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Patterns of inheritance

Back in the day, Mendel crossed different varieties of pea plants to establish rules of inheritance. He didn't know what we know today about genes and DNA. So what do we know, and what did he find out?

The entirety of genetic material in an organism is called a genotype. It can also refer to specific things, like a genotype for a certain trait in a given organism.

The genotype refers to the physical constitution of a little part of DNA. Its expression, however (that is what protein a gene encodes, and what that protein ends up doing in the organism) is a separate entity which is subject to environmental influence. This is called the phenotype.

Humans have 2 sets of chromosomes, so for each distinct chromosome e.g. chromosome 1, there are two copies. How do the same genes on both homologous chromosomes interact if they result in different phenotypes? Which has priority?

If you crossed a green pea plant with a yellow pea plant, what colour would the offspring be? What about their offspring's offspring?

This is precisely what you'll be able to answer by thee end of this topic.


Basics

Versions of the same gene that give rise to different phenotypes are called alleles. For example, the gene responsible for ear shape in a cat may have 2 alleles: pointy shape and oval shape.

One of these alleles may be expressed at the expense of another, where both are present together in a cat. Say that the oval shape allele is dominant while the pointy shape is recessive.

Because cats also have 2 copies of each chromosome (and therefore gene), these alleles are written as 2 letters. 

If the gene for ear shape is abbreviated as E or e for ear, then the alleles would be:

E (dominant) for oval shape and 
e (recessive) for pointy shape

These upper case - dominant, lower case - recessive notation rules are used universally. So what combinations may be present in a cat?

EE, ee or Ee

The first two examples are called homozygous because the same allele (E or e) is present twice, while the last example is heterozygous because different alleles (E and e) are present.

So what happens in crossing?

EE x ee gives rise to 4 combinations: Ee, Ee, Ee and Ee! 100% heterozygous where the cats will appear oval-ear shaped, yet also carry the recessive allele for pointy ears. Let's do a second cross.

Ee x Ee gives rise to 4 combinations: EE, Ee, eE and ee. That's 50% homozygous and 50% heterozygous. 3/4 will have oval ears while 1/4 will have pointy ears.





Now see what happened in Mendel's pea plant experiments?

It's also possible to have multiple (more than 2) alleles for a given gene. Say there is also a round ear allele. It could be that this allele is codominant with the pointy ear allele, so that both traits are simultaneously expressed.

Multiple alleles involve three or more variations (alleles) of a gene. A common example is blood type: A, B, AB or 0 given by three alelles, i, IA and IB.


Relative to type 0 (i-i), both A (i-IA or IA-IA) and B (i-IB or IB-IB) are dominant, while A and B are codominant enabling option AB (IA-IB).

These cases represent monohybrid inheritance. Regardless of how many alleles there are for one gene, we are only looking at one gene and its associated trait - hence monohybrid.




Dihybrid inheritance refers to the inheritance of two genes, each with multiple alleles. Increasing the number of compared genes therefore produces a greater variety of genotypes in the offspring.

This showcases Mendel's first law that states factors are segregated. Remember, in that time DNA and the concept of a gene weren't known. Segregation of factors referred to the factors (genes) being inherited independently from each other. The second law refers to the independent assortment of these factors during inheritance. This resonates in particular to the process of meiosis where chromosomes are assorted into offspring cells independently of each other. That is, small heritable units e.g. genes are subject to their own heritability, and individuals do not simply inherit their parents' genetic information in bulk.

It is possible that some allelic combination are lethal and do not result in viable offspring.




If a dominant individual is not known to be homozygous or heterozygous, a test cross can be done where the unknown individual is crossed with a recessive (and hence homozygous) individual. The phenotype proportion of the offspring can reveal whether the dominant parent is homozygous or heterozygous.

In addition to the AB0 blood type example, multiple alleles are showed in the human leukocyte antigen (HLA) complex. This is a cluster of genes on chromosome 6 that codes for the major histocompatibility complex in humans. The MHC governs the immune function of recognising the body's own cells from invading pathogens.



These over 200 genes are highly variable and are classified into 3 classes (I, II and III), each of which has specific genes that are considered major. For example, the major genes in Class I are HLA-A, HLA-B and HLA-C. They are considered major because they are expressed on the surface of almost all cells in the body.




The number of variant alleles of major genes in Class I is very high. For example, there are 3,589 different versions of the HLA-B gene. Given this great variation and the sheer number of different genes, the outcomes of crossing two people results in many different HLA combination outcomes. This is the type of screening that is important in organ transplantation. It is also why close relatives are not necessarily compatible from this point of view.


Chi-squared test

The chi-squared (c2) test is a measure of expected frequency versus observed frequency to determine how closely aligned they are; whether what is observed would be expected or whether it is different to what would be expected.

The default expectation is the null hypothesis which states that no difference exists between the things we are experimenting with, observing or comparing and their default, or control state.

The chi-squared value we obtain from the chi-squared test is put against a probability scale. The probability refers to the probability that for a given chi-squared value (which is defined by how different our observation is from what we would expect), what we observe really is different to what we expect to a significant extent that enables us to reject the null hypothesis.

For example, our expected values for the eye colour of 154 flies in a population would be:

Eye colour: 77 white and 77 red

The expected values cannot be below 1 for the chi-squared test.

Say our study reveals that in fact there are:

Eye colour: 98 white and 56 red

The way to carry out a chi-squared test is to take the difference between the observed (O) and expected (E) values, square it, and then divide by the expected number (E). This is done for both categories and then added together for the final chi-squared value. The extra 0.5 taken away is know as the Yates correction and is used if our comparison only has two groups.

(O-E-0.5)2 / E for white = (98-77-0.5)2 / 77

5.46

(O-E-0.5)2 / E for red = (56-77-0.5)2 / 77

6.00

We then add the two, 0.03 + 1 and get 11.46. The reference table for the chi-squared values looks something like this:




The most often used threshold for the significant probability value is 0.05, or 5%. This means as long as the probability of mistaking whether there is a difference between observed and expected is less than 5%, we will assume the difference is indeed real.

The degree of freedom refers to the number of groups being compared - 1. So in our white-red example we get 2 - 1 = 1. Our degree of freedom is 1.

The p value for 1 degree of freedom at 0.05 is 3.84. Our chi-squared value for eye colour is above this, so we can reject the null hypothesis and say that there is a significant difference between the observed and expected numbers of white and red eye colour.


Mutation

The Cause of Mutations

Mutations are a random occurrence during DNA replication and the rate of mutation is influenced by external factors such as UV radiation. There are different types of mutation:

1. Deletion where a nucleotide base is deleted. AGTCA becomes AGCA.

2. Substitution where a nucleotide base is replaced by another. AGTCA becomes AGTCG.

3. Insertion where a nucleotide base is added as extra. AGTCA becomes ATGTCA. 




The Effect of Mutations

Since the genetic code is degenerate, it's possible that a mutation won't have any effect whatsoever! This represents silent mutations. If 2 different triplet codes translate into the same amino acid, the polypeptide chain will remain unchanged. This of course only applies to substitutions.

Another scenario where a mutation may cause no effect is if it arises in an intron. Since these are removed before mRNA is translated, no mutations would be carried along.

What happens if a base is deleted or added? The genetic code is non-overlapping, so the error cannot simply be overlooked and the following triplets read correctly. The entire subsequent code will be shifted. This is called a frameshift

Deletion: AGT GGC TTA... --> lose the first G --> ATG GCT TA...

Insertion: AGT GGC TTA... --> insert an A after the first A --> AAG TGG CTT A...

The code is affected significantly!!! In fact, it may be totally ruined. One way this can happen is by a nonsense mutation which by a frameshift causes the code to arrive at a stop codon earlier than it's supposed to. This will result in a shorter polypeptide and therefore truncated protein which may malfunction.

missense mutation is when a substitution changes the amino acid encoded. This does not necessarily impact the overall protein, but it may result in a protein with an altered binding site and therefore affect its activity.




Sickle cell anaemia

Sickle cell anaemia is a part of sickle cell disease which is a genetic condition affecting the haemoglobin in our red blood cells. This impairs its function of carrying oxygen in the blood and hence can cause symptoms of anaemia such as dizziness, rapid heart rate and fatigue.

Quite rarely, a condition is caused by a simple point mutation of just one DNA base. This is the case in sickle cell anaemia. The single change, in this case a substitution, happens to result in a different amino acid being coded for altogether, as the codon the mutated base is part of codes for valine instead of glutamic acid in this case.


This results in different properties in the new haemoglobin, and as red blood cells contain millions of haemoglobin molecules, it alters the red blood cell structure and function too.



They become sticky and compromise circulation. The different shape of the cell, resembling a sickle, gives this condition its name. In areas where HIV is endemic, sickle cell disease has spread significantly. Despite it being a detrimental feature, it seems to confer some resistance if HIV infection has taken place in the same individual. In this way the condition has persisted since it is advantageous to those who also have HIV.


Cystic fibrosis

Cystic fibrosis (CF) is also caused by a mutation in one gene (monogenic). Carriers only have one mutated copy, while those with CF have two mutated copies of the CFTR gene on human chromosome 7.



The CFTR (cystic fibrosis transmembrane conductance regulator) protein is a chloride ion channel, key in multiple processes such as the secretion of sweat, digestive juices and mucus.




Inactivity of this transporter results in the accumulation of thick mucus in various parts of the body such as lungs, sinuses, sweat ducts and bowels. This creates the CF symptoms of recurring chest infections, difficulty breathing, frequent coughing, diarrhoea and difficulty gaining weight.

The mucus makes tissues more prone to infections, so antibiotics must be taken. Due to the specific infectious agents carried by people with CF, it is also not indicated for them to contact each other, in order to minimise cross-transmission.

Over time, lung damage is accrued. This is life-threatening and may only be counteracted by a lung transplant. Due to these symptoms, life expectancy for people with CF is not as high as for the general population. With increasing life expectancy generally, and improving management of the condition, those born more recently can expect a longer life expectancy.


Phenylketonuria (PKU)

PKU is a condition caused by a mutation on chromosome 12 of the PAH gene. PAH stands for phenylalanine hydroxylase which is responsible for the metabolism of the amino acid phenylalanine to the amino acid tyrosine.

People with two copies of the mutation exhibit the symptoms of PKU if left untreated. Failure to metabolise phenylalanine results in high buildups of the amino acid, which are detrimental to the brain. In developing children, this can have severe and permanent effects due to intellectual disability, microcephaly and mood disorders, in addition to symptoms of musty odour and very light skin.

Management of PKU must start in infancy soon after birth and continue throughout life. This is why screening for PKU is carried out after a baby is born by taking blood samples. If after a couple of days of normal feeding the baby has elevated phenylalanine levels, PKU is suspected and further tests are carried out to confirm the diagnosis.

PKU is managed by a diet low in phenylalanine, alongside supplements of protein that might be lacking due to the low-phenylalanine diet.




With an adequate diet and regular blood monitoring of phenylalanine levels, people with PKU can prevent symptoms and expect an average lifespan.


Huntington's disease

Unlike the previous conditions, Huntington's disease (HD, named after its discoverer) is autosomal dominant. This means just one copy of a mutated gene coding for the protein huntingtin is sufficient to cause the disease. This mutation is an insertion of a 3-base repeat (CAG) beyond the normal number of repeats i.e. 36.



CAG codes for the amino acid glutamine which becomes part of the primary structure of the protein.

The mutated version of hungtingtin starts damaging specific brain cells that are susceptible to it in the basal ganglia and cerebral cortex. Symptom onset is around 30-50 years old, but may occur at any age. The progression of the disease spans 10-20 years.

These symptoms include jerky movements and a host of cognitive impairments that progress from difficulty planning, thinking in abstract and using rules, to memory loss that eventually progresses to dementia and requires full-time care.

The range of psychological symptoms is very wide and includes anxiety, depression, aggression and compulsive behaviour.

If a family history of HD exists, an expecting parent may undergo prenatal testing to check if the foetus has the disease. As this condition is classified as a terminal illness, the testing is only carried out if the parent is willing to terminate the pregnancy in the case of a positive HD result.

This is done in order to avoid a child finding out they have a terminal illness that was carried through without their ability to consent.


Sex linkage and autosomal linkage

Sex linkage refers to a trait that is carried on a sex chromosome like the X chromosome. Because someone might have a different number or combination of sex chromosomes such as a single X chromosome or two X chromosomes, the expression of various traits can differ.




If for example the allele on the affected X chromosome means that an essential protein isn't being made, the carrier XX child has another unaffected X chromosome to fall back on and be able to produce the essential protein. The carrier XY child only has the affected X chromosome and cannot make the protein. This results in an illness for example, such as haemophilia. Haemophilia is a blood clotting disorder in which excessive bleeding takes place because the platelet plug and fibrin which are supposed to stop bleeding do not work fully.




Another example of an X-linked condition is Duchenne muscular dystrophy which affects around 1 in every few thousand children with an XY genotype. It is a progressive muscle degeneration condition that affects mobility, and in the long term requires assistive ventilation devices, with an overall impact on life expectancy. 

The inheritance pattern matches that of haemophilia.

Autosomal linkage is the other option. An autosome is a chromosome that isn't a sex chromosome. In humans this could be chromosome 1, chromosome 2, etc.




Nail patella syndrome is an example of an autosomal linkage (alongside some previously covered conditions such as phenylketonuria). It is an autosomal dominant condition, so only one mutated gene is sufficient to cause the disease. It is also possible for the mutation to have occurred spontaneously in someone rather than to have been inherited.

Its name comes from the symptoms of small, underdeveloped nails, and an absent, small or misshapen kneecap (a.k.a. patella) that may be easily dislodged. The name is somewhat misleading, as this condition presents many symptoms in other areas of the body. These include glaucoma (high pressure in the eyes), bloody urine due to impaired kidney function which may progress onto kidney disease, digestive problems, tingling or burning sensation in the hands and feet, osteoporosis and others.

Treatment involves the specific alleviation of each symptom e.g. surgery on the patella, physical therapy for joint pain, and dialysis in the case of loss of kidney function.


Investigating inheritance with model organisms

Due to their observable characteristics, ease of handling and breeding, and fast generation times, model animals such as Drosophila melanogaster have been used to discover the rules of inheritance. Pea plants are not the only ones to do the honour!

The black/grey body, and long/vestigial wing in Drosophila follows autosomal inheritance. Because the autosomes are subject to changes in meiosis, unpredictable offspring can result from crossing a heterozygous wild type with a recessive mutant. In this case, the yellow (or grey) fly with long wings is the wild type.




If the two traits were linked up (yellow with long; black with vestigial), the only possible offspring here would be those two combinations. However, upon breeding them, we find some offspring that are yellow have vestigial wings, while some offspring that are black have long wings. This is possible due to crossing over of genes during meiosis.

Since autosomes are inherited evenly, the outcome for the offspring follows the same pattern as for dominant/recessive interactions. This scenario is also an example of dihybrid inheritance, previously covered.


Down's syndrome, Turner's syndrome and Klinefelter's syndrome

During meiosis, different chromosome distribution in the gametes can occur which can leave them without the expected number of chromosomes. If there are more chromosomes than expected (2 of each in humans), this is termed polysomy and can result in conditions such as Down's syndrome. If there are fewer chromosomes than expected, it is monosomy and can result in conditions such as Turner's syndrome.

Down's syndrome involves an extra chromosome 21, and expresses itself in terms of many different features, some of which are detrimental to health. Common outcomes include unique facial features, slower overall development, higher incidence of congenital heart abnormalities, decreased or absent fertility and overall lower life expectancy.



Turner's syndrome is in a way the "reverse" of Down's syndrome as it presents one fewer chromosome rather than one extra. Specifically, it is a diminished or absent X chromosome. Since XY embryos missing their only X chromosome would not be viable, this syndrome only presents itself in births of would-be XX babies who end up having just one X chromosome or one X and a partial X.

As many as 99% of Turner's syndrome cases are thought to terminate via miscarriage or stillbirth. For those who survive and are born alive, common features include a webbed neck, low-set ears, short stature, lack of puberty without hormonal treatment and heart defects. Their overall life expectancy is shorter due to the development of heart disease, diabetes, thyroid problems and others, and constant health monitoring is required.




Klinefelter's syndrome is a relatively common chromosomal variation (up to 1 in 500 male assigned births) where an XY individual has an extra X chromosome, hence being an XXY individual. Life expectancy is comparable to XY individuals. 



Symptoms of the condition include reduced fertility or infertility, lower levels of testosterone, increased height, reduced muscle strength and coordination, breast growth and learning and speech difficulties. Interventions include speech therapy, testosterone replacement therapy, breast surgery and assisted reproductive technology.


Chromosomal mutations

Mutations do not only occur at the DNA sequence level. They can also take place chromosome-wide, as seen in Down's, Turner's and Klinefelter's syndromes.

Translocation is a type of chromosomal mutation where one or more nucleotide bases are moved between non-homologous chromosomes e.g. AAGCTT on human chromosome 1 is moved and becomes AAGCTT on human chromosome 3




Not assigning the expected chromosome or chromatid during meiosis is called chromosome non-disjunction and results in a cell with a different number of chromosomes.




Screening and conducting genetic tests for genetic conditions has ethical considerations, as seen previously with Huntington's disease. The purpose of screening is to detect conditions ahead of time to be able to better inform decisions regarding the patient's health. Genetic testing can provide information on genetic conditions before conception, and inform reproductive choices and methods.

A variety of human conditions are caused by a single gene. This means that the diagnosis of certain diseases, as well as the predisposition to them, and probability of passing them on to a child can all be found out pretty easily. This has implications that extend to blood relations. While someone might jump at the opportunity of being better informed, their relative might prefer not to know so much, and be able to live without worrying or trying to control things.

Genetic counselling can take place for couples with genetic conditions who wish to have a child and be fully informed about the risk of their child inheriting that condition - whether just carried or expressed (recessive alleles).

Ok byeeeeeee

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