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Understanding the Human Genome and Genetics

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The Human Genome

  • The structure of the DNA molecule was discovered in 1953 by James D. Watson and Francis Crick.
  • A human genome is made of 3,200 million base pairs, split into 46 chromosomes.
  • The first complete human genome was only decoded in 2003 and published in 2007. The first two individuals who had their genome sequenced that year were James Watson, whose genome was sequenced by the Human Genome Project funded by the U.S. Government, and Craig Venter, CEO of Celera Genomics, funded by the private sector.
  • A human genome is 98% identical to a chimpanzee's genome, and 97% to a gorilla's. In comparison, two random human beings are in average 99.5% identical. Gorillas are in fact 97% identical to either humans or chimps, meaning that humans are more chimp-like than gorillas.
  • Most of our genome is made of noncoding DNA, sometimes called "junk DNA". Only approximately 2% of our genome encodes proteins. This so-called junk DNA is composed either of deactivated genes that were once useful for our non-human ancestors (like a tail), or parasitic DNA from virus that have entered our genome and replicated themselves hundreds or thousands of times over the generations, but generally serve no purpose in the host organism. One famous retrovirus that copies itself into the human genome is HIV.
  • Genome size is not related to the complexity of life. For example, the genome of Polychaos dubium, a microscopic unicellular being, has been reported to contain more than 200 times the amount of DNA found in the human genome.

       

Base pairs & mutations

  • Nucleotides are the alphabet of DNA. There are only four "letters" in DNA, called bases. The four bases are adenine (A), thymine (T), guanine (G) and cytosine (C). A always pairs with T, while G always pairs C. Such pairs are called base pairs. In RNA, thymine (T) is replaced by uracil (U).
  • Almost every cell in our body contains a complete copy of our genome. The exceptions are gametes (ovocytes and sperm cells), which only carry half of our genome, as well as red blood cells, which have no nucleus and therefore no DNA at all.
  • If the DNA contained in each cell's nucleus was completely unfolded, it would measure nearly 2 metres in length. Humans have an estimated 100 trillion (1012) cells. In other words, if the all the DNA from every cell in a person's body were patched up together they would form a strand of 200 billion kilometres, or more than 1,000 times the distance between Earth and the Sun.
  • Mitochondrial DNA is found outside the cell's nucleus, inside the mitochondria - organelles that provide energy to the cell. It consists of only 16,569 base pairs, or 0,000005% of the human genome.
  • Mitochondrial DNA (mtDNA) is inherited only through one's mother. As it does not recombine like chromosomes, it can be used in population genetics to trace back ancestry on the matrilineal side and to divide populations into haplogroups. The same can be done on the patrilineal side using the Y-chromosome (Y-DNA), which is inherited exclusively from father to son and does not recombine with the X chromosome. Only a few mutations distinguish the Y chromosome of a man and his father. These mutations are cumulative from generation to generation, so it is easy to trace the family tree of humanity by analyzing these mutations (SNPs) on the Y chromosome and mtDNA.
  • A SNP (single nucleotide polymorphism) is a mutation in a single base pair. Depending on what section of DNA is affected, these mutations can alter the physical appearance, have a positive effect on health (e.g. better immunity), cause malfunctions or diseases, cause genetic diseases (e.g., cystic fibrosis), or have no effect at all (silent mutation). This will depend on whether the mutation occurs in a coding region of a gene, and if this is the case, on the nature of the replaced amino acid (e.g. hydrophilic instead of hydrophobic).

The Chromosomes

  • Humans have 23 pairs of chromosomes, each person inheriting a maternal and paternal copy of each chromosome. Pairs of chromosomes are numbered from the largest (chromosome 1) to the smallest (chromosome 21). Chromosome 22 ought to be the smallest, but it was later discovered than chromosome 21 was smaller, and the established ordered was kept.
  • The sex-determining chromosomes (X and Y) are the only pair that is not symmetrical in size. The Y-chromosome possess 60 millions bases, against 153 millions for the X chromosome.
  • The reason why the Y chromosome is so much smaller than the X chromosome is that the latter possess genes that "attack" the Y chromosome. In response the Y chromosome has had to shut down a lot of its non-coding DNA so as to better protect itself.
  • In some rare cases people are born with one extra chromosome. Those born with three chromosome 21 have Down's syndrome. Other possibilities is an extra X chromosome, leading to Klinefelter's syndrome (XXY), XYY syndrome, Triple X syndrome, XXYY syndrome, 48, XXXX, or 49, XXXXX. An extra copy of any other chromosome normally results in miscarriages. Some very rare cases of autosomal trisomies can survive to birth, notably when it affects chromosomes 13 or 18, but result in seriously shortened life expectancy.
  • Humans, like most animals, are diploid, meaning that they have only two sets of chromosomes. However that is not the case of all life beings. Plants in particular are often polyploid. There are varieties of wheat that are tetraploid (four sets of chromosomes) and others that are hexaploid (six sets of chromosomes). Some strawberries can be decaploid (ten sets of chromosomes). Polyploid animals include the goldfish, salmons, and salamanders. Polyploidy occurs in some human tissues like muscles or the liver. When two or three spermatozoids fertilise an ovum at the same time, a human foetus will be triploid or tetraploid. However almost all such pregnancies end as miscarriage and those that do survive to term typically die shortly after birth.

Heredity & Genetic Diseases

  • Virtually all diseases, syndroms, and medical or psychological conditions have at least partially a genetic origin. These are called risk factors for a condition. Adding up the risks over different genes gives the level of genetic predisposition to a disease or condition. The genetic risk profile is determined by a DNA test and leads to personalized medicine and pharmacogenetics, which aim inter alia to adapt his lifestyle and treatments based on the specifics of his own genome.
  • the so-called genetic diseases are caused exclusively by genes and are usually caused by a single mutation or series of mutation making an ineffectif gene. The only possible treatment to cure a genetic disease is the gene therapy (or gene therapy), which is to change the DNA sequence in the genome of the individual. These techniques are in full swing and, currently, treatments have already done successfully for ten genetic disorders, including cystic fibrosis (the most common genetic disease in Europe) and Thalassemia (which is common in the Mediterranean). In the near future it will be possible to use gene therapy to modify one's genome "on demand", for example to increase physical and mental abilities, or extend its life expectancy.
  • Although autosomal DNA is inherited equally from each parent, a few genetic diseases seem to be worse when inherited from one's father (e.g. Huntingdon's disease), because mutations occur or repeat themselves at a higher rate in men, and increase with the father's age. This is also why older fathers (over 40 years old) have higher chances of having children suffering from schizophrenia, depression or autism.
  • Some genes have different functions depending on whether they are inherited from one's father or mother. These are called imprinted genes. For example, the maternal copy of a gene on chromosome 15 is known as UBE3A, while the paternal copy is called SNRPN. Inheriting two paternal copies or missing the maternal copy causes Prader-Willi syndrome, whereas two maternal copies or a deletion of the paternal copy leads to the very different Angelman syndrome.
  • Rather than inheriting a homosexual gene, studies have observed that gay men tended to have several older brothers (including abortions and miscarriages). The reason is that the mother's body accumulates antibodies against genes responsible for the masculinisation of the foetus' brain at each pregnancy with a boy. The risk of male homosexuality therefore increases with the number of boy carried by a mother before. This does not apply to girls.

       

Genetics of the brain

  • Neurotransmitters such as serotonin, dopamine, histamine, or gamma-Aminobutyric acid, influence our mood and personality. Their levels is influenced by our nutrition and interactions with our environment, but also depends on genetic factors. The sensitivity of the brain to these neurotransmitters is entirely genetically determined, notably by the number of receptors and transporters for each of these neurotransmitters.
  • Low serotonin levels increase depression, anxiety, risk of suicide and violence. Carbohydrates and cholesterol both increase serotonin levels.
  • Excessive dopamine can lead to schizophrenia. Too low dopamine levels engender boredom and low activity, and in extreme cases Parkinson Disease. The long variants (7-repeat or more) of the dopamine receptor D4 (DRD4) causes dopamine to be consumed more quickly by the brain. People with this variant will usually have more novelty-seeking, thrill-seeking and adventurous personality than average to compensate for naturally lower dopamine levels. Similarly, the number of dopamine receptor D2 (DRD2) influences the risk of alcoholism, nicotine dependence, and schizophrenia. It is easy to know what variants one carries with a DNA test.

Immunity & Evolution

  • Some people possess a deletion on the CCR5 gene, which makes them more resistant (if inherited from only one parent) or completely immune (if inherited from both parents) to smallpox, HIV, plague and other viruses (e.g. West Nile virus). This mutation is commonest in north-east Europe, notably in Baltic countries, Finland and Sweden.
  • The ABO blood type is related to cholera resitance, with AB confering the strongest resistance, and O the weakest. On the other hand, the O blood group seems to be the most resistant against malaria and syphilis, and less susceptible to many kinds of cancers. The ABO blood type influences many other disease risks.
  • Many genetic diseases survived natural selection because they confer immunity against epidemic diseases. For instance, the CFTR mutation causing cystic fibrosis protects against the dysentry and fever of typhoid. Sickle-cell anaemia and thalassaemia are both protective against malaria. Genetic resistance to TB has for side-effect an increased susceptibility for osteoporosis. Tay-Sachs disease, mostly found among people of Ashkenazi Jewish ancestry, is also protective against TB.
  • Studies have shown that men and women are most attracted to the smell of people with the most different immune system from their own. This is also a way of Nature to prevent inbreeding. Differences in immune systems can be identified by comparing our HLA types, among other genes of the major histocompatibility complex (MHC).

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