IBDP Biology Unit 3 Genetics – Inheritance (SL & HL)

D3.2.1 Production of haploid gametes in parents and their fusion to form a diploid zygote as the means of inheritance.

  • Inheritance: Trait passed from parent to offspring during reproduction.
  • DNA (Deoxyribonucleic Acid): Molecule of inheritance for all living organisms.
  • DNA is inherited by the passing of chromosomes between generations of cells.
  • Diagram shows the relationship between Nucleus, Chromosome, DNA (double helix), Histone proteins, Nucleosomes, and Base pairs.

Inheritance in the Sexual Life Cycle

  • All eukaryotic organisms with a sexual life cycle produce haploid gametes.
  • Gametes: Haploid, having only one chromosome of each type.
  • Male and female gametes fuse at fertilization to form a zygote.
  • Zygotes: Diploid, having two chromosomes of each type.
  • By uniting two gametes with half the number of chromosomes, the full chromosome number is restored each generation.
  • At fertilization the two haploid gametes combine to form a zygote which again has the full complement of 2n = 46 chromosomes.
  • Gametes: Haploid cells that fuse together at fertilization to produce the single-cell zygote.
  • Zygote: The diploid cell produced at fertilization when gametes fuse
  • Male Gametes (Sperm): Small, self-propelling cells.
  • Female Gametes (Egg/Ovum): Large, passively moved cells.

D3.2.2 Methods for conducting genetic crosses in flowering plants

  • Gregor Mendel (1822-1884): Austrian monk who studied heredity in plants.
  • Heredity: Passing down of traits from one generation to another.
  • At the time, there was no understanding of DNA or genes.
  • People could just observe that offspring resemble their parents but did not understand the mechanism of inheritance.
  • Blending Inheritance (Widely Accepted Hypothesis): Predicted that the traits of parents blended in offspring.
  • Example: A white-flowered plant and a purple-flowered plant would produce an intermediate, or light purple flowered plant.
  • Mendel carried out a series of experiments on the common pea plant in his monastery’s experimental garden plot between 1856 and 1863 to Test this hypothesis.

Methods for Performing Crosses in Plants

  • Reproduction in flowering plants is sexual.
  • Male gametes are found in pollen grains on the flower anther.
  • Female gametes are inside the ovules of the flower ovary.
  • Pollen is transferred from the anthers of one plant to the stigma of another plant.
  • Genetic crosses in flowering plants are commonly used to breed new varieties of crops or ornamental plants, in addition to demonstrating patterns of inheritance.
  • Cross-pollination: When one plant fertilizes another plant of the same species.
  • Mendel pollinated the pea plants by hand, using pollen from parent plants of his choice and purposefully cross-pollinated pea plants based on their different features to make important discoveries on how traits are inherited between generations.

Mendel’s Crosses - Parent (P) Generation

  • Mendel’s first step was to establish pea plant populations with two different features, such as tall vs. short height, breeding them until they always produced offspring identical to the parent.
  • After this, he crossed the plants with each other to observe how the offspring inherited the traits.
  • He performed seven different crosses.
  • The parent plants in the experiments are referred to as the P (for parent) generation

Mendel’s Crosses - F1 Generation

  • All of the resultant plants (the F1) were identical in shape to one of the parents.
  • The results directly contradicted the blending inheritance hypothesis.
  • Mendel concluded that one of the phenotypes masked the expression of the other phenotype.
  • He termed the expressed phenotype of the F1 as the dominant phenotype, whereas the repressed phenotype was termed the recessive phenotype.
  • The F1 generation results from cross-pollination of two parent (P) plants.
  • F1 stands for “first filial.” The word filial means “relating to a son or daughter”, so the F1 offspring are the first generation of offspring.

Mendel’s Crosses - F2 Generation

  • Mendel wondered what had happened to the recessive characteristic in the F1 generation.
  • He assumed some type of “inherited unit” produced each phenotype.
  • To test this, Mendel allowed the F1 generation plants (that displayed only the dominant trait) to self-fertilize.
  • In self-fertilization, pollen grains from anthers on one plant are transferred to stigmas of flowers on the same plant.
  • The self-pollination of the F1 resulted in an F2 generation in which the recessive trait reappeared!
  • There was a 3:1 ratio for plants that showed the dominant trait for every plant that showed the recessive trait.
  • The F2 generation results from self-pollination of F1 plants.
  • F2 stands for “second filial.” The word filial means “relating to a son or daughter”, so the F2 offspring are the second generation of offspring.
  • From his study, Mendel concluded that the phenotypes he was studying (i.e. seed shape, flower color, etc.), were determined by the combination of what he referred to as “discrete heritable units.”
  • This concept, known as the particulate inheritance hypothesis, was in direct contrast to blending inheritance, which predicted that phenotypes of offspring are intermediate to the parents.
  • We now refer to Mendel’s inherited units as alleles, alternate versions of a gene.

Punnett Grids

  • Reginald Crundall Punnett (1875-1967): British geneticist who devised the "Punnett Square," a visual representation of Mendelian inheritance.
  • Punnett’s book Mendelism (1905) is sometimes said to have been the first textbook on genetics; it was probably the first popular science book to introduce genetics to the public.

Steps for Completing a Punnett Grid

  1. Determine gene, alleles, and parental diploid genotypes.
  2. Determine the unique gametes from each parent that result from segregation of alleles during meiosis.
  3. Draw a Punnett grid using unique gametes only.
  4. Fill in the Punnett grid with the possible genotypes of the offspring.
  5. Summarize possible genotypes and phenotypes of offspring, with expected ratios.

  • Punnett Grid is more appropriate because not all have to be “squares.” Depending on the genotypes of the parents, a “rectangle” might be more appropriate.

  • Example: A homozygous tall pea plant is crossed with a heterozygous tall pea plant.

    • Gene = pea plant height
    • Alleles = T for tall, t for dwarf
    • Parent = Homozygous tall is TT genotypes, Heterozygous tall is Tt
    • Parent diploid genotype, meaning what the parent cell genotype is before it does meiosis and makes gametes
    • Homozygous tall parent (TT) produces all gametes with the T allele.
    • Heterozygous tall parent (Tt) can make gametes with T or t.

  • For each parent, examine how many unique genotypes the gametes can be given the parent genotype.

    • AA parent - all gametes will have “A”, so there is ONE type of unique gamete
    • Aa parent - gametes can have either “A” or “a”, so there are TWO types of unique gametes
    • aa parent - all gametes will have “a”, so there is ONE type of unique gamete

  • Then, make a Punnett grid with only the types of unique gametes.

    • AA x aa --> 1 gamete type X 1 gamete type = 1 box Punnett
    • AA x Aa --> 1 gamete type X 2 gamete types = 2 box Punnett
    • Aa x Aa --> 2 gamete types X 2 gamete types = 4 box Punnett

  • Each box of the Punnett grid represents an equal probability of a genetic outcome for an offspring of a cross between these two parents.

    • Offspring genotypes = 1/2 TT, 1/2 Tt
    • Offspring phenotypes = 4/4 tall plants

D3.2.3 Genotype as the combination of alleles inherited by an organism

  • Gene: A sequence of DNA nucleotides that codes for an RNA or protein product. Genes are located on chromosomes. There are many genes located on each chromosome.
  • Transcription is the synthesis of RNA using the gene as a template.
  • Translation is the synthesis of a polypeptide from mRNA.
  • The sequence of nitrogenous bases in nucleic acids forms a code that stores information that is used to make proteins in the process of gene expression.
  • Alleles: Different versions of the same gene.
  • Because they are the same gene, alleles code for the same type of protein.
  • Alleles of a gene may be different by a single base in the sequence of the gene or by large sections.
  • New alleles are generated by mutation which can form single-nucleotide polymorphisms.
  • Alleles are often dominant or recessive to other alleles.
  • Diploid Organisms: Have two copies of each chromosome, one inherited from each parent. As a result, diploid organisms have two copies of each gene.
  • Genotype: The combination of alleles for the two copies of a gene within a diploid cell.
  • Homozygous: The two copies of the gene are of the same allele (AA or aa).
    • Having two of the same alleles of a particular gene.
    • The individual's mom and dad passed on the same versions of the gene.
    • Notated by two capital letters (XX) for the dominant alleles, and two lowercase letters (xx) for the recessive alleles.
  • Heterozygous: The two copies of the gene are different alleles (Aa).
    • Having two different alleles of a particular gene.
    • The individual's mom and dad passed on different versions of the gene.
    • Notated by one capital letter for the dominant allele and one lowercase letter for the recessive allele (Xx).

D3.2.4 Phenotype as the observable traits of an organism resulting from genotype and environmental factors

  • Phenotype: The observable traits or characteristics of an individual.
    • Morphology (physical structures)
    • Developmental processes
    • Biochemical processes
    • Physiology
    • Behaviors
  • Both genes and the environment influence phenotype.
  • Examples of Human Phenotypes:
    • Determined by Genotype Only: ABO blood group, PKU disease, Haemophilia disease
      • Gene expression mechanism by which information in genes has effects on phenotype.
    • Determined by Environment Only: Scars, Body art (piercings and tattoos), Language spoken
      • "Environment" refers to the physical environment, as well as social influences and life experiences.
    • Determined by Interaction of Genotype with the Environment: Height, Development of Type II diabetes, Tanning of skin, Development of coronary heart disease

D3.2.5 Effects of dominant and recessive alleles on phenotype

  • Humans are diploid organisms, which means that we have two copies of each chromosome and therefore two copies of each gene (that is on an autosome (non-sex chromosomes).
  • People who are chromosomally male will have only one copy of any gene that is on the X and Y chromosomes!
  • A karyogram depicts the chromosomes of an organism, arranged in pairs
  • Genotypes can Influence Phenotype
  • Phenotypes that are influenced by genes will depend on which two versions of the gene (alleles) are present in the genotype.
  • Alleles are often described as “dominant” or “recessive” over other alleles.
  • Dominant Allele: A variation of a gene that will produce a certain phenotype, even if the individual only has one copy. Notation is a capital letter.
    • A dominant allele typically encodes for a functioning protein.
    • The allele is dominant because one copy of the allele is all that is needed in order to make enough of the protein coded for the by the gene.
    • Example: Dark hair (R) is dominant over blonde or red hair (r) because having even one copy of the dark hair allele will code for enough melanin protein for the hair to look dark (this is a simplified example, in reality hair color is polygenic, meaning it is coded for by multiple genes).
  • Recessive Allele: A variation of a gene that must be homozygous when inherited in order to be expressed in the phenotype. Notation as a lowercase letter.
    • Cause #1: The recessive allele codes for a non functioning protein.
      • Example: A protein called MC1R functions to get rid of red pigment. The dominant allele of the MC1R gene (R) codes for a functional protein. As long as there is one working MC1R gene, the hair won’t be red. The recessive allele for the MC1R gene (r) codes for a nonfunctioning MC1R protein. If both copies of the MC1R gene are the recessive allele, then no functional protein is made and no red pigment is removed, so the hair is red.
    • Cause #2: The recessive allele is the normal one, and the dominant allele is a mutated version, and we need two good copies of the allele for normal function.
      • Example: Achondroplasia, or dwarfism, is caused by a broken version of the FGFR3 gene. The normal job of the FGFR3 gene (allele a) is to code for a protein that prevents bone growth. The broken version of FGFR3 (allele A) is hyperactive -- it tells bones to stop growing even when they should be growing. The hyperactive FGF3 protein causes a person's bones to be much shorter than normal. Even if a person has a normal copy of FGFR3 (a), the broken version sends a signal that's just too strong (making A dominant).

D3.2.6 Phenotypic plasticity as the capacity to develop traits suited to the environment experience by an organism, by varying patterns of gene expression.

  • Phenotypic Plasticity: Ability of an organism to express different phenotypes depending on the biotic or abiotic environment
  • Involves regulatory genes that switch on structural genes given the appropriate stimulus.
  • The environment of an organism impacts gene expression. For example, human hair and skin color are impacted by the exposure to sunlight and high temperatures.
  • Similarly, pigments in the fur of Himalayan rabbits (Oryctolagus cuniculus) are regulated by temperature.
    • Gene C controls fur pigmentation in Himalayan rabbits.
    • The gene is active when environmental temperatures are between 15 and 25°C. At higher temperatures, the gene is inactive.
    • In warm weather, no pigment is produced and the fur is white.
    • In low temperatures, Gene C becomes active in the rabbit's colder extremities (ears, nose, and feet) and produces a black pigment.

D3.2.7 Phenylketonuria as an example of a human disease due to a recessive allele

  • Genetic Disease: An illness that is caused in whole or in part by a change in the DNA sequence away from the normal sequence.
  • In single-gene diseases, a mutation in just one gene is responsible for disease.
  • There are “normal” alleles of the gene and a “disease-causing” alleles of the gene.
  • Genetic diseases can be dominant or recessive; autosomal or sex-linked
    • Dominant: If a person has one dominant allele, then they themselves will develop the disease (e.g., Huntington’s disease).
    • Recessive: The disease only develops in individuals that do not have the dominant allele of the gene (e.g., Cystic fibrosis, Phenylketonuria).
    • Codominant: Heterozygotes have a different phenotype than individuals with two copies of either allele (e.g., Sickle cell disease).
    • Autosomal: The gene is located on an autosome, so males and females are equally affected.
    • Sex-linked: The gene is located on a sex chromosome, resulting in a different pattern of inheritance in males and females (e.g., Red-green colorblindness, Hemophilia).
  • Genetic diseases are relatively rare in a population
  • Most genetic diseases are caused by a recessive allele of a gene. The disease, therefore, only develops in individuals that do not have the dominant allele of the gene.
  • Genetic diseases caused by a recessive allele usually appear “unexpectedly.” Both parents of a child with the disease may be carriers.
  • Carriers have one recessive allele for the genetic disease and one dominant normal allele. They will not show symptoms of the disease, but they can pass on the recessive allele to their offspring.
  • Phenylketonuria (PKU): Inherited in an autosomal recessive pattern.
  • The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but they typically do not show signs and symptoms of the condition because they have a normal allele.
  • Two healthy parents who are carriers of the disease causing PKU allele can have a child with PKU disease.
  • There is a 1 in 4 chance the offspring of two carriers will have PKU disease.
  • PKU is caused by mutations in the PAH gene. The PAH gene is located on chromosome 12, which is an autosome (a non-sex determining chromosome). Males and females are, therefore, equally likely to be born with PKU if both of their parents are carriers.
    • Normal Allele (dominant): The normal allele codes for functioning phenylalanine hydroxylase, an enzyme that converts the amino acid phenylalanine to another amino acid called tyrosine.
    • Disease Allele (recessive): Mutations in the PAH gene have formed an allele that codes for a non-functioning phenylalanine hydroxylase. If phenylalanine hydroxylase does not function, phenylalanine from the diet is not processed effectively. A person with two recessive copies of the PKU allele cannot produce functioning enzyme. As a result, phenylalanine accumulates and tyrosine becomes deficient. Nerve cells in the developing brain are particularly sensitive to phenylalanine levels, so excessive amounts of this substance can cause brain damage.
  • PKU was the first condition for which widespread newborn testing was implemented.
  • PKU is treatable. The treatment consists of a diet containing little or no phenylalanine. If children with the condition are placed on this diet at birth, they grow normally and usually show no symptoms or health problems.
  • A newborn screening, in which a sample of blood is taken from a heel prick, and multiple genetic diseases are tested for.

D3.2.8 Single-nucleotide polymorphisms and multiple alleles in gene pools

  • Single Nucleotide Polymorphism (SNP): A variation at a single position in a DNA sequence among individuals.
  • The DNA code is formed from a chain of four nucleotide bases: A, C, G, and T.
  • If a SNP occurs within a gene, then the gene is described as having more than one allele.
  • SNPs are formed through point mutations to the DNA. A point mutation occurs when a single base pair is added, deleted, or changed.
  • While most point mutations are silent, they can also have various functional consequences, including altering the structure and function of the protein the gene encodes (D1.2.11).
  • SNPs result in many different alleles (versions) of each gene in the entire population of a species; there is no limit to the number of alleles of a gene in the population.
  • Each minor change (mutation) in the DNA sequence of a gene can result in a new allele!
  • In the human genome, genes involved with the immune response have the greatest number of alleles. For example, there are more than 32,000 known alleles of the Major Histocompatibility Complex (MHC) genes.
  • Gene Pool: The collection of all the genes and the various alleles of those genes within a population.
  • Natural selection will act on the alleles within the gene pool, maintaining alleles that provide an advantage, and selecting out alleles that negatively impact survival and/or reproduction.
  • Even if there are more than two alleles in the gene pool, there are a maximum of two alleles in any single individual.
  • An example of a gene with multiple alleles in the gene pool is called the “S-gene.” This gene is found in the gene pool of many tree fruit crops (such as apples, Malus domesticus).
  • There are over 50 known alleles of the S- gene in apples. The alleles are numbered S1, S2, S3, etc.
  • Each apple cultivar has a unique combination of two of the alleles. A cultivar is a variety of a plant for which people have selected for desired traits and which retains those traits when propagated.
  • The S-gene is an example of a genetic mechanism used by plant species to ensure that male and female gametes fusing during fertilization are from different plants.
  • In species with the S-gene, cross-pollination is necessary to achieve sexual reproduction.
  • During pollination, if a pollen grain lands on the stigma of a flower with the same allele of the S-gene, the pollen is rejected, and fertilization will not occur.

D3.2.9 ABO blood groups as an example of multiple alleles

  • The ABO gene is an example of a gene with multiple alleles. The gene codes for an enzyme that alters the structure of a glycoprotein on the red blood cell membrane.
  • The gene has three alleles, IA, IB, and i.
    • Allele IA alters the glycoprotein by adding a molecule called acetylgalactosamine
    • Allele IB alters the glycoprotein by adding a molecule called galactose.
    • Allele i adds nothing to the glycoprotein.
  • Within this entire gene pool, all three blood type alleles (IA , IB and i) are present.
  • With three alleles of a gene, there are six possible allele combinations in an individual: IAIA, IAi, IBIB, IBi, IAIB, ii.
  • ABO Blood Type Depends on the Combination of Alleles
  • Alleles IA and IB each show complete dominance over i.
  • Alleles IA and IB are codominant.
  • Phenotypes and Genotypes:
    • Type A: IAIA or IAi
    • Type B: IBIB or IBi
    • Type AB: IAIB
    • Type O: ii
  • ABO Blood Type Crosses

D3.2.10 Incomplete dominance and codominance

  • Incomplete Dominance: Sometimes, one allele is not completely dominant over the other alleles of a gene. With incomplete dominance, the heterozygous phenotype is intermediate.
  • For example, in the snapdragon (Antirrhinum majus), flower color is influenced by a gene with two alleles, red (CR) and white (CW).
  • If cross-pollination (D3.1.10) occurs between a homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR), the offspring will have pink flowers (CRCW).
  • The basis for the intermediate color in the heterozygote is simply that the pigment produced by the red allele (anthocyanin) is diluted in the heterozygote and, therefore, appears pink because of the white background of the flower petals.
  • Note that different genotype notation is used to distinguish incomplete dominance from simple dominance and recessiveness.
  • The capital letter is for the gene (C for color), and the superscript letters are for the alleles (CW for white and CR for red).
  • Codominance: With codominance, the heterozygote expresses the phenotype of two alleles equally.
  • The phenotype is not a blending, rather equal and independent expression of two phenotypes.
  • For example, roan coat color in many organisms is the result of having red hair (CR) interspersed with white hairs (CW). Both hair color alleles are expressed.
  • If fertilization occurs between a homozygous white parent (CWCW) and a homozygous red parent (CRCR), the offspring will have an intermixing of both red and white-colored hairs (CRCW).
  • Note that different genotype notation is used to distinguish codominance from simple dominance and recessiveness.
  • Codominance in ABO Antigens: Red blood cells have glycoproteins on their plasma membranes that distinguish ABO blood type. The glycoproteins are coded for by one gene with three alleles, IA, IB, and i. Both the IA and IB alleles of the gene show dominance over i. However, neither IA or IB is dominant over the other; they are codominant.

D3.2.11 Sex determination in humans and inheritance of genes on sex chromosomes

  • Sperm cells determine the sex of offspring.
  • The inheritance of sex can be shown using a genetic diagram (known as a Punnett square), with the X and Y chromosomes taking the place of the alleles usually written in the boxes
  • Inheritance of sex depends upon which sex chromosomes a person has, so this is the only time we use chromosomes, rather than alleles.

D3.2.12 Haemophilia as an example of a sex-linked genetic disorder

  • Genes carried by X and Y chromosomes
  • The X chromosome is larger than the Y and has its centromere more central than on the Y chromosome.
  • Fewer genes are coded for on the Y chromosome as a result.
  • The X carried around 16x more genes than the Y chromosome.
  • Non-sex phenotypic traits, including certain blood clotting factors, are coded for on the X chromosome but not on the Y.
  • The Y chromosome carries genes that code for male characteristics
  • One of these genes is the SRY gene which in involved in:
    • Development of testes in male embryos and production of testosterone
    • Females don’t receive these genes, so instead ovaries develop and female sex hormones are expressed.
  • Sex-Linked Genes: Those found on either the X or Y chromosome. Most sex-linked traits are due to genes located on the X chromosome because there are many more genes on the X chromosome than on the Y chromosome.
  • In males one recessive allele is sufficient to cause the condition (because they have only one X chromosome).
  • Sex Linked Gene Notation
    • Male: XA Y
    • Female: XA Xa
  • Because it is unlikely that females (who have two X chromosomes) will have two copies of a rare recessive allele, it is very rare for females to have hemophilia.
  • Hemophilia is inherited in an sex-linked recessive pattern.
  • A female with one altered copy of the gene is a carrier. Carrier females have about half the usual amount of coagulation factor VIII or coagulation factor IX, which is generally enough for normal blood clotting.

D3.2.13 Pedigree charts to deduce patterns of inheritance of genetic disorders

  • A pedigree chart is a diagram that shows the occurrence and appearance of phenotypes of a particular gene from one generation to the next.
  • Deducing Patterns of Inheritance from Pedigree Charts
    • Does the trait skip generations?
      • Yes - the trait is recessive
      • No - the trait is dominant
    • Is the trait found much more often in males?
      • Yes - the trait is sex linked
      • No - the trait is autosomal

D3.2.15 Box-and-whisker plots to represent data for a continuous variable such as student height.

  • When performing an investigation, a scientist will record both quantitative and qualitative data.
    • Quantitative: Data that is in the form of a number obtained in a count or measurement.
    • Qualitative: Data that is descriptive using words and is open to interpretation
  • Quantitative measurements are more objective than qualitative observations, but all measurements are limited in precision and accuracy.
  • Quantitative data is further classified as either discrete or continuous.
    • Discrete: A finite value that can be counted.
    • Continuous: An infinite number of possible values can be measured.
  • A data set is a collection of data.
  • Data sets can also be statistically compared to other data sets to determine if there is a statistically significant relationship or difference between them.
  • Quantitative data sets can be represented and compared graphically using:
    • Histogram
    • Bar Chart
    • Box and Whisker
    • Line/Curve Plot
  • Box-and-whisker plots display six aspects of data:
    • Outliers
    • Minimum
    • First quartile
    • Median
    • Third quartile
    • Maximum
  • Quartiles divide a dataset ordered from smallest to largest into four equal parts.
  • The median is the middle number of the ordered data set (the second quartile, Q2).
  • The interquartile range (IQR) describes the difference between the third quartile (Q3) and the first quartile (Q1), indicating the range of the middle half of the scores in the distribution.
  • An outlier is an observation that lies an abnormal distance from other values in a random sample from a population.
  • A data point is categorized as an outlier if it is more than 1.5
    umber* IQR (interquartile range) above the third quartile or below the first quartile.
  • There are online calculators to determine if a data set contains an outlier. Use your search engine to look up “outlier IQR calculator”
  • IQR and Outliers
    • If a data set containers an outlier and is skewed, then the data is best:
      • Described with the median as the central tendency of the data set
      • Described with the IQR as the measure of spread within the data set
      • Represented with a box-and-whisker plot
      • Statistically compared to other groups with a Kruskal-Wallis test
    • If a data set does not container an outlier and is not skewed, then the data is best:
      • Described with the mean as the central tendency of the data set
      • Described with the standard deviation as the measure of spread within the data set
      • Represented with a bar chart or line plot
      • Statistically compared to other groups with a T-test or ANOVA test