Ch.3_Bioenergetics, Enzymes, & Metabolism_Final

7/27/2019 Ch.3_Bioenergetics, Enzymes, & Metabolism_Final

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BIOENERGETICS,

ENZYMES, &

METABOLISMChapter 3


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What is Bioenergetics?

The study of energy transformations occurring in

living organisms


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Energy Capacity to do work, or to change ormove something

Thermodynamics the study of the changes inenergy that accompany events in the universe

Laws of Thermodynamics


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1st Law of Thermodynamics

Energy cannot be created or destroyed onlytransferred from one form to another

Total amount of energy in the universe isconstant

Examples of Energy Transduction

Chemical

mechanical (moving organelles) Chemical electrical (proton gradients)

Chemical thermal (muscle contraction)

Chemical light (fireflies & fish)


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The System vs. The Surroundings

The universe can be divided into systems &

surroundings

System a subset or section of the universe

under study

Surroundings everything else

The energy of the systeminternal energy (E)

Its change during a transformation is called E


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Energy Conversion & Heat

When there is energy conversion (E) in a system,heat content (Q) may increase or decrease

Reactions that lose heat are exothermic

Reactions that gain heat are endothermic

The energy conversion in a system can becalculated with a mathematical formula

E = Q W


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E Can Be Positive or Negative


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The 2nd Law of Thermodynamics

Events in the universe tend to proceed from a state of

higher energy to a state of lower energy

Such events are called spontaneous, they can occurwithout the input of external energy

Exergonic Release or Produce energy during reaction

Endergonic Uses or Requires energy for reaction to proceed

Entropy (S) Measure of randomness & disorder

It is the energy NOT available to do work


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Entropy increases withevery energy transfer

Entropy is associatedwith random movementsof particles or matter

Living systems maintain

a state of order, or lowentropy

Entropy in the Universe is Increasing


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But Living Organisms Are

OrganizedHow Do You Explain That?

During every energy transfer (even nonspontaneous ones) heat is lost to the

environment

Heat = energy in most disordered form

Therefore the total entropy (Cell + environment) increases


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Free Energy (G)

The 1st and 2nd laws of thermodynamics can be

combined and expressed mathematically

Equation:H =G + TS

Total energy (H) = Free Energy (G) + Entropy (TS)

Spontaneity

IfG < 0 then the rxn is favorable

IfG > 0 then the rxn is not favorable


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Free-Energy Changes in Chemical Rxns

All chemical reactions are theoretically reversible

All chemical reactions spontaneously proceed

toward equilibrium (Keq = [C][D]/[A][B])

The rates of chemical reactions are proportional

to the concentration of reactants

At equilibrium, the free energies of the products

and reactants are equal (G = 0)


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Standard free energy changes are calculated based on

equilibrium conditions

G = -RT ln KeqG = -RT ln [C] [D]/[A][B]

Standard conditions are not representative of cellular conditions,but are useful to make comparisons

Non-standard conditions are corrected for

prevailing conditions

G =G + RT ln Keq

G =G + RT ln [C] [D]/[A][B]


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Conditions in the Cell are NOT Standard

Laws of thermodynamics say rxns are

spontaneous/favorable

Unfavorable reactions are still necessary

Unfavorable reactions occur b/c ofcoupled reactions


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Coupling Endergonic & Exergonic Rxns


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Example of Endergonic & Exergonic Rxns

Glutamic acid + NH3 Glutamate

Endergonic

G = +3.4 kcal/mol

unfavorable

ATP + H2O ADP + PiExergonic

G = -7.3 kcal/mol

Glutamic acid + NH3 + ATP Glutamate + ADP + Pi

G = -3.9 kcal/mol


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Equilibrium vs. Steady-State Metabolism

Cellular metabolism is

nonequilibrium

metabolism

Cells are open

thermodynamic systems

Cellular metabolism

exists in a steady state


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ENZYMESBiological Catalysts


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Basic Properties of Enzymes

Required only in small amounts

Are not permanently altered during the course of a reaction

Do NOT affect the thermodynamics of rxns, only the rates

Are highly specific for theirsubstrates

Produce only appropriate metabolic products

Can be regulated to meet the needs of a cell


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Why Dont Thermodynamically Favorable

Reactions Happen on Their Own?

Molecules are in a relatively stable state

Bonds are not going to break or formwithout the input of some energy

There is an energy barrierthat prevents

the reaction from proceeding

Activation Energy (EA)

The amount of kinetic energy needed to

start a rxn

Copyright The McGraw Hill Companies Inc Permission required for reproduction or display


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Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

EnergyStateofReaction

Energy of activation in the

absence of enzyme

Energy of activation in thepresence of enzyme

Progress of Reaction

Final state

Products

Initial

state

Reactant


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Enzymes Lower the Activation Energy

No enzyme = only a

few substrate

converted

(Pink/Orange)

Enzyme = large

proportion of

substrate converted

(Blue)


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The Enzymatic Reaction

Substrate binds to aportion of the enzymeactive site


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Substrate & active

sites have

complementary

shapes

Substrate is often

taken into a

hydrophobic cleft

of the enzyme


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Mechanisms of Enzyme Catalysis

1. Substrate Orientation

Optimal position for rxn

2. Changing Substrate Reactivity

R groups manipulate interactions

3. Inducing Strain in the Substrate

Stresses covalent bonds


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Shifts in theconformation afterbinding cause aninduced fit between

enzyme and thesubstrate

Covalent bonds of thesubstrate are strained

Destabilizes substrate

Substrate must adopttransition state

Inducing Strain in the Substrate


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Enzyme Reaction Catalyzed

Hydrolases Catalyze a hydrolytic cleavage reaction

Nucleases Break down nucleic acid by hydrolyzing nucleotides

Proteases Break down proteins by hydrolyzing amino acids

Synthases Synthesize molecules in anabolic reaction sby condensing two

smaller molecules together

Isomerases Catalyze the rearrangement of bonds within a single molecule

Polymerase Catalyze polymerization reaction such as the synthesis of DNA

Kinases Catalyze the addition of phosphate groups to moleculesPhosphatases Catalyze the hydrolytic removal of a phosphate group from a

molecule

Oxido-Reductases Catalyze reactions in which one molecule is oxidized while the

other is reduced

ATPases Hydrolyze ATP

Some Common Types of Enzymes


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Enzymes May Have Helpers

May be conjugated with

nonprotein components

Cofactors

Inorganic metals that help bring the

active site & substrate closer

together

Coenzymes

Organic compounds that helpperform a chemical alteration to the

substrate


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Some Common Cofactors


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Some Common CoenzymesVitamin Coenzyme Enzyme-Catalyzed Reaction

Requiring These Coenzymes

Thiamine

(Vitamin B1)

Thiamine

pyrophosphate

Activation & transfer of aldehydes

Riboflavin

(Vitamin B2)

FADH Oxidation-reduction

Niacin NADH, NADPH Oxidation-reduction

Pantothenic acid Coenzyme A Acyl group activation & transfer

Pyridoxine Pyridoxal phosphate Reactions involving amino acid

activation

Biotin Biotin CO2 activation & transfer

Lipoic acid Lipoamide Acyl group activation; oxidation-

reduction

Folic acid Tetrahydrofolate Acitvation & transfer of single

carbon groups

Vitamin B12 Cobalamin coenzymes Isomerization & methyl group

transfers


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Enzyme Kinetics

The rate at which enzymes catalyze reactions

Must be determined under controlled conditions

Enzyme kinetics is interested in the initialvelocity

the speed at

which the enzyme works before any product is produced

Rate of enzymatic reaction will increase until the enzyme has

reached saturation

Saturation = enzymes maximum capacity

This statement assumes that substrate conc. is increasing


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Vmax = Speed of rxn at saturation

Turnover # = max # of molecules that can be converted to product by 1enzyme

The Michaelis constant (KM) can tell the affinity of enzyme for the substrate

(KM) = substrate conc. at of Vmax


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Lineweaver-Burk Plot can make it easier to

determine Vmax and KM.


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Temperature & pH can Affect Enzymatic

Reaction Rates


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Enzyme Inhibitors

Inhibitors slow down enzymatic rxns

Ir reversible inhibi to rs Tightly bound to the enzyme

Reversib le inh ibi to rs

Loosely bound to the enzyme


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Competitive vs. Noncompetitive Inhibition


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Competitive

Similar in structure to

substrate

Bind to the active site toslow enzyme activity

Can be overcome with

high substrate/inhibitorratios

Noncompetitive

Bind to sites other than

active sites and inactivate

the enzyme

The maximum velocity of

enzyme molecules cannot

be reached

Cannot be overcome with

high substrate/inhibitor

ratios.


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METABOLISM


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Chemical rxns are organized into metabolic

pathways

Anabolism Assembling/building macromolecules that the cell needs

Uses/consumes energy

Catabolism Breaking down/destroying organic compounds to obtain energy

Releases/makes energy

Metabolism Overview


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Metabolic Pathways

Metabolic rxns occur in aseries of steps

The products of some rxns

are the reactants/substratesfor the next

Each step is catalyzed by an

enzyme

Enzymes of a metabolicpathway are usually confinedto one location in a cell


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Anabolic & Catabolic Pathways are Interconnected


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The Capture & Utilization of Energy

Cells obtain energy by oxidizing organic molecules

Exergonic reaction a rxn thatproduces orreleases energy (G < 0)

Endergonic reaction a rxn that requires or usesenergy (G > 0)


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Transferring Electrons Moves Energy

Oxidation Reduction Reactions

OILRIG

Redox reactions always occur in pairs An electron donor = reducing agent (red) An electron acceptor = oxidizing agent (blue)

Fe0 + Cu2+ Fe2+ + Cu0

e-

e-

e-

e-Reduced Oxidized Oxidized Reduced


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CELLS USE ENERGY INFOOD TO MAKE ATP


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Glycolysis


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Probably the most ancient metabolic pathway

Splitting of Sugar

Uses & makes

2 Phases

Energy Investment

Energy Production

No O2 needed

ATP

Glycolysis

654321

Glucose (6C)

Pyruvate (3C) Pyruvate (3C)

Glycolysis


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Glycolysis and ATP Formation

10 Rxns

All but 3 are near

equilibrium (G ~ 0)under cellular

conditions

These 3 rxns drive

glycolysis


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Transfer Potential

ATP formation is onlymoderately endergonic

compared with other phosphate

transfer in cells

Transfer potential shown whenmolecules higher on the scale

have less affinity for the group

being transferred than are the

ones lower on the scale.

The less the affinity, the better

the donor.


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Glycolysis and ATP Formation Cont.

Glucose is phosphorylated to glucose 6-phosphate byusing ATP

Glucose 6-phosphate is isomerized to fructose 6-

phosphate

Fructose 6-phosphate is phosphorylated to fructose 1,6-bisphophate using another ATP

Fructose 1,6-bisphosphate is split into two three-carbonphosphorylated compounds.


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NAD+ is reduced to NADH when glyceraldehyde 3-phosphate is converted to 1,3-bisphosphoglycerate

Dehydrogenase enzymes oxidize and reduce cofactors

NAD+ is a nonprotein cofactor associated withgluceraldehyde phosphate dehydrogenase

NAD+ can undergo oxidation and reduction at differentplaces in the cell

NADH donates electrons to the electron transport chain inthe mitochondria


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ATP is formed when 1,3-bisphosphoglycerate is

converted to 3-phosphoglycerate by 3-phosphoglycerate

kinase

Kinase enzymes transfer phosphate groups

Substrate-level phosphorylation occurs when ATP is formed by a

kinase enzyme

3-phosphoglycerate is converted to pyruvate via three

sequential reactions, in one of them a kinase

phosphorylates ADP


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Glycolysis can generate a net of 2 ATPs for each glucose

Glycolysis occurs in the absence of oxygen, it is ananaerobic pathway

The end product, pyruvate, can enter aerobic oranaerobic catabolic pathways.


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Pyruvate is Versatile


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Anaerobic Oxidation of Pyruvate: The

Process of Fermentation Fermentation restores NAD+ from NADH

Under anaerobic conditions, glycolysis depletes thesupply of NAD+ by reducing it to NADH

In fermentation, NADH is oxidized to NAD+ by reducingpyruvate

In muscle and tumor cells pyruvate is reduced to lactate

In yeast and other microbes, pyruvate is reduced andconverted to ethanol

Fermentation is inefficient with only about 8% of theenergy of glucose captured as ATP


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The Process of Fermentation


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Reducing Power

Anabolic pathways require a source of electrons to formlarger molecules

NADPH donates electrons to form large biomolecules

NADPH is a coenzyme similar to NADH

The supply of NADPH represents the cells reducing power

NADP+ is formed by phosphate transfer from ATP to NAD+


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Reducing Power Cont.

NADPH and NADH are interconvertible, but have

different metabolic roles

NADPH is oxidized in anabolic pathways

NAD+ is reduced in catabolic pathways

The enzyme transhydrogenase catalyzes the transfer

of hydrogen atoms from one cofactor to the other

NADPH is favored when energy is abundant

NADH is used to make ATP when energy is scarce


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Metabolic Regulation

Cellular activity is regulated as needed

Regulation may involve controlling key enzymes of metabolicpathways

Enzymes are controlled by alteration in active sites

Covalent modification of enzymes regulated by phosphorylationsuch as protein kinases

Allosteric modulation by enzymes regulated by compoundsbinding to allosteric sites.

In feedback inhibition, the product of the pathway allostericallyinhibits one of the first enzymes of the pathway.


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Feedback Inhibition

Build up of product has a negative effect Turns pathway off


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Separating Catabolic & Anabolic Pathways

Glycolysis and gluconeogenesis are the catabolicand anabolic pathways of glucose metabolism

Synthesis of fructose 1,6-bisphosphate is coupled tohydrolysis of ATP

Breakdown of fructose 1,6-bisphosphate is via hydrolysis byfructose 1,6-bisphosphatase in gluconeogenesis

Phosphofructokinase is regulated by feedback inhibition withATP as the allosteric inhibitor

Fructose 1,6-bisphosphatase is regulated by covalentmodification using phosphate binding

ATP levels are highly regulated


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Separating Catabolic & Anabolic Pathways


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Separating Catabolic and Anabolic Pathways

Anabolic pathways do not proceed via the same reactionsas the catabolic pathways even though they may have

steps in common

Some catabolic pathways are essentially irreversible due to largeG values

Irreversible steps in catabolic pathways are catalyzed by different

enzymes from those in anabolic pathways

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Ch.3_Bioenergetics, Enzymes, & Metabolism_Final