Alleles, Genotype and Phenotype

What this lesson covers in the specification

Incandio is aligned to this specification. It is not published by, endorsed by or affiliated with Pearson, and it reproduces none of Pearson's wording — the statement numbers are given so you can check every lesson against your own copy.

• 3.19 — Alleles as alternative forms of genes giving rise to inherited differences
• 3.20 — The terms dominant, recessive, homozygous, heterozygous, phenotype and genotype
• 3.21 — The meaning of codominance (bold B statement — Paper 2 only)

Specification section 3(b) Inheritance — also taught in DNA, Genes and Chromosomes, Protein Synthesis, Monohybrid Inheritance and Probability, Pedigrees and Sex Determination.

1 · Understand it

No exam language yet. The only question this section answers is: do I actually understand what is happening?

Everything on this page follows from one fact established earlier: chromosomes come in pairs, one of each pair from each parent. So you have TWO copies of every gene — one at the same position on each chromosome of the pair. Those two copies need not be the same, and when they differ, something has to decide which version shows.

An ALLELE is one version of a gene. The gene is the thing — the section of DNA at a particular position that codes for a particular protein; the alleles are the alternative forms that gene comes in. Take a gene for flower colour: the gene is 'flower colour', and the alleles might be 'red' and 'white'. Everyone with that gene has it at the same place on the same chromosome; what differs between individuals is which alleles they carry.

Think of it like a form with two copies of every answer

Imagine a questionnaire where each question has been filled in twice, once by each of your parents. The QUESTION is the gene — the same question appears on everybody's form, in the same place. The ANSWERS given are the alleles, and yours may be the same as each other or different. And there is a rule for what happens when the two answers disagree: usually one of them is simply the one that counts. What you can read off the finished form is not the two answers themselves but the single result they produce — and that is the difference between genotype and phenotype.

The six words, in the order they build on each other

1. GENOTYPE — the alleles an organism has for a gene, written as a pair of letters, such as RR, Rr or rr. It is what is written on the form.
2. PHENOTYPE — the observable characteristic that results, such as 'red flowers'. It is what you can actually see.
3. HOMOZYGOUS — the two alleles are the SAME: RR (homozygous dominant) or rr (homozygous recessive).
4. HETEROZYGOUS — the two alleles are DIFFERENT: Rr.
5. DOMINANT — an allele that is expressed in the phenotype whenever it is present, even if there is only one copy. Written as a CAPITAL letter.
6. RECESSIVE — an allele that is only expressed in the phenotype when BOTH alleles are recessive. Written as the same letter in lower case.

Two conventions are worth getting right at the start because they save time forever. First, use the SAME letter for both alleles of a gene, capital for dominant and lower case for the recessive — R and r, never R and w. Second, choose a letter whose capital and lower case look clearly different: C and c are a poor choice, and B and b or A and a are better. Examiners can only credit what they can read.

The three genotypes and what each one shows — the whole of monohybrid inheritance in four lines

1. RR — homozygous dominant. Two dominant alleles, so the dominant characteristic shows. Red flowers.
2. Rr — heterozygous. One of each; the dominant allele is expressed whenever present, so the dominant characteristic shows. Red flowers.
3. rr — homozygous recessive. The only way to have no dominant allele at all, so the recessive characteristic shows. White flowers.
4. So a recessive characteristic appears in ONE genotype out of three, and a dominant characteristic in two — which is why recessive conditions can skip generations and dominant ones cannot.

That last point deserves a sentence of its own, because it is the most useful consequence of the whole system. RR and Rr look identical. You cannot tell them apart by looking, which means a red-flowered plant may be carrying a hidden white allele and passing it on unnoticed for generations — until two carriers happen to cross and a white flower appears from nowhere. Nothing has been created; a hidden allele has simply met another one.

Finally, a case where the usual rule does not apply. In CODOMINANCE, neither allele is dominant over the other, and a heterozygote shows BOTH characteristics at once. Cross a red snapdragon with a white one and the offspring are pink — not because the colours have blended chemically, but because both alleles affect the phenotype. (Strictly, biologists call the snapdragon case INCOMPLETE dominance, because the white allele makes no pigment; it is often treated as codominance at this level, and the cattle below are the cleaner example.) In cattle, a red bull crossed with a white cow gives calves with a coat of mixed red and white hairs, which is the same thing more visibly: both alleles expressed, side by side.

Codominance has its own notation, and using it is worth a mark. Because neither allele is dominant you cannot use a capital and a lower case letter — that would state the very thing being denied. Instead the gene gets a capital letter and each allele a raised label: C^R for red and C^W for white, giving genotypes C^R C^R, C^R C^W and C^W C^W. Three genotypes, and here three DIFFERENT phenotypes, because the heterozygote no longer hides behind one of them.

2 · Grade 9 Notes

A different job from the section above. You have already understood it; this is the precise set of things to LEARN — definitions to reproduce word for word, processes in order, equations with units, and the answers that score full marks.

Learn this definition · Allele

One of the alternative forms of a gene, occupying the same position on a chromosome and giving rise to inherited differences.

Statement 3.20 — the six terms, exactly as they must be defined

Genotype

The alleles an organism has for a particular gene, such as RR, Rr or rr.

Phenotype

The observable characteristics of an organism, resulting from its genotype and its environment.

Dominant

An allele that is expressed in the phenotype whenever it is present, even in a heterozygote. Written as a capital letter.

Recessive

An allele that is only expressed in the phenotype when both alleles present are recessive. Written as a lower-case letter.

Homozygous

Having two identical alleles for a gene — RR or rr.

Heterozygous

Having two different alleles for a gene — Rr.

Learn this definition · Codominance

Where neither allele is dominant over the other, so that a heterozygous individual shows both characteristics in its phenotype.

The three genotypes — what each one is called and what it shows

Genotype against phenotype — the pair that decides most marks on this topic

A. GENOTYPE is the alleles present, written as letters: RR, Rr or rr. It cannot be seen, and two different genotypes can look identical.

B. PHENOTYPE is the observable characteristic that results — 'red flowers'. It is what you can see, and it is affected by the environment as well as by the genotype.

Homozygous against heterozygous — say SAME or DIFFERENT

A. HOMOZYGOUS: the two alleles are the SAME. RR or rr. Such an organism can only pass on one kind of allele.

B. HETEROZYGOUS: the two alleles are DIFFERENT. Rr. Such an organism can pass on either one, which is why heterozygotes are what make crosses interesting.

Writing genotypes — the conventions that are worth marks in themselves

• Use the SAME letter for both alleles of a gene: R and r, never R and w
• CAPITAL for the dominant allele, lower case for the recessive
• Choose a letter whose capital and lower case are clearly different — A/a or B/b rather than C/c or S/s
• Always write TWO letters for a genotype, because every body cell has two alleles of every gene (genes on the sex chromosomes are the exception)
• For CODOMINANCE, use a capital letter for the gene with raised labels for the alleles: C^R and C^W, since neither is dominant

Model answer [2 marks]

Explain the difference between the genotype and the phenotype of an organism. [2]

The genotype is the combination of alleles an organism has for a particular gene, such as Rr. The phenotype is the observable characteristic that results from those alleles, such as red flowers — and it is influenced by the environment as well as by the genotype.

Model answer [3 marks]

A plant with red flowers is crossed with a white-flowered plant, and all the offspring have pink flowers. Explain what this shows about the alleles for flower colour. [3]

The offspring are all heterozygous, having received one allele from each parent. They show a phenotype different from either parent, and both parental characteristics are contributing to it, so neither allele is dominant over the other. The alleles are therefore codominant, and both are expressed in the heterozygote.

Model answer [3 marks]

Explain why two plants that look identical may produce offspring that look different from both of them. [3]

A plant with the dominant phenotype may be homozygous dominant or heterozygous, because the dominant allele is expressed whenever it is present and the two genotypes therefore look the same. If both parents are heterozygous, each can pass on a recessive allele. An offspring receiving a recessive allele from each parent is homozygous recessive, and shows the recessive characteristic that neither parent showed.

Mark-losing trap. A genotype is TWO letters (except for genes on the X chromosome in males). One letter describes a gamete, not an organism.

Mark-losing trap. Use the same letter in both cases — R and r. Two different letters describe two different genes.

Mark-losing trap. Homozygous means the two alleles are the SAME, not that the organism shows the dominant characteristic.

Mark-losing trap. Codominance is not blending. BOTH alleles are expressed — in cattle you can see red hairs and white hairs separately.

Mark-losing trap. Say an allele is a VERSION of a gene. Calling it 'a type of gene' or 'a gene for a characteristic' loses the mark.

3 · Prove it — the five questions

The five questions climb Grade 6 → Grade 7 → Grade 8 → Grade 9 → Grade 9 challenge, and are marked inside Incandio on your own device, by rule, with an authored diagnosis of the mistake you actually made. The mark schemes stay in the app so that the practice is worth doing; the questions themselves are here.

1. Grade 6 · Define [1 mark] — What is an allele?
2. Grade 7 · Identify [2 marks] — In pea plants, the allele for tall (T) is dominant and the allele for short (t) is recessive. A plant has the genotype Tt. What is its phenotype, and what is this genotype called?
3. Grade 8 · Explain [5 marks] — Two red-flowered plants of the same species are crossed and one of the offspring has white flowers. Explain how this is possible, given that neither parent had white flowers. Select every statement that belongs in a full-mark explanation.
4. Grade 9 · Apply [4 marks] — In a breed of cattle the coat colour alleles are codominant: C^R gives red hairs and C^W gives white hairs, and a heterozygous animal has a coat of mixed red and white hairs called roan. A roan bull is crossed with a roan cow. Out of 200 calves, how many would be expected to be roan?
5. 9+ · Analyse [5 marks] — A breeder has a herd of red, white and roan cattle, and a separate flock of sheep in which black wool is dominant to white. The breeder says: 'In both animals I can tell exactly which alleles an animal carries just by looking at it.' Select every statement that belongs in a full-mark evaluation of this claim.

The people behind this science

Two ways into the same idea — the one who discovered every word on this page, and the one whose theory needed exactly this and never found it. Inside Incandio each of them answers knowing exactly which lesson you have just finished.

Gregor Mendel — the one who discovered every word on this page

This entire vocabulary describes what Mendel found. Crossing tall pea plants with short ones, he got offspring that were all tall — and then, crossing those with each other, short plants reappeared in the next generation in a ratio of about one in four. That result is only explicable if each plant carries two factors, if one can mask the other without destroying it, and if the two separate when gametes are made. Dominant, recessive, homozygous and heterozygous are the modern names for the things he had to invent in order to explain his own numbers.

• “How can a characteristic vanish in one generation and come back in the next?”
• “What made you conclude each plant carries two factors rather than one?”
• “Why did you cross the offspring with each other rather than stopping?”
• “What ratio did you find, and why did that number matter so much?”
• “Did you know how any of it physically worked?”

Charles Darwin — the one whose theory needed exactly this and never found it

Darwin's theory required inherited variation to persist, and the inheritance he believed in would have destroyed it. Like almost everyone then, he assumed the characteristics of two parents blend in their offspring — and a critic pointed out that blending would halve any new variation every generation until nothing was left to select. He never solved it. The answer is on this page: alleles are discrete, and a recessive allele hidden in a heterozygote is not diluted at all, only unseen. Mendel published it in 1866; Darwin died in 1882 without reading it.

• “What did you think happened when two parents' characteristics were inherited together?”
• “Why was blending inheritance a problem for your theory?”
• “How did you answer the objection that variation would be diluted away?”
• “What difference would it have made to know inheritance came in units?”

Carry on through the course

• Previous lesson: Protein Synthesis
• Next lesson: Monohybrid Inheritance and Probability
• Sexual and Asexual Reproduction — Two ways to make a new organism — one produces copies, the other produces something that has never existed before. Why any species would want both.
• Flowers, Pollination and Fertilisation — Two completely different solutions to one problem — a plant that cannot move has to get its male gamete to another plant's female gamete.
• Seeds and Germination — What a seed needs to start growing, what it lives on before it has a single leaf — and why light is not on the list.
• The Human Reproductive Systems — Two systems built around the same problem — making gametes and bringing them together — and the hormones that switch them on.
• The Menstrual Cycle — Four hormones, two organs and one repeating question — should the uterus lining be built up, held, or let go?
• All of Biology · Biology key terms · required practicals · Incandio Science · The 4BI1 specification