BSCI 170 - Energy, ATP, and Enzymes (End of Unit 1)

The ability to _______ and ___ energy is a fundamental property of all living organisms

• Remember: Energy is the capacity to make a ______ against a _________ _____

  • In a biological context, energy is the ability to do ____.

acquire, use, change, resistant force, work

All reaction pathways for biological work are __________.

endergonic

Monomer + Monomer ←→ Dimer + H₂O (delta G = +)

• This reaction spontaneously moves ____

• Making this reaction move forward (to the right) requires an _____ __ ______

left, input of energy

Monomer + Monomer + Energy ←→ Dimer + H₂O (delta G = -)

• Why does this work?

many endergonic reactions are driven forward by free energy released from the hydrolysis of the nucleotide ATP

What is adenosine triphosphate composed of?

three phosphate groups, ribose sugar, and an adenine

ATP has a similar monomer to a __________

nucleotide

What will the hydrolysis of ATP do?

• pop off one of the phosphate groups

What does ATP change to when it loses a phosphate group?

adenosine diphosphate (ADP)

Phosphate groups have 3 negative charges next to each other from the oxygens. Why is this important?

• When you try to put two sides of a magnet together, they push against each other

• Energy is stored since they are pushing against each other

• Energy is released when you go down to ADP

What are the roles of ATP in the cell?

• subunit for synthesis of RNA (and DNA)

• starting product for synthesis of cyclic AMP (adenosine monophosphate)

  • intracellular signaling molecule

• Energy coupler for endergonic reactions

True or False: Humans get their energy directly in the form of ATP

false

Where do organisms get ATP from?

Some organisms absorb energy from the sun and convert it into ATP or into other organic molecules that other organisms can consume and convert into ATP

• ATP is an inherently _______ molecule

  • multiple, closely set _________ charges on phosphate groups ______ each other

unstable, negative, repel

What role does hydrolysis play in increasing ATP’s stability?

The hydrolysis of the terminal phosphate group creates a more stable product

Going from a less-stable structure to a more stable structure ___________ ______ _______.

releases free energy

What is characteristic of ATP hydrolysis?

it is highly exergonic

What is the change in free energy associated with ATP hydrolysis?

-7300 cal/mol (-7.3 kcal/mol)

Any energy that is not captured and used is released as _____.

• Is this a useful form of energy?

• What does it mean for energy to be useful?

heat

• no since it results in increased entropy

• to be useful, energy must be captured. By “captured,” this means that it should be used by the cell to do biological work before it is released as heat

An exergonic ATP hydrolysis is usually coupled with a _______, __________ reaction

second, endergonic

The coupled reaction moves forward (to the right) if the change in free energy of ATP hydrolysis (7.3 kcal/mol) is _______ than the change in free energy of the endergonic reaction

greater

ATP as Energy Coupler

Consider the following reaction:

A + B ←→ C (delta G = +)

• The reaction cannot move to the ________

• couple the reaction with ___ ________

  • A + ATP —> A~P + ADP (delta G₁ = -)

  • A~P + B —> C + P_i (delta G₂ = +)

• If delta G₁ + delta G₂ = -, then total reaction sequence is ___________ (________)

right, ATP hydrolysis, spontaneous, exergonic

Life is driven by chemical reactions operating under controlled conditions.

• A —> B

• Reactant —→ Product

• Substrate ——> Product

For your reference

All reactions are theoretically ________.

• A ←→ B

reversible

Only _______ (spontaneous) reactions can move forward

• If a reaction cannot move forward, then it is at…

  • ___________ (delta G = 0), or

  • ___________ (delta G = +)

favorable, equilibrium, endergonic

The hydrolysis of sucrose has a delta G of -7000 cal/mol, is this reaction favorable?

highly favorable

Sucrose + Water =

• Nothing happens for many _____!

• Remember: A reaction may be thermodynamically _________ but not occur at an appreciable rate.
  

years, spontaneous

What does the reaction of sucrose and water result in?

sucrose and water

• The Laws of Thermodynamics can tell us if a reaction can move _______ or not

• The Laws of Thermodynamics can tell us nothing about ________ ____

• Most biochemical reactions progress too _______ on their own to support life

  • How is this problem solved?

forward, reaction rate, slowly, catalysts

• Catalysts accelerate a reaction without being ________ or ____________ _________

  • neither a ________ nor a _________

• Biological catalysts are called _________

  • usually a _______

  • may be a catalytic ___

    • _________

  • can be regulated: __ and _____

consumed, permanently changed, substrate, product, enzymes, protein, RNA, ribozyme, up, down

Enzymes Accelerate Reactions

• Reaction goes to completion in ________

seconds

Anatomy of a Chemical Reaction

• All chemical reactions involve _____ or __________ chemical bonds

  • ________ bonds

  • _________ bonds

• Process requires a higher-energy, unstable, intermediate step called the _________ ______

• Reactants must have sufficient ________ to reach the transition state'

• Think of it like raising a bowling ball so you can roll it down a hill

breaking, rearranging, covalent, noncovalent, transition state, energy

Energy Profile of a Favorable Reaction

• (Reactants) AB + CD —> AC + BD (Products)

• For a favorable reaction, the free energy of AB + CD (Reactants) will be ______ than the free energy of AC + BD (products)

• The delta G will be a _______ number

greater, negative

Activation Energy (E_A)

For a reaction to go to completion:

• Energy must be present and available to raise reactants to the __________ ______

  • Transition state has more energy than the ___________

• Energy is released when old bonds are _______, new bonds are ________, and the product assumes a ______-energy, more-_______ state
  

transition state, reactants, broken, formed, lower, stable

Activation Energy (E_A)

• Activation energy serves as a barrier to reaction progression and completion

  • Low Barrier: _____ reactant molecules have sufficient energy

    • the reaction proceeds rapidly

  • High Barrier: ___ reactant molecules have sufficient energy

    • the reaction proceeds slowly

many, few

Accelerating Favorable Reactions

• Most important favorable reactions have significant ________ ______ barriers

• How can you get reactants across the barrier?

  • Solution 1: increase _______ ________ of reactants by _________ _________

    • increases the percentage of molecules with sufficient energy to get over the barrier

    • this works well in lab; not in living systems

    • must increase temperature above dangerous levels to work

  • Solution 2: _______ the barrier

    • More reactants will have sufficient energy at the start of the reaction

      • this is what enzymes do

activation energy, average energy, increasing temperature, reduce

What is the role of enzymes?

decrease the activation energy

• enzymes and reactants form an enzyme-substrate (ES) complex

• E + S ←→ ES ←—→ E + P

• interaction between enzyme and substrate usually highly specific

• delta G is unaffected by an enzyme

What is the active site?

substrates bind at the active site

• it is a groove or pocket exposed on the surface of the enzyme

• not a rigid structure

• small fraction of enzyme molecule

What is the active site formed from?

noncontiguous amino acids

• The amino acids that form the active site are often far apart in the linear sequence of the unfolded enzyme

• Protein folding brings specific amino acids close to each other to form the active site

What are the mechanisms of catalysis?

• bending the bonds

• moving the substrates closer together to get into the transition state

• provide the right charge environment (the charges can pull apart the parts of the molecule —> go from substrates to products)

What is induced fit?

a model for enzyme-substrate binding where the active site of the enzyme undergoes a conformation change upon substrate binding. This change enhances the fit between the enzyme and substrate, facilitating the catalysis of the reaction

Regulating Chemical Reactions

• Allowing all reactions to proceed without regulation would be __________

• Many mechanisms exist for controlling the ________, ________, and _____ of chemical reactions in cells

disastrous, location, timing, rates

Controlling Reaction Rate: I

• One way is to operate enzymes under ________ conditions

optimal

Enzymes have optimal __________

• What is the optimal temperature for a typical human enzyme?

• What is the optimal temperature for an enzyme of thermophilic (heat-tolerant) bacteria?

temperatures, 37 degrees Celsius, much higher (77 degrees Celsius)

Enzymes have optimal ____

• The optimal pH for a stomach enzyme would be much ______ than the optimal pH for an intestinal enzyme

pHs, lower

Controlling Reaction Rate: II

• The rate of a reaction can generally be controlled by altering the [_______]

  • brackets signify ___________

substrate, concentration

Initial Reaction Velocity vs. [Substrate]

• As [Substrate] ________ ______ some value, rate of product formed ______ ______

increases above, slows down

What does saturation mean?

• The rate of product formation is at a ___________

• All functional enzyme molecules are binding _________ and converting it into produce as _____ as possible

• The only ways to increase the rate of product formation are to _________ more enzyme or ________ enzyme already present

maximum, substrate, fast, synthesize, activate

Controlling Reaction Rate: III

• ________ _______ _________ bind to the enzyme and regulate its activity

  • ___________: increase the rate of product formation

  • ___________: decrease the rate of product formation

enzyme effector molecules, activators, inhibitors

Cofactors

• Cofactors are ________ enzyme __________

• Cofactors may be ________ (such as a metal in ionic form) or _________

• An organic cofactor is called a __________

  • These include ________

nonprotein, activators, inorganic, organic, coenzyme, vitamins

Enzyme Inhibitors

• Affect the ability of an enzyme to ________ a reaction

  • Two Types:

    • ________ inhibitors

    • _________ inhibitors

catalyze, irreversible, reversible

Irreversible Inhibitors

• _________ attachment to enzyme

• usually at _____ ____

covalent, active site

Reversible Enzyme Inhibitors

• ___________ attachment to enzyme

• Several types

  • ___________ inhibitor

  • ___________ inhibitor

noncovalent, competitive, noncompetitive

Competitive Inhibitor

• The effect of a competitive inhibitor can be reduced by ___________ ___ ___________ __ __________.

increasing the concentration of substrate

FOR YOUR REFERENCE:
Analogy: Competitive Inhibitor

• A plug is a substrate and an outlet is an enzyme

  • When plugged into an outlet, an enzyme-substrate complex is formed

• An outlet plug and an outlet is like a competitive inhibitor and an enzyme

N/A

____________ Inhibitor: binds to enzyme away from active site

• changes ________ of enzyme

• reduces the ability of an enzyme to _______ normally

• the inhibitory effect is unrelated to the concentration of the ________.

noncompetitive, structure, function, substrate

FOR YOUR REFERENCE:

Analogy: Noncompetitive Inhibitor

• A noncompetitive inhibitor is like changing the power board to interfere with an enzyme-substrate complex

N/A

Controlling Reaction Rate: IV

• Use _________ molecules to change the ___________ (and ______) of the enzyme

• _________ regulatory molecules bind to an enzyme _____ from the active site

regulatory, conformation, activity, allosteric, away

Allosteric Regulation

• __________ enzymes often exist in two distinct conformations.

  • One conformation: __________

  • One conformation: ___________

• Enzyme __________ between two shapes

• Binding an ________ effector stabilizes the enzyme in one state or the other

  • _________: stabilizes in active conformation

  • _________: stabilizes in inactive conformation

multisubunit, functional, nonfunctional, oscillates, allosteric, activator, inhibitor

For your reference:

N/A

What is endproduct inhibition?

when a metabolic pathway is turned off by an enzyme at the front of the pathway binding its endproduct

What is an example of endproduct inhibition?

• when a 5-enzyme pathway that converts threonine into isoleucine

• when isoleucine builds up, it binds to Enzyme 1 and inhibits it and the entire pathway