Chapter 6 - Energy and Enzymes

Slides 2-3: Types of Energy in the Cell

• Chemical Energy

  • ATP/GTP

  • NADH/FADH2

  • Other high-energy molecules

• Ion Gradients

  • Energy from ion concentration differences across membranes

• Solar Energy

  • Energy harnessed from sunlight

Types of Chemical Energy

• ATP/GTP (Most common)

  • Primary energy carriers in cells

• NADH/FADH2

  • Electron carries in metabolic reactions

• Other High Energy Molecules

  • Various molecules that store energy

Slides 4-5: ATP: Adenosine Triphosphate

• Structure of ATP

  

  • Composed of adenine, ribose, and phosphate groups

• ATP has High-energy bonds between the phosphate groups

• When the P-P bonds are broken the energy released can be used for enzyme reactions.

Slides 6-7: ATP Hydrolysis

• ATP Hydrolysis provides energy needed for many essential process in organisms and cells

  • Including intracellular signaling, DNA and RNA synthesis and more

• Hydrolysis Reaction

  • ATP + H2O → ADP + Pi + Energy

• Energy released can drive cellular processes

  

Slides 8-16: Electron Carriers: NADH, NADPH, FADH2 —Oxidation-Reduction Reactions —

• Redox Reactions (OILRIG)

  • Oxidation-Reduction reactions

  • Some molecules alternate between reduced and oxidized forms

    • Ex. NADH + B -> NAD⁺ + BH

• NADH and NAD+

  • NADH is the reduced form, high energy that has accepted a pair of electrons

    

  • NAD+ is the oxidized form, low energy that has lost a pair of electrons

    

• Reduced cmpd loses e-s and becomes oxidized

• Oxidized cmpd gains e-s and becomes reduced

  • When a cmpd gains e-s is sometimes picks up an H as well

• NADH _(reduced) + B_(ox) -> NAD+ _(oxidized) +BH_(reduced)

  • The NADH +B donates a pair of e- to B

  • NADH loses a pair of e- and becomes oxidized — NADH → NAD+

  • B gains a pair of e- and becomes reduced — B → BH

  NAD⁺ + 2e^- + 2H⁺ -> NADH

  

• Oxidized form lost a pair of e-s low energy form (left) — Reduced form Gains 2e-s (+ 2H +) high energy form (right)

• OILRIG: Oxidation Is Loss, Reduction Is Gain of electrons

Slides 17-19: Ion Gradients as Energy

• Ion Gradient: When the concentration of an ion is high on one side of the membrane

• Ion gradients create potential energy

• Energy is released as ions flow down their concentration gradient

• As ions move down their concentration gradient, enough energy is released to move some other substance, or make ATP

Slides 20-22: Solar Energy and Photosynthesis

• Photosynthesis Overview

  • Light energy converted into chemical energy (ATP and NADPH)

• Energy from sunlight can be used for electron transport during photosynthesis

• Light Reactions

  • Involved water splitting and electron transport

• Light reactions of photosynthesis — sunlight → Electron transport H+ Gradient → ATP + NADPH chemical energy

  

• Overall reaction: CO2 + H2O + light energy → sugar + O2

Slides 23-27: Laws of Thermodynamics

• 1st Law: Energy cannot be created or destroyed, it can only be transformed

• 2nd Law: Any Energy transformations increases the disorder of a system (entropy)

  • Entropy is a measure of randomness or disorder

Slides 28-32: Metabolic Pathways and Chemical Reactions

• Reactions are part of metabolic pathways

  • Enzymes catalyze each step

  • The activity of all 3 enzymes is needed to make the final product

• Reactants = substrates is the starting compound in a reaction

• Product: Compound made at the end of a reaction

Slides 33-38: Chemical Equilibrium

• Chemical equilibrium occurs when the rate of formation of products equals the rate of formation of the reactants

  • aA + bB <—>cC + dD

• Equilibrium constant (Keq) indicates favorability of product formation

  • The larger the Keq the more product is made relative to reactant at equilibrium

• Example: ATP breakdown to ADP + Pi

• Equilibrium greatly favors formation of products

  K_eq =  [ADP][Pi] / [ATP]

• ATP rapidly breaks down to make ADP + Pi

• At equilibrium there will be tiny amounts of ATP and very large amounts of ADP + Pi

Slides 39-44: Free Energy and Reactions

• Free energy (G) is the energy that can be used to do work

  • Reactions tend to proceed in the direction that causes a decrease in the free energy of the system

    • (ΔG = negative)

• Exergonic Reactions: Energy is released can occur spontaneously (ΔG < 0 ) ΔG = negative

• Endergonic Reactions: Requires energy input in order to occur reaction is not spontaneous (ΔG > 0) ΔG = Positive

• Reactions can be coupled

  • Coupled reactions over all ΔG is negative; together reactions are spontaneous

    • ATP → ADP + P

    • Glucose+ P -: Glucose-6P

      • Glucose + ATP → Glucose-6-p + ADP

Slides 45-52: Enzymes as Catalysts

• Catalysts increase the rate of reaction

  • Catalysts are not used up in the reaction (reusable!!)

    • A catalyst does not equal reactant

• Catalysts do not alter the equilibrium of a reaction

  • They decrease the amount of time required to reach equilibrium

  Special Features of Enzymes

• Enzymes are specific, efficient and regulated

• Specific : Enzymes perform one reaction or type of reaction

• Efficient : Enzymes increase the rate of reaction dramatically

• Regulated : Enzymes can be turned ON and OFF.

  • Enzymes work in path way that can be interconnected and flow thru a pathway can be regulated

• Enzymes are proteins that speed up reactions

• Catalysts are not consumed in reactions

Slides 54-57: Mechanism of Enzyme Activity

• Enzymes interact with substrates to form an enzyme-substrate complex

• Transition state is an intermediate with higher free energy (G) compared to that of the reactant

• Substrates must go through an activated transition state

  • E + S -> E^.●S -> E^.●P -> E + P

    

Slides 59-65: Activation Energy

• Activation energy (EA) is the energy needed to start a reaction

• Enzymes lower the activation energy(EA), speeding up the reactions

  • Enzymes can interact with the substrate providing an alternate transition state

    • Alternate state = different intermediate

      • Enzyme catalyzed reaction goes through a transition state/intermediate whose free energy is lower than the intermediate of the uncatalyzed reaction

        • To lower the activation energy enzymes can interact with the substrate and provide an alternate transition state

        • They can also hold the substates in the proper orientation for the reaction to occur

Slides 66-74: Enzyme Specificity and Function

• Enzymes specificity is determine by the shape of the active site

  • Active site: location in enzyme where reaction takes place

    

• Lock and Key Model: Only specific substrates fit

  • Specificity: only molecules that can fit into the active site of an enzyme are substrates for the reaction

    • Substrate fit into the active site of an enzyme like a lock into a key

• Substrates are oriented so the bond can be cleaved in a certain position

  

• Induced Fit Model: Enzyme shape changes upon substrate binding to improve catalytic activity of the enzyme

  -Catalytic Efficiency and the Active Site-

• Substrates are held in close proximity and proper orientation

• Formation of covalent intermediates

• Active site contains functional groups that temporarily donate H+s or e-s

• Binding of a substrate to a enzyme induces the strain on the substrate molecules and makes it more reactive

  

• The active site lower the activation energy

• Acts as a template for the reaction

• It stresses the substrate

• Stabilizes the transition state

  • Participates in catalytic reaction

Slides 75-95: Factors Influencing Enzyme Activity

• A proteins shape is essential to its function

• A denatured protein loses its 3D shape, and becomes an unfolded chain of amino acids

  • A denatured protein will not function properly

• During denaturation the ionic, H bonds and disulfide bonds that hold the protein in its 3D shape are broken, and the enzymes unfolds

  • The amino acids are still connect in a chain by peptide bonds

    -What Causes Protein Denaturation-

• Large change in pH

  • Acidic or basic

• High temperature

  Denaturation is usually permanent

• When an enzyme reaches past its optimal temperature or pH the enzyme are permanently inactivated when they are denatured

  -Small Changes in pH (<1 pH unit)

• Will change the charge on the substrate and the charge on the enzyme (active site)

• The substrate may no longer be able to bind as well, so the enzyme will be less active

• pH optimum: The pH at which the enzyme performs the reaction on the maximum rate

  • The enzyme becomes denatured above and below the pH optimum, so its is less active

    

    • Most enzymes have a pH optimum that matches the pH of the environment the enzyme is designed to work in

    -Large changes in pH (>1 pH unit)

• Will break the ionic and H bonds that hold protein in its 3D shape

• Enzymes may partially unfold and become less active

• Enzymes may completely unfold (denature) and become totally inactive

  -Temperature and Enzyme Activity-

• Many enzymes have a temperature optimum that is equal to the body temperature of the organism they are from

Slides 96-101: Kinetic Energy and Reaction Rates

• Kinetic Energy: energy associated with movement

• Molecules are always moving: they have kinetic energy

  • More kinetic energy → more collisions between molecules → Faster reaction rate

• The colder the temperature the mess kinetic energy a molecule has

  • Which result in fewer collisions between molecules → lowers reaction rate

    • If there are fewer collision between reactant molecules at a low temperature the reaction rate will be slower

Slides 97-106: Additional Factors for Maximal Enzyme Activity

• Prosthetic Group: small organic molecules permanently bound to a enzyme

• Coenzymes: small organic molecule (vitamin derivaties), bind temporarily to enzymes

  • Cofactors or Metal Ions: ex. Fe, Mg

  -Function-

• May be required for proper 3D shape of protein

• May be directly involved in chemical reaction

• Coenzymes may change the shape of the active site

  • Coenzymes may make a temporary bond between 2 substrates

• Inhibitor: molecule or ion that binds to a enzyme and decreases its activity

• Competitive inhibitor binds to the active site of a enzyme

  • The inhibitor must resemble the substrate in order to bind to the active site

    • If the inhibitor binds to the active site the substrate can’t bind, so no reaction will occur

  • The more inhibitor is added, the more the reaction is inhibited, there are mnay enzyme molecules in the cell

    • The more inhibitor binds to the active site the lower the reaction rate

  • The inhibitor binds to the active site, so it must have a similar structure to the normal substrate

• Noncompetitive Inhibitors: Bind to allosteric site noncovalently, altering enzyme shape

  • Some proteins have more than one subunit

  • Catalytic subunit: contains the active site and performs reactions

  • Regulatory subunit: contains the allosteric site and regulates enzyme activity

• Inhibitor binds to allosteric site on regulatory subunit

  • Changes the shape of regulatory subunit and the catalytic subunit

    • Enzyme activity decreases

Page 122-138: Allosteric Regulation

• Catalytic Subunit: Binds substrate at the active site, performs enzyme reaction

• Regulatory subunit: binds an effector at the allosteric site, controls activity of enzyme

• Effector: small organic molecule that controls the activity of the enzyme

  • The effector binds to the allosteric site

• Active form: form of the enzyme that performs its function (ON)

• Inactive form: nonfunctional form of enzyme (OFF)

• Effector controls activity of enzyme

• Regulatory molecules / effectors binds to regulatory subunit and causes it to change shape

• A change in shape of the regulatory subunit causes catalytic subunit to change its shape

  • Catalytic subunit no in inactive form (OFF)

• Regulatory subunit may still be bound to catalytic subunit but both change its shape

• An inhibitor binds to the regulatory subunit

  • inhibitor = effector

• Inhibitor binding causes regulatory subunit to change shape

  • Change of shape of regulatory subunit causes catalytic subunit to change shape, from active form to inactive form

    

• Accumulation of product of a metabolic pathway inhibits one of the enzymes at the beginning of the pathway

  Feedback inhibition is a kind of allosteric inhibition

• Inhibitor = product of pathway

• Inhibitor binds to allosteric site on regulatory subunit of enzyme 1

• Regulatory subunit changes shape

• Catalytic subunit changes shape → inactive form

• When a product made at the end of a pathway binds to one of the enzyme near the beginning of the pathway, and inactivates the enzyme

• Product binds to enzyme 1 at the allosteric site and changes the enzymes shape

  • Enzyme 1 : Active → inactive (OFF!)

• Allosteric regulation is a kind of noncompetitive inhibition

  • it is used to regulate enzymes in pathways

• Feedback inhibition is a kind of allosteric inhibitor

• Allosteric inhibitor: binding of the effector makes enzyme less active

  • Active enzyme → inactive (OFF)

• Allosteric activator: binding of the effector makes enzyme more active

  • Inactive enzyme → Active (ON)

Page 139: Summary of Allosteric Regulation

• Allosteric regulation is crucial for maintaining metabolic balance

• Involves both activation and inhibition mechanisms