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Biochemistry and Molecular Biology

The study of structures and processes that form the foundation for all living matter.

Members of the The American Society for Biochemistry and Molecular Biology have worked with CourseSource to create a Learning Framework for the Biochemistry and Molecular Biology Course. The table below lists the learning goals and objectives that the Society agrees any undergraduate biological sciences major should know about Biochemistry and Molecular Biology by the time they graduate. 

 

 

The following group worked to develop this society approved Biochemistry and Molecular Biology Learning Framework:

The core concepts, underlying concepts, and student learning objectives were developed by the ASBMB community through multiple workshops and working groups funded by the NSF (#0957205) and the ASBMB Education and Professional Development Committee.

Special message from the Editors:

The partnership of the American Society of Biochemistry and Molecular Biology with CourseSource is a logical next step in the Society’s involvement with science education reform and has developed from the RCN-UBE funded project from the National Science Foundation that the three of us have been involved with over the past 5 years. This project, the Society’s accreditation program, and the “Vision and Change” initiative have focused undergraduate education in biochemistry and molecular biology on foundational concepts and skills using evidence based active learning approaches. As resources with aligned concept areas and best practices of teaching are developed, publication in CourseSource provides an excellent avenue for dissemination of these materials to the educational community. We are excited to help CourseSource become the first stop resource for faculty wishing to adopt student-centered approaches to teaching biochemistry and molecular biology.

Biochemistry and Molecular Biology Learning Framework

Society Learning Goals Articles Sample Learning Objectives
Energy is required and transformed in biological systems
What is the nature of biological energy?
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  • 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).
  • Identify and explain instances when energy is converted from one form to another.
  • Write a general chemical reaction and the corresponding mathematical expression that approximates its equilibrium constant (Keq).
  • Explain the relationship between equilibrium constants and reaction rate constants
  • Apply knowledge of basic chemical thermodynamics to biologically catalyzed systems.
  • 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.
  • Explain the properties of biomolecules with high-energy transfer potential that make them suitable as energy currency.
How do enzymes catalyze biological reactions?
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  • Identify the factors contributing to the activation energy of a reaction.
  • Explain transition state stabilization.
  • Calculate the rate enhancement of an enzyme-catalyzed reaction.
  • Explain what a substrate is in terms of being a reactant.
  • Differentiate between the activation energy, the free energy and standard free energy of a reaction.
  • Use kinetic parameters to compare enzymes.
  • Distinguish the different forms of catalytic inhibition and explain how and why they differ.
  • Quantitatively model how catalyzed reactions occur and calculate kinetic parameters of enzymes from experimental data.
  • Explain how catalytic parameters vary as one varies substrate or enzyme concentration.
  • 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
How is energy of chemical processes coupled in metabolic pathways?
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  • Discuss the concept of Gibbs free energy and how to apply it to chemical transformations
  • Explain how endergonic and exergonic pathways can be coupled and how this applies to metabolism.
  • Calculate the overall ΔG for a coupled reaction given the ΔG values for the component reactions.
  • 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.
  • Predict how perturbing a system affects the actual free energy (both mathematically and conceptually).
  • Explain evolutionary conservation of key metabolic pathways.
  • Explain differences in energy use and production in different cells and different biological systems.
  • Explain the role of gene duplication in the evolution of energy production and utilization by different organisms.
Macromolecular Structure Determines Function and Regulation
What factors contribute to the size and complexity of biological macromolecules?
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  • Discuss the diversity and complexity of various biologically relevant macromolecules and macromolecular assemblies in terms of evolutionary fitness.
  • Describe the basic units of the macromolecules and the types of linkages between them.
  • Compare and contrast the processes involved in the biosynthesis of the major types of macromolecules (proteins, nucleic acids and carbohydrates).
  • Compare and contrast the processes involved in the degradation of the major types of macromolecules (proteins, nucleic acids and carbohydrates
  • Understand that proteins are made up of domains and be able to discuss how the protein families arise from duplication of a primordial gene.
What factors determine structure?
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  • Recognize the repeating units in biological macromolecules and be able to discuss the structural impacts of the covalent and non-covalent interactions involved.
  • Discuss the composition, evolutionary change and hence structural diversity of the various types of biological macromolecules found in organisms.
  • Discuss the chemical and physical relationships between composition and structure of macromolecules.
  • Compare and contrast the primary, secondary, tertiary and quaternary structures of proteins and nucleic acids.
  • Use various bioinformatics approaches to analyze macromolecular primary sequence and structure.
  • Compare and contrast the effects of chemical modification of specific amino acids on a three dimensional structure of a protein.
  • Compare and contrast the ways in which a particular macromolecule might take on new functions through evolutionary changes.
  • Use various bioinformatics and computational approaches to compare primary sequences and identify the impact of conservation and/or evolutionary change on the structure and function of macromolecules.
  • Predict the effects of mutations on the activity, structure or stability of a protein and design appropriate experiments to assess the effects of mutations.
  • Propose appropriate chemical or chemical biology approaches to explore the localization and interactions of biological macromolecules.
  • Discuss how mutations of a duplicated gene generate functional diversity.
  • Evaluate chemical and energetic contributions to the appropriate levels of structure of the macromolecule and predict the effects of specific alterations of structure on the dynamic properties of the molecule.
How are structure and function related?
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  • Use mechanistic reasoning to explain how an enzyme or ribozyme catalyzes a particular reaction.
  • Calculate enzymatic rates and compare these rates and relate these rates back to cellular or organismal homeostasis.
  • Discuss various methods that can be used to determine affinity and stoichiometry of a ligand-macromolecule complex and relate the results to both thermodynamic and kinetic data.
  • Critically assess contributions to specificity in a ligand-macromolecule complex and design experiments to both assess contributions to specificity and test hypotheses about ligand specificity in a complex
  • Discuss the basis for various types of enzyme mechanisms.
  • Predict the biological and chemical effects of either mutation or ligand structural change on the affinity of binding and design appropriate experiments to test their predictions.
What is the role of noncovalent intermolecular interactions?
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  • Discuss the impact of specificity or affinity changes on biological function and any potential evolutionary impact.
  • Discuss the various methods that can be used to determine affinity and stoichiometry for a ligand-macromolecule complex and relate the results to both thermodynamic and kinetic data
  • Discuss the interactions between a variety of biological molecules (including proteins, nucleic acids, lipids, carbohydrates and small organics, etc.) and describe how these interactions impact specificity or affinity leading to changes in biological function.
  • Predict the effects of either mutation or ligand structural change on the affinity of binding and design appropriate experiments to test their predictions.
  • Discuss the relationship between the temperature required for denaturation (Tm) and macromolecular structure.
How is macromolecular structure dynamic?
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  • Discuss the time scales of various conformational effects in biological macromolecules and design appropriate experiments to investigate ligand induced changes in conformation and dynamics.
  • Discuss the structural basis for the dynamic properties of macromolecules and predict the effects of changes in dynamic properties that might result from alteration of primary sequence.
  • Predict whether a sequence is ordered or disordered and discuss potential roles for disordered regions of proteins.
  • Critically discuss the evidence for and against the roles of dynamics in macromolecular function.
How is the biological activity of macromolecules regulated?
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  • Compare and contrast various mechanisms for regulating the function of a macromolecule or an enzymatic reaction or pathway.
  • Discuss the advantages and disadvantages of regulating a reaction allosterically
  • Discuss examples of allosteric regulation, covalent regulation and gene level alterations of macromolecular structure-function.
  • Use experimental data to assess the type of regulation in response to either homotropic or heterotropic ligands on a macromolecule.
  • Design a model to explain the regulation of macromolecule structure-function.
  • Describe how evolution has shaped the regulation of macromolecules and processes
  • Describe how changes in cellular homeostasis affect signaling and regulatory molecules and metabolic intermediates.
How is structure (and hence function) of macromolecules governed by foundational principles of chemistry and physics?
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  • Relate basic principles of rate laws and equilibria to reactions and interactions and calculate appropriate thermodynamic parameters for reactions and interactions.
  • Explain how a ligand, when introduced to a solution containing a macromolecule to which it can bind, interacts with the macromolecule.
  • Explain, using basic principles, the effects of temperature on an enzyme catalyzed reaction
  • Discuss the dynamic properties of a macromolecule using foundational principles of physics
How are a variety of experimental and computational approaches used to observe and quantitatively measure the structure, dynamics and function of biological macromolecules?
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  • Propose a purification scheme for a particular molecule in a mixture given the biophysical properties of the various molecules in the mix.
  • Explain how computational approaches can be used to explore protein-ligand interactions and discuss how the results of such computations can be explored experimentally
  • Either propose experiments that would determine the quaternary structure of a molecule or interpret data pertaining to tertiary and quaternary structure of molecules
  • Compare and contrast the computational approaches available to propose a three dimensional structure of a macromolecule and discuss how the proposed structure could be validated experimentally.
  • Analyze kinetic or binding data to derive appropriate parameters and assess the validity of the model used to describe the phenomenon.
Information storage and flow are dynamic and interactive
What is a genome?
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  • Define what a genome consists of and how the information in the various genes and other sequence classes within each genome is used to store and express genetic information.
  • Discuss how the genome is organized and packaged in prokaryotes and eukaryotes.
  • Discuss tools used to study expression, conservation and structure of an organism at the genome level.
  • Explain the role of repetitive and non-repetitive DNA and how its relative abundance varies from prokaryotes to eukaryotes.
How does the nucleotide sequence of the gene lead to biological function?
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  • Explain the role of repetitive and non-repetitive DNA and how its relative abundance varies from prokaryotes to eukaryotes.
  • Explain the process of gene regulation connecting how extracellular signals can result in a change of gene expression.
  • Discuss how genes are organized and contrast the different approaches used in prokaryotic and eukaryotic organisms.
  • Explain how mRNA processing occurs and how splicing affects the diversity of gene products in eukaryotic organisms.
How do genomes transmit information from one generation to the next?
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  • Explain the differences of mitosis and meiosis and relate them to the process of cellular division.
  • Illustrate how DNA is replicated and genes are transmitted from one generation to the next in multiple types of organisms including bacteria, eukaryotes, viruses and retroviruses.
  • Apply the concepts of segregation and independent assortment to traits inherited from parent to offspring and discuss how they increase genetic variation.
How are genomes maintained?
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  • State how the cell ensures high fidelity DNA replication and identify instances where the cell employs mechanism for damage repair.
  • Explain what a mutation is at the molecular level, how it arises and how it could potentially affect the organism from gene expression to fitness.
  • Relate how the cell cycle and genome maintenance are coordinated and how disruptions in this coordination could affect the organism.
  • List events that result in genomic instability and explain how the cell responds to restore order and stability.
  • Construct relationships between chromosome and cellular structures (e.g. telomere, centromeres and centrosomes) and explain how these structures are responsible for and/or involved in genomic stability.
Discovery requires objective measurement, quantitative analysis and clear communication
What is the scientific process?
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  • Accurately prepare and use reagents and perform the required experiments.
  • When presented with an observation, develop a testable and falsifiable hypothesis.
  • When provided with a hypothesis, identify the appropriate experimental observations and controllable variables.
  • Determine averages and standard deviations to relate the significance of experimentally obtained data.
  • Use equations and models to predict outcomes of experiments.
  • Use appropriate equations to analyze experimental data and obtain parameters.
What skills are needed to access, comprehend and communicate science?
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  • Identify, locate and use the primary literature.
  • Use databases and bioinformatics tools.
  • When provided with appropriate background information, identify consistencies and inconsistencies.
  • Explain the big picture aspects of current challenges in the molecular life sciences.
  • Use visual and verbal tools to explain concepts and data.
  • Translate science into everyday examples.
What constitutes a scientific community of practice?
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  • Explain the importance of and keep an accurate laboratory notebook.
  • Given a case study, identify both scientific and societal ethical aspects.
  • Explain cross-disciplinary concepts such as modularity, energy, modeling scientific phenomena, change over time and the differences between stochastic and deterministic phenomena
  • Access and interpret safety information and conduct lab work safely and ethically.
  • Give and take directions to be an effective team member.
Evolution
What is the significance of evolution?
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  • Describe evolution as genetic change in a population over time.
  • Analyze preexisting and novel data and relate the findings in light of evolution.
  • Relate evolution to concepts in biochemistry and molecular biology.
What are the mechanisms of evolution?
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  • Explain how mechanisms of evolution cause variation within a population.
  • Distinguish between random and nonrandom evolutionary processes.
  • Demonstrate their understanding of the mechanisms of evolution to relevant issues, such as antibiotic resistance, the occurrence of genetic disorders or cancer therapeutics.
How is natural selection a key evolutionary mechanism?
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  • Describe the process of natural selection.
  • Distinguish between individual fitness and adaptation of populations.
  • Explain how selection of phenotypes affects genotype transmission.
  • Synthesize and evaluate supporting evidence for the theory of natural selection
What is the molecular basis of evolution?
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  • Explain how cells can acquire new genetic material.
  • Explain how mutations and epigenetic changes influence gene expression, structure and function of gene products and the fitness of an organism.
  • Using genetic information, categorize organisms and establish phylogenetic relationships.
Homeostasis
What is the biological need for homeostasis?
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  • Describe why maintenance of homeostasis is advantageous to an organism.
  • Define homeostasis in a biochemical context to both scientifically trained and lay audiences.
  • Describe how homeostatic pathways and mechanisms have been conserved throughout evolution
  • Appraise the costs and benefits of different homeostatic mechanisms to an organism.
  • Relate different environmental factors necessitating homeostasis to a specific adaptation.
How are steady state processes and homeostasis linked?
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  • Explain that a system at chemical equilibrium (or just equilibrium) is stable over time, but no energy or work is required to maintain that condition.
  • Apply the principles of kinetics to describe flux through biochemical pathways.
  • Discuss a metabolic pathway in terms of equilibrium and Le Chatelier’s principle.
  • Relate the laws of thermodynamics to homeostasis and explain how the cell or organism maintains homeostasis.
  • Model how perturbations to the steady state can result in changes to the homeostatic state.
  • Propose how resources stored in the homeostatic state can be utilized in times of need.
How is homeostasis quantified?
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  • Describe experiments discussing how signaling and regulatory molecules and metabolic intermediates can be quantitated in the laboratory.
  • Relate concentrations of key metabolites to steps of metabolic pathways and describe the roles they play in homeostasis.
  • Calculate enzymatic rates and compare these rates and relate these rates back to cellular or organismal homeostasis.
  • Explain that organismal homeostasis can be measured in multiple ways and over different time scales (seconds, minutes, hours, days and months).
  • Given a metabolic network and appropriate data, predict the outcomes of changes in parameters of the system such as increased concentrations of certain intermediates or the changes in the activity of certain enzymes.
How is homeostasis controlled?
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  • Discuss how chemical processes are compartmentalized in the organism, organ and the cell.
  • Explain why biochemical pathways proceed through the intermediates that they do (gradual oxidation or reduction) and why pathways share intermediates
  • Summarize the different levels of control (including reaction compartmentalization, gene expression, covalent modification of key enzymes, allosteric regulation of key enzymes, substrate availability and proteolytic cleavage) and relate these different levels of control to homeostasis.
  • Compare the temporal aspect of different control mechanisms (e.g. how quickly phosphorylation occurs versus changes in gene expression).
  • Hypothesize why and how organs evolved with specialized function in metazoans.
  • Discuss different models of allosteric regulation.
  • Formulate models relating changes in flux through a pathway to other pathways and overall homeostasis.
  • Defend why anabolic and catabolic pathways are compartmentalized in the cell.
How do cells and organisms maintain homeostasis?
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  • Describe how the cell and organism store resources (both in terms of stored energy and chemical building blocks) for times of need and how they mobilize these resources.
  • Integrate homeostasis from the cellular to the organismal level. In other words, students should be able to describe how a complex metazoan can have both a cellular and organismal response to maintain homeostasis.
  • Compare and contrast homeostasis in different organisms.
  • Describe homeostasis at the level of the cell, organism or system of organisms and hypothesize how the system would react to deviations from homeostasis.
  • American Society for Biochemistry and Molecular Biology logo

American Society for Biochemistry and Molecular Biology

  • The American Society for Biochemistry and Molecular Biology (ASBMB), founded in 1906, advances the science of biochemistry and molecular biology through publication of scientific and education journals, organizes scientific meetings, advocates for funding of basic research and education, supports science education at all levels and promotes the diversity of individuals entering the scientific workforce. 

     

    Course Editor(s):

    • Editor, Neena Grover
      Editor Degrees: 

      Ph.D., Biochemistry/Bioinorganic Chemistry, University of North Carolina, Chapel Hill

      M.S., Biophysical Chemistry, University of Illinois, Chicago

      M.Sc., Chemistry, Indian Institute of Technology, Kanpur, India

      About Teaching and Course Source: 

      My teaching philosophy involves facilitating learning through careful organization of the material and activities that allow students to connect new information to their prior learning.  By applying the newly learned concepts to real-life problems students’ build their foundational knowledge and begin recognizing the common patterns that drive molecular processes.  Seventeen years of teaching have confirmed my belief that students in our classrooms can perform at higher level on Bloom’s taxonomy if we can model the right approaches to learning, set clear expectations and only grade things that we value. Students’ ability to ask good questions should be nurtured at every stage of learning so that they can integrate and critically evaluate new developments in the field. Students should also be provided with opportunities to use their scientific knowledge to make meaningful contributions to their community.

    • Associate Editor, Ellis Bell
      Editor Degrees: 
      • Ph.D., M.A. and B.A. from Oxford University, UK

      About Teaching and Course Source: 

      After almost 40 years of teaching students everything from introductory biology and chemistry, to biochemistry, to advanced topics in protein structure, function and biophysics I have found that each year I lecture less and less and try to engage students in more active learning activities. I try to align my teaching with the concepts of “Vision and Change” with a focus on foundational concepts and the skills necessary to be a scientist. For me, the most effective scenarios involve interdisciplinary aspects of biochemistry and molecular biology, integrating meaningful research projects into a student's education via courses and independent research, and encouraging and enabling students to communicate science in a variety of ways to different audiences.

    • Associate Editor, Kristin Fox
      Editor Degrees: 

      Ph.D. in Biochemistry, Cornell University, New York

      B.S. in Chemistry with Honors, Lafayette College, Pennsylvania

      About Teaching and Course Source: 

      Over the last 15 years, I have continually shifted my biochemistry teaching from primarily lecture-based to more interactive modes of learning. We do a variety of activities, from students working in groups on questions related to the topic in class, to discussing papers, to using computers to visualize proteins. Over the last two years I have worked to make the last two weeks of class essentially lecture-free. When we reach this point in the term the students are comfortable with biochemical terminology and with my instructional style. This allows me the freedom to use more open-ended pedagogical techniques. The students work in groups to answer questions, then we share answers and I give a brief discussion of areas they have questions about. I am still honing these activities because teaching is always a work in progress.

Announcements

American Society for Biochemistry and Molecular Biology

  • ASBMB accreditation provides an independent assessment of BMB programs and nationally recognizes those programs that meet the society’s expectations. The next application submission deadline is Oct. 15, 2017. More information is available at http://www.asbmb.org/accreditation/overview/.

     

  • Renew or establish an ASBMB Student Chapter:

    The ASBMB Student Chapters is devoted to building a national network of undergraduate students and faculty for the advancement of research, education and science outreach. Our mission is to provide networking opportunities and career development opportunities at regional and national conferences, access to research and science outreach, as well as grants and awards to facilitate these aims. Renew or establish a new chapter today!