Prescott’s Microbiology, 9 th Edition
10
This chapter discusses energy and the laws of thermodynamics. The participation of energy in cellular metabolic processes and the role of adenosine-5

-triphosphate (ATP) as the energy currency of cells are examined. The chapter concludes with a discussion of enzymes as biological catalysts: how they work, how they are affected by their environment, and how they are regulated.
After reading this chapter you should be able to:
• list the features common to all types of metabolism
• describe the three types of work carried out by cells
• state the relationship between cellular work and energy
• paraphrase the first and second laws of thermodynamics
• use the equation for free energy change and the equation that links standard free energy change to a reaction’s equilibrium constant and explain their importance
• infer from a standard free energy change whether a reaction is exergonic or endergonic
• describe ATP’s role as a coupling agent that links exergonic and endergonic reactions
• compare ATP’s phosphate transfer potential to that of glucose-6-phosphate and phosphoenolpyruvate (PEP) and relate this to ATP’s function in cells
• describe the energy cell observed in all organisms
• describe the metabolic functions of three nucleoside triphosphates (other than ATP)
• describe a redox reaction, noting the role of the two half reactions and identifying the electron donor, electron acceptor, and conjugate redox pairs of the reaction
• relate the standard reduction potential of a conjugate redox pair to its tendency to act as an electron-donating half reaction
• state the equation that links standard free energy change to the difference in standard reduction potentials of the two half reactions of a redox reaction
• predict which molecule will act as an electron donor, which molecule will act as an electron acceptor, and the relative amount of energy released by a redox reaction, using the standard reduction potentials of the reaction’s conjugate redox pairs
• list the molecules that are commonly found in electron transport chains (ETCs) and indicate if they transfer electrons and protons or just electrons
• arrange electron carriers in an ETC using their standard reduction potentials
• indicate the location of ETCs in bacterial, archaeal, and eukaryotic cells
• describe the components of a biochemical pathway and how they are organized.
• state the function and chemical makeup of enzymes
• distinguish apoenzyme from holoenzyme and prosthetic group from coenzyme
• draw a diagram that shows the effect of an enzyme on the activation energy of a chemical reaction
• describe the effects of substrate concentration, pH, and temperature on enzyme activity
• differentiate competitive and noncompetitive inhibitors of enzymes
• discuss the importance of the discovery of ribozymes
• compare and contrast ribozymes and enzymes
• list two examples of ribozymes and the reactions they catalyze
• list the three methods cells use to regulate metabolism
1
© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.

Prescott’s Microbiology, 9 th Edition
• describe metabolic channeling and one example of how it is accomplished; predict whether it is an important regulatory mechanism in bacterial, archaeal, and eukaryotic cells
• distinguish allosteric regulation and covalent modification
• describe the structure of an allosteric enzyme
• create a concept map that illustrates how positive allosteric and negative allosteric effectors regulate the activity of an enzyme
• list the three chemical groups commonly used to covalently modify an enzyme and its activity
• explain how feedback inhibition is used to control the functioning of biosynthetic pathways
• predict which enzymes of a biochemical pathway are likely to be regulated by either allosteric control or covalent modification
• develop a model illustrating how feedback inhibition can be used to regulate a multiply branched biosynthetic pathway
I.
Metabolism: Important Principles and Concepts
A.
Cellular work and energy transfers
1. Living cells carry out three major types of work a.
chemical work—synthesis of complex molecules b.
transport work-take up nutrients, eliminate wastes and maintain ion balances c.
mechanical work –cell motility and the movement of structures within cells
2. Energy is the capacity to do work or to cause particular changes
B.
Laws of Thermodynamics
1.
First law of thermodynamics—energy can be neither created nor destroyed a.
The total energy in the universe remains constant b.
Energy may be redistributed either within a system or between the system and its surroundings
2.
Second law of thermodynamics—physical and chemical processes proceed in such a way that
the disorder of the universe (entropy) increases to the maximum possible a.
Energy is measured in calories where 1 calorie is the amount of heat energy needed to raise the temperature of 1 gram of water from 14.5 to 15.5

C b.
one calorie of heat equals about 4.2 joules
C.
Free Energy and Reactions
1.
The changes in energy that can occur in chemical reactions are expressed by the equation for free energy change (ΔG = ΔH − T∙ΔS); free energy change (Δ G ) is the amount of energy in a system that is available to do work
2.
The change in free energy of a chemical reaction is directly related to the equilibrium constant of the reaction
3.
The standard free energy change (Δ G 0

) is the change in free energy under standard conditions of concentration, pH, pressure, and temperature
4.
When Δ G 0

is negative, the equilibrium constant is greater than one and the reaction goes to completion as written; the reaction is said to be exergonic and releases energy (spontaneous)
5.
When Δ G 0

is positive, the equilibrium constant is less than one and little product will be formed at equilibrium; the reaction is said to be endergonic and requires energy (not spontaneous)
II.
ATP: The Major Energy Currency of Cells
A.
ATP is a high-energy molecule used to capture, store, and provide chemical energy; removal of the terminal phosphate by hydrolysis goes almost to completion with a large negative free energy change (i.e., the reaction is strongly exergonic); ATP has high phosphate group transfer potential
B.
These characteristics make ATP well suited for its role as the energy currency; ATP is formed from ADP and P i
(inorganic phosphate) by energy-trapping processes; exergonic breakdown of ATP can be coupled with various endergonic reactions to facilitate their completion
III.
Redox Reactions: Reactions of Central Importance in Metabolism
2
© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.

Prescott’s Microbiology, 9 th Edition
A.
The release of energy during metabolic processes normally involves oxidation-reduction reactions
1.
Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor to an electron acceptor (conjugate redox pairs)
2.
The equilibrium constant for an oxidation-reduction reaction is called the standard reduction potential ( E
0
) and is a measure of the tendency of the electron donor to lose electrons; the more negative the reduction potential, the better it is as an electron donor
B.
When electrons are transferred from an electron donor to an electron acceptor with a more positive reduction potential, free energy is released that can be used to form ATP
IV.
Electron Transport Chains: Sets of Sequential Redox Reactions
A.
An electron transport chain (ETC) is a series of electron carriers, each with a different redox potential
B.
Electron transport is important in a variety of metabolic processes (e.g., respiration and photosynthesis); cells move electrons by using a variety of electron carriers organized into a chain
C.
Electron carriers include NAD + , NADP + , flavoproteins (FAD, FMN), quinones, iron-sulfur centers
(ferredoxin), and cytochromes (hemes); these carriers differ in terms of how they carry electrons, and this impacts how they function in electron transport chains
V.
Biochemical Pathways
A.
Products of reactions are called metabolites
B.
Metabolite flux is the rate of turnover of a metabolite
VI.
Enzymes and Ribozymes
A.
Enzyme Structure
1.
Enzymes are protein catalysts with great specificity for the reaction catalyzed and the molecules acted upon a.
A catalyst is a substance that increases the rate of a reaction without being permanently altered b.
The reacting molecules are called substrates and the substances formed are products
2.
An enzyme may be composed only of protein or it may be a holoenzyme, consisting of a protein component (apoenzyme) and a nonprotein component (cofactor) a.
Prosthetic group—a cofactor that is firmly attached to the apoenzyme b.
Coenzyme—a cofactor that is loosely attached to the apoenzyme; it may dissociate from the apoenzyme and carry one or more of the products of the reaction to another enzyme
B.
How enzymes speed up reactions
1.
Enzymes increase the rate of a reaction but do not alter the equilibrium constant (or the standard free energy change) of the reaction
2.
Enzymes lower the activation energy required to bring the reacting molecules together correctly to form the transition-state complex; once the transition state has been reached the reaction can proceed rapidly
3.
Enzymes bring substrates together at the active site to form an enzyme-substrate complex; this can lower activation energy in several ways: a.
Local concentrations of the substrates are increased at the active (catalytic) site of the enzyme b.
Molecules at the active site are oriented properly for the reaction to take place
C.
Substrate concentration and enzyme activity
1.
The amount of substrate present affects the reaction rate, which increases as the substrate concentration increases until all available enzyme molecules are binding substrate (saturated) and converting it to products as rapidly as possible a.
When no further increase in reaction rate occurs with increases in substrate concentration, a reaction is said to be proceeding at maximal velocity ( V max
) b.
The Michaelis constant ( K m
) of an enzyme is the substrate concentration required for the reaction to reach half maximal velocity; it is used as a measure for the apparent affinity of an enzyme for its substrate
2.
Enzyme activity is affected by alterations in pH and temperature; each enzyme has specific pH and temperature optima; extremes of pH, temperature, and other factors can cause denaturation (loss of activity due to disruption of enzyme structure)
D.
Enzyme Denaturation
1.
pH and temperature can effect enzyme activity a.
if pH deviates too much from optimum activity slows and the enzyme may be damaged
3
© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.

Prescott’s Microbiology, 9 th Edition b.
if temperature rises too much activity can be lost
2.
pH and temperature often reflect the pH and temperature of the organism’s habitat
E.
Enzyme Inhibition
1.
Competitive inhibition occurs when the inhibitor binds at the active site and thereby competes with the substrate (if the inhibitor binds, then the substrate cannot, and no reaction occurs); this type of inhibition can be overcome by adding excess substrate
2.
Noncompetitive inhibition occurs when the inhibitor binds to the enzyme at some location other than the active site and changes the enzyme’s shape so that it is inactive or less active; this type of inhibition cannot be overcome by the addition of excess substrat
F.
Ribozymes:Catalytic RNA molecules
1.
Catalytic RNA molecules are called ribozymes; often they act on RNA substrate molecules
2.
The shape is essential to catalytic activity
VII.
Regulation of Metabolism
A.
Regulation is essential for microorganisms to conserve energy and material and to maintain metabolic balance despite frequent changes in their environment
B.
Metabolic processes can be regulated in three major ways:
1.
Metabolic channeling—the localization of metabolites and enzymes in different parts of a cell
2.
Increasing or decreasing the number of enzyme molecules present (regulation of gene expression)
3.
Stimulation or inhibition of critical enzymes in a pathway (posttranslational regulation)
C.
Metabolic channeling
1.
Compartmentation is a common mechanism for metabolic channeling; enzymes and metabolites are distributed in separate cell structures or organelles
2.
Channeling can occur within a compartment
3.
Channeling can generate marked variations in metabolite concentrations and therefore directly affect enzyme activity
VIII.
Posttranslational Regulation of Enzyme Activity
A.
Allosteric regulation—regulation of enzyme activity by an effector or modulator, which binds reversibly and noncovalently to a regulatory site on the enzyme; the regulatory site is distinct from the catalytic site; the effect can be positive or negative
B.
Covalent modification of enzymes—regulation of enzyme activity by the reversible covalent addition or removal of a chemical group (e.g., phosphate, methyl group, adenylic acid); the effect can be positive or negative
C.
Feedback Inhibition
1.
Every pathway has at least one pacemaker enzyme that catalyzes the slowest (rate-limiting) reaction in the pathway; often this is the first reaction in a pathway
2.
In feedback inhibition (end product inhibition), the end product of the pathway inhibits the pacemaker enzyme
3.
In branched pathways, balance between end products is maintained through the use of regulatory enzymes at branch points; multiple branched pathways often use isoenzymes, each under separate and independent control
1. Consider the following diagram of the energy flow for a particular reaction. Is the reaction exergonic or endergonic? What does the diagram indicate? How would the use of an enzyme catalyst affect the energy flow?
Indicate this on the diagram, and also indicate the energy of activation and the free energy change of both the catalyzed and uncatalyzed reactions.
4
© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.

Prescott’s Microbiology, 9 th Edition
A + B C + D
Time
2. Each of the following two diagrams indicates the rate of a reaction as a function of substrate concentration. In each case an inhibitor is present (not the same one) and the substrate concentration is not saturating the enzyme.
Explain the difference between the two situations.
{Substrate} {Substrate}
5
© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.

Prescott’s Microbiology, 9 th Edition
3. Considering that ATP is used as a common substrate in many reactions to allow energetically
unfavorable reactions to proceed in a forward direction, explain why regulation of ATP levels is
crucial to metabolism.
4. How is ATP utilized in the feedback inhibition of glycolysis?
Construct a concept map that summarizes metabolic processes. Use the concepts that follow, any other concepts or terms you need and your own linking words between each pair of concepts in your map. anabolism, catabolism, ATP, endergonic reaction, exergonic reaction, entropy, free energy change, redox reactions, ETC, enzyme.
6
© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.