Chapter 6

1
Chapter 6 An Introduction to Metabolism

• -Metabolism, Energy, and Life
• -Enzymes
• -Control of Metabolism

2
Metabolism

• Metabolism is the totality of an organisms
  chemical reactions
• Includes all processes that involve breaking down
  energy sources
• Ex. cellular respiration, digestion, etc.
• Arises from interactions between molecules and
  cellular environments.
• Is concerned with managing the material and
  energy resources of the cell.

3
Metabolic Pathways

• Are intricate and numerous.
• Utilize steps to minimize loss of energy (most
  efficient paths are used).
• Are selectively accelerated by presence of
  enzymes (biological catalysts).

4
Figure 6.1  The Complexity of Metabolism
Dots represent molecules Lines represent
chemical reactions that transform those
molecules Inset shows first two steps of glucose
breakdown Diagram represents a few hundred of
the thousands of metabolic reactions that occur
in a cell.
5
Two Types of Metabolic Pathways

• Catabolic degradative processes, where complex
  molecules are broken down into simpler compounds
  and energy is released.
• Ex. Cellular respiration
• Anabolic consume energy to build complicated
  molecules from simpler ones.
• Ex. Protein synthesis
• these pathways intersect in such a way that the
  energy released from Catabolic can be used to
  drive Anabolic
• this transfer of energy is called Energy Coupling

6
Energy Bioenergetics

• Defined as capacity to do work (move matter
  against opposing forces).
• Exists in a variety of forms, and work of life
  depends on ability of cells to transform energy
  from one type into another.
• Bioenergetics is the study of how organisms
  manage their energy resources.

7
Potential vs. Kinetic vs. Activation

• Potential Energy stored energy that matter
  possesses because of its location or structure
• Ex. Chemical energy in organic molecules, water
  in reservoir behind dam
• Kinetic Energy energy of motion
• Ex. Water gushing through dam, light energy, heat
  energy
• Activation Energy energy required to start a
  chemical reaction.

8
Figure 6.2x1 Kinetic and Potential Energy Dam
9
Activation Energy

• Activation energy converts potential energy to
  kinetic energy the push to get a reaction
  started
• Ex. Boulder on top of hill, give a push to start
• -OR-
• Boulder on top of hill, use a lever to get
  boulder rolling

10
Energy Transformations are Subject to Laws of
Thermodynamics

• Thermodynamics study of the energy
  transformations that occur in a collection of
  matter
• Scientists use terms system and surroundings to
  describe
• system is the matter under study
• surroundings are everything outside of the system
• Closed vs. Open Systems closed systems are
  isolated from surroundings, and in open systems,
  energy can be transferred between the system and
  its surroundings

11
First Law of Thermodynamics

• Energy can be transferred and transformed, but it
  cannot be created or destroyed.
• Known as Principle of Conservation of Energy
• Energy of universe is constant!

12
Second Law of Thermodynamics

• Every energy transfer or transformation makes the
  universe more disordered
• ENTROPY measure of disorder or randomness.
• The more random a collection of matter, the
  greater its entropy.
• So, restate as
• Every energy transfer or transformation increases
  the entropy of the universe.

13
Free Energy

• The portion of a systems energy that can perform
  work when temperature is uniform throughout the
  system.
• Systems that are rich in energy are unstable.
• Systems that are highly ordered are unstable.
• In any spontaneous process, the free energy of a
  system decreases.
• Organisms can live only at the expense of free
  energy acquired from the surroundings.

14
Free energy portion of a systems energy that
can perform work when temperature is uniform
throughout the systemIs free because is
available for work, not because it does not cost
the universe something!See page 91 in textbook.
Scientists use free energy as a standard for
measuring the spontaneity of a system alone.
15
?G ?H - T ?S

• G ? systems quantity of free energy
• H ? systems total energy
• T ? absolute temperature in Kelvin
• S ? systems total entropy
• So, for a process to occur spontaneously, the
  system must either give up energy (decrease H),
  give up order (increase S), or both. The change
  in G must be negative.
• In other words, nature runs downhill in the sense
  of a loss of useful energy the capacity to
  perform work.

16
Equilibrium

• State of maximum stability.
• In chemical reactions, as the reaction proceeds
  toward equilibrium, the free energy of the
  mixture of reactants and products decreases.
• Free energy increases when a reaction is pushed
  away from equilibrium.
• A chemical reaction or physical process at
  equilibrium performs no work.

17
Exergonic Endergonic Reactions

• Classification of reactions is based on the
  free-energy changes
• Exergonic energy outward proceed with a net
  release of free energy -- usually releases energy
  in form of heat these reactions occur
  spontaneously
• (? G is negative)
• Endergonic energy inward absorbs free energy
  from its surroundings, containers for these
  reactions tend to feel cool
• (? G is positive)

18
Figure 6.6  Energy Changes in Exergonic and
Endergonic Reactions
Exergonic Reaction ?G lt 0 Reaction proceeds
with a net RELEASE of free energythese reactions
occur spontaneously.
Endergonic Reaction ?G gt 0 Reaction proceeds
with an ABSORPTION of free energythese reactions
are not spontaneous.
19
Metabolic Disequilibrium

• Reactions in a closed system eventually reach
  equilibrium and can do no work.
• Because systems at equilibrium have a ?G of zero
  and can do no work, a cell that has reached
  metabolic equilibrium is dead.
• Thus, metabolic disequilibrium is a defining
  feature of life!
• See pages 93 and 94 in textbook for open vs.
  closed system

20
Figure 6.7 Disequilibrium and Work in Closed and
Open Systems
21
ATP and Energy Coupling

• 3 kinds of work in cell
• 1. mechanical
• 2. transport
• 3. chemical
• Energy Coupling use of an exergonic process to
  drive and endergonic process.
• ATP mediates most energy coupling in cells!

22
Figure 6.8 The Structure and Hydrolysis of ATP
All are negatively charged crowded and repel,
creating instability!
When bonds are broken from ATP to ADP
(hydrolysis), 7.3 kcal/mol of energy is released
is exergonic
23
Phosphorylation

• Recipient of phosphate group when ATP loses it.
• This phosphorylated intermediate is more reactive
  (less stable) than the original molecule.
• Nearly all cellular work depends on ATPs
  energizing of other molecules by transferring
  phosphate groups.

24
Figure 6.10 The ATP Cycle
ATP is a renewable resource that can be
regenerated
ENERGY COUPLING The use of exergonic processes
to drive endergonic processes.
Is fast working muscle cell recycles its entire
ATP pool once each minute Turnover represents 10
million molecules of ATP generated per second in
a cell.
25
Enzymes

• http//www.sumanasinc.com/webcontent/animations/co
  ntent/enzymes/enzymes.html
• Catalysts are chemical agents that change the
  rate of reaction without being consumed by the
  reaction.
• Enzymes are catalytic proteins.
• Enzymes keep chemical traffic through the
  pathways of metabolism from getting too congested
  and bogged down.

26
Figure 6.11 Example of an enzyme-catalyzed
reaction Hydrolysis of sucrose
A solution of sucrose dissolved in sterile water
will sit for years at room temp with no
appreciable hydrolysis occurring.BUT, if add
SUCRASE (an enzyme), the sucrose will be
converted in seconds
27
Figure 6.12 Energy profile of an exergonic
reaction
Uphill - Reactants A B must absorb enough
energy from the surroundings to surmount the hill
of activation energy and reach the unstable
transition state. Downhill Bonds break, and
new bonds form. Energy is released to
surroundings during this process (EXERGONIC - ?G
negative) products have less energy than
reactants. THIS IS WITH NO ENZYME ACTIVITY!!!
28
Figure 6.13 Enzymes lower the barrier of
activation energy
Without affecting the free-energy change (?G) for
the reaction, an enzyme speeds the reaction up by
lowering the activation energy required to start
the reaction. Black Curve shows course of
reaction w/out enzyme. Red Curve shows course
of reaction with enzyme.
29
Enzymes

• Read 1st 2nd paragraph on page 97 under Enzymes
  and Activation Energy
• AN ENZYME SPEEDS A REACTION BY LOWERING THE
  ACTIVATION ENERGY REQUIRED TO START THE REACTION.
• Cannot change the ?G for a reaction.
• Cannot make an endergonic reaction exergonic.
• Can only hasten reactions that would occur
  normally, regardless!
• Enzymes ARE NOT USED UP during the course of the
  reaction!

30
Enzymes

• The reactant an enzyme acts on is its substrate.
• Enzymes are substrate specific, and can
  distinguish its substrate from even closely
  related isomers!
• Each enzyme has an active site the catalytic
  center of the enzyme!
• Rate of conversion of substrate into new products
  depends on initial concentration of substrate!
• But there is a limit to total speed of reaction
  all enzyme molecules may be working (saturated),
  so only way to increase reaction speed is to ADD
  MORE ENZYME!
• Soto speed up reactionadd MORE substrate or add
  more enzyme!!!

31
Figure 6.14 The induced fit between an enzyme
and its substrate
The specificity of an enzyme is attributed to a
compatible fit between the shape of its active
site and the shape of the substrate. Active site
of enzyme can be seen in computer model as groove
on surface of protein (blue) On entering the
active site, the substrate (red) induces a change
in the shape of the protein that causes the
active site to embrace the substrate.
32
Figure 6.15 The Catalytic Cycle of an Enzyme
Substrates enters active site binds to protein
enzyme enzyme changes shape to embrace
substrate (induced-fit)
33
Physical and Chemical Environment Affects Enzyme
Activity

• Temperature too high, denatures protein
• pH too high or too low, denatures protein
• Cofactors inorganic nonprotein helper bound to
  active site must be present for some enzymes to
  function (zinc, iron, copper)
• Coenzymes organic nonprotein helper bound to
  active site again, must be present (vitamins)
• http//www.sumanasinc.com/webcontent/animations/co
  ntent/proteinstructure.html

34
Inhibitors

• Enzyme Inhibitors stop enzyme from working!
• 2 types competitive and noncompetitive
• Competitive blocks active site, mimics substrate
• Noncompetitive bind to another part of enzyme and
  change shape of enzyme so cant work on
  substrate
• http//bcs.whfreeman.com/thelifewire/content/chp06
  /0602001.html

35
Figure 6.17 Inhibition of Enzyme Activity
Mimics the substrate and competes for the active
site.
Binds to the enzyme at a location away from the
active site, but alters the shape of the enzyme
so that the active site is no longer fully
functional.
36
Control of Metabolism

• Cell regulates metabolic pathways by controlling
  when and where enzymes are active.
• Does this by
• switching on or off the genes for production of
  specific enzymes
• -OR-
• regulating enzymes once made

37
Figure 6.18 Allosteric regulation of enzyme
activity
By binding to allosteric site, can either
inhibit or stimulate Most allosterically
regulated enzymes are made up of one or more
polypeptide subunits each having its own active
site.
38
Figure 6.19 Feedback inhibition
Feedback Inhibition Switching off of a metabolic
pathway by its end product, which acts an
inhibitor of an enzyme within the pathway.
39
Figure 6.20 Cooperativity
Similar to allosteric activation amplifies the
response of enzymes to substrates One substrate
molecule primes an enzyme to accept more
substrate molecules