Modern Biology

Learning objectives by module

Unit 2: Biological Chemistry

• Module 2: Atoms, Functional Groups, and Water
  • After delving into the functional grouping of molecules, students will be able to identify different functional groups, and characterize each, by category (i.e. polar, non polar, neutral, or charged).
  • Define a buffer and its utility to the biological system.
  • Define a hydrogen bond and draw possible hydrogen bonds between any two appropriate molecules.
  • Define and draw the structure of a hydrogen bond between any two appropriate molecules.
  • Define, and draw the structure of, a hydrogen bond between any two appropriate molecules.
  • Describe an instance of bioselectivity resulting from the structure and bonding of carbon.
  • Describe how water, as a solvent, buffers the structure of ions in solution.
  • Describe properties of water that make it the most suitable to support living systems.
  • Describe the difference between covalent and non-covalent bonds.
  • Describe the energy associated with breaking covalent and non-covalent bonds.
  • Describe the hydrophobic effect and its significance in biological systems.
  • Describe the properties of water that are critical for the support of living systems.
  • Describe the results of the hydrophobic effect, which is the interaction of hydrophobic molecules to the exclusion of water.
  • Determine the charge on functional groups at a given a pH level.
  • Determine the total number of hydrogen bonds possible from a given electronegative atom.
  • Distinguish between a strong electrolyte and a weak electrolyte.
  • Explain the basic structure of a water molecule and how it can form a three dimensional structure.
  • Explain the significance of having electronegative atoms in a molecule.
  • Identify different functional groups and characterize each by category (i.e. polar/nonpolar,charged/uncharged).
  • Identify the electronegative atoms found in biological systems.
  • Identify the more electronegative atom when comparing two atoms.
  • List at least 4 of the major trace elements found in cells and the ionic state in which they exist naturally.
  • List atoms (elements) found in biological systems that are most important to life, including the most common atoms and trace elements.
  • List the six major atoms found in the composition of biological systems and describe the properties that make them essential for life.
  • Recognize and describe a covalent and an ionic bond structurally.
  • Recognize and describe a covalent bond and inter-molecular forces (an ionic, a hydrogen bond, and van der Waals interactions) both structurally and energetically.
  • Recognize and describe a covalent, an ionic, and a hydrogen bond, both structurally and energetically.
• Module 3: Equilibrium and pH
  • Define a weak electrolyte and write an expression for the equilibrium constant.
  • Describe the dynamics of equilibrium.
  • Describe the relationship between pH and proton concentration.
  • Distinguish acids from bases, and explain their relationship to acid dissociation.
  • Explain the relationship between the concentration of acid and conjugate base at equilibrium.
  • Upon completing this review, students will be able to describethe significance of Ka and pKa, and explain the relationship between them.
• Module 4: Carbohydrates and Polysaccharides
  • After examining carbohydrate molecules, students will be able to describe the three major functions of carbohydrates.
  • Characterize the functional groups in carbohydrates.
  • Define a glycosidic bond and the relationship between condensation and hydrolysis.
  • Define the criteria for formation of a glycosidic bond.
  • Describe condensation and hydrolysis.
  • Describe the anomeric carbons of the hemiacetal form of the carbohydrates.
  • Designate functions for the mono-, di-, and polysaccharides, given in the text.
  • Distinguish aldose (aldehydes) from ketoses (ketones).
  • Distinguish and describe the differences between the plant cell wall and bacterial cell wall.
  • Distinguish between an aldose and a ketose.
  • Distinguish characteristic structural differences among homopolysaccharides.
  • Distinguish primary, secondary, tertiary, and quaternary structures.
  • Distinguish, and characterize the differences, between cellulose, starch and glycogen.
  • Explain alpha helix and beta structures.
  • Explain why all amino acids are the L-isomer and why glycine is not.
  • Explain why carbohydrates are well suited for signaling and cell recognition functions.
  • Identify a glycosidic bond.
  • Identify and describe characteristics of the molecules marked.
  • Identify asymmetric (chiral) centers.
  • Identify enantiomers of all carbohydrates as D.
  • Identify the basic structure of all amino acids.
  • Identify the molecules: glyceraldehyde, dihydroxyacetone, ribose, glucose, galactose and fructose.
  • Identify which steroisomer of carbohydrates are found in nature.
  • Illustrate the different types of bonding responsible for holding the tertiary structure of protein together.
  • Place any amino acid into one of the four categories of properties, based on the structure of its side chain.
  • Recognize a peptide (amide bond) and list the structural properties of it.
  • Recognize alpha and beta orientation of hydroxyl on anomeric carbon.
  • Recognize and describe structure and function of sucrose, lactose, cellulose, glycogen, amylose, amylopectin, and starch.
  • Recognize the anomeric carbon in the hemiacetal form of the carbohydrates.
• Module 5: Amino Acids and Proteins
  • Classify amino acid side chains based on polarity and ionization.
  • Define and describe the primary structure of a protein.
  • Define the driving force for the folding of a polypeptide in water and in a non-polar solvent.
  • Define the structural properties of a peptide bond that will put constraints on the folding of a protein.
  • Describe how a quaternary structure is dynamic.
  • Describe specific examples of secondary structure in detail.
  • Describe specific structural restrictions that characterize secondary structure.
  • Describe structural domains.
  • Describe the bonding involved in the folding of proteins.
  • Describe the type of reaction responsible for the formation anddegradation of the peptide bond.
  • Describe what is necessary to form a quaternary structure.
  • Explain how primary structure defines the final structure of a protein.
  • Explain the covalent bonds possible in stabilizing a tertiary structure.
  • Explain why most naturally occurring amino acids are the L-isomers and why glycine is not.
  • Give at least one example of a quaternary structure.
  • Identify and draw hydrogen bonding between peptide bonds.
  • Identify the basic structure of amino acids.
  • Identify the functional groups involved in formation of a peptide bond.
• Module 6: Protein Function – Binding and Catalysis
  • Define activation energy and the effect an enzyme hasupon it.
  • Define equilibrium binding and describe how it is dynamic.
  • Describe how pH affects enzyme kinetics.
  • Describe how temperature affects enzyme kinetics.
  • Describe the effect of changing ligand concentration on an equilibrium.
  • Describe the general reaction for an enzyme catalyzed reaction.
  • Describe the interactions that stabilize the protein-ligandcomplex.
  • Discern the difference between a ligand and a substrate.
  • Draw a graph of equilibrium binding.
  • Explain the parallels between protein-ligand binding and weak electrolyte dissociation.
  • Explain what happens before and after the formation of the ES complex.
  • Explain, and graphically illustrate, the effect of each inhibitor type on a velocity vs. substrate concentration graph: a) non-competitive and b) competitive.
  • Graphically represent the relationship, between each of the following, for an enzyme catalyzed reaction: 1) velocity and substrate concentration; 2) velocity and enzyme concentration; 3) velocity and pH; and, 4) velocity and temperature.
  • Recognize, and describe, the reversible binding of proteins with their ligands.
  • Upon completion of this topic, students will be able to recognize, and describe, the reversible binding of proteins with their ligands.

Unit 3: Cell Biology

• Module 7: Lipids and Membranes
  • Define the amphipathic character of a phospholipid and glycolipid.
  • Define the functions of each of the classes of lipids.
  • Describe and diagram the characteristic features of the fluid mosaic membrane.
  • Describe and identify the difference between a liposome and a micelle.
  • Explain how the different structural features of fatty acids influence their role in phospholipids and fats.
  • Name and identify the ester bonds between fatty acids and glycerol and the glycerol and phosphate.
• Module 8: Membrane Transport
  • Characterize the environmental changes necessary to allow recycling of intermediates in receptor mediated endocytosis.
  • Describe a set of criteria for selective transport of a given molecule to pass through a membrane channel.
  • Describe a typical source of energy (general and specific examples).
  • Describe how osmotic pressure is generated and what conditions are necessary to create high osmotic pressure in a cell.
  • Describe the difference between general endocytosis and protein transduction.
  • Describe the factors that affect simple diffusion
  • Describe the fate of a molecule taken into a cell by receptor mediate endocytosis.
  • Describe the fate of the material undergoing endocytosis.
  • Describe the general structural features of a membrane transport protein.
  • Describe the solute differences between isotonic, hypertonic and hypotonic solutions.
  • Describe the spontaneous direction of the movement of molecules
  • Describe the structural and chemical characteristics of a typical ‘facilitator’.
  • Describe why the process requires energy.
  • Disntiguish how receptor mediated endocytosis differs from protein transduction.
  • Distinguish between facilitated diffusion and active transport.
  • Distinguish between simple diffusion and facilitated diffusion.
  • Distinguish the mechanisms of uniports, symports and antiports.
  • Explain how receptor mediated endocytosis differs from phagocytosis.
  • Explain the affect of an isotonic, hypertonic and hypotonic solution on the shape of a cell.
  • Explain the difference between pinocytosis and phagocytosis.
  • Explain why the description of osmosis emphasizes the solvent hanges.
  • Expound on how the inside surface of the endocytic vesicle is the same as the outside surface of the cell and why that is important to the cell.

Unit 4: Basis of Molecular Biology

• Module 10: DNA Replication
  • Characterize the direction of DNA synthesis.
  • Describe one method of editing that takes place during DNA synthesis.
  • Describe the formation of the Open Complex at the origin of replication.
  • Describe the process of connecting the Okazaki fragments into a continuous strand of DNA.
  • Describe the results of semiconservative replication.
  • Differentiate the multiple origins of replication that are used to reduce the time of replication of Eukaryotic chromosomes.
  • Discuss how competitive binding is used in DNA sequencing using dideoxy-NTPs.
  • Distinguish the difference between continuous and discontinuous DNA synthesis.
  • Explain how the appropriate substrate for DNA polymerase at the replication fork is established.
  • Explain how the the length of DNA amplified during PCR is defined.
  • Explain the substrate requirements for DNA synthesis by DNA polymerase.
  • Expound on why Okazaki fragments are formed on the lagging strand.
  • Specify how telomerase uses the rules for DNA synthesis to overcome shortening of the chromosome.
• Module 11: DNA Transcription
  • Describe a post-transcriptional modification that takes place with each of the classes of transcription products.
  • Describe the difference between a eukaryotic and prokaryotic Operon
  • Describe the differences between the substrate requirements for DNA polymerase and RNA polymerase
  • Describe the process of RNA splicing including the splicesome, introns, exons and lariats.
  • Describe the role of the 5′-cap and the 3′-polyA tail in the functioning of mRNA.
  • Describe the similarities between the functioning of DNA plymerase and RNA polymerase
  • Describe the steps in the process of transcription (RNA synthesis) starting with RNA polymerase binding to the promoter and ending with the release of polymerase from the terminator
  • Describe where the information (signal) for splicing is and why it might lead to alternative splicing.
  • Explain the difference between a weak and a strong promoter including the basis for the difference in “strength” of the promoter
  • Name the products of transcription and differentiate each from the others
• Module 12: RNA Translation-Protein Synthesis
  • Define the genetic code.
  • Define the role of each RNA molecule used in translation.
  • Describe the process of translation as a step-wiseprocess.
  • Describe what post-transcriptional modification must take place beforetranslation.
  • Distinguish between prokaryotic and eukaryotictranslation.
• Module 9: DNA and RNA
  • Correctly draw the hydrogen bonding between DNA and RNA bases.
  • Correctly identify and specifically name all of the nucleotides.
  • Define which helix type describes DNA and RNA.
  • Describe 3 common structural characteristics of DNA/RNA polymer backbones.
  • Describe the criteria for determining the most stable structure between two DNA molecules, two RNA molecules, between a DNA and a RNA molecule.
  • Describe the difference and identify the difference between a nucleotide and a nuceloside.
  • Describe the hydrogen bonding that exists between complimentary base pairs in DNA and RNA.
  • Describe the major characteristics of the B-DNA double helix
  • Describe the structural differences between the A-helix and B-helix.
  • Describe why AT and AU base pairs are weaker than GC base pairs.
  • Describe why purines are always paired with pyrimidines to form the helix structures of DNA and RNA.
  • Explain the major difference between the DNA and RNA backbone structures.
  • Give two examples of bioselectivity in the formation of the RNA or DNA backbone.
  • Identify a phosphodiester bond.
  • Identify correct base pairing between DNA and RNA bases.
  • Identify the difference between a purine and pyrimidine.
  • Identify the structure of each of the nitrogenous bases: A, T, G, C,U.
  • Identify which bases are incorporated into DNA and RNA.

Unit 5: Metabolism

• Module 13: Pathways
  • Describe a linear, branched, and circular pathway.
  • Describe the common features of metabolic pathways.
  • Describe the major differences between a competitive and uncompetitive inhibitor.
  • Distinguish regulation by non-covalent and covalent modification of enzymes.
  • Explain activation of enzymes by allosteric compounds as a method of regulation.
  • State the major differences between catabolic and anabolic pathways.
• Module 14: Energetics
  • Calculate the Gibbs free energy change, given the state of the system and the standard energy changes.
  • Describe how a pathway with a positive Gibbs free energy can be reversed by coupling to an energy releasing reaction.
  • Describe the direction of electron transfer in oxidation/reduction reactions.
  • Determine the spontaneous direction of a reaction from the Gibbs free energy.
  • Explain how to balance redox reactions.
  • Explain the difference between direct and indirect coupling.
  • Explain the major energy storage methods in metabolism – phosphorylated compounds, redox carriers, and proton gradient.
  • Explain the relationship between the equilibrium point of a system and the difference in standard energies.
  • Identify and describe the source of “high-energy” phosphate bonds in ATP.
  • Specify the difference between standard energy and Gibbs free energy.
  • State the name of two common organic electron carriers and show familiarity with changes in the structure that occurs on oxidation/reduction.
  • Tell how the energy stored in a thioester can be used for ATP synthesis or organic addition reactions.
• Module 15: Enzyme Nomenclature
  • Describe the reactions catalyzed by dehydrogenases, hydratases, isomerases, and synthetases.
  • Explain the difference between a kinase and a phosphatase
• Module 16: Glycolysis
  • Define glycolysis and identify its celluar location.
  • Describe anaerobic metabolism and how it effects glycolysis.
  • Describe how energy released by oxidation is stored.
  • Distinguish how direct and indirect coupling are used to make glycolysis spontaneous.
  • Explain what happens when glucose is metabolized through glycolysis.
• Module 17: TCA Cycle
  • Describe how glycolysis connects to the TCA cycle and where the TCA cycle occurs.
  • Describe how intermediates in the TCA cycle are used to synthesize a wide range of compounds.
  • Explain where CO2 is released.
  • Expound on where, and in what form, the energy released by the TCA cycle is stored.
• Module 18: Electron Transport and Ox. Phos.
  • Explain ATP synthase and the effects of allosteric changes during proton translocation.
  • Explain the role of the four complexes, coenzyme Q, and cytochrome C in electron transport.
  • Explain what happens when electrons transport through complexes I, III, and IV.
  • Identify the pathway of the electrons from FADH2 to oxygen resulting in the formation of water.
  • Identify the pathway of the electrons from NADH to oxygen resulting in the formation of water.
  • Predict whether the free energy stored in the non-equilibrium hydrogen ion gradient is sufficient to sythesize ATP from the transport of 3 protons.
• Module 19: Integrated Metabolism
  • Describe how glycolysis and gluconeogenesis are coordinately regulated by sensing energy levels in the cell.
  • Describe how select amino acids enter the oxidative pathways.
  • Describe indirect coupling in glycogen synthesis and how glycogen synthase is controlled by protein phosphorylation.
  • Describe receptor mediated signal transduction and explain the role of G-proteins and adenyl cyclase.
  • Explain how glucose can be synthesized from pyruvate.
  • Explain how glycogen degradation by glycogen phosphorylase is controlled by protein phosphorylation.
  • Explain how hormone controlled phosphorylation of enzymes affect fructose 2,6 phosphate (F-26-P) levels.
  • Explain how the disaccharides sucrose and lactose enter glycolysis.
  • Explain the physiological role of the hormones epinephrine, glucagon, and insulin.
  • Explain the role of the protein kinases and phosphatases in regulating the enzyme function.
  • Express how glycogen and glucose metabolism in the liver effects the glucose demand of the organism and the liver cell.
  • Identify the role of phosphofructose kinase and fructose-1,6-bisphosphatase in gluconeogenesis pathways.
  • Indicate the number of steps in glycolysis that are too energetically unfavorable to reverse in gluconeogenesis and describe how the steps are reversed.
  • Recognize the structure of glycogen.
  • Specify how fats (triglycerides) are metabolized by fatty acid oxidation.
  • Specify the number of steps in glycolysis with Gibbs free energies that are close to zero and can be reversed in gluconeogenesis.
  • Summarize how fructose 2,6, phosphate levels regulate glycolysis and gluconeogenesis.
  • Tell how carbons atoms from the excess consumption of any dietary source can be incorporated into fats.