Molecular, Cellular, and Developmental Biology

learning Goals:

We have established course and topic level Learning Goals for the following courses. Click on a course name to view its related Learning Goals:
MCDB 1041-Fundamentals of Human Genetics (non majors)
MCDB 1150-Introduction to Molecular and Cellular Biology
MCDB 2150–Genetics
MCDB 4650-Developmental Biology

MCDB 1041-Fundamentals of Human Genetics (non majors): Learning Goals (with syllabus topics)

You should be able to:
Cells

Name the different domains of life, and know about relative sizes of cells
Recognize the components of a cell and describe why each is necessary for the function of a cell
Briefly describe why organelles are present and what their general functions are, including the contents of the nucleus

Mitosis
Describe the basic principle of mitosis (why do cells undergo mitosis?).
Diagram how an exact replica of the genetic material is made, including the numbers of chromosomes present at each phase of mitosis.
Distinguish between chromosome, replicated chromosomes, and sister chromatids.
Propose a reason why cells need to go through a "cell cycle".

Meiosis
Describe how gametes are made, and what kinds of cells they arise from.
Compare the two phases of meiosis, and justify why the chromosomes separate differently in each phase.
Compare mitosis to meiosis: what are the differences and similarities?
Justify the importance of crossing over.
Predict the possible outcomes of various mistakes in meiosis.

Gamete maturation and embryonic development
Define what stem cells are, and be able to defend their importance in the human body. 
Compare how the maturation of spermatocytes and ooctyes.
Appreciate the amazing events of fertilization and human embryonic development.

Transmission of Genes – Segregation and Independent Assortment
Justify how Mendel arrived at his laws of inheritance
Define and use correctly the terms: homozygous, heterozygous, dominant and recessive
Describe the basic principles of inheritance (segregation and independent assortment)
Calculate the probability of inheritance of particular genes or traits based on probability
Distinguish between "independent" and "dependent" events

Modes of inheritance and pedigrees
Construct a pedigree from given information
Calculate the likelihood of a genetic event based on a pedigree
Determine which mode of inheritance is most likely based on information in a pedigree

Variations and Extensions of Mendel's laws
Explain how having multiple alleles for a single gene results in multiple distinguishable traits (rather than two for two alleles).
Explain how alleles can have different relationships besides simple recessiveness or dominance.
Explain several possible reasons why a given genotype does not always result in the same phenotype.
Compare inheritance of the mitochondrial genome with the nuclear genome.
Contrast the inheritance of linked genes with unlinked genes.

Sexual development and dosage compensation
Distinguish how "phenotypic" sex is different from "gonadal" sex
Explain how the outward sex characteristics can be mismatched with genetic sex (the sex chromosomes)
Describe what dosage compensation is, and the basic mechanism for how it works in humans.
Compare the impact of dosage compensation on individuals with sex chromosomal abnormalities.

Molecular Genetics
Explain the "central dogma" of genetic information transfer
Describe the relationship between chromosomes, genes and DNA
Distinguish between the theories for how DNA replication might work, and explain how it does work
Draw the process of transcription and explain its utility
Diagram the processing of mRNA transcripts before translation and explain why they happen
Demonstrate how we know the "code" is non-overlapping and redundant.
Interpret how mutations might affect protein structure

Mutations
Recognize different kinds of mutations (frameshift, insertions, deletions, point mutations), and predict their effect on amino acid sequence and protein structure. 
Predict the likelihood of a region of DNA incurring a mutation
Give examples of how DNA can be mutated
Explain why most of us are relatively normal despite the fact that mutations occur in our DNA

Applications of DNA technology
Describe the basic idea of PCR, and how/why it is used.
Explain how gel electrophoresis works, and interpret data from a gel.
Recognize palindromic restriction enzyme sites, and explain why restriction enzymes might be used.
Explain the significance of variable regions in DNA
Interpret gel electrophoresis data, and explain how gels can be used
Explain what an STR is, and HOW STRs can be used in DNA fingerprint analysis

Transgenics and Cloning
Design a transgenic animal, where a protein of interest is specifically produced in some cells.
Explain how cloning can be done, and why one might want to clone an animal.
Describe the differences between a clone and the organism it was cloned from.
Justify reasons for using therapeutic cloning vs. reproductive cloning.

Gene Therapy
Explain the relevance of gene therapy
Compare different kinds of gene therapies
Justify reasons for continuing gene therapy research despite setbacks

Cancer
Describe how cancer begins and how it spreads.
Connect the cell cycle to how cancer initiates.
Apply the principles of genetics to cancer (what genes are mutated, what else is wrong with cancer cells, etc.).
Analyze the possible efficacy of cancer treatments.

MCDB 1150-Introduction to Molecular and Cellular Biology: Course Learning Goals

After completing an introductory MCDB course, students should be able to:

1.  Explain what makes living organisms unique among the complex systems we are familiar with, in terms of how they process information, matter, and energy, and indicate whether both living and non-living things obey the same laws of chemistry and physics.

2.  Contrast the features that distinguish viruses, bacterial cells, and eukaryotic cells from each other.

3.  Explain the theory of evolution through variation and natural selection, and cite evidence that it is an ongoing process affecting our daily lives.

4.  Recognize structures of the four major classes of building-block molecules (monomers) that make up cellular macromolecules and membranes.

5.  Describe how the properties of water affect the three-dimensional structures and stabilities of macromolecules, macromolecular assemblies, and lipid membranes.

6.  Distinguish between equilibrium, non-equilibrium, and steady-state biochemical systems using flow diagrams, and indicate which of these systems can explain the homeostasis that living organisms exhibit.

7.  Outline the flow of matter and energy in the processes by which organisms fuel growth and cellular activities, and explain how these processes conform to the laws of thermodynamics.

8.  Explain how an enzyme increases the rate of a biochemical reaction in terms of thermodynamics and molecular interactions.

9.  Explain how coupled reactions allow an energetically favorable process (e.g. ATP hydrolysis) to drive an energetically unfavorable process (e.g. phosphodiester bond formation).

10.  Explain the importance of membranes in compartmentalizing cellular activities and describe the essential functions that are carried out by the major organelles in a eukaryotic cell.

11.  Using diagrams, describe in general terms how the information in a gene is stored, accessed for expression of a specific protein, replicated, and transmitted to daughter cells.

12.  Describe the general mechanism by which chemical signals from outside a cell are transduced across the cell membrane to influence cell behavior and gene expression.   

13.  Explain in general terms how different types of cells in the same organism can produce different proteins, even though all cells carry the same DNA sequence information.

14.  Explain the roles of the soma and the germ line in the life cycle of a typical multicellular organism.

15.  Describe, using diagrams, the process of meiosis, and explain how it contributes to genetic diversity.

16. Given a well-designed scientific experiment, identify the positive and negative controls and   explain their purpose.

17. Analyze and draw conclusions from numerical and graphical data.

18. Explain the difference between a hypothesis and a theory.

 

MCDB 2150–Genetics: Course and Topic Learning Goals

After completing this course, students should be able to:
1. Analyze phenotypic data and deduce possible modes of inheritance (e.g. dominant, recessive,
autosomal, X-linked, cytoplasmic) from family histories.
Draw a pedigree based on information in a story problem.
Calculate the probability that an individual in a pedigree has a particular genotype.
Define the terms "incomplete penetrance," "variable expressivity," and "sex-limited
phenotype," and explain how these phenomena can complicate pedigree analysis.

2. Describe the molecular anatomy of genes and genomes.
Recognize that a given gene is generally situated at the same chromosomal locus in a
species.
Differentiate between a gene and an allele.
Diagram a typical eukaryotic gene and indicate the locations of (a) regions that are
genic but are not coding, (b) regions that are transcribed but not translated, and (c)
regions that are both transcribed and translated.
Describe the general organization, possible function, and frequency of genes and non-gene
DNA sequences in a typical eukaryotic genome.
Explain the functional significance of packaging DNA into chromosomes and the lack of
correlation between chromosome number and genetic information content.

3. Describe the mechanisms by which an organism’s genome is passed on to the next generation.
Define somatic and germline cells, and list similarities and differences between them.
Recognize why germline mutations can be passed onto the next generation, whereas somatic
mutations cannot.
Describe, using diagrams, the sequence of events involving DNA in meiosis from
chromosome duplication through chromosome segregation.
Describe the phenomena of linkage and independent assortment of alleles during
meiosis, and explain why some pairs of alleles exhibit linkage and others do not.
Explain how independent assortment can lead to new combinations of alleles of unlinked
genes.
Diagram the process of homologous recombination during meiosis and explain how it can
lead to new combinations of linked alleles.
Explain how a specific combination of linked alleles (haplotype) can persist through
many generations.

4. Extract information about genes, alleles, and gene functions from genetic crosses and human
pedigree analysis.
Design genetic crosses to provide information about genes, alleles, and gene functions.
Explain why it is advantageous to use true-breeding organisms in crosses.
Predict progeny genotypic frequencies given the genotypes of the parental gametes.
Identify an allele’s mode of inheritance from progeny phenotypes.
Place genes in a functional order based on the phenotypes of double mutants, and explain the
assumptions that must be made when interpreting these results.
Determine gene linkage and genetic map distances by analyzing progeny with
recombinant phenotypes.
Use statistical analysis to determine how well data from a genetic cross or human pedigree
analysis fits theoretical predictions.
Determine if two mutations affect the same gene using complementation tests, and explain
the requirements and the basis for interpreting results from these tests.

5. Describe the processes that can influence the frequency of alleles in a population.
Determine allele frequencies based on phenotypic data for a population in equilibrium.
Explain how natural selection and genetic drift can affect the elimination or maintenance of
deleterious alleles in a population.

6. Cite examples of gene dosage variation (ploidy), and explain why it affects phenotype.
Discuss why alterations in chromosome number can be detrimental.
Describe the process of X inactivation in mammals, and explain its function.

7. Compare different types of mutations and describe how each can affect genes, mRNA and
proteins.
Explain, using diagrams, how nucleotide changes result in the alteration of protein
activity.
Explain why some mutations do not affect protein structure or function.
Describe how deletions, inversions, translocations, and the movement of transpositional
elements can affect gene function, gene expression, and genetic recombination.
Describe how mutations arise and how environmental factors can increase mutation rate.
Cite examples of mutations that can be beneficial to organisms.
Explain why some DNA damage does not result in mutation.
Distinguish between a DNA replication error and a mutation.
Explain what is meant by a single-nucleotide polymorphism (SNP) and how SNPs can be
used as genetic markers even if they do not affect protein structure or function.

8. Explain the molecular basis at the protein level for allele types with different genetic behaviors.
Describe the differences between loss of function and gain of function mutations and their
potential phenotypic consequences.
Predict the most likely effects on protein structure and function of null, reduction-of-function,
overexpression, dominant-negative and gain-of-function mutations.

9. Justify the value of studying genetics in organisms other than humans.
Explain why it is useful to investigate functions of many human genes by studying simple
model organisms such as yeast, nematode worms, and fruit flies.
Describe the benefits and limitations of using model systems to study human diseases.
Use bioinformatic data to compare homologous genes in different species and infer relative
degrees of evolutionary relatedness.

10. Describe the steps that are taken to determine the molecular identity of a human gene that
when mutated can underlie a disease.
Use information from model organisms to identify candidate genes in humans.
Use pedigree information and DNA markers to track a disease trait in a family.
Explain, correctly apply, and interpret results from molecular genetic tools such as
DNA sequencing, SNP analysis, and microarrays.

 

MCDB 4650-Developmental Biology: Course Learning Goals                                                                   

Topics we expect you to be familiar with when you begin (at the level covered in Alberts et al., Molecular Biology of the Cell or equivalent):

  • molecular biology of eukaryotic gene expression; classes of transcription factors.
  • Eukaryotic protein synthesis and secretion.
  • Transmembrane signaling; classification of signaling pathways.
  • structure and function of: cellular components, extracellular matrix, epithelial and mesenchymal cells. 
  • The roles of cytoskeletal components in cell motility.
  • Mendelian genetics.
  • DNA markers.
  • mitosis and meiosis.
  • chromosome structure.
  • standard techniques of modern molecular biology [restriction digests, gel electrophoresis, Southern, "Northern" and "Western" blots, hybridization with nucleic acid probes, autoradiography, footprinting analysis, gel shift (EMSA) analysis, co-immunoprecipitation, making genomic and cDNA libraries, DNA sequencing, polymerase chain reaction (PCR), RNA interference]. 

What we expect you to be able to do when you finish:

  • Compare combinatorial control of transcription during development to combinatorial control of cell signaling during development.
  • Predict different mechanisms that could be responsible for control of gene expression in development.
  • Design experiments that would demonstrate the principles of cell fate, cell commitment (determination), and differentiation.
  • Compare the roles of different transmembrane signaling pathways in development
  • Discuss eukaryotic genome organization and information content. 
  • Justify the importance of "model organisms" in the study of development, and the advantageous biological features of C. elegans, Drosophila, Xenopus, chick, and mouse.
  • Compare the uses of forward and reverse genetics.
  • Explain fertilization and cleavage, and justify why cleavage is an important step in development.
  • Design experiments that would demonstrate the cell movements of gastrulation .
  • Evaluate experiments that demonstrate the establishment and patterning of axes in embryos.
  • Explain how the neural tube and the nervous system form and are patterned.
  • Interpret the effects of lateral inhibition in establishing neural fates.
  • Compare how vertebrates and invertebrates become segmented or divided into repeating units.
  • Explain how Hox genes control patterning along the anterior-posterior axis and in many developing organs.
  • Compare how different organ systems are established and patterned.
  • Explain the mechanisms of 1° and 2° sex determination, dosage compensation, and imprinting in vertebrates, and compare these processes to those in invertebrates.
  • Describe how transgenics, genomics, proteomics, and cultured stem cells can be used to study development, and be able to design experiments using these techniques.
  • Describe some of some major still unanswered questions in development.

Throughout the course we stress experimental approaches. We expect you to understand the evidence for what is known and the available methods for approaching what is unknown in modern developmental biology.  We also expect you to be able to read developmental biology papers in current journals and understand the methods and the evidence presented well enough to judge the validity of the conclusions. 

We hope you will achieve these non-content goals by the end of the course.  Be able to:

  1. Explain where the information in the textbooks comes from and judge how reliable it is.
  2. Describe how research is supported, done, communicated, evaluated, and validated or invalidated.
  3. Look at other sources beyond the textbook for additional information.
  4. Read a research paper in the current developmental biology literature.
  5. Gauge how much new understanding you have gained through this course.
  6. Verbalize how you learn best.