Mutation, polymorphism, and DNA damage Flashcards
Describe the different kind of mutations. If possible, make some examples.
Dominant versus recessive: depending on whether one or two copies of the mutant allele are needed to express the phenotype.
Germ-line versus somatic: depending on whether they occur in the cells that produce gametes or in the other cells of the body.
Harmful/lethal versus beneficial: depending on whether they reduce or increase the fitness of the organism.
Loss of function versus gain of function: depending on whether they decrease or increase the activity or expression of a gene product.
Small scale versus large scale: depending on whether they affect one or a few nucleotides or a large part of a chromosome.
Examples of mutations are:
sickle cell anemia a recessive, harmful, loss of function, small scale mutation (in the beta-hemoglobin gene),
lactase persistence, a dominant, beneficial, gain of function, small scale mutation (in the lactase promoter),
What are the different kinds of large-scale mutations?
Change in chromosome number: when an organism has variations in the number of chromosomes, such as monosomy (loss of a single chromosome),
trisomy (gain of a single chromosome), or
tetrasomy (gain of an extra chromosome pair).
Change in chromosome set: when an organism has variations in the number of sets of chromosomes, such as
polyploidy (more than two sets of chromosomes) or
aneuploidy (abnormal number of chromosomes).
Chromosomal mutation: when a part of a chromosome is altered in its structure or position, such as
inversion (reversal of a segment within a chromosome),
deletion (loss of a segment of a chromosome),
duplication (gain of an extra copy of a segment of a chromosome),
amplification (multiple copies of a segment of a chromosome),
insertion (addition of a segment from another chromosome),
translocation (exchange of segments between non-homologous chromosomes),
chromothripsis (shattering and reassembly of a chromosome), or
copy number variation (variation in the number of copies of a segment of DNA among individuals).
How can you study the risk of a monogenic versus a polygenic disease?
The risk of a monogenic versus a polygenic disease can be studied by different methods, such as:
Family studies: tracing the inheritance of a trait or a disease in a family and calculating the recurrence risk or the heritability of the trait or disease.
Linkage analysis: identifying chromosomal regions that are co-inherited with a trait or a disease in a family and mapping the genes that are responsible for the trait or disease.
Association studies: comparing the frequency of genetic variants between individuals with and without a trait or a disease in a population and identifying the variants that are associated with the trait or disease.
Sequencing studies: identifying the exact sequence of DNA bases in individuals with and without a trait or a disease and detecting the variants that cause or contribute to the trait or disease.
What are the most common sources of DNA damage?
Endogenous sources: those that originate from within the cell or the organism, such as spontaneous reactions (e.g., depurination, deamination, oxidation, alkylation), reactive oxygen species (ROS), replication errors, or programmed cellular events (e.g., meiosis, immunoglobulin maturation).
Exogenous sources: those that originate from outside the cell or the organism, such as ultraviolet (UV) light, ionizing radiation, environmental exposure, or chemical agents.
How are mismatched generated and repaired?
Mismatches are generated when DNA bases are incorrectly incorporated during replication or recombination. They are repaired by the mismatch repair (MMR) pathway, which involves the following steps:
Recognition: the mismatch is recognized by a complex of proteins called MutS, which binds to the mismatch and recruits another complex of proteins called MutL.
Excision: the newly synthesized strand of DNA is distinguished from the template strand by the presence of nicks or gaps, and the mismatched segment of DNA is excised by an endonuclease and an exonuclease.
Resynthesis: the gap in the DNA is filled by a DNA polymerase and sealed by a DNA ligase, restoring the correct base pairing.
How are mismatched generated and repaired?
Methylated cytosines are mutagenic because they can undergo spontaneous deamination, which converts them into thymines. This creates a mismatch between the original guanine and the new thymine, which can lead to a permanent mutation if not repaired by the base excision repair (BER) pathway.
Describe what is a Double strand break, its possible consequences and how can it be repaired
A double strand break (DSB) is a breakage of the phosphodiester bonds on both strands of DNA, creating two free ends. It can be caused by endogenous sources (e.g., ROS, programmed cellular events) or exogenous sources (e.g., radiation, chemical agents). It can have serious consequences for the cell, such as chromosome loss, mutations, or rearrangements, if left unrepaired or misrepaired. It can be repaired by two main pathways: non-homologous end joining (NHEJ) or homologous recombination (HR).
NHEJ: a quick and simple but error-prone pathway that directly ligates the two ends of the DSB, often with loss or gain of nucleotides at the junction. It does not require a homologous template and can operate throughout the cell cycle.
HR: a precise and accurate but complex and slow pathway that uses a homologous template (usually the sister chromatid) to copy the missing information and restore the original sequence of the DSB. It requires a homologous template and can only operate in the late S and G2 phases of the cell cycle, when the sister chromatid is available.
Describe a DNA repair mechanism of your choice
A DNA repair mechanism of my choice is nucleotide excision repair (NER), which repairs bulky lesions in the DNA, such as pyrimidine dimers or intrastrand crosslinks, that distort the normal structure of the DNA and block transcription or replication. It involves the following steps:
Recognition: the lesion is recognized by a complex of proteins called XP (xeroderma pigmentosum), which binds to the lesion and recruits another complex of proteins called TFIIH, which unwinds the DNA around the lesion.
Incision: the damaged strand of DNA is cut on both sides of the lesion by two endonucleases, XPG and XPF-ERCC1, creating a gap of about 30 nucleotides.
Excision: the excised segment of DNA is removed by a helicase, XPB, and degraded by an exonuclease, RPA.
Resynthesis: the gap in the DNA is filled by a DNA polymerase and sealed by a DNA ligase, restoring the normal structure of the DNA.
Which cells induced programmed Double Strand Breaks? Why? And how do they repair
them?
Some cells induce programmed double strand breaks (DSBs) in order to fulfill their tasks, such as developing T and B cells of the adaptive immune system, or germ cells during gametogenesis.
T and B cells: These cells generate unique receptors that can recognize different types of molecules (antigens) by randomly assembling different gene segments through a process called V(D)J recombination. This process involves the induction of DSBs by an enzyme called RAG (recombination activating gene) and the repair of DSBs by NHEJ, creating diversity and specificity in the antigen recognition. Another process that involves the induction of DSBs by an enzyme called AID (activation-induced cytidine deaminase) and the repair of DSBs by BER or MMR is class switch recombination (CSR), which changes the class of the antibody without changing its antigen specificity.
Germ cells: These cells generate haploid gametes (sperm or egg) from diploid cells through a process called meiosis. This process involves the induction of DSBs by an enzyme called SPO11 and the repair of DSBs by HR, creating diversity and recombination in the genetic material. The DSBs are repaired using the homologous chromosome (not the sister chromatid as in mitosis), which allows the exchange of genetic material between the paternal and maternal chromosomes and increases the genetic diversity of the offspring.
Why Double Strand breaks are fundamental in Meiosis?
Double strand breaks (DSBs) are fundamental in meiosis because they trigger the pairing and recombination of homologous chromosomes, which is essential for the correct segregation of chromosomes and the generation of genetic diversity. The DSBs are induced by an enzyme called SPO11 and are repaired by HR using the homologous chromosome as a template. The recombination results in the exchange of genetic material between the paternal and maternal chromosomes and creates new combinations of alleles in the gametes.
Which regions of the eukaryotic genome look as Double strand Breaks? Why is this a
problem? How is it solved
Some regions of the eukaryotic genome, such as telomeres and centromeres, can look like DSBs because they have a similar structure or sequence1. This can be a problem because it can trigger the DNA damage response and the repair pathways, which can lead to chromosome fusions, rearrangements, or loss. This problem is solved by specific proteins and mechanisms that protect these regions from being recognized and repaired as DSBs. For example, telomeres are protected by a complex of proteins called shelterin, which binds to the telomeric repeats and prevents the activation of the DNA damage response. Centromeres are protected by a complex of proteins called kinetochore, which binds to the centromeric repeats and facilitates the attachment of the spindle fibers during mitosis or meiosis.
