Enzyme Regulation in Metabolic Pathways

Lloyd Wolfinbarger

• Publisher: Wiley-Blackwell
• Year: 2017
• ISBN:
  9781119155416
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Cell Biology
• Index: Biological Sciences

Enzyme Regulation in Metabolic Pathways shows the reader how to understand the roles of enzymes and their kinetic constants in intermediary metabolism. It provides a means of correlating data obtained in experimental studies to multiple possible mechanisms through which some enzyme may catalyze the conversion of a substrate to a product. Although not the most appropriate means of determining some potential kinetic mechanism, quasi-equilibrium assumptions are used throughout the book, keeping the rate equation derivations simple. Actual metabolic pathways with known (presumed) positive and negative regulation events are linked to these potential kinetic mechanisms using both rate equation derivations and data plots illustrating how the rate equation derivations can be used to explain the data plots.

This book will be a valuable reference for students in biological sciences and biochemistry majors required to take a core course in enzymology.

Part I

Beyond this point there be dragons.

Admonition on old seafaring maps

1
Characteristics of Enzymes

At university, Enzymology was the class that most biochemistry or biology majors dreaded taking. Those students who liked the class were typically math majors who took the class for the thrill of solving complex rate equation derivations. Those students who had to take the class against their will were those who might need to understand the role of enzymes as they pertained to other aspects of biochemistry, but otherwise had little desire to sit through boring lectures involving lots of equations and the occasional molecular structures on the white board. As a professor teaching biochemistry to undergraduate and graduate students the task fell to me to keep my students’ attention, so they didn’t fall asleep, yet challenge them to understand why what I was teaching them could be both fun and useful.

I started teaching traditional enzymology as it was presented in the textbooks of the day (and I’m sorry to say is still being presented today). I found my students were passing the tests, but failing to understand how to interpret data and more importantly how to fit the data they were obtaining in their research into something meaningful and exciting. I eventually adopted a strategy of engaging the minds of my students with challenging, but improbable, enzymatic mechanisms and found that steady state kinetics, while more relevant, hindered the understanding of some of the more basic principles associated with enzyme kinetics. I finally hit upon the use of quasi‐equilibrium assumptions and my students began to question and challenge my lectures—I had finally arrived as a professor.

Enzymology can be the study of enzymes as protein molecules with specific folding patterns of the amino acid polymer and unique binding sites wherein intra‐ and inter‐molecular distances define the specificity of the molecule to attract, bind to, and change some substrate molecule. Computer‐aided molecular modeling is a wonderful aspect of both biochemistry and enzymology in providing visuals essential to understanding, but does little to help with data analysis. Alternatively, enzymology can be the study of how these protein molecules control and mediate the flow of metabolites through intermediary metabolism affecting what we call metabolic viability to life forms. It is this latter study of enzymes that will be the focus of this book.

Enzymes are mostly proteins that are of variable length (with respect to amino acid sequences) and molecular weight. These amino acid polymers typically fold into some conformation that is most energetically favored based on the nature of the amino acids making up the protein and the aqueous environment in which they find themselves. For the most part, hydrophobic amino acids such as leucine or phenylalanine, as examples, are to be found in what might be called the hydrophobic core of the protein, whereas the hydrophilic amino acids such as histidine or aspartic acid, again as examples, will preferentially be found on those surfaces of the protein more exposed to an aqueous (hydrophilic) environment. The arrangement of hydrophobic and ionizable side groups of these hydrophilic amino acids is typically described as being present in some molecular organization that forms a region complementary to some low molecular weight solute. This region of the protein is generally regarded as constituting the substrate‐ (or modifier‐) binding site. Whether this binding site tends to bind an unstable form of the substrate, stabilizing the unstable intermediate, and in so doing promoting its conversion to product; or whether this binding site tends to bind a stable form of the substrate and in so doing causes the substrate to shift into some less stable configuration promoting its conversion to product, will be discussed in detail. We will enter into this aspect of the basics of enzymology in detail in Chapter 2. For now, I only wish to stipulate that this enzyme with a substrate‐binding site will be referred to as free enzyme (E) in subsequent sections. When free enzyme (E) binds with the substrate, it will be referred to as the enzyme/substrate complex (ES). As the enzyme facilitates the conversion of substrate to product via some unknown or unspecified mechanism, the product (P) released from the substrate‐binding site will result in the (ES) complex reverting to free enzyme (E). Thus within the context of this book, the sum of the concentration of free enzyme (E) and enzyme/substrate complex (ES) will be referred to as the total amount (or quantity) of enzyme (E_t). When introducing modifiers of enzyme activity, I will use the simple connotation of a modifier (M) being either an activator (Ma) or an inhibitor (Mi). Modifiers will typically bind to free enzyme (E) to form a modified enzyme as either (MaE) or (MiE). Where substrate (S), enzyme (E), substrate/enzyme complex (ES), and so forth, are bracketed with square brackets, such as [S], the intent will be to express the molecule as some concentration. I will try to restate this point throughout the text, more to remind and help you than to irritate you with what will appear as my being overly redundant. Repetition is a good learning tool.

I would also like to emphasize one more point. I will make reference to “saturating” concentrations of substrate or modifier in the text. As you will see in later figures, as you add increasing concentrations of substrate (or modifier) to an enzymatic reaction, the rate of conversion of substrate to product will gradually increase until such time as that concentration approaches the capacity of that enzyme to bind to substrate converting it to product. At such a time where increasing the concentration of substrate no longer significantly increases the rate of conversion to product, it is generally assumed (described) as a saturation of enzyme by substrate. This will make more sense later, but I also want to emphasize that we will operate under the premise that the amount of substrate at any given concentration of that substrate will be inexhaustible. This means basically that you can crystallize salt out of sea water, but you will never run out of sea water where there is an infinite amount of salt. This is the difference between the concentration of salt in sea water and the amount of salt in the sea.

I shall take a rather simplistic approach to the overall mathematical equation subject with respect to enzymes by defining a few selected terms. As you get deeper into the study of enzym...

Table of contents

• Cover
• Title Page
• Table of Contents
• Preface
• Author’s Review
• Part I
• Part II
• Index
• End User License Agreement