AP Biology

Metabolism & Enzymes

AP Biology

Day 1 - Flow of energy through life

Life is built on chemical reactions transforming energy from one form to

another

organic molecules ATP & organic molecules

organic molecules ATP & organic molecules

sun

solar energy ATP & organic molecules

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Reactions in a closed system Eventually reach equilibrium

Figure 8.7 A

(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until

the system reaches equilibrium.

∆G < 0 ∆G = 0

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Reactions in an open system Cells in our body

Experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium

Figure 8.7

(c) A multi-step open hydroelectric system. Cellular respiration is analogous to this system: Glucose is broken down in a series

of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction

reaches equilibrium.

∆G < 0∆G < 0

∆G < 0

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Metabolism A cell is a miniature factory where

thousands of reactions occur

Metabolism is the totality of an organism’s chemical reactions Arises from interactions between molecules Transforms matter and energy, subject to

the laws of thermodynamics

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1st Law of Thermodynamics

Figure 8.3 

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).

(a)

Chemicalenergy

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2nd Law of Thermodynamics

Figure 8.3 

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’s

surroundings in the form of heat and the small molecules that are the by-productsof metabolism.

(b)

Heat co2

H2O+

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Living systems

Increase the entropy of the universe

Use energy to maintain order

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Metabolism Chemical reactions of life

forming bonds between molecules dehydration synthesis synthesis anabolic reactions

breaking bonds between molecules hydrolysis digestion catabolic reactions

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Examples dehydration synthesis (synthesis)-anabolic

hydrolysis (digestion) - catabolic

enzyme

enzyme

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∆G is Gibbs Free EnergyCalculation to tell us if a reaction will proceed to the left or to the right…..

The sign of ∆ G tells us in what direction the reaction has to shift to reach equilibrium.

Reactions go towards a NEGATIVE ∆ G

The magnitude of ∆ G tells us how far the reaction is from equilibrium at that moment.

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Chemical reaction. In a cell, a sugar molecule is

broken down into simpler molecules.

.

Diffusion. Molecules in a drop of dye diffuse until they are randomly

dispersed.

Gravitational motion. Objectsmove spontaneously from a

higher altitude to a lower one.

• More free energy (higher G)• Less stable

• Greater work capacity

• Less free energy (lower G)• More stable

• Less work capacity

In a spontaneously 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

(a) (b) (c)

Figure 8.5 

At maximum stability-The system is at equilibrium

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Endergonic vs. exergonic reactionsexergonic endergonic- energy released- digestion

- energy invested- synthesis

-G

G = change in free energy = ability to do work

+G

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Energy & life Organisms require energy to live

where does that energy come from? coupling exergonic reactions (releasing energy)

with endergonic reactions (needing energy)

+ + energy

+ energy+

digestion

synthesis

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ATP – Adenosine Tri-phosphate ATP powers cellular work by

coupling exergonic reactions to endergonic reactions

A cell does three main kinds of work Mechanical Transport Chemical

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The Structure and Hydrolysis of ATP

Provides energy for cellular functions

Figure 8.8

O O O O CH2

H

OH OH

H

N

H H

O

NC

HC

N CC

N

NH2Adenine

RibosePhosphate groups

O

O O

O

O

O

-- - -

CH

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Energy is released from ATPWhen the terminal phosphate bond is brokenand the negative charge on the PO4 groups repel

Figure 8.9

P

Adenosine triphosphate (ATP)

H2O

+ Energy

Inorganic phosphate Adenosine diphosphate (ADP)

PP

P PP i

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ATP hydrolysiscan be coupled to other reactions

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/molFigure 8.10

ATP hydrolysis

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ATP drives endergonic reactionsBy phosphorylation, transferring a phosphate to other molecules

(c) Chemical work: ATP phosphorylates key reactants

P

Membraneprotein

Motor protein

P i

Protein moved(a) Mechanical work: ATP phosphorylates motor proteins

ATP

(b) Transport work: ATP phosphorylates transport proteins

Solute

P P i

transportedSolute

GluGlu

NH3

NH2

P i

P i

+ +

Reactants: Glutamic acid and ammonia

Product (glutamine)made

ADP+

P

Figure 8.11

Three types of cellular work are powered by the

hydrolysis of ATP

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The Regeneration of ATP Catabolic pathways

Drive the regeneration of ATP from ADP and phosphate

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 yielding

processes)

ATP hydrolysis to ADP + P i yields energy

Figure 8.12

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∆ G = -7.3 kcal/mol

∆ G = +7.3 kcal/mol

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Day 2

Enzymes and Activation Energy

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What drives reactions? If reactions are “downhill”, why don’t

polymers spontaneously digest into their monomers because covalent bonds are stable bonds

starch

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Activation energy Breaking down large molecules

requires an initial input of energy activation energy large biomolecules are stable must absorb energy to break bonds

energycellulose CO2 + H2O + heat

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Too much activation energy for life Activation energy

amount of energy needed to destabilize the bonds of a molecule

moves the reaction over an “energy hill”

Not a match!That’s too much energy to expose

living cells to!

glucose

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Catalysts So what’s a cell got to do to reduce

activation energy? get help! … chemical help… ENZYMES

G

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Reducing Activation energy Enzymes are Biological Catalysts

reduce the amount of energy to start a reaction

reactant

product

uncatalyzed reaction

catalyzed reaction

NEW activation energy

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Enzymes are proteins (& RNA)

facilitate chemical reactions increase rate of reaction without being consumed reduce activation energy don’t change free energy (G) released or required

required for most biological reactions highly specific

thousands of different enzymes in cells control reactions

of life

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Naming conventions 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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Enzymes vocabularysubstrate

reactant which binds to enzyme enzyme-substrate complex: temporary association

product end result of reaction

active site enzyme’s catalytic site; substrate fits into active site

substrate

enzyme

productsactive site

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The active site can lower an EA barrier by:

Orienting substrates correctly Synthesis: brings substrate closer

together so they can bond to one another Straining substrate bonds

Digestion: active site binds substrate and puts stress on bonds that must be broken, making it easier to separate molecules

Providing a favorable microenvironment

Covalently bonding to the substrate

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Properties of enzymes Reaction specific

each enzyme works with a specific substrate chemical fit between active site & substrate

H bonds & ionic bonds

Not consumed in reaction single enzyme molecule can catalyze

thousands or more reactions per second enzymes unaffected by the reaction

Affected by cellular conditions any condition that affects protein structure

temperature, pH, salinity

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Lock and Key model Simplistic model of

enzyme action substrate fits into 3-D

structure of enzyme’ active site H bonds between

substrate & enzyme like “key fits into lock”

In biology…Size

doesn’t matter…Shape matters!

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Induced fit model More accurate model of enzyme action

3-D structure of enzyme fits substrate substrate binding cause enzyme to

change shape leading to a tighter fit “conformational change” bring chemical groups in position to catalyze

reaction

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Factors that Affect Enzymes

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Factors Affecting Enzyme Function Enzyme concentration Substrate concentration Temperature pH Salinity Activators Inhibitors

catalase

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Factors affecting enzyme function Enzyme concentration

as enzyme = reaction rate more enzymes = more frequently collide with

substrate reaction rate levels off

substrate becomes limiting factor not all enzyme molecules can find substrate

enzyme concentration

reac

tio

n r

ate

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Factors affecting enzyme function

substrate concentration

reac

tio

n r

ate

Substrate concentration as substrate = reaction rate

more substrate = more frequently collide with enzyme

reaction rate levels off all enzymes have active site engaged enzyme is saturated maximum rate of reaction

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Factors affecting enzyme function Temperature

Optimum T° greatest number of molecular collisions human enzymes = 35°- 40°C

body temp = 37°C Heat: increase beyond optimum T°

increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate H, ionic = weak bonds

denaturation = lose 3D shape (3° structure) Cold: decrease T°

molecules move slower decrease collisions between enzyme & substrate

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Factors affecting enzyme function pH

changes in pH adds or remove H+

disrupts bonds, disrupts 3D shape disrupts attractions between charged amino acids affect 2° & 3° structure denatures protein

optimal pH? most human enzymes = pH 6-8

depends on localized conditions pepsin (stomach) = pH 2-3 trypsin (small intestines) = pH 8

720 1 3 4 5 6 8 9 10 11

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Factors affecting enzyme function Salt concentration

changes in salinity adds or removes cations (+) & anions (–) disrupts bonds, disrupts 3D shape

disrupts attractions between charged amino acids affect 2° & 3° structure denatures protein

enzymes intolerant of extreme salinity Dead Sea is called dead for a reason!

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Compounds which help enzymes Activators

cofactors non-protein, small inorganic

compounds & ions Mg, K, Ca, Zn, Fe, Cu bound within enzyme molecule

coenzymes non-protein, organic molecules

bind temporarily or permanently toenzyme near active site

many vitamins NAD (niacin; B3) FAD (riboflavin; B2) Coenzyme A

Mg inchlorophyll

Fe inhemoglobin

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Compounds which regulate enzymes Inhibitors

molecules that reduce enzyme activity competitive inhibition noncompetitive inhibition irreversible inhibition feedback inhibition

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Competitive Inhibitor Inhibitor & substrate “compete” for active site

penicillin blocks enzyme bacteria use to build cell walls

disulfiram (Antabuse)treats chronic alcoholism blocks enzyme that

breaks down alcohol severe hangover & vomiting

5-10 minutes after drinking

Overcome by increasing substrate concentration saturate solution with substrate

so it out-competes inhibitor for active site on enzyme

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Non-Competitive Inhibitor Inhibitor binds to site other than active site

allosteric inhibitor binds to allosteric site causes enzyme to change shape

conformational change active site is no longer functional binding site

keeps enzyme inactive some anti-cancer drugs

inhibit enzymes involved in DNA synthesis stop DNA production stop division of more cancer cells

cyanide poisoningirreversible inhibitor of Cytochrome C, an enzyme in cellular respiration

stops production of ATP

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Irreversible inhibition Inhibitor permanently binds to enzyme

competitor permanently binds to active site

allosteric permanently binds to allosteric site permanently changes shape of enzyme nerve gas, sarin, many insecticides

(malathion, parathion…) cholinesterase inhibitors

doesn’t breakdown the neurotransmitter, acetylcholine

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Allosteric regulation Conformational changes by regulatory

molecules inhibitors

keeps enzyme in inactive form activators

keeps enzyme in active form

Conformational changes Allosteric regulation

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Metabolic pathways

A B C D E F G enzyme

1

enzyme

2

enzyme3

enzyme4

enzyme5

enzyme6

Chemical reactions of life are organized in pathways divide chemical reaction

into many small steps artifact of evolution efficiency

intermediate branching points control = regulation

A B C D E F G

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Efficiency Organized groups of enzymes

enzymes are embedded in membrane and arranged sequentially

Link endergonic & exergonic reactions

AP Biology allosteric inhibitor of enzyme 1

Feedback Inhibition Regulation & coordination of production

product is used by next step in pathway final product is inhibitor of earlier step

allosteric inhibitor of earlier enzyme feedback inhibition

no unnecessary accumulation of product

A B C D E F G enzyme

1

enzyme2

enzyme3

enzyme4

enzyme

5

enzyme6

X

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Feedback inhibition Example

synthesis of amino acid, isoleucine from amino acid, threonine

isoleucine becomes the allosteric inhibitor of the first step in the pathway as product

accumulates it collides with enzyme more often than substrate does

threonine

isoleucine

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Review Feedback Loops Learned about feedback loops at the

start of school (August) Negative Feedback Loops Positive Feedback Loops

The END!

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7

pH

pH

reac

tio

n r

ate

20 1 3 4 5 6 8 9 10

pepsin trypsin

What’shappening here?!

11 12 13 14

pepsin

trypsin

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Enzymes and temperature Different enzymes function in different

organisms in different environments

37°Ctemperature

reac

tio

n r

ate

70°C

human enzymehot spring

bacteria enzyme

(158°F)