Chapter 06

Lecture Outline

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Chapter 6 Energy, Enzymes, and Metabolism

  Energy and Chemical Reactions

  Enzymes and Ribozymes

  Overview of Metabolism

  Recycling of Organic Molecules

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Key Concepts:

  Energy = ability to promote change or do work

  Two forms  Kinetic Energy – associated with movement

 Potential Energy – due to structure or location

  Chemical energy, the energy in molecular bonds, is a form of potential energy

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Energy and Chemical Reactions

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(a) Kinetic energy (b) Potential energy a: © moodboard/Corbis RF; b: © amanaimages/Corbis RF

Laws of Thermodynamics

  First Law of Thermodynamics   “Law of conservation of energy”   Energy cannot be created or destroyed,

but can be transformed from one type to another

  Second Law of Thermodynamics   Transfer of energy from one form to another

increases the entropy (degree of disorder) of a system

  As entropy increases, less energy is available for organisms to use to promote change

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H = G + TS

H = enthalpy or total energy

G = free energy or amount of energy for work

S = entropy or unusable energy

T = absolute temperature in Kelvin (K)

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ΔG = Δ H – T Δ S

Spontaneous reactions

  Occur without input of additional energy

  Not necessarily fast, can be slow  Breakdown of sucrose to CO2 and H2O is

spontaneous, but will take a long time for sugar in a sugar bowl to break down

  Key factor is the free energy change – if ΔG is negative, then process is exergonic and spontaneous

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Change in free energy determines direction of chemical reactions

  Total energy = Usable energy + Unusable energy

  Energy transformations involve an increase in entropy (disorder that cannot be harnessed to do work)

  Free energy (G) = amount of energy available to do work  Also called Gibbs free energy

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  Metabolism: Sum total of all chemical reactions in an organism.

  Anabolic reactions: Complex molecules are built from simple molecules; energy input is required.

  Catabolic reactions: Complex molecules are broken down to simpler ones and energy is released.

8.1 What Physical Principles Underlie Biological Energy Transformations?

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Increase

More disordered

in entropy

Highly ordered

Figure 8.3 Exergonic Reactions

  Exergonic Reactions:   Releases free energy, (-ΔG) (spontaneous)   Catabolic reactions   Order/complexity decreases; Entropy increases +ΔS

Figure 8.3 Endergonic Reactions

  Endergonic Reactions   Consume free energy (+ΔG) (not spontaneous)

  Anabolic reactions

  Complexity, order increases -ΔS

•  Living systems increase the entropy of the universe

–  Use energy to maintain order

–  As they increase order, the order in the surroundings decreases

50µm

Detailed anatomy of a root tissue from a buttercup plant.

Biological Order and Disorder

An Analogy for Cellular Respiration

A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucose is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium.

∆G < 0

∆G < 0

∆G < 0

Input: Glucose Output: CO2

and ATP

•  Living cells do not reach equilibrium

•  Catabolic Pathways in a cell releases free energy in a series of reactions not just one

  No net change in concentration or chemical activities of products and reactants with time.

  At chemical equilibrium, ΔG=0

  Rate of the forward and reverse reactions are equal:

  The concentrations of A and B determine the direction of the reaction.

Chemical Equilibrium

•  A cell that reaches metabolic equilibrium is:

DEAD or ALIVE?

Figure 8.4 Chemical Reactions Run to Equilibrium

  A spontaneous reaction is not necessarily a fast reaction

  Catalyst – an agent that speeds up the rate of a chemical reaction without being consumed during the reaction

  Enzymes – protein catalysts in living cells

  Ribozymes – RNA molecules with catalytic properties

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Enzymes and Ribozymes

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Progress of an exergonic reaction

Fre

e en

erg

y (G

)

Transition state

Reactants

Reactant molecules

Enzyme

ATP Glucose

Products

Activation energy (EA) without enzyme

Activation energy (EA) with enzyme

Change in free energy (ΔG)

How enzymes lower activation energy

  Straining bonds in reactants to make it easier to achieve transition state

  Positioning reactants together to facilitate bonding

  Changing local environment  Direct participation through very temporary bonding

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Figure 8.9 Enzyme and Substrate

Substrate binding

  Enzymes have a high specificity for their substrate

  Lock and key metaphor for substrate and enzyme binding – only the right key (substrate) will fit in the lock (enzyme)

  Induced fit phenomenon – interaction also involves conformational changes

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Enzyme reactions

  Saturation  Plateau where nearly all active sites are occupied by

substrate

 Vmax = velocity of reaction near maximal rate

  Michaelis constant, KM  Substrate concentration where velocity is half

maximal value

 High KM enzyme needs higher substrate concentration

  Inversely related to affinity between enzyme and substrate 22

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Vel

oci

ty

(pro

du

ct/s

eco

nd

)

[Substrate]

A

B Vmax

2

Vmax C

D

A 60 sec Low

B 60 sec Moderate

C 60 sec High

D 60 sec

Reaction velocity in the absence of inhibitors

0

Amount of enzyme

Tube

Incubation time

Substrate concentration

Very high

1 µg 1 µg 1 µg 1 µg

KM

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Enzyme Regulation

  Irreversible inhibition: Inhibitor binds to enzyme and has irreversible effects.

  Reversible inhibition: Effect of inhibitor is reversible. (This is what cells do)

 Competitive inhibition

 Noncompetitive inhibition

Figure 8.15 Irreversible Inhibition

DIPF: Diisopropyl Phosphorofluoridate

Inhibition

  Competitive inhibition  Molecule binds to active site

  Inhibits ability of substrate to bind

 Apparent KM increases – more substrate needed

  Noncompetitive inhibition  Lowers Vmax without affecting Km

  Inhibitor binds to allosteric site, not active site

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KM with inhibitor [Substrate] Competitive inhibition

Vel

oci

ty

(pro

du

ct/s

eco

nd

) Plus competitive inhibitor

Substrate Inhibitor Enzyme

Vmax

KM [Substrate] Noncompetitive inhibition

Vel

oci

ty

(pro

du

ct/s

eco

nd

)

Substrate Inhibitor

Enzyme Allosteric site

0

0

KM

Vmax

V max with inhibitor

Plus noncompetitive inhibitor

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Competitive inhibition

Vmax

KM [Substrate] Noncompetitive inhibition

Vel

oci

ty

(pro

du

ct/s

eco

nd

)

Substrate Inhibitor

Enzyme Allosteric site

0

V max with inhibitor

Plus noncompetitive inhibitor

KM with inhibitor [Substrate]

Vel

oci

ty

(pro

du

ct/s

eco

nd

)

Plus inhibitor

0 KM

Vmax No inhibitor

Other requirements for enzymes

  Prosthetic groups – small molecules permanently attached to the enzyme

  Cofactor – usually inorganic ion that temporarily binds to enzyme

  Coenzyme – organic molecule that participates in reaction but is left unchanged afterward

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Enzymes are affected by environment

  Most enzymes function maximally in a narrow range of temperature and pH

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0 0

10 20

Rat

e o

f a

chem

ical

rea

ctio

n

30 40 50 60

High

Temperature (ºC)

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  Chemical reactions occur in metabolic pathways

Redox reactions Substrate level phosphorylation reactions

  Each step is coordinated by a specific enzyme

  Catabolic pathways   Breakdown cellular components   Exergonic

  Anabolic pathways   Synthesis cellular components   Endergonic   Must be coupled to exergonic reaction

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Overview of Metabolism

Catabolic reactions

  Breakdown of reactants

  Used for recycling building blocks

  Used for energy to drive endergonic reactions  Energy stored in intermediates such as ATP, NADH

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Anabolic reactions

  Biosynthetic reactions

  Make large macromolecules or smaller molecules not available from food

  Require energy inputs from intermediates (NADH or ATP) to drive reactions

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Adenine (A)

Ribose

Phosphate groups

Phosphate (Pi) Adenosine diphosphate (ADP)

Adenosine triphosphate (ATP)

+ ~

H H

OH

O

OH

H H

O O O

H2C O–

NH2

N

N H

N

N

P OH O

O–

P O–

O

O–

P HO

~ ~

H H

OH

O

OH

H H

O O O

H2C O–

NH2

N

N H

N

N

P O O

O–

P O

O–

P O–

H2O Hydrolysis of ATP

  ΔG = -7.3 kcal/mole

  Reaction favors formation of products

  The energy liberated is used to drive a variety of cellular processes

Hydrolysis of ATP

Figure 8.7 Coupling of ATP Hydrolysis to an Endergonic Reaction

Redox Reactions

  Oxidation-reduction reaction or Redox reaction

 Reduction: Gain of one or more electrons (hydrogens)

 Oxidation: Loss of one or more electrons (hydrogens)

 Both processes occur together

  C6H12O6 + 6O2 6CO2 + 6H2O + free energy

  Reducing agent becomes oxidized

  Oxidizing agent becomes reduced

Reducing Agent

Oxidizing Agent

  Redox is also defined as loss/gain of H atoms   Loss of H atoms = Oxidation

  Gain of H atoms = Reduction

  The more reduced a molecule, the more energy is stored in its chemical bonds.

  NAD+ acts as an electron carrier

  Participates in redox reactions

  Highly exergonic ΔG = 50 kcal/mol where as ATP ΔG = 12 kcal/mol

  NAD+ + H+ + 2e- NADH

  FAD+ is similar carrier

Nicotinamide Adenine Dinucleotide (NAD+)

Figure 9.3 NAD+/NADH is an Electron Carrier in Redox Reactions

NAD+ + H+ + 2e- NADH

Two ways to make ATP

1.  Substrate-level phosphorylation   Enzyme directly transfers phosphate from one

molecule to another molecule

2.  Chemiosmosis   Energy stored in an electrochemical gradient is

used to make ATP from ADP and Pi

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Feedback Inhibition of Metabolic Pathways

Committed Step Several Reactions

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Feedback Inhibition

Enzyme 3 Enzyme 1

Initial substrate

Conformational change

Allosteric site

Intermediate 1 Intermediate 2 Final product

Enzyme 2 Active site

Final product

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Feedback Inhibition: If the concentration of the final product becomes high, it will bind to enzyme 1 and cause a conformational change that inhibits the enzyme’s ability to convert the initial substrate into intermediate 1.

Regulation of metabolic pathways

  Gene regulation   Turn genes on or off

  Cellular regulation   Cell-signaling pathways like hormones

  Biochemical regulation   Feedback inhibition – product of pathway inhibits

early steps to prevent over accumulation of product

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  Most large molecules exist for a relatively short period of time

  Half-life – time it takes for 50% of the molecules to be broken down and recycled

  All living organisms must efficiently use and recycle organic molecules

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Recycling of Organic Molecules

Recycling Mechanisms

  Exonucleases (Exosome Complex)-mRNA degradation

  Proteosome-Protein degradation

  Lysosome-Molecule degradation

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