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Intro to Metabolism Campbell Chapter 8. http://www.youtube.com/watch?v=Xy0UBpagsu8. http://www.gifs.net. http://ag.ansc.purdue.edu/sheep/ansc442/Semprojs/2003/spiderlamb/eatsheep.gif. Metabolism is the sum of an organism’s chemical reactions - PowerPoint PPT Presentation
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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