• All living things obtain energy from the
  environment.
• Energy can be transformed from one type to
  another.
• Living cells carry out energy transformations.

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Energy

• Several forms exist
• Chemical energy
• Light energy
• Mechanical energy
• All energy is either
• Kinetic energy- energy of movement
• Alters the state or motion of matter
• Potential energy- stored energy
• Can be stored in chemical bonds, as a
  concentration gradient, as electric potential

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Energy Conversions and Work
Kinetic energy of river is converted to potential
energy by a dam.
Generator converts kinetic energy of released
water to electric energy.
In cells, energy can be stored in chemical bonds.
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Metabolism

• 2 types of activities
• Anabolic reactions
• Link simple molecules together to make complex
  ones
• Energy storing process
• Reactions consume energy
• Catabolic reactions
• Break down complex molecules into simpler ones
• Some reactions provide energy for anabolic
  reactions
• Reactions release energy
• Anabolic and catabolic reactions are often linked
  to do biological work.

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Figure 6.2 The Laws of Thermodynamics
Energy is neither created nor destroyed.
Amount of free energy available to do work is
always less than the amount of original energy)
Free energy decreases and unusable energy
increases. (entropy-measure of the disorder of a
system
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• Total energy (H) usable energy (G) unusable
  energy (S)
• Usable energy to do work is called free energy
  (G)
• In a chemical reaction if ?G is negative- free
  energy is released
• If ?G is positive- free energy is required

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• The amount of energy taken up or released is
  directly related to the tendency of the reaction
  to run to completion (the point at which all
  reactants are converted to products.)

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Chemical reactions release or take up energy

• A spontaneous reaction will go more than halfway
  to completion without input of energy.
• Spontaneous reactions are called exergonic.
• Release energy
• Non-spontaneous reactions are called endergonic.
• Consume energy

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?G is negative
?G is positive
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ATP Transferring Energy in Cells

• All living cells use ATP for capture, transfer
  and storage of energy.
• Energy currency
• Energy released by reactions is captured in ATP
  ATP can then release energy to drive other
  reactions.

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• Why ATP?
• Releases a relatively large amount of energy when
  hydrolyzed
• Free energy of the P-O bond between phosphate
  groups is much higher than the energy of the H-O
  bond after hydrolysis
• It takes energy to get phosphate groups near
  enough together to link them to make ATP from
  ADP.
• Can phosphorylate many different molecules

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ATP hydrolysis releases energy

• Structure of ATP
• Adenine bonded to ribose, carbon 5 of ribose has
  3 phosphate groups attached.
• ATP can hydrolyze to form ADP plus an inorganic
  phosphate ion (Pi)
• ATP H20 ----? ADP Pi

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Figure 6.5 ATP (Part 1)
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Formation of ATP

• Making ATP from ADP involves overcoming repulsive
  negative charges on the phosphates to be joined.
• The energy to do this is stored in glucose or
  other fuel molecules.
• ADP Pi free energy----? ATP H2O
• Each cell requires millions of molecules of ATP
  per second to drive its biological machinery.

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Synthesis of glutamine from glutamate and NH4 is
endergonic and must be coupled to exergonic
hydrolysis of ATP.
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Enzymes Biological Catalysts

• Living cells use biological catalysts (enzymes)
  to increase and control rates of chemical
  reactions.
• A catalyst speeds up a reaction without being
  permanently altered.
• A chemical reaction will occur spontaneously if
  it releases free energy, but it may occur to
  slowly to be effective in living cells.

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• Activation energy
• Energy which must be invested to initiate a
  reaction.
• This energy is absorbed by reactants to break
  chemical bonds.
• All reactions have activation energy
  requirements.

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Activation energy is small compared to the
overall change in free energy.
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Over the Energy Barrier
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Enzymes

• Heating the reactants may increase their kinetic
  energy and thus lower the activation energy.
• Not efficient or specific, would speed up all
  reactions
• Could denature proteins
• Enzymes can lower required energy of activation.
• but they do not initiate reactions that could not
  eventually take place on their own.

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Enzyme and Substrate
E S ? ES ? E P
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How do enzymes speed up reactions?

• At the active site, enzymes and substrates
  interact by breaking old bonds and forming new
  ones.
• Enzyme may change chemically, but is restored to
  its original form after reaction is catalyzed.

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Enzymes Lower the Energy Barrier
?G is not affected by Ea
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How do enzymes lower the activation energy?

• 1. Orienting substrates
• Two substrates bound to an enzyme are more likely
  to be oriented so that a reaction can occur.
• 2. Inducing strain in substrates
• Substrate enters active site of enzyme, and the
  substrate shape is changed. Stretching of bonds
  makes them more reactive.
• 3. Temporarily adding chemical groups to
  substrates
• Enzymes may transfer hydrogen ions, form covalent
  bonds with substrate, may lose or gain electrons

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Orientation
Substrates are oriented so that they can react.
Physical strain
Enzyme strains the substrate
Chemical change
Enzyme adds charges to the substrate
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Enzyme structure and size

• The active site of an enzyme is usually small.
• 6-12 amino acids
• The whole enzyme is usually composed of hundreds
  of amino acids.
• The active site is the site where the specific
  substrate binds.
• Induced fit-
• Many enzymes change their structure when they
  bind their substrates
• Induced fit brings reactive side chains together
  from the active site into alignment with the
  substrate.

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Glucose ATP ------? glucose-6-phosphate ADP
hexokinase
Hexokinase changes shape when substrate binds.
2nd substrate is ATP
Enzyme-hexokinase
Empty active site
Water is excluded from active site.
Shape changes result in an induced fit, improving
the catalytic activity of the enzyme.
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Non-protein molecules associated with enzymes

• Some enzymes require the presence of other
  non-protein molecules in order to function
• Cofactors
• Inorganic ions copper ions, zinc ions and iron
  ions.
• Bind to the enzyme and are essential to function
  of some enzymes
• Coenzymes
• Small carbon-containing molecules which
  temporarily bind to enzymes
• Must collide with enzyme and bind to active site
• Prosthetic groups
• Molecular groupings permanently bound to enzymes

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Metabolic pathways are regulated by enzymes

• Burning of glucose would be an inefficient way to
  extract energy from its bonds
• Step-by-step pathways catalyzed by enzymes allow
  the energy to be extracted in a form that is
  usable by cells.

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Metabolism is organized into pathways

• A-----?B------?C-----?D
• Each step is catalyzed by enzymes.
• One enzyme converts A to B a second enzyme
  converts B to C, and so forth.
• Pathways can be anabolic or catabolic.

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Regulation of enzyme activity

• Enzyme activity can be inhibited by natural and
  artificial inhibitors.
• Natural-regulate metabolism
• Artificial
• Treat disease
• Kill pests
• Study how enzymes work
• DIPF inhibits an enzyme essential for propagation
  of nerve impulses
• DIPF is a nerve gas related to Sarin

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• Irreversible inhibitors
• Occurs when inhibitor destroys the enzymes
  ability to interact with substrate
• Aspirin permanently inactivates cyclooxygenase
• Reversible inhibitors- more likely to occur in
  nature
• Reversible inhibitors involved in regulation of
  metabolic pathways.

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• Competitive inhibitors
• Bind to active site of enzyme
• Compete with the natural substrate for the active
  site
• Enzymes function is disabled as long as the
  protein remains bound.
• Reversible

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Figure 6.18 Reversible Inhibition (Part 2)
Inhibitor of enzyme succinate dehydrogenase
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• Non-competitive inhibitors
• Inhibitor binds at a site distinct from the
  active site
• Binding causes as conformational change in the
  active site so that substrate cannot bind (or
  cannot bind as well).
• Reversible

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Inhibitor binding may change shape of enzyme so
that substrate no longer fits.
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Figure 6.18 Reversible Inhibition (Part 4)
Isoleucine binds to enzyme away from the active
site, but enzyme is altered so that it cannot
interact with substrate.
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Allosteric enzymes

• Allo- different, stery- shape
• Enzymes may exist in more than one possible
  shape.
• Allosteric enzymes
• 1. Binding of inhibitor induces enzyme to change
  shape, or, more commonly,
• 2. Enzymes already exist in cell in different
  shapes.
• Active form
• Inactive form
• Forms can interconvert, regulated by allosteric
  enzymes.
• Positive regulators stabilize active form of
  enzyme.
• Negative regulators stabilize inactive form.

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Figure 6.19 Allosteric Regulation of Enzymes
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Figure 6.19 Allosteric Regulation of Enzymes
Conformational change
Inactive form
Active form
The enzyme switches back and forth between the
two forms. They are in equilibrium.
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Figure 6.19 Allosteric Regulation of Enzymes
Conformational change
Inactive form
Active form
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Figure 6.19 Allosteric Regulation of Enzymes
Allosteric regulation
Inactive form
When the enzyme is in its inactive form, the
allosteric sites on the regulatory subunits can
accept inhibitor.
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Figure 6.19 Allosteric Regulation of Enzymes
Allosteric regulation
Inactive form
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Figure 6.19 Allosteric Regulation of Enzymes
Allosteric regulation
Active form
When the enzyme is in its active form, the active
sites on the catalytic subunits can accept
substrate.
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Figure 6.19 Allosteric Regulation of Enzymes
Cooperativity
Once a site is filled with a substrate or
inhibitor, binding at a second site of the same
type is favored.
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Figure 6.19 Allosteric Regulation of Enzymes
Cooperativity
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Enzymes are affected by their environment

• Enzymes are highly sensitive to
• Temperature
• pH

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pH Affects Enzyme Activity
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Temperature Affects Enzyme Activity
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Allosteric effects regulate metabolism

• End-product or feedback inhibition
• First step in a metabolic pathway is called the
  commitment step.
• What if the cell has no need for the end-product?
• The final product may allosterically inhibit the
  enzyme that catalyzes the commitment step.

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Inhibition of Metabolic Pathways