Chapter VIII -Medical Biology - course content Genetics 2023-2024.pdf

Exercise 8 Topic: The cell cycle. Mendelian genetics; dominant/recessive inheritance in humans. Glossary: Allele – one of the possible alternative variants of a given gene often distinguished from other alleles by phenotypic effects; gene variant lying in the same locus on homologous chromosomes. Ca...

Exercise 8 Topic: The cell cycle. Mendelian genetics; dominant/recessive inheritance in humans. Glossary: Allele – one of the possible alternative variants of a given gene often distinguished from other alleles by phenotypic effects; gene variant lying in the same locus on homologous chromosomes. Carrier - heterozygous individual with respect to recessive traits. Centromere - region of chromosome where microtubules of a mitotic spindle attach during mitosis and meiosis; structure that holds together sister chromatids. Chromatid - one of two parallel strands (sister chromatids) of a duplicated chromosome joined by a single centromere. Chromosome - a threadlike structure composed of DNA and protein; carries hereditary information in the form of genes. Codominance - a relationship between two versions of a gene: both alleles are expressed fully and simultaneously in heterozygote phenotype (both features are revealed). Complementary genes (complementation) - genes present on different genetic loci but interacting to express a single character; together produce a particular phenotypic trait in an individual Complete dominance (full) - a relationship between two versions of a gene: in heterozygotes one allele – or “version” – of a gene (dominant allele) completely masks another (recessive allele). Crossing over – the meiotic process where two homologous non-sister chromatids (coming from two homologous chromosomes) pair up with each other and exchange different segments of genetic material; results in new allelic combinations (random shuffling of genetic material during the process of gamete formation) Cumulative genes (polygenes, multifactorial, additive, multiple) - genes from different independent loci, which affect the same characteristics but in an additive fashion (summing effects); genes determining the formation of quantitative traits; they inherit according to Mendel's laws Diploid (2n) - cellular condition where each chromosome type is represented by two homologous chromosomes Dominant allele - an allele that manifests itself in the diploid organism phenotype both in the homozygous and heterozygous genotype; an allele that is fully expressed in the phenotype of a heterozygote. Epistasis - the phenomenon of the impact of one gene expression products on other genes that are not alleles to them (a feature in this situation is conditioned by several pairs of alleles). Epistatic genes - genes that inhibit (mask) the expression of genes from another pair of alleles (hypostatic - masked genes). F1 generation – the first filial or hybrid generation; the offspring resulting from interbreeding of the P generation. F2 generation – the offspring resulting from interbreeding of the hybrid F1 generation. Gene – a basic unit of heredity; hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses) codes for a specific trait; a unit of genetic information corresponding to the DNA fragment necessary for the formation of a functional RNA molecule. Gene expression - the process of gene product formation (e.g., proteins, microRNAs). Gene polymorphism - the occurrence of multiple variants of a given gene due to changes in a single nucleotide, changes in coding or non-coding sequences; may lead to differences in the structure and action of the protein encoded by this gene. Genome - the total hereditary genetic material of an organism; consists of DNA (or RNA in RNA viruses). Genotype - a set of genes of a given organism; genetic structure of the organism; in a narrower sense - the allelic system of a given gene. Haploid (n) – the cellular condition where each chromosome type is represented by only one chromosome. Haplotype - a group of closely-coupled alleles that are usually entirely inherited from each parent (gene loci are in the same chromosome). Heterozygous – having two different alleles for a given gene (also called hybrid). Homologous chromosome – a chromosome of the same size and shape which carries the same type of genes Homozygote – there is a given (same) allele in both homologous chromosomes of a given subject. Homozygous – having two identical alleles for a given gene (also called pure). Hybridization – mating or crossing of two true-breeding varieties (individuals from genetically distinct populations) to receive a hybrid – individual who carry two different alleles of the same gene. Hypostasis - in genetics, the phenomenon of non-appearance of a condition determined by a specific gene (hypostatic gene) due to the masking effect of the gene from another pair of alleles (epistatic gene) Inbreeding- the production of offspring from the mating or breeding of individuals or organisms that are closely related genetically. Incomplete domination (also: partial dominance)– type of relationship between alleles: the dominant allele does not fully mask the effects of the recessive allele expression; both alleles at a gene locus are partially expressed (in the heterozygote phenotype an intermediate feature between the dominant homozygote trait and the homozygous recessive trait) Incomplete (reduced) penetrance – some individuals will not express the trait even though they carry the allele. Kinetochores - a large protein assemblies that form on a chromatids during cell division, connect them to microtubules of the mitotic and meiotic spindles. Lethal gene (lethal allele) - a gene (allele) that causes the body's death; the dominant lethal allele induces the death of dominant and heterozygous homozygotes; the recessive lethal allele causes the death of recessive homozygotes. Linkage - the condition in which genes are present on the same chromosome, causing them to be inherited as a unit; gene alleles go together in subsequent generations; provided that they are not separated by crossing-over during meiosis; the distance that separates them is small enough. Locus - the specific location of a gene on a chromosome (locus - plural loci) Monogenic (monogenic) traits - features conditioned by one pair of allelic genes. Multigenic (polygenic) traits - features by multiple non-allelic genes (genes from different loci). Multifactorial features (complex features) - characteristics conditioned by genetic factors (many gene pairs from different loci, whose effects add up - cumulative genes) and environmental factors; Multiple alleles - the occurrence of more than two gene forms/varieties lying in the same locus on homologous chromosomes; there may be only two alleles in a given organism, and there may be many in the gene pool of the population. Nondisjunction - no disintegration of two homologous chromosomes or sister chromatids during the anaphase of cell division. P generation – the parent individuals from which offspring are derived; P = parental generation, parents in the genetic sense: individuals of pure lines (homozygotes) showing opposite characteristics - dominant and recessive. Penetration - the frequency of the phenotypic expression of a given genotype; determines the percentage of individuals revealing the phenotype characteristic of a given genotype. Phenocopy - a phenotypic trait or disease that resembles the trait expressed by a particular genotype, but in an individual who is not a carrier of that genotype; induced by the environment falsely mimic the genetically determined trait / disease. Phenotype - the observable characteristics in an individual resulting from the expression of genes; the expressed physical and physiological traits of an organism which are determined by its genetic makeup; the clinical presentation of an individual with a particular genotype; a set of revealing features/traits of a given individual. Pleiotropy - a phenomenon in which one factor has more than one effect; one gene influences two or more seemingly unrelated phenotypic traits; the effect of pleiotropic genes. Pleiotropic gene - a gene that affects more than one phenotypic trait. Polygenic traits – see multigenic traits Punnett square – a diagram used in the study of inheritance to show the results of random fertilization in genetic crosses. Pure line - a breed or strain of animals or plants which are obtained after multiple rounds of inbreeding selection or selffertilization; in pure lines, descendants from inbred line show a certain specific character similar in all the later generations Recessive allele - an allele that appears phenotypically only in the case of a recessive homozygote; the allele whose phenotypic expression is masked by a dominant allele; an allele whose phenotypic effect is not observed in a heterozygote. Sex coupling - inheritance of the gene transmitted on the sex chromosome; linkage with sex chromosome. Somatic cells - all body cells except reproductive cells. Total penetration - all individuals with the same genotype show the same phenotype. True-breeding varieties – a kind of breeding in which the parents with a particular phenotype produce offspring only with the same phenotype; the parents are homozygous for every trait; e.g. plants that produce offspring of the same variety when they self-pollinate. Variable expression, variable expressivity - variation in the manner in which a trait is manifested; a phenotype is expressed to a different degree among individuals with the same genotype; varied intensity of a genetically determined characteristic (e.g. as a result of changes in non-coding sequences). All cellular organisms (prokaryotes and eukaryotes) arise from pre-existing cells. The generation–to–generation sequence of stages in the reproductive history of a cell, is named a cell cycle. The cell division reproduces an organism enables sexual and asexual reproduction of the organisms, and also enables tissue renewal and repair in the adult organism. The basis for asexual reproduction and generation of new somatic cells is a process of cell division named mitosis. The species cells derived from mitosis contain an identical number of chromosomes. In sexual reproduction, specialized reproductive cells, gametes with haploid number of chromosomes, are generated in the process named meiosis. The cell cycle of the eukaryotic cell life is the ordered sequence of events – from the cell origin in the division of a parent cell until its own division into two and is composed of the M (mitosis), and interphase (during which G 1, S, and G2 phases may be distinguished). During the interphase, the cell grows and copies its DNA. The duration of interphase often accounts for about 90% of the cycle. Figure 1. Phases of cell cycle. Interphase: G1 phase metabolic changes prepare the cell for division. At a certain point - the restriction point - the cell is committed to division and moves into the S phase. S phase DNA synthesis replicates the genetic material; each chromosome now consists of two sister chromatids. G2 phase metabolic changes assemble the cytoplasmic materials necessary for mitosis and cytokinesis. The process of cell division starts with karyokinesis – the division of the cell nucleus and equal distribution of nuclear material, and precedes the division of the cytoplasm (cytokinesis). The process of karyokinesis (karyomitosis) involves four stages: prophase, metaphase, anaphase, and telophase. Prophase - nuclear chromatin condenses to form visible chromosomes, nucleoli disappear, the nuclear membrane dissolves, the centrioles are formed and move toward opposite ends of the cell ("the poles"), the mitotic spindle forms: the mitotic spindle is created (from the centrioles in animal cells), Spindle fibres (made of microtubules) from each centriole attach to each sister chromatid at the kinetochore (contains motor proteins that can shorten spindle fibres and facilitate the chromosome movement during anaphase). Metaphase - chromosomes align in the metaphase plate - line up in the middle of the cell ("the equator"); the centrioles complete their migration to the poles, kinetochores of two sister chromatids of one chromosome move in opposite directions. Anaphase - separation of chromatids, migration of chromatids to the opposite poles; spindle fibres attached to kinetochores begin to shorten as a result of the loss of tubulin subunits, this exerts a force on the sister chromatids that pulls them apart; spindle fibres continue to shorten, pulling chromatids to opposite poles, this ensures that each daughter cell gets identical sets of chromosomes. Telophase - reconstitution of nuclear envelope (membrane) around chromatids (2n chromosomes) near each pole, decondensation of chromosomes, nucleolus reformation. Cytokinesis creating two daughter cells is different in animal (cleavage furrow formation and a constriction of the cytoplasm) and plant cells (cell plate formation), Cytokinesis progresses into G1 or G0 phase. Meiosis is a form of eukaryotic cell division that produces haploid sex cells or gametes (which contain a single copy of each chromosome) from diploid cells (which contain two copies of each chromosome). As in mitosis, meiosis is preceded by a process of DNA replication that converts each chromosome into two sister chromatids. Then two successive nuclear and cellular divisions (Meiosis I and Meiosis II) take place. Meiosis: reduces the number of chromosome sets from diploid (2n) to haploid (n), gives 4 daughter cells – reproductive cells = gametes. Meiosis I - reductional division that reduces the cell from diploid to haploid: 4n DNA/chromosome → 2n DNA/chromosome (2n chromosome →1n chromosome), crossing-over → genetic diversity. Prophase I - the homologous chromosomes pair and exchange DNA to form recombinant chromosomes; divided into five phases:  Leptotene: chromosomes start to condense.  Zygotene: homologous chromosomes become closely associated (synapsis) to form pairs of chromosomes (bivalents) consisting of four chromatids (tetrads).  Pachytene: crossing over between pairs of homologous chromosomes to form chiasmata (sing. chiasma).  Diplotene: homologous chromosomes start to separate but remain attached by chiasmata.  Diakinesis: homologous chromosomes continue to separate, and chiasmata move to the ends of the chromosomes. Prometaphase I - spindle apparatus is formed, and chromosomes attached to spindle fibres by kinetochores. Metaphase I - homologous pairs of chromosomes (bivalents) are arranged as a double row along the metaphase plate. The arrangement of the paired chromosomes with respect to the poles of the spindle apparatus is random along the metaphase plate - each chromosome segregates randomly. This is a source of genetic variation through random assortment, as the paternal and maternal chromosomes in a homologous pair are similar but not identical. The number of possible arrangements is 2n, where n is the number of chromosomes in a haploid set. Human beings have 23 different chromosomes, so the number of possible combinations is 223, which is over 8 million. Anaphase I - the homologous chromosomes in each bivalent are separated and move to the opposite poles of the cell. Telophase I - the chromosomes become diffuse and the nuclear membrane reforms. Cytokinesis - is the final cellular division to form two new cells, followed by Meiosis II. Meiosis I is a reduction division: the original diploid cell had two copies of each chromosome; the newly formed haploid cells have one copy of each chromosome. Meiosis II - separates each chromosome into two chromatids: 2n DNA → 1n DNA, 1n chromosome → 1n chromosome  Prophase: the same as mitosis  Metaphase: the same as mitosis - centromeres dividing, chromosomes formed only by one chromatid;  Anaphase: the same as mitosis  Telophase: the same as mitosis A Comparison between Mitosis and Meiosis www.uic.edu The bases of modern genetics are the works of Grzegorz Mendel, who in 1866 published the results of his observations of the pea (Pisum sativum) in the article “Research on plant hybrids” and proposed the theory of inheritance units (proposed that the units responsible for inheritance were discrete particles - particulate theory of inheritance). He formulated the principles of heredity defined as Mendel's laws: I - the law of purity of gametes: the two alleles for a trait separate (or segregate) during the formation of gametes, II - the law of independent assortment (segregation) of alleles during gamete formation: alleles pair independently, meaning a particular allele for one character can be paired with either allele of another character. Inheritance units, today called genes, may be present in given individual in two forms - alleles (allelomorphic genes) lying in the same locus (site) on homologous chromosomes. Somatic cells contain one pair of such alleles for each trait, while generative cells contain one of the alleles. Traits conditioned by one pair of gene alleles on chromosomes are called monogenic (Mendelian). In humans, such traits are numerous diseases inheriting predominantly or recessively autosomal or conjugated to the X or Y chromosome. Genetic research conducted by many scientists in subsequent years led to the formulation of a chromosomal theory of heredity (T. Morgan et al.), Cognitive genes (Nilsson-Ehle), interactions between non-allelic genes, e.g. epistasis, hypostasis, complementation, codominance phenomena, incomplete domination, multiple alleles, pleiotropy, differential gene expression and penetration, as well as mitochondrial inheritance. The simple translation of one gene into one phenotypic trait (as in Mendel) is rare. Many different genes interact with the formation of many traits. Complex interdependency networks arise - the complexity built by the interactions and combinations, not the number of constituent elements. Designations used in genetic analyses: P - Parentes (Latin: parents); parental generation, parents in the genetic sense: individuals of pure lines showing opposite characteristics; homozygotes opposing: dominant and recessive; F1 - Filius, Filia (Latin: son, daughter, plural filii - children, descendants, kids); the first generation of hybrids; heterozygotes; F2 - the second generation of hybrids (grandkids); Fn - further generations. Gene designations: a pair of allelomorphic genes: e.g. A - dominant allele, a - recessive allele; Genotype record: homozygote AA or A/A or heterozygote Aa or A/a or A A ; aa or a/a or A a a a ; ; recording of the occurrence of two different genes on different chromosomes: AA BB or A/A B/B or recording of the occurrence of two different genes on the same chromosome (linked genes) AB/AB or AB AB AB AB. ; Mendelian crosses (Table 1): - Parental cross (Parentes with opposite traits) AA x aa - crossword F1 Aa x Aa - back crosses: an individual from generation P with a subject from F1 generation: AA x Aa and aa x Aa (test cross for finding what genotype is individual with dominant phenotype) Table 1. Inheritance in accordance with Mendel's laws. Parental cross(P) AA Gametes aa A A First generation (F1) genotype F1 cross x Aa a Aa Aa Aa 100% children with a dominant trait (phenotype 𝐴̅ ) Aa x Gametes A Second generation (F2 ) AA genotypes Genotype ratio 1 a Aa A Aa : 2 Phenotype ratio a 3 a Aa aa : 1 : 1 75% of children with a dominant trait (𝐴̅), 25% - with a recessive trait (𝑎̅) Test cross aa x Aa Gametes Genotypes a Aa a A a Aa aa aa Genotype ratio 1 : 1 Phenotype ratio 1 : 1 50% of children with a dominant trait (𝐴̅), 50% - with a recessive trait (𝑎̅) Extensions of Mendelian genetics – gene interactions Codominant alleles - both alleles are fully expressed: an example is in human ABO blood types: the heterozygote blood type AB produces both A and B antigens. Incomplete dominance – is a condition when neither allele is dominant over the other, therefore the organism’s resulting physical appearance shows a blending of both alleles. If a red flowered plant is crossed with a white flowered one, the progeny will all be pink. When pink is crossed with pink, the progeny are one red, two pink, and one white. Multiple alleles - many genes have more than two alleles, such as the ABO blood groups in humans - alleles IA, IB, IO. Multiple alleles result from different mutations of the same gene. Epistasis - the expression of one gene interferes with the expression of another, therefore,by which it is modified e.g., masked, inhibited or suppressed or combine to produce an entirely new trait. Pleiotropy - the effect of a single gene on more than one characteristic. Sickle-cell anaemia is a human disease resulting of a mutation in the beta-globin gene. The mutation results in red blood cells that are sickle-shaped, which causes them to clump together and blocking normal blood flow. This causes various health complications and damages many organs, including the heart, brain and lungs. Similarly phenylketonuria, resulting from mutation of the phenylalanine hydroxylase gene, may result in infants in intellectual disabilities, seizures, heart problems, and developmental delays. Polygenic Inheritance - traits are governed by the cumulative effects of many genes and Multifactorial inheritance– where not only many genes at different loci, but also the influence of the environment causes a trait or health problem. Pedigree analysis Pedigree is a graphical representation of generations of a given family and clinical data on the occurrence of a feature or disease over the years. It allows to determine the mode of the trait / disease inheritance and the genetic risk of the occurrence or recurrence of the disease in the family. It also allows to determine which of the family members bears an increased genetic risk and decides on the type and scope of diagnostic tests. Proper design and pedigree analysis is therefore an important element in the practice of genetic counselling. In pedigree, the arrow indicates the proband - the first member of the family in whom the genetic disease was detected. Proband is also sometimes referred to as an indicator case (propositus / proposita). Presentation of only a single parent in the pedigree means that the partner is healthy or is not relevant for the analysis. Preparing pedigree, drawing and analyzing begins from the bottom, from the youngest generation, moving up towards the earlier generations (older). All family members should be included in the pedigree, including miscarriages, perinatal deaths, children put up for adoption, deceased persons. The symbols used in the construction of pedigrees are shown in Figure 3. Figure 3. Pedigree symbols. Difficulties in analysing pedigrees: genetic heterogeneity - the appearance of the same phenotype with different genotypes (different genetic basis) e.g. albinism, polycystic kidney disease (autosomal dominant trait, mutation in chromosome 4 (PKD2) or chromosome 16 (PKD1) - clinically identical diseases); phenocopy; rare cases in few families; uncertainty of paternity. The risk of the offspring with recessive trait is rising in the situation of consanguineous mating - the mating of very closely related individuals, defined as a union between two individuals who are related as second cousins or closer. As relatives share a proportion of their genes, it is much more likely that related parents will be carriers of an autosomal recessive gene, and therefore their children may inherit identical gene copies from both parents – they are at a higher risk of an autosomal recessive disorder. In monogenic diseases and chromosomal aberrations, the risk of disease in the offspring of a given parental pair is constant and does not change depending on the number of healthy or sick children already in possession. For example, in autosomal recessive inheritance, the risk of recurrence in siblings is always 25%, because the child's parents are heterozygous; in autosomal dominant inheritance, if one of the parents is sick (heterozygote), the risk will be 50%; in a disease conditioned by a recessive gene conjugated to the X chromosome - if the mother is heterozygous - the risk of a sick son will be 50%. In the cases mentioned, one should also always remember about a possible new mutation, not present in the examined family. Selected human monogenic features / diseases Congenital spherocytosis (HS, congenital microspherocytosis, Minkowski-Chauffard's disease, Latin anaemia, microspherocytica congenita). It is the most common congenital haemolytic anaemia in Northern Europe (incidence of about 1: 5,000 births). It is caused by mutations in the genes encoding erythrocyte membrane proteins that cause quantitative deficiencies or improper structure of the spectrin - the main element of the membrane skeleton. The molecular basis of hereditary spherocytosis is beyond the mutations of α-spectrin and β-spectrins, also mutations in the genes encoding other proteins of the erythrocyte backbone membrane: ankyrin. It is estimated that 45% of HS cases are related to ankyrin depletion, 28% with spectrins depletion, 22% with anion transfer proteins depletion, and 5% with 4.2 protein depletion. Depending on the type of mutation, the disease may be inherited in an autosomal recessive (worse prognosis, 25% of cases) or autosomal dominant inheritance (better prognosis 75% of cases). In the course of the disease in the peripheral blood, besides normocytes, there are spherocytes characterized by: a small diameter (about 2/3 diameter of normocytes), a spherical shape, a smaller ratio of the area to the volume of the blood cell, a higher haemoglobin concentration, a shorter lifetime. Spherocytes are destroyed in the spleen, which causes splenomegaly, haemolytic anaemia and increased serum bilirubin. They are more susceptible to decay in conditions of low osmotic pressure in the blood. A common complication of congenital microspherocytosis is cholecystolithiasis. Sickle cell anaemia (SCA) A blood autosomal recessive genetic disorder in which an abnormality in haemoglobin - the oxygen-carrying protein is observed. It occurs when a person inherits two abnormal copies of the haemoglobin gene (locus 11p). It is caused by a mutation in the β-globin chain of haemoglobin, replacing glutamic acid with less polar valine at the sixth amino acid position, β 6Glu→Val (normal haemoglobin HbA has α 2 β2 amino acid chains). The association of two α-globin subunits with two mutant β-globin subunits (α2 β2S) forms haemoglobin S (HbS), which polymerises under low oxygen conditions causing distortion of red blood cells and a tendency for them to lose their elasticity. Normal red blood cells are quite elastic, which allows the cells to deform to pass through capillaries. Repeated episodes of sickling causes loss of this elasticity and the cells fail to return to the normal shape when oxygen concentration increases. These rigid red blood cells are unable to flow through narrow capillaries, causing vessel occlusion and ischemia.  A person who receives the defective gene from both father and mother develops the disease (HbS/HbS)  A person who receives one defective and one healthy allele (HbA/HbS) remains healthy, but can pass on the disease and is known as a carrier (sickle cell trait SCT). Signs and symptoms of sickle cell disease usually begin in early childhood. Characteristic features of this disorder include a low number of red blood cells (anaemia), repeated infections, and periodic episodes of pain. The severity of symptoms varies from person to person, some patients have mild symptoms while others have severe ones. Pain and swelling in hands and feet, fatigue and shortness of breath, retinal damage, yellowing of the skin and eyes, delayed growth and puberty in children are some of the common symptoms. The individuals who are carriers of the sickle cell disease (heterozygotes) are relatively protected against the risk of dying from malaria. As a result, the frequencies of sickle cell carriers are high in malaria-endemic areas. The highest frequency of sickle cell disease is found in tropical regions, particularly sub-Saharan Africa, tribal regions of India and the Middle East. The carrier frequency ranges between 10% and 40% across equatorial Africa, decreasing to 1–2% on the North African coast and