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An organisms metabolism transforms matter and energy, subject to the laws of thermodynamics
Metabolism is the totality of an organisms chemical reactions Metabolism is an emergent property of life that arises from interactions between molecules within the cell
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A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme
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Enzyme 1
Enzyme 2 B C Reaction 2
Enzyme 3 D Reaction 3
A
Reaction 1
Starting molecule
Product
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Catabolic pathways release energy by breaking down complex molecules into simpler compounds Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism
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Anabolic pathways consume energy to build complex molecules from simpler ones The synthesis of protein from amino acids is an example of anabolism Bioenergetics is the study of how organisms manage their energy resources
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Forms of Energy
Energy is the capacity to cause change Energy exists in various forms, some of which can perform work
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Kinetic energy is energy associated with motion Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules Potential energy is energy that matter possesses because of its location or structure
A diver has more potential energy on the platform than in the water.
Free
A diver has less potential energy in the water Powerpoint than Templates on the platform.
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Thermodynamics is the study of energy transformations A closed system, such as that approximated by liquid in a thermos, is isolated from its surroundings In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems
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According to the first law of thermodynamics, the energy of the universe is constant:
Energy can be transferred and transformed, but it cannot be created or destroyed
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During every energy transfer or transformation, some energy is unusable, and is often lost as heat According to the second law of thermodynamics:
Every energy transfer or transformation increases the entropy (disorder) of the universe
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Heat
Chemical energy
CO2 + H2O
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Living cells unavoidably convert organized forms of energy to heat 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
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The evolution of more complex organisms does not violate the second law of thermodynamics Entropy (disorder) may decrease in an organism, but the universes total entropy increases
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The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously
Biologists want to know which reactions occur spontaneously and which require input of energy To do so, they need to determine energy changes that occur in chemical reactions
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An exergonic reaction proceeds with a net release of free energy and is spontaneous An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous
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Energy
Products
Progress of the reaction (a) Exergonic reaction: energy released Products Free energy Amount of energy required (G > 0)
Energy
Reactants
Progress of the reaction (b) Endergonic reaction: energy required Free Powerpoint Templates
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Fig. 8-6a
Reactants
Amount of energy released (G < 0)
Energy
Free energy
Products
Fig. 8-6b
Products
Free energy
Reactants
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ATP (adenosine triphosphate) is the cells energy shuttle ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups
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Fig. 8-8
Adenine
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The bonds between the phosphate groups of ATPs tail can be broken by hydrolysis Energy is released from ATP when the terminal phosphate bond is broken This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
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Fig. 8-9
H2O
Pi
Energy
Inorganic phosphate
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ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant The recipient molecule is now phosphorylated
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Fig. 8-11
Membrane protein
Pi
Solute
Solute transported
ADP
+ P
Vesicle
Cytoskeletal track
ATP
Motor protein
Protein moved
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(b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed Free Powerpoint Templates
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Fig. 8-12
ATP + H2O
ADP + P i
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Enzymes
1. 2. 3. 4. Enzymes speed up metabolic reactions by lowering energy barriers Enzymes are substrate specific The active site in an enzymes catalytic center A cells physical and chemical environment affects enzyme activity
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Anabolism: Aspect of metabolism simpler substances are combined to form complex substances for storage of energy for the production of new cellular materials and growth. Catabolism: Aspect of metabolism complex substances are broken down to simpler substance releasing chemical energy. Metabolism = Catabolism + Anabolism
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Chemical reactions between molecules involve both bond breaking and bond forming.
To hydrolyze sucrose, the bond between glucose and fructose must be broken and then new bonds formed with a hydrogen ion and hydroxyl group from water.
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In an exergonic reaction, the reactants must still absorb energy from the surroundings, the activation energy (EA), to break the bonds.
This energy makes the reactants unstable, increases the speed of the reactant molecules, and creates more powerful collisions.
In exergonic reactions, the activation energy released back to the surroundings, more energy is released with the formation of new bonds.
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Activation energy is the amount of energy necessary to push the reactants over an energy barrier.
At the summit the molecules are at an unstable point, the transition state. The difference between free energy of the products and the free energy of the reactants is the delta G.
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For some processes, the barrier is not high and the thermal energy provided by room temperature is sufficient to reach the transition state. In most cases, EA is higher and a significant input of energy is required.
A spark plug provides the energy to energize gasoline. Without activation energy, the hydrocarbons of gasoline are too stable to react with oxygen.
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The laws of thermodynamics would seem to favor the breakdown of proteins, DNA, and other complex molecules.
However, in the temperatures typical of the cell there is not enough energy for a vast majority of molecules to make it over the hump of activation energy. Yet, a cell must be metabolically active. Heat would speed reactions, but it would also denature proteins and kill cells.
Denature: To alter the physical properties and three dimensional structure of protein, usually by treating it with excess heat, strong acid or strong base. Reactant: substrate that participate in a chemical reaction.
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Fig. 8-14
Transition state
A C
B D
EA
Reactants
A
C
B
G < O D
Products
Progress of the reaction
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Enzymes catalyze reactions by lowering the EA barrier Enzymes do not affect the change in free energy (G); instead, they hasten reactions that would occur eventually
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EA without enzyme
Products
Progress of the reaction
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The shape of active site matches the shape of a specific part of the substrate molecule. Induced Fit
Substrate molecule upon binding to the active site of the enzyme induces a slight change in the shape of both molecule, substrate and enzyme. Once substrate molecule has made contact with the active site and has initiated the change in shape, the enzyme initiates the actual reaction of the substrate molecule. Once the reaction complete, attraction between substrate and enzyme cease, freeing the enzymes from the product enabling to catalyzed the second reaction of the same type.
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The active site of an enzymes is a groove on the surface of the protein into which the substrate fits. The specificity of an enzyme is due to the fit between the active site and the substrate. As the substrate binds, the enzyme changes shape leading to a tighter induced fit, bringing chemical groups in position to catalyze the reaction.
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The reason a particular enzyme will combine only with one kind of substrate is that the fit between the two is very precise. In fact, the fit is so precise, the combining of the enzyme and substrate results in a slight change in the shape of both. This precise fit that modifies both original molecules is called an induced fit. This "strained" fit acts to break old chemical bonds and form new ones, resulting in the formation of the product from the substrate. Once this change has occurred, the product is released from the enzyme, and the enzyme can combine with another molecule of substrate.
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In most cases substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds.
R groups of amino acids on the active site catalyze the conversion of substrate to product.
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In an enzymatic reaction, the substrate binds to the active site of the enzyme The active site can lower an EA barrier by
Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate
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Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzymecatalyzed reaction
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Fig. 8-16
Substrate
Active site
Enzyme-substrate complex
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A single enzyme molecule can catalyze thousands or more reactions a second. Enzymes are unaffected by the reaction and are reusable. Most metabolic enzymes can catalyze a reaction in both the forward and reverse direction.
The actual direction depends on the relative concentrations of products and reactants. Enzymes catalyze reactions in the direction of equilibrium.
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Enzymes use a variety of mechanisms to lower activation energy and speed a reaction.
As the active site binds the substrate, it may put stress on bonds that must be broken, making it easier to reach the transition state.
R groups at the active site may create a conducive microenvironment for a specific reaction.
The active site orients substrates in the correct orientation for the reaction.
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The rate that a specific number of enzymes converts substrates to products depends in part on substrate concentrations. At low substrate concentrations, an increase in substrate speeds binding to available active sites. However, there is a limit to how fast a reaction can occur. At some substrate concentrations, the active sites on all enzymes are engaged, called enzyme saturation. The only way to increase productivity at this point is to add more enzyme molecules.
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Km
Substrate concentration at V
max
[S]
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ATP + H2O
ADP + P i
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Fig. 8-13
Sucrose (C12H22O11)
Sucrase
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Fig. 8-17
2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 3 Active site can lower EA
Substrates
Enzyme-substrate complex
6
Active site is available for two new substrate molecules.
Enzyme
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100
10
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Cofactors
Cofactors are nonprotein enzyme helpers Cofactors may be inorganic (such as a metal in ionic form) or organic An organic cofactor is called a coenzyme Coenzymes include vitamins
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Enzyme Inhibitors
Competitive inhibitors bind to the active site of an enzyme, competing with the substrate Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective Examples of inhibitors include toxins, poisons, pesticides, and antibiotics
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Fig. 8-19
Noncompetitive inhibitor (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition
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If the inhibitor binds to the same site as the substrate, then it blocks substrate binding via competitive inhibition.
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If the inhibitor binds somewhere other than the active site, it blocks substrate binding via noncompetitive inhibition. Binding by the inhibitor causes the enzyme to change shape, rendering the active site unreceptive or less effective at catalyzing the reaction. Reversible inhibition of enzymes is a natural part of the regulation of metabolism.
Reversible inhibitor: A substance that forms a weak bonds with an enzyme, temporarily interfering with its function. A reversible inhibitor can be competitive or non competitive. Irreversible inhibitor: A substance that permanently inactivates an enzyme.
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Chemical chaos would result if a cells metabolic pathways were not tightly regulated A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes
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Fig. 8-20
Activator
Active form
Oscillation
Inactive form
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Fig. 8-20a
Oscillation
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Cooperativity is a form of allosteric regulation that can amplify enzyme activity In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits
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Fig. 8-20b
Substrate
Inactive form
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In enzymes with multiple catalytic subunits, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits, a process called cooperativity. This mechanism amplifies the response of enzymes to substrates, priming the enzyme to accept additional substrates
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Some allosteric regulators, activators, stabilize the conformation that has a functional active site. Other regulators, inhibitors, stabilize the conformation that lacks an active site.
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Metabolic control often depends on allosteric regulation In many cases, the molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors. These molecules often bind weakly to a allosteric site, a specific receptor on the enzyme that is not the active site. Binding by these molecules can either inhibit or stimulate enzyme activity.
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Most allosterically regulated enzymes are constructed of two or more polypeptide chains. Each subunit has its own active site and allosteric sites are often located where subunits join. The whole protein oscillates between two conformational shapes, one active, one inactive.
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As the chemical conditions in the cell shift, the pattern of allosteric regulation will shift as well. In many cases both inhibitors and activators are similar enough in shape that they compete for the same allosteric sites.
These molecules may be products and substrates of a metabolic pathway. For example, some catabolic pathways have allosteric sites that are inhibited when ATP binds and activated when AMP binds. When ATP levels are low, AMP levels are high, and the pathway is turned on until ATP Free levels Powerpoint Templates Page 88 levels rise, AMP fall and inhibition by
Fig. 8-21
RESULTS Caspase 1
Active form
Free
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Fig. 8-21a
EXPERIMENT
Caspase 1 Active site Substrate
SH Allosteric
SS
Hypothesis: allosteric inhibitor locks enzyme in inactive form Free Powerpoint Templates Page 90
Fig. 8-21b
RESULTS
Caspase 1
Inactive form
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Structures within the cell help bring order to metabolic pathways Some enzymes act as structural components of membranes In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria
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Fig. 8-23
Mitochondria
1 m
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EA without enzyme
A cells physical and chemical environment affects enzyme activity The three-dimensional structures of enzymes (almost all proteins) depend on environmental conditions. Changes in shape influence the reaction rate. Some conditions lead to the most active conformation and lead to optimal rate of reaction.
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2. Because pH also influences shape and therefore reaction rate, each enzyme has an optimal pH too. This falls between pH 6 - 8 for most enzymes. However, digestive enzymes in the stomach are designed to work best at pH 2 while those in the intestine are optimal at pH 8, both matching their working environments.
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Fig. 8-UN4
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Feedback Inhibition
In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed
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One of the common methods of metabolic control is feedback inhibition metabolic pathway is turned off by its end product. The end product acts as an inhibitor of an enzyme in the pathway. When the product is abundant the pathway is turned off, when rare the pathway is active.
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Systematic names for each enzyme have been made in an international claasification of enzymes.
Oxidoreductase: are involved in oxidation/reduction. Transferase: transfer functional groups between donor and receptor. Hydrolases transfer water that is they catalysed the hydrolysis of a substrate. Lyases: add or remove the element of water, ammonia or CO2 to form double bond. Isomerase: catalyzed changes within one molecule. Ligase (synthetases): join two molecule together at the expense of a high-energy phosphate bond of ATP.
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