1. Nucleotides and nucleic acids
Lecture 5
Dr. Mamoun Ahram

2. Nucleic acids
Monomers
Polymers

3. Chemical composition and bonds

4. DNA vs. RNA

5. Nitrogenous bases

6. Other nucleotides Xanthine, hypoxanthine and uric acid
intermediates in purine metabolism)
N6-methyl adenine
5-methyl-cytosine and N4-methyl cytosine
pseudouracil
has the ribose attached to C5 instead of N1 of uracil
Pseudouridine
1,3,7-trimethylxanthine (caffeine)

8. Nucleotides are acidic

9. Nucleotides vs. Nucleosides

12. Nucleic acid polymer

13. A new era

14. DNA structure A double helix Backbone vs. side chains Antiparallel
Specific base-pairing
Chargaff's rules
Stable
Flexible
Groovings
Stability vs. flexibility

15. Chemical forces Ionic interactions Hydrogen bonds
van der Waals interactions
Hydrophobic interactions (Base stacking)
Both van der Waals and hydrophobic interactions drive the formation of DNA (and RNA) double helices

16. B-DNA

17. Other forms

18. Chromosomal packaging
2 meters of DNA/cell
40 km of thread in a tennis ball!
How?
Histones

19. What is a chromatin? Chromatin = DNA molecule + proteins
The proteins that bind to the DNA:
histones (H1, H2A, H2B, H3, and H4)
nonhistone chromosomal proteins

20. Nucleosomes

21. Chromatosome
H1 is bound to the DNA forming with the octamer and wrapped DNA a chromatosome

22. DNA-histone interaction
Histones are positively charged
Interaction
Charge neutralization

23. RNA
Vs. DNA
Secondary structures

24. Molecular processes

25. Types of RNA Messenger RNA (mRNA)
Localization
Modification
Variable size

26. Types of RNA Ribosomal RNA (rRNA)
Ribosomal RNA molecules comprise 65 to 70% of the mass of the ribosome
The rRNA maintains the structure of the ribosome and provides sites for the binding of mRNA and protein synthesis

27. Types of RNA Transfer RNA (tRNA)
tRNA is a ~75 base molecule that carries the amino acids, and transfers them to the growing protein
tRNAs have a common tertiary structure

28. Modified nucleotides in tRNA
tRNAs contain modified bases

29. Other RNA molecules Small nuclear RNA (snRNA) RNA processing
MicroRNA (miRNA)
Natural
translation regulation
Small interfering RNA (siRNA)
Synthetic
Translation regulation

30. Light absorbance of nucleic acids
Aromatic pyrimidines and purines can absorb UV light
The peak absorbance is at 260 nm wavelength

31. The unit of absorbance The absorbance of 260 nm (A260) is constant
dsDNA: A260 of 1.0 = 50 ug/ml
ssDNA: of 1.0 = 30 ug/ml
ssRNA: A260 of 1.0 =40 ug/ml

32. Exercise
What is the concentration of a double stranded DNA sample diluted at 1:10 and the A260 is 0.1? DNA concentration = 0.1 x 10 x 50 µg/ml = 50 µg /ml

33. Denaturation-renaturation

34. Observation of denaturation

35. Factors influencing Tm
G·C pairs pH
Salt and ion concentration
Destabilizing agents (alkaline solutions, formamide, urea)

36. G-C content