Welcome to Genome 351! Human Genetics April 1, 2013

1. Welcome to Genome 351! Human Genetics April 1, 2013 There is still space available in this course; if you are not registered and wish to take this course, see me during the break, or immediately after class

2. Welcome to Genome 351! Human Genetics March 28, 2011 There is still space available in this course; if you are not registered and wish to take this course, see me during the break, or immediately after class

3. Course goals -Basic understanding of the concepts of (human) genetics -Be able to critically read the science section of the New York Times -Informed citizen, voter, health consumer

4. Genome 351 – Human Genetics Instructors: Leo Pallanck (4/1-5/3) Evan Eichler (5/6-6/7) Office hours (by appointment): Fridays 1:00-2:00PM Teaching Assistants: Adam Gordon; Office hours: Thursdays 4:00PM - 5:00PM S-110 Blake Hovde; Office hours: Wednesdays 2:30PM – 3:30 PM S-110 Evan Eichler on 4/5 Discussion Section (AA) Wednesday 10:30-11:20 AM S110 Discussion Section (AB) Wednesday 1:30-2:20 PM S110 NO DISCUSSION SECTION THIS WEEK

5. General course information Suggested Textbook: The Human Genome -- A User’s Guide, Julia E. Richards & R. Scott Hawley Elsevier Science in Society Series, 3rded. 2010 This week: Chapters 1 & 2 Course website: http://courses.washington.edu/gen351/ Will use course website to post: -announcements (e.g., room changes) -suggested reading -lectures; problem sets; answer keys

6. Course content 4/1-5/3: Basic Genetics/Molecular Biology (Leo Pallanck) -Mendel’s Laws & Segregation -Cell Cycle, Mitosis & Meiosis -DNA Replication -Recombination & Aneuploidy -Transcription, Splicing & Translation -Mutations 5/6-6/7: Human Genetics/Disease (Evan Eichler) -Human Genome -Disease Mechanisms -Human Molecular Evolution -Cancer Genetics -Population Genetics -Stem Cells&Gene Therapy -Mapping Genetic Traits

7. Grading • • Midterm exam (125 points) • • Final exam (125 points) – not cumulative, but… • Six problem sets (60 total points) – handed out on Fridays, due the following Friday • 2-3 Discussion section debates (40 points) • Grading on curve; mean = 2.8 • To pass the course you must receive a minimum of 175 points • No make-up Exams!

8. How to succeed in this course • Attend class (lecture and discussion section) • If you don’t understand something, don’t wait… ask for help! Can you explain today’s lecture to your non-scientist parents/friends without referring to the notes? • Use the book as a resource to understand the lectures • Work the problem sets/make sure you understand the answers • Form study/discussion groups • Make use of help time!

9. Genome 351, 1 April 2013, Lecture 1 Today… • Outline of course • Pedigrees (example: cystic fibrosis) • Mendel’s experiments with pea plants • Proteins • Cells

10. Cystic fibrosis -Inherited disease that affects the lungs and digestive system -Affects ~30,000 children and adults in the United States (~70,000 worldwide). -A defective gene and its corresponding protein product cause the body to produce unusually thick, sticky mucus that: * clogs the lungs and leads to life-threatening lung infections; and * obstructs the pancreas and stops natural enzymes from helping the body break down and absorb food.

11. A simple pedigree Two unaffected individuals have three children, the youngest of whom has cystic fibrosis (CF) = cystic fibrosis = Normal How can you tell if CF is a genetic disorder?

12. A larger family Two unaffected individuals have eight children, two of whom have cystic fibrosis Does this tell you that CF is a genetic disorder? What else might you want to know?

13. Another generation

14. Building pedigrees Horizontal line = mating Vertical line = offspring = Unaffected male = Affected male = Unaffected female = Identical twins = Affected female = Deceased male = sex unspecified

15. Building pedigrees (cont’d) =

16. Building pedigrees (cont’d) I II = III Proband: affected individual who first brings attention to the trait

17. Some early theories on heredity • Blending of traits • Vital spark (paternal or maternal) • Sperm carries preformed individual (homunculus) Gregor Mendel (1822–1884) introduces a more systematic approach

18. Reasons why Mendel was successful: • Choice of a good model organism—garden pea • relatively short generation time—one per year • lots of progeny per cross • self-pollination and out-crossing possible • - true-breedingstrains readily available from local merchant • Choice of clear character differences to track • Yellow vs. green seed pods, round vs. wrinkled seeds, purple vs. white flowers, etc. • Careful mathematical analysis of the results • allowed him to develop and test specific models

19. Mendel’s experiments crosses within the true-breeding population yield progeny that show the same trait as the parent Establish true-breedingstrains, each of which exhibit clear character differences x x Make crosses between different true-breeding strains Identify and count the progeny traits (phenotypes) x ?? Make crosses between the progeny… …are the progeny traits (phenotypes) like one parent or the other? How many of each class are there?

20. Results of Mendel’s experiments: True-breeding green pea pod strain True-breeding yellow pea pod strain x Generation I: Reciprocal cross gave same result Predictions of: Blending Hypothesis Greenish/yellow Vital spark Hypothesis All Green or yellow What happened to the yellow seed pod trait? Homunculus Hypothesis All Green or yellow Actual results: Hybrid pea plants Generation II:

21. The yellow trait returns in generation III True-breeding green pea pod strain True-breeding yellow pea pod strain x Generation I: Hybrid pea plants Generation II: Cross hybrid plants to one another (or self-cross) was this just a peculiarity of the seed pod color trait? Generation III: in 3:1 ratio (green:yellow)

22. Yellow 6022 yellow 2. Yellow X green seed 3.01 : 1 2001 green Purple 705 purple 3. Purple X white petal 3.15 : 1 224 white Inflated 882 inflated 4. Inflated X pinched pod 2.95 : 1 299 pinched Round 5474 Round 5. Round X wrinkled seed 2.96 : 1 1850 wrinkled Axial 651 axial 6. Axial X terminal flowers 3.14 : 1 207 terminal Long 787 long 7. Long X short stem 2.84 : 1 277 short Identical findings seen with other traits… Parental Phenotypes Gen II Gen III Ratio (gen III) Green 428 Green 1. Green X yellow pod 2.82 : 1 152 yellow How did Mendel interpret these findings?

23. Mendel’s interpretations Both parents contribute a “determinant” (gene) that influences the seed pod color trait The “G” or “g” gene True-breeding green pea pod strain True-breeding yellow pea pod strain x Each parent randomly donates only one of their two genes for any given trait to their offspring

24. Mendel’s interpretations There are two forms of a gene (alleles) for the seed pod color trait; the trait conferred by one allele (recessive) can be masked by the trait conferred by the other allele (dominant) True-breeding green pea pod strain True-breeding yellow pea pod strain x alleles: variants of a gene recessive dominant The g allele (which confers yellow seed pods) is recessive to the dominant G allele (which confers green seed pods).

25. Mendel’s interpretations Genes are particulate (i.e., do not mix); recessive traits that are not evident in heterozygotes can be unmasked in progeny True-breeding (homozygous) green pea pod strain True-breeding (homozygous) yellow pea pod strain x Generation I: Hybrid (heterozygous) pea plants Generation II: Cross hybrid plants to one another (or self-cross) The recessive trait reappears intact in generation III Generation III:

26. G g How did Mendel explain the 3:1 ratio? -The Punnett Square gametes = sperm or eggs x female gametes G g Explains the 3:1 ratio in the Generation III offspring from Mendel’s crosses male gametes

27. General conclusions of Mendel’s work 1. Many traits (phenotypes) are determined by genes Gene variants (alleles) can confer dominant or recessive traits (phenotypes) There are two copies of each gene Each parent randomly transmits only one of their two alleles of a given gene to their offspring

28. Some vocabulary Gene: unit of information passed from one generation to the next. Alleles : variants of a gene (e.g., yellow vs. green) Homozygote: both copies of the gene are the same Heterozygote: the two copies of the gene are different Genotype: the information specifying a trait Phenotype: the manifestation of the trait itself Genotypes? GG Gg gg Gg Phenotypes? green green yellow green

29. Information passes from one generation to the next!

30. cc C? C? cc C? C? C? C? Applying Mendel’s principles to CF Two unaffected individuals have eight children, two of whom have cystic fibrosis C = common allele c = cystic fibrosis allele What are the odds that this child is a carrier? Cc Cc

31. C c C c The Punnett Square Cc Heterozygous parents CC Cc Cc Cc cc

32. cc C? C? cc C? C? C? C? Applying Mendel’s principles to CF Two unaffected individuals have eight children, two of whom have cystic fibrosis C = common allele c = cystic fibrosis allele What are the odds that this child is a carrier? Cc Cc

33. The cystic fibrosis gene specifies a membrane protein

34. Proteins are the workhorses of the cell • Many sizes and shapes • Rod-like, globular • Single subunit, multimeric • Many distinct properties • Water soluble, lipid loving • Many functions • Structure, catalysts, motors, signals, pumps • Mutations often alter proteins Including cystic fibrosis

35. CFTR+ CFTR+ CFTR+ CFTR- CFTR- CFTR- Cystic fibrosis is recessive The allele that predominates in the population Cystic Fibrosis NO Homozygous (wild-type) Heterozygous NO A rare allele in the population Homozygous (mutant) YES One wild-type version of the gene is sufficient

36. But what are proteins (chemically)? Polymers of 20 different amino acids (only 11 can be made by humans, others must be obtained from the diet) Have a repeating backbone structure Distinguished by their side chains (R groups)

37. The 20 amino acids

38. Proteins adopt a variety of structures • Average protein = 300 to 400 aa’s • Variety of linear amino acid sequences is almost infinite... • e.g., a protein of 100 amino acids made with the 20 different known amino acids can have 20100different linear sequences • Frequently have globular (spherical) 3-D shapes & are negatively charged • E. coli (human intestinal bacteria) makes about 3,000 proteins • humans make about 100,000 different proteins with 25,000 genes (WOW!)

39. Distinct proteins are different length chains of different amino acids Insulin -- Met-ala-leu-trp-met … glu-gln-tyr-cys-gln (110 aa) Collagen -- Met-his-pro-gly-leu … cys-met-lys-ser-leu (1678 aa) ß-Hemoglobin -- Met-val-his-leu … ala-his-lys-tyr-his (147 aa)

41. Collagen G6PD Albumin

42. Cells -- the basic unit of life • Organisms can be single cells (e.g., bacteria, yeast) or collections of many cells • Prokaryotes (bacteria) lack a nucleus • Eukaryotes have a nucleus and other compartments The Basic Unit of Life

43. An animal cell • Surrounded by the plasma membrane • Contains a nucleus (where >99% of the genes are located) and cytoplasm with specialized organelles • Come in many different shapes

44. The plasma membrane

45. The cystic fibrosis gene specifies a membrane protein

46. Mitochondria • Site of ATP (energy) production • Has its own circular DNA (<1% of the cellular genes located here) • Mitochondrial genes are inherited from the mother

47. Human Cells • Hundreds of cell types • Several categories • Epithelial (skin, intestinal, lung, but also pancreas, liver, kidney) • Muscle • Nerve • Connective • Blood

48. Levels of Organization • Organism • Organ systems • Organs • Tissues • Cells

49. Next time… DNA is the genetic material Structure of DNA reveals a digital code Replication of DNA

50. CFTR regulates Cl- transport across membranes