Intro to Metabolism Campbell Chapter 8

Intro to MetabolismCampbell Chapter 8

http://www.gifs.nethttp://ag.ansc.purdue.edu/sheep/ansc442/Semprojs/2003/spiderlamb/eatsheep.gifhttp://www.youtube.com/watch?v=Xy0UBpagsu8

• Metabolism is the sum of an organism’s chemical reactions

• Metabolism is an emergent property of life that arises from interactions between molecules within the cell

http://www.encognitive.com/images/metabolic-pathways.png

Bond Energies and the Big Picture

• 1. http://www.angelfire.com/ak2/chemists/project5.html(photosynthesis/cell respiration cycle)

• 2. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BondEnergy.html#Gibbs

• (bond energies and Delta G. follow link to electronegativity and bond energy table)

• 3. http://www.saskschools.ca/curr_content/chem30_05/1_energy/energy3_3.htm

• (advanced Delta G problems for the interested student..)

A metabolic pathway begins with a specific molecule and ends with a product

• Each step is catalyzed by a specific enzyme

BIOCHEMICAL PATHWAYVIDEO

ENZYMES THAT WORK TOGETHER IN A PATHWAY CAN BE

Soluble with free floating intermediates

Covalently bound incomplex

Attached toa membranein sequenceBiochemistry Lehninger

Concentrated in specific location

CATABOLIC PATHWAY (CATABOLISM)Release of energy by the breakdown of complex molecules to simpler compoundsEX: digestive enzymes break down food

ANABOLIC PATHWAY (ANABOLISM)consumes energy to build complicated molecules from simpler onesEX: linking amino acids to form proteins

http://www.sciencelearn.org.nz/var/sciencelearn/storage/images/contexts/nanoscience/sci_media/images/chemical_reactions_involve_making_new_combinations/53823-2-eng-NZ/chemical_reactions_involve_making_new_combinations_full_size_landscape.jpg

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/I/IntermediaryMetabolism.html

Krebs Cycle connects the catabolic and anabolic pathways

Forms of Energy

• ENERGY = capacity to cause change

• Energy exists in various forms (some of which can perform work)

• Energy can be converted from one form to another

KINETIC ENERGY – energy associated with motion– HEAT (thermal energy) is kinetic

energy associated with random movement of atoms or molecules

POTENTIAL ENERGY = energy that matter possesses because of its location or structure

– CHEMICAL energy is potential energy available for release in a chemical reaction

On the platform, the diver hasmore potential energy.

Diving convertspotential energy to kinetic energy.

Climbing up converts kinetic energy of muscle movement to potential energy.

In the water, the diver hasless potential energy.

THERMODYNAMICS = the study of energy transformations

• CLOSED system (EX: liquid in a thermos) = isolated from its surroundings

• OPEN system energy + matter can be transferred between the system and its surroundings

• Organisms are open systems

http://ag.ansc.purdue.edu/sheep/ansc442/Semprojs/2003/spiderlamb/eatsheep.gif

The First Law of Thermodynamics

= energy of the universe is constant

– Energy can be transferred and transformed

– Energy cannot be created or destroyed

• The first law is also called the principle of CONSERVATION OF ENERGY

http://www.pxleyes.com/photoshop-picture/4a3b747566555/remote-control.htmlhttp://www.suncowboy.com/solar101.php

The Second Law of Thermodynamics

During every energy transfer or transformation•entropy (disorder) of the universe INCREASES

•some energy is unusable, often lost as heat

http://hyperphysics.phy-astr.gsu.edu/hbase/therm/entrop.html

http://www.janebluestein.com/articles/whatswrong.html

Chemical energy

Heat

CO2

First law of thermodynamics Second law of thermodynamics

H2O

ORGANISMS are energy TRANSFORMERS!

Spontaneous processes occur without energy input; they can happen quickly or slowly

For a process to occur without energy input, it must increase the entropy of the universe

Free-Energy Change (ΔG) can help tell which reactions will happen

∆G = change in free energy ∆H = change in total energy (enthalpy) or change ∆S = entropy (amount of “disorder”)T = temperature

∆G = ∆H - T∆S

•Only processes with a negative ∆G are spontaneous

•Spontaneous processes can be harnessed to perform work

http://2ndlaw.oxy.edu/gibbs.html (link to discussion for the advanced biology/physics student)

Exergonic and Endergonic Reactions in Metabolism

• EXERGONIC reactions (- ∆G)

• Release energy

• are spontaneous

ENDERGONIC reactions (+ ∆G)

• Absorb energy fromtheir surroundings

• are non-spontaneous

Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions• A cell does three main kinds of work:

– Mechanical

– Transport

– Chemical

• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

• Overall, the coupled reactions are exergonic

Phosphate groups

Ribose

Adenine

ATP (adenosine triphosphate) is the cell’s renewable and reusable energy shuttle

ATP provides energy for cellular functions

Energy to charge ATP comes from catabolic reactions

LE 8-9

Adenosine triphosphate (ATP)

Energy

P P P

PPP i

Adenosine diphosphate (ADP)Inorganic phosphate

H2O

+ +

P

i

ADP

Energy for cellular workprovided by the loss ofphosphate from ATP

Energy from catabolism(used to charge upADP into ATP

ATP

+

Endergonic reaction: DG is positive, reaction is not spontaneous

Exergonic reaction: DG is negative, reaction is spontaneous

ΔG = +3.4 kcal/mol

ΔG = –7.3 kcal/mol

ΔG = –3.9 kcal/mol

NH2

NH3Glu Glu

Glutamicacid

Coupled reactions: Overall DG is negative;Together, reactions are spontaneous

Ammonia Glutamine

ATP H2O ADP P i

+

+ +

Coupled Reactions: Minimize energy loss• The proximity of molecules (enzymes, reactants) in biochemical

pathways allow the maximum harnessing of the motion created by electronic binding rearrangements (aka “bond formation/creation) so the the amount of energy lost as heat is reduced.

• Maximum capture of translational energy and less entropy gain; maximizing the amount of USEFUL WORK THAT CAN BE DONE.

• Picture gears in an engine in proximity, as one gear turns, another turns; although heat is always lost, the proximity of the gears is critical for the operation of the system. The same is true for biochemical pathways; only the gears are molecules.

• Coupled Reaction Animation: http://www.indiana.edu/~oso/animations/useATP.html

– 1st the enzyme provides a surface to bring reactants into proximity.

– 2nd, the translational (kinetic energy) transfer is captured as one molecule experiences a bond rearrangement a.k.a “electronic binding reconfiguration.

– 3rd, another molecule captures the kinetic energy to do work.

Coupled Reaction Videos• http://www.youtube.com/watch?v=VxuQ71l5rEw&feature=results_vi

deo&playnext=1&list=PL496A22971EDE9E61

• (ATP Synthesis animation; coupled reaction)

• http://www.youtube.com/watch?v=5sGqbnQoyrI&feature=results_video&playnext=1&list=PL496A22971EDE9E61

• ATP Synthase animation #2

• http://www.youtube.com/watch?v=VxuQ71l5rEw&feature=results_video&playnext=1&list=PL496A22971EDE9E61

• (lecture video)

LE 8-11

NH2

Glu

P i

P i

P i

P i

Glu NH3

P

P

P

ATPADP

Motor protein

Mechanical work: ATP phosphorylates motor proteins

Protein moved

Membraneprotein

Solute

Transport work: ATP phosphorylates transport proteins

Solute transported

Chemical work: ATP phosphorylates key reactants

Reactants: Glutamic acidand ammonia

Product (glutamine)made

+ +

+

Every chemical reaction between molecules involves bond breaking and bond forming

ACTIVATION ENERGY = amount of energy required to get chemical reaction started

Activation energy is often supplied in the form of heat from the surroundings

http://www.chuckwagondiner.com/art/matches.jpghttp://plato.acadiau.ca/COURSES/comm/g5/Fire_Animation.gif

IT’S LIKE PUSHING A SNOWBALL UP A HILL . . . Once you get it up there, it can roll down by itself

Free energy animation

LE 8-14

Transition state

C D

A B

EA

Products

C D

A B

ΔG < O

Progress of the reaction

Reactants

C D

A B

Free e

nerg

y

The Activation Energy Barrier

http://www.learnerstv.com/animation/animation.php?ani=161&cat=Biology (animation)

CATALYST = a chemical agent that speeds up a reaction without being consumed by the reaction

ENZYMES = biological catalystsMost enzymes are PROTEINS Exception = ribozymes (RNA) Ch 17 & 26

Enzyme Activity Animations• The red ball in the animation represents a reactant that exhibits kinetic motion

in response the its surroundings.

• At cell temperatures, the motion (kinetic, translational or “collision” energy) is often not enough to allow a reaction to occur.

• The enzyme (protein with specific “charged or uncharged amino acids) provide a surface the forces the proximity of the reactants.

• The enzyme thereby reduces the amount of kinetic energy required to initiate a reaction (REDUCED Ea).

• http://www.indiana.edu/~oso/animations/SN2%2BE.html (animation)

• NOTE: enzymes cannot perform a reaction that is thermodynamically impossible. Only the RATE of the reaction is changed.

• In mitochondria...the electron transport chain comprises an enzymatic series of electron donors and acceptors. Each electron donor passes electrons to a more electronegative acceptor, which in turn donates these electrons to another acceptor, a process that continues down the series until electrons are passed to oxygen, the most electronegative and terminal electron acceptor in the chain. Passage of electrons between donor and acceptor releases energy, which is used to generate a proton gradient across the mitochondrial membrane by actively “pumping” protons into the intermembrane space, producing a thermodynamic state that has the potential to do work. The entire process is called oxidative phosphorylation, since ADP is phosphorylated to ATP using the energy of hydrogen oxidation in many steps.

Course ofreactionwithoutenzyme

EA

without enzyme

ΔG is unaffectedby enzyme

Progress of the reaction

Free e

nerg

y

EA withenzymeis lower

Course ofreactionwith enzyme

Reactants

Products

ENZYMES LOWER ACTIVATION ENERGY BY:

– Orienting substrates correctly

– Straining substrate bonds

– Providing a favorable microenvironment

Enzymes change ACTIVATION ENERGY

but NOT energy of REACTANTS or PRODUCTS

http://sarahssureshots.wikispaces.com/Focus+on+Proteinshttp://www.ac-montpellier.fr/sections/personnelsen/ressources-pedagogiques/education-artistique/consultation-avis-du

http://www.learnerstv.com/animation/animation.php?ani=161&cat=Biology

ENZYMES• Most are proteins • Lower activation energy• Specific• Shape determines function• Reusuable• Unchanged by reaction

Image from: http://www.hillstrath.on.ca/moffatt/bio3a/digestive/enzanim.htm

• The REACTANT that an enzyme acts on = SUBSTRATE

• Enzyme + substrate = ENZYME-SUBSTRATE COMPLEX

• Region on the enzyme where the substrate binds = ACTIVE SITE

• Substrate held in active site by WEAK interactions (ie. hydrogen and ionic bonds)

TWO MODELS PROPOSED

• LOCK & KEYActive site on enzymefits substrate exactly

• INDUCED FITBinding of substrate causes changein active site so it fits substratemore closely

http://www.grand-illusions.com/images/articles/toyshop/trick_lock/mainimage.jpghttp://commons.wikimedia.org/wiki/File:Induced_fit_diagram.png

– General environmental factors, such as temperature, pH, salt concentration, etc.

– Chemicals that specifically influence the enzyme

http://www.desktopfotos.de/Downloads/melt_cd.jpg http://www.nealbrownstudio.com/adm/photo/163_nb_fried_egg.jpg

See a movieChoose narrated

Enzyme Activity can be affected by:

TEMPERATURE & ENZYME ACTIVITY

Each enzyme has an optimal temperature at which it can function (Usually near body temp)

http://www.animated-gifs.eu/meteo-thermometers/001.htm

Increasing temperature increases the rate of an enzyme-catalyzed reaction up to a point.Above a certain temperature, activity begins to decline because the enzyme begins to denature.

http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm

pH and ENZYME ACTIVITYEach enzyme has an optimal pH at which it can

function

COFACTORS = non-protein enzyme helpers

• EX: Zinc, iron, copper

COENZYMES = organic enzyme helpers

• Ex: vitamins

http://www.wissensdrang.com/media/wis9r.gif

http://www.elmhurst.edu/~chm/vchembook/595FADcoq.html

Enzyme Kinetics: Studies RATES of reactions;usually measures ∆substrate concentration over ∆ Time

V MAX←

Adding substrate increases activity up to a point

REGULATION OF ENZYME PATHWAYS

• GENE REGULATIONcell switches on or off the genes that code for specific enzymes

REGULATION OF ENZYME PATHWAYS

• FEEDBACK INHIBITIONend product of a pathway interacts with and “turns off” an enzyme earlier in pathway

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

FEEDBACK INHIBITION

NEGATIVE FEEDBACK

– An accumulation of an end product slows the process that produces that product

B

A

C

D

Enzyme 1Enzyme 1

Enzyme 2

Enzyme 3

DD D D

D

D

DD

DD

C

B

A Negative feedback

Example: sugar breakdown generates ATP; excess ATP inhibits an enzyme near the beginning of the pathway

Negative Feedback or Feedback Inhibition Examplesa. In Feedback inhibition (a.k.a., negative feedback) is the Inhibition of

enzyme activity in which the products of a reaction or series of reactions acts upon the enzyme(s) responsible for the generation of that product.

b. Thus, the more product there is, the less product which is produced. If similarly, the less product there is, the more product which is produced, then there should exist a stable product concentration which is (or range of concentrations which are) maintained over time.

c. Feedback inhibition generally leads to well controlled metabolic pathways.

d. Your furnace and thermostat at home constitute a negative feedback system. The furnace heats things up. At a given temperature the furnace is shut down by the thermostat. The system only starts up again when the inhibitor (the heat) is lost from the system.

e. Example: driving at the speed limit:

f. An analogy is driving down the highway:

a. If you are going too fast, you slow down.

b. If you are going too slowly, you speed up.

g. Here your velocity is the product, your car is the enzyme (gasoline and air are your substrates), and you are translating your knowledge of your vehicle's velocity into feedback inhibition of the rate at which your car acts upon gasoline and air.

h. The science of control which includes such constructs as negative feedback is called cybernetics.

http://www.northland.cc.mn.us/biology/biology1111/animations/enzyme.html

POSITIVE FEEDBACK (less common)

– The end product speeds up production

WW

X

Y

Z

ZZ

ZZ

Z

Z Z Z

Z Z Z Z

Z

ZZ Z

ZZ

Y

X

Enzyme 4

Enzyme 5

Enzyme 6

Enzyme 4

Enzyme 5

Enzyme 6

Positivefeedback

EXAMPLE: Chemicals released by platelets that accumulate at injury site, attract MORE platelets to the site.

Positive Feedback Examples:• The product of one or a series of enzymatic reactions acts upon the

enzymes responsible for the generation of that product to increase the activity of one or more of these enzymes.

-Positive feedback can lead to out of control situations. Positive feedback tends to be employed by life only under circumstances in which a gross over response (often destructive) is desirable.

-A car analogy would have you accelerating even if you were already driving too fast.

-Inflammation response during injury, allergic response, bee stings are another examples.

-Positive feedback occurs durign childbirth as the pressure of the infant's head against the exit from the womb stimulates stretch-sensitive receptors. These receptors signal for the release of a hormone from the brain (oxytocin) that intensifies labor contraction. The contractions cause the release of additional hormone and continue until stretching is stopped by the infant's birth."

http://mansfield.osu.edu/~sabedon/biol1045.htm Practice Quiz..scroll down to #21

S

REGULATION OF ENZYME ACTIVITY• ALLOSTERIC REGULATION

protein’s function at one site is affected by binding of a regulatory molecule at another site

• Allosteric regulation can inhibit or stimulate an enzyme’s activity

http://bio.winona.edu/berg/ANIMTNS/allostan.gif

Allosteric enzyme inhibition

SOME ALLOSTERIC ENZYMES HAVE MULTIPLE SUBUNITS

• Each enzyme has active and inactive forms

• The binding of an ACTIVATOR stabilizes the active form

• The binding of an INHIBITOR stabilizes the inactive form

Substrate

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

Cooperativity another type of allosteric activation

Stabilized active formInactive form

COOPERATIVITY = form of allosteric regulation that can amplify enzyme activity

Binding of one substrate to active site of one subunit locks all subunits in active conformation

COMPETITIVE inhibitor REVERSIBLE; Mimics substrate and competes with substrate for active site on enzyme

ENZYMEANIMATION

Enzyme Inhibitors

Enzyme Inhibitors

NONCOMPETITIVE inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

ENZYMEANIMATION