Print Version

Effective: Summer 2013

Prerequisites: Prerequisite: BIOL 1A.
Advisory: Advisory: Students taking the biology majors' sequence (BIOL 1A, 1B, 1C, 1D) are strongly advised to take the sequence in order and in its entirety.
Grade Type: Letter Grade, the student may select Pass/No Pass
Not Repeatable.
FHGE: Non-GE Transferable: CSU/UC
4 hours lecture. (48 hours total per quarter)

Student Learning Outcomes -
  • Explain the relationship between structure and function as observed in key enzymes used in DNA replication, transcription and translation.
  • Demonstrate an understanding of how experimental evidence is used to draw conclusions regarding the structure and function of important genetic molecules.
  • Demonstrate the ability to examine current scientific literature, and draw conclusions based on published current research
  • Demonstrate the ability to understand the link between DNA structure, and it's function as the molecule of heredity, and evolutionary change
Description -
Intended for students wishing to transfer to a four year school with a major in molecular biology, biochemistry, or molecular genetics. An introduction to molecular genetics with an emphasis in genome organization, DNA replication and repair, mutation, transcription, translation and the regulation of gene expression.

Course Objectives -
The student will be able to:
  1. explain the key experiments that led to the discovery of DNA structure and function
  2. describe the role of genes within cells
  3. discuss the evolution of the three domains Archaea, Bacteria, and Eukarya.
  4. compare and contrasts DNA organization of prokaryotes and eukaryotes.
  5. describe the steps of DNA replication and explain the molecular basis for DNA replication's remarkable fidelity.
  6. compare and contrast bacterial and eukaryotic DNA polymerase and DNA replication.
  7. describe the various mechanisms that cause DNA damage and mutation.
  8. describe DNA repair systems, comparing and contrasting eukaryotic and bacterial systems.
  9. explain the mechanisms and importance of recombination, repair and transposition.
  10. describe transcription in bacteria
  11. describe transcription in eukaryotes
  12. compare and contrast transcription and RNA processing in bacteria and eukaryotes.
  13. describe the various types of post-transcriptional processing.
  14. describe protein translation.
  15. compare and contrast control of gene expression in eukaryotic and bacterial genomes.
  16. describe basic methods in molecular genetics and discuss their applications.
  17. describe some of the contributions made by eminent scientists, including women and minorities, to the fields of molecular and cell biology
  18. critically read and discuss original scientific papers
  19. explore and discuss scientific questions for which there is as yet no single, generally accepted answer.
Special Facilities and/or Equipment -
  1. Multimedia lecture room and student access to computers.
  2. Students need internet access.

Course Content (Body of knowledge) -
  1. Brief history of molecular genetics.
    1. Experiments that identified DNA as the molecule of inheritance
    2. Discovery of the structure of DNA
    3. Experiments that led to our initial understanding of transcription
    4. Experiments that led to our initial understanding of translation
    5. Elucidation of the genetic code
  2. Molecular nature of genes.
    1. Storing and using genetic information
    2. Replication
    3. Mutation
    4. Recombination
  3. Evolutionary relationship between Archaea, Bacteria, and Eukarya
    1. Molecular evolution
    2. Conserved sequences
    3. Molecular clocks
      1. rRNA
      2. histone genes
      3. subunits of DNA polymerase
      4. subunits of RNA polymerase
  4. Genome organization
    1. Review prokaryotic organization
    2. Eukaryotic organization
      1. Nucleosomes and chromatin packaging into chromosomes
      2. Introns and exons
      3. Nonrepetitive DNA, moderately repetitive DNA, and highly repetitive DNA
      4. Gene clusters
      5. Organelle DNA: mitochondria and chloroplast
  5. DNA Replication
    1. Replicons
    2. DNA structure and the primer:template junction
    3. Enzymology
      1. helicase and helicase loader
      2. single stranded binding proteins
      3. topoisomerases
      4. Primase
      5. RNAse H
      6. ligase
      7. histone chaperones
      8. sliding clamp and sliding clamp loaders
    4. DNA polymerase
      1. Three dimensional structure - palm, finger, and thumb domains
      2. Processivity
      3. Fidelity of replication (molecular basis of proof-reading function)
      4. Holoenzyme - catalytic core, tao, sliding clamp, clamp loader
    5. Initiation
    6. Elongation - trombone model
    7. Termination
    8. Regulation of DNA replication
  6. Comparing eukaryotic and bacterial systems and molecules
    1. Origins of replication - replicators and initiators
    2. DNA polymerases - similarities and differences
    3. Regulation - similarities and differences
  7. Mutation and DNA damage
    1. Types of mutation
    2. Estimating mutation rates
    3. Base pair modifications
      1. tautomers
      2. alkylation
      3. deamination
      4. depurination
      5. oxidation
      6. intercalating agents
      7. base analogs
      8. UV radiation and dimers
      9. ionizing radiation and chromosome breaks
  8. DNA repair systems
    1. Direct repair
    2. Mismatch repair
    3. Base excision repair
    4. Nucleotide excision repair
    5. Recombination
    6. Nonhomologous end joining
    7. Translesion synthesis
  9. Recombination and transposition
    1. Homologous recombination
    2. RecA protein
    3. Holliday junctions
    4. Meiotic recombination
    5. Transposition
      1. transposons
      2. retrotransposons
      3. transposable elements in different genomes
  10. Transcription in bacteria
    1. Transcription overview and transcription bubbles
    2. Bacterial promoters
    3. Bacterial RNA polymerase
    4. Initiation, elongation, and termination
    5. Regulation of transcription
  11. Transcription in eukaryotes
    1. Eukaryotic RNA polymerases
    2. Transcription factors
    3. TATA box binding protein
    4. Eukaryotic promoters
      1. Class I
      2. Class III
      3. Class II
    5. CTD tail and mediator complex
    6. Regulation of transcription
  12. Compare and contrast transcription in bacteria, archaea, and eukarya
    1. RNA polymerases
    2. RNA processing
  13. Post-transcriptional processing
    1. 5' cap
    2. Poly A tail
    3. Splicing
      1. Spliceosome
      2. Splicing reactions
      3. Splicing errors
      4. Alternative splicing
  14. Translation
    1. Ribosomes, messenger RNA, and transfer RNA
    2. The genetic code
    3. Initiation
    4. Elongation
    5. Termination
    6. Protein structure and localization
  15. Regulation of gene expression
    1. Negative and positive control
    2. Operons
    3. Eukaryotic regulation
      1. chromatin modification
      2. control elements and transcription factors
      3. enhancers and activators
      4. post-transcriptional regulation
    4. Nondcoding RNAs
      1. microRNAs
      2. small interfering RNAs
      3. chromatin remodeling and silencing
  16. Laboratory Methods - description and discussion only
    1. Tools for recombinant DNA technology
      1. Vectors
      2. Restriction enzymes
      3. Ligase
    2. Cloning
    3. Selected applications
      1. Centrifugation and Svedberg units
      2. Melting curves and C0t curves
      3. Electrophoresis
      4. DNA fingerprints
      5. DNA footprints
Methods of Evaluation -
  1. One or more objective written midterm exams.
  2. Frequent quizzes that include both short answer and objective questions.
  3. Short essay.
  4. Written objective comprehensive final exam
Representative Text(s) -
Required text:
Reece, Jane B., Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Petr V. Minorsky, and Robert B. Jackson. Campbell Biology. 9th ed. San Francisco, CA.: Benjamin/Cummings Publishing, Inc., 2011.
Krebs, Jocelyn E., Elliott S. Goldstein, and Stephen T. Kilpatrick. Lewin's Essential Genes. 2nd ed. Sudbury, MA.: Jones and Bartlett Publishers, 2010.
Duncan, Kathleen. Study Guide for Biology 1D. Foothill College, 2011.
Supplemental Text:
Alberts, Bruce, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walter. Molecular Biology of The Cell. 5th ed. New York, NY.: Garland Science, 2008.
Watson, James D., Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, and Richard Losick. Molecular Biology of the Gene. 6th ed. San Francisco, CA.: Benjamin/Cummings Publishing, Inc., 2008.
Nelson, David L. and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York, N. Y.: W. H. Freeman and Company, 2008.

Disciplines -
Biology or related fields
Method of Instruction -
Lecture, Discussion, Cooperative learning exercises.
Lab Content -
Not applicable.
Types and/or Examples of Required Reading, Writing and Outside of Class Assignments -
  1. Reading Assignments
    1. Weekly reading assignments from primary text and supporting texts
    2. Supplemental reading assignments from web sources relevant to course material
  2. Writing Assignments
    1. Weekly assignment to answer objective set questions and define vocabulary
    2. Participation in online discussion forums
  3. Computation and writing
    1. Construct and interpret graphs.
    2. Interpret melting curves and C0t curves.
    3. Interpret DNA footprint and DNA fingerprint data.
    4. Calculate and interpret recombination frequencies.
    5. Interpret laboratory data from relevant key experiments in the field of molecular genetics.