Genetic terminology

Monohybrid inheritance

• The inheritance of a single gene, such as the gene controlling cat coat colour or eye colour.

• Mendel famously studied this using garden pea plants, using contrasting traits to breed with and how these are expressed in their offspring. The characteristic he chose, height, colour and seed shape were all examples of discontinuous variation, making them easy to study.

  • Using this, he generated his first law of inheritance, the law of segregation: ‘the characteristics of an organism are determined by factors which occur in pairs. Only one of a pair is present in each gamete.‘

• When drawing inheritance in a diagram, F stands for filial.

  • Parents is the first generation, F1 is the first set of offspring, and the numbers go upwards.

• When showing the genotype, use the same letter in capitals and lowercase for alleles of the same gene.

• For each set of offspring, calculate the ratio of the phenotypes.

• Punnett squares can be used to calculate the genotypes of the offspring.

• Test crossing is used to determine an organism with a dominant gene is heterozygous or homozygous.

  • This is done by breeding the organism with another with a recessive phenotype. If any present the recessive trait, the dominant organism is heterozygous.

  • For peas, a tall plant could be crossed with a dwarf plant. If some are dwarf, it is heterozygous.

No dominant alleles

• There are two possibilities when this occurs:

  • Co-dominance - Where both alleles are expressed individually.

    • For example, cats who have both a ginger and black allele will become calico. This means they will have both black and ginger on their coat.

  • Incomplete dominance - The alleles reach an intermediate between two phenotypes.

    • For example, a carnation with red and white alleles will be pink.

• In cases of multiple dominant genes, they are written as one shared letter capitalised and a small letter in the corner.

  • For the plant example, this would be C^W and C^R.

• From these experiments, Mendel made his first law of inheritance, the law of segregation - ‘The characteristics of an organism are determined by factors (alleles) which occur in pairs. Only one of a pair is present in each gamete.‘

Dihybrid inheritance

• Simultaneous inheritance of two unlinked genes, such as genes on different chromosomes. To test this, Mendel crossed plants with contrasting characteristics in two phenotypes:

  • A plant with wrinkled seeds (rr) and green seeds (yy) and a plant with round seeds (RR) and yellow seeds (YY).

  • He found that all the F1 seeds were yellow and round, with a genotype of RrYy. These were then crossed, resulting four different phenotypes:

  • Round and yellow, round and green, wrinkled and green, wrinkled and green. This was in the ratio of 9:3:3:1.

  • For singular traits, such as colour, the ratio would be 3:1.

• This led to the second law of inheritance - ‘Either one of a pair of contrasting pairs may combine with either of another pair.‘

  • In modern genetics terms, this means that each member of an allele pair can combine randomly with another allele pair on a different chromosome.

• A testcross for this would involve crossing a plant with two dominant alleles with one that is homozygous recessive for both, as Mendel did.

  • The resulting ratios indicate the genotype of the parent.

Linkage

• Alleles of different genes on the same chromosome cannot segregate by moving to opposite poles during meiosis.

  • This is because they are on the same physical structure, and therefore must move together. They are then described as linked.

• Crossing over can occur, where certain parts of a chromosome switch genes. The original genotypes are known as parental genotypes, and those post-crossing over are known as recombinant genotypes.

  • Crossing over is rare and does not happen in most cells, meaning most gametes are parental.

  • The further apart genes are, the more opportunity for crossing over. This increases the amount of offspring with recombinant phenotypes.

• If the offspring with different characteristics do not correspond with Mendelian ratios, the characteristics are likely to be linked. This is a common reason for rejecting a null hypothesis.

• For example, a dihybrid genetics experiment on fruit flies does not follow the 9:3:3:1 ratio, meaning the lowest traits are recombinant as this is a rare occurrence.

• The crossover value (COV) - the percentage of linked genes that experience crossing over - can be calculated as:

  • Number of recombinants ÷ number of overall offspring/progeny × 100.

Probability

• The ratios as calculated via a punnett square are a prediction of outcomes, however the actual results are unlikely to exactly mimic these.

• The probabilities can be calculated using fractions. For example, the probability of the allele combinations in Mendel’s dihybrid crosses are:

  • Round and yellow: 9/16

  • Round and green: 3/16

  • Wrinkled and yellow: 3/16

  • Wrinkled and green: 1/16

  • This can be calculated using the ratios.

The chi2 (x*2) test

• This tests whether the ratios of a genetics cross are close enough to expected ratio to support the genetic explanation of how they occured.

  • If the numbers are not close enough, a different explanation is responsible for genes.

• There are two possible hypothesis:

  • Null hypothesis - There is no difference between the expected and observable results. These are based on Mendelian inheritance laws.

  • Alternative hypothesis - There is a difference between the expected and observed results, meaning there is a different explanation for the gene presentation (such as linked genes).

• The formula is: Σ(O-E)*2 ÷ E

• This is calculated using a table:

• The expected is calculated using the ratio. For wrinkled green, the ratio is 1/16, which can be replaced with 556/16 = 35. This can be calculated for the rest of them in the same way.

• Degrees of freedom are used to measure the values that can vary independently . For monohybrid and dihybrid class, this is one less than the number of data classes. In this case, it is 4-1 = 3.

• Statisticians say that if the predicted results happen 5% or more of the times the experiment is run, the biological reasoning is correct and all deviation is due to chance.

  • If it is less than 5% (0.5), the deviation is significant and the biological assumptions are incorrect.

• By comparing the degrees of freedom and calculated Chi2 the probability the deviation is due to chance can be found.

  • In this case, the probability is between 99%-50%.

• A conclusion must include:

  • The chi2 value is less than the critical value of 7.82 (if higher than this, it is below 5%).

  • This is equivalent to a probability over 5%.

  • The null hypothesis is accepted at the 5% level of significance.

  • The inheritance is therefore Mendelian, and deviation from the predicted ratio is due to chance.

Sex determination

• Most angiosperm species are hermaphrodite, meaning they make both pollen and ovules. There are two other strategies:

  • Monoecious plants have separate male and female flowers on the same plant.

  • Dioecious plants have separate male and female individuals.

• In animals, hermaphrodites are in the phylum Mollusca (garden snail) and Annelida (earthworm). Hermaphrodite vertebrates are extremely rare, most have separate male and female individuals.

• Whether they are male or female can be controlled by many factors:

  • Temperature - Lizard, alligator and crocodile eggs hatch as male when above 32 degrees, and female when below.

    • Conversely, sea turtle eggs are female if laid directly in the sun, but males if born in the shade.

  • Sequential hermaphroditism - Animals change between male and female throughout their lives. For example, the common slipper limpet makes stacks of individuals. Those at the top are male, and when new organisms join the stack the ones below will change to female.

    • Male sewage sludge worms can become hermaphrodite and fertilise themselves if females are not available.

    • If the dominant female clownfish dies, the dominant male changes sex and takes her place.

  • Ploidy level - Non-fertilised bee, aphid and grasshopper eggs are haploid and develop as males. Fertilised eggs become diploid and develop as female.

  • Chromosome structure - In mammals, females have XX chromosomes and males have XY. In birds, moths and some fish the male chromosomes are ZZ and the female chromosomes are ZW.

Human sex determination

• Humans have 23 chromosomes from each parent, which can be arranged in homologous pairs.

  • Each pair contains chromosomes of the same size and shape, with genes in the same order and coding for the same characteristics.

  • The arrangement of homologous pairs in decreasing size order is known as a karyotype.

• Of the 23 pairs, 22 pairs have a identical genes (although the alleles may differ). These are known as autosomes.

  • The 23rd pair is the sex chromosomes, an identical XX in females and XY in males, with the Y being much shorter.

  • Two regions on the XY are homologous and can pair with each other at meiosis, known as pseudoautosomal regions - PAR1 and PAR2.

  • These reflect the evolutionary loss of genes from one sex chromosomes, leaving a large X and small Y.

    • Their different sizes mean the sex chromosomes are heterosomes.

  • The Y has a gene the X does not, the SRY gene, which is the sex-determining region. It’s role is to switch the genes on the other chromosomes which are responsible for the expression of male characteristics.

    • This means all it takes is a single Y chromosome, no matter the amount of Xs, to make a person male.

  • Abnormalities of sex chromosomes are the most common.

• In females, all secondary oocytes contain an X making the female the homogametic sex (identical gametes in terms of sex chromosomes).

  • In males, at meiosis 1, an X chromosome passes into one secondary spermatocyte and a Y into the other.

  • Therefore, half of a males gametes are male, and half are female. This makes males the heterogametic sex (different gametes in terms of sex chromosomes).

• During fertilisation, an oocyte can be fertilised by an X or Y carrying sperm with equal probability.

Sex linkage

• As most lengths of XY chromosomes are not homologous, females have two copies of each gene and males have only one copy.

  • For females, dominant and recessive genetic rules apply. For males, as there is no other Y chromosome, whatever trait it carries will be expressed.

• Haemophilia, a potentially lethal condition where an individual cannot produce enough of one of the 13 blood clotting proteins. This causes blood to clot slowly, if able to at all, causing persistent bleeding.

  • This is associated to a gene on the X chromosome, which codes for the blood clotting protein Factor VIII. The normal version is X^H, and the mutant gene is X^h.

  • Females can have:

    • The normal genes - X^hX^h.

    • Carry the gene, as X^H is dominant haemophilia would not be the phenotype - X^HX^h.

    • Haemophilia - X^HX^H.

  • Males can have:

    • The normal genes - X^hY.

    • Haemophilia - X^HY.

• This means males are more likely to have haemophilia, making it a sex-linked condition.

• Another example is Duchenne muscular dystrophy (DMD) which is caused an X-linked recessive allele of a gene which codes for the protein dystrophin, which is a component of a glycoprotein which stabilises the cell membranes of muscle fibres.

  • These symptoms begin around 2-3 years old, and include progressive muscle weakness and loss of muscle mass.

• The inheritance works the same way with haemophilia. A female can only get DMD if their mother has the gene, either as a carrier or a sufferer, and if their father also has the gene.

  • However, if the father suffers and the mother doesn’t, their son will be unaffected as the DMD gene is attached to the X.

  • This again means sons are more likely to have the gene, as it takes only one gene from the mother.

Mutations

• This is a change in the amount, structure or arrangement in the hereditary material of an organism; either DNA or RNA (happens with some viruses).

• They are:

  • Spontaneous, as they can happen without an apparent cause.

  • Random, as they can happen with equal probability anywhere in the genome of a diploid organism.

• They can occur in all cells, but are only inherited if they occur in the gametes.

• Beneficial mutations are rare, but give individuals a selective advantage.

  • Mutations contribute to variation.

• In haploid organisms, any mutation is expressed.

  • In diploid, dominant mutations are expressed, but these are rare.

  • Mutations are mostly recessive, so are not expressed if alongside a dominant gene.

  • Mutations in diploid organisms have a lessened impact on evolution than other sources of variation.

Mutation rate

• Mutations can occur during DNA replication, prior to cell division, so organisms with short life spans and therefore frequent meiosis have a greater rate of mutations.

• Mutation rates have a low baseline, but can be increased by:

  • Ionising radiation - Gamma rays, X-rays and UV light.

    • UV light of wavelength 260 nm is particularly mutagenic, as it is the wavelength DNA absorbs most efficiently.

    • Radiation joins adjacent pyrimidine (thymine and cytosine) bases in a DNA strand, meaning that at replication, DNA polymerase may insert an incorrect amino acid.

  • Mutagenic chemicals - Polycyclic hydrocarbons in cigarette smoke, methanol, mustard gas.

    • Acridine is a mutagen which works as it’s flat molecules slide between base pairs in the double helix and prevents DNA polymerase inserting the correct nucleotide at replication.

• They can happen in various ways:

  • Gene/point mutation - DNA is not copied accurately in S phase (before cell division).

    • This involves one or a small number of bases.

  • Chromosome mutation - Chromosomes may get damaged and break.

    • They can repair themselves and the DNA and protein rejoin, however they can repair incorrectly, altering their structure and potentially affecting a large number of genes.

  • Aneuploidy - A whole chromosome lost or added.

    • This occurs due to non-disjunction, when chromosomes fail to separate to the poles of dividing cells at anaphase 1, or when chromatids fail to separate at anaphase 2.

  • Polyploidy - Chromosome number may double if the cell fails to divide following the first nuclear division after fertilisation.

Gene/point mutations

• This occurs when DNA polymerase changes the base sequence. There are 5 types:

  • Addition - A base is added, and if this happens in three places, an extra amino acid will be added to the polypeptide chain at translation.

  • Duplication - The same base is added twice.

  • Subtraction - A base is deleted, and if this happens in three places, there will be one less amino acid in the polypeptide.

  • Substitution - A different base is incorporated.

  • Inversion - Adjacent bases on the same DNA strand swap positions.

• This changes the allele on which it occurs, therefore the bases of the messenger RNA codon.

• The effect this has on the overall polypeptide produced, and therefore the phenotypic effects, depends on the nature of the mutation:

  • The new codon may code for the same amino acid, meaning there is no change to the polypeptide.

    • This is a silent mutation.

  • An amino acid with a similar chemical nature may be substituted, meaning it has a small effect.

  • If the mutation is at a significant site on the protein molecule, it can make a significant difference to it’s activity.

    • If the protein is an enzyme, the structure of the active site may be destroyed.

Sickle cell anemia

• A substitution point mutation in the gene which codes for the B polypeptide of haemoglobin results in sickle cell anemia.

• A DNA triplet on the coding strand, CTC, codes for glutamate.

  • If T is substituted for A (CAC), valine is added instead.

  • Glutamate is large and hydrophilic, whereas valine is small and hydrophobic.

  • When oxygen tension is low, affected haemoglobin in the red blood cell aggregates.

  • This causes the cell membrane to collapse on the precipitated haemoglobin, causing the red blood cell to become sickle shaped.

  • Cells are therefore fragile and can break within the capillaries.

• Normal haemoglobin is symbolised by HbA, with the allele Hb^A.

• Sickle cell, or mutant haemoglobin, is symbolised by HbS, with the allele Hb^S.

• Individuals with Hb^SHb^S alleles have sickle cell disease and are often severely affected, with joint pain and organ damage.

  • Their red blood cells have a reduced ability to carry oxygen causing anaemia and possible death.

• Individuals with Hb^SHb^A alleles have both types of haemoglobin, as they are co-dominant alleles.

  • They have sickle cell trait, with at least 50% of their haemoglobin being sickle cell, and with less severe symptoms than those with both alleles.

Chromosome mutations

Changes in structure

• Mutation arises when chromosomes do not rejoin accurately to its homologous partner.

  • The homologous chromosomes, and the gametes they enter, therefore have different genes.

• Gametes may fuse and produce an organism, but further meiosis will be impossible as mutant chromosomes will be unable to create homologous pairs at meiosis.

Aneuploidy

• When there are extra chromosomes, or too little, they are known as aneuploid.

• This is most likely to occur during meiosis, when chromosomes separate at anaphase 1, or chromatids at anaphase 2.

  • A faulty spindle can cause chromosomes to be shared unequally between daughter cells, which is known as non-disjunction.

  • This means one daughter cell gets two copies of a chromosome, and the other gets none.

Down’s syndrome

• This affects 1/1000 people.

• It occurs when a secondary oocyte experiences non-disjunction during oogenesis, therefore having either 2 copies or 0 of chromosome 21.

  • Those with no chromosome 21 cannot produce a viable embryo.

• Those with 2 copies can fuse with a normal sperm, with a viable embryo produced with 3 copies of chromosome 21, a total of 47 chromosomes.

• This is known as trisomy 21, and produces Down’s syndrome.

• 5% of people with Down’s syndrome have 46 chromosomes, and this is known as translocation Down’s.

  • Translocation occurs when a fragment of one chromosome attaches to another, in this case a fragment of chromosome 21 attaches to chromosome 14. This can happen in meiosis of either gamete.

  • This produces an embryo with two normal copies of chromosome 21, and an additional one attached to chromosome 14.

Polyploidy

• Cells with complete sets of chromosomes are known as euploid.

• If they have several sets of chromosomes, they are polyploid.

• This can occur in many ways:

  • A spindle defect during meiosis can result in all the chromosomes at anaphase 1, or all the chromatids at anaphase 2, moving to the same pole of a cell.

    • This makes gametes with 2 of each chromosome.

    • When this is fertilised by a normal haploid gamete, a triploid zygote is formed.

    • It may survive, but cannot make homologous pairs at meiosis, making it infertile.

    • Most plants reproduce asexually, meaning triploidy does not prevent their reproduction.

  • If two diploid gametes fuse, a tetraploid (4n) is produced.

  • Endomitosis is the replication of chromosomes which is not followed by cytokinesis.

    • If this happens in an early embryo, four sets of chromosomes are incorporated into the new nuclear envelope and successive rounds of mitosis continue to produce tetraploid cells.

    • In rare cases, infertile triploids undergo endomitosis, forming hexaploids (6n). This makes them fertile, as they can make homologous pairs during meiosis.

• This is common in flowering plants, and is associated with beneficial characteristics such as vigour and disease resistance.

• It is much more common in plants, as:

  • They reproduce asexually.

  • Are hermaphrodite and do not determine sex via chromosomes.

Carcinogens and genes

• A carcinogen is an agent that causes cancer, and this agent is therefore carcinogenic.

• Some mutagens are carcinogenic.

Tumour suppressor genes

• There are genes that control cell division, and halt this when enough cells have been produced for growth and repair.

• Genes that regulate mitosis and prevent cells dividing too quickly are called tumour suppressor genes.

• Mutations can affect these genes, preventing it from fulfilling it’s regulatory function.

• The cell can then go through rapid and repeated mitosis, which characterises cancer.

  • If the cell then escapes the attack of the immune system, it produces a collection of cells known as a tumour.

  • Tumours can be harmless or benign, but sometimes they are able to spread around the body and invade other tissues, making secondary tumors, or metastases.

    • This is a malignant tumour.

• Abnormalities in the TP53 tumour suppressor gene, which codes for the p53 protein, have been identified in more than half of all human cancers.

  • Normally, this protein activates repair of damaged DNA, prevents cells from entering S phase by holding it in G₁ while damaged DNA is repaired, and initiates apoptosis if DNA cannot be repaired.

  • Without it, DNA is not repaired, and cells replicate DNA and undergo mitosis even if DNA is damaged.

Oncogenes

• A proto-oncogene codes for a protein that contributes to cell division.

  • Mutation may switch on this gene permanently, causing excessive amounts of the protein, causing rapid and repeated mitosis.

  • This is therefore known as an oncogene, as it causes cancer.

• This can happen if:

  • A mutation rearranges chromosomes, placing the proto-oncogene next to a DNA sequence that permanently activates it.

  • There is an extra copy of the proto-oncogene, resulting in too much of it being made, causing excess mitosis.

• Tobacco has over 4000 chemicals, including tar, nicotine, carbon monoxide, 40 carcinogens and 400 toxic genes.

  • Tar collects in the lungs as tobacco smoke cools, tar itself made up of many chemicals such as polycyclic hydrocarbons.

    • These can enter the nuclei of alveolar cells and slide between DNA base pairs, causing mutation by preventing accurate replication.

  • This is one way in which tobacco smoke is carcinogenic.

Gene expression control

• Variation has been historically been related to:

  • Differences in DNA nucleotide sequence (alleles).

  • Physiological effects of the environment (resource availability).

• Evidence has accumulated that the environment can alter expression of genes, by affecting their transcription, without changing the nucleotide sequence.

  • These are epigenetic changes - they affect the genes but not the nucleotide sequences.

Epigenetic modifications

DNA methylation

• Cytosine can have a methyl or hydroxymethyl group added.

• Methylated cytosine can be read as cytosine, and pairs with guanine.

• If regions of DNA are heavily methylated, however, cytosine is less likely to be transcribed.

Histone modification post-translation

• This can occur when an acetyl group attaches to the amino acid lysine, a methyl group to lysine and arginine or a phosphate group to serine and threonine.

• These changes affect their interaction with DNA, via changing nucleosome arrangement.

• When unmodified, nucleosomes pack more tightly, reducing their access to enzymes and reducing transcription.

  • When modified, coiling is more relaxed and transcription factors and RNA polymerase have access to the DNA, increasing transcription.

Variation

• Embryo stem cells progressively differentiate, switching off genes coding for enzymes that are not needed.

• This means differentiated cells only express genes necessary for their own activity.

  • For example, skin cells produce melanin and retinal cells produce rhodopsin.

• Epigenetic changes can occur to cells within the same tissue and different tissues, causing the vast difference in gene expression in different cells of an organism.

• Epigenetic changes can be caused at the site of repaired damage

  • This damage occurs around 60,000 times a day in each cell of the human body.

• Monozygotic twins provide evidence of these changes:

  • They have the same nucleotide frequencies, but as they grow, their histone DNA methylation and histone acetylation differences increase.

Consequences

• Genomic imprinting:

  • If genes are inactivated in gametes, the inactivation can be transferred to the next generation.

  • A gene may be permanently switched off due to DNA methylation on the chromosome of one parent, which could cause a medical condition.

  • An example is the NOEY2 gene, which increases the risk of ovarian and breast cancer if not expressed.

• X inactivation:

  • These changes can switch off a whole chromosome.

  • Cells of female mammals use only one X chromosome, and the other is inactivated, becoming a mass of densely staining chromatin known as the Burr body.

  • An example is tortoiseshell cat coats, which reflect random inactivation of either X chromosome.

• These changes have also been implicated in autoimmune conditions, mental illness, diabetes, and many cancer.

  • Epigenetics is likely to become very important in disease detection, treatment and prevention.