Bio 161 Ch. 8 Energy, Enzymes, and Metabolism

Enthalpy (H)

Total energy in biological systems, cannot measure absolutely

Feedback Inhibition

(AKA End-Product Inhibition) Mechanism in which when the end product is present at high concentration some of it binds to an allosteric site on the commitment step enzyme thereby inactivating it, thus the final product acts as a noncompetitive inhibitor, this prevents the cell from wasting energy and producing a product it already has enough of

Enthalpy Equation

(H = G + TS rearranged to:) Delta G = Delta H - T(Delta S) -if delta G is positive, then products have more energy than reactants and there must have been some input of free energy (b/c of first law) -if delta G is negative, then free energy is released **If necessary free energy not available then reaction does not occur!

Endergonic

(endothermic) Reactions that require or consume free energy (positive delta G) (see graph 8.3)

Exergonic

(exothermic) Reactions that release free energy (negative delta G), catabolic (see graph 8.3)

Reaction Rate in Catalyzed VS Uncatalyzed Reaction

-With no enzyme present, the reaction rate increases with substrate concentration -With an enzyme present, a saturation phenomenon occurs: *at low substrate concentration, the enzyme greatly increases reaction rate *at high substrate concentration, the enzyme reaches maximum rate LOOK AT 8.13 GRAPH!

Mechanisms Used by Enzymes to Catalyze a Reaction

-orient substrates: active site has just the right shape to bind substrates in a way that atoms that interact are adjacent, as substrates are normally moving randomly in solution -induce strain in substrate: can cause bonds in substrate to stretch thereby putting it in an unstable transition state, promoting certain bonding types rather than others -temporarily add chemical groups to substrate: acid base, covalent, or metal ion catalysis

Factors Affecting Delta G

-point of equilibrium -beginning concentrations of reactants and products -temp -pH -pressure

Nonprotein Chemical Partners Required for Certain Enzymes to Function

-prosthetic groups -inorganic factors -coenzymes

Why are enzymes so large? What are possible roles of the rest of the macromolecule?

-provide a framework so that the amino acids of the active site are properly positioned in relation to the substrate -participate in significant changes in protein shape and structure that result in induced fit -provide binding sites for regulatory molecules

Standard Laboratory Conditions

1 atm, 25 degrees C, 1 M, pH 7 (delta G 0)

2 Types of Metabolism

1. Anabolic Reactions 2. Catabolic Reactions **Catabolic and anabolic reactions are often linked, so energy released in catabolic reactions is often used to drive anabolic reactions (biological work)

2 Factors Affecting Sign and Magnitude of Delta G

1. Delta H: total amount of energy added to or released from system 2. Delta S: affects sign and size of term TS showing influence of entropy on delta G

2 Types of Energy

1. Potential Energy 2. Kinetic Energy

Why does ATP release free energy when one or two of its phosphate groups are lost?

1. because phosphate groups are negatively charged and therefore repel each other, it takes energy to get 2 phosphates near enough to each to make the covalent bond that links them together, some of this energy is stored as potential energy 2. the free energy in P-O bond is much higher than energy of O-H bond that forms in hydrolysis so some energy is therefore released

What regulates enzyme activity?

1. gene expression, many signal transduction pathways end with changes in gene expression which then often switches the encoding of enzymes on or off 2. activating/inactivating enzymes Regulating enzymes and their rates contributes to homeostasis

Why is the complexity of organisms not in conflict with the 2nd law of thermodynamics?

1. the construction of complexity is coupled to the generation of disorder (metabolism creates far more disorder than the amount of order stored in 1 kg flesh) 2. life requires a constant input of energy to maintain order, otherwise complex structures would just breakdown - so energy is used to generate and maintain order

Covalent Catalysis

A functional group in a side chain forms a temporary covalent bond with a portion of the substrate

Entropy (S)

A measure of the disorder in a system, cannot measure absolutely -positive delta S if there are more products than reactants and they can move around freely -negative delta S if there are fewer products and more bonds preventing free movement

Regulatory Sites

AKA allosteric sites, site where inhibitors and activators bind on enzyme, very specific

Acid-Base Catalysis

Acidic or basic side chains of the amino acids in the active site transfer H+ to or from the substrate, destabilizing a covalent bond in the substrate and permitting it to break

Forms an Enzyme can Exist in in a Cell

Active Form = proper shape for substrate binding Inactive Form = shape that cannot bind the substrate

ATP

Adenosine triphosphate, two main roles: 1. "energy currency", cells rely on ATP for the capture and transfer of the free energy they require to do chemical work, some of the free energy released by exergonic reactions is captured in the formation of ATP from ADP and inorganic phosphate, ATP hydrolyzed to release free energy to drive endergonic reactions 2. ATP can be converted into a building block for nucleic acids, structure is similar to that of other nucleoside triphosphate but 2 things make it especially useful for cells: 1) ATP releases a large amount of energy when hydrolyzed to ADP and Pi 2) ATP can phosphorylate many different molecules, which then gain some of the energy that was stored in ATP

Laws of Thermodynamics

Apply to all matter and energy transformations, derived from studies of the fundamental physical properties of energy and the ways it interacts with matter 1. Energy is neither created nor destroyed 2. Disorder tends to increase

Chemical Equilibrium

Balance between forward and reverse reactions (occur at same rate), no net change but individual molecules are still forming and breaking, delta G = 0, each chemical reaction has a specific equilibrium point related to the free energy released by the reaction under specified conditions, look at product:reactant ratio at equilibrium to determine if reaction has gone to completion, change in free energy for any reaction is related directly to its point of equilibrium

Energy Barrier

Barrier between the reactants and the products, represents the amount of energy needed to start the reaction (activation energy)

Energy

Capacity to do work, capacity for change (EX: energy changes, in biochemical reactions associated with changes in chemical compositions and properties of molecules), comes in many forms: chemical, electrical, heat, light, mechanical (TABLE 8.1!)

Inhibitors

Chemical inhibitors can bind to enzymes to slow down the rates of the reactions they catalyze, natural inhibitors regulate metabolism and artificial inhibitors can be used to treat diseases, kill pests, or to study how enzymes work, some inhibitors can permanently deactivate the enzyme while others are reversible

Reactant

Chemical substance that enters into a chemical reaction with another substance, bonds broken and formed

Anabolic Reactions

Collectively anabolism, link simple molecules to form more complex molecules, require input of energy, energy is captured in chemical bonds formed and thereby stored as potential energy, generate order, endergonic EX: synthesis

Catabolic Reactions

Collectively catabolism, break down complex molecules into simpler ones and release the energy stored in chemical bonds, released energy may be recaptured in new chemical bonds or it may be used as kinetic energy to move atoms, molecules, cells, organism, etc., generate disorder, exergonic EX: hydrolysis

Prosthetic Groups

Distinct, non amino acid atoms or molecular groupings that are permanently bound to their enzymes

Commitment Step

First step in metabolic pathway, once this enzyme catalyzed reaction occurs the other reactions happen in sequence leading to the end product

Biological Catalyst

Either an enzyme or an RNA, framework within which chemical catalysis takes place, this molecular framework binds the reactants and sometimes participates in reaction itself but is not permanently changed, cells usually use proteins to catalyze because they have greater diversity in 3D structure and in chemical function due to functional groups, highly specific unlike nonbiological catalysts, enzymes have Kds (10^-5 or 10^-6) means binding is reversible but the enzyme catalyzes reaction so quickly that reactant does not leave before reaction occurs

Names of Enzymes

End in "ase", name reflects function

Kinetic Energy

Energy of movement, type of energy that does work/makes things change, can be converted into potential energy

Potential Energy

Energy of state or position, stored energy (can be stored in many forms), can be converted in kinetic energy

Cellular Respiration

Energy released from fuel molecules captured in ATP, conversion of ADP to ATP is endergonic

Unusable Energy

Entropy times absolute temperature (T)

Effect of pH on Enzyme Activity

Enzyme activity decreases as solution gets more acidic or more basic than its optimal pH, pH also effects which R groups are ionized (in neutral/acidic pHs amino groups become + and in neutral/basic pHs carboxyl groups become -) so in neutral pHs amino groups electrically attract to carboxyl groups but if pH changes these bonds do not occur and instead a negative carboxyl might be protonated or vice versa and thus the active site has different R groups

How do the reaction rates of nonallosteric enzymes versus multisubunit allosteric enzymes differ compared to substrate concentration?

For nonallosteric enzymes - the plot is hyperbolic, so the reaction rate increases sharply at first and then tapers off at a constant max rate when enzymes are saturated For allosteric enzymes - graph is sigmoid (S) shaped, at low substrate concentrations the reaction rate increases only gradually but after the substrate binds to the first active site there's a change in quaternary structure such that other sites become more likely to bind so the reaction rate speeds up rapidly almost vertically, once sites are saturated then graphs plateau - basically within a certain range the reaction rate is extremely sensitive to relatively small changes in substrate concentration and also very sensitive to low concentrations, BECAUSE OF THIS SENSITIVITY ALLOSTERIC ENZYMES ARE IMPORTANT IN REGULATING ENTIRE METABOLIC PATHWAYS

Isozymes

Group of enzymes that catalyze the same reaction but have different amino acid compositions and physical properties, help organisms adapt to changes in environment because isozymes might have different optimal temperatures

Irreversible Inhibition

If an inhibitor covalently binds to certain side chains at the active site of an enzyme it will permanently inactivate the enzyme by destroying its capacity to interact with its normal substrate, this form of regulation not common in cell because the enzyme is permanently inactivated and cannot be recycled EX: DIPF, used in biological warfare as a gas

First Law of Thermodynamics

In an energy conversion, energy is neither created nor destroyed: -in other words, total energy before and after conversion is the same

Transition State

In an enzyme catalyzed reaction the reactive condition of the substrate after there has been sufficient input of energy to initiate the reaction

Metabolism

Sum of all the chemical reactions occurring in a biological system at a given time, metabolic reactions involve energy changes

Reversible Inhibition

Inhibitor similar enough to a particular enzyme's natural substrate to bind noncovalently to its active site but different enough that the enzyme catalyzes no chemical reaction

Inorganic Factors

Ions (Cu, Zn, Fe) that are permanently bound to certain enzymes, called "cofactors"

Are enzymes small or large?

Large!

Regulation via Reversible Phosphorylation

Like in epinephrine signal transduction pathway phosphorylation via a kinase can activate a protein via shape change and then this phosphate can be removed by a phosphatase so the enzyme becomes inactive again

What does specificity of an enzyme result from?

The 3D shape and structure of its active site, only certain substrates can fit

Metal Ion Catalysis

Metal ions (Cu/Fe/Mn) in side chains of enzymes can lose or gain electrons without detaching from the enzymes, important in redox reactions

Noncompetitive Inhibitor

Molecule that binds to an enzyme at a site distinct from the active site, this binding causes a change in the shape of the enzyme thereby altering its activity as the enzyme may no longer bind to the substrate or if it still can bind the rate of product formation is reduced, reversible as they can be unbound

Uncompetitive Inhibitor

Molecule that binds to the enzyme-substrate complex thereby preventing the complex from releasing products, unlike competitive inhibition this cannot be overcome by addition more substrate

Effector Molecules

Molecules that can influence which form an enzyme takes: -binding of an inhibitor to a site other than the active site can stabilize the inactive form of the enzyme, making it less likely to convert to the active form -the active form can be stabilized by the binding of an activator to another site on the enzyme

Do enzymes affect equilibrium?

NO! The final equilibrium state is the same with or without the enzyme, similarly enzymes do not change delta G

Systems Biology

New field of biology in which computer algorithms are used to model metabolic pathways and show how they mesh in an interdependent system, these models can help predict what will happen if the concentration of one molecule or another is altered

Structure of ATP

Nitrogenous base adenine bonded to ribose (a sugar) which is attached to a sequence of 3 phosphate groups

Coenzymes

Nonprotein carbon-containing molecule that is required for the action of one or more enzymes, usually relatively small compared with the enzyme to which is temporarily binds, moves from enzyme to enzyme to add/remove chemical groups from the substrate, it binds to active site change chemically during the reaction and then separates from the enzyme to participate in other reactions, because of this behavior sometimes coenzymes can be confused with substrates themselves

Allosteric Regulation

Occurs when an effector molecule binds to a site other than the active site of an enzyme thereby inducing the enzyme to change its shape, change in shape alters the affinity of active site for the substrate and so the rate of the reaction is changed, most enzymes that are allosterically regulated are proteins with quaternary structure so they have catalytic and regulatory subunits, can be positive regulation like if an enzyme has multiple subunits containing active sites the binding of a substrate to one active site causes allosteric effects which make the next active site more likely to bind to another substrate so the reaction speeds up as the sites become sequentially activated

Chemical Reaction

Occurs when atoms have sufficient energy to combine or change their bonding partners, theoretically reversible, concentrations determine which direction will be favored

Active Site

Particular site on an enzyme to which substrate molecules bind, this is where catalysis takes place, usually small compared to size of enzyme (only 6-12 amino acids), specific to its substrate

Catalytic Subunit

Polypeptide with the active site

Regulatory Subunit

Polypeptide with the allosteric site

How is the active site specific?

Precise interlocking of molecular shapes and interactions of chemical groups at the active site, binding depends on H-bonds/electric attraction or repulsion/hydrophobic interactions

Enzyme-Substrate Complex

Produced by the binding of a substrate to the active site of an enzyme, held together by several transient interactions, gives rise to product and free enzyme, free enzyme always the same as beginning of reaction even if it changes chemically in ES E + S -> ES -> E + P

Bioluminesence

Production of light by a living organism, an endergonic reaction driven by ATP hydrolysis that involves an interconversion of energy forms (chemical to light), light is generally used to avoid predators or attract potential mates

Disorder

Randomness due to the thermal motion of particles, this energy is of such low value and is so dispersed that it is unusable

Substrates

Reactants in an enzyme-catalyzed reaction, small molecule or a small part of a large molecule that binds to active site of enzyme

What does delta G tell us nothing about?

Reaction rate

Induced Fit

Shape changes that alter the shape of the active site upon the binding of its substrate, brings substrate reactive side chains together and also prevents outside molecules from getting to close to interact (EX: water), partly explains why enzymes are so large

Reaction Rate

Speed at which reaction moves toward equilibrium, reactions that cells depend on have spontaneous rates that are so slow that cells would not survive without a way to speed them up

Catalysts

Substances that speed up reactions without themselves being permanently altered, does NOT cause a reaction to occur that would not proceed without it just allows equilibrium to be reached more rapidly, most biological catalysts are proteins called enzymes but some are RNA molecules called ribozymes

Activation Energy (Ea)

The energy input required for substrate to reach transition state, energy needed to start the reaction and overcome the energy barrier, energy needed to change the reactants into unstable transition-state intermediates, this amount of energy is often small compared to the delta G of reaction, recovered in "downhill" phase of reaction so not part of net free energy change (delta G)

Energy Coupling Cycle

The formation and hydrolysis of ATP, ADP picks up energy from exergonic reactions to become ATP which then donates energy to endergonic reactions, ATP is thus a common coupling agent, coupling of exergonic and endergonic reactions is very common in metabolism, free energy is captured and retained in P-O bonds and then ATP diffuses to another site in cell where its hydrolysis releases the free energy to drive an endergonic reaction, reactions often proceed exergonically when they are coupled

Relationship between Delta G and Point of Equilibrium

The further toward completion the point of equilibrium lies, the more free energy is released -a large + delta G means the reaction will hardly proceed in the forward direction -delta G near 0 means reaction is readily reversible, reactants and products have almost same free energy -more negative delta G means the further the reaction proceeds towards completion

How do enzymes speed up reactions?

They lower the energy barrier by bringing reactants closer together, when reactants are bound to enzyme they require less activation energy than the transition state intermediates, this speeds up both forward and reverse reactions so reaction proceeds toward equilibrium more rapidly,

Products

The molecules that result from the completion of a chemical reaction, different chemical properties than those of reactants

Metabolic Pathways

The product of one reaction is a reactant for the next, these pathways interact extensively, each reaction in each pathway is catalyzed by a specific enzyme, thus enzymes determine the flow of chemicals through different metabolic pathways

Transition State Intermediates

Unstable molecular forms that have higher free energies than either the reactants or the products

Free Energy (G)

Usable energy that can do work, cells require this for chemical reactions, cannot measure absolutely

Effect of Temperature on Enzyme Activity

Warming increases reaction rate by increasing kinetic energy to provide activation energy, however when temp gets too hot enzymes might be deactivated because they could vibrate and twist so rapidly that some of their noncovalent bonds break thus breaking tertiary structure and losing function, most enzymes are stable at high temperatures than those of the bacteria that infect us so that a moderate fever tends to denature bacterial enzymes but not our own

Change in G/H/S

We cannot measure G/H/S absolutely but we can determine the change in each at a constant temp., energy changes are measure in calories (cal) or joules (J) and is represented by a delta

Maximum Rate of Catalyzed Reaction

When all the enzyme molecules are bound to substrate molecules, the enzyme is working as fast as it can, increasing substrate concentration has no effect at this point, maximum rate of catalyzed reaction can be used to measure efficiency of enzyme, measure in # if substrate molecules that one enzyme can convert to product per unit time

Second Law of Thermodynamics

When energy is converted from one form to another, some of that energy becomes unavailable for doing work: -in other words, no physical process or chemical reaction is 100% efficient -some released energy is lost to a form associated with disorder -unless energy is applied to a system, it will be randomly arranged and disordered (favors entropy) -predicts that as a result of energy transformations, disorders tends to increase (entropy increases) -- this explains the directionality of reactions

Competitive Inhibitor

While this molecule is bound to the enzyme the natural substrate cannot enter the active site and the enzyme is unable to function, thus competes with natural substrate for active site, degree of inhibition depends on the relative concentrations of the substrate and the inhibitor and thus inhibition is reversible and can be changed by concentrations

Hydrolysis of ATP

Yields free energy, ADP, and an inorganic phosphate ion OR AMP and a pyrophosphate ion (P2O7 4-), an exergonic reaction, delta G in lab conditions = -7.3 and in cellular conditions = -14 kcal/mol, gives energy to: -active transport -condensation reactions that use enzymes to form polymers -modifications of cell signaling proteins by protein kinases -motor proteins