Biochemistry

Raymond S. Ochs

• Publisher: CRC Press
• Year: 2021
• ISBN:
  9781000428124
• Edition: 2
• Topic: Biological Sciences
• Subtopic: Biochemistry
• Index: Biological Sciences

Biochemistry Second Edition, is a single-semester text designed for undergraduate non-biochemistry majors. Accessible, engaging, and informative, it is the perfect introduction to the subject for students who may approach chemistry with apprehension. Its unique emphasis on metabolism and its kinetic underpinnings gives the text up-to-the-minute relevance for students investigating current public health concerns, such as obesity and diabetes. Biochemistry Second Edition will encourage students to explore the basics of chemistry and its influence on biological problems.

Key Features:

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• Provides an understanding of (mostly) enzymatic reactions that are responsible for the function and maintenance of living things.

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• This innovative text for non-biochemistry majors includes introductory material at the beginning of each chapter that contextualizes chapter themes in real-life scenarios.

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• Online supporting materials with further opportunities for research and investigation.

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• Synthesis questions at the end of each chapter that encourage students to make connections between concepts and ideas, as well as develop critical-thinking skills.

About the Author:

Raymond S. Ochs is a biochemist with a career-long specialty in metabolism spanning 30 years. Previously, he has written the textbook Biochemistry, contributed the metabolism chapters to another text, Principles of Biochemistry, and co-edited a collection of articles published as Metabolic Regulation, and the recent monograph Metabolic Strucure and Regulation. His research interests concern major pathways of liver and muscle, including glycolysis, gluconeogenesis, ureogenesis, fatty acid metabolism, glycogen metabolism, and control by cAMP, Ca2+, diacylglycerol, and AMPK. He is currently professor of pharmacy at St. John's University in New York, teaching biochemistry, physiology, and medicinal chemistry.

1 Foundations

Biochemistry is the study of the chemical nature of biology. Biochemists use chemical ideas and tools to elucidate living systems. We begin with a review of some chemical concepts: reactions, kinetics, equilibrium, steady-state, and energy. Next, we introduce acid–base and redox reactions. Some foundational ideas of biology complete the chapter: cell theory, evolution, and species hierarchies.

1.1 Origins of Biochemistry

Compared to its component sciences, biochemistry itself is a young discipline. Hoppe-Seyler coined the word Biochimie in 1877. He also edited the first biochemistry journal, Biological Chemistry, still in existence today. In this period – the later part of the 19th century – both the notions of spontaneous generation and vitalism were dispelled, clearing the way for a discipline that required new thinking.

According to the hypothesis of spontaneous generation, living systems arose from nothingness, as bacteria seem to do in a nutrient-rich broth. In the 1860s, however, Louis Pasteur demonstrated that bacteria exist in the air; no bacteria appear in the broth if the container is isolated from the atmosphere. This discovery led to the cell theory, which holds that cells are the fundamental unit of living systems and arise from other cells. Despite this advance, Pasteur himself was a vitalist, believing that living systems do not obey the same chemical principles as inert objects.

Two challenges to vitalism bracketed the work of Pasteur. In 1828, Wohler discovered that urea could be synthesized in a laboratory from ammonia cyanate. The strictly in vitro synthesis of an organic compound did not need the “aid of a kidney” as Wohler put it (see Box 1.1). In 1897, the German chemists (and brothers) Eduard and Hans Buchner showed that fermentation occurs in extracts from ruptured cells, thus dispelling the notion that cellular organization is required for processes that occur in living systems.

In the 20th century, biochemistry was dominated first by organic chemistry, as metabolic pathways were discovered, then by enzymology, then bioenergetics, and later by molecular biologists as the study of DNA intensified. As biochemistry plays an increasingly large role in physical and chemical sciences today, these disciplines overlap considerably. What remains distinctive about biochemistry is the chemical perspective of biological phenomena. Biochemical principles are presented in the following chapters. In the present one, we consider some fundamental concepts of chemistry and biology.

1.2 Some Chemical Ideas

To determine if you might need a review or can instead skip to the next section, take the following self-test:

• Without specifying a value, what is the meaning of Avogadro’s number?
• Distinguish between atoms, electrons, molecules, and moles.
• When is it appropriate to use mole units as opposed to grams?
• Why is the equilibrium constant for a reaction expressed as the equilibrium concentrations of the products multiplied together, divided by the equilibrium concentrations of the substrates multiplied together?
• How does equilibrium relate to kinetics?

Box 1.1 Word Origins: Organic

Among its rich meanings, the word organic also implies a sense of the whole, as in organism, which also implies animate, living, or vital. The root word stems from the Greek ergon, meaning work in the sense that an organism is a collection of working entities. Vitalists identified substances believed to be produced only by a living organism. After vitalism was discounted, organic was redefined rather than cast aside. Today, organic chemistry is defined as a branch of chemistry that focuses on compounds of carbon. Strictly speaking, inorganic chemistry refers to molecules containing other elements. In recent times, another meaning for organic has emerged that is closer to its historical roots. In this context, organic is a label for farming methods that do not use synthesized chemicals (e.g., fertilizers and pesticides for plants, antibiotics and hormones for animals). Thus, growing plants and raising animals in this way is said to produce organic food. Whether this is a definite health benefit is debatable. For example, the absence of pesticides can lead to greater bacterial content in food. Moreover, there is no settled agreement on exactly what organic farming is, so products vary. Despite the various uses of the word, we are concerned with only the definition of organic chemistry as the chemistry of carbon compounds.

The ideas of the mole, Avogadro’s number, atoms, and molecules are presented in Appendix A.1. Here, we consider here the notions of kinetics and thermodynamics and other chemical principles with the assumption that those ideas are well in hand.

1.2.1 Reactions and Their Kinetic Description

Suppose substances A and B react to form substances C and D. This is a generic reaction, which can be written in the form:

A + B ⇌ C + D

(1.1)

A and B are called substrates; C and D are products. Each represents a chemical species and can also be called a compound or a metabolite. To visualize what is happening, let us relax our molecular thinking and describe the molecules pictorially as Figure 1.1. In this representation, the reaction involves removing a piece of molecule A and affixing it to B, thus creating C and D. This is a mechanistic view. To more fully characterize the reaction, we consider each direction separately. Fixing a direction allows us to define the rate of a reaction, a characterization known as kinetics. Consider first the forward direction, which proceeds from left to right. This reaction is written:

FIGURE 1.1 A generic reaction.

A + B → C + D

(1.2)

Suppose there are 3 A molecules and 4 B molecules, as shown in Figure 1.2. Each A can combine with any of 4 Bs. This procedure follows Equation (1.2), which excludes the reaction of A with itself or B with itself. There are 12 possible collisions (3 × 4). Another way of expressing the situation is that the reaction is proportional to 3 × 4. This analysis is formally known as collision theory: the rate of a reaction is proportional to the number of...