AP Biology Day 13

Wednesday, September 17, 2014

AP BIOLOGY DAY 13

DO-NOW 1.  Take out your composition lab notebook 2.  Sit together in your groups 3.  Make your final observations for your lab 4.  If time, begin the post-lab questions.

ANNOUNCEMENTS •  Tutoring

•  If you are not receiving passing scores, it is expected that you attend tutoring and complete re-takes to improve your grade to a 70% or higher

•  Mornings beginning at 7am or lunch

CW/HW ASSIGNMENTS 7.  Ch. 8 Lecture Notes

PLANNER •  Finish Enzyme Investigation lab

•  Complete Enzyme Activity Pre-Lab (on weebly)

FLT •  I will be able to explain how order in

living things is maintained by constant free energy by completing Ch. 8 Notes

ESSENTIAL KNOWLEDGE •  2.A.1: All living systems require

constant input of free energy.

NOTES PROTOCOL

•  Noise level 0

•  Raise hand to question/comment

•  Do not copy notes word for word – just the main ideas

•  You may write notes in your subject notebook or you may use the notes outline provided on the website (for binder use)

•  Quiz will be based on reading and notes

CH. 8: INTRODUCTION TO METABOLISM

I. METABOLISM •  Metabolism =

•  All of the chemical reactions in an organism •  Involves the transformation of matter and energy

II. ENERGY D.  Free Energy •  All living organisms require a constant input of free

energy, which is used for organization, growth, and reproduction (Big Idea 2)

II. ENERGY D.  Free Energy •  Some reactions occur spontaneously and others require

the input of energy •  Gibbs free energy (G) = Energy that can do work at a

constant P and T (such as in a living cell) •  Gibbs free energy helps us identify whether or not a

reaction is spontaneous by looking at the potential driving forces behind a chemical reaction

II. ENERGY D.  Free Energy •  ΔG = change in free energy during a process •  ΔH = Change in enthalpy (total energy)

•  ΔS = change in entropy (disorder) •  T = Temperature in Kelvin

ΔG = ΔH – TΔS - ΔG = spontaneous reaction (requires no input of energy to occur)

NOTE •  This equation is on your AP Biology equation sheet so

you do not need to memorize it – just how to interpret it

II. ENERGY D.  Free Energy

ΔG = ΔH – TΔS 1.  Significance of Free Energy •  Spontaneous reactions = free E decreases (-ΔG) and

the stability of a system increases •  Less free energy = more stable

•  Equilibrium = state of maximum stability •  There is no net change in the concentration

of reactants or products because the forward and reverse reactions at occur at the same rate

•  Systems never spontaneously move away from equilibrium

III. ENERGY AND LIFE

III. ENERGY AND LIFE A.  Exergonic Rxn vs. Endergonic Rxn

•  Exergonic reaction: Spontaneous (–ΔG ) •  Endergonic reaction: Nonspontaenous (+ΔG)

Energy

(a) Exergonic reaction: energy released

Progress of the reaction

Free

ene

rgy

Products

Amount of energy released (∆G < 0)

Reactants

Energy

(b) Endergonic reaction: energy required


Free

ene

rgy

Products

Amount of energy required (∆G > 0)

Reactants

III. ENERGY AND LIFE B.  Equilibrium and Metabolism

•  Reactions in a closed system eventually reach equilibrium and then do no work ΔG = 0

!  An open system exchanges matter & energy with the environment

!  A closed system does not exchange matter

III. ENERGY AND LIFE B.  Equilibrium and Metabolism

•  Cells are not in equilibrium; they are open systems experiencing a constant flow of materials.

•  Metabolism is NEVER at equilibrium

•  A catabolic (breaks down molecules) pathway in a cell releases free energy in a series of reactions

IV. ATP •  ATP powers cellular work via ENERGY COUPLING =

coupling exergonic reactions to endergonic reactions •  In other words, energy from the exergonic reaction of

ATP hydrolysis can be used to drive an endergonic reaction!

IV. ATP B.  Energy Coupling

•  Most energy coupling in cells is mediated by the exergonic hydrolysis of ATP

•  Overall, the coupled reactions are exergonic

IV. ATP A.  Three types of work done by ATP:

•  Chemical •  Ex/ Phosphorylation of reactants to make rxns proceed

•  Transport •  Ex/ Phosphorylation of transport proteins/pumps

•  Mechanical •  Ex/ Phosphorylation of motor proteins

IV. ATP C.  Structure and the Hydrolysis of ATP

•  ATP = Adenosine Triphosphate •  Made of ribose, adenine, and 3 phosphate groups

•  Modified nucleotide

IV. ATP C.  Structure and the Hydrolysis of ATP

•  E is released from ATP when the terminal phosphate bond is broken by hydrolysis

•  This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

Hydrolysis of ATP releases energy to do work

Inorganic phosphate

Energy

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

P P

P P P

P + +

H2O

i

IV. ATP D.  Regeneration of ATP

•  Hydrolysis of ATP: ATP " ADP + Pi + Energy •  ATP can be renewed!

#  ADP + Pi + E ATP •  The energy to phosphorylate ADP comes from

catabolic reactions (that release energy) in the cell

PAIR-SHARE-RESPOND 1.  What can Gibbs free energy tell us about a

reaction? 2.  Distinguish between an exergonic and

endergonic reaction. 3.  What effect will an increase in entropy

have on Gibbs free energy? 4.  How does ATP release energy? 5.  What is meant by the term “energy

coupling”?

V. ENZYMES Enzymes increase the rate of metabolic rxns by lowering E barriers. End in –ase (usually) Enzymes are named after their substrate (ex/ sucrase is an enzyme for sucrose)

•  In the next class, we’re going to be looking at an enzyme that acts on the substrate hydrogen peroxide. What do you think the enzyme is called?

V. ENZYMES A.  Catalyst

•  Catalyst = increases the rate of a reaction without being consumed by the rxn

•  Enzymes = proteins that act as catalysts

V. ENZYMES B.  Enzymes and activation energy

1.  Free energy of activation •  Every chemical reaction between molecules involves

bond breaking and bond forming •  Activation Energy (Ea) = initial energy needed to start

a chemical reaction •  Enzymes lower the amount of Ea needed, thus

increasing the reaction rate

The effect of an enzyme on activation energy


Products

Reactants

∆G is unaffected by enzyme

Course of reaction without enzyme

Free

ene

rgy

EA without enzyme EA with

enzyme is lower

Course of reaction with enzyme


2.  Transition state •  = Highly unstable state where bonds can break

The effect of an enzyme on activation energy


Products

Reactants

∆G is unaffected by enzyme

Course of reaction without enzyme

Free

ene

rgy

EA without enzyme EA with

enzyme is lower

Course of reaction with enzyme


Note:

•  Enzymes do NOT affect ΔG

•  Enzymes increase the rate of reactions that would already occur eventually

V. ENZYMES C.  Enzyme Specificity

V. ENZYMES C.  Enzyme Specificity 1.  Substrate = the reactant that an enzyme acts on

•  When an enzyme binds to its substrate, it forms an enzyme-substrate complex (reaction occurs)

2.  Active Site = region on enzyme where substrate binds. Complementary to its specific substrate.


3.  Induced Fit •  When an enzyme binds to the matching substrate,

the active site changes its orientation to enhance its ability to catalyze the rxn

Induced fit between an enzyme and its substrate

Substrate

Active site

Enzyme Enzyme-substrate complex

(b) (a)


4.  Active site can lower an Ea barrier by: •  Orienting substrates correctly

•  Straining substrate bonds/tension •  Providing a favorable microenvironment •  Covalently bonding to the substrate


5.  Catalytic Cycle of an Enzyme = !  Substrates enter active site " induced fit

!  Held together by weak interactions !  Active site lowers Ea/increases rxn rate !  Substrates are converted into products

!  Products are released !  Active site is once again available


5.  Catalytic Cycle of an Enzyme =

PAIR-SHARE-RESPOND 1.  What is a catalyst? 2.  What effect do enzymes have on the

energy profile of a reaction? 3.  Distinguish between an active site and a

substrate 4.  Explain the induced-fit model for enzymes. 5.  What type of interactions hold together

substrates and enzymes?

V. ENZYMES D.  Factors Affecting Enzyme Activity

•  An enzyme’s activity/reaction rate can be affected by environmental factors

•  Key question: How do biotic and abiotic factors affect an enzyme’s ability to function?

•  We’ll be looking at this in tomorrow’s lab :D


1.  Environmental factors affecting enzyme activity: a.  Temperature

•  Enzyme activity tends to increase with temperature until it reaches its optimum temp


1.  Environmental factors affecting enzyme activity: b.  pH

•  Most enzymes perform best within pH 6-8, but there are some exceptions.

Environmental

factors affecting enzyme

activity R

ate

of re

actio

n

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


1.  Environmental factors affecting enzyme activity: c.  Cofactors/Coenzymes

•  Cofactors = nonprotein enzyme helpers (such as metals) bound to the enzyme

•  Coenzymes = organic cofactors (such as vitamins)


1.  Environmental factors affecting enzyme activity: c.  Cofactors/Coenzymes

•  Certain enzymes may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites


2.  Enzyme Inhibitors •  Inhibitors are chemicals that covalently bond to

enzymes in order to limit that enzyme’s function


2.  Enzyme Inhibitors a.  Competitive Inhibitors

•  Bind to the active site of an enzyme, competing with the substrate


2.  Enzyme Inhibitors a.  Noncompetitive Inhibitors

•  Bind to another part of an enzyme & cause the enzyme to change shape

•  The active site is then less able to bind with substrates

Inhibition of enzyme activity

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

Noncompetitive inhibitor

Active site Competitive inhibitor

Substrate

Enzyme


•  Metabolism includes ALL of the body’s chemical reactions

•  They cannot occur all at once!

•  A cell regulates metabolism by: !  Switching on or off the genes that encode specific

enzymes !  Or by regulating the activity of enzymes


3.  Allosteric Regulation •  Can inhibit OR stimulate an enzyme’s activity

•  Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site


3.  Allosteric Regulation •  Allosteric site = site where molecule binds

•  Activation/Inhibition: •  Activator = Stabilizes active enzyme form •  Inhibitor = Stabilizes inactive enzyme form

V. ENZYMES D.  Factors Affecting Enzyme Activity 3.  Allosteric Regulation

c.  Cooperativity •  A substrate binding to one active site causes all of

the other subunits to change to the favorable conformation

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

V. ENZYMES D.  Factors Affecting Enzyme Activity 3.  Allosteric Regulation

f.  Feedback Inhibition •  = The end product of a metabolic pathway acts as

an allosteric inhibitor. It binds to an enzyme in the pathway to inhibit it.

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

Feedback Inhibition

Intermediate C

Feedback inhibition

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

PAIR-SHARE-RESPOND 1.  How does temperature (generally) affect

enzyme activity? 2.  How does pH (generally) affect enzyme

function? 3.  Distinguish between competitive and

noncompetitive inhibitors. 4.  Describe feedback inhibition. Be sure to

specify its purpose.

CW •  Finish notes •  Work on lab •  Begin “Enzyme activity” pre-lab

YOU SHOULD NOW BE ABLE TO:

1.  Distinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and endergonic reactions.

2.  In your own words, explain the second law of thermodynamics and explain why it is not violated by living organisms.

3.  Explain in general terms how cells obtain the energy to do cellular work.

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

4.  Explain how ATP performs cellular work. 5.  Explain why an investment of activation energy is

necessary to initiate a spontaneous reaction. 6.  Describe the mechanisms by which enzymes

lower activation energy. 7.  Describe how allosteric regulators may inhibit or

stimulate the activity of an enzyme.

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

AP Biology Day 13

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