Mendel and the Gene Idea: Discovering the Basics of Genetics

1. SGN 17 Mendel and the Gene Idea

2. Genetics – the study of biological inheritance; the study of gene expression

3. Review… - homologous chromosomes vs sister chromatids - mitosis vs meiosis - gene vs allele - genotype vs phenotype - characteristic vs trait - monogenic vs polygenic characteristic - heterozygous versus homozygous

4. Gregor Mendel’s work is notable for several reasons He questioned traditional presumptions of biological inheritance He used experimental methods that produced data that could be quantitatively analyzed (statistics, probability, etc.); choice of model organism; importance of large sample size in biological studies He made several remarkable conclusions regarding biological inheritance and gene expression Blending

5. A summary of Mendel’s experiments and his conclusions Initial experiments Monohybrid cross between true – breeding parents; self fertilization of F1 Worked with pea plants that are true-breeding (self pollinate – offspring have same traits as parents) and 7 characteristics that only occurred in two traits; characteristics were monogenic (traits determined by one gene), unknown to Mendel Removed anthers and cross pollinated plants with different traits of the same characteristic and then recorded results in F1 generation; then he crossed or self-pollinated the F1 gen to produce the F2 generation P1 F2 F1

6. Found that in F1 only one trait showed up (100%) called the dominant trait, while the other was referred to as the recessive, while in the F2 generation both traits were evident in a 3:1 ratio (dom:rec)

7. Mendel was trying to figure out the relationship between genotype and phenotype But nothing was known about genotype, so in one sense he was trying to figure out what “genotype “ could be

8. Mendel looked at his data and concluded… Two factors are involved in determining each characteristic, one factor inherited from the male parent and one from the female parent; factors and traits are discrete units and do not blend

9. Sometimes inherited factors are the same (homozygous) and sometimes different (heterozygous) If different, Mendel concluded in regard to his 7 traits, one factor and trait (100% in F1) is dominant and one is recessive

10. What we know today Alleles – Mendel’s “factors”; genes that share the same locus on homologous chromosomes and have nucleotide sequences coding for the same protein product, although the sequences may or may not be identical

11. Mendel was describing meiotic cell division and fertilization Meiosis reduces the chromosome number by ½ Fertilization restores the diploid number

12. Dominant alleles make functional proteins, recessive alleles don’t; in Mendel’s experiments, one active allele gives same result as two

13. Mendel proposed two fundamental ideas Idea (Law) of Segregation – paired alleles (factors) segregate (separate) independently (randomly) during gamete formation; today we know it is paired, homologous chromosomes, which contain the alleles, that actually segregate independently) Separation of homologous alleles (and chromosomes) during meiosis 1

14. Mendel tested this idea with monohybrid crosses; he could explain his data if “factors” always segregated independently This is always true as we know it today

15. Idea (Law) of Independent Assortment tested with multihybrid crosses 9:3:3:1 9 = one P type 1 = the other P type 3, 3 = recombinant types

16. Alleles at different loci (different sets of paired alleles or genes) separate into gametes independently (according to Mendel) This is only true in regard to nonhomologous alleles and chromosomes, although Mendel’s results suggested it is always true By chance, Mendel chose 7 characteristics that are either determined by alleles on nonhomologous chromosomes, or if on the same chromosome, so far apart that crossing over makes them appear to be on separate chromosomes (more on this later)

17. Independent assortment only applies when considering loci on different pairs of homologous chromosomes (unlinked loci); does not apply when genes are linked on the same chromosome Assortment occurs during meiosis 1 Also complicated by crossing over (which can make linked alleles appear unlinked)

18. Mendel tested this idea with multihybrid crosses and found separation of one pair of alleles was not related to separation of pair of alleles for second trait Mendel found this happened; independent assortment If assorted dependently (linked) this would happen

19. See Daily Agenda 1/24/18

20. Crossing over adds complexity and, as we will see, messes up our data Crossing over produces recombinant DNA Recombinant DNA – chromosome that is produced by fusing DNA from non sister chromosomes (naturally and artificially), so offspring have different chromosome than either parent Also produced by… Chromosomal translocation or fusion (to be discussed in the future) Genetic engineering

21. Recombinant offspring – combination of traits for different characteristics seen in the offspring that were not seen in parents Example: a plant that makes only yellow, wrinkled seeds mates with a plant that makes only green, smooth seeds  Which would be the recombinant offspring?

22. Mendel’s work and other discoveries in genetics are based on statistics and probability The outcomes of monohybrid and multihybrid crosses can be predicted because of the random nature of separation of alleles and their recombination The simple Punnett square can be used to determine probability of offspring phenotype and genotype based on parental genotype for monohybrid crosses

23. Multihybrid test crosses are predicted using statistical probabilities, based upon two rules The Rule of Multiplication What is the probability of multiple possible independent events happening together? If you and I flip a coin at the same time what is the probability of both turning up tails? What is the probability that a zygote will inherit dominant alleles from each heterozygous parent? (… that both parents flip tails when making gametes)

24. The Rule of Multiplication Since the chances of any unlinked allele winding up in a gamete is independent of the chances of any other unlinked allele winding up in the same gamete, probability can be used to calculate the chances of producing any number of combinations of unlinked alleles The odds of having any number of unlinked events occur simultaneously is equal to the product of the odds of occurrence of each event multiplied together

25. Recap Principle of Segregation Factor pairs/paired alleles always separate randomly (each gamete has a 50/50 shot of receiving either) Always true because paired alleles are on paired homologues, which do separate randomly Involves monohybrid cross Principle of Independent Assortment Separation of one pair of factors/paired alleles is independent from the separation of a second pair of factors/alleles (to Mendel all genes behaved as if they were unlinked) Only true when different pairs of alleles are on different pairs of homologous chromosomes (not if the two different pairs are on the same homologues) Involves multihybrid crosses Random = just as likely one way or the other In a large enough sample size, you’ll get approximately 50/50 The Rules of Multiplication and Addition allow us to predict, or explain the results of cross breeding Rule of Multiplication – 2 or more unrelated things happening at the same time Rr x Rr The chance one gamete that makes an organism is R (50%) and the other is R (50%), meaning the organism will be RR (.5 x .5 = .25 or ¼)

26. What is the chance that a PpYy x PpYy will produce ppyy(what portion of offspring will be ppyy)? Pp x Pp 1/4 chance offspring will be pp Yy x Yy 1/4 chance offspring will be yy 1/4 x 1/4 = 1/16th chance (or 1 out of 16 offspring) Chance offspring is PPYy? PpYyRr x ppyyrr what chance PpYyRr? Practice Problem: Rule of Multiplication

27. The Rule of Addition The probability of an event that can occur in two or more different ways is the sum of the separate probabilities ( rule of multiplication) of those ways (the rule of addition)

29. What is the chance that a PpYy x Ppyy will produce a PpYy or Ppyy? What is the chance that PpYy x PpYy will produce offspring with the dominant phenotype for each trait? • Practice Problem: Rule of Addition What is the chance that a PpYy x PpYy will produce offspring with at least 2 recessive alleles?

30. What is the chance that a PpYy x Ppyy will produce a PpYy or Ppyy? PpYy1/2 x 1/2 = 1/4 Ppyy1/2 x 1/2 = 1/4 2/8 or 1/2 • What is the chance that PpYy x PpYy will produce offspring with the dominant phenotype for each trait? PPYY1/4 x 1/4 = 1/16 PPYy1/4 x 1/2 = 1/8 = 2/16 PpYY1/2 x 1/4 = 1/8 = 2/16 PpYy1/2 x 1/2 = 1/4 = 4/16 9/16 • What is the chance that a PpYy x PpYy will produce offspring with at least 2 recessive alleles? ppyy1/4 x 1/4 = 1/16 PpYy1/2 x 1/2 = 4/16 PPyy1/4 x 1/4 = 1/16 ppYY1/4 x 1/4 = 1/16 Practice problems in book!! Yypp1/2 x 1/4 = 2/16 yyPp1/4 x 1/2 = 2/16 11/16

31. Probability tells us the ideal number of offspring of each genotype, but statistics tell us numbers will never be ideal Other statistical analysis is needed to determine whether observed numbers are statistically the same as ideal numbers, for example chi – square analysis

32. Mendel discovered the particulate behavior of genes, but only described the simplest of cases (monogenic characteristics, 2 different alleles only, 3 genotypes, 2 phenotypes; in multihybrid crosses compared unlinked genes on different autosomes,)

33. How do we explain Mendelian Complete dominance? The protein product of only one allele is enough to obtain dominant phenotype; heterozygous shows dominant phenotype

34. Complex genetics – in most instances, biological inheritance and gene expression is much more complicated than is seen in simple Mendelian genetics More complex monogenic characteristics have different inheritance patterns and complicating influences that lead to more numerous possible phenotypes Many characteristics are polygenic, which produce a range of traits within a characteristic The level at which a characteristic is considered also effects how the its genetics are described

35. Monogenic characteristics are characteristics that are determined by one gene, or one pair of alleles, such as the pea plant characteristics studied by Mendel More complex patterns seen in monogenic characteristics give more than two phenotypes Codominance – alleles each produce a product; both phenotypes expressed in heterozygote; 3 genotypes, 3 phenotypes A, B and AB blood types (more on O later)

36. Incomplete dominance – typically heterozygote is an intermediate phenotype due to only ½ of protein produced; 3 genotypes, 3 phenotypes

37. Recap and discussion (slides 37 – 40) What is the molecular and biochemical basis for the different patterns of gene expression and inheritance that we see in monogenic characteristics? Molecular basis = what is going on at the gene/DNA level? Biochemical basis = what is the affect seen in cellular biochemistry? Organismal level = what is the affect on the observable phenotype? What are the three different organismal patterns of gene expression and inheritance that we’ve described? What is one way to explain ____________ at the molecular and biochemical level? Dominant and recessive traits; the heterozygous = dominant trait

38. How might we explain incomplete dominance at the molecular and biochemical level? Heterozygote shows intermediate phenotype Snapdragon color – why is the heterozygote pink, while the homozygotes are red or white? Hypercholesterolemia – why do heterozygotes show higher levels of blood cholesterol and mild disease symptoms? Sickle cell anemia – at organismal level we see some disease symptoms, and at biochemical level we see some cells sickling – but what is happening at the molecular level? (as we will see later, it is not incomplete dominance)

39. How might we explain codominanceat the molecular and biochemical level? In heterozygote both phenotypes expressed How do we explain A, B and AB blood types in regard to codominance? How do we explain checkered chickens, roan cattle and calico cats? At the cellular level some cells are expressing one allele and some cells are expressing the other allele

41. Multiple alleles at a particular loci can also increase number of phenotypes, especially if different alleles show different inheritance patterns

42. And at each locus there might be complex inheritance patterns, multiple alleles, and other factors influencing gene expression Polygenic inheritance – phenotypes determined by additive effects of 2 or more genes on a single characteristic; gives a continuum of variation (versus 2 or a few discrete phenotypes)

43. For any characteristic the dominance/recessiveness relationship we observe depends on the level at which we examine phenotypes In regard to sickle cell anemia Organismal and Biochemical level = Incomplete dominance – heterozygote shows some symptoms Molecular level = Codominance at - both normal and mutated hemoglobin produced Organismal level = affect on organism Biochemical level = affect on biochemical activity Molecular level = affect on gene and protein production Molecular (protein) production  Biochemical activity  Organismal effect

44. In regard to Tay-Sachs disease Organismal level = Mendelian dominance – heterozygote and homozygous dominant show no symptoms Biochemical level = incomplete dominance – activity of Hex - A enzyme reduced in heterozygotes Molecular level = codominance – equal number of active and malformed (dysfunctional) enzymes produced

45. Other factors to consider in regard to gene expression Pleiotropy – one gene affects more than one phenotypic characteristic

46. Epistasis– a gene at one locus alters the phenotypic expression of a gene at another locus Alters expected ratio of offspring

47. Epigenetics Chemical alterations of the chromosomes can affect gene expression Often established in utero due to environmental conditions affecting development, such as nutritional status or other stresses

48. Examples involve… • Methylation Typically silences genes Transcription factors can’t bind to DNA • RNA interference Typically silences genes Blocks mRNA from binding to ribosomes • Histone acetylation Typically allows for gene expression Euchromatin vs Heterochromatin Methylation – attachment of methyl (CH3) group Acetylation – attachment of acetyl (COCH3) group

50. Temperature sensitive enzymes Ambient environment can also influence immediate gene expression and phenotype For example, temperature activated genes or flower color effected by soil pH