Biochemistry — Open & Free

Learning objectives by module

Unit 2: Biochemistry

Module 2: Introduction and Water Structure

• 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

 

Module 3: Acids and Buffers

• Calculate the amount of a weak acid and its conjugate base to make a buffer system.
• Calculate the amount of an acid that is protonated at any given pH.
• Calculate the net charge on a molecule, at any pH.
• Understand the relationship between the structure and acidity of an acid.
• Understand why solutions of weak acids resist pH changes.

 

Module 4: Protein Structure

• Characterize molecular forces between antibody and antigen.
• Define the terms antigen, epitope, and hapten.
• Describe the process of antibody production by B-cells.
• 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.
• Interpret changes in ΔH and ΔS.
• Join two amino acids into a dipeptide.
• Obtain ΔH and ΔS for protein unfolding from experimental data.
• Predict degree of protein unfolding given ΔH and ΔS.
• Predict the result of treating a protein with different cleavage reagents.
• 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 relationship between primary, tertiary, and quaternary structure of antibodies.
• 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 5: Binding

• Calculate amount of oxygen delivered from binding curves.
• Compare and contrast homotropic and heterotropic allosteric effectors.
• Compare and contrast structures and binding curves of myoglobin and hemoglobin.
• Construct Hill plot and obtain KD and Hill coefficient.
• Describe how the amount of ligand bound is affected by the ligand concentration, both at low and high [L].
• Determine the dissociation constant, KD directly from binding data.
• How allosteric activators and inhibitors affect binding.
• Interpret KD in terms of inter-molecular interactions.
• Relate the Hill coefficient to the molecular behavior of the system.
• Understand role of allosteric modulators in oxygen delivery.
• Understand the molecular basis of oxygen transport.

 

Module 6: Enzymes

• Be able to describe how the substrate concentration affects the rate of enzymatic reactions.
• Be able to obtain kinetic parameters from experimental data
• Calculate the rate enhancement due to transition state stabilization.
• Compare and contrast the structure and mechanism of HIV protease to serine proteases.
• Define steady-state conditions
• Describe the factors that contribute to stabilization of the transition state.
• Determine the dissociation constant for inhibitors.
• Distinguish between enthalpic and entropic stabilization of the transition state.
• 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.
• 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: Protein Purification and Structure Determination

• Calculate and interpret specific activity.
• 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.
• Understand the principles of separation techniques.

 

Module 8: Carbohydrates

• Compare and contrast the structure of glycogen and cellulose
• Describe how ring structures of saccharides are formed.
• Describe the structure of bacterial cell walls.
• Draw and name disaccharides.
• Draw the chemical structure of aldoses and ketoses.
• Identify the anomeric carbon in cyclic monosaccharides.

 

Module 9: Lipids

• Calculate the energetics of membrane-protein interactions.
• Describe the thermodynamics of self-assembly of membranes.
• 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: Metabolism

• 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.
• Describe a linear, branched, and circular pathway.
• Describe the common features of metabolic pathways.
• Enzyme Regulation: Role of protein kinases and phosphatases in control of enzyme function.
• Hormonal Control: Understand physiological role of hormones epinephrine, glucagon, and insulin.
• How the energy stored in a thioester can be used for ATP synthesis or organic addition reactions.
• Identify that glycolysis oxidizes the six carbon glucose to produce two three-carbon pyruvate molecules.
• Identify the cellular location of glycolysis.
• Identify the role of direct and indirect coupling in metabolic pathways.
• 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 direction of reactions using Gibbs free energy.
• Predict the product of oxidative decarboxylations
• Signal transduction: Understand the role of G-proteins and adenyl cyclase in receptor mediated signal transduction.
• State the major differences between catabolic and anabolic pathways.
• 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 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 major differences between a competitive and uncompetitive inhibitor.
• Understand the major energy storage methods in metabolism – phosphorylated compounds, redox carriers, proton gradient.
• Understand the mechanism of ATP synthase, how allosteric changes that occur during proton translocation lead to the conversion of ADP and Pi to ATP.
• 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 source of “high-energy” phosphate bonds in ATP
• Understand the structure of glycogen.

 

Module 11: Recombinant DNA and Central Dogma

• Be able to utilize the lac repressor/operator to control gene expression
• Calculate TM of a double stranded DNA molecule.
• Compare and contrast the major factors that stabilize dsDNA and Proteins.
• 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.
• Discuss the major features that affect the energetics of DNA-protein interactions.
• Discuss the role of each element in an expression vector.
• 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 how PCR leads to the amplification of DNA.
• Explain how proofreading occurs during DNA synthesis.
• Explain the basis of DNA sequencing.
• Explain the difference in the chemical stability of RNA versus DNA.
• 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 major and minor group of a base pair.
• Identify the non-Watson-Crick hydrogen bonds in A-T and G-C basepairs.
• Identify the Watson-Crick hydrogen bonds in A-T and G-C basepairs.
• Include the appropriate signals to cause export of the protein out of the cell
• List the essential elements of an expression vector.
• Provide a description of the structural features of B-DNA.
• The describe the mechanism of RNA polymerase
• Use restriction enzymes and DNA ligase to generate recombinant DNA molecules.

 

Module 12: DNA Replication

• Describe the activities of each protein involved in replication.
• Understand the enzymatic differences in polymerases and the importance of these differences in functionality