Graduate Concentration in Molecular Biology and Genetics: Comprehensive Exam Guidelines

Good sources for review of these topics are:

1. Molecular Biology of the Cell by Alberts et al. or Molecular Cell Biology by Lodish et al. (Textbooks used for BISC 401)
2. Genetics: From Genes to Genomes LH Hartwell, L Hood, ML Goldberg, AE Reynolds, LM Silver, RC Veres (Textbook for BISC 403)
3. Biochemistry by Garrett and Grisham (Textbook for CHEM 641)

Also, you may attend lectures in either BISC 401 or 403 this spring if you wish to prepare more formally.

Molecular Biology (BISC 401 and BISC 602)

Note sets which give more specific details of these topics are available from Dr. Simmons' BISC 401 web site. At the password box, type in your UDelNet ID and password.

• Molecular interactions and bioenergetics
• Amino acids, Protein structure and function
  

1. Classes of amino acids
   
2. Protein folds-motifs, domains, etc.
   
3. Examples and representations of protein 3D structure
   
4. Mechanisms of enzyme action
   

• The structure and chemistry of DNA and RNA
• Methods in molecular and cell biology

1. General methods
1. Gel electrophoresis
2. Sedimentation
3. Hybridization
4. Column chromatography and fractionations
5. Microscopy (e.g. Confocal)
2. Molecular methods
1. Cloning
2. Blotting (dot, Western, Southern, etc.)
3. PCR, sequencing and other nucleic acid methods
4. Microarray technology
5. Antisense and RNAi attenuation of gene expression
6. Methods for overexpression of genes in cells
7. Methods for protein production

• Genetic code and protein biosynthesis
  1. Initiation of protein synthesis in eukaryotes and prokaryotes
  2. Elongation of protein synthesis
  3. Redundancy in genetic code and base pair rules at Wobble position
• DNA replication

1. The replication fork
2. Initiation and elongation in bacteria, yeast, mammalian and virus systems
3. Replication and cell cycle regulation

• RNA synthesis and processing in eukaryotes

1. The general transcription machinery
2. Promoters and enhancers
3. Activators and repressors of transcription
4. Mediators, co-activators and co-repressors
5. Chromatin remodeling

• Control of gene expression

1. At transcription level
2. At postranscriptional level
3. At translational level

• Membrane Structure and Function

1. Basic structure and properties of lipid classes
2. Lipid Rafts and their function
3. GPI anchored proteins

• Synthesis of proteins on the ER membrane, modification, sorting and transport

1. The secretory pathway
2. Vesicular transport
3. Glycosylations and their role in protein structure and function

• Receptor mediated endocytosis and internalization of molecules
• The cell cycle and its regulation in yeast and mammalian cells

1. Cyclin kinase complexes
2. Polyubiquitination complexes

• Cell signaling

1. G protein coupled receptors
2. Tyrosine kinase receptors
3. Nuclear hormone receptors
4. Cytokine receptors

• Apoptosis
  • Intrinsic and extrinsic pathways
    
• Oncoproteins and tumor suppressors

Genetics (BISC 403 and BISC 654)

• Mendelian inheritance, dominant and recessive traits, co-dominance
• Pleiotropy and epistasis
• Phenotype versus genotype
• Quantitative traits, allele frequency and the definitive of "wildtype"
• Chromosome structure and function
• Meiosis, linkage, recombination
• DNA repair and mechanisms of mutation
• Genetic screens, purpose and methods
• Cloning vectors and the use of selectable markers
• Methods for cloning genes mutated in genetic screens
• Bacterial genetics and genetic engineering of bacteria

1. Conjugation, transduction, and transformation
1. Gene transfer - efficiency, uses, and difficulties
2. F-factor and F plasmid families
2. Insertion elements and how is transposition controlled in bacteria
1. Mapping genes using IS elements and three-point crosses

• Yeast as a model organism

1. Advantages and disadvantages
2. The structure of the genome
3. Design of genetic screens and cloning of mutant genes

• Drosophila as a model organism

1. Advantages and disadvantages
2. The genome and its unusual characteristics
3. Genetic manipulation
1. Balancer Chromosomes
2. Elements and transformation trans/cis effects
4. Ectopic expression and its use in genetics and gene discovery
   

• Mouse as a model organism

1. Advantages and disadvantages
2. Outbred and inbred mouse strains, mouse species definitions
3. Developmental pattern and at what stage can we do genetics?
1. Transgenic
2. Knock-out/knock-in

• Human genetics

1. What sort of biological questions can be asked in humans
2. Identification of disease causing genes in humans
1. Single gene mutation
2. Quantitative traits

• Evolution

1. Definition and proof that it occurs
2. Use of genetic models in its study
3. Similarity versus homology as concepts in gene and phenotypic evolution

Biochemistry (CHEM 641)

• Water, pH and ionic equilibrium
• Thermodynamics
• Amino acid structure
• Nucleic acid structure
• Membrane structure
• Protein structure and its control
• Enzyme regulation, specificity, mechanisms and kinetics
• Molecular motors
• Basic metabolism/energetics