1. BIOL 2416 CH 4: Gene Function

2. How do biochemical reactions take place in a cell? Each reaction in a metabolic pathway must be catalyzed by its own enzyme Enzymes are proteins encoded in the cellular DNA (by a gene) If the gene is functional, functional enzyme is made, and food substrate A can be turned into product B: gene 1 functional enzyme 1 helps convert A B If the gene has been mutated, the reaction cannot take place in real time, no functional enzyme is made, and A cannot be turned into B (mutant cell dies) Adding B will overcome the mutation, adding more A will not.

3. So there is a relationship: 1 gene = 1 enzyme (polypeptide)

4. Archibald Garrod, 1902 Alkaptonuria- urine turns black upon exposure to air Inborn error of metabolism

5. One Gene - One Enzyme Hypothesis Discovered by George Beadle and Edward Tatum (1942) Used Neurospora crassa (orange bread mold) = HAPLOID mycelial-form fungus (means mutations cannot be masked) Bombarded wild-type cells with X-rays to induce random mutations in enzyme-coding genes –Each metabolic pathway involves its own set of enzymes/genes; idea is to create one mutant for every step (gene) in the pathway –Isolate all mutants concerning one specific pathway –Order the mutants to start to discover the gene and enzymes involved in the pathway

6. Mutant analysis: first make sure each mutant we study has one and only one mutated gene We cannot study the effects of more than one mutated gene at a time Ensure heritable single gene mutants by performing specific mating bread mold experiments Mate wild type (A) and mutant (a) together: –produces A/a ascus –A/a ascus undergoes meiosis and 1 round of mitosis –produces 4 A and 4 a “ascospores –Ascospores can be germinated into 8 babies Examine the babies: if 4 babies are wild-type (A), and 4 are mutant (a), by definition there is a mutation in a SINGLE gene

7. Life cycle of Neurospora crassa

8. Figure 3-10b The linear meiosis of Neurospora

9. Out of the single-gene mutants, how do we pick the ones in the same pathway? Done by testing different growing conditions (media):

10. Wild-Type (non-mutated) Neurospora is prototrophic Needs only minimal media with: Inorganic salts (including Nitrogen source) Organic Carbon source (sugar) Biotin (a vitamin)

11. Minimal media –Supports growth of wild-type organisms –Wild-type organisms can make whatever is not supplied using raw materials in minimal media –Requires functional genes to make functional protein enzymes Complete media –Has everything plus the kitchen sink –Supports wild-type and auxotrophic mutants –Supplies anything mutants cannot make due to faulty genes/enzymes

12. Auxotrophic Mutant Mutants are produced by X-ray exposure Already seen how potential mutants are mated to wild- type strain to ensure X-ray damage is heritable and in only one gene And how progeny spores that can be germinated Auxotrophic mutants can no longer grow on minimal medium In order to grow, mutant needs –minimal media PLUS particular nutrient supplement to overcome the gene mutation –Or can grow on complete medium (not diagnostic)

13. Method to isolate auxotrophic mutations in N. crassa

14. How do we pick the correct auxotrophic mutants? Consider the biosynthetic pathway: A > B > C > D > E –Bread mold needs E to live –Wild type bread mold can make E from D from C from B from A in minimal media –But only if all genes/enzymes are OK If any one step (>) in the pathway leading to E is blocked (due to a mutation in that enzyme gene), no E is made and the mutant dies on minimal media So for this pathway, test mutants to see if they will live when given E –If adding E overcomes the mutation: bingo! –If not, it must be a mutant in a different pathway

15. E.g. Methionine (E) Biosynthesis Involves 4 protein enzymes in a linear pathway Encoded by 4 wild-type DNA genes: met-2 +, met- 3 +, met-5 +, and met-8 +: (met-5 + ) (met-3 + ) (met-2 + ) (met-8 + ) enz 1 enz 2 enz 3 enz 4 A B C DE (substrate)(intermediates) (end product Methionine)

16. Identifying Auxotrophic Mutants in the E Pathway Germinate all spores on complete medium (so everything, mutant or wild type will grow) Switch to arrays of minimal media with B, C, D, or E food supplements All mutants DIE on minimal media with NO food supplements E pathway mutants die on minimal, but live on minimal + E supplement

17. Ordering E pathway mutants: Again, all mutants CAN GROW as soon as supplement E (methionine) is added Because supplement E overrides any defects in “upstream” enzyme genes: A X B X C X D X E GROW anyway Add E (met-5 (met-3) (met-2) ( met-8)

18. Ordering E pathway mutants: Mutants can grow if they receive a downstream supplement to override an upstream enzyme defect: Met-8 mutation can only be overcome by adding E food supplement; means it must concern the last enzyme/gene in the E pathway Met-2 mutation can be overcome by adding D or E; must concern the next-to- last enzyme/gene in the E pathway Met-3 mutation can be overcome by adding C, D, or E Met-5 mutation can be overcome by adding B, C, D, or E (met-5) (met-3) (met-2) (met-8) A B C D E grow (BCDE) (CDE) (DE) (E)

19. Genetically based enzyme deficiencies in humans - usually recessive Phenylketonuria (PKU) –Cannot convert excess phenylalanine to needed tyrosine –Convert to harmful phenylpyruvic acid instead –Mental retardation, unless on PKU-restricted diet –Guthrie testing on newborns Albinism –Mutated tyrosinase gene prevents normal pigmentation –No melanin

20. Lesh-nyhan syndrome –Only males (sex-linked) –Self-mutilation –Eventually fatal –Accumulate excess purines due to purine-processing enzyme defect Tay-sachs disease –hexA defect causes ganglioside accumulation in brain –Progressive neurological degeneration –Fatal by age 3-4 –Ashkenazi Jews - registry

21. Sickle cell anemia –Hemoglobin defect –Causes sickling of red blood cells > get stuck in capillaries > Oxygen deficiency –Pleiotropic (wide-ranging) effects –Milder sickle cell “trait” Cystic fibrosis –Abnormal active transport of ions across cell membranes –Causes thick mucus > must be dislodged –Eventually fatal

22. Practice Problem Q4.1 A number of auxotrophic mutant strains were isolated from wild-type, haploid yeast. These strains responded to the addition of certain nutritional supplements to minimal culture medium either by growth (+) or no growth (0). The following table gives the growth patterns for single-gene mutant strains: