bio - module 7

Genetics  

  • Is the branch of biology concerned with heredity and variation of inherited characteristics (- the transmission of genetic information from parent to offspring) 

  • "blending" theory of inheritance: the genetic materials contributed by the male and female parents mix in forming the offspring, and the progeny inherits any characteristic as the average of the parents' values of that characteristic 

  • Inheritance of acquired characters: it was believed that an organism acquires some traits during its life time and they are then passed on to the offspring  

 

The Modern Science of Genetics – Mendel's principles 

  • The principles (basic roles) of inheritance were first demonstrated by Gregor Johann Mendel (1822-1884), an Austrian monk who bred pea (pisium sativum) plants 

  • Mendel was raised on a farm and worked on breeding of vegetables and fruits. After entering the monastery, he was ordained as a priest. Then, Mendel worked for a short time as a school teacher. He continued his study on mathematics and botany among others at the University of Vienna 

  • Shortly after his university training, Mendel began his experiments with garden pea. He planned hif experiments carfully, recorded the data, and subjected the results to mathematical analysis. Mendel was the first scientist to effectively apply quantitative methods to the study of inheritance 

  • His major discoveries, including those now known as Mendel's Principles of Segregation and Independent Assortment, became the foundation of the science of genetics 

  • His work was unappreciated in his lifetime, it was rediscovered in 1900 

 

Mendel's Principles 

Mendel's experimental materials 

  • The plant – garden pea (pisium sativum) 

  • Mendel chose the materials for several reasons: 

    • Pea plant could be easily cultivated in the garden 

    • Pea plant has many varieties with distinguishable heritable features or characters (traits) 

    • Pea plants are diploid, vegetative cells contain two sets of seven chromosomes 

    • Pea plant is self-pollinated in nature 

    • Pea plant can be cross-pollinated by hands between varieties, itself alone would self-pollinate. Thus, both cross – and self – pollinations are possible  

 

 

Phenotype  

  • The physical appearance of an organism 

  • Observable/expressed trait or traits of an individual, including the organism's appearance, development, biochemical and physiological properties, and behaviour 

 

Genotype 

  • Refers to the genetic makeup of an organism 

  • Can be used to refer to the alleles or variants of a gene, that are carried by an organism 

  • Contributes to phenotype 

  • Is one of the three factors that determine phenotype, along with epigenetic factors and non-inherited environmental factors 

 

Single Trait Crosses  

  • Mendel first performed experiments to determine the pattern of inheritance of single traits. Such experiments are called monohybrid cross 

  • Mendel chose seven traits including flower color, flower position, seed color, seed shape, pod shape, pod color and plant height 

    • The traits chosen had pairs 

    • Pairs were clearly distinguished 

    • Varieties with these traits are true-breeding lines (a genetically pure line of organism; organisms for which sexual reproduction produces offspring with inherited trait(s) identical to those of parents) 

  • Cross (hybridization) - the cross-fertilixation of two different varieties/ species 

  • Hybrid – the offspring of parents ( P genreation) of two different varieties/species 

  • F1 generation – the first gen. Resulting from a cross (F stands for filial and F1 for first filial) 

  • F2 generation – the next generation of plants from self-fertilization of the F1 offspring 

Mendel's Experimental Results (i.e. flower color) 

  • F1 generation: 

    • When he crossed a plant with purple flowers to a plant with white flowers, regardless of which of the parents provided, all progeny produced plants with purple flowers 

    1. No blending of traits observed 

    2. What happened to the white flower trait? Lost or not allowed to be expressed? 

  • F2 generation  

    • Produced both purple and white flower plants 

    • Out of 929 plants, 705 purple flowers and 224 white flowers, a ratio of approx. 3:1 

  • Mendel tested all seven traits. In all cases, in F1 generation only one of the teo traits was expressed, and in F2 '75% of the generation was the same as in F1' and 25% the other  

  • Mendel proposed: 

    • For each trait there is a pair (alleles) of heritable factors (what we now call genes) in each parent 

    • During the formation of gametes (male or female sex cells), the two factors for a trait separate, and only one factor is passed on to a gamete 

    • When male or female gametes fuse during fertilization, each parent contributes one of the factors for a trait, so that the offspring has a pair of factors 

    • For a cross between individual with different traits of a pair, factors for both traits are present but one is masked by its partner 

 

Alleles 

  • Alternative forms of a gene 

  • Genes governing variation of the same character that occupy corresponding positions (loci) on homologous chromosomes 

  • Dominant: an allele that is always expressed when it is present, regardless of whether it is homozygous or heterozygous 

  • Recessive: an allele that is not expressed in the heterozygous state 

 

Homozygous  

  • A true breeding organism having two identical alleles for a given characteristic 

 

Heterozygous 

  • Having two different alleles for a given characteristic 

 

Hemizygous 

  • A condition in which only one copy of a gene ot DNA sequence is present in diploid cells 

 

Punnet Square 

  • The punnet-square explains the Mendel's hypotheses at the genotype level 

  • P generation: 

    • Dominant homozygous     PP 

    • Recessive homozygous    PP 

  • F1 generation: 

    • Hybrid (heterozygous)       Pp 

    • Two types of gametes       P, p 

  • F2 generation: 

  • Two phenotypes                Purple, white 

  • Three phenotypes             PP, Pp, pp 

Genotypes 

(1:2:1) 

Phenotypes 

(3:1) 

PP 

25% 

purple 

1 

Pp 

50% 

purple 

2 

pp 

25% 

white 

1 

  • Punnet square, a tool to predict the probability of possible genotypes of offspring 

 

Association between genotypes and phenotypes 

 

Testcross 

  • A cross of an individual of unknown genotype (which may be either heterozygous or homozygous) for a particular characteristic with a homozygous-recessive individual for that same characteristic  

 

Mendel's First Law- the law of segregation: 

  • Why an individual produces gametes, the alleles separate, so that each gamete receives only one member of the pair of alleles 

 

Mendel's experiment – two trait cross 

  • A genetic cross in which the parents differ with respects to the alleles of two loci (genes) of interest, called dihybrid cross 

  • Mendel performed the two trait crosses to see if the two traits of a parent are passed on together in gametes, or whether they segregate independently  

  • The phenotypes were:   

  • In this cross, both parents were homozygous  

  • Traits round and yellow were dominant over wrinkled and green  

  • Mendel considered that in F2, there were two possibilities of the types of gametes produced from F1 plants (YyRr) 

  • If the two traits (genes) passed on together, then only two types of gametes would be formed (YR and yr) 

  • 2 types of gametes: 

    • Yellow/Round (YR) 

    • Green/Wrinkled (yr) 

    • In this case, self-fertiliziation of F1 (YyRr) will yield two phenotypes: 75% yellow and round, and 25% green and wrinkled (3:1) 

  • The 2nd possibility Mendel considered was that the two traits (genes) segregated independent of each other during gamete formation. Thus, 4 types of gametes could be formed in equal numbers (YR, Yr, yR, yr – 1:1:1:1) 

  • 4 types of gametes: 

    • Yellow/round 

    • Yellow/wrinkled 

    • Green/round 

    • Green/wrinkled  

    • When these gamtes combine, there is a possibility of 4 types of phenotypes:  

  • Results:  

    • The phenotypes ratio Mendel obtained 9: 3: 3: 1 

    • In F2, Mendel fot 2 phenotypes similar as original parents, and two new mixed phenotypes appeared 

    • The genotypes of these 4 phenotypes can be predicted using punnet-square 

    • Nine genotypes out of 16 combinations were: 
      YYRR, YYRr, YyRR, YyRr, yyRR, yyRr, YYrr, Yyrr, yyrr 
          (1)      (2)       (2)      (4)      (1)      (2)    (1)     (2)   (1) 

    • Corresponding to four phenotypes: 
      (yellow/round, yellow/wrinkled, green/round, green/wrinkled) 

               9                     3                     3                      1 

    • In various dihybrid combinations of seven pea traits, Mendel observed that each of two traits produced a 3:1 ratio of phenotypes in the F2, and two trait combination always showed a 9: 3: 3: 1 ratio.  

    • Mendel's Second Law – the law of independent assortment 

      • Alleles of two (or more) different genes get sorted into gametes independently of one another 

Variations of Mendel's Principles 

  • Incomplete dominance – a type of inheritance in which one allele for a specific trait is not completely expressed over its paired allele in F1 hybrids. This resuslts in a third phenotype in which the expressed physical trait is a combination of the phenotypes of both alleles   

 

Variations of Mendel's Principles 

  • Codominance – with codominance, a cross between organisms with two different phenotypes produces offspring with a third phenotype in which both of the parental traits appear together   

  • Multiple alleles - occurrence of a gene that exists as three or more alleles in a population  

  • Pleiotropy – the determination of more than one character by a single gene  

  • Epitasis – occurs when two or more different gene loci contribute to the same phenotype, but not additively. It is often described as when one gene masks or modifies the phenotype of a second gene 

  • Polygenic inheritance – the additive effect of two or more gene loci on a single phenotypic characteristic  

    Chromosomal Basis of Inheritance 

    • Genes are located based on chromosomes 

    • Behaviour of chromosomes during meiosis accounts for Mendel's principles of inheritance patterns 

      • Diploid individual, as in pea plant or human, possesses two sets of homologous chromosomes 

      • Two chromosomes bear two alleles (the same or different) at the same positions  

      • Each set comes from male or female parent  

      • When any individual produces gametes, the alleles separate, so that each gamete receives only one member of the pair of alleles  

       

       

    • After Mendel's experiments, other workers discovered an inheritance pattern that seemed totally inconsistent with Mendelian principles. In F2 of dihybrid crosses, phenotype ratios other than 9: 3: 3: 1 were obtained 

     

    Baetson-Punnet's experiment (1908) 

    • Two traits in sweet peas (lathyrus odoratus): flower color and pollen shape 

    • One parent – homozygous for recessive purple flower (PP) and long pollen grains (LL); another parent – homozygous for recessive flower (pp) and round pollen (ll) 

    • Cross of heterozygous plants (PpLl) that expressed the dominant traits – purple flower and long pollen grains 

    • Picture 

    • Results of F2 generation: 

      • Single trait segregated following Mendel's segregation principle, producing a phenotypic ratio of roughly 3:1 

      • Two trait segregation, however, did not produce the 9:3: 3:1 ratio that is predicted for a dihybrid cross 

      • Instead, a larger portion of plants with purple flower and long pollen (284 of 381, ~75%) and red flower and round pollen (55 of 381 ~15%) were observed  

       

       

       

     

    Explanation:  

    • The factors (genes) for the two traits may nnot be segregating evenly in all of the gametes formed. In this experiment, meiosis in the heterozygous (PpLl) pea plant produces two predominant types of gametes (PL and pl) rather than equal numbers of the 4 types of gametes formed 

    • The large numbers of plants with purple/long and red/round traits resulted from reunion (fertilization) among PL and pl gametes  

    • Several years later, it was revealed that the dominant genes for purple color and long pollen are located on the same parental chromosome 

    • Generally, many genes do not follow Mendel's principle of independent assortment 

      • In an organism, each chromosome possesses many genes 

        • Human genome revealed 26,588 protein-encoding genes, but 23 pairs of chromosomes 

        • Arabisopsis plant has 25,498 protein-encoding genes, encoding proteins within 5 chromosomes 

        • Fission yeast contains 4,824 protein-containing genes distributed in 3 chromosome 

      • During meiosis, close localized genes on a chromosome tend to be passed on together to a gamete 

      • Thus, the genes that are located close together on the same chromosome are linked, called linked genes 

     

    Question:  

    • What about the less numbers of plants with purple round and reed long traits? - recombinants 

    • In Bateson-Punnet's experiments, some Pl and pL gametes were also formed. Crossing over accounts for the recombinant gamete formation, and recombines linked genes into assortments of alleles not found in parents 

    • Crossing over is the exchange of segments between chromatids of homologous chromosomes during the prophase of meiosis I 

     

    Recombination of Linked Genes: Crossin-over accounts for recombination of alleles  picture 

     

     

     

     

     

    Linkage Map  

    • Using segregation ratios to predict recombination frequencies (percentage of recombinants), linkage maps could be developed to help determining the position of different genes or loci on the same chromosome  

     

    • Using recombinant frequency as measurement, Alfred H. Sturtevant, one of Morgan's students, created the first linkage map showing the arrangement of 5 genes on chromosome 2 of drosophila 

     

    • The unit of a linkage map, called a map unit, is equivalent to a recombinant offspring frequency of 1%  

    • The map unit is also called the centimorgan (cM) in honour of Morgan's discovery of linkage and recombination 

     

    Morgan Genetics- the chromosomal basis of inheritance  

    • Morgan's results revealed that if many traits are on the same chromosome, it contradicted Mendel's claim of independent assortment. Morgan and his colleagues confirmed the chromosla theory of inheritance that genes carried on the same chromosomes follow the mechanical basis of heredity 

    • Mendel's theory of dominance and recessive variations could not account for the inheritance of sex in the observed one-to-one ratio  

     

    Sex Chromosome  

    • For many organisms, including human, sex of organisms is determined by one of the chromosomes – the sex of chromosme  

    • Different species, the chromosomes are different in numbers or kinds: 

      • In humans ♀ has XX and all gametes have X; ♂ has XY and produces 2 types of gametes: X and Y. Therefore, the sex of the offspring is determined by the gametes from ♂ 

      • In some insects such as grasshoppers and flies, ♀ as XX, but ♂ has only one X; Y chromosome is absent. Here ♂is designated XO 

      • In birds and fishes,  is XX (called ZZ) and ♀ has XY (called ZW). Thus, the situation is opposite of humans: the ♀ (egg) determines the sex of offspring  

      • In other insects such as ants, and bees, sex id determined by chromosome numbers. ♀ develops from the fertilized egg (diploid); ♂ develops from the unfertilized egg (haploid)  

      • An autosome is any chromosome that is not a sex chromosome 

     

    Sex-linked Inheritance 

    • Human individuals with abnormal sex chromosomes could be physically normal, but sterile 

      • Human XO individuals are females who could be physically moderately abnormal and mentally normal, but sterile (turner syndrome)  

      • XXY individuals are males who be physically normal, but always sterile (Klinefelter syndrome) 

      • XYY individuals, which occurs every 1 in 1000 male births show normal clinical phenotype (jacobs syndrome). Most males with 47 chromosomes (XYY) have normal sexual development and have normal fertility 

       

    • Many of the genes on sex chromosomes are for non-sexual traits 

    • In humans, Y chromosome  contains less than 200 genes, among them are the maleness determinants. However, X chromosome contains a large number of genes (over 1000 genes) 

    • Earlier we learnt that chromosomes exist in homologous pairs in a diploid organism. Males however contain a single X and Y chromosomes. Several important human diseases are inherited as X-linked recessives, including muscular dystrophy, color blindness and hemophilia which are expressed much more frequently in men than in women  

     

    X-linked Recessive Inheritance  

     

     

     

    Extranuclear Inheritance (cytoplasmic transmission)  

    • Some traits in eukaryotes do not adhere to expected patterns associated with the biparental inheritance characteristic of Mendelian genetics 

    • Transmission could be associated with female parent:  

      • Mitochondrial and chloroplast genomes that affect the offspring's phenotype  

      • Maternal gene products that influence early development – epigenetics 

      • Infectious particles - able to mediate horizontal gene transfer  

      • Mitochondria: energy-converting organelles of  eukaryotes evolved from prokaryotes (proteobacteria) that were engulfed by primitive eukaryotic cells and developed a symbiotic relationship (endosymbiosis) with them about 1.5 x 109 years ago.  

        • e.g. the human mitochondrial genome contains 16,569 bp and encodes 37 genes 

        • Maternal inheritance 

        • High mutation rate  

        • Threshold effect for disease 

        • Age-related mutations  

      • Chloroplast: an organelle in land plants, algae and some protists where photosynthesis takes place. It is believed to be originated from cyanobacteria through endosymbiosis  

        • Land plant chloroplast genomes typically contain around 110-120 unique genes 

        • Maternal inheritance 

     

    Maternal Inheritance in the four-o'clock plant (mirabilis jalapa) 

    • Carl Erich Correns (1864-1933), a german botanist and geneticist, who rediscovered and independently verified the work of Mendel in a separate model organism. In addition, he also discovered cytoplasmic inheritance, an important extension of Mendel's principles 

    • This non-mendelian inheritance pattern was later traced to a gene named iojap that codes for a small protein (chloroplsatic) required for proper assembly of chloroplast ribosomes