Lecture 4 (2015)Apunte Español
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Ingrid Guarro Marzoa
Lecture 4-human genome: complexity and dynamics
Genes and DNA:
A gene is a segment of DNA that is able to produce a polypeptide under
regulated conditions. These genes are not placed in specific positions of the
chromosomes. In a gene we can find:
1. Regulatory sequences
2. The transcriptional unit: The region that is going to be transcribed into
RNA: this region is formed by exons and introns.
• Definitions: o Locus: place in a chromosome. Plural=loci o Diploid: 2n chromosomes. Human cells are diploid except egg and sperm cells.
o Alleles: different variantss of a gene.
§ Homozygote: when both copies contain the same allele.
§ Heterozygote: when the two copies contain different alleles.
Genome size varies between different species. It is usual that the more evolved an organism the larger the size of its genome (exception: plants and amphibious). The gene number between species also is bigger in more evolved organisms.
• Repetitive DNA sequences: Repetitive DNA sequences are tandem repeated sequences over and over again. We can’t find this DNA in bacteria and in humans we can find it in: o Telomeric sequences (AGGGTT repeat unit in human) Highly repetitive o Centromeric sequences (satellite DNA) o Variable number tandem repeats (VNTRs, minisatellite DNA) § VNTRs are routinely used for genetic identification.
o Di-and trinuclotide repeats (microsatellite DNA) o Non-adjacent repeats of modules with diverse sizes dispersed between and retrotransposons).
within genes (likely originated from 2014/2015 • Molecular Biology Ingrid Guarro Marzoa DNA processes: o Homologous recombination or general recombination: is a genetic exchange that takes place between a pair of homologous DNA sequences. Homologous DNA sequences are DNA sequences which are similar or identical in nucleotide sequence. It is used to repair double-strand breaks and to exchange bits of genetic information between two different chromatides to create new combinations of DNA sequences in each chromosome during meiosis. There is an enzyme that ensures that two chromosomes are perfectly lined.
o Transposition: is the process in which a wide variety of specialized segments of DNA (mobile genetic elements) are moved from one position in a genome to another. This mobile genetic elements that move by way of transposition are called transposons and they move thanks to an enzyme called transposase. This enzyme acts on a specific DNA sequence at each end of the transposon, causing it to insert into a new target DNA site. Transposition has a key role in the life cycle of many viruses (basically retroviruses) and also it is considered a source of mutation.
2014/2015 Molecular Biology Ingrid Guarro Marzoa o Mutation: mutation is a any change in DNA, many of them being random errors that occur during replication. Mutations can be caused by: § Tautomerism in nitrogen bases: a spontaneous mutation inherent to the DNA chemistry. It can cause the wrong incorporation of a base pair during replication that will become a fixed mutation in the following generations if not repaired.
§ Deamination § Replication errors § External chemical and physical agents such as oxidation of UV light.
Depending on altered sequence of DNA we can find: § Point mutations: caused by: o Transitions: a nucleotide change of one nitrogen base for the same type of nitrogen base. Ex: change of a purine for a purine.
o Transversions: a nucleotide change of one nitrogen base for a different type of nitrogen base. Ex: change of a purine for a pyrimidine § Insertions: inserting an extra nucleotide.
§ Deletions: deleting a nucleotide.
§ Translocations: move a nitrogen base from one place to another.
Repair: there are mechanisms that allow DNA to be repaired before mutations become stable. Mutations can cause different structural distortions into DNA (such as mutations created by UV light). The repair mechanisms the only thing they do is to look to distortions on DNA. They look on places where de double helix structure is not okay. Different kind of lesions wil be detected in different ways and will have different ways of getting it repaired. Once detected, mutations are repaired by a mechanism quite general for all mutations. First, when one base can’t fit with the pair one, it creates a distortion on the hydrogen bonds. An exonuclease cuts the fragment in which there is the error and removes it. This creates a gap and the fragment will be repaired by the DNA 2014/2015 Molecular Biology Ingrid Guarro Marzoa polymerase as if it was a Okazaki fragment and the ligase will close it. There is one particular case: cytosine deamination into uracil. Cytosine can be oxidazed and become uracil. This explains why DNA has thymine instead of cytosine. If DNA had uracils and one cytosine converts into a uracil it will be imposible for the cell to detect which uracil is wrong.
There is a mutation that prevents the complex from detecting the thymine dimers. If both parents have damaged genes for the protein that detects this dimer, their following generations may have skin cancer very easily. This skin cancer is called xeroderma pigmentosum. This fact underlines very clearly the importance of our systems to correct errors on DNA. This means that in all of us if we take some sun we require these proteins to remove the errors of our DNA, removing thymine dimers and thus decreasing the risk of skin cancer.
We have proteins that find DNA sites that have a wrong structure and tells (avisa) other proteins to cut the region that is affected. It only cuts one of the strands and so how does the cell know whether to cut one strand or the other one? We have some enzymes (common on bacteria) that recognize specific sequences and add methyl groups to some bases. This methyl group does not affect the base (it’s not going to cause any mutation). This methyl groups is going to be added to the same base in the other strand. The enzymes that look for these sequences are slow, so during some time after replication only one strand (the parental) is methylated. The proteins that detect these changes on the structure check which strand is methylated and which is not, and they cut the strand that DOESN’T have methyl groups, in other words, the newer one.