Nucleic Acids - Triple helices – H-DNA (Hoogsteen base pairing), a long

segment of polypurine hydrogen bonded to a long segment

DNA Structure
of polypyrimidine.
Dimensions of Crystalline DNA - Supercoils

1. One turn of the double helix spans 3.4 nm and consists of Organelle DNA
approximately 10.4 base pairs. (Changes in pH and salt
- Chloroplast
concentrations affect these values slightly.)
- Mitochondria
2. The diameter of the double helix is 2.4 nm. Note that the
interior space of the double helix is only suitable for base Mutation
pairing a purine and a pyrimidine. Pairing two pyrimidines
Transition Mutation
would create a gap, and pairing purines would destabilize
the helix. - Tautomeric Shift – imino form bond with cytosine
3. The distance between adjacent base pairs is 0.34 nm.
Base Modification
Stability
- Ionizing Radiation – formation of pyrimidine dimers, free
1. Hydrophobic interaction – base ring π cloud of electrons radicals
between stacked purine and pyrimidine is nonpolar
2. Hydrogen bonds – three between GC pairs and two Spontaneous Hydrolytic Reactions
between AT pairs - Depurination Reaction – N-glycosyl linkage between a
3. Base stacking – parallel stacking of nearly planar purine base and deoxyribose is cleaved (point mutation)
heterocyclic bases by Van de Waals forces
4. Electrostatic interactions – sugar-phosphate backbone’s Xenobiotics
repulsion between negatively charged phosphate group - Base Analogues – caffeine base analogue of thymine
stabilized by divalent cations such as Mg+2 and polycationic (transition mutation)
histones and polyamines - Alkylating Agents – electrophilic substances attack
Some parts of the DNA have higher-order structures molecules that possess unshared pair of electrons,
methylguanine pairs with T instead of C, dimethylsulfate
- Cruciforms – cross-like structures due to palindrome and dimethylnitrosamine are alkylating agents, add methyl
sequences, form inverted repeats group
 - Nonalkylating agents – nitrous acid deaminates bases,
adenine to xanthine, guanine to hypoxanthine, cytosine to
uracil, ex. benzo[a]pyrene
- Intercalating agents – planar molecules that can insert
themselves between stacked DNA base pairs, adjacent base
pairs are deleted or new base pairs are inserted, causes
frameshift mutation
RNA vs. DNA
- Sugar is ribose instead of deoxyribose
- Uracil instead of thymine
- Single stranded not double stranded
Transfer RNA
- tRNA transport amino acids to ribosomes for assembly to
proteins
- 15% cellular RNA; 75 nucleotides
- At least one RNA for each of the 20 amino acids
- Important components: 3’-terminus and anticodon loop
- Variable loops
- Modified bases
Ribosomal RNA
- rRNA is the most abundant form of RNA in living cells
- 80% of the total RNA
- 3D structure is conserved
- Prokaryotes and eukaryotes have the same shape and
function of RNA but different size and chemical composition
- Both types contain two subunits of unequal size
- S (Svedberg, sedimentation units, sedimentation velocity in
a centrifuge) dependent on molecular weights and size of
particles
- Prokaryotes 70S = 50S 30S
- Eukaryotes 80S = 60S 40S
Messenger RNA
- mRNA are the carrier of genetic information from the DNA
for protein synthesis
- 5% of cellular RNA
- Cistron – a DNA sequence that contains the coding
information for polypeptides and several signals required
for ribosome function
- Prokaryotic RNA are polycistronic; contain coding
information for several polypeptide chain
- Eukaryotic RNA are monocistronic
- Prokaryotic RNA are translated into ribosomes immediately
or during synthesis
- Eukaryotic RNA are modified extensively
o Capping (linkage of 7-methylguanosine to the 5’-
terminal residue)
o Splicing (removal of introns)
o Attachment of adenylate polymer known as poly-A
tail
Heterogenous RNA and Small Nuclear RNA
- In Eukaryotes
o hnRNA are primary transcripts of DNA and are
precursors of mRNA
o hnRNA are processed by splicing and modification
to form mRNA
o Splicing – enzymatic removal of introns from the
primary transcripts
o snRNA are complexed with proteins; 90 to 300
nucleotides
 o snRNA are involved in splicing activities and other
forms of RNA processing

Central Dogma

Replication – Semi-conservative

Replication of DNA: Origin and Replication Forks

A. Small Prokaryotic Circular DNA

B. Very Long Eukaryotic DNA

Proteins responsible for maintaining the separation of the parental

strands and unwinding the double helix ahead of the advancing
replication fork.

- Rich A-T Base Pairs – DNA A Protein

- Single-stranded DNA binding proteins
- DNA Helicases