Biochemistry

Free Energy, Relative Substrate Concentrations, and Coupled Reactions in Biochemistry

Introduction

In a recent article, I introduced the concept of the Gibbs energy of a chemical reaction. Before building on the content of that post, I’d like to recap its most salient points: Gibbs energy change is an important and broadly applicable thermodynamic concept which provides a reliable way of determining the conditions under which specific reactions or processes will occur spontaneously. Gibbs energy change values have been tabulated for many different reactions under standardized conditions. Since it’s a state function, various linear combinations of those values can be added and subtracted like algebraic equations to calculate the values of still other reactions. As was the case with enthalpy, (which I covered here and here), there exist ways of adjusting those standardized values so that they still yield viable answers under non-standard reaction conditions. The Gibbs energy of a reaction is closely tied with its equilibrium constant (K), whose numeric value represents the ratio of products to reactants at which the reaction equilibrates at a given temperature. This provides a thermodynamic explanation for why the relative concentrations of substrates for a given reaction affects whether it will occur spontaneously (and to what extent). In turn, this dependence of a reaction’s spontaneity on relative substrate concentrations is one of the ways in which biological organisms naturally perform many processes that would otherwise be thermodynamically unfavorable. My goal for this post is to use a couple of examples to illustrate how the spontaneity of some biochemical processes can be affected by relative substrate concentrations, and/or by the coupling of an endergonic (non-spontaneous) process with an endergonic (spontaneous) one. (more…)

By Credible Hulk, ago
Chemical Equilibrium

Gibbs Free Energy and Spontaneity

Introduction

In my previous couple of blog posts, I talked about a thermodynamic state function called enthalpy, and how it is used by scientists and engineers. This included covering a principle called Hess’s Law, which has led to the tabulation of enthalpy values for certain reactions under a set of standardized conditions, such that the idea could be generalized to make thermodynamic predictions about a huge variety of processes. Those posts laid the groundwork for the following topic.  (more…)

By Credible Hulk, ago
Enthalpy and Hess’s Law

Applying Hess’s Law, and Generalizing it to Different Physical Situations

Introduction

In a recent post, I introduced a thermodynamic state function called enthalpy and introduced something called Hess’s Law. That post was following up on two previous posts, the first of which covered the 1st and 2nd Laws of Thermodynamics, entropy, and the distinction between state functions vs path functions, and the second of which covered the concepts of work, heat transfer, reversibility, and internal energy in thermodynamic systems. Just to recap, enthalpy H is a state function that scientists and engineers use to analyze the thermodynamic properties of certain physical processes (particularly chemical reactions). More accurately, it’s the change in this function that we’re most interested in, particularly at constant pressure, which is the case for most biological processes as well as many experimental situations. You can check out the previous article for the gory details, but the take home message was that the change in enthalpy at constant pressure is equal to the heat transferred to or from the system, and that its status as a state function led to an important general result called Hess’s Law. The tl; dr version of Hess’s Law is that the change in enthalpy for a reaction is the sum of the enthalpies of formation of the products, each multiplied by its corresponding coefficient (n) from its balanced chemical equation, minus the enthalpies of formation of the reactants, each (again) multiplied by its corresponding coefficient. Hess’s Law can also be concisely summarized by the following equation which uses sigma (summation) notation:  (8). This is important to scientists and engineers because it has permitted the tabulation of many experimentally-derived ΔH values under a set of standardized conditions. Adding and subtracting various combinations of these can facilitate convenient thermodynamic predictions for a wide variety of reactions. The remainder of this article deals with how Hess’s Law is applied and generalized to a variety of physical situations. (more…)

By Credible Hulk, ago
Enthalpy and Hess’s Law

Enthalpy: Exothermic vs Endothermic Processes

Introduction

In a recent article, I talked about the 1st and 2nd Laws of Thermodynamics, entropy, and the distinction between state functions vs path functions. More recently, I wrote another one in which I talked about heat, work, reversibility, and internal energy in thermodynamic systems. At the end of the latter post, I mentioned in passing that the path-dependence of heat and work done by non-conservative forces makes it desirable to work with state functions whenever feasible, because it’s not always easy to know the precise path by which a system arrived at its current state from a prior one. That’s where a function called enthalpy comes into play. (more…)

By Credible Hulk, ago
Heat

Work, Heat, and Internal Energy

Heat, and internal energy

In a recent article, I mentioned in passing that the internal energy of a system is a state function. Just to quickly recap, state functions are properties of a physical system whose values do not depend on how they were arrived at from a prior state of the system. They depend only on the starting and ending states of the system. I then contrasted state functions with path-dependent functions, which can take on very different values depending on the path by which the system arrived at its current state from its previous state (the history of the system matters). Perhaps counter-intuitively, while it’s true that internal energy is a state function, the change in a system’s internal energy is the sum of two path-dependent functions. (more…)

By Credible Hulk, ago
Entropy

State Functions, Entropy, Path Dependence, and Energy Conservation in Thermodynamic Systems

State Functions vs Path Dependent Functions

In thermodynamics, scientists distinguish between what are called state functions vs path functions. State functions are properties of a system whose values do not depend on how they were arrived at from a prior state of the system. They depend only on the starting and ending states of the system. On the other hand, path functions can take on very different values depending on the path by which the system arrived at a state from its previous state. (more…)

By Credible Hulk, ago
Science Communication

Admin Reflections (July 2018)

Since I started doing science blogging and skeptical outreach, I’ve noticed that my most popular posts usually involve topics that are considered controversial by the general public, even if they aren’t considered as controversial by actual experts: i.e. genetically engineered foods, anthropogenic climate change, the safety and efficacy of municipal water fluoridation, the importance of vaccines, and anti-science conspiracy speculationism. (more…)

By Credible Hulk, ago
General Skepticism

The Streisand Threshold

The Streisand Threshold: Choosing one’s battles

There is a tremendous amount of pseudoscience and other misinformation that circulates-- seemingly unimpeded-- on the internet. Consequently, it can be a daunting task for those of us who fight against it to know which targets are an effective use of our time and effort. There are various considerations that might inform one’s decision about where (or toward whom) to direct one’s science advocacy or skeptical outreach: (more…)

By Credible Hulk, ago
Philosophy of Science

Incommensurability, The Correspondence Principle, and the “Scientists Were Wrong Before” Gambit

Introduction

One of the intrinsic features of the scientific process is that it leads to modifications to previously accepted knowledge over time. Those modifications come in many forms. They may involve simply tacking on new discoveries to an existing body of accepted knowledge without really contradicting prevailing theoretical frameworks. They may necessitate making subtle refinements or adjustments to existing theories to account for newer data. They may involve the reformulation of the way in which certain things are categorized within a particular field so that the groupings make more sense logically, and/or are more practical to use. In rare cases, scientific theories are replaced entirely and new data can even lead to an overhaul of the entire conceptual framework in terms of which work within a particular discipline is performed. In his famous book, The Structure of Scientific Revolutions, physicist, historian, and philosopher of science, Thomas Kuhn referred to such an event as a “paradigm shift.” [1],[2]. This tendency is a result of efforts to accommodate new information and cultivate as accurate a representation of the world as possible. (more…)

By Credible Hulk, ago
Chemophobia

Glyphosate and the Gut Microbiome: Another Bad Argument Annihilated

Introduction:

Glyphosate is a broad spectrum herbicide that was first introduced by the Monsanto company in the 1970s under the brand name Roundup. The already popular product grew even more popular among farmers upon the introduction of various commodity crops which were genetically engineered to resist the herbicide while it killed the surrounding weeds with which the crops would otherwise compete for water and nutrients. Glyphosate went off patent back in the year 2000, and since then many manufacturers have cashed in on its popularity [1]. Although it is of unusually low toxicity, glyphosate receives a level of scrutiny and vehemence of criticism that is disproportionate to its actual established risks [2],[3],[4]. This is attributable in part to its ubiquity in modern conventional farming, but it's likely even more attributable to its association with Monsanto, against which a large and well-organized counter-movement has emerged [5]. (more…)

By Credible Hulk, ago