Topics: DNA Structure, Replication & Central Dogma

1. GENETICS : Introduction to IEM Topics: DNA Structure, Replication & Central Dogma

2. Studies of Heridity • By geneticists • - describe patterns of inheritance • traits (phenotypes) • heritable (passed from parents to offspring) • cytogeneticists knew that trait inheritance is associated with the cell nucleus and with chromosomes • biochemists knew that chromosomes are composed of DNA and protein

3. Parent trait Offspring trait Q. What is the molecular/biochemical basis of inheritance? How is it known that DNA contains genetic information ???

4. Some Important Definitions • Gene: • - segment of DNA that contains all the information needed for regulated synthesis of an RNA or protein product. • Genome: • - the entire DNA sequence content of an organism (nuclear DNA)

5. DNA Structure: Double Helix • 1953 - Watson and Crick 3-D structure of DNA • DNA is a double helix (ll-stranded) • Polymer of nucleotides (phosphate, sugar, base) • DNA has 4 base types (adenine, thymine, guanine, cytosine)

6. 4 DNA Nucleotides THYMINE (T) ADENINE (A) base phosphate sugar CYTOSINE (C) GUANINE (G)

7. A - T G - C Base pairing Strands have different polarity & antiparallel

8. equal (randam) base composition AT rich GC rich 5’ 3’ or or 3’ 5’ 1 bp

9. DNA Replication parental strand as a template daughter strand has complement bases

10. Clones due to replication from 1 cell

11. How does DNA relate to proteins? 1908: Garrod inborn errors of metabolism (hereditary disease) Alkaptonuria (AKU): accumulation of homogentisic acid 1:200,000

12. blocked in PKU 1:8,000 Phenylalanine/Tyrosine degradative metabolic pathway II blocked in Tyrosenemia III blocked in AKU 1:200,000

13. A defective enzyme results from a mutant gene HOW????

14. Central Dogma of Genetics Replication DNA RNA Protein Transcription Reverse Transcription Translation aa aa aa aa aa aa

18. Genes and Proteins • Inborn Errors of Metabolism shown by Garrod to cause hereditary disease. • Study of Biochemical Pathways lead to understanding that mutant genes result in defective proteins (enzymes).

19. further metabolites homogentisic acid Tyr Accumulation of homogentisic acid Biochemical Genetics Archibald Garrod (1902) - an English doctor Described “alkaptanurea” disease Symptom: urine turns black when exposed to air Found it was due to oxidation of homogentisic acid in urine homogentisic acid = an intermediate in Phe degradation Phe

20. Biochemical Genetics Archibald Garrod : important contributions Described “alkaptanurea” disease Deduced that it is due to a defective metabolic enzyme Disease is a hereditary condition (ran in his patients’ families) Led to concept of “inborn errors of metabolism” A novel phenotype may reflects a discrete biochemical difference

21. Biochemical Genetics

22. Aspartame = a dipeptide: aspartyl-phenylalanine methyl ester “Real-World Biochemistry” Aspartame is metabolized in the body to its components: aspartic acid, phenylalanine, and methanol. Like other amino acids, it provides 4 calories per gram. Since it is about 180 times as sweet as sugar, the amount of aspartame needed to achieve a given level of sweetness is less than 1% of the amount of sugar required. Thus 99.4% of the calories can be replaced. Look on your diet soda cans and read the warning

23. defective enzyme Parent trait Offspring trait Biochemical Genetics Archibald Garrod : important contributions Proposed that inheritance of a defective metabolic enzyme leads to inheritance of a phenotype (disease)

24. George W. Beadle • born in Wahoo, Ne • undergraduate degree at UNL • did graduate work at Cornell • got a faculty position at CalTech • ended up as the president of the Univ of Chicago • did work in the 1930’s & 40’s on Drosophila eyes • and on Neurospora (bread mold) • “one gene - one enzyme” hypothesis (1941) • awarded Nobel prize in 1958 (with research colleagues J. Lederberg and E. Tatum)

25. sucrose Inorganic salts biotin George W. Beadle • Bread Mold: Neurospora crassa • can grow on minimal media • Beadle selected for nutritional mutants (auxotrophs) • irradiated fungal spores, grew these up on complete • media, and transferred part of the stock to minimal media • He looked for mutants that can grow on complete media but NOT on minimal media • These mutants are lacking an enzyme for the synthesis of an essential nutrient

26. Beadle’s Experiment Summary • Beadle could identify mutants in specific steps of a pathway • Assuming each mutant was defective in a single gene, Beadle postulated that the different mutant classes each lacked a different enzyme for Arg biosynthesis • Therefore, he could show a one-to-one correspondance between mutation and absence of an enzyme. • one gene specifies/encodes one enzyme

27. Parent trait defective gene defective enzyme Offspring trait Beadle’s experiment gave rise to a new field called Biochemical Genetics

28. Mutations • Mutation = change in the base sequence of DNA • Any mutation that causes the insertion of an incorrect amino acid in a protein can impair its function • Base substitutions alter the genetic code which specifies amino acid placement in proteins

33. Genes and Environment • One gene can affect more than one trait: pleiotropy • Any trait can be affected by more than one gene: epistasis

35. Pedigree Analysis • The analysis of an unknown trait from a family history (pedigree)  • Is the trait dominant • does every affected offspring have an affected parent • Is the trait determined by a single gene • affected progeny born to heterozygous parents (carriers) should occur with a frequency of 3:1 (unaffected to affected) • Is the trait sex-linked • is it expressed more frequently in males • not, if expressed at equal frequency in male and female progeny

36. Autosomal Dominants • At least one parent of the index case (proband) is affected, both male and female progeny are affected equally and can transmit the condition, when an affected person has offspring, they have a one chance in two of inheriting the trait •  For dominantly inherited traits: • generations not skipped • some patients do not have affected parents, the result of a new mutation • clinical features: • reduced penetrance - reduced fraction of individuals show the phenotype • variable expressivity – trait is expressed to different extents among affected individuals • for many dominant traits the age of onset is delayed beyond reproductive age 

37. Mechanisms of dominant disorders • Usually a loss of function mutation • Loss of a component of an enzymatic, regulatory or signaling pathway • Loss of a structural protein such as collagen • These can produce a dominantly active phenotype by: • reducing function below a level necessary to maintain a normal phenotype (familial hypercholesterolemia, LDL receptor) • acting as a “dominant negative” (Marfan Syndrome, fibrillin-1 or some forms of Ehlers-Danlos Syndrome, collagen) which prevents the function of the normal allele in the heterozygous state • Gain of Function Mutation • Huntington disease results from a mutation in the Huntington gene which gives rise to an over-expression of an altered protein that is toxic to neural cells

38. Autosomal Dominant Genetic Disease

40. Autosomal Recessive • The trait does not usually affect the parents, but siblings may show the disease • Siblings have a 1-in-4 chance of inheriting the disease • The majority of the mutant genes in the gene pool are in heterozygous “carriers” • If the mutant gene occurs with a low frequency in the population, there is a likelihood the proband is the product of a consanguineous marriage

41. Mechanisms of Recessive Disorders • Features of autosomal recessive disorders • Complete penetrance • Early age of onset • Molecular change usually results in a loss of function • In the heterozygous carrier the presence of 50% of the protein is sufficient to provide a normal phenotype • Essentially all inborn errors of metabolism are inherited as autosomal recessive traits

42. Autosomal Recessive Genetic Disease