1. Nucleotides and Nucleic Acids - Lehninger Chapter8
8.1 Basics
8.2 Structure
8.3 Chemistry
8.4 Nucleotide Function

2. 8.1 Basics
Building Blocks
Canonical and Minor Bases
Phosphodiester bonds
Naming and Drawing
Base Stacking and Pairing

3. Building Blocks Nucleotides = Base + Sugar + Phosphate
Nucleosides = Base + Sugar
Nitrogen Bases
Purines (5 + 6 membered rings) – numbering
Adenine Guanine
Pyrimidines (6 membered ring) – numbering
Thymine Cytosine Uracil
Pentose Sugars (numbering)
– Ribose
– Deoxy Ribose

6. Ribose

7. Canonical and Minor Bases
DNA A, G, C, T
RNA A, G, C, U
Modified bases
Methylation in DNA
Lots of Mods in RNA

8. Purines

9. Pyrimidines

12. Phosphodiester bonds Formed by Polymerase and Ligase activities
C-5' OH carries the phosphate in nucleotides
C5' - O - P - O - C3'
Phosphate pKa ~ 0
Natural Oligonucleotides have 5' P and 3' 0H
Base hydrolysis due to ionizaiton of 2' OH in RNA

15. Oligonucleotide naming / drawing conventions
5’ - Left to Right - 3’
pACGTOH
ACGT

16. Base Stacking and Base Pairing
Bases are very nearly planar
Aromaticity => large absorbance at 260nm
Epsilon 260 ≈ 10,000 (M-1 cm-1 )
The A260 ≈ 50 μg /ml for DS DNA
The A260 ≈ 40 μg /ml for SS DNA or RNA
Flat surfaces are hydrophobic
Dipole-Dipole and Van Der Waals interactions also stabilize stacked structures
Bases have hydrogen bond donors and acceptors
H-bonding potential satisfied in paired structures

18. 8.2 Structure DNA contains genetic Information
Distinctive base composition foretells base pairing patterns
Double helical structures
Local structures
mRNAs - little structure
Stable RNAs - complex structures

19. DNA contains genetic Information
Purified DNA can "transform" Bacteria
Avery, MacLeod & McCarty transferred the virulence trait to pneumococci
The genetic material contains 32P (DNA) and not 35S (protein – C, M)
Hershey and Chase grew bacteriophage on either 32P or 35S
Bacteriophage infection resulted in transfer of 32 P and not 35S

22. Distinctive Base composition foretell base pairing patterns
Hydrolysis of DNA and analysis of base composition
Same for different individuals of a given species
Same over time
Same in different tissues
%A = %T and %G = %C (Chargaff's Rules)
Amino acid compositions vary under all three conditions
No quantitative relationships in AA composition

23. Structural Basis of Chargaff’s Rules
Two Strands have complementary sequences
2 logical operations to obtain complementary strand 5' to 3'
1. Reverse: Rewrite the sequence, back to front
2. Complement: Swap A with T, C with G

24. Double helical structures
Potentially Right or Left Handed
Actually Mostly Right Handed
Potentially Parallel or Anti-parallel
Actually anti-parallel
Sugar Pucker + 6 rotatable bonds gives 3 families
A, B, Z structures
KING 3D display software:

25. B-DNA

26. Semi-conservative Replication

27. A, B and Z DNA A form – favored by RNA
B form – Standard DNA double helix under physiological conditions
Z form – laboratory anomaly,
Left Handed
Requires Alt. GC
High Salt/ Charge neutralization
A, B & Z DNA Kinemages

28. Local structures Palindromes – Inverted repeats Direct Repeats
Not quite the same as (Madam I’m Adam)
Symmetrical Sequence Elements Match Symmetry of Protein Homo-Oligomers
Symmetry often incomplete/imperfect
Direct Repeats
Hairpin and Cruciform Structures

32. Messenger RNAs Contain protein coding information
ATG start codon to UAA, UAG, UGA Stop Codon
A cistron is the unit of RNA that encodes one polypeptide chain
Prokaryotic mRNAs are poly-cistronic
Eukaryotic mRNAs are mono-cistronic
Base pairing/3D structure is the exception
Can be used to regulate RNA stability termination, RNA editng, RNA splicing

33. The Genetic Code G A C U GG[GACU] code for Glycine
arg
ser
trp
cys
glu
asp
lys
asn
gln
his
tyr
ala
thr
pro
val
met
ile
leu
phe
GG[GACU] code for Glycine
UGG codes for Tryptophan
UGA, UAG, UAA are stop codons
AG[CU] and UC[GACU] code for Serine

34. mRNA coding patterns

35. Stable RNAs with complex structures

36. RNA Helices are short, bulges, loops

37. tRNA-Phe 2° Structure

38. 8.3 Chemistry Denaturation and reannealing Hybridization
Spontaneous Chemical Reactions
Methylation
Sequencing
Chemical Synthesis

39. Denaturation and reannealing

40. Tm (transition midpoint) as a function of base composition
Salt dependence is more dramatic

41. Hybridization
DNA sequences can spontaneously re-anneal and form helices
Basis for many of molecular biology techniques.
PCR, DNA sequencing