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

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Fig. 8-1

Concept 8.1: 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

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Why is Patrick Paralyzed?

Maureen Knabb Department of Biology

West Chester University

4

Why did Patrick lose his ability to move?

Patrick at 2:

Patrick at 21: Movie in QuickTime (mov)

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Patrick’s History • When Patrick was 16 years old, his hand started

twitching as he picked up a glass at dinner.

• Five months later (in February 2001), he fell down the steps at his home and was unable to climb the steps to the bus. He went to the ER for his progressive weakness.

• At Children’s Hospital of Philadelphia he was initially diagnosed with a demyelinating disease.

• He was treated with anti-inflammatory drugs and antibodies for 2 years with no improvement.

• What was wrong with Patrick?

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CQ1: What could be responsible for Patrick’s loss of mobility?

A: His nervous system is not functioning properly.

B: His muscles are not functioning properly.

C: He cannot efficiently break down food for energy.

D: All of the above are possible causes. Answer: D 7

CQ2: Which of the following processes requires energy?

A: Creating ion gradients across membranes.

B: Muscle shortening.

C: Protein synthesis.

D: All of the above. Answer: D

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Why do nerve and muscle cells need energy?

• Synthetic work = building macromolecules – (e.g., Making protein)

• Mechanical work = moving molecules past each other – (e.g., Muscle shortening)

• Concentration work = creating chemical gradients – (e.g., Storing glucose)

• Electrical work = creating ion gradients – (e.g., Unequal distribution of sodium and potassium ions)

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What is energy?

• Energy is the capacity to cause change • Energy exists in various forms, some of

which can perform work

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Forms of Energy

• Potential Energy = stored energy – Chemical bonds – Concentration gradients – Electrical potential

• Kinetic Energy = movement energy – Heat = molecular motion – Mechanical = moving molecules past each other – Electrical = moving charged particles

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The Second Law of Thermodynamics

• During every energy transfer or transformation, some energy is unusable, and is often lost as heat

• According to the second law of thermodynamics: – Every energy transfer or transformation

increases the entropy (disorder) of the universe

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• Kinetic energy is energy associated with motion • Heat (thermal energy) is kinetic energy

associated with random movement of atoms or molecules

• Potential energy is energy that matter possesses because of its location or structure

• Chemical energy is potential energy available for release in a chemical reaction

• Energy can be converted from one form to another

Animation: Energy Concepts Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Cycling between stored chemical versus movement energy

• Stored chemical energy must be released – Processes that RELEASE energy

• Catabolic/ Exergonic • Energy released > Energy required

• Movement requires energy

– Processes that REQUIRE energy • Anabolic/ Endergonic

• ATP plays a central role

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The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously

• Biologists want to know which reactions occur spontaneously and which require input of energy

• To do so, they need to determine energy changes that occur in chemical reactions

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Exergonic and Endergonic Reactions in Metabolism

• An exergonic reaction proceeds with a net release of free energy and is spontaneous

• An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous

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Fig. 8-6a

Energy

(a) Exergonic reaction: energy released

Progress of the reaction

Free

ene

rgy

Products

Amount of energy released (∆G < 0)

Reactants

Fig. 8-6b

Energy

(b) Endergonic reaction: energy required

Progress of the reaction

Free

ene

rgy

Products

Amount of energy required (∆G > 0)

Reactants

ATP powers cellular work by coupling exergonic reactions to endergonic reactions

• A cell does three main kinds of work: – Chemical – Transport – Mechanical

• To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

• Most energy coupling in cells is mediated by ATP

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The Structure and Hydrolysis of ATP

• ATP (adenosine triphosphate) is the cell’s energy shuttle

• ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-8

Phosphate groups Ribose

Adenine

The Regeneration of ATP

• ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

• The energy to phosphorylate ADP comes from catabolic reactions in the cell

• The chemical potential energy temporarily stored in ATP drives most cellular work

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CQ4: What would happen if Patrick lost his ability to make ATP?

A: His muscles would not be able to contract.

B: His neurons would not be able to conduct electrical signals.

C: Both A and B. Answer: C 23

How is ATP generated?

• ATP is formed through metabolic

pathways.

• In metabolic pathways, the product of one reaction is a reactant for the next.

• Each reaction is catalyzed by an enzyme.

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• Movie

What are enzymes?

• Enzymes (usually proteins) are biological catalysts, highly specific for their substrates (reactants).

• Enzymes change reactants into products through transition state intermediates.

• Enzymes are not consumed in the reaction. • Movie

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Enzymes speed up metabolic reactions by lowering energy barriers

• A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction

• An enzyme is a catalytic protein • Hydrolysis of sucrose by the enzyme

sucrase is an example of an enzyme-catalyzed reaction

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Enzymes as Catalysts

• Enzymes “speed up” reactions by lowering the “activation energy” of a reaction.

• Enzymes DO NOT change the overall energy released in a reaction.

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The Activation Energy Barrier

• Every chemical reaction between molecules involves bond breaking and bond forming

• The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA)

• Activation energy is often supplied in the form of heat from the surroundings

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-14

Progress of the reaction

Products

Reactants

∆G < O

Transition state

EA

D C

B A

D

D

C

C

B

B

A

A

How Enzymes Lower the EA Barrier

• Enzymes catalyze reactions by lowering the EA barrier

• Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually

Animation: How Enzymes Work Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-15

Progress of the reaction

Products

Reactants

∆G is unaffected by enzyme

Course of reaction without enzyme

EA without enzyme EA with

enzyme is lower

Course of reaction with enzyme

Substrate Specificity of Enzymes

• The reactant that an enzyme acts on is called the enzyme’s substrate

• The enzyme binds to its substrate, forming an enzyme-substrate complex

• The active site is the region on the enzyme where the substrate binds

• Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-16

Substrate

Active site

Enzyme Enzyme-substrate complex

(b) (a)

Catalysis in the Enzyme’s Active Site

• In an enzymatic reaction, the substrate binds to the active site of the enzyme

• The active site can lower an EA barrier by – Orienting substrates correctly – Straining substrate bonds – Providing a favorable microenvironment – Covalently bonding to the substrate

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-17

Substrates

Enzyme

Products are released.

Products

Substrates are converted to products.

Active site can lower Eand speed up a reaction.

Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds.

Substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit).

Active site is

available for two new

substrate molecules.

Enzyme-substrate complex

5

3

2 1

6

4

Effects of Local Conditions on Enzyme Activity

• An enzyme’s activity can be affected by – General environmental factors, such as

temperature and pH – Chemicals that specifically influence the

enzyme

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Effects of Temperature and pH

• Each enzyme has an optimal temperature in which it can function

• Each enzyme has an optimal pH in which it can function

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-18

Rat

e of

reac

tion

Optimal temperature for enzyme of thermophilic

(heat-tolerant) bacteria

Optimal temperature for typical human enzyme

(a) Optimal temperature for two enzymes

(b) Optimal pH for two enzymes

Rat

e of

reac

tion

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

CQ5: Which statement about enzymes is correct?

A: Enzymes are always proteins. B: Enzymes are consumed in a reaction. C: Enzymes are always active. D: All are correct. E: None are correct. Answer: E

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Enzyme Regulation • Enzymes turn “on” and “off” based on the

need of the organism – “ON” = Activators

• Positive allosteric regulation

– “OFF” = Inhibitors • Irreversible = must make new enzyme! • Reversible = inhibitor can “come off”

– Competitive = active site – Noncompetitive = “other” site = allosteric site

• Feedback Inhibition 41

Cofactors

• Cofactors are nonprotein enzyme helpers • Cofactors may be inorganic (such as a

metal in ionic form) or organic • An organic cofactor is called a coenzyme • Coenzymes include vitamins

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Enzyme Inhibitors

• Competitive inhibitors bind to the active site of an enzyme, competing with the substrate

• Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

• Examples of inhibitors include toxins, poisons, pesticides, and antibiotics

• http://science360.gov/obj/tkn-video/28df391b-8455-4c17-9ab2-abb30ff0dfa5

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-19

(a) Normal binding (c) Noncompetitive inhibition (b) Competitive inhibition

Noncompetitive inhibitor

Active site Competitive inhibitor

Substrate

Enzyme

Allosteric Activation and Inhibition

• Most allosterically regulated enzymes are made from polypeptide subunits

• Each enzyme has active and inactive forms • The binding of an activator stabilizes the

active form of the enzyme • The binding of an inhibitor stabilizes the

inactive form of the enzyme

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• Cooperativity is a form of allosteric regulation that can amplify enzyme activity

• In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

How are metabolic pathways regulated?

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Feedback inhibition animation http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter8/animations.html#

Feedback Inhibition

• In feedback inhibition, the end product of a metabolic pathway shuts down the pathway

• Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

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Fig. 8-22

Intermediate C

Isoleucine used up by cell

Enzyme 1 (threonine deaminase)

End product (isoleucine)

Enzyme 5 Intermediate D

Intermediate B

Intermediate A

Enzyme 4

Enzyme 2

Enzyme 3

Initial substrate (threonine)

Threonine in active site

Active site available

Active site of enzyme 1 no longer binds threonine; pathway is switched off.

Isoleucine binds to allosteric site

Feedback inhibition

CQ6: In competitive inhibition… A: the inhibitor competes with the normal

substrate for binding to the enzyme's active site.

B: an inhibitor permanently inactivates the enzyme by combining with one of its functional groups.

C: the inhibitor binds with the enzyme at a site other than the active site.

D: the competing molecule's shape does not resemble the shape of the substrate molecule.

Answer: A 50

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

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 8-23

1 µm

Mitochondria

• http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter8/animations.html#

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DNA mutations can disrupt

metabolic pathways

• Patrick suffered from a genetic disease that altered the structure of one protein.

• The protein was an enzyme. • The enzyme could potentially:

• lose its ability to catalyze a reaction. • lose its ability to be regulated.

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CQ7: Consider the following metabolic pathway: A C D

B If the enzyme responsible for converting A to C was

mutated and nonfunctional, what would happen?

A: A levels would increase; B, C, and D levels would decrease.

B: A and B levels would increase; C and D levels would decrease.

C: A, B and C levels would increase; D levels would decrease.

D: A, B, C, and D levels would all decrease. Answer:B 55

Fig. 8-UN1

Enzyme 1 Enzyme 2 Enzyme 3 D C B A

Reaction 1 Reaction 3 Reaction 2 Starting molecule

Product

Metabolic Pathways: Glycolysis

• Pathway present in almost every cell!

• Takes place in the cytoplasm of the cell.

• Occurs with or without oxygen.

• Oxidizes glucose (6 C) to 2 pyruvate (3 C).

• Overall yield = 2 ATP and 2 NADH + H+

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Important Electron Acceptors Coenzymes

• NAD (Nicotinamide Adenine Dinucleotide) – NAD+ + 2H+ + 2 e- --> NADH+ + H+

• FAD (Flavin Adenine Dinucleotide) – FAD + 2H+ + 2 e- --> FADH2

• Both molecules serve as coenzymes in many reactions.

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Fermentation: Recycles NADH

• Occurs in the cytoplasm without O2 • NADH + H+ is reoxidized to NAD+

• Alcoholic Fermentation = yeast cells – Converts pyruvate to ethanol and CO2 – Overall yield = 2 ATP

• Lactate Fermentation = animal cells – Converts pyruvate to lactate – Overall yield = 2 ATP

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CQ8: Consider the following metabolic pathway: Pyruvate Acetyl CoA TCA cycle Lactate If Patrick’s enzyme responsible for converting pyruvate to acetyl CoA was inhibited, what would happen? A: Pyruvate levels would increase; acetyl CoA and lactate levels would decrease.

B: Pyruvate and lactate levels would increase; acetyl CoA levels would decrease.

C: Pyruvate, acetyl CoA, and lactate levels would increase.

D: Pyruvate, acetyl CoA, and lactate levels would all decrease.

Answer: B 60

Patrick suffered from lactate acidosis

• Lactate (lactic acid) and pyruvate accumulated in his blood.

• Acidosis led to: – Hyperventilation – Muscle pain and weakness – Abdominal pain and nausea

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What happened to Patrick? • He inherited a mutation

leading to a disease called pyruvate dehydrogenase complex disease (PDCD).

• Pyruvate dehydrogenase is an enzyme that converts pyruvate to acetyl CoA inside the mitochondria.

• The brain depends on glucose as a fuel. PDCD degenerates gray matter in the brain.

• Pyruvate accumulates, leading to alanine and lactate accumulation in the blood (lactate acidosis). 62

CQ9: Why did Patrick become paralyzed? A: He inherited a genetic disease that resulted in the

partial loss of an enzyme necessary for aerobic breakdown of glucose.

B: The enzyme that is necessary for metabolizing fats was defective.

C: He was unable to synthesize muscle proteins due to defective ribosomes.

D: He suffered from a severe ion imbalance due to a high salt diet.

Answer: A 63

CQ10: Which food(s) can be metabolized to generate acetyl CoA?

A: Carbohydrates

B: Fats

C: Proteins

D: Both carbohydrates and fats

E: Carbohydrates, fats and proteins

Answer: E 64

Are there any treatment options for PDH deficiency?

• High fat, low carbohydrate diet (ketogenic diet)

• Fatty acids can form acetyl CoA which can enter

the Krebs cycle

Fatty acids

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Are there any treatment options for PDH deficiency?

• Dichloroacetate (DCA) blocks the enzyme that converts PDH from active to inactive forms

• PDH remains in the active form

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DCA blocks here

CQ11: Dichloroacetate (DCA) administration would lead to…

A: Increased production of acetyl CoA. B: Decreased lactate accumulation. C: Increased ATP production. D: All of the above. Answer: D

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CQ12: The loss of which of the following molecules was the most critical for Patrick’s paralysis?

A: Pyruvate dehydrogenase B: Acetyl CoA C: Lactate D: ATP Answer: D

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What happened to Patrick?

• Although his family tried to care for him at home, Patrick remained in hospitals and nursing homes until he died in 2006.

• Patrick died due to pneumonia, sepsis, and renal failure when he was only 21 years old.

• His family mourns his loss but feels grateful that he was able to survive for 5 years on a respirator, 4 years beyond his doctor’s predictions.

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