Vocabulary for Part 1: Chapter 6: Microbial Metabolism-Fuelling Cell Growth (September 25-October 2)

3-phosphoglycerate

A three-carbon intermediate in both glycolysis and the Calvin cycle, playing a pivotal role in energy metabolism and biosynthesis. In glycolysis, it is formed from 1,3-bisphosphoglycerate by the enzyme phosphoglycerate kinase, generating one molecule of ATP in the process. 3-PGA is then converted into 2-phosphoglycerate by phosphoglycerate mutase, continuing the pathway toward pyruvate formation. In photosynthetic organisms, 3-PGA is the first stable product of carbon fixation via the Calvin cycle, formed when ribulose-1,5-bisphosphate reacts with CO₂. Beyond energy metabolism, it serves as a precursor for amino acid biosynthesis, particularly serine.

a-ketoglutarate 

A five-carbon dicarboxylic acid that serves as a key intermediate in the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle. It is formed by the oxidative decarboxylation of isocitrate via isocitrate dehydrogenase and is subsequently converted into succinyl-CoA by the α-ketoglutarate dehydrogenase complex, releasing CO₂ and generating NADH. Beyond its role in energy metabolism, α-ketoglutarate is a precursor for amino acid biosynthesis—especially glutamate—and participates in nitrogen assimilation and cellular redox balance. It also functions as a co-substrate for dioxygenases involved in epigenetic regulation and collagen synthesis.

Acetyl coenzyme A (acetyl-CoA)

A central metabolic intermediate that links carbohydrate, fat, and protein catabolism to energy production and biosynthesis. It consists of a two-carbon acetyl group bound to coenzyme A, a thiol-containing molecule derived from pantothenic acid (vitamin B₅). Acetyl-CoA is primarily formed from pyruvate via the pyruvate dehydrogenase complex, from fatty acid β-oxidation, or from amino acid degradation. It enters the tricarboxylic acid (TCA) cycle by combining with oxaloacetate to form citrate, initiating a series of reactions that generate ATP, NADH, and FADH₂. Beyond energy metabolism, acetyl-CoA serves as a precursor for lipid synthesis and is a donor of acetyl groups in protein acetylation, influencing gene expression and enzyme activity.

Activation energy 

The minimum amount of energy required for reactant particles to undergo a chemical reaction, serving as the threshold that must be overcome for bonds to break and new ones to form. It represents the energy barrier between reactants and products, and only collisions with energy equal to or greater than this value can lead to a successful transformation. This concept explains why reactions proceed faster at higher temperatures or in the presence of catalysts, which lower the activation energy and increase the number of effective collisions. Activation energy is central to understanding reaction rates and the dynamics of chemical change.

Adenosine diphosphate (ADP)

A nucleotide made up of the nitrogenous base adenine, the sugar ribose, and two phosphate groups. It is formed when adenosine triphosphate (ATP) loses one of its three phosphate groups through hydrolysis, releasing energy for cellular processes. ADP can be converted back into ATP by the addition of a phosphate group during cellular respiration or photosynthesis, making it a central molecule in the cell’s energy cycle.

Adenosine triphosphate (ATP)

A high-energy molecule that serves as the primary energy currency of the cell. It is composed of the nitrogenous base adenine, the sugar ribose, and three phosphate groups linked by high-energy bonds. When one of these bonds is broken (usually converting ATP to ADP + P_i), energy is released to power essential cellular processes such as muscle contraction, active transport, and biosynthesis.

Alcohol fermentation

An anaerobic metabolic process in which glucose is first broken down into pyruvate via glycolysis, and then converted into ethanol and carbon dioxide by yeast or certain bacteria. This occurs through two enzymatic steps: pyruvate is decarboxylated to acetaldehyde, which is then reduced to ethanol by alcohol dehydrogenase, regenerating NAD⁺ to sustain glycolysis. The process yields a net gain of two ATP per glucose molecule and is crucial for energy production in oxygen-limited environments. Alcohol fermentation underpins the production of beer, wine, and spirits, and also contributes to breadmaking, where CO₂ causes dough to rise and ethanol evaporates during baking.

Anabolism 

The set of metabolic processes in living organisms that build complex molecules from simpler ones, requiring energy input to drive biosynthesis and support growth, repair, and cellular function. These reactions construct macromolecules such as proteins, nucleic acids, lipids, and carbohydrates from smaller units like amino acids and sugars, using energy typically supplied by ATP or NADPH. Anabolism is essential for tissue development, enzyme production, and maintaining structural integrity, and it operates in balance with catabolism, which breaks down molecules to release energy that fuels anabolic activity.

Carbohydrate

An organic macromolecule made of carbon (C), hydrogen (H), and oxygen (O), usually in a ratio close to 1:2:1. Carbohydrates are built from simple sugar units called monosaccharides (like glucose, fructose, and galactose). They can form larger molecules such as disaccharides (sucrose, lactose) and polysaccharides (starch, glycogen, cellulose). Their main functions are to provide energy, store energy, and, in some cases, give structural support (like cellulose in plant cell walls).

Carbohydrate catabolism

The metabolic process by which complex carbohydrates like starch and glycogen are broken down into simpler sugars such as glucose, which are then oxidized to release energy in the form of ATP. This process involves a series of enzymatic pathways, primarily glycolysis, the citric acid cycle, and oxidative phosphorylation, through which glucose is converted into pyruvate and further metabolized to carbon dioxide and water. Along the way, high-energy electron carriers like NADH and FADH₂ are generated, feeding into the electron transport chain to drive ATP synthesis. Carbohydrate catabolism is central to cellular respiration and provides the primary energy source for most organisms.

Catabolism

The set of metabolic processes that break down complex molecules such as carbohydrates, lipids, and proteins into simpler units like glucose, fatty acids, and amino acids, releasing energy that cells use for vital functions. These reactions are typically exergonic, producing ATP and other energy carriers through pathways like glycolysis, the citric acid cycle, and oxidative phosphorylation. Catabolism supports cellular activities including muscle contraction, biosynthesis, and thermoregulation, and it operates in dynamic balance with anabolism to maintain metabolic homeostasis.

Catalyst

A substance that accelerates the rate of a chemical reaction by lowering the activation energy required for the reaction to proceed, without being consumed or permanently altered in the process. It achieves this by providing an alternative reaction pathway that is energetically more favorable, allowing reactants to convert into products more efficiently. Catalysts are essential in both industrial and biological contexts—for example, enzymes are biological catalysts that facilitate vital cellular reactions. Importantly, while catalysts speed up how quickly equilibrium is reached, they do not affect the final equilibrium position or the overall energy change of the reaction.

Cellular respiration

A biochemical process in which cells convert glucose and other nutrients into energy in the form of ATP (adenosine triphosphate), using oxygen and releasing carbon dioxide and water as byproducts. It involves a series of metabolic pathways—glycolysis, the citric acid cycle, and oxidative phosphorylation—that systematically extract energy from organic molecules by transferring electrons through redox reactions. This process is essential for sustaining life in aerobic organisms, as ATP powers nearly all cellular functions, from muscle contraction to active transport and biosynthesis.

Collision theory

Explains that chemical reactions occur when reactant particles collide with enough energy and the correct orientation to break existing bonds and form new ones. The minimum energy required for a successful collision is called the activation energy, and only collisions that meet this threshold are considered effective. Factors such as temperature, concentration, and surface area influence the frequency and energy of collisions, thereby affecting reaction rates. This theory helps predict and interpret how molecular motion and energy distribution impact the likelihood of reactions, especially in gases and solutions.

Dihydroxyacetone phosphate

A three-carbon intermediate in carbohydrate metabolism, formed during glycolysis and the Calvin cycle. In glycolysis, it arises from the cleavage of fructose 1,6-bisphosphate by the enzyme aldolase, yielding DHAP and glyceraldehyde 3-phosphate (G3P). Although only G3P continues directly through glycolysis, DHAP is rapidly isomerized into G3P by triose phosphate isomerase, ensuring efficient energy extraction from glucose. DHAP also serves as a precursor in lipid biosynthesis, contributing to the formation of glycerol-3-phosphate, which is essential for triglyceride and phospholipid synthesis. Its central role in both energy metabolism and biosynthetic pathways highlights its metabolic versatility.

Electron transport chain (ETC)

A series of protein complexes (I–IV) and mobile electron carriers embedded in the inner mitochondrial membrane that facilitate the transfer of electrons from NADH and FADH₂ molecular oxygen, the terminal electron acceptor. As electrons move through the chain, energy is released and used to pump protons from the mitochondrial matrix into the intermembrane space, creating an electrochemical gradient known as the proton motive force. This gradient drives protons back into the matrix through ATP synthase (complex V), catalyzing the synthesis of ATP from ADP and inorganic phosphate—a process called oxidative phosphorylation. The ETC is tightly regulated and essential for efficient aerobic energy production, while also contributing to reactive oxygen species signaling and cellular redox balance.

Enzyme 

A biological catalyst, usually a protein (though some are RNA), that speeds up chemical reactions in living organisms without being consumed in the process. Enzymes work by lowering the activation energy needed for a reaction, making biological processes—such as digestion, energy production, and DNA replication—happen efficiently and at body temperature. Each enzyme is highly specific, typically acting on only one type of substrate or reaction.

Erythrose 4-phosphate

A four-carbon sugar phosphate that functions as a key intermediate in the pentose phosphate pathway and serves as a precursor metabolite in anabolic biosynthesis. It is generated through transaldolase and transketolase reactions and plays a crucial role in the synthesis of aromatic amino acids—phenylalanine, tyrosine, and tryptophan—via the shikimate pathway in plants, fungi, and bacteria. E4P also contributes to the biosynthesis of vitamins and cofactors, linking carbohydrate metabolism to essential cellular functions. Its presence underscores the metabolic versatility of sugar phosphates in bridging energy production and biosynthetic demand.

Fermentation

A metabolic process in which organisms convert sugars like glucose into energy without using oxygen, typically producing byproducts such as ethanol, lactic acid, or carbon dioxide. It occurs in anaerobic conditions and allows cells to regenerate NAD⁺ from NADH, enabling glycolysis to continue producing ATP. Fermentation is essential in many microorganisms and also occurs in human muscle cells during intense exercise when oxygen is scarce. Beyond biology, fermentation has industrial and culinary significance, underpinning the production of bread, yogurt, beer, and biofuels.

Food catabolism

The biochemical process by which complex macronutrients—carbohydrates, proteins, and fats—are broken down into simpler molecules to release energy and provide metabolic intermediates. It begins with digestion, where enzymes hydrolyze polymers into absorbable units like glucose, amino acids, and fatty acids. These are then metabolized within cells through pathways such as glycolysis, β-oxidation, and deamination, producing acetyl-CoA and other intermediates that enter the TCA cycle. The cycle generates NADH and FADH₂, which feed electrons into the electron transport chain, driving ATP synthesis via oxidative phosphorylation. Catabolism is tightly regulated by hormones and cellular energy demands, ensuring efficient energy production and integration with anabolic processes.

Fructose 6-phosphate

A phosphorylated six-carbon sugar that serves as a key intermediate in both glycolysis and gluconeogenesis. It is formed from glucose 6-phosphate by the enzyme phosphoglucose isomerase and can be further phosphorylated by phosphofructokinase-1 (PFK-1) to form fructose 1,6-bisphosphate, a committed step in glycolysis. In anabolic pathways, F6P can also be diverted into the pentose phosphate pathway or used for amino sugar and nucleotide biosynthesis. Its central role in carbohydrate metabolism makes it a crucial regulatory node, especially in energy homeostasis and biosynthetic flux.

Glucose 

A simple sugar (monosaccharide) with the molecular formula C₆H₁₂O₆ that serves as a primary energy source for living organisms. It is a key product of photosynthesis in plants and a crucial fuel in cellular respiration for animals and humans. Structurally, glucose exists in both linear and cyclic forms, with the D-glucose isomer being biologically active. In the bloodstream, glucose levels are tightly regulated by hormones like insulin and glucagon, and imbalances can lead to conditions such as diabetes. Its role extends beyond metabolism, contributing to biosynthesis pathways and serving as a building block for complex carbohydrates like starch and cellulose.

Glucose 6-phosphate

An intermediate compound produced during central catabolic pathways—such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle—that serves as a starting material for anabolic biosynthesis. Instead of being fully oxidized for energy, these molecules are diverted into synthetic pathways to construct essential cellular components like amino acids, nucleotides, lipids, and carbohydrates. Examples include pyruvate, acetyl-CoA, and ribose-5-phosphate, which link energy metabolism to macromolecular synthesis, making precursor metabolites critical nodes in the metabolic network.

Glycolysis (1^st step in cellular respiration)

A ten-step anaerobic metabolic pathway that occurs in the cytoplasm, where one molecule of glucose (a six-carbon sugar) is enzymatically broken down into two molecules of pyruvate (three-carbon compounds), yielding a net gain of two ATP molecules and two NADH molecules. The pathway is divided into an energy investment phase, which consumes ATP to phosphorylate glucose intermediates, and an energy payoff phase, which generates ATP through substrate-level phosphorylation and reduces NAD⁺ to NADH. Glycolysis is highly conserved across species and functions as the universal entry point for carbohydrate catabolism, feeding into aerobic respiration when oxygen is available or fermentation pathways under anaerobic conditions.

Gonorrheal opthalmia

A severe eye infection caused by Neisseria gonorrhoeae, typically affecting newborns exposed to the bacteria during childbirth or adults through direct contact with infected genital secretions. It manifests as intense conjunctival inflammation, swelling, and thick purulent discharge, often appearing within 2 to 5 days after exposure. In infants, the condition—also called ophthalmia neonatorum—can lead to corneal damage and blindness if untreated, making early intervention critical. Prophylactic treatment at birth, such as silver nitrate or antibiotic eye drops, is commonly used to prevent infection. In adults, gonorrheal ophthalmia is rare but can occur through autoinoculation or contaminated hands, requiring prompt systemic and topical antibiotic therapy.

Lactic acid fermentation

An anaerobic metabolic process in which glucose is converted into pyruvate via glycolysis, and then reduced to lactic acid by the enzyme lactate dehydrogenase. This reduction regenerates NAD⁺ from NADH, allowing glycolysis to continue producing ATP in the absence of oxygen. It occurs in certain bacteria (e.g., Lactobacillus) and in animal cells like muscle tissue during intense activity when oxygen is limited. While it yields only 2 ATP per glucose molecule, it provides a rapid energy source and plays a role in food production, contributing to the flavor and preservation of fermented products like yogurt and sauerkraut.

Lactobacillus

A genus of Gram-positive, rod-shaped, facultatively anaerobic bacteria known for converting sugars into lactic acid through fermentation, a trait that makes them essential in food production and microbial ecology. Commonly found in fermented foods like yogurt, kefir, and sauerkraut, these bacteria contribute to acidity, flavor, and preservation. In the human microbiome, certain Lactobacillus species colonize the gut and urogenital tract, where they help maintain pH balance, inhibit pathogens, and support immune function. Their probiotic properties have made them valuable in therapeutic applications, and recent genomic studies have led to taxonomic reclassification of many species within the genus.

Lipase 

An enzyme that catalyzes the hydrolysis of triglycerides into glycerol and free fatty acids, playing a central role in lipid digestion, transport, and metabolism. Produced primarily by the pancreas and secreted into the small intestine, lipase acts at the oil–water interface of emulsified fat droplets, a process enhanced by bile salts. In humans, several types of lipases exist, including pancreatic lipase, hepatic lipase, and lipoprotein lipase, each with distinct roles in breaking down dietary fats or processing lipoproteins in the bloodstream. Lipase activity is essential for nutrient absorption and energy homeostasis, and its measurement is clinically relevant in diagnosing pancreatic disorders such as acute pancreatitis.

Lipid

A broad class of naturally occurring organic molecules that are insoluble in water but soluble in nonpolar solvents (like oils or alcohols), due to their largely hydrophobic structure. They include fats, oils, phospholipids, steroids, and waxes, and are made mostly of carbon, hydrogen, and a small amount of oxygen. Lipids play essential roles in living organisms, such as serving as a major energy storage source, forming cell membranes (phospholipid bilayers), and acting as signaling molecules (like steroid hormones).

Metabolism 

The totality of chemical reactions within a living organism that convert energy and matter to sustain life, encompassing both catabolic processes that break down molecules to release energy and anabolic processes that use energy to build complex molecules for growth and repair. These reactions are catalyzed by enzymes and organized into pathways that regulate cellular function, maintain homeostasis, and adapt to environmental changes. Metabolism powers essential activities such as respiration, nutrient assimilation, and biosynthesis, operating continuously to support survival and biological complexity.

Nicotinamide adenine dinucleotide (NAD⁺, NADH⁺, H⁺)

A coenzyme found in all living cells that plays a central role in redox reactions, acting as an electron carrier in metabolic pathways like glycolysis, the citric acid cycle, and oxidative phosphorylation. It exists in two forms: NAD⁺, the oxidized form that accepts electrons, and NADH, the reduced form that donates electrons. Structurally, NAD consists of two nucleotides joined through their phosphate groups—one containing an adenine base and the other a nicotinamide. By cycling between NAD⁺ and NADH, this molecule facilitates energy transfer and supports biosynthetic reactions, making it essential for cellular respiration and other biochemical processes.

Oxaloacetate

A four-carbon dicarboxylic acid that plays a central role in cellular metabolism, particularly in the tricarboxylic acid (TCA) cycle and gluconeogenesis. In the TCA cycle, it condenses with acetyl-CoA to form citrate, initiating the cycle that generates ATP, NADH, and FADH₂ for energy production. Oxaloacetate is regenerated at the end of the cycle, maintaining its continuity. It also serves as a key intermediate in gluconeogenesis, where it is converted to phosphoenolpyruvate for glucose synthesis, and acts as a precursor for several amino acids, including aspartate. Its ability to shuttle carbon and nitrogen between pathways underscores its metabolic versatility.

Oxidation

A chemical process in which an atom, ion, or molecule loses electrons, resulting in an increase in its oxidation state and often involving the addition of oxygen or removal of hydrogen. It is a key component of redox reactions, where one species is oxidized and another is reduced. Oxidation plays a central role in biological energy production, such as cellular respiration, as well as in industrial processes like combustion and corrosion. The concept extends beyond oxygen involvement to any electron loss, making it fundamental to understanding chemical reactivity and energy transfer.

Oxidative phosphorylation

The final stage of cellular respiration in which ATP is synthesized using energy derived from the transfer of electrons through the electron transport chain, coupled with the movement of protons across the inner mitochondrial membrane. As electrons from NADH and FADH₂ pass through protein complexes in the membrane, protons are pumped into the intermembrane space, creating an electrochemical gradient. This proton motive force drives protons back into the mitochondrial matrix through ATP synthase, a molecular turbine that catalyzes the formation of ATP from ADP and inorganic phosphate. Oxygen serves as the final electron acceptor, combining with electrons and protons to form water, making this process both aerobic and highly efficient.

Phosphoenolpyruvate

A high-energy, three-carbon intermediate in glycolysis and gluconeogenesis, characterized by its unstable enol phosphate bond. In glycolysis, PEP is formed from 2-phosphoglycerate via the enzyme enolase and is subsequently converted into pyruvate by pyruvate kinase, a reaction that generates one molecule of ATP. In gluconeogenesis, the reverse occurs, with pyruvate being carboxylated and then converted back to PEP by PEP carboxykinase. PEP also plays roles in other metabolic pathways, such as the shikimate pathway in plants and bacteria, and in bacterial phosphotransferase systems for sugar uptake. Its high phosphoryl transfer potential makes it a key energy donor in cellular metabolism.

Phosphorylation

The biochemical process of attaching a phosphate group (PO₄^3-) to a molecule, typically mediated by enzymes called kinases, and it plays a crucial role in regulating cellular functions such as metabolism, signal transduction, and energy transfer. This modification can activate or deactivate proteins, alter their interactions, or change their location within the cell, thereby acting as a molecular switch in pathways like cell division or apoptosis. In energy metabolism, phosphorylation is central to ATP synthesis and usage, as phosphate groups are transferred to drive reactions. The process is reversible, with phosphatases removing phosphate groups to fine-tune cellular responses.

Precursor metabolite

An intermediate compound produced during central catabolic pathways—such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle—that serves as a starting material for anabolic biosynthesis. Instead of being fully oxidized for energy, these molecules are diverted into synthetic pathways to construct essential cellular components like amino acids, nucleotides, lipids, and carbohydrates. Examples include pyruvate, acetyl-CoA, and ribose-5-phosphate, which link energy metabolism to macromolecular synthesis, making precursor metabolites critical nodes in the metabolic network.

Protein

A large, complex molecule made up of chains of amino acids linked by peptide bonds. Proteins perform a wide variety of essential functions in living organisms, including structural support, enzyme activity, transport, cell signaling, immune defense, and movement. The function of a protein depends on its unique three-dimensional shape, which is determined by the sequence and properties of its amino acids.

Pyruvate

A three-carbon molecule that serves as a key metabolic intermediate at the crossroads of several biochemical pathways, most notably glycolysis, where it is produced from glucose. Under aerobic conditions, pyruvate is transported into mitochondria and converted into acetyl-CoA, entering the citric acid cycle for further oxidation and ATP production. In anaerobic environments, pyruvate can be reduced to lactate in animals or ethanol in yeast, regenerating NAD⁺ to sustain glycolysis. It also participates in gluconeogenesis, amino acid synthesis, and fatty acid metabolism, making it a versatile node in cellular energy and biosynthetic networks.

Reduction

A chemical process in which an atom, ion, or molecule gains electrons, resulting in a decrease in its oxidation state and often involving the removal of oxygen or the addition of hydrogen. It is the counterpart to oxidation in redox reactions, where one species is reduced while another is oxidized. Reduction plays a central role in biological systems, such as cellular respiration, where molecules like NAD⁺ are reduced to NADH to carry energy. This process is also fundamental in industrial applications like metal refining and electrochemical reactions.

Ribose 5-phosphate

A five-carbon sugar phosphate that serves as a crucial intermediate in the pentose phosphate pathway, linking carbohydrate metabolism to nucleotide and amino acid biosynthesis. It is synthesized from glucose 6-phosphate through oxidative reactions and can also be interconverted with other sugars via transketolase and transaldolase enzymes. R5P is the precursor for the ribose moiety in nucleotides and nucleic acids, making it essential for DNA, RNA, and coenzyme synthesis (e.g., NAD⁺, FAD). Its availability influences cell proliferation and anabolic activity, especially in rapidly dividing cells.

Streptococcus

Streptococcus is a genus of Gram-positive, spherical bacteria that typically form chains or pairs and are known for their diverse roles in human health, ranging from harmless commensals to serious pathogens. These facultative anaerobes are classified based on hemolytic properties (alpha, beta, gamma) and Lancefield grouping, which identifies surface antigens. Pathogenic species like Streptococcus pyogenes cause diseases such as strep throat, scarlet fever, and rheumatic fever, while Streptococcus pneumoniae is a major cause of pneumonia and meningitis. Other species, such as Streptococcus mutans, contribute to dental caries by metabolizing sugars into acid. Despite their pathogenic potential, some streptococci are part of the normal flora of the mouth, skin, and respiratory tract.

Substrate-level phosphorylation

A metabolic process in which a phosphate group is directly transferred from a phosphorylated intermediate (substrate) to ADP, forming ATP without the involvement of the electron transport chain. This occurs during specific steps of glycolysis and the citric acid cycle, where enzymes catalyze the transfer of phosphate groups from high-energy compounds like 1,3-bisphosphoglycerate or phosphoenolpyruvate to ADP. Unlike oxidative phosphorylation, which relies on a proton gradient and membrane-bound ATP synthase, substrate-level phosphorylation is a simpler, enzyme-driven mechanism for generating ATP in both aerobic and anaerobic conditions.

Tricarboxylic acid cycle (TCA cycle)

A mitochondrial pathway that oxidizes acetyl-CoA into two molecules of carbon dioxide while generating high-energy electron carriers—three NADH, one FADH₂—and one GTP (or ATP) per turn. This cycle begins with the condensation of acetyl-CoA and oxaloacetate to form citrate, which undergoes a series of enzymatic transformations that progressively release CO₂ and regenerate oxaloacetate. The reduced cofactors produced feed electrons into the electron transport chain, driving oxidative phosphorylation and ATP synthesis. Beyond energy production, the TCA cycle supplies key intermediates for biosynthetic pathways, including amino acid, nucleotide, and heme synthesis, making it a central hub of both catabolism and anabolism.