Genetics - Appunti esame

Intercalating agents: proflavine, acridine orange and ICR

They mimic base pairing by intercalating between nitrogen bases -> insertion if on newly synthesized strand; -> deletion if on template strand.

Damage a base so it won’t pair with anyone:

1. UV:

   Creates 2 lesions (photoproducts) on pyrimidine bases: cyclobutene photo dimer (interaction between 2 pyrimidines) and T-T interaction (6-4 photoproduct). This code cannot be read.

2. Ionizing radiation (X and γ rays):

   They form ionized molecules and superoxide radicals (O2-, OH-) which cause double stranded breaks in DNA. γ rays can lead to deletion. X rays dose is cumulative (linear relation between radiation and dosage) and has no efficient repair system.

Repair mechanisms

1. Photoreactivation DNA repair (for UV lesions):

   White light + enzyme photolyase -> opens T-T dimer

2. General excision repair (for UV lesions):

   Uvr pathway. UvrA recruits UvrB to the damaged site -> B and C recognise the photo dimer, make...

cuts -> helicase II takes away the damaged part -> polymerase I repairs the missing piece -> ligase binds everything together

3. Specific excision pathway, AP endonuclease repair pathway (for lesions not recognised by Uvr): DNA glycosylase (cleaves N-glycosidic base-sugar bond) recognises the damage -> takes out the damaged base, creating AP site (apurinic or apyrimidinic), recognised by AP endonuclease which cuts 1 strand -> exonuclease cuts DNA sequence next to AP site -> polymerase I synthesises a new strand. There are different glycosylases, like uracil glycosylase, which removes a U resulted from spontaneous deamination of C

Post replication repair

1. Mismatch repair: during replication an incorrect nucleotide was placed (eg T-C). The one to correct is the one on the newly synthesized strand (not methylated one), which gets replaced with a correct base.

2. Recombinational repair: when there is a photo dimer, after replication it's still there but the newly synthesized strand

has a gap -> there is an exchange of DNA between the gaped strand and the normal strand of another DNA molecule, which because of this, now has a gap -> repaired

3. SOS repair mechanism: bypass system to prevent breakages in DNA, it inserts random nucleotides just to have a correct number of them -> prone to mistakes

Chromosome mutations:

➔ Karyotype: complete set of chromosomes of a cell in mitotic metaphase. In prophase I of meiosis homologous regions have strong pairing affinity, form many structures. Broken chromosome ends pair with other like that, they are very sticky. To study chromosomes, Drosophila's 4 polytene chromosomes which chromatids don't separate, are perfect for that. 1 chromosome= 5000 bands. 1 band = 30 kbps

4 types of changes in chromosome structure

1. Deletion or deficiency (loss of part/whole chromosome, induced by X or γ rays) with 2 mechanisms: interstitial (inside the chromosome, must contain 2 cuts) and terminal (1 cut is enough BUT there are

telomers to conserve, so a 2 cut is neededfor them to stick back after). The piece cut is acentric, thus lost. In polytenechromosomes, the loss of a piece means the forming of a loop (no part to stick to thechromatid)

a. Intragenic: small deletion in a gene, similar to a null point mutation

b. Multigenic: lethal if homozygous (when all 2 copies of a gene are deleted),sometimes viable when heterozygous (1 copy of gene still remains), but thereis pseudodominance: bc there’s only 1 copy, a recessive allele will act as thedominant one. Deletion in humans at the end of chr5 -> chi du chat

2. Duplication (increase of gene doses): less sever effects than deletions, whenheterozygous they form loop at meiosis. Williams syndrome: chromosome-PMS-17genes-PMS-chromosome. An uneven crossover between 2 wrong PMSs leads to 1chromosome with a deletion (syndrome) + 1 with 2 copies of 17 genes and 3 PMSs.

Bar mutation in Drosophila (tandem duplication of 16A chr region) reduces n of eyefacets.

Duplication is useful for evolution (see haemoglobin evolution). Thalassemia's blood disease: α is on chr 16, β on 11. Due to an uneven crossover, a subunit of haemoglobin is part beta and part delta -> Lepore (anemia) + antilepore3. Inversion (≠ order of genetic material): often don't show abnormal phenotype. 2 types: pericentric (includes the centromere -> arm ratio changes; in meiosis bc of loops, gametes will have duplications and deletions, thus not viable) and paracentric (=arm ratio; in meiosis 1 gamete will be dicentric, other acentric thus lost). If heterozygous (1 out of 2 chromatids inverted), a loop is formed (no crossing over within it, very low for near regions). Inversions are better tolerated if homozygous. 4. Translocation: intra (chr piece changes position inside its own chromosome) or interchromosomal (chr piece moves to a non-homologous chr), which can be non-reciprocal (moving in 1 direction) and reciprocal (exchange caused by breaks in chromosomes,

which ends become very sticky). It can be homozygous (both chromatids exchange the same material with the other 2 chromatids) or heterozygous (1 chromatid exchanges info with another). In heterozygous case, there are effects in meiosis with 3 types of segregation:

1. Alternate: normal chromatids (1,2) and translocated ones (1',2') are pulled away to opposite poles -> gametes: 1,2 (normal) + 1',2' (translocated) -> both viable. 'a' and 'b' have 1/2 of happening: Mendel
2. Adjacent 1: 1 and 2' are moved to the same pole -> gametes are 1-2' and 1'-2, both not viable
3. Adjacent 2 (very rare): 1 and 1' move to the same pole -> gametes are 1-1' and 2-2' -> not viable

Conclusion: reciprocal translocations cause half sterility and apparent linkage of genes known to be independent. Human translocations are always heterozygous. Rare Down syndrome form is the Robertsonian one (5%) which can be inherited

andis caused by translocation: 2 21 chromosomes + 1 sane 14 + 1 14-21 fused together.Translocations appear also in cancer cells – Burkitt’s lymphoma: proto-oncogene c-myc gets translocated next to a gene which enhances the production of antibodies ->antibody producing B cells become cancer

Mutations in chromosome number:
➔ Numbers can change for whole chromosome sets or for parts of the set, calledaneuploidy (eg trisomy of chr 21). Number of chromosomes in a basic set ismonoploid number X (humans=23). Organisms with multiple monoploid sets arecalled euploids (diploid is normal euploidy). More than 2 sets -> polyploids. Haploidnumber is n of chromosomes in the gametes (n). eg: wheat has 42 chr, it’s hexaploid=> n=21, X=7. In most organisms X=n.
➔ Male bees develop parthenogenetically: they are monoploid, thus sterile (cannot domeiosis) -> bypass this by forming gametes by mitosis.
➔ In breeding, all pure lines are wanted, to do that monoploids are used:

take the pollen out of a 2n plant (n)-> culture it with cold treatment -> grown an (n) plant ->add colchicine to meristematic cells so that going into mitosis, DNA is duplicated but cells don’t do cytokinesis -> diploid and pure homozygous plant➔ Triploids can develop spontaneously (autopolyploids) or be constructed by crossing a 4n individual (2n gametes) x diploid (n gametes) -> 3n is sterile (no equal division in anaphase meiosis: can be a trivalent or a bivalent 2n + univalent n. All chr have to divide in the same way (all bivalents to 1 pole), otherwise it leads to gametes with chr n between haploid and diploid -> aneuploid, non viable). Calculate balanced n gametes: 2(½) (n=haploid number). In polyploids, if n is even (2,4) then it’s mostly fertile; if uneven, mostly sterile➔ Tetraploids are bigger and more robust -> induced by colchicine. Sterile if chr don’t divide in 2 bivalents➔ Allopolyploids synthesized by Karpechenko in 1928:

1. radish (2n=18) x cabbage(2n=18) which can inter cross-> sterile hybrid (chr in meiosis don’t align correctly, too different) -> spontaneousgenome doubling -> fertile hybrid that cannot cross with the parental species = newspecies (offspring not predictable)
2. Allopolyploids are synthesized in plant breeding: species A x B = sterile hybrid -colchicine-> duplication -> fertile allopolyploid. Polyploids (wheat) act like diploids inmeiosis thanks to Ph1 locus which prevents pairing of related chromosomes (samechr of another set) -> thanks to evolution.
3. Aneuploidy (often caused by non-disjunction in mitosis/meiosis I): nullisomic (2copies of 1 chr are erased), monosomic (1 copy of 1 chr missing), double monosomic(1 copy of 2 chr missing), trisomic (1 extra copy of 1 chr), double trisomic (1 extracopy of 2 chr), tetrasomic (2 extra copies of 1 chr), nullitetrasomic (2 copies of 1 chrerased + 2 extra copies of another chr). Trisomy is well tolerated in plants.

Increased non-disjunction with age – why? There is a meiotic arrest of oocytes in prophase I which continues only at menstruation, so tetrads have to be maintained for decades (they break in time)➔ Sex chromosomes tolerate better aneuploidy: nullisomic spermatozoa x F normal = XO (Turner); trisomic spermatozoa x F normal = XXY Klinefelter➔ Barr bodies (condensed X chromosomes): females use only 1 of the 2 X chromosomes. One is randomly inactivated (in every cell, in ≠ cells ≠ Xs can be inactivated), except for germinal tissue, with XIC locus which produces RNA that coats the whole X transforming it into heterochromatin by acetylation of H3 and H4. A male with a Barr body is Klinefelter. A XXX female has 2 of them. In cats, X chr determines the coat pattern of the fur -> calico cat is the result of alternate inactivation of X in different parts of the body. In humans, anhidrotic ectodermal dysplasia is the result of the same alternative inactivation.

Gene expression: lac