1. Nucleic Acids: Cell Overview and Core Topics

2. Outline I.Cellular Overview II.Anatomy of the Nucleic Acids 1.Building blocks 2.Structure (DNA, RNA) III.Looking at the Central Dogma 1.DNA Replication 2.RNA Transcription 3.Protein Synthesis

3. Cellular Overview DNA and RNA in the Cell

4. Classes of Nucleic Acids: DNA  DNA is usually found in the nucleus  Small amounts are also found in: mitochondria of eukaryotes chloroplasts of plants  Packing of DNA: 2-3 meters long histones  genome = complete collection of hereditary information of an organism

5. Classes of Nucleic Acids: RNA FOUR TYPES OF RNA mRNA - Messenger RNA tRNA - Transfer RNA rRNA - Ribosomal RNA snRNA - Small nuclear RNA

6. Anatomy of Nucleic Acids THE BUILDING BLOCKS

7. Nucleic acids are linear polymers. Each monomer nucleotide consists of: 1. a sugar 2. a phosphate 3. a nitrogenous base

8. Nitrogenous Bases

9. DNA (deoxyribonucleic acid): adenine (A)guanine (G) cytosine (C)thymine (T) RNA (ribonucleic acid): adenine (A)guanine (G) cytosine (C)uracil (U) Why ?

10. Properties of purines and pyrimidines: 1.keto – enol tautomerism 2.strong UV absorbance

11. Pentoses of Nucleic Acids This difference in structure affects secondary structure and stability. Which is more stable?

12. Nucleosides linkage of a base and a sugar.

13. Nucleotides - nucleoside + phosphate - monomers of nucleic acids - NA are formed by 3’-to-5’ phosphodiester linkages

14. Shorthand notation: - sequence is read from 5’ to 3’ - corresponds to the N to C terminal of proteins

15. Nucleic Acids: Structure DNA

16. Primary Structure nucleotide sequences

17. DNA Double Helix Maurice Wilkins and Rosalind Franklin James Watson and Francis Crick Features: two helical polynucleotides coiled around an axis chains run in opposite directions sugar-phosphate backbone on the outside, bases on the inside bases nearly perpendicular to the axis repeats every 34 Å 10 bases per turn of the helix diameter of the helix is 20 Å Secondary Structure

19. Double helix stabilized by hydrogen bonds. Which is more stable?

20. Axial view of DNA

21. A and B forms are both right-handed double helix. A-DNA has different characteristics from the more common B-DNA.

22. left-handed backbone phosphates zigzag Z-DNA

23. Comparison Between A, B, and Z DNA:  A-DNA: right-handed, short and broad, 11 bp per turn  B-DNA: right-handed, longer, thinner, 10 bp per turn  Z-DNA: left-handed, longest, thinnest, 12 bp per turn

24. Major and minor grooves are lined with sequence-specific H-bonding.

25. Supercoiling relaxed DNA supercoiled DNA Tertiary Structure

27. Consequences of double helical structure: 1. Facilitates accurate hereditary information transmission 2.Reversible melting melting: dissociation of the double helix melting temperature (T m ) hypochromism annealing

28. Structure of Single-stranded DNA Stem Loop

29. Nucleic Acids: Structure RNA

30. Secondary Structure transfer RNA (tRNA) : Brings amino acids to ribosomes during translation

31. Transfer RNA Extensive H-bonding creates four double helical domains, three capped by loops, one by a stem Only one tRNA structure (alone) is known Many non-canonical base pairs found in tRNA

32. ribosomal RNA (rRNA) : Makes up the ribosomes, together with ribosomal proteins. Ribosomes synthesize proteins All ribosomes contain large and small subunits rRNA molecules make up about 2/3 of ribosome Secondary structure features seem to be conserved, whereas sequence is not There must be common designs and functions that must be conserved

33. messenger RNA (mRNA) : Encodes amino acid sequence of a polypeptide

34. small nuclear RNA (snRNA) :With proteins, forms complexes that are used in RNA processing in eukaryotes. (Not found in prokaryotes.)