BIOL 101 Chp 8: An Introduction to Metabolism

An Introduction

to Metabolism

BIOL 101: General Biology I

Chapter 8

Rob Swatski Associate Professor of Biology

HACC – York Campus 1

Overview: The Energy of Life

• The living cell is a miniature chemical factory where thousands of reactions occur

• The cell extracts energy and applies energy to perform work

• Some organisms even convert energy to light, as in bioluminescence

3

Bioluminescence

5

6

An organism’s metabolism transforms matter and energy, subject to the

laws of thermodynamics

• Metabolism is the totality of an organism’s chemical reactions

• Metabolism is an emergent property of life that arises from interactions between molecules within the cell

8

Chemical Reactions

Metabolism

Physiology

Emergent Properties

Metabolic Pathways 9

10

11 http://www.metabolicvisualizer.org/

Enzyme 1 Enzyme 2 Enzyme 3

B A

Reaction 1 Reaction 3 Reaction 2

Starting Molecule

(Substrate)

Product

B C D

Bioenergetics: study of how organisms manage their energy resources

Metabolic Pathway

12

AB A B

Catabolic Pathways

13 …release energy

Light energy

ECOSYSTEM

Photosynthesis in chloroplasts

CO2 + H2O

Cellular respiration in mitochondria

Organic molecules

+ O2

ATP powers most cellular work

Heat energy

ATP

exergonic

endergonic

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15

A B AB

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Anabolic Pathways

…gain energy

Light energy

ECOSYSTEM

Photosynthesis in chloroplasts

CO2 + H2O

Cellular respiration in mitochondria

Organic molecules

+ O2

ATP powers most cellular work

Heat energy

ATP

exergonic

endergonic

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18

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Energy

Potential

Chemical

Kinetic & Heat

(thermal energy)

A diver has more potential energy on the platform

than in the water.

Diving converts potential energy to

kinetic energy.

Climbing up converts the kinetic energy of muscle movement

to potential energy.

A diver has less potential energy in the water

than on the platform.

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Thermodynamics

Closed systems

Open systems

22

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First Law of Thermodynamics

= Principle of Conservation of

Energy

The energy of the universe is constant

Energy can be transferred &

transformed, but…

…it cannot be created or destroyed

First law of thermodynamics

26

Total Energy of Reactants

Total Energy of Products

First Law of Thermodynamics

27

Second Law of Thermodynamics

During every energy transfer or

transformation…

…some energy is unusable & is often lost

as heat

Every energy transfer or transformation increases the entropy (disorder) of

the universe

Heat

Second Law of Thermodynamics

29

Spontaneous Processes

Occur without any energy input

Can be fast or slow

Must always increase the entropy of the

universe

30

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Biological Order & Disorder

Cells create order from disorder

Energy flows into an ecosystem as light…

…and flows out of an ecosystem as heat

Primary producers

Energy flow

Chemical cycling

Primary consumers

Secondary consumers

Tertiary consumers

Microorganisms and other

detritivores

Detritus

Sun

Heat

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34

Why doesn’t the evolution of more

complex forms of life violate the Second

Law?

35

Effie Sue

36

Entropy may decrease in an individual

organism, but the total entropy of the universe is still

increasing

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38

Energy and Chemical Reactions

Which reactions are spontaneous?

Which reactions require an input of energy?

How does energy change during a

chemical reaction?

39

Free Energy

Energy in a living cell that can do

work when temperature &

pressure are uniform

Change in free energy (∆G)

- ∆G reactions are spontaneous & can

be harnessed to do work

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∆G = ∆H – T∆S

∆H = the change in enthalpy (total energy)

T = temperature in degrees Kelvin

∆S = the change in entropy

42

Free Energy

Free energy measures a system’s

stability

Unstable systems tend to become

more stable

- ∆G reactions: free energy decreases & stability increases

Moves toward equilibrium

(maximum stability)

Less free energy (lower G) More stable

Less work capacity

More free energy (higher G) Less stable

Greater work capacity

In a spontaneous change: The free energy of the system

decreases (∆G < 0) The system becomes more

stable The released free energy can

be harnessed to do work

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Spontaneous change

Spontaneous change

Spontaneous change

Diffusion Chemical reaction Gravitational motion

44

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Energy Energy Exergonic Reaction

Spontaneous: releases free energy

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Energy Energy Endergonic Reaction

Nonspontaneous: absorbs free energy

Energy

Exergonic reaction

Progress of the reaction

Fre

e e

ne

rgy

Products

Amount of energy

released (∆G < 0)

Reactants

47

Energy

Endergonic reaction

Progress of the reaction

Fre

e e

ne

rgy

Products

Amount of energy

required (∆G > 0)

Reactants

48

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Closed Systems

Reactions in closed systems

eventually reach

equilibrium and…

…cannot do any more work

Closed hydroelectric system

∆G < 0 ∆G = 0

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Open Systems

Life consists of open systems that do not

reach equilibrium

Materials are constantly flowing in

and out

Metabolism is never at equilibrium

∆G < 0

Open hydroelectric system

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∆G < 0

∆G < 0

∆G < 0

Open multistep hydroelectric system

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Cellular Work

Chemical

Transport Mechanical

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Kinesin

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Endergonic

Exergonic

Energy Coupling

ATP

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ATP: Adenosine

Triphosphate Main energy

molecule of the cell

Ribose (sugar)

Adenine (nitrogenous base)

3 Phosphate groups

Phosphate groups Ribose

Adenine

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ATP Hydrolysis

Breaks the terminal

phosphate bond of ATP

Releases energy to power all

cellular work

ATP is now in a state of lower

free energy

Inorganic phosphate

Energy

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

P P

P P P

P + +

H2O

i

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Phosphorylation

How ATP drives endergonic reactions

Transfers a phosphate group to

another molecule

The recipient molecule is now phosphorylated

P

(b) Coupled with ATP hydrolysis, an exergonic reaction

Ammonia displaces the phosphate group, forming glutamine.

(a) Endergonic reaction

(c) Overall free-energy change

P P

Glu

NH3

NH2

Glu i

Glu ADP +

P

ATP +

+

Glu

ATP phosphorylates glutamic acid, making the amino acid less stable.

Glu NH3

NH2

Glu +

Glutamic acid

Glutamine Ammonia

∆G = +3.4 kcal/mol

+ 2

1

63

Mechanical work: ATP binds non-covalently to motor proteins, then is hydrolyzed

P i

ADP +

P P i

Transport work: ATP phosphorylates transport proteins

ATP

ATP

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P i ADP + Energy from catabolism (exergonic)

Energy for cellular work

(endergonic) H2O ATP + ATP

ATP = Renewable Resource

Phosphorylation of ADP

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Enzymes

Catalysts: speed up a reaction

Are not consumed by the reaction

Enzyme-catalyzed reaction

67

Increase Reaction Rate

Decrease Activation

Energy

Catalysts

68

Enzymes as Catalysts

69

Sucrose (C12H22O11)

Glucose (C6H12O6) Fructose (C6H12O6)

Sucrase

Sucrose Hydrolysis by Sucrase

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Activation Energy (EA)

Energy needed to start a chemical

reaction

Often supplied by surrounding heat

Activation energy barrier

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Progress of the reaction

Products

Reactants

∆G < O

Transition state

EA

D C

B A

D

D

C

C

B

B

A

A

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Enzymes and EA

Enzymes lower the EA barrier

Do not affect the change in free

energy (∆G)

Enzymes accelerate reactions that would

eventually occur

Course of reaction without enzyme

EA without enzyme EA with

enzyme is lower

Course of reaction

with enzyme

Reactants

Products

G is unaffected by enzyme

Progress of the reaction

Fre

e e

ne

rgy

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Enzyme & Substrate Specificity

Substrate = Reactant

Enzyme-substrate complex

Active site

Substrates

Active Site

Enzyme

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Enzymes = Catalysts

Induced fit

78

How Do Enzymes Lower the EA barrier?

Form multiple bonds with substrates

Properly orient substrate

Provide a favorable microenvironment

Strain substrate bonds

Substrates

Enzyme

Products are released

Products

Substrates converted into

products

Lower EA speeds up reaction

Hydrogen bonds & ionic bonds form between

enzyme & substrates

Substrates enter active site

Active site is open

for new substrates

Enzyme-substrate complex

5

3

2

1

6

4

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Enzyme Activity &

Environmental Factors

Temperature

pH

Cofactors

Rat

e o

f re

acti

on

Optimal temperature for enzyme of thermophilic

(heat-tolerant) bacteria

Optimal temperature for typical human enzyme

Optimal temperature for two enzymes

Optimal pH for two enzymes

Rat

e o

f re

acti

on

Optimal pH for pepsin (stomach enzyme)

Optimal pH for trypsin (intestinal enzyme)

Temperature (ºC)

pH 5 4 3 2 1 0 6 7 8 9 10

0 20 40 80 60 100

Effects of Temperature & pH on Enzyme Activity

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Cofactors

Nonprotein enzyme helpers

Inorganic: metal ions

Organic: coenzymes (vitamins)

83

Enzyme Inhibitors

Competitive Inhibitors

Noncompetitive Inhibitors

Toxins, pesticides, antibiotics

Normal binding Noncompetitive inhibition Competitive inhibition

Noncompetitive inhibitor

Active site

Competitive inhibitor

Substrate

Enzyme

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85

Allosteric Regulation of

Enzyme Activity

May stimulate or inhibit enzyme

activity

Regulatory protein binds to enzyme at

one site…

…and affects enzyme function at

another site

Activators & inhibitors

Inhibitor

Non- functional active site

Stabilized inactive

form

Inactive form

Oscillation

Activator Active form

Stabilized active form Regulatory

site (1 of 4)

Allosteric enzyme with 4 subunits

Active site (1 of 4)

Allosteric Activators & Inhibitors 86

87

Cooperativity

Another type of allosteric activation

Amplifies enzyme activity

Substrate binds to one active site…

…and stabilizes favorable shape

changes at all other active sites

Substrate

Inactive form

Stabilized active form

Cooperativity

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Identification of Allosteric Regulators

Attractive drug candidates for

enzyme regulation

Example: inhibit proteolytic

enzymes (caspases)

May help manage inappropriate inflammatory

responses

SH

Substrate

Hypothesis: allosteric inhibitor locks enzyme

in inactive form

Active form can bind substrate

S–S SH

SH

Active site

Caspase 1

Known active form

Known inactive form

Allosteric binding site

Allosteric inhibitor

EXPERIMENT

90

Caspase 1

RESULTS

Active form Allosterically inhibited form

Inactive form

Inhibitor

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Feedback Inhibition

End product of enzymatic pathway…

…shuts down the pathway

Prevents a cell from wasting

resources

Active site available

Isoleucine used up by

cell

Feedback inhibition

Active site of enzyme 1 is

no longer able to catalyze the

conversion of threonine to intermediate A;

pathway is switched off. Isoleucine

binds to allosteric

site.

Initial substrate

(threonine)

Threonine in active site

Enzyme 1 (threonine deaminase)

Intermediate A

Intermediate B

Intermediate C

Intermediate D

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

End product (isoleucine)

Tonyjaase Enzyme

Substrate 1

Substrate 2

Active Sites

Tonyjaaase Enzyme

in Action video

94

Specific Localization of Enzymes Within the Cell

• Structures within the cell help bring order to metabolic pathways

• Some enzymes act as structural components of membranes

• In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria

Mitochondria

The matrix contains enzymes in solution that are involved in one stage

of cellular respiration.

Enzymes for another stage of cellular

respiration are embedded in the inner membrane.

1 m