Biochemistry

Hydrogen Bonding

Hydrogen Bonding A particularly important type of dipole-dipole interaction is hydrogen bonding. It’s the main reason for the stability of the double-helix secondary structure of DNA, the unusual phase diagram of water, and the secondary structure of proteins in our bodies. Strictly speaking, hydrogen bonds are a special case of Read more…

By Credible Hulk, ago
Chemistry

Ion-Dipole Interactions and Hydrophilicity

Ion-Dipole Interactions and Hydrophilicity Ion-dipole forces are generally stronger than dipole-dipole interactions because at least one of their participants is an ion, which means it has a net electric charge, whereas dipole-dipole forces involve polar molecules with no net electric charge. These interactions explain why ionic compounds tend to be Read more…

By Credible Hulk, ago
Chemistry

Dipole-Dipole Interactions

Dipole-dipole interactions Many covalently bonded molecules have a net neutral electric charge, but do not distribute their charge evenly. Some parts of their structure have greater electron density than others. This is again a result of differences in electronegativity. For example, chlorine is more electronegative than carbon. Consequently, bonds between Read more…

By Credible Hulk, ago
Chemistry

Ion-Ion Interactions

Ion-ion interactions Recall that ions are atoms or molecules that have lost or gained one or more electrons with respect to their electrically neutral counter-parts, such that they have a net electric charge. As a result, two or more ions can exert electrostatic forces on each other. This is the Read more…

By Credible Hulk, ago
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