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Chapter 3

Energy and Catalysis

The First Law of Thermodynamics
The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. In…
The Second Law of Thermodynamics
In the quest to identify a property that may reliably predict the spontaneity of a process, a promising candidate has been identified: entropy.…
Enthalpy within the Cell
Enthalpy (H) is used to describe the thermodynamics of chemical and physical processes. Enthalpy is defined as the sum of a system's internal…
Entropy within the Cell
A living cell's primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics…
An Introduction to Free Energy
How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these…
Endergonic and Exergonic Reactions in the Cell
If energy releases during a chemical reaction, then the resulting value will be a negative number. In other words, reactions that release energy…
The Equilibrium Binding Constant and Binding Strength
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is…
Free Energy and Equilibrium
The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the…
Non-equilibrium in the Cell
An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in…
Oxidation and Reduction of Organic Molecules
Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction…
Introduction to Enzymes
The use of enzymes by humans dates to 7000 BCE. Humans first used enzymes to ferment sugars and produce alcohol without knowing that this was an…
Enzymes and Activation Energy
The activation energy (or free energy of activation), abbreviated as Ea, is the small amount of energy input necessary for all chemical reactions to…
Introduction to Enzyme Kinetics
Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various…
Turnover Number and Catalytic Efficiency
The turnover number of an enzyme is the maximum number of substrate molecules it can transform per unit time. Turnover numbers for most enzymes range…
Catalytically Perfect Enzymes
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions…
Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the…
Ligand Binding and Linkage
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the…
Cooperative Allosteric Transitions
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand…
Ribozymes
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower…
ATP Energy Storage and Release
ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP and inorganic phosphate (Pi), and the…
ATP and Macromolecule Synthesis
Biological macromolecules are organic compounds, predominantly composed of carbon atoms. The carbon atoms are covalently bonded with hydrogen,…
Coupled Reactions
Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions…
Rapid Determination of Antibody-Antigen Affinity by Mass Photometry
Measurements of the specificity and affinity of antigen-antibody interactions are critically important for medical and research applications. In this…
Measuring Lactase Enzymatic Activity in the Teaching Lab
Understanding how enzymes work, and relating this to real life examples, is critical to a wide range of undergraduate degrees in the biological and…
Application of Biolayer Interferometry (BLI) for Studying Protein-Protein Interactions in Transcription
A transcription factor (TF) is a protein that regulates gene expression by interacting with the RNA polymerase, another TF, and/or template DNA.…

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