Part I.          Genomics - The New Genetics

Part II.         Classical Mendelian Genetics

    Part IIa.     Classical Genetics

    Part IIb.     Genetic Linkage

Part III.        Chromosomes

Part IV.        Population and Quantitative Genetics

Part V.       Molecular Genetics and Mutagenesis

A: The Science of Genetics.

1. Genetics is a scientific subdiscipline of Biology
2. The Scientific Method uses:   Observation - Hypothesis - Experimentation.
3. The scientific goal is to determine the "Truth" of the Natural World.
4. Inheritance of traits is the major theme of Genetics
5. Genotypes and Phenotypes are the major scientific concepts in Genetics.

B: Genomes.

1. Each biological species has a unique genome.
2. A genome is all of the genetic information contained within the cell or organism.
3. DNA is the organic molecule that contains the genetic information
4. DNA is linear, digital information. 
5. The Genetic Code is the language of life.
6. Genomes are analyzed and understood using the tools of Bioinformatics

C: Functional Genomics.

1. Functional genomics is the expression of genetic information.
2. The Central Dogma describes of flow of biological information: DNA -> RNA -> Protein.
3. The linear DNA information is expressed in 3-demensions in the form of proteins.
4. Proteins are responsible for Biochemistry and Cellular life.
5. RNA is the intermediary "Master Control" molecule in the cell.
6. The expression of RNA is central to the concept of a "Gene".
7. DNA is the Genotype.
8. Proteins are the Phenotype.
9. RNA is the bridge between DNA/genotype and protein/phenotype.

D: Molecular Biotechnology

1. Molecular Biology has explained how genetic information "works"
2. Replication -Transcription - Translation - Protein folding.
3. Molecular mutagenesis explains genetic variation.
4. Genetic Engineering (Recombinant DNA) allows us to manipulate genetic information.
5. Biotechnology industry is still relatively young.
6. Cloning technology is beginning to "come on line".
7. Microarray technology allows us to profile global gene expression patterns.
8. Forensic profiling, Biowarfare potential, and Genetic disease prediction.
9. Ethical and moral problems with manipulating genetic information.

A: Gregor Mendel and Model Systems.

1. Pre-Mendelian theories suggest that "Blending" was responsible for inheritance.
2. Gregor Mendel published the first accurate and quantitative work on inheritance in 1866.
3. Model systems are key to the study of genetics:  variations - generation time - low cost.
4. E. coli - Yeast - C. elegans - Drosophila - Zebrafish - Mouse - Arabidopsis.
5. The study of Human health and disease has established many genetic concepts.
6. Mendel's model system was the pea plant: seven (7) phenotypes.
7. Each phenotype is characterized as a trait.
8. True Breeding populations (strains, types, purebreds) express only that trait.
9. Different types (or flavors) of a trait are called Alleles.
10. A Monohybrid cross is the mating of two parents of different trait types (alleles).
11. The progeny (babies) are the F1 generation.  Mating of the F1's results in the F2 generation.
12.   Principle of Segregation:  genotype is composed of two alleles that separate (Aa -> A or a).
13. Homozygote is (AA or aa).  Heterozygote is (Aa). 
14. Alleles behave quantitatively and show Dominant and Recessive characteristics.
15. The Punnett Square technique allows us to model the genotypes of a genetic cross.
16. 3:1 ratio of phenotypes (dominant : recessive) in F2 progeny from a F1 heterozygote cross.
17. The Gene is the unit of inheritance.
18. A Testcross is a mating with a homozygote recessive and is used to determine genotype.
19. Backcross is a mating with a parent.
20. A wild type phenotype is the most common phenotype in a population (not always dominant).

B: The Dihybrid Cross and Mendelian Deviations.

1. A Dihybrid cross contains two (2) traits that differ in the parental generation.
2. New combinations of phenotypes that were not present in parental generation.
3. 9:3:3:1 combination of traits in F2 from a F1 dihybrid heterozygote cross.
4. Principle of Independent Assortment:  genes assort independently from each other.
5. Trihybrid cross: three (3) different traits, use cross-line method of genotype modeling.
6. Multiple alleles: more than two gene types, eg ABO blood system.
7. Codominance:  both parental genotypes (alleles) are expressed equally in heterozygotes.
8. Incomplete dominance:  partial expression of each phenotype in heterozygotes.
9. Pleiotropy:  more than one distinct phenotype is expressed from a unique genotype.
10. Epistasis:  more than one gene is responsible for a particular phenotype (trait).
11. Variable Expressivity:  genes are expressed at different degrees in different individuals.
12. Penetrance:  phenotype is not always expressed even though individual has genotype.
13. Complementation Test is used to determine how many different genes code for phenotype.
14. Generate a matrix of all recessive mating to calculate the number of complementation groups.

C: Pedigree Analysis and Genetic Probability.

1. Most animals cannot be used as model genetic systems (eg, humans, dogs, cattle).
2. The study of inheritance in these species requires a visual tree of descendants.
3. Rules for Pedigree analysis:  generations - individuals - mating - births - symbols.
4. Probability:  number of occurrences / total number of possible outcomes.
5. Addition rule:  the probability (%) of mutually exclusive events is the sum of each event %.
6. Multiplication rule:  the probability of 2 or more independent events is the product of each %.
7. Predictions in pedigree analysis combine the Addition and Multiplication rules.
8. Since many life forms are diploid, use a binomial probability (2ⁿ⁾ to model genetic crosses.
9. A coin toss (heads or tails = A or a), is useful to model segregation of alleles in mating.
10. Binomial Distribution:  (p + q)ⁿ   eg. N =3   (p + q)³  =  p³ + 3(p + q)² + 3(p + q)² + q³
11. To determine coefficients in binomial distribution use: Pascal's Triangle or Factorial method.
12. Chi Square analysis is used to estimate the quality of the data fit to a specific hypothesis.
13. A Probability value (P-value) of less than 5/100 (<0.05) results in a rejection of the hypothesis.
14. Use Chi square table, determine degrees of freedom, solve for the c² value, calculate P-value.
15. Chi square equation: 

D: Life Cycles, Meiosis, Genetic Recombination and Linkage.

1. The life cycle of each diploid life form contains a stage of chromosome reduction (Meiosis).
2. Chromosomes carry the genetic information from generation to generation.
3. Sexually mature adult - gametogenesis - fertilization - zygote - somatic development.
4. The Cell cycle:  (G⁰) Interphase [2n] (Gap1 -> Synthesis [4n] -> Gap2) -> Mitosis [2 x 2n].
5. Mitosis:  (Prophase -> Metaphase -> Anaphase -> Telophase)  -> Cytokinesis.
6. Meiosis: [2n] -> [4n] -> [2 x 2n] -> [4 x n].
7. Prophase I of meiosis genetic recombination occurs: sister chromatids, tetrads, crossing over.
8. Leptotene ->  Zygotene -> Pachytene -> Diplotene -> Diakinesis.
9. Sex determination is based on chromosome type, ratio, or environmental conditions.
10. Humans use X and Y,  Drosophila uses autosome #: X,  reptiles use temperature.
11. Phenotypes linked to genes on sex chromosomes have altered inheritance patterns.
12. Human males are haploid for X-linked genes.  X-linked traits often skip a generation!
13. Genetic linkage between two genes when they are inherited at greater than 50% frequency.
14. If genes assort independently (= 50% frequency) then they are NOT linked.
15. Recombination frequency (RF%) calculation: number of recombinants / total number  x  100.
16. Recombination frequency is related to the distance between genes on the same chromosome.
17. One percent (1%) recombination frequency is equal to 1 centimorgan (1cM) or map unit.
18. Genetic map units are related to physical distance on chromosomes:  1 cM = ~ 10⁶ base pairs.
19. Multiple crossing over between homologous chromosomes prevents recombination % >50%.
20. Genetic maps can be generated for each chromosome by calculating recombination frequency.
21. Each gene has a position or locus (plural = loci) on a particular chromosome.
22. The Three-Point testcross is used to generate RF% and relative position.
23. Method: parental genotype = highest RF%, double-crossover = gene in middle = lowest RF%.
24. Finish Three-Point testcross by calculating the RF% for each of the outside genes.
25. Genetic Interference is the lower percentage of double crossovers compared to expected.
26. Genetic recombination is very rare in mitotic cell division.  X and Y chromosomal differences.
27. Tetrad Analysis is a technique for genetic mapping in certain fungi species.
28. During meiosis, these fungi generate ascospores that contain individual haploid cells.
29. Measure First division and Second division segregation patterns.
30. Determine gene distance from centromere. Calculation:  RF = 0.5 x 2^nd Division patterns  x 100

                                                                                                                  total number of patterns

E: Chromosome Structure and Abnormalities.

1. Genomes are organized into structures called Chromosomes (single to hundreds).
2. Chromosomes are organized into Genetic maps (cM, map units) and Physical maps (bp).
3. Molecular structure differs between Prokaryotes and Eukaryotes.
4. Bacterial chromosomes are supercoiled and folded into loops (domains).
5. Eukaryotic chromosomes are "relatively" unorganized in Interphase.
6. During Metaphase, chromosomes become highly condensed. (1 meter into 10 mm)
7. Chromatin (nucleic acid and protein) is organized into Euchromatin or Heterochromatin.
8. Nucleosomes are the first level of condensation ("beads on a string").
9. Histone octamer contains highly conserved cationic amino acids (core = 145-160 bp).
10. Histone H1 is more variable and connects beads by a linker (20 - 100 bp).
11. Nucleosomes are organized in a helical structure called the 30 nm fiber or solenoid.
12. Domains are larger regions of folded chromatin.  Has functional organization.
13. Chromosome structures include; centromere, telomere (TTAGGG), arms (p and q).
14. Sequence organization; highly repetitive, moderate repetitive, unique DNA sequence.
15. DNA hybridization kinetics gives sequence annealing profiles.  Cot-curves.
16. Transposable elements (jumping genes) can expand in genomes (LINES, SINES).
17. Polytene (giant) chromosomes in Drosophila allow for easy gene mapping.
18. Cytogenetics is the study of abnormal chromosomal structure and numbers.
19. Karyotype is a microscopic visualization of stained metaphase chromosomes (FISH).
20. Chromosome structure can change by; Deletion, Addition, Inversion, Translocation.
21. Reciprocal translocations are balanced, Robertsonian translocations fuse centromeres.
22. Loss of Heterozygosity (LOH) is the deletion of a chromosomal segment (cancer).
23. Philadelphia chromosome: reciprocal translocation ch22 to ch9, results in CML.
24. Chromosome numbers are counted as autosomes and sex chromosomes.
25. Most animals are diploid, some monoploid (male bees).
26. An increase in complete chromosome sets is called Polyploidy.
27. Many plants are polyploid (tetraploid = 4X).  Triploids are sterile (bananas and oysters).
28. Polysomy and monosomy is due to the gain or loss of a single chromosome.
29. In humans monosomy is lethal and polysomy is very harmful (eg. Trisomy 21).
30. Chromosomal nondisjunction during meiosis is responsible for poly/monosomy.
31. The age of the mothers oocytes is correlated to frequency of polysomy.
32. The X chromosome experiences dosage compensation due to X-inactivation.
33. Sex chromosomes abnormalities are more common (XO, Turners syndrome).
34. Mosaic phenotypes (Lyonization) is due to X-inactivation.  (eg. Calico cat).

A: Population Genetics.

1. Population genetics is the study of the extent and pattern of genetic variation in a population.
2. A population is a geographically constrained group of individuals of the same species.
3. The individuals in a population are able to mate with one another.
4. The Gene Pool is all of the genes and alleles in a population.
5. A Polymorphism is an allele different from wild type that is relatively frequent (~5%).
6. Genetic variation is calculated by genotypic frequency (Aa) and allelic frequency (A or a).
7. Allele frequency is measured by; phenotype, allozymes (proteins), DNA (SNP, STR, RFLP).
8. Mating strategies; Random (gamete dispersal), Assortive (positive and negative), Inbreeding.
9. Hardy-Weinberg Principle; allele frequencies will NOT change from generation to generation
10. if;  Random mating, No selection, No mutation, No migration, Large population (no drift).
11. Hardy-Weinberg equation: p + q = 1,   p² + 2pq +q² =1,   where p² = AA, 2pq = Aa, q² = aa.
12. Rare recessive alleles are much more frequent in heterozygotes than in homozygotes.
13. Rare alleles on sex chromosomes (X) are expressed in males (haploid) more frequently.
14. Inbreeding generates more homozygotes (reduction in heterozygosity).  "Identical by descent".
15. Inbreeding coefficient (F):   F = 1 Ð H/2pq    H = # of heterozygotes. Total inbreeding F = 1.

B: Evolution.

1. Evolution is the changes in the population gene pool resulting in adaptation to the environment.
2. Evolution occurs over relatively long time periods punctuated by rapid periods of change.
3. Charles Darwin's "Origin of the Species" in 1859 set the foundation for modern biology.
4. Natural Selection favors individuals who survive and reproduce under prevailing conditions.
5. "Biological Fitness":  overall fitness of an organism = Viability and Fertility.
6. In any generation many more offspring are produced that can survive and reproduce.
7. Individual organisms differ (genotypes) in their ability to survive and reproduce.
8. Organisms that do reproduce pass their genetic information to progeny at higher frequency.
9. Selection against very rare recessive alleles is very inefficient (most are heterozygotes).
10. Heterozygote superiority can increase the frequency of a negative allele in the population.
11. Mutation is the spontaneous or induced heritable change in the DNA sequence (gene).
12. Mutations can be Neutral (neither good or bad), Negative, and Positive (least likely).
13. Selection - Mutation Balance explains the frequency of negative alleles in a population.
14. Migration is the movement of individuals from one population to another.
15. Migration is important in introducing new alleles into a population.
16. Genetic Drift concerns the changes in allele frequency due to small mating populations.
17. Alleles become "fixed" due to random sampling of gametes in small populations.

C: Quantitative Genetics.

1. Most phenotypes are due to complex interactions between genes and the environment.
2. Multifactorial genetic interactions are best studied using a quantitative approach to genetics.
3. Types of traits:  Continuous, Meristic (counting), and Threshold.   "QTL's".
4. Almost any biological trait can be quantified:  intelligence, ability, physical trait, etc.
5. Method:  Determine the Distribution of the trait in a population sample (Normal distribution).
6. Calculate the mean (average x) value for the trait in question.  Median value is the midpoint.
7. Determine the Variance (spread of the distribution) and calculate the square root of variance.
8. The square root of the variance is the Standard Deviation: 1SD = 68%, 2SD = 95%, 3SD =99%
9. In a normal distribution the phenotypes cluster around the mean.  "Mutants = > 3 SD's" ????
10. Artificial Selection involves the selection of specific parents for the next generation.
11. Generate some type of quantitative parameter to select parents (Truncation point).
12. Continue selection process until no further increase in phenotype (Selection Limit).
13. Selection limit can be due to fixation of all "good" alleles or to a decrease in fitness.
14. Inbreeding depression occurs when bad alleles become prevalent in selected population.
15. Heterosis (hybrid vigor) is when different types of inbreed parents produce superior offspring.
16. Quantitative estimate of Artificial Selection is the Narrow Sense Heritability (h²).
17. Narrow Sense Heritability is the phenotypic variance due to genotype: h² = M' - M/M* - M.
18. Twin Studies use Identical and Fraternal twins to study environmental effects on genotypes.
19. Broad Sense Heritability is the genetic variation related to the environment.
20. Broad Sense Heritability  H² =  S²g (genetic)

A: DNA as Genetic Information.

1. Deoxyribonucleic acid is a long organic polymer made up of nucleotide subunits.
2. Discovery of DNA: Meischer (1869), Griffith (1928), Avery (1944), Hershey-Chase (1952).
3. The molecular structure of DNA discovered by Watson and Crick (1953).
4. DNA is a polar (5'-> 3'), usually double-stranded, complementary and antiparallel helix.
5. Hydrogen bonding between (guanine-cytosine) and (adenine-thymine) results in base pairs.
6. DNA can form different physical structures: circular, linear, supercoiling, B-DNA, Z-DNA.
7. Genetic information is carried in the sequence of base pairs in DNA.  4ⁿ possible sequences!
8. DNA is like digital information in that a string of O's and 1's are bits and bytes.
9. Genetic information must: Replicate, control cell organization, be able to change (evolution).
10. All cellular life forms use DNA as the information molecule.  Viruses use DNA or RNA.

B: DNA Replication.

1. Replication occurs in a bidirectional manner after priming by small RNA oligonucleotides.
2. The Meselson-Stahl experiment (1958) showed that DNA replication is semi-conservative.
3. DNA synthesis is performed by DNA polymerase (bacteria = 1000bp/sec.) (eukary.=50bp/sec.)
4. Essential components: DNA polymerase, DNA template, nucleotide primer, dNTP's.
5. The polymerase chain reaction (PCR) amplification: Denaturation - Annealing - Synthesis.
6. In the cell DNA replication begins at an Origin of replication (bacteria =1) (eukary. = many).
7. Replication fork: Helicase, Topoisomerase, SSB, Primosome, DNA polymerase 5' -> 3'.
8. Leading and Lagging strands: Okazaki fragments, Nuclease, DNA polymerase, DNA ligase.

C: Mutagenesis and DNA Repair.

1. A mutation is a heritable change in the genetic material.  Germ line or Somatic cells.
2. Mutation types: Spontaneous occur during DNA replication. Induced caused by DNA damage.
3. Base substitution mutations: Transition (eg. C -> T) and Tranversion (eg. C -> A).
4. Single base changes can result in Misense, Nonsense and Silent mutations.
5. Insertions and Deletions (Indels) are caused by replication, repair or Transposable elements.
6. Frameshift mutations are caused by deletion or addition (non-3) of nucleotides within an ORF.
7. Spontaneous mutation rates differ in prokaryotes (~ 1 in 10⁶) and eukaryotes (~ 1 in 10⁹) bp.
8. The fidelity of DNA replication is based on: Base paring, Proofreading, Mismatch repair.
9. Mutation "hot spots" occur in DNA that is prone to mutation. Eg. Repeated sequences.
10. Trinucleotide repeats are important to some Genetic diseases (eg. Huntington disease).
11. Induced mutations are grouped by the type of chemical agent or environmental exposure.
12. Types: nucleotide base analogs, chemically reactive compounds, intercalators, radiation.
13. The Ames Test is used to screen for mutagenic compounds.  Not a carcinogenic screen!
14. Cells have sophisticated DNA repair systems to deal with spontaneous and induced mutations.
15. Mismatch repair uses the methylation status of the parental DNA stand to correct errors.
16. UV light causes pyrimidine dimers to form. Photoreactivation reverts damage to normal.
17. Excision repair is a general mechanism to remove damaged bases. 
18. SOS repair is an error prone repair system that bacteria use with excessive DNA damage.
19. DNA recombination is a important tool for repairing damaged DNA.  Gene conversion.
20. Reversion of mutations occur by direct reversion or suppressor mutations (eg. tRNA^amber).

D: Gene Expression.

1. Global gene expression patterns are the "Symphony of Life".  Genes are the notes!
2. Flow of genetic information is: DNA -> RNA -> Protein.  Genotype -> Phenotype.
3. What is a gene?   An Open Reading Frame (ORF) codes for a polypeptide.
4. Some genes code for structural or regulatory functional RNAs. (rRNA, tRNA, iRNA).
5. A typical prokaryotic gene: promoter - ribosome binding site - ORF - terminator.
6. Eukaryotic genes are often split into Exons and Introns.  Much longer than transcript (mRNA).
7. Messenger RNA (mRNA) has polarity: 5'-> 3'.  DNA can be transcribed in 6 possible frames.
8. Transcription is organized by: Initiation, Elongation, and Termination.
9. Transcription begins by RNA polymerase binding to a gene Promoter.
10. A RNA copy of the DNA is made from the template or non-coding strand.
11. Termination occurs when a stem-loop structure forms on the growing RNA transcript.
12. In prokaryotes, transcription and translation are often coupled.  Rapid protein production.
13. Eukaryotes have a more complex transcription machinery.  RNA processing occurs in nucleus.
14. RNA processing includes: splicing of exons, capping of 5' nucleotide, poly-A tail at 3' end.
15. Control of gene expression is primarily at the level of transcription (to make mRNA).
16. Promoter binding strength and transcription factors regulate mRNA synthesis.
17. Negative regulation (repressors), Positive regulation (activators). Prokaryotic = operator.
18. In eukaryotes gene regulation DNA signals (cis acting elements) are enhancers and silencers.
19. Eukaryotic gene expression control is very complicated.  Domains and gene networks.
20. The lactose (lac) operon is a good model system to study gene expression in prokaryotes.

E: The Genetic Code and Protein Synthesis

1. The final step of the Central Dogma is to decode the RNA information into Proteins.
2. The Genetic Code is universal ("almost") and uses 3 nucleotide codons for each amino acid.
3. An ORF is defined by the start codon (ATG) and a stop codon (TAA, TAG, TGA).
4. The Genetic Code is degenerate in that multiple codons can code for the same amino acid.
5. Transfer RNA (tRNA) is the bridge between mRNA and protein.
6. Each class of tRNAs are charged with the correct amino acid by Aminoacyl tRNA Synthetase.
7. Translation uses a protein synthesizing molecular machine called a Ribosome.
8. Ribosomes are made of two subunits (large and small) and contain rRNA and many proteins.
9. Translation proceeds by: Initiation, Elongation, and Termination.
10. Numerous protein co-factors are used in the different steps of Translation.  (Eg. EF-Tu).
11. mRNA is translated in the 5'-> 3' direction with no gaps in the Open Reading Frame.
12. The nascent polypeptide must fold into the correct 3D structure to be functional.
13. Protein structure is based on: Primary, Secondary, Tertiary, Quaternary levels of organization.
14. Protein folding is based on thermodynamic properties and active processes (Chaperones).
15. Post-Translation modification must occur for many proteins to be functional.
16. Disulfide bonds, glycosylation (sugar), and phosphate attachment (kinases) are most common.
17. Phenotypes are changed by changing the structure and/or function of Proteins.