ENERGY: Energy is required by and transformed in biological systems.

Core concepts of energy and matter transformation

The learning goals below are categorized as introductory {A}, intermediate {B} and upper {C}.

1. The nature of biological energy
Many forms of energy are involved in biological processes: light, chemical, conformational, mechanical and gradients. These forms can be understood in terms of the principles of thermodynamics. Energy is utilized for diverse purposes, such as the work required to synthesize biomolecules, create electrical and chemical gradients, perform mechanical work or stored within biomolecules.


Associated learning goals
• Students should be able to compare and contrast biologically relevant forms of energy (e.g. kinetic energy versus potential energy, energy stored in bonds versus potential energy of concentration gradients). {A}
• Students should be able to identify and explain instances when energy is converted from one form to another. {A}
• Students should be able to write a general chemical reaction and the corresponding mathematical expression that approximates its equilibrium constant (Keq). {A}
• Students should be able to explain the relationship between equilibrium constants and reaction rate constants. {B}
• Students should be able to apply their knowledge of basic chemical thermodynamics to biologically catalyzed systems. {B}
• Students should be able to account for energy changes in the intermediate steps that define a biological process and predict the spontaneity of the overall process or an intermediate step. {C}
• Students should be able to explain the properties of biomolecules with high-energy transfer potential that make them suitable as energy currency. {C}
 

2. Catalysis
 Enzymes, which can be proteins or RNA, are macromolecules with catalytic functions. They do not alter reaction equilibria; instead, they lower the activation energy barrier of a particular reaction allowing it to proceed more rapidly. Key concepts of enzyme kinetics are typically defined in terms of the initial rate of product formation, Vo, and various catalytic kinetic parameters, such as Vmax or Kcat and Km, which are either mathematically defined for enzymes that follow Michaelis-Menten kinetics or defined empirically for more complicated enzyme models.

Associated learning goals
• Students should be able to identify the factors contributing to the activation energy of a reaction. {A}
• Students should be able to explain transition state stabilization
. {A}
• Students should be able to calculate the rate enhancement of an enzyme-catalyzed reaction. {A}
• Students should be able to explain what a substrate is in terms of being a reactant. {A}
• Students should differentiate between the activation energy, the free energy and standard free energy of a reaction. {B}
• Students should be able to use kinetic parameters to compare enzymes
. {B}
• Students should be able to distinguish the different forms of catalytic inhibition and explain how and why they differ. {B}
• Students should be able to quantitatively model how catalyzed reactions occur and calculate kinetic parameters of enzymes from experimental data
. {C}
• Students should be able to explain how catalytic parameters vary as one varies substrate or enzyme concentration. {C}
• Students should be able to interpret the physical meaning of various kinetic parameters and describe the underlying assumptions and conditions (such as steady state or equilibrium) on which different parameters depend.
{C}
 
 
3. Energetic coupling of chemical processes in metabolic pathways

Biochemical systems couple energetically unfavorable reactions with energetically favorable reactions. These reactions can be part of catabolic pathways where complex substances are broken into simpler ones with the release of energy or anabolic pathways where complex molecules are synthesized with an input of energy.

Associated learning goals
• Students should be able to discuss the concept of Gibbs free energy and how to apply it to chemical transformations. {A}
• Students should be able to explain how endergonic and exergonic pathways can be coupled and how this applies to metabolism
. {A}
• Students should be able to calculate the overall ΔG for a coupled reaction given the ΔG values for the component reactions. {A}
• Students should be able to explain the simplifying assumptions made in biochemistry that are consistent with physiological conditions and make "biochemical standard conditions" (steady state) different from the standard conditions (equilibrium conditions) normally referred to in chemistry
. {B}
• Students should be able to predict how perturbing a system affects the actual free energy (both mathematically and conceptually). {B}
• Students should be able to explain evolutionary conservation of key metabolic pathways. {C}
• Students should be able to explain differences in energy use and production in different cells and different biological systems. {C}
• Students should be able to explain the role of gene duplication in the evolution of energy production and utilization by different organisms. {C}