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Macromolecular Structure Determines Function and Regulation

Biochemistry and Molecular Biology Learning Framework

Society Learning Goals Articles Sample Learning Objectives
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.

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