DNA + RNA

1. DNA + RNA Dan Graur

2. The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA) molecules.

3. DNA is made of four nucleotides adenine (A) guanine (G) cytosine (C) thymine (T) 2 purines (R): 2 pyrimidines (Y):

4. DNA is made of four nucleotides adenine (A) guanine (G) cytosine (C) thymine (T) 2 purines (R): 2 pyrimidines (Y): sugar (deoxyribose) phosphate

5. DNA is made of four nucleotides 2 purines (R): 2 pyrimidines (Y): A G C T one ring two rings

6. The nucleotides are covalently linked in tandem by asymmetrical 5’-3' phosphodiester bonds. The DNA is, thus, polarized.

7. Thus, the sequence 5’-GCAAT-3’ is different from the sequence 3’-GCAAT-5’

8. Deoxyribonucleic acid (DNA) consists of two complementary strands twisted around each other to form a right-handed double helix. The two chains are joined throughout their lengths by hydrogen bonds between pairs of nucleotides.

9. Weak bond Strong bond A purine always pairs with a pyrimidine.

10. Theantiparallelstructure of double-stranded DNA

11. upstream downstream 5’ 3’ 3’ 5’ downstream upstream

12. A preponderance of purines 3’ 5’ heavy chain light chain 3’ 5’ A preponderance of pyrimidines

13. 3’ 5’ 3’ 5’ CTGGA

14. The length of a single-stranded nucleic acid is measured in number of nucleotides.

15. The length a double-stranded sequence is measured in base pairs (bp), thousands of base pairs (kilobases, Kb), millions of base pairs (megabases, Mb), or billions of base pairs (gigabases, Gb).

16. The entire complement of genetic material carried by an individual is called the genome. Eukaryotic cells usually have more than one genome: nuclear1, mitochondrial2, & plastid3. Some eukaryotes have a single genome; some have 4 or more genomes . 3 1 2

17. Genome Genic DNA Nongenic or intergenic DNA

18. Replication DNA  DNA

19. 1958: Matthew Meselson & Franklin Stahl

21. The origin of replication is at the replication bubble, a local region where the two strands of the DNA helix have been separated from each other. Replication proceeds in both directions as two replication forks.

22. Bacteria have one origin of replication. A bacterial genome can replicate in ~40 minutes. In eukaryotes, many replication origins exist. They are spaced at intervals of up to 300,000 bp from one another. Replication in eukaryotic cells may take several hours.

23. DNA replication occurs only in the 5'-to-3' direction.

24. The leading strand is replicated continuously. The lagging strand is replicated as Okazaki fragments. Okazaki fragments Bacteria = 1,000 - 2,000 nucleotides Vertebrates = 100 - 200 nucleotides

25. What is a Gene? When Wilhelm Johannsen coined the word “gene” in 1909, the term meant “a unit of heredity.” Its material basis was unimportant for its usefulness as a concept.

26. What is a Gene? “Where the meaning of most four-letter words is all too clear, that of gene is not. The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.” Helen Pearson

27. What is a Gene? “A gene is a sequence of DNA that is essential for a specific function.” (1) Protein-codinggenes, which are transcribed into RNA and subsequently translated into proteins (2) RNA-specifyinggenes, which are only transcribed into RNA (3) Untranscribed genes.

28. What is a Gene? (1) Protein-coding genes (2) RNA-specifying genes Structural or Productive Genes

29. Transcription DNA  RNA

30. RNA differs from DNA by having ribose instead of deoxyribose…

31. standard nucleotides RNA differs from DNA by using uracil instead of thymine…

32. DNA is mostly double-stranded. RNA is mostly single-stranded.

33. Transcription antisense The 5’ to 3’ DNA is transcribed into 3’ to 5’ RNA sense

34. RNA Coding RNA = mRNA Non-coding RNA Non-functional RNA (transcriptional noise)

35. Non-coding RNAs

36. RNA processing pre-RNA mature-RNA

37. Examples of RNA processing: 1. Capping of 5' end. 2. Polyadenylation of 3' end. 3. Postranscriptional modifications. 4. Splicing. 5. RNA editing.

38. Capping is the addition of a 7’-methylated guanine to the 5’ end via a 5’ to 5’ bond.

39. Polyadenylation of 3' end

40. I: Inosine (needed for wobble). Ψ: Pseudouridine (only in Eukarya and Archaea). D: Dihydrouridine. T: Thymine (unusual for RNA). Y: Wybutosine (found just after the anticodon). Postranscriptional modifications

41. Splicing

42. Protein-coding genes The number of introns varies greatly from gene to gene. The distribution of intron sizes in vertebrate genes is very broad. The distribution of exon sizes is much narrower with a peak at around 150 bp. The vast majority of protein-coding genes in vertebrates consist mostly of introns.

43. acceptor donor

44. The human factor-IX gene Total length of exons = 1,386 bp Total length of introns = 29,954 bp 5' untranslated region = 30 bp 3' untranslated region = 1,389 bp Only about 4% of the pre-mRNA sequence actually encode the protein. Note the uneven distribution of exons.

45. Homo sapiens Rattus rattus Arabidopsis thaliana Mean size = 144 bp Mean size = 123 bp Mean size = 165 bp exons Mean size = 2364 bp Mean size = 733 bp Mean size = 171 bp introns

46. Intron and exon lengths

47. The nuclear divide:

49. Substitution Insertion/deletion RNA editing • Mononucleotide insertion (C, G, U) • Mononucleotide deletion (U) • Dinucleotide insertion (GC, GU, CU, AU, AA) • Substitutions (UA, UG, UC, AG, CU, CA, GA) • Modifications to a nonstandard nucleotide (AI)

50. Substitution editing