7: Microbial Biochemistry

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The earth is estimated to be 4.6 billion years old, but for the first 2 billion years, the atmosphere lacked oxygen, without which the earth could not support life as we know it. One hypothesis about how life emerged on earth involves the concept of a “primordial soup.” This idea proposes that life began in a body of water when metals and gases from the atmosphere combined with a source of energy, such as lightning or ultraviolet light, to form the carbon compounds that are the chemical building blocks of life. In 1952, Stanley Miller (1930–2007), a graduate student at the University of Chicago, and his professor Harold Urey (1893–1981), set out to confirm this hypothesis in a now-famous experiment. Miller and Urey combined what they believed to be the major components of the earth’s early atmosphere—water (H₂O), methane (CH₄), hydrogen (H₂), and ammonia (NH₃)—and sealed them in a sterile flask. Next, they heated the flask to produce water vapor and passed electric sparks through the mixture to mimic lightning in the atmosphere (Figure \(\PageIndex{1}\)). When they analyzed the contents of the flask a week later, they found amino acids, the structural units of proteins—molecules essential to the function of all organisms.

Diagram of the Miller-Urey experiment. A flask of water (to simulate the ocean) is heated. This is connected via glass tubing in a closed loop to: a vacuum pump, a flask containing gases (water, methane, hydrogen, ammonia), and an electric spark (to simulate lightning), and final to a condenser that cools the water. The cooled water contains organic compounds. — Figure \(\PageIndex{1}\): Scientist Stanley Miller and Harold Urey demonstrated that organic compounds may have originated naturally from inorganic matter. The Miller-Urey experiment illustrated here simulated the effects of lightning on chemical compounds found in the earth’s early atmosphere. The resulting reactions yielded amino acids, the chemical building blocks of proteins. (credit: modification of work by Courtney Harrington)

7.1: Organic Molecules
Biochemistry is the discipline that studies the chemistry of life, and its objective is to explain form and function based on chemical principles. Organic chemistry is the discipline devoted to the study of carbon-based chemistry, which is the foundation for the study of biomolecules and the discipline of biochemistry. Both biochemistry and organic chemistry are based on the concepts of general chemistry.
7.2: Carbohydrates
The most abundant biomolecules on earth are carbohydrates. From a chemical viewpoint, carbohydrates are primarily a combination of carbon and water, and many of them have the empirical formula (CH₂O)ₙ, where n is the number of repeated units. This view represents these molecules simply as “hydrated” carbon atom chains in which water molecules attach to each carbon atom, leading to the term “carbohydrates.”
7.3: Lipids
Although they are composed primarily of carbon and hydrogen, lipid molecules may also contain oxygen, nitrogen, sulfur, and phosphorous. Lipids serve numerous and diverse purposes in the structure and functions of organisms. They can be a source of nutrients, a storage form for carbon, energy-storage molecules, or structural components of membranes and hormones. Lipids comprise a broad class of many chemically distinct compounds, the most common of which are discussed in this section.
7.4: Proteins
Amino acids are capable of bonding together in essentially any number, yielding molecules of essentially any size that possess a wide array of physical and chemical properties and perform numerous functions vital to all organisms. The molecules derived from amino acids can function as structural components of cells and subcellular entities, as sources of nutrients, as atom- and energy-storage reservoirs, and as functional species such as hormones, enzymes, receptors, and transport molecules.
7.5: Using Biochemistry to Identify Microorganisms
Accurate identification of bacteria is essential in a clinical laboratory for diagnostic and management of epidemics, pandemics, and food poisoning caused by bacterial outbreaks. In this section, we will discuss a few methods that use biochemical characteristics to identify microorganisms.
7.E: Microbial Biochemistry (Exercises)

Thumbnail: An enzyme binding site that would normally bind substrate can alternatively bind a competitive inhibitor, preventing substrate access. Dihydrofolate reductase is inhibited by methotrexate which prevents binding of its substrate, folic acid. Binding site in blue, inhibitor in green, and substrate in black (PDB: 4QI9). (CC BY 4.0; Thomas Shafee).