Biology 101

1. Biology 101 Fall, 2007 Week 4 – Genetics Inherited traits

2. GENETICS - before and after Mendel Josef Kölreuter discovered in the 1760’s that offspring could have features of only one parent, or could be intermediate between both. Karl Friederich von Gaertner did >10,000 hybridization experiments in the 1820's. Some of these identified the traits in peas (purple flower color, pod color and seed shape) that were subsequently used by Mendel in his "laws" of inheritance. Gregor Mendel (1822-1884) is generally regarded as the father of genetics.

3. Barbara McClintock The textbook (Stern) accentuates the work of Barbara McClintock. This was certainly important: McClintock was awarded a Nobel Prize in 1983 However, the transposable elements she discovered relate more directly to epigenetics than to genetics.

4. Mendelian Genetics Gregor Mendel was an Augustinian monk with training in agricultural science and mathematics. Several individuals had studied inheritance of traits, but Mendel applied what is now known as “the Scientific Method” to address what was a puzzling situation. In particular, he:

5. 1. Tested a specific hypothesis and planned his experiments carefully, using clear examples. 2. Obtained pure-breeding lines for starting his experiments. 3. Followed not only the offspring of the first cross, but also those of subsequent crosses. 4. Counted offspring from each cross and analyzed the results mathematically. 5. Kept accurate records of his experiments and results, enabling others to repeat them.

6. Mendel derived two basic “laws”: • SEGREGATION • Hereditary traits are determined by discrete factors (genes) that occur in pairs, one from each parent. • INDEPENDENT ASSORTMENT • The inheritance of a pair of factors for one trait is independent of that for other factors.

7. In fact, various situations cause variations in the above events so that many scientists no longer consider the above situations “laws”. Importantly: (a) The involvement of a gene pathway (polygenes) for a trait means that it may not be governed by a single, discrete, factor. (b) Genes are present in linear arrays on chromosomes. If two genes are close together on the same chromosome (i.e., linked), there is relatively little chance that they will assort independently.

8. Segregation: Paired factors segregate during the formation of reproductive cells (meiosis I) so that each cell gets one of the factors. Dominance: Sometimes one factor dominates the other factor. A dominant trait masks/suppresses the alternative (recessive) trait for a particular feature. Conversely, a recessive trait is masked or suppressed by the dominant trait for the feature in question. Independent assortment: When considering two or more pairs of traits, the factors for each pair of traits assort independently to the reproductive cells. Gene is the modern term for one of Mendel's paired "factors".

9. Allelesare genes at the same position (locus) on homologous chromosomes (i.e. chromosomes that carry the same genes and that pair up early in meiosis I). Homologous chromosomes in an individual may carry the same or different alleles at a given locus. A plant ishomozygousfor a given gene if it has identical alleles for that gene on both homologous chromosomes bearing the gene. A plant is heterozygous for a given gene if it has different alleles for that gene on the two homologous chromosomes bearing the gene.

10. Genotype: the genetic constitution of an organism. Phenotype: the physical form or appearance of an organism. This may differ from the genotype because of dominance and other regulatory events that mask the full expression of the genotype.

11. Punnett squareis a useful diagram for determining the predicted ratios of offspring resulting from a genetic cross. (see Stern, p. 246). – Make one yourself at: http://www.usoe.k12.ut.us/curr/science/sciber00/7th/genetics/sciber/punnett.htm Progeny ratiosof phenotypes often reveal the genetic state of plants that were crossed Thus: a phenotypic ratio of 3:1 is typical for the progeny of a monohybrid cross between two parents heterozygous for a dominant trait. The genotypic ratio for the same progeny is 1:2:1

12. P P P P W. Bateson (worked with Punnett)

14. A phenotypic ratioof 9:3:3:1 is typical for the progeny of a dihybrid cross between parents that are both heterozygous for two dominant/recessive traits. Gametes are reproductive cells, e.g. egg cells & sperm.

17. MUTATIONS Mutations can arise in many ways. Most are point mutations, consisting of single base substitutions, insertions or deletions that occur as nucleotide “typographical errors” during DNA replication: single base substitution error: CCTGAGG ® GGACACC ® CCTGTGG single base deletion error: CCTGAGG ® GGACCC ® CCTGGG • single base insertion error: • CCTGAGG ® GGACTTGG ® CCTGAAGG

18. Sickle cell anemia is a clear example of the effects that can arise from what appears to be a very minor change in DNA – a single base substitution error: • mRNA sequences: CCUGAGG ® CCUGUGG • amino acids coded for: Glu®Val In normal β‑globin (one of the two polypeptides in hemoglobin), the sixth amino acid is Glutamic acid, a charged amino acid residue. As a result of the error, the codon for the sixth amino acid is changed so that Valine, a nonpolar amino acid, is incorporated into β‑globin instead of glutamic acid, during messenger translation. As a result, β‑globin does not assume its correct tertiary structure, hemoglobin function is deficient, and the affected erythrocytes are deformed, with a “sickle” shape.

19. Exposure to chemicals and radiation can give rise single base changes. Exposure to sunlight radiation can lead to methylation or other chemical modifications of DNA that prevent proper expression of genetic information, e.g., cytosine methylation: CCTGAGG® CmCTGAGG

20. Since the process of selection of the fittest has optimized most systems, the vast majority of mutations are harmful. However, some will be beneficial, and the cell with the new genetic information resulting from the mutation will be able to outperform other cells. This enhanced fitness at the cellular level may increase the survival and reproductive performance of the organism, and in that case the mutation will be conserved. Changes that occur during chromosomal segregation, and especially during synapsis, involve large segments of genetic information. Large changes are typically lethal and are therefore not propagated/conserved, but many heritable defects result from such events.

21. Transpositionoccurs when genetic information is moved from one chromosomal location to another. This can result from: movement of transposable elements, chromosome breakage, such as incorrect pairing of chromosomes (namely pairing of non-homologous chromosomes instead of homologous ones) in meiosis I. or errors during meiosis

22. chromosome 1 chromosome 2 =A=B=C=·=D=E=F= + =J=K=L=·=M=N=O=® =A=B=C=·=D=E=F=M=N=O= + =J=K=L=·= chromosome 1 chromosome 2 Translocationsare large transposition events, usually by chromosome breakage and incorrect reattachment: Note that chromosome 1 has become longer (gained genes) and chromosome 2 has lost genes and is shorter Inversion: Genes are rearranged, by processes such as those given above: =A=B=C=·=D=E=F= ® =A=E=D=·=C=B=F=

23. Duplication:Segments of a chromosome are duplicated: =A=B=C=·=D=E=F=® =A=B=C=·=D=E=F=D=E=F= Polyploidy: Multiple copies of all chromosomes are present. This can result from failure of chromosomes to separate after crossing-over. Aneuploidy:Certain chromosomes are present in extra copies or are deficient in number.

24. COMPLEX INHERITANCE Mendel's observations are only accurate for dominant/recessive genes. There are many ways in which progeny ratios can differ from those obtained for a single dominant monohybrid cross: Incomplete dominance Codominance Multiple genes Serial genes Polygenic inheritance Pleiotropic genes

25. Incomplete dominance ...results when the expression of a gene is additive rather than dominant

26. Codominance ...similar to incomplete dominance, but genes may encode a noncompeting phenotype, as in the case ofallozymes(i.e., slightly different functional enzymes made by different genes at the same locus on homologous chromosomes). Multiple genes May encode the same or similar protein (trait). They are not allelic, as each of the multiple genes is at a different locus (not all of the loci necessarily in the nucleus). Isozymes are the products of such multiple genes.

27. Serial genes ...often act in concert to produce a phenotype. Thus, a series of genes may be needed to complete a metabolic pathway, e.g. the development of flower color. Such interaction of two or more serial genes is epistasis. Polygenicinheritance Complex traits such as yield (e.g. tons of wheat per hectare) and plant height often involve the interaction of several genes. Pleiotropic genes ...may affect more than one phenotypic characteristic. For example, the purple flowers and seed coat of peas is probably pleiotropic.

28. In tobacco the sizes and shapes of leaves, flowers, anthers and fruits are controlled by the S gene. Plants with at least one dominant S allele (SS or Ss) grow longer and narrower organs (ss plants have short, broad structures). In tobacco, many genes are involved in the development of inflorescence and leaf color and shape. However, their effect may be overriden by S, a pleiotropic gene.

29. NON-MENDELIAN INHERITANCE Linkage When genes are located in close physical proximity they do not assort independently. Most of Mendel's traits are on separate chromosomes, or are on distant parts of the same chromosome. However, pod shape and plant height are linked traits in pea. Mendel did not report results for hybrids involving these traits. They did not conform to his “laws” of inheritance.

30. Cytoplasmicinheritance This results when a trait is entirely or partially encoded by an organelle (e.g. chloroplast or mitochondrion) genome. Transposons Transposable elements have the ability to move from one place in the genome to another. Typically, a transposon contains only a few genes. However, a gene that is interrupted by the presence of a transposon can be inactivated or changed in its function.

31. Epigenetics Because the nucleotides of DNA can be modified, e.g. by methylation, the same sequence may or may not be available for transcription Further, the association of DNA with chromatin depends on the chemical status of the histones Histones can be modified in several ways, including acetylation, methylation, phosphorylation, ubiquitination, glycosylation, and ADP ribosylation. These modifications alter the availability of DNA, and hence genes, for expression

32. Histone Tail Core Two loops of DNA (~150 bp) per nucleosome Spacer DNA (~50 bp) between each nucleosome Histone proteins (blue and yellow) form the core of a nucleosome. One end (tail) of the histones can wrap round the DNA (blue nucleosomes), making it inactive, or be in an open and active configuration (yellow nucleosomes).

33. The Hardy-Weinberg Equilibrium The study of events that occur in gene pools that modify gene frequencies is known as Population Genetics. The mathematical model developed by G.H. Hardy and W. Weinberg predicts that: the proportional frequencies of dominant and recessive alleles will be maintained from generation to generation in a randomly mating population. This holds good when: (1) The population is large (2) Individuals do not move in or out of the population (3) Mutations do not occur (4) Reproduction is random, not selective (5) All alleles and combinations of alleles have equal fitness; i.e. there is no natural selection.