Review for Genetics Lab final

Protein Sequence vs Nucleotide Sequence

• Students often confuse nucleotide sequences with protein sequences.
• Protein BLAST (Basic Local Alignment Search Tool) is used for comparing sequences.

Using Protein BLAST

• Input the protein sequence into the central window of Protein BLAST.
• Utilize the reference proteins database, specifically the "RefSeq Proteins" database for accurate results.
• Leaving the organism input blank allows comparison against all known sequences, albeit a longer processing time.

Fly Base Introduction

• The FlyBase database offers user-friendly access to genetic information.
• Example Gene: "Lozenge" (lz)
• Defined as a transcription factor.
• Part of the RAD-related transcription factor family, crucial for eukaryotic gene expression regulation.

Gene Information

• Location is significant: For the lozenge gene in Drosophila, it is X-linked on chromosome 1.
• Genetic linkage is central to Mendelian inheritance.
• Two linked genes will recombine less likely than unlinked genes.
• Map units indicate distance between genes on chromosomes; e.g. genes 10 map units apart equate to a 10% recombination frequency.

Understanding Genetic Mapping

• To find distance between genes:
• Formula: \text{Distance} = \frac{\text{Number of Recombinants}}{\text{Total Offspring}} \times 100
• Test cross analysis helps visualize potential offspring phenotypes.
• Parentals: Original phenotypes, Recombinants: New phenotypes resulting from crossover.

Phenotype and Genotype Relationship

• Utilize correct genotyping for accurate predictions: e.g. upper case for dominant traits.
• Example for the taster phenotype:
• Dominant (T) for taster, recessive (t) for non-taster.

Searching with BLAST

• Returning results from BLAST requires proper identification of gene names as presented in results, including percentage of amino acid identity.
• Finding orthologs (genes in different species) and paralogs (genes within the same species) is crucial in evolutionary studies.

Alternative Splicing

• Genes like lozenge can produce multiple isoforms through alternative splicing, altering protein function.
• Example: Lozenge has two isoforms due to splicing differences.

Population Genetics

• Understand key definitions and formulas for allele frequencies within populations.
• Example: Hardy-Weinberg equilibrium where p + q = 1 ; and p^2 + 2pq + q^2 = 1 for genotype frequencies.

Tetrad Analysis

• Yeast tetrad analysis provides insight into meiotic events. Important for understanding genetic recombination.

Summary of Mendelian Genetics

• Knowledge of genetic linkage, gene mapping, and gene function is essential for genetic predictions and experiments.
• Proper notation is crucial for clarity in genetic crosses and predictions.