Fundamentals of Biochemistry is designed to help readers understand many topics across a broad range of area. It covers the the biochemistry foundational concepts recommended by the American Chemical Society (ACS), the American Society for Biochemistry and Molecular Biology (ASBMB) and for the Medical College Admissions Test (MCAT) written by the American Association of Medical Colleges (AAMC). The foundational concepts recommended by these organizations broadly overlap. The ASBMB is the only organization that has also defined specific learning objectives for each of the foundational concepts.
These strongly emphasize scientific inquiry and reasoning skills, which are perhaps best assessed by open-ended questions derived from the literature in which students must employ higher level Bloom skills of application and analysis.
The ability to apply, analyze, and evaluate information and concepts are at the heart of scientific inquiry and reasoning skills which are central to the competency standards.
Each chapter and chapter section will (by 2023) contain learning goals and objective and for each chapter, literature-based assessment question and answers that address the foundational concepts and learning goals.
Biochemistry Foundational Concepts and Learning Goals/Objectives
We will present the biochemistry foundational concepts and learning goals/objectives recommended by the following professional organizations.
American Chemical Society (ACS)
The American Chemical Society does not describe learning goals and objectives, but rather suggest concepts in three general areas that should be covered in a biochemistry course. These include:
Biological Structures and Interactions
- Fundamental building blocks (amino acids, carbohydrates, lipids , nucleotides, and prosthetic groups)
- Biopolymers (nucleic acids, peptides/proteins, glycoproteins, and polysaccharides)
- Supramolecular architecture
- Kinetics and mechanisms of biological catalysis
- Biosynthetic pathways and strategies/metabolic engineering
- Metabolic cycles, their regulation, and metabolomics
- Organic and inorganic cofactors
Biological Equilibria and Thermodynamics
- Acid-base equilibria
- Thermodynamics of binding and recognition
- Oxidation and reduction processes Electron transport and bioenergetics
- Protein conformation/allostery, folding, oligomerization, and intrinsically disordered proteins (IDPs)
American Society for Biochemistry and Molecular Biology
Of the three professional organization, the ASBMB is the only one that offers both core concepts and learning objectives. Applicable ASBMB learning objectives will be listed at the beginning of each chapter sections (in 2023).
Core Concept 1: Energy is required by and transformed in biological systems.
1.1. Given knowledge of common mechanisms of regulation for biomacromolecules, students should be able to predict the sites and nature of regulation in pathways that transform energy
1.2. Given a knowledge of the basic structure of fatty acids, triglycerides, nucleotides, and carbohydrates; students should be able to compare and contrast the synthesis, storage, and transformation of macromolecules from which living organism harvest derive energy
1.3. Given a macromolecule, students should be able to explain the contribution of entropy, enthalpy and temperature of a macromolecule and water (associated and in bulk solvent) in a folded versus unfolded state
1.4. Given a biological example, students should be able to explain how thermodynamically unfavorable processes can occur.
1.5. Given an enzyme reaction, students should be able to differentiate the effect of an enzyme on the change in free energy of a reaction versus the change in transition state
1.6. Given entropy, enthalpy and temperature, students should be able to justify why evolutionary selection is constrained by the laws of thermodynamics
Core Concept 2: Macromolecular structure determines function and regulation
2.1. Given the knowledge of bio macromolecules, students should be able to identify, draw(sketch) and know properties (functions) of biomacromolecules
2.2. Given a list of macromolecules, students should be able to devise an experiment on how they interact or interpret results of experiments on their interactions
2.3. Given structural changes of a macromolecule, students should be able to predict the impact of structural substitution would have on macromolecule structure and function
2.4. Given experimental data, students should be able to assess how enzymes facilitate biochemical reactions
2.5. Given that evolutionary forces such as gene duplications and genomic mutations can provide changes in protein structure(s) and function(s) students should be able to explain how protein structures might change while retaining an evolutionarily conserved function
Core Concept 3: Information storage and flow are dynamic and interactive
3.1. Given an understanding of replication, transcription and translation, students should be able to determine how changes in DNA sequence affect the amino acid sequence of the protein it encodes
3.2. Given an understanding of common mechanisms of gene regulation, students will be able to explain or predict changes in transcription in response to biologic variables.
3.3. Given an understanding of genetic information transfer, students should be able to explain the role of RNA in the flow of genetic information
3.4. Given an understanding of evolution and natural selection, students should be able to make predictions on how environmental factors will affect information flow over generations.
3.5. Given an understanding of commonly encountered signal transduction mechanisms, students will be able to predict or design models for information transfer cascades
American Association for Medical Colleges (AAMC) - MCAT
The AAMC has defined the core concepts and content areas covered in their latest version (2015) of the MCAT. These are listed below.
Biological and Biochemical Foundations of Living Systems
Foundational Concept 1: Biomolecules have unique properties that determine how they contribute to the structure and function of cells and how they participate in the processes necessary to maintain life. The content categories for this foundational concept include:
1A. Structure and function of proteins and their constituent amino acids.
1B. Transmission of genetic information from the gene to the protein.
1C. Transmission of heritable information from generation to generation and the processes that increase genetic diversity.
1D. Principles of bioenergetics and fuel molecule metabolism.
Foundational Concept 2: Highly organized assemblies of molecules, cells, and organs interact to carry out the functions of living organis
2A. Assemblies of molecules, cells, and groups of cells within single cellular and multicellular organisms.
2B. The structure, growth, physiology, and genetics of prokaryotes and viruses.
2C. Processes of cell division, differentiation, and specialization.
Foundational Concept 3: Complex systems of tissues and organs sense the internal and external environments of multicellular organisms, and through integrated functioning, maintain a stable internal environment within an ever-changing external environment.
3A. Structure and functions of the nervous and endocrine systems and ways these systems coordinate the organ systems.
3B. Structure and integrative functions of the main organ systems.
Chemical and Physical Foundations of Biological Systems Section
Foundational Concept 4: Complex living organisms transport materials, sense their environment, process signals, and respond to changes using processes understood in terms of physical principles.
4A. Translational motion, forces, work, energy, and equilibrium in living systems.
4B. Importance of fluids for the circulation of blood, gas movement, and gas exchange.
4C. Electrochemistry and electrical circuits and their elements.
4D. How light and sound interact with matter.
4E. Atoms, nuclear decay, electronic structure, and atomic chemical behavior.
Foundational Concept 5: The principles that govern chemical interactions and reactions form the basis for a broader understanding of the molecular dynamics of living systems.
5A. Unique nature of water and its solutions.
5B. Nature of molecules and intermolecular interactions.
5C. Separation and purification methods.
5D. Structure, function, and reactivity of biologically relevant molecules.
5E. Principles of chemical thermodynamics and kinetics.