8.1: Energy, Matter, and Enzymes

Learning Objectives

• Define and describe metabolism
• Compare and contrast autotrophs and heterotrophs
• Describe the importance of oxidation-reduction reactions in metabolism
• Describe why ATP, FAD, NAD⁺, and NADP⁺ are important in a cell
• Identify the structure and structural components of an enzyme
• Describe the differences between competitive and noncompetitive enzyme inhibitors

The term used to describe all of the chemical reactions inside a cell is metabolism (Figure \(\PageIndex{1}\)). Cellular processes such as the building or breaking down of complex molecules occur through series of stepwise, interconnected chemical reactions called metabolic pathways. Reactions that are spontaneous and release energy are exergonic reactions, whereas endergonic reactions require energy to proceed. The term anabolism refers to those endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy. Conversely, the term catabolism refers to exergonic pathways that break down complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules, which are used to drive anabolic pathways. Thus, in terms of energy and molecules, cells are continually balancing catabolism with anabolism.

Figure \(\PageIndex{1}\): Metabolism includes catabolism and anabolism. Anabolic pathways require energy to synthesize larger molecules. Catabolic pathways generate energy by breaking down larger molecules. Both types of pathways are required for maintaining the cell’s energy balance.

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Classification by Carbon and Energy Source

Organisms can be identified according to the source of carbon they use for metabolism as well as their energy source. The prefixes auto- (“self”) and hetero- (“other”) refer to the origins of the carbon sources various organisms can use. Organisms that convert inorganic carbon dioxide (CO₂) into organic carbon compounds are autotrophs. Plants and cyanobacteria are well-known examples of autotrophs. Conversely, heterotrophs rely on more complex organic carbon compounds as nutrients; these are provided to them initially by autotrophs. Many organisms, ranging from humans to many prokaryotes, including the well-studied Escherichia coli, are heterotrophic.

Organisms can also be identified by the energy source they use. All energy is derived from the transfer of electrons, but the source of electrons differs between various types of organisms. The prefixes photo- (“light”) and chemo- (“chemical”) refer to the energy sources that various organisms use. Those that get their energy for electron transfer from light are phototrophs, whereas chemotrophs obtain energy for electron transfer by breaking chemical bonds. There are two types of chemotrophs: organotrophs and lithotrophs. Organotrophs, including humans, fungi, and many prokaryotes, are chemotrophs that obtain energy from organic compounds. Lithotrophs (“litho” means “rock”) are chemotrophs that get energy from inorganic compounds, including hydrogen sulfide (H₂S) and reduced iron. Lithotrophy is unique to the microbial world.

The strategies used to obtain both carbon and energy can be combined for the classification of organisms according to nutritional type. Most organisms are chemoheterotrophs because they use organic molecules as both their electron and carbon sources. Table \(\PageIndex{1}\) summarizes this and the other classifications.

Table \(\PageIndex{1}\): Classifications of Organisms by Energy and Carbon Source

Classifications		Energy Source	Carbon Source	Examples
Chemotrophs	Chemoautotrophs	Chemical	Inorganic	Hydrogen-, sulfur-, iron-, nitrogen-, and carbon monoxide-oxidizing bacteria
	Chemoheterotrophs	Chemical	Organic compounds	All animals, most fungi, protozoa, and bacteria
Phototrophs	Photoautotrophs	Light	Inorganic	All plants, algae, cyanobacteria, and green and purple sulfur bacteria
	Photoheterotrophs	Light	Organic compounds	Green and purple nonsulfur bacteria, heliobacteria

Video: Autotrophs and Heterotrophs

Curious about modes of nutrition? Join the Amoeba Sisters in learning about autotrophs and heterotrophs. Video explains these terms as well as how their carbon source differs. Photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs, and their energy sources, are also discussed!

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Oxidation and Reduction in Metabolism

The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy incrementally; that is, in small packages rather than a single, destructive burst. Reactions that remove electrons from donor molecules, leaving them oxidized, are oxidation reactions; those that add electrons to acceptor molecules, leaving them reduced, are reduction reactions. Because electrons can move from one molecule to another, oxidation and reduction occur in tandem. These pairs of reactions are called oxidation-reduction reactions, or redox reactions.

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Energy Carriers: NAD⁺, NADP⁺, FAD, and ATP

The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile electron carriers, molecules that bind to and shuttle high-energy electrons between compounds in pathways. The principal electron carriers we will consider originate from the B vitamin group and are derivatives of nucleotides; they are nicotinamide adenine dinucleotide, nicotine adenine dinucleotide phosphate, and flavin adenine dinucleotide. These compounds can be easily reduced or oxidized. Nicotinamide adenine dinucleotide (NAD⁺/NADH) is the most common mobile electron carrier used in catabolism. NAD⁺ is the oxidized form of the molecule; NADH is the reduced form of the molecule. Nicotine adenine dinucleotide phosphate (NADP⁺), the oxidized form of an NAD⁺ variant that contains an extra phosphate group, is another important electron carrier; it forms NADPH when reduced. The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH₂. Both NAD⁺/NADH and FAD/FADH₂ are extensively used in energy extraction from sugars during catabolism in chemoheterotrophs, whereas NADP⁺/NADPH plays an important role in anabolic reactions and photosynthesis. Collectively, FADH₂, NADH, and NADPH are often referred to as having reducing power due to their ability to donate electrons to various chemical reactions.

A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms ATP (Figure \(\PageIndex{2}\)). Adding a phosphate group to a molecule, a process called phosphorylation, requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. Thus, the bonds between phosphate groups (one in ADP and two in ATP) are called high-energy phosphate bonds. When these high-energy bonds are broken to release one phosphate (called inorganic phosphate [P_i]) or two connected phosphate groups (called pyrophosphate [PP_i]) from ATP through a process called dephosphorylation, energy is released to drive endergonic reactions (Figure \(\PageIndex{3}\)).

Figure \(\PageIndex{2}\): The energy released from dephosphorylation of ATP is used to drive cellular work, including anabolic pathways. ATP is regenerated through phosphorylation, harnessing the energy found in chemicals or from sunlight. (credit: modification of work by Robert Bear, David Rintoul)

Figure \(\PageIndex{3}\): Exergonic reactions are coupled to endergonic ones, making the combination favorable. Here, the endergonic reaction of ATP phosphorylation is coupled to the exergonic reactions of catabolism. Similarly, the exergonic reaction of ATP dephosphorylation is coupled to the endergonic reaction of polypeptide formation, an example of anabolism.

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Interactive Element

Case Study Preview: "Meningitis in the Sun"

When 15-month-old Hannah starts acting strangely during a summer trip to Gambia - fatigue, light sensitivity, and vomiting - her parents assume it’s a mild virus. But when her symptoms worsen, a local physician suspects something more serious: meningitis. With her life on the line, doctors start treatment before test results come back.

In this case, you’ll track how a tiny gram-negative diplococcus - Neisseria meningitidis - can rapidly invade the body and why quick diagnosis and treatment are critical. You'll also explore how biochemical tests are still essential tools in resource-limited settings and learn why travel vaccinations matter more than ever.

Sometimes the scariest bugs don’t cause stomach aches - they go straight for the brain.

Chapter 8 Case Study - Meningitis in the Sun

 

Key Concepts and Summary

• Metabolism includes chemical reactions that break down complex molecules (catabolism) and those that build complex molecules (anabolism).
• Organisms may be classified according to their source of carbon. Autotrophs convert inorganic carbon dioxide into organic carbon; heterotrophs use fixed organic carbon compounds.
• Organisms may also be classified according to their energy source. Phototrophs obtain their energy from light. Chemotrophs get their energy from chemical compounds. Organotrophs use organic molecules, and lithotrophs use inorganic chemicals.
• Cellular electron carriers accept high-energy electrons from foods and later serve as electron donors in subsequent redox reactions. FAD/FADH₂, NAD⁺/NADH, and NADP⁺/NADPH are important electron carriers.
• Adenosine triphosphate (ATP) serves as the energy currency of the cell, safely storing chemical energy in its two high-energy phosphate bonds for later use to drive processes requiring energy.