A course that focuses on topics at the forefront of experimentation in the fields of cellular biology, molecular biology, biochemistry, and genetics.
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Modern Biology — Open & Free
A course that focuses on topics at the forefront of experimentation in the fields of cellular biology, molecular biology, biochemistry, and genetics.
- What students will learn
- Learning objectives by module
- Course outline
- Other course details
- System requirements
- Open & Free features
What students will learn
- Biological Chemistry
- Cell Biology
- Molecular 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.
UNIT 1: Introduction to Modern Biology
Module 1: Introduction
UNIT 2: Biological Chemistry
Module 2: Atoms, Functional Groups, and Water
Module 3: Equilibrium and pH
Module 4: Carbohydrates and Polysaccharides
Module 5: Amino Acids and Proteins
Module 6: Protein Function – Binding and Catalysis
UNIT 3: Cell Biology
Module 7: Lipids and Membranes
Module 8: Membrane Transport
UNIT 4: Basis of Molecular Biology
Module 9: DNA and RNA
Module 10: DNA Replication
Module 11: DNA Transcription
Module 12: RNA Translation-Protein Synthesis
UNIT 5: Metabolism
Module 13: Pathways
Module 14: Energetics
Module 15: Enzyme Nomenclature
Module 16: Glycolysis
Module 17: TCA Cycle
Module 18: Electron Transport and Ox. Phos.
Module 19: Integrated Metabolism
UNIT 6: Appendix
Module 20: Appendix
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