BIO 171 - Introduction to Molecular and Cellular Biology

1. Demonstrate skills associated with the common student learning outcomes for Delta College.
   1. Competently communicate in the language of the discipline.
   2. Demonstrate the ability to think critically through scientific and quantitative reasoning.
   3. Use cooperative interactions to learn and accomplish complex tasks
   4. Access scientific information from a variety of sources for purposes learning and critical evaluation.
2. Demonstrate the process of science in order to engage in scientific investigations.
   1. Outline the steps of the scientific method.
   2. Plan an experiment using the steps of the scientific method.
   3. Classify data as either qualitative or quantitative.
   4. Emphasize the use of safety during scientific investigation.
   5. Use of spreadsheets to track and analyze data.
   6. Demonstrate competency in performing specific laboratory techniques, including spectrophotometry, use of standard curves, microscopy, cell transformation, sterile technique, gel electrophoresis and tests for various carbohydrates.
   7. Analyze data from specific laboratory approaches including DNA sequencing, restriction mapping, Edmund degradations, reciprocal crosses and genetic chromosome mapping.
3. Recognize the broad unifying themes in the study of living things.
   1. List the characteristics of life which are common to all organisms/cells.
   2. Provide several examples of the correlation of structure and function at the organismal, cellular and sub-cellular level.
   3. Explain the common aspects of the inheritance of biological information as based in nucleic acids and base pairing.
   4. Discuss evolution as a core theme of biology noting that its effects can be seen at the molecular, subcellular, and organismal levels.
4. Demonstrate an understanding of how the living properties of cells are manifest from the physical properties of macromolecules and systems of organelles.
   1. CLASSIFICATION
      1. Classify cells into different kingdoms based on structure, specialization and metabolic characteristics.
      2. List three parts of the cell theory and briefly describe its development.
      3. Explain why cells are small, and be able to calculate the surface area to volume ratio as it relates to the size of the cell.
      4. List five basic differences between prokaryotic and eukaryotic cells.
      5. Using a microscope, distinguish between cell types characteristic of the five kingdoms.
      6. Prepare materials for microscopic observation and demonstrate the correct procedure for using and storing a compound microscope.
   2. MACROMOLECULES
      1. Apply the basic concepts regarding the structure and organization of matter and energy to biological systems as typically presented in the fields of chemistry and physics.
      2. Identify the biologically important functional groups and their chemical properties.
      3. Identify and describe the structure and function of carbohydrates, lipids, nucleic acids and proteins as classes of macromolecules.
      4. Discuss how carbohydrates, lipids, nucleic acids and proteins support cell structure, energy use, information storage and chemical catalysis.
      5. Describe the consequences of dehydration and hydrolysis reactions and how they are dependent upon water.
      6. Describe the four levels of protein structure and the forces that help maintain the integrity of each.
      7. Discuss the various ways that organisms/cells interact with their environment.
   3. MEMBRANES
      1. Understand the biochemistry of phospholipids and how they are organized into membranes.
      2. Compare and contrast the terms diffusion, facilitated diffusion and osmosis.
      3. Predict the behavior of a cell in an isotonic, hypertonic, and hypotonic environment.
      4. Define active transport.
      5. Discuss the membrane models involved in diffusion, facilitated diffusion, and active transport.
      6. Differentiate between endocytosis and exocytosis.
      7. Describe the operation of sodium-potassium pumps and the proton pumps.
   4. CELL SIGNALLING
      1. Discuss the signal hypothesis.
      2. Indicate the functions of cell surface receptors and cell surface markers.
   5. ORGANELLES
      1. Describe techniques and tools used to study cells such as microscopy, centrifugation, and radioactive tracers.
      2. Identify and describe the cell organelles and how they function.
      3. Identify which organelles belong to the endomembrane system.
      4. Identify the path of a secreted protein through the cell.
5. Demonstrate an understanding of the metabolic strategies that cells utilize.
   1. ENERGETICS AND ENZYMES
      1. Discuss the energetics of coupling reactions.
      2. Identify different types of potential energy within a cell. (concentration gradients, electronegativity, repulsion of like-charges, order)
      3. Identify cellular processes that convert one type of stored energy into another type of energy.
      4. Apply the principles of entropy, enthalpy, endergonic, exergonic, catabolism, anabolism, dehydration reactions, and hydrolysis reactions with macromolecule metabolism.
      5. Explain how energy is stored in the structure of ATP.
      6. Define activation energy and describe how it is related to reaction rate and how it can be altered.
      7. Describe the role of enzymes as chemical catalysts in biological systems.
      8. Explain in terms of chemical properties of amino acids how an enzyme is capable of possessing substrate specificity.
      9. Identify that pH, temperature, enzyme concentration, substrate concentration and inhibitors can all affect the activity of an enzyme.
      10. Explain in chemical terms how pH, temperature, enzyme concentration, substrate concentration and inhibitors can all affect the activity of an enzyme.
      11. Explain in terms of the Law of Mass Action the difference between competitive and non-competitive inhibitors.
      12. Diagram a generalized biochemical pathway.
      13. Explain the role of kinases in the cell.
   2. RESPIRATION AND FERMENTATION
      1. Describe glycolysis in general terms, including initial reactants, products, as well as net vs. total ATP production.
      2. Explain the chemical consequences of the early phosphorylation events of glycolysis.
      3. Describe the role of the citric acid cycle, the electron transport chain and oxidative phosphorylation in cellular respiration.
      4. Compare the overall energy efficiency of the complete aerobic degradation of one molecule of glucose with the efficiency of glycolysis alone.
      5. Explain the role of NADH and FADH in glycolysis and the citric acid cycle as electron carriers.
      6. Explain the relative ATP yields or NADH and FADH in terms of oxidative potential and the electron transport chain.
      7. Distinguish between substrate and oxidative phosphorylation.
      8. Explain the significance of oxygen and hydrogen in biological redox reactions.
      9. Briefly describe the role of the citric acid cycle in intermediary metabolism touching on deamination and beta-oxidation.
      10. Describe alcoholic fermentation in terms of needing to recycle electron acceptors, its energy output and its end products.
      11. Describe three ways in which living organisms generate ATP and indicate which is more efficient.
      12. Describe the process of anaerobic respiration as it occurs in human muscle.
      13. Identify the stage of glycolysis, respiration and/or fermentation in which these intermediates are produced or involved: glucose, pyruvate, acetyl, acetyl CoA, oxaloacetate, citrate, oxygen, water, carbon dioxide, hydrogen ions.
      14. Identify the cellular location of the different stages of glycolysis, citric acid cycle, and fermentation.
   3. PHOTOSYNTHESIS
      1. Describe the properties of light in terms of energy content and photons.
      2. Name the stages of eukaryotic photosynthesis and indicate which processes require light and why.
      3. State the overall equation for photosynthesis and explain why water is included on both sides of the equation.
      4. Explain how photosynthesis I and II produce ATP and NADH.
      5. Compare and contrast non-cyclic and cyclic electron flow.
      6. Describe how RUDP, glyceraldehyde-3 phosphate and PGAL fit into the Calvin Cycle.
      7. Define photorespiration and its potential hazard to plants.
      8. Discuss how CAM and C4 plants combat excessive photorespiration.
      9. Identify the location of the light and dark reactions inside the chloroplast.
      10. Discuss the complementary nature of photosynthesis and aerobic respiration.
6. Demonstrate an understanding of how cells use genetic information for protein synthesis.
   1. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
      1. Recognize and properly label the chemical components of a DNA molecule.
      2. Identify the contributions of: Griffiths, Avery et al., Hershey and Chase, Chargaff, Wilkins and Franklin, Watson and Crick to the discovery of DNA as the information molecule.
      3. Explain what is meant by semi-conservative replication.
      4. Explain the experiments which lead to understanding that DNA is replicated semi-conservatively.
      5. Discuss the role of the following in DNA replication: origin of replication, strand separation, priming, polymerase, Okazaki fragments, ligase, proofreading and DNA repair.
      6. List five differences between DNA and RNA.
      7. Describe diagrammatically the processes of DNA replication, RNA
   2. PROTEIN SYNTHESIS
      1. Explain transcription, and translation. (The central dogma.)
      2. Given a DNA coding strand and a table of codons/amino acids, determine the complimentary mRNA strand, tRNA anticodons, and the amino acid sequence that would be translated.
      3. Discuss the contributions of Garrod, Beadle and Tatum to our current understanding of the gene.
      4. Compare and contrast eukaryotic and prokaryotic genes and genomes.
      5. Discuss signal sequences, RNA splicing and processing, spliceosomes and ribozymes.
      6. Predict the impact of various types of mutation on protein sequence.
   3. GENE STRUCTURE and REGULATION
      1. Describe the five regions of the lac operon and how they work together to regulate lactose metabolism.
      2. Identify the stages in the central dogma at which regulation of gene expression can occur.
      3. Describe generally the source of antibody diversity.
      4. Describe the effects of chemical modification of nucleic acids on gene expression.
      5. Compare and contrast oncogenes and tumor suppressor genes.
      6. Describe three different levels associated with the control of gene expression.
      7. Discuss the features specific to eukaryotic genes which allow them to evolve more quickly than prokaryotic genes.
      8. Discuss development at the organismal level. Include the following in your discussion: totipotent, differentiation, and homeotic genes.
      9. Compare and contrast eukaryotic and prokaryotic chromosome structures.
      10. Identify factors in the environment which can act as mutagens and/or carcinogens.
7. Demonstrate an understanding of how biotechnology uses genetic information.
   1. Identify viral structures and replication, distinguish between DNA viruses, RNA viruses and retroviruses.
   2. Discuss the lytic and lysogenic cycles of bacteriophage
   3. Discuss the bacterial genome, plasmids, transformation, transduction, and conjugation.
   4. Define a transposon and name several organisms in which transposons have been identified.
   5. Distinguish between applied and basic research using examples from recombinant DNA technology.
   6. Understand how plasmids and lambda viruses are used as vectors to introduce DNA to a cell.
   7. Know the natural function of restriction endonucleases and how a normal bacterial cell protects its DNA from their activity.
   8. Explain the basic steps of gene cloning.
   9. Explain selection of transformed colonies.
   10. Explain Southern blot hybridization.
   11. Explain the theory of genetic diagnosis based on RFLPs.
   12. Explain the theory of PCR.
   13. Identify the role of HUGO in molecular genetics today.
   14. Discuss the implication of gene therapy in society from both practical and ethical views.
8. Demonstrate understanding of the relationships between cell division and patterns of genetic inheritance.
   1. MITOSIS
      1. Describe and identify the major events of each stage of mitosis and interphase.
      2. Discuss cancer at the cellular level in terms of cell cycle control, signal transduction, the multiple-hit hypothesis, treatment strategies and specific genes such as p53.
   2. MEIOSIS
      1. Describe and identify the major events in each stage of meiosis.
      2. Understand the genetic consequences of crossing over and independent assortment.
      3. Indicate the evolutionary advantages and disadvantages of sexual reproduction and describe the most current explanation for its initial development.
      4. Define aneuploidy and polyploidy and discuss three human conditions resulting from abnormal chromosome number.
      5. Interpret human karyotypes. 
      6. Differentiate between the products of mitosis and meiosis in number and genetic composition.
   3. TRANSMISSION GENETICS
      1. Identify the stage of meiosis where the following genetic process occur: crossing-over, independent assortment, segregation and non-disjunction.
      2. Define and properly use the terms: dominance, recessive, hybrid, monohybrid, dihybrid, genotype, allele, locus, sex-influenced, sex-limited, mutation, linkage group, crossing over, and non-disjunction.
      3. Utilize the principles of probability in predicting outcomes of genetic crosses involving: monohybrid, dihybrid, sex-linked, incomplete dominance, and multiple alleles.
      4. Perform pedigree analysis.
      5. Apply the product rule to calculate the probability of independent event occurring together in a genetic cross involving more than one gene pair.
      6. Describe modifications of Mendel's principles based on the acquisition of new data: i.e. polygenic inheritance, multiple alleles, sex-linked traits, epistasis, and incomplete dominance penetrance.
      7. Describe the role of the genetic counselor and explain the importance of diagnostic testing and family history in the counseling process.
      8. Discuss current potentials and problems associated with recent advances in the field of genetics.
      9. Explain and state the evidence for the chromosome theory of heredity.
      10. Explain how the recombination of linked genes can be used to map chromosomes.
      11. Discuss different chromosomal sex determination systems.
      12. Relate the concept of dosage compensation and the observation of Barr Bodies with the Lyon Hypothesis.