Nucleic Acid Structure & Function Part 2

perpendicular

temperature at which 50% of dDNA becomes single stranded or half-denatured
-increases with G-C content
-influenced positively by iconic strength

via hydrogen bond formation

depends on the size and complexity of the DNA strands

sequence of nucleotides (bases) along the polynucleotide chain
5'-ACGTTAATGGC-3'

3', 5' phosphodiester bond

3D structure of backbone
(Double helix of DNA)

includes supercoiling of the secondary strxr

Watson & Crick in 1953

interaction of nucleic acids with proteins

-messenger RNA that directs amino acid sequence of proteins
-linear single stranded molecule
-post transcriptionally modified
-2% of total cellular RNA

-transfer RNA
-folded stem loop strxrs or hair pins (shaped like a clover) formed by intramolecular H-bonding
-3' end containing sequence CGA = point of attachment of AA (at terminal A residue)
-anticodon seq (triplet) basepairs with a specific codon on the mRNA to facilitate polypeptide synthesis during translation
-adaptor molecules
-carries amino acid to ribosome during translation
-16% of total RNA

tRNA

-ribosomal RNA
-linear single stranded, folded molecule
-complexes with protein to form ribosome
-component of the strxr of ribosome
-82% of total RNA
-rRNA responsbile for overall strxr of ribosome & catalytic activity (forming covalent peptide bonds)

rRNA

Small Nuclear Ribonucleic Acid-snRNA
-involved in generation of mature mRNA transcripts
-mRNA splicing & gene regulation
-central components of splicing apparatus that removes non-coding introns and joins together protein coding exons
-associate with specific proteins to form small nuclear ribonucleoproteins (snRNP)
-<1% in cellular RNA

U1, U2, U4, U5, & U6
Short in length (106-185 nucleotides)

involved in the regulation of gene expression

3% of genome

Primary miRNA transcript (nuclear processing)--> Pre-miRNA (cytoplasmic processing) --> mature miRNA --> miRNA + RNA-induced silencing complex (RISC) --> Translation of target DNA is repressed or Target mRNAs are degraded

5' end of a phosphate group bound to 5' carbon of sugar and 3' end of a OH group attached to 3' carbon on sugar

-favored when DNA sol'n is dehydrated
-right handed double helix with 11 bp/turn & diameter of 2.6nm
-planes of bases not perpendicular--> deeper major groove and shallower minor groove
-observed in short DNA molecules, double-stranded RNA, and DNA/RNA hybrids

-left handed helix with 12bp/turn
-backbone has zig-zag pattern
-sequence of alternating purine & pyrimidines
-present in eukaryotes and prokaryotes
-has a role in recombination and regulation of gene expression

-single stranded ribonucleic acid polymers
-however, tRNA & rRNA fold and form intramolecular H bonding that result to regions of dsRNA

DNA denaturation
Renaturation
Melting temperature Tm
Hybridization

breaking of H bonds and unstacking of bases--> separation of strands
-n vitro can be achieved by heating or exposing to alkali

-annealing of strands with slow cooling after denaturation
-rate depends on the DNA conc, time, & DNA complexity
-rate is inversely proportional to the complexity of DNA

formation of hybrid DNA cules or DNA/RNA hybrids btw single stranded molecules containing certain amts of complimentarity
-marks the foundation for a number of molecular bio reactions and analysis

-2nd messengers in the signal transduction from hormones to intracellular enzymes in euks
-in proks, involved in intracellular signalling & gene expression

Azidothymidine (AZT) & Didanosine (ddI)
Acyclovir

-nucleoside analogs that lack a free 3'OH group
-high affinity for reverse transcriptase enzyme & inhibit their activity
-used in tx for retro-viral infections such as HIV

-open chain strxr in place of sugar strxr
-potent inhibitor of viral DNA polymerase--> causing termination of DNA replication
-used in tx of Herpes virus

Tenofovir

-nucleotide analogs
-open chain strxr in place of sugar strxr
-potent reverse transcriptase inhibitor
-used to tx HIV infection

Tenofovir (nucleotide analog)
Azidothymidine (AZT) & Didanosine (ddl) (nucleoside analog)

-two types: Cytosine & adenosine arabinoside
-unusual planar strxrs
-inhibit activity of DNA polymerase
-induce DNA damage by incorporating into a DNA during replication
-used as anti-cancer drugs by selectively destroying the rapidly dividing cancer cells

-disrupt the epigenetic process of DNA methylation
-has a N atom at position 5 of cytidine and prevents DNA methyl-transferase enzymes from methylation cytosine at position 5
-direct inhibitors of DNA methyl-transferase enzymes
-5-aza-2'deoxycytdine
-5-azacytidine

gene regulation (transcription) in eukaryotes

-anti-cancer agent
-converted to FdUMP which inhibits thymidylate kinase
-inhibits synthesis of thymine nucleotides required for DNA synthesis

-metabolized to 6-mercaptopurine which suppresses rejection during organ transplantation

-txt for gout
-inhibitis xanthine oxidase
-lowers conversion of purine bases to uric acid end products
-purines are excreted as xanthine and hypoxanthine which are more soluble that uric acid

-txt supraventricular tachycardia
-slows heart rate
-plays a role in sleep regulation
-so high levels = extended periods of wakefulness
-low levels= periods of sleep