Proteins, phenotypes, mutation, and genetic diversity

1. Proteins, phenotypes, mutation, and genetic diversity

2. A quick review of enzymes • Biological catalysts • Reactions are connected to form metabolic pathways • Metabolism: sum of all biochemical reactions (pathways)

3. Metabolic pathways An unbranched pathway A branched pathway

4. Pathways and phenotypes • Defect in an enzyme can change phenotype and cause disease • Enzyme 1 defect: PKU • Enzyme 5 defect: alkaptonuria • Enzyme 6: albinism • How? • Why? See Fig. 10.5; this is a partial list “enzyme 1” is phenylalanine hydroxylase

5. PKU: Phenylketonuria (OMIM 261600) • Body can’t convert phenylalanine to tyrosine • Phenylpyruvic acid accumulates and causes brain damage • Phenylalanine is in all proteins, so strict diet must be imposed immediately • Is inherited as a recessive trait • more about PKU

6. Newborn testing for PKU • Required by all states in U.S. • Over 10,000 identified out of 100 million screened • No cure, but brain damage can be avoided with immediate treatment • This is one of many diseases for which screening is available • Not all are performed routinely

7. How metabolic disorders cause disease • Intermediate builds up and causes damage • A needed substance isn’t synthesized

8. Enzyme defects are found in other metabolic pathways • Carbohydrate metabolism • Galactosemia • Glycogen storage disorders • These are accumulation disorders • Lactose intolerance • Enzyme becomes less active over time

9. Lipid metabolism disorders Many are storage disorders- can’t break down lipids for energy Familial hypercholesterolemia (OMIM 144010) Transport disorder

10. Lesch-Nyhan Syndrome (OMIM300322) Inability to metabolize purines Accumulation of uric acid instead Gout, liver and kidney failure Mental retardation Self-mutilation X-linked recessive Inability to metabolize vitamins and minerals also documented

11. Structural disorders of proteins • Hemoglobin • Sickle cell anemia • Hemoglobin variant- there are many • Some have no effect • Autosomal recessive • Thalassemias • Insufficient production of hemoglobin • Mild or severe anemia • Autosomal recessive

12. Sickle cell anemia Anticancer drugs have been effective

13. Phenotypic variations are not always so drastic • Allergies • Sensitivities • Pharmacogenetics: genetic basis for sensitivities to drugs • Resistance • Toxicity • Predisposition to cancer • Tasters, nontasters, supertasters

14. Ecogenetics • What is toxic (or carcinogenic) to whom? • Some people have “resistance” genes • How many (allelic frequency) • What is the distribution of the allele in the population? • How did these mutations arise in the first place?

15. What is a mutation? • A heritable change in DNA • Somatic • Affects all daughter cells of affected cell • Underlying cause of cancers • Not transmitted to offspring • Germline • Single genes • Chromosomes

16. How are mutations discovered? • Pedigree analysis (Is the change observed in the generations that follow?) • Recessive mutations are hard to spot! • Direct genetic analysis • See Table 11.1 in book for rates- range from <1 to over 100 per million gametes • Some calculated rates are 1 in 1012

17. How does mutation occur? • Spontaneously? • It’s complicated • Species (viruses mutate very rapidly) • Some genes mutate more frequently than others • Size • Presence of many repeats • Presence of many G/C pairs

18. Types of mutations: base substitution

19. Frameshift mutations • Remember the triplet codon • Adding or removing bases changes the “reading frame”

20. Transposable elements • Discovered in corn; studied in bacteria • 40% of human genome may be transposable elements http://www.nature.com/scitable/topicpage/transposons-or-jumping-genes-not-junk-dna-1211 • Disrupt gene expression • May play regulatory role

21. Induced mutations: chemicals and radiation Modify, substitute, intercalate Used to study mutation Some are used as drugs Handle with care!

22. Base analogs and intercalating agents

23. Multiple repair mechanisms

24. Mismatch repair • Error often occur when DNA is being replicated • Replicating enzyme has proofreading function • Studied in bacteria- occurs in humans too, but with different mechanism • DNA repair is critical to survival!

25. How do you know if a chemical causes mutations? • Ames test- developed in 1970’s • Uses bacteria, not animals • Has been modified to simulate processes in animals and find “promutagens” • Mutagen: chemical that causes mutations in DNA • Carcinogen: chemical that causes cancer • Many mutagens are carcinogens • Effect in animals; dose levels; often difficult to assess

26. The Ames test

27. Mutations, genotypes, and phenotypes • Diploid individuals have two copies of a gene • In some disorders, a single mutation is the cause (sickle cell anemia) • In others, many different mutations have been found • Example: over 1600 mutations of CTFR (cystic fibrosis) gene • What is the effect of having a different mutation on each allele?

28. Genomic imprinting • Generally, male and female alleles are required for normal development • Genes are “silenced” by methylation (imprinting) • In humans, a limited number of genes are imprinted In imprinting, one copy of a gene is silenced Implicated in certain diseases

29. http://universe-review.ca/I10-46-imprint1.jpg

30. Why imprinting? • Not fully understood • Implicated in diabetes mellitus, autism, schizophrenia, and other disorders • Is only seen in placental mammals • There is still much to learn about gene silencing and gene regulation

31. Summary • Cell metabolism is a collection of biochemical pathways • Many inherited metabolic disorders have been described • Genetic variation arises through mutation • Mutations can be spontaneous or induced • Phenotypes are affected by epigenetic factors as well as Mendelian inheritance

32. A final word (for now) on the epigenome • epigenome song