Title: InkBiology / Inheritance and population genetics
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Homozygous.
Back: Carrying two identical alleles of a gene.

Front: DEFINE
Define: Genotype.
Back: The alleles an organism carries, for the gene or genes under discussion.

Front: CHECK YOURSELF
In cattle, coat colour is controlled by a single gene with two codominant alleles: C^RC^R cattle are red, C^WC^W are white, and C^RC^W are roan, a mixture of red and white hairs. A farmer crosses a roan bull with a roan cow and gets 24 calves. Set out the cross and state how many calves of each colour you would expect. The farmer then crosses the same bull with a white cow: state the expected ratio for that cross.
Back: Roan × roan is C^RC^W × C^RC^W. Each parent produces gametes carrying C^R or C^W in equal numbers, so the offspring are 1 C^RC^R : 2 C^RC^W : 1 C^WC^W.
That is 1 red : 2 roan : 1 white, so of 24 calves you would expect 6 red, 12 roan and 6 white.
Roan × white is C^RC^W × C^WC^W. The white cow can only give C^W, so the offspring are half C^RC^W and half C^WC^W: 1 roan : 1 white, with no red calves at all.
The give-away that these alleles are codominant rather than showing incomplete blending is the roan coat itself: it is red hairs and white hairs side by side, both alleles expressed, rather than a pink blend.

Front: CHECK YOURSELF
A recessive allele causes a metabolic disorder that affects 1 in 10 000 newborns. Assuming Hardy-Weinberg equilibrium, calculate the frequency of the recessive allele and the percentage of the population who are carriers. Then explain why a screening programme that identifies and counsels affected individuals would have almost no effect on the frequency of the allele.
Back: The affected newborns are homozygous recessive, so q² = 1 ÷ 10 000 = 0.0001 and q = 0.01. Then p = 1 − 0.01 = 0.99.
Carriers are the heterozygotes: 2pq = 2 × 0.99 × 0.01 = 0.0198, so about 2% of the population, or roughly 1 person in 50, carries the allele.
Comparing the two figures answers the second part. For every affected individual there are around 198 carriers, so the overwhelming majority of copies of the recessive allele are in heterozygotes, who show no symptoms and would not be identified by a programme based on phenotype.
Removing the affected individuals from the breeding population therefore removes only a tiny fraction of the allele's copies, and the frequency falls very slowly. This is the general rule for rare recessive alleles: the rarer the allele, the larger the proportion of it that is hidden in heterozygotes.

Front: DEFINE
Define: Crossing over.
Back: The exchange of equivalent sections of DNA between non-sister chromatids of a homologous pair during prophase I.

Front: DEFINE
Define: Phenotype.
Back: The observable characteristics of an organism, produced by its genotype interacting with its environment.

Front: DEFINE
Define: Heterozygous.
Back: Carrying two different alleles of a gene.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A 3 : 1 ratio means three out of every four offspring show the dominant characteristic.
Back: A ratio is a statement about probability, not a promise about a family. Each fertilisation independently has a 3 in 4 chance of the dominant phenotype, and only over large numbers does the count settle near 3 : 1. A pea plant obliges; three children need not.

Front: DEFINE
Define: Recessive.
Back: An allele whose effect appears only when two copies are present.

Front: CHECK YOURSELF
In a species of rodent, coat colour is controlled by two genes. Allele A is needed for any pigment to be made and is dominant to a; allele B produces black pigment and is dominant to b, which produces brown. Two rodents of genotype AaBb are crossed and produce 96 offspring. Predict the numbers of each coat colour, name the phenomenon involved, and state what a chi-squared test with 2 degrees of freedom would need to show for the prediction to stand.
Back: The dihybrid classes from AaBb × AaBb are 9 A_B_ : 3 A_bb : 3 aaB_ : 1 aabb. Without allele A no pigment is made, so aaB_ and aabb are both white and merge into one class of 4.
The prediction is therefore 9 black : 3 brown : 4 white. Of 96 offspring, one sixteenth is 6, so the expected numbers are 54 black, 18 brown and 24 white.
The phenomenon is recessive epistasis: the homozygous recessive genotype aa at the first locus masks the expression of the gene at the second locus.
There are three phenotype classes, so degrees of freedom is 3 − 1 = 2 and the critical value at p = 0.05 is 5.99. For the prediction to stand, the calculated χ² must be below 5.99, so that the difference between observed and expected is not significant and the null hypothesis is accepted.

Front: DEFINE
Define: Chiasma.
Back: The visible point at which two non-sister chromatids cross during a bivalent's crossover.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A dominant allele spreads through a population, because dominant alleles get passed on more.
Back: Dominance describes what happens inside one heterozygote and says nothing about how common an allele is. Polydactyly is dominant and rare; blood group O is recessive and commonest. With no selection or mutation and random mating, frequencies do not change at all.

Front: DEFINE
Define: Dominant.
Back: An allele whose effect appears in the phenotype even when only one copy is present.

Front: DEFINE
Define: Reduction division.
Back: A division that halves the chromosome number. Meiosis I is one; meiosis II is not.

Front: DEFINE
Define: Bivalent.
Back: The structure formed when a homologous pair comes together in prophase I: two chromosomes, four chromatids.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Meiosis is mitosis done twice, so learning it means learning the same four stages again with roman numerals attached.
Back: The second division really is mitosis in miniature; the first has no counterpart in mitosis at all. Homologous chromosomes pair, exchange lengths of DNA, and separate as whole chromosomes with centromeres intact. Every ratio later in the unit comes from that division.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A significant chi-squared result is the one that supports your genetic hypothesis.
Back: The test runs the other way round. Chi-squared measures how badly the observed numbers disagree with the ones the hypothesis predicted, so a large value is evidence against it. Proposing a 9 : 3 : 3 : 1 ratio, you want a small value and a difference that is not significant.

Front: DEFINE
Define: Homologous pair.
Back: Two chromosomes of the same length carrying the same genes at the same loci, one from each parent, though not necessarily the same alleles.

Front: DEFINE
Define: Recombinant.
Back: A chromatid, or an offspring, carrying a combination of alleles that neither parental chromosome carried.

Front: DEFINE
Define: Allele frequency.
Back: The proportion of all the alleles of a gene in a gene pool that are of one particular kind.

Front: DEFINE
Define: Haploid.
Back: Having one chromosome from each homologous pair, written n.

Front: DEFINE
Define: Population.
Back: A group of organisms of the same species living in the same place at the same time and able to interbreed.

Front: CHECK YOURSELF
A mouse has a diploid number of 40. State the number of chromosomes and the number of chromatids in one cell at the end of meiosis I, and in one cell at the end of meiosis II. Then state how many different chromosome combinations its gametes could carry, ignoring crossing over, and explain where that number comes from.
Back: At the end of meiosis I each cell has 20 chromosomes and 40 chromatids. The homologous pairs have separated, so the chromosome number has halved, but the centromeres have not divided and each chromosome is still two chromatids.
At the end of meiosis II each cell has 20 chromosomes and 20 chromatids. The centromeres have now divided and the sister chromatids have gone to opposite poles, so each is a chromosome in its own right.
A diploid number of 40 means 20 homologous pairs, so n = 20 and the number of combinations is 2^20 = 1 048 576.
The exponent is 20 rather than 40 because each homologous pair is decided once, at metaphase I, and the pairs are decided independently of one another. Twenty independent two-way choices give 2^20 outcomes.

Front: DEFINE
Define: Gene pool.
Back: All the alleles of all the genes present in a population at a given time.

Front: DEFINE
Define: Carrier.
Back: An individual heterozygous for a recessive allele, so not showing the characteristic but able to pass the allele on.

Front: DEFINE
Define: Diploid.
Back: Having chromosomes in homologous pairs, written 2n.