A molecular simulation environment lets students explore the effect of molecular interactions on the biochemical properties of systems. Biochemistry is an introductory course, designed for both biology and chemical engineering majors.
- Additional information
- What students will learn
- Learning objectives by module
- Course assessments, activities, and outline
- Other course details
- System requirements
- Included instructor tools
What students will learn
By the time they finish this course, students will learn about or be able to:
- Predict how changes in structure affect function.
- Utilize quantitative approaches to characterize structure-function relationships in biochemical systems.
Learning objectives by module
Unit 1: Lectures
- Module 1: Week 1
- Calculate the amount of an acid that is protonated at any given pH.
- Characterize functional groups.
- Describe molecular orbitals.
- Explain the molecular structure of Water.
- Identify hydrogen bond donors and acceptors.
- Predict the solubility of compounds in water.
- Predict the strength of hydrogen bonds based on geometry.
- Provide a general overview of biochemistry based on component parts.
- Recognize chiral centers
- Understand the relationship between the structure and acidity of an acid.
- Module 2: Week 2
- Calculate the amount of a weak acid and its conjugate base to make a buffer system.
- Calculate the net charge on a molecule, at any pH.
- Determine the interaction of each amino acid with water.
- Distinguish between primary, secondary, tertiary and quaternary structure.
- Draw the structure of all amino acids.
- Generate the primary sequence from sequencing data.
- Identify chiral centers on amino acids.
- Join two amino acids into a dipeptide.
- Predict the result of treating a protein with different cleavage reagents.
- Understand why solutions of weak acids resist pH changes.
- Module 3: Week 3
- Interpret changes in ΔH and ΔS.
- Obtain ΔH and ΔS for protein unfolding from experimental data.
- Predict degree of protein unfolding given ΔH and ΔS.
- Predict the secondary structure of a residue from the Ramachandran plot
- Relate thermodynamic forces to the stability of super-secondary structures.
- Understand conformational entropy.
- Understand consequences of orbital overlap on the configuration of the peptide bond.
- Understand dominant enthalpic forces that stabilize proteins.
- Understand geometrical properties of linear polymers.
- Understand the role of hydrogen bonds in the stability of secondary structures.
- Understand the role of the hydrophobic effect in protein folding.
- Understand why trans peptide bonds are more stable.
- Module 4: Week 4
- Calculate amount of oxygen delivered from binding curves.
- Characterize molecular forces between antibody and antigen.
- Compare and contrast structures and binding curves of myoglobin and hemoglobin.
- Define the terms antigen, epitope, and hapten.
- Describe how the amount of ligand bound is affected by the ligand concentration, both at low and high [L].
- Describe the process of antibody production by B-cells.
- Determine the dissociation constant, KD directly from binding data.
- Interpret KD in terms of inter-molecular interactions.
- Understand the molecular basis of oxygen transport.
- Understand the relationship between primary, tertiary, and quaternary structure of antibodies.
- Module 5: Week 5
- Compare and contrast homotropic and heterotropic allosteric effectors.
- Construct Hill plot and obtain KD and Hill coefficient.
- How allosteric activators and inhibitors affect binding.
- Relate the Hill coefficient to the molecular behavior of the system.
- Understand role of allosteric modulators in oxygen delivery.
- Module 6: Week 6
- Calculate the rate enhancement due to transition state stabilization.
- Define steady-state conditions
- Describe the factors that contribute to stabilization of the transition state.
- Distinguish between enthalpic and entropic stabilization of the transition state.
- Understand the basis of substrate specificity.
- Understand the difference between reaction rates and KM and kcat.
- Understand the mechanism of serine proteases.
- Understand the relationship between substrate concentration and the rate of product formation.
- Module 7: Week 7
- Be able to describe how the substrate concentration affects the rate of enzymatic reactions.
- Be able to obtain kinetic parameters from experimental data
- Compare and contrast the structure and mechanism of HIV protease to serine proteases.
- Determine the dissociation constant for inhibitors.
- Explain the difference between competitive and non-competitive inhibitors.
- Identify steps in viral replication that are suitable for inhibition with drugs.
- Interpret KI values within the context of molecular interactions.
- Module 8: Week 8
- Calculate and interpret specific activity.
- Describe how ring structures of saccharides are formed.
- Determine quaternary structure of a protein.
- Develop a purification scheme.
- Distinguish between molecular weight determination methods.
- Distinguish between the importance of amplitude and phase in X-ray structure determination.
- Draw the chemical structure of aldoses and ketoses.
- Identify the anomeric carbon in cyclic monosaccharides.
- Understand the principles of separation techniques.
- Module 9: Week 9
- Calculate the energetics of membrane-protein interactions.
- Compare and contrast the structure of glycogen and cellulose
- Describe the structure of bacterial cell walls.
- Describe the thermodynamics of self-assembly of membranes.
- Draw and name disaccharides.
- Draw the structure of Phospholipids.
- Draw the structure of saturated and unsaturated fatty acids.
- Draw the structure of triglycerides.
- Predict membrane permeability of compounds.
- Predict the critical micelle concentration of fatty acids, based on structure.
- Predict the melting temperature of fatty acids, based on structure.
- Predict the melting temperature of model bilayers, based on structure.
- Module 10: Week 10
- Describe a linear, branched, and circular pathway.
- Describe the common features of metabolic pathways.
- How the energy stored in a thioester can be used for ATP synthesis or organic addition reactions.
- Identify the role of direct and indirect coupling in metabolic pathways.
- Predict the direction of reactions using Gibbs free energy.
- State the major differences between catabolic and anabolic pathways.
- Understand the major energy storage methods in metabolism – phosphorylated compounds, redox carriers, proton gradient.
- Understand the source of “high-energy” phosphate bonds in ATP
- Module 11: Week 11
- Enzyme Regulation: Role of protein kinases and phosphatases in control of enzyme function.
- Hormonal Control: Understand physiological role of hormones epinephrine, glucagon, and insulin.
- Identify that glycolysis oxidizes the six carbon glucose to produce two three-carbon pyruvate molecules.
- Identify the cellular location of glycolysis.
- Signal transduction: Understand the role of G-proteins and adenyl cyclase in receptor mediated signal transduction.
- Understand activation of enzymes by allosteric compounds as a method of regulation.
- Understand anaerobic metabolism and its role in allowing glycolysis to continue in the absence of oxygen.
- Understand coordinated regulation of opposing steps in synthetic and degradative pathways.
- Understand glucose can be synthesized from pyruvate.
- Understand how both direct and indirect coupling are used to make glycolysis spontaneous.
- Understand how glycogen degradation and synthesis is controlled by protein phosphorylation.
- Understand how the energy released by the oxidation is stored as ATP and “high-energy” electrons.
- Understand regulation by non-covalent and covalent modification of enzymes.
- Understand the major differences between a competitive and uncompetitive inhibitor.
- Understand the relationship between the Gibbs free energy change of a step in the pathway and whether the step can be accomplished by the same enzyme in the reverse direction.
- Understand the structure of glycogen.
- Module 12: Week 12
- Be able to describe how intermediates in the TCA cycle are used to synthesize a wide range of compounds.
- Be able to describe how sugar and fatty acid oxidation are connected to the TCA cycle.
- Be able to describe where, and in what form, the energy is stored that is released by the TCA cycle.
- Distinguish between a purine and a pyrimidine.
- Draw the monomeric structure of a nucleotide.
- Explain how a polymer of nucleic acid is formed from nucleoside triphosphates.
- Explain the difference in the chemical stability of RNA versus DNA.
- Identify the major and minor group of a base pair.
- Identify the Watson-Crick hydrogen bonds in A-T and G-C basepairs.
- Know that electron transport flows through complexes I, III, and IV leads to generation of a hydrogen ion gradient across the inner mitochondrial membrane.
- Know the pathway of the electrons from FADH2 to oxygen, resulting in the formation of water.
- Know the pathway of the electrons from NADH to oxygen, resulting in the formation of water.
- Know the role of the four complexes, coenzyme Q, and cytochrome C in electron transport.
- Predict the product of oxidative decarboxylations
- Provide a description of the structural features of B-DNA.
- Understand that the free energy stored in the non-equilibrium hydrogen ion gradient is sufficient to sythesize ATP from the transport of 3 protons.
- Understand the mechanism of ATP synthase, how allosteric changes that occur during proton translocation lead to the conversion of ADP and Pi to ATP.
- Module 13: Week 13
- Calculate TM of a double stranded DNA molecule.
- Compare and contrast the major factors that stabilize dsDNA and Proteins.
- Discuss the major features that affect the energetics of DNA-protein interactions.
- Discuss the role of each element in an expression vector.
- Explain how proofreading occurs during DNA synthesis.
- Explain the effect of salt concentration on the melting temperature of DNA.
- Explain why DNA synthesis is always in the 5′-3′ direction.
- Explain why there is a high mutation rate in the HIV virus.
- Identify the non-Watson-Crick hydrogen bonds in A-T and G-C basepairs.
- List the essential elements of an expression vector.
- Use restriction enzymes and DNA ligase to generate recombinant DNA molecules.
- Module 14: Week 14
- Be able to utilize the lac repressor/operator to control gene expression
- Describe the overall process of amino acid synthesis on the ribosome
- Describe the role of tRNA structure in protein synthesis.
- Design a coding sequence with the correct signals for protein synthesis
- Design primers for PCR DNA amplification.
- Determine a protein sequence given a sequencing gel.
- Explain how PCR leads to the amplification of DNA.
- Explain the basis of DNA sequencing.
- Include the appropriate signals to cause export of the protein out of the cell
- Read a DNA sequencing gel.
- The describe the mechanism of RNA polymerase
Course assessments, activities, and outline
Other course details
This is a semester-long course, so it averages approximately three modules/week.
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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