Genetics Terminology

Terminology

• Phenotype refers to any measurable characteristic or distinctive trait possessed by an organism.
• Genotype constitutes all of the genes possessed by an individual.
• Pure line is a group of individuals with similar genetic backgrounds, produced by self-fertilization or mating closely related individuals for many generations.
• Homozygous is produced by the union of gametes carrying identical alleles, where a homozygote produces only one kind of gamete.
• Heterozygous is produced by the union of gametes carrying different alleles.
• Recessive factor can come to phenotypic expression only in a homozygous genotype.
• Dominant factor can phenotypically express itself in the heterozygote as well as in the homozygote.

Mendel's First Law: Law of Segregation

• Members of a pair of factors segregate from each other during the formation of sex cells in an individual.

Complete Dominance

• An allele can phenotypically express itself in the heterozygote as well as in the homozygote.
• Upper letters designate the dominant and lowercase letters the recessive alleles.
• As an example, the presence of red is dominant to white.
• One allele masks the effect of another completely.
• For the first filial, F1 generation of the parents RR and rr, the offspring produce Rr that are red.
• The second filial, F2 generation produces: RR (red), Rr (red), Rr (red), and rr (white).
• There are two gametes.
• There are two phenotypes.
• There are three genotypes.
• Phenotypic ratio is ¼ red : ¼ white.
• Genotypic ratio is ¼ AA: ¼ Aa : ¼ aa.

Testcross

• A testcross distinguishes between homozygous dominant and heterozygous individuals (since they both have the same phenotype).
• In a testcross, the unknown individual is mated to a homozygous recessive individual.
• A testcross of Rr X rr produces ½ Rr (red) : ½ rr (white).

Incomplete Dominance

• An allele does not completely mask the other one, so the heterozygous phenotype is an intermediate character of both homozygous phenotypes.
• For example, plumage color in chickens.
• Black (BB) crossed with white (bb) parents results in a gray (Bb) F1 generation.
• An F2 generation produces BB (black), Bb (gray), Bb (gray), and bb (white).
• There are two gametes.
• There are three genotypes.
• There are three phenotype.
• Phenotypic ratio = ¼: ¼: ¼.
• Genotypic ratio = ¼: ¼: ¼.

Codominance

• Both alleles express their phenotype in heterozygous individuals.
• For example, cattle coat color.
• Red (CRCR) crossed with white (CWCW) parents results in roan (CRCW mixture of red and white) F1 generation.
• An F2 generation produces CRCR (red), CRCW (roan mixture of red and white), CRCW (roan mixture of red and white), and CWCW (white).
• There are two gametes.
• There are three genotypes.
• There are three phenotype.
• Phenotypic ratio = ¼: ¼: ¼.
• Genotypic ratio = ¼: ¼: ¼.

Lethal Alleles

• These genes cause the death of homozygous individuals.
• Recessive lethal occurs when the homozygous is lethal.

Recessive lethal with dominant phenotype

• For example, yellow coat color in mice.
• Yy crossed with Yy parents results in YY (die), Yy (yellow), Yy (yellow), and yy (agouti).
• There are two gametes.
• There are two genotypes.
• There are two phenotype.
• The phenotypic ratio = 2/3: 1/3.
• The genotypic ratio = 2/3 : 1/3.

Recessive lethal with recessive phenotype

• For example, sickle cell anemia.
• Ss crossed with Ss parents results in SS (normal), Ss (carrier), ss, (die).
• SS is found 1/3 of the time.
• Ss is found 1/3 of the time.

Multiple Alleles

• Genes have more than two alleles, however only two express the diploid number in an individual.
• Multiple alleles are expressed in the population.
• Number of genotypes = n (n+1) / 2.
• Number of heterozygous genotype = n (n-1) / 2.
• Number of homozygous genotype = n, where n = number of alleles.
• A multiple allelic series is ((A>B > C > D> E > F)) .
• The number of of genotypes = n (n+1) / 2 = 6 (6+1) / 2 = 21.
• The number of heterozygous genotype = n (n-1) / 2 = 6 (6-1) / 2 =15.
• The number of homozygous genotype = number of alleles = 6.

Sex Determination in Drosophila

• The presence of a Y chromosome does determine maleness in Drosophila.
• Sex determination is determined by a balance between genes on the autosomes and genes on the X chromosome.
• The determination is determined by the number of X chromosomes divided by the number of haploid sets of autosomal chromosomes (X: A ratio).
• An X: A ratio of 1.0 produces a female.
• An X: A ratio of 0.5 produces a male.

Chemicals and Equipment

• Fetal calf serum is used for nutrition of cells.
• Penicillin and streptomycine protect from infection.
• Phytohaemagglutinin M activates cell division.
• Denaturation temperature is 94-98 °C.
• Annealing temperature 50-65 °C.
• Extension temperature 72 °C.
• Proteinase K solution destructs protein.
• Lysis buffer breaks the cell wall of cells.
• Wash buffer is used for washing the disc in spin column.
• Elution Buffer facilitates the dissolving of the DNA and the cross from the spin column.
• Absolute alcohol participates in DNA extraction.
• Heat block incubates the samples at a specific temperature to facilitate the lysis process.
• An eppendorf centrifuge is used for centrifuging the samples at a high speeds to extract the DNA.
• A vortex is for mixing the sample with lysis solutions.
• Pipettes with different ranges are used to measure different solutions used in reactions.
• TAE Buffer ensures electrical conductivity in gel electrophoresis.
• DNA Marker (ladder) is DNA of known molecular weight used to compare DNA bands in samples with their molecular weight.
• Agarose powder dissolves in buffer, it is heated, then cools and forms gelatinous solid molecules.
• Ethidium bromide is a fluorescent chemical that enters between base pairs in a double stranded DNA molecule.
• This is used to detect DNA following gel electrophoresis.

PCR Reaction and Temperatures

• The PCR master mix includes 25 μ Volume 50, 10 μ Volume 20 and 20 μ Volume 40.
• The PCR DNA includes 4 μ Volume 50, 2 μ Volume 20 and 4 μ Volume 40.
• The PCR forward primer includes 1.5 μ Volume 50, 1 μ Volume 20 and 1.5 μ Volume 40.
• The PCR reverse primer includes 1.5 μ Volume 50, 1 μ Volume 20 and 1.5 μ Volume 40.
• The PCR distilled water includes 18 μ Volume 50, 6μ Volume 20 and 13 μ Volume 40.
• DNA amplification is done by Taq Polymaerase enzyme.
• Step 1, initial denaturation, temperature is at 95 c, in 10 min, for 1 cycle.
• Step 2, cycling steps consist of denaturation at 95 c for 30 sec.
• Annealing occurs at 55 c for 30 sec.
• Extension occurs at 72 c for 30 sec, for 35 cycles.
• Step 3, final extension, occurs at 72 for 10 min, for 1 cycle.
• Step 4, final hold, occurs at 4 c for Indefinite time.
• The melting temperature is calculate by: Tm = {4°(G+C) + 2°(A+T)} C

Gene Expression

• The length of the primary DNA is 100 X 9 = 900 base.
• The length of the primary RNA transcript (before any processing) for the gene is DNA – promotor = 900 – 100 = 800 base.
• The length of mRNA in the cytoplasm, assuming a poly A tail of 200 nucleotides, is (5 x 100) + 200 = 700 base after removing promoter and introns, then adding poly A tail.
• The number of amino acids in the encoded protein is: (Sum of Exons ÷ 3) – 1 = Sum of Exons = 3 x 100 = 300, then (3003) -1 = 99 amino acid.
• This gene belongs to eukaryotes, because it contain introns in its structure.