chapter 8: an introduction to metabolism. 1.what is metabolism? all of an organisms chemical...

sites of cellular respiration

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Chapter 8: An Introduction to Metabolism


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1. What is metabolism?• All of an organisms chemical processes

2. What are the different types of metabolism?• Catabolism – releases energy by breaking down complex

molecules• Anabolism – use energy to build up complex molecules• Catabolic rxns – hydrolysis – break bonds• Anabolic rxns – dehydration – form bonds

3. How is metabolism regulated?- Enzymes


Enzyme 1 Enzyme 2 Enzyme 3

A B C DReaction 1 Reaction 2 Reaction 3

Startingmolecule

Product


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4. What are the different forms of energy?

- Kinetic – energy from molecules in motion

- Potential – energy based on location or structure

- water behind a dam

- bonds in gas/oil/fats/starch

- Chemical energy – bio speak for potential energy from release in a catabolic rxn



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Figure 8.2 Transformation between kinetic and potential energy

On the platform, a diverhas more potential energy.

Diving converts potentialenergy to kinetic energy.

Climbing up converts kinetic

energy of muscle movement

to potential energy.

In the water, a diver has less potential energy.


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5. What are the 2 laws of thermodynamics?

- 1st law – Energy is constant. It can be transferred or transformed but it cannot be created or destroyed.

- 2nd law – Every transfer or transformation of energy increases the entropy (disorder) of the universe.


(a) First law of thermodynamics: Energy can be transferred or transformed but neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

(b)

Chemicalenergy

Heatco2

H2O+


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6. What is the difference between exergonic & endergonic rxns?

- Exergonic – releases energy

- Endergonic – require energy

- Catabolic rxns – hydrolysis – break bonds – exergonic

- Anabolic rxns – dehydration – form bonds – endergonic

7. Where does the energy come from to drive rxns in the body?

- ATP


CH–O O O O CH2

H

OH OH

H

N

H H

O

NC

HC

NC

C

N

NH2Adenine

Ribose

O–

O O

O–

O

O–

P P P

Phosphate groups


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8. How does ATP provide energy?

- hydrolysis of ATP


P

Adenosine triphosphate (ATP)

H2O

+ Energy

Inorganic phosphate Adenosine diphosphate (ADP)

PP

P PP i+


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Figure 8.10 Energy coupling using ATP hydrolysis

Endergonic reaction: ∆G is positive, reaction is not spontaneous

∆G = +3.4 kcal/molGlu Glu

∆G = –7.3 kcal/molATP H2O+

+ NH3

ADP +

NH2

Glutamicacid

Ammonia Glutamine

Exergonic reaction: ∆ G is negative, reaction is spontaneous

P

Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol


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Figure 8.11 How ATP drives cellular work

+

P

Motor protein

P i

Protein moved

(a) Mechanical work: ATP phosphorylates motor proteins

Membraneprotein

ATP

Solute

P P i

P i

ADP+

Solute transported

(b) Transport work: ATP phosphorylates transport proteins

GluGlu

NH3

NH2

P i

P

+

(c) Chemical work: ATP phosphorylates key reactants

Reactants: Glutamic acid and ammonia

Product (glutamine)made


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ATP synthesis from ADP + P i requires energy

ATP

ADP + P i

Energy for cellular work(endergonic, energy-consuming processes)

Energy from catabolism(exergonic, energy yieldingprocesses)

ATP hydrolysis to ADP + P i yields energy

Figure 8.12 The ATP cycle


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9. What is an enzyme?

- biological catalyst made of protein

10. How do enzymes work?

- lower energy of activation (EA)

- EA - energy reactants must absorb before the rxn can start



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A

C D

A

A

B

B

B

C

C

D

D

Transition state

Products

Progress of the reaction

∆G < O

Reactants

Fre

e en

ergy

EA

The reactants AB and CD must absorbenough energy from the surroundingsto reach the unstable transition state,where bonds can break.

Bonds break and newbonds form, releasingenergy to thesurroundings.

Figure 8.14 Energy profile of an exergonic reaction


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Progress of the reaction

Products

Course of reaction without enzyme

Reactants

Course of reaction with enzyme

EA

withoutenzyme

EA with enzymeis lower

∆G is unaffected by enzyme

Fre

e e

ne

rgy

Figure 8.15 The effect of enzymes on reaction rate.


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11. Some enzyme terms

- substrate – what the enzyme works on – substrate specific

- active site – where the substrate binds to the enzyme

- induced fit – molecular handshake – when the enzyme binds to the substrate, it wraps around the substrate


Substrate

Active site

Enzyme

(a) (b)

Enzyme- substratecomplex


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1 Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).

Substrates

Products

Enzyme

Enzyme-substratecomplex

5 Products areReleased.

2 Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.

3 Active site (and R groups ofits amino acids) can lower EA

and speed up a reaction by• acting as a template for substrate orientation,• stressing the substrates and stabilizing the transition state,• providing a favorable microenvironment,• participating directly in the catalytic reaction.

4 Substrates are Converted intoProducts.

6 Active siteis available fortwo new substratemolecules.

Figure 8.17 The active site and catalytic cycle of an enzyme


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12. What affects enzyme activity?

- temperature

- pH


Optimal pH for two enzymes

Ra

te o

f re

act

ion

Ra

te o

f re

act

ion

0 20 40 60 80 100Temperature (Cº)

(a) Optimal temperature for two enzymes

(b) Optimal pH for two enzymespH

Optimal temperature fortypical human enzyme

Optimal temperature for enzyme of thermophilic

Optimal pH for pepsin (stomach enzyme)

Optimal pHfor trypsin(intestinalenzyme)

10 2 3 4 5 6 7 8 9 10

(heat-tolerant) bacteria


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- temperature

- pH

- cofactors – non-protein helpers of enzyme activity (Zn, Fe, Cu)

- coenzymes (vitamins)

- inhibitors

- competitive – compete w/ substrate for active site

- non-competitive (allosteric) – bind remotely changing enzyme shape & inhibiting activity



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A noncompetitiveinhibitor binds to the

enzyme away fromthe active site, altering

the conformation ofthe enzyme so that its

active site no longerfunctions.

Competitiveinhibitor

(a) Normal binding

(b) Competitive inhibition

A substrate canbind normally to the

active site of anenzyme.

A competitiveinhibitor mimics the

substrate, competingfor the active site.

Substrate

Active site

Enzyme

Noncompetitive inhibitor

(c) Noncompetitive inhibition

Figure 8.19 Inhibition of enzyme activity


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13. How are enzymes regulated?

- allosteric inhibitors

- allosteric activators


Stabilized inactiveform

Allosteric activaterstabilizes active fromAllosteric enyzme

with four subunitsActive site

(one of four)

Regulatorysite (oneof four)

Active formActivator

Stabilized active form

Allosteric inhibiterstabilizes inactive form

InhibitorInactive formNon-functionalactivesite

(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again.

Oscillation


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- cooperativity


Binding of one substrate molecule toactive site of one subunit locks all subunits in active conformation.

Substrate

Inactive form Stabilized active form

(b) Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate.


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- cooperativity

- feedback inhibition

- compartmentalization in the cell


Active siteavailable

Isoleucineused up bycell

Feedbackinhibition

Isoleucine binds to allosteric site

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

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threoninedeaminase)

Intermediate A

Intermediate B

Intermediate C

Intermediate D

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

End product(isoleucine)

chapter 8: an introduction to metabolism. 1.what is metabolism? all of an organisms chemical...

Documents

law energy

transformation of energy

energy transfer

energy coupling

chemical potential energy

motion potential energy

catabolism releases

different forms of energy