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sites of cellular respiration

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Please pick up your lab notebooks from the table by the door.


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Overall 1st Quarter Grades (AVG) (updated w/ Unit 2 Test included)

• 1st period: 85%

• 2nd period: 89%

• 3rd period: 86%

• 4th period: 88%

• 6th period: 90%

• 8th period: 86%

• WOW!!!


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Pre-Lab Preparation!!!• Go to “Labs & Lab Notebook” link on my website.• Click on “LabBench” link.• Click on “Lab 1: Diffusion & Osmosis.”• Read through Concepts #1-5, Design Exercises

#1-2, and Self-Quiz ?s #1-3 of the Pre-Lab.• Answer the general questions COMPLETELY that

are listed on your Lab Notebook Guidelines sheet.– Remember to ignore the “Water Potential”

section and calculations– Due on Friday!!!


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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?

Chapter 8: An Introduction to Metabolism

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

- Chemical energy – bio speak for potential energy that can be released 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 – dehydr. syn. – 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: Use an exergonic reaction to fuel an endergonic reaction!!!

Endergonic reaction (dehydration synthesis of NH2 and Glu): ∆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 (hydrolysis of ATP): ∆ 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 (endergonic)

ATP

ADP + P i

Energy for cellular work (such as dehydration synthesis!)

Energy from catabolism(breaking down food molecules via hydrolysis)

ATP hydrolysis to ADP + P i yields energy (exergonic)

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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Figure 8.17 The active site and catalytic cycle of an enzyme


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How does it work?

• Variety of mechanisms to lower activation energy & speed up reaction– Dehydration synthesis

• active site orients substrates in correct position for reaction/brings substrates closer together

– Hydrolysis • active site binds substrate & puts stress on

bonds that must be broken, making it easier to separate molecules


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Enzymes in REAL LIFE!• Enzymes named for reaction they catalyze

– sucrase breaks down sucrose

– proteases break down proteins

– lipases break down lipids

– DNA polymerase builds DNA• adds nucleotides

to DNA strand

– pepsin breaks down proteins (polypeptides)


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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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12. What affects enzyme activity?- temperature- pH- cofactors – inorganic non-protein helpersof enzyme activity (Zn, Fe, Cu)

- coenzymes – organic cofactors (vitamins)

- inhibitors- competitive – compete w/ substrate for active site

-PENICILLIN – blocks enzyme that bacteria use to build cell walls

- non-competitive – bind remotely (not to active site, but to secondary site called ALLOSTERIC SITE,) thus changing enzyme shape & inhibiting activity

-CYANIDE – changes shape of enzyme necessary to make ATP during cellular respiration



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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

-keeps enzyme inactive

- allosteric activators

-keeps enzyme active


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

Oscillation


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- feedback inhibition

-final product is inhibitor

of earlier step!

-prevents unnecessary

accumulation of product


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)

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Documents

law energy

transformation of energy

energy transfer

chemical potential energy

motion potential energy

catabolism releases

different forms of energy

metabolism slide