7.013 Recitation 4 – Spring 2018

7.013: Spring 2018: MIT 7.013 Recitation 4 – Spring 2018 (Note: The recitation summary should NOT be regarded as the substitute for lectures) Summary of Lectures 5 (2/16) and 6 (2/20): Note: Some commonly used terms in genetics along with their definition are given below. Terms Gene Definitions (abstractly) a fundamental unit of inheritance; (chemically) a sequence of DNA that encodes an RNA or protein. Allele Different forms or variants of a gene Homozygous Presence of identical alleles at one loci between homologous chromosomes Heterozygous Presence of different alleles at one loci between homologous chromosomes Genotype Set of alleles; genetic make-up Phenotype Physical appearance, trait or characteristic imparted by the genotype Pure- or true- breeding Contains homozygous alleles at the gene of interest Trait One or more detectable variants in a genetic character Dominant Phenotype that is expressed in a heterozygote Recessive Phenotype that is NOT expressed in heterozygote Cell cycle: The cell cycle is the process by which one cell becomes two identical cells. The cell cycle is the chain of events that occur in a dividing cell. Cells preparing to undergo cell division must first copy each of their double-stranded DNA molecules (or chromosomes) by DNA replication. The duplicated homologs remain attached to each other by cohesin protein. The cell cycle consists of four stages – G1, S (DNA synthesis/ replication), G2, and M (mitosis). G1 phase is when the cells are preparing to replicate their DNA, which occurs in S phase. G2 is when the cells are preparing to divide, which occurs in M phase. Of these, the G1 phase shows variable length in different cell types. Hartwell & Nurse received the Nobel Prize in 2001 for their contribution. Please see the link below. © Clinical Tools, Inc. All rights reserved. Link: http://www.nobelprize.org/nobel_prizes/medicine/laureates/2001/illpres/index.html Cell division: Mitosis is the division of a diploid somatic cell (2n) to form two daughter cells (2n) that are similar to the parental somatic cell. Meiosis has two divisions; meiosis 1 looks different from mitosis, but meiosis II looks similar to mitosis. In Meiosis I a parent cell (2n) duplicates its genome (4n) and then divides to form two daughter cells (2n), this involves the separation of duplicated homologs. In meiosis II, each daughter cell (2n) divides to form two daughter cells (n), this involves the separation of chromatids. So the end result of meiosis is the production of four haploid gamete cells/ reproductive cells such as eggs or sperm, each of which has half the number of chromosomes (n) as a diploid somatic cell (2n). Link: http://www.pbs.org/wgbh/nova/body/how-cells-divide.html Non-disjunction and its effect: It is important to note that failure of separation of duplicated chromosomes (non-disjunction) during cell division may result in daughter cells with abnormal number 1 DR 7.013: Spring 2018: MIT of chromosomes. If non-disjunction occurs during Mitosis, it results in both daughter cells having an abnormal number of chromosomes (n+1 for one daughter cell and n-1 for the other), which may be transferred to subsequent daughter cells and can result in diseases such as cancer. However nondisjunction in mitosis is never passed on to the offspring of the next generation. In comparison, nondisjunction either during Meiosis -1 or Meiosis-II can result in gametes with abnormal number of chromosomes and is the cause of genetic disorders such as Downs syndrome, Edwards syndrome, Turner’s syndrome, Kleinfelter’s syndrome etc. Recombination and crossing over: Homologous recombination is the reciprocal exchange of DNA between two homologous chromosomes that occurs only during metaphase of meiosis I. During homologous recombination, two homologs (e.g. the chromosome #7 inherited from dad and the chromosome #7 inherited from mom) break at the same place and switch ends with each other. Homologous recombination results in a change in which alleles are on the same chromosomes together (e.g. a cell with “AB” on the maternal homolog and “ab” on the paternal homolog can give rise to gametes containing “Ab” or “aB” chromosomes). The two recombinants (“Ab” and “aB”) will always be created in equal frequencies because one of each kind is created by a single recombination event. Mendel’s laws; Monohybrid cross: Here you cross/ mate two true-breeding (i.e. homozygous for the alleles of a gene(s)) organisms that differ by a single characteristic that is regulated by one gene, such as plants that produce round versus wrinkled seeds. The two organisms you cross are called the P or FO (parental) generation. For example, a cross between two plants, which are both homozygous and differ from each other with respect to one gene, can be represented as AA X aa where “A” and “a” are the two alleles of the same gene. The offspring that represent the F1 (filial) generation will all receive one allele from each parent and will have the “Aa” genotype, which makes them heterozygous. These F1 offspring will display whichever of the two phenotypes is dominant i.e. such as round seeds. If you cross two F1 plants together (Aa x Aa), you create the F2 generation. The ratios of different genotypes (AA:2Aa:aa) and phenotypes (Round 3: wrinkled 1) within the F2 generation can be derived either by using the basic probability (the sum rule and the product rule) or by using a Punnett Square. Mendel’s laws; Dihybrid cross: A dihybrid cross is when you cross/ mate two true-breeding organisms that differ by two characteristics each being controlled by a single gene, such as pea plants that produce round versus wrinkled seeds (controlled by Gene R, that can exist as allele R or r) and green or yellow peas (regulated by Gene Y that exists as allele Y or allele y). For example, a cross between two pea plant P1 (genotype: RRYY) and P2 (genotype: rryy) can result in F1 offspring (genotype: RrYy), which are heterozygous for the alleles of both genes and which display the dominant phenotypes (in this case round and green). If you cross two F1 organisms together (RrYy x RrYy), you create the F2 generation with the phenotypes: Round/ Yellow (9): Round/ Green (3): Wrinkled/Yellow (3): wrinkled/ Green (1). The ratios of different genotypes and phenotypes within the F2 generation can be derived either by using the probability rule or by using a Punnett Square. Test cross: This is used to determine whether an individual showing a dominant trait is homozygous or heterozygous for the allele(s) of a gene(s). The individual in question is crossed with an individual that is homozygous for the recessive trait- this is easy to identify, because all individuals with the recessive phenotype are homozygous for that trait. If the individual in question is homozygous then all the offspring resulting from the test cross will be heterozygous and will exhibit the dominant trait. In comparison, if the individual in question is heterozygous, then the back cross will produce offspring showing the dominant trait and offspring showing the recessive trait in the ratio of 1:1. Linked and Unlinked genes: During prophase of Meiosis I, genes at different loci on the same chromosome can be separated from one another and recombined by crossing over. When crossing over occurs between two linked genes, not all the progeny of a cross have the parental phenotypes. Instead the recombinant offspring appear as well, in proportions called recombination frequency, which is calculated by dividing the number of recombinants by the total number of progeny. Recombination 2 7.013: Spring 2018: MIT frequency is greater for loci that are far apart on the chromosome than for the loci that are close to each other. For example during crossing over/ homologous recombination, two homologs (e.g. the chromosome #7 inherited from dad and the chromosome #7 inherited from mom) break at the same place and switch ends with each other. Homologous recombination results in a change in which alleles are on the same chromosomes together (e.g. a cell with “AB” on the maternal homolog and “ab” on the paternal homolog can give rise to gametes containing “Ab” or “aB” chromosomes). The two recombinants (“Ab” and “aB”) will always be created in equal frequencies because one of each kind is created by a single recombination event. Again you can identify the offspring with recombinant phenotypes by doing a test cross (crossing with a homozygous recessive parent)! Two genes can either be unlinked, completely linked or somewhat linked. Genes that are unlinked are usually located on different chromosomes from each other or are located far apart (50cM or 50 map units) from each other on the same chromosome. Genes that are completely linked are very close to each other on the same chromosome (map distance = 0cM). Genes that are somewhat linked are located on the same chromosome with a map distance of <50cM. Unlinked genes assort independently from each other; this means that an AaBb parent would create their four possible gametes (AB, ab, Ab, and aB) each 25% of the time. Genes that are completely linked always segregate with each other. This means that an AaBb parent would create only two (parental types and no recombinants) of the four possible gametes. Genes that are somewhat linked to each other show a pattern that is in between what is seen for unlinked genes and completely linked genes. Questions: 1. Below is pictured the nucleus from a skin cell taken from a mouse (named Mouse #1), with the chromosomes shown in bold. a) Is the cell haploid or diploid? _________ b) Let’s say we blew up a region of the longest chromosome to look at its sequence at one small gene. i. Is Mouse #1 homozygous or heterozygous for this gene? ii. When you zoom in on the same locus on the long chromosome in a cell from Mouse #2 you find that its two homologous chromosomes have the sequences. How might we write the genotypes of Mouse #1 and Mouse #2 if Sequence #1 encodes a functional protein but Sequence #2 encodes a protein that no longer works? (Note: Use the upper case or lowercase A while writing the genotypes). 5’-CCAGTATACGGAGTACGTAC-3’ Sequence 1 3 5’-CCAGTATACGGATTACGTAC-3’ Sequence 2