S. BIS101 O'Neill I.
Genes and Gene Expression - Outline
page 1
Introduction A. B. C. D. E. F. G. H. I. Genetics Gene Central dogma Genotype and phenotype Genetic variation Environment- gene interaction Gene networks and Systems Biology Epigenetics/Epigenomics Genomics
II.
Mendelian Genetics (handouts #1 & 2) A. B. Mendel's experimental design (handout #1) Principle of segregation 1. 2. C. Monohybrid cross Test cross
Principle of independent assortment 1. Probability a. b. 2. 3. Product rule Sum rule
Dihybrid cross Calculating genetic ratios
D.
Mendelian genetics in humans 1. Pedigree analysis a. b. c. Recessive traits Dominant traits Two examples: handout #3
BIS101 S. O'Neill III.
Genes and Gene Expression - Outline
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Chromosomal Basis of Inheritance A. Mitosis and meiosis 1. 2. 3. 4. 5. 6. Chromosome complement of eukaryotes Asexual/sexual reproduction Cell cycle Stages of mitosis (handout #4) Stages of meiosis (handout #5) Genetic significance of mitosis and meiosis
B.
Sex-linked traits 1. Sex chromosomes a. b. 2. Drosophila Human
Sex linkage a. b. Defined Reciprocal cross
3.
Sex determination a. b. Drosophila Humans i. ii. Y chromosome mechanism X chromosome inactivationdosage compensation
4.
Sex-linked traits in humans a. b. c. X-linked recessive X-linked dominant Y-linked
BIS101 S. O'Neill IV.
Genes and Gene Expression - Outline
page 3
Mendelian Extensions A. Multiple alleles 1. 2. Drosophila eye color ABO blood groups
B.
Modifications of dominance relationships 1. Incomplete dominance a. 2. Snapdragon flower color b.
Codominance
C.
Gene interactions (modified Mendelian ratios) 1. 2. New phenotypes-comb shape in chickens Epistasis a. b. recessive epistasis duplicate recessive epistasis -complementary gene action
D.
Essential genes and lethal alleles 1. 2. 3. Dominant lethal allele Recessive lethal allele Pleiotropic genes
E.
Penetrance and expressivity
BIS101 S. O'Neill V.
Genes and Gene Expression - Outline
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Genetic Linkage/Recombination/Mapping A. Linkage
B.
Recombination 1. Result of crossing over during meiosis a. b. 2. Input/output genotypes Parent/recombinant products of meiosis
Two-point test cross (handout #6)
C.
Genetic map 1. 2. Recombination frequency Map units
D.
Three-point test cross (handout #7) 1. 2. 3. 4. Single and double crossovers Gene order Coefficient of coincidence/interference Map units are additive
E.
Tetrad analysis 1. Life cycle of Neurospora a. b. 2. 3. Asexual reproduction Sexual reproduction
Ordered versus unordered tetrads Cross (handout #8)
BIS101 S. O'Neill F.
Genes and Gene Expression - Outline
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Mapping genes in human chromosomes 1. 2. X chromosome linkage (handout #9) Somatic cell hybridization technique
VI.
Chromosomal Mutations A. Structural aberrations 1. 2. 3. 4. Deletion Duplication Inversion Translocation
B.
Numerical aberrations 1. 2. Aneuploidy-nondisjunction (handouts #10 and #11) Polyploidy
BIS101 S. O'Neill VII.
Genes and Gene Expression - Outline
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Genetic Analysis of Bacteria A. Genotype analysis 1. 2. 3. Lethal and conditional mutants Auxotrophs and prototrophs Replica plating (handout #12)
B.
Transformation
C.
Conjugation 1. 2. 3. 4. F factor Hfr strains Interrupted mating Hfr X Fgene order (handout #13) map distances in recombination units 5. F' : partial diploid
D.
Transduction 1. 2. 3. 4. Bacteriophage structure Life cycle of virulent phage (handout #14) Generalized transduction Mapping-cotransduction (handout #15)
BIS101 S. O'Neill
Genes and Gene Expression - Outline
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Note: we may skip the next section if we are running behind schedule. Thus there will be no time to cover this information in class.
VIII. Genetic Analysis in A. Bacteriophages Phage growth and markers
B.
Benzer experiments 1. 2. 3. 4. Recombination analysis Deletion mapping Complementation Complementation vs. Recombination
BIS101 S. O'Neill IX.
Genes and Gene Expression - Outline
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Genes as Functional Units A. Protein structure/function
B.
Genetic dissection of biochemical pathway (handout #16)
C.
Complementation 1. 2. Flower color Drosophila body color
X.
Genetic Material-DNA and RNA A. DNA as genetic material 1. 2. 3. Griffith experiment Avery, MacLeod, and McCarty experiment Hershey and Chase experiment
B.
Chemical composition of DNA/RNA 1. 2. Nucleotides (handout #17) Phosphodiester bond (handout #18)
C.
Double Helix Model 1. 2. 3. 4. X-ray diffraction (Franklin and Wilkens) (handout #19) Chargaff's rules (handout #19) Base pairing (handout #20) Watson and Crick model (handout #19)
D.
RNA structure
BIS101 S. O'Neill XI.
Genes and Gene Expression - Outline
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Chromosome Structure A. Prokaryotes
B.
Eukaryotes 1. 2. 3. Nucleosomes 30 nm chromatin fiber Nuclear scaffold
XII.
DNA Replication A. Semiconservative model
B.
Replication in E. coli Overview (handout #21) 1. 2. 3. 4. 5. 6. 7. Origin of replication Denaturation of double helix Stabilization of DNA in replication fork Initiation of synthesis Elongation Joining of Okazaki fragments Proofreading
C.
Rolling circle replication (handout #22)
D.
Replication in eukaryotes (animations) 1. 2. Replicons Chromosome ends; telomerase (handout #23)
BIS101 S. O'Neill
Genes and Gene Expression - Outline
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XIII. Molecular Recombination A. Holliday Model (handout #24 and animations) 1. 2. 3. 4. 5. Single strand break Strand invasion Heteroduplex DNA Branch migration Resolution
B.
Gene conversion and mismatch repair (handout #25 and animations)
XIV. Transcription A. Introduction
B.
Prokaryotes (E. coli) 1. 2. 3. Initiation Elongation Termination a. b. rho dependent rho independent
C.
Eukaryotes (animations) 1. 2. 3. Multiple polymerases Transcription factors Posttransciptional modification (mRNA) a. b. 5' cap (handout #26) 3' poly(A) tail (handout #26)
BIS101 S. O'Neill
Genes and Gene Expression - Outline
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c. 4. tRNA a. b.
Splicing
Structure/function Post transcriptional modification
XV. Genetic Code and Translation A. Genetic code 1. 2. 3. Codons Wobble hypothesis Suppressor mutations a. b. Frameshift mutation Nonsense suppressor mutation
B.
Protein synthesis 1. 2. 3. 4. 5. Ribosome structure/function (handout #27) Activation of amino acids (handout #28) Initiation (handout #28) Elongation (handout #28) Termination (handout #28)
BIS101 S. O'Neill
Genes and Gene Expression - Outline
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XVI. Regulation of Gene Expression A. Prokaryotes 1. Iac operon a. b. Negative control Positive control
B.
Eukaryotes 1. 2. Comparison with prokaryotes Levels of regulation (handout #30) a. b. c. d. e. f. 3. 4. Transcription RNA processing mRNA transport mRNA translation RNA degradation Protein degradation
The GAL system in yeast Chromatin a. Chromatin remodeling b. The histone code c. Epigenetic marks
5.
Gene silencing a. RNA interference
BIS101 S. O'Neill
Genes and Gene Expression - Outline
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XVII. Recombination DNA Technology A. Polymerase chain reaction (PCR) 1. End-point PCR 2. Real Time PCR
B. Analysis of genes 1. Nucleic acid hybridization (done in week one)
C.
DNA sequencing 1. Sanger sequencing (handout #31) 2. Next Generation Sequencing
XVIII. Genomic Analysis A. Genomics overview
B.
Genome Projects 1. 2. 3. Microbial Plant Animal
C.
Human Genome Project 1. 2. Online Mendelian Inheritance in Man (OMIM) Human HapMap Project
D.
Predictive, preventive and personalized medicine. 1. Nutritional Genomics.