Lecture notes study book Harper's Illustrated Biochemistry Thirty-First Edition of Victor Rodwell, David Bender - ISBN: 9781259837944, Edition: 31, Year of publication: - (medicine notes)
CHEMISTRY OF NUCLEIC ACIDS, DNA ORGANIZATION & GENOME SEQUENCE CLASSES
1. Chemical Structure
2. Differentiate RNA and DNA based on their structural and chemical charateristics
DNA RNA
Chemical Structure - pentose sugar: deoxyribose - pentose sugar: ribose
- monomeric deoxynucleotide units: - lacks a methyl group -> uracil
> deoxyadenylate, deoxyguanylate, deoxycytidate, - ribose comes in fully hydroxylated form
thymidylate - 2’ –OH
- held together by 3’, 5’ phosphodiester bonds - exists as a single strand; does not form analogous
- polymer has a polarity (direction): one end has 5’- double helix
hydroxyl (phosphate terminal), one end has 3’- - single strand is capable of folding back on itself
phosphate (hydroxyl terminal) (hairpin) thus acquiring double-stranded characteristics
- polarity – antiparallel (one strand runs in 5’ to 3’ - G content does not necessarily equal C content
direction and other in 3’-5’ direction) - binds to template strand
- A = T, C = G
- 2 strands are held together by hydrogen bonds bet - “primary structure” – sequence of purine and
purine and pyrimidine pyrimidine nucleotides -> complementary to the
- van der Waals & hydrophobic interactions hold template strand of the gene from which it was
together stacked / adjacent base pairs transcribed
- right-handed; spiral in a clockwise direction - d/t complementarity, an RNA molecule can bind
- restrictions: rotation about phosphodiester bond specifically via base-pairing rules to its template DNA
(anticonfiguration of glycosidic bond) strand
- genetic information – template strand (copied during - hybridization – not bind to coding strand of its gene
RNA synthesis – transcription) aka noncoding strand
- coding strand – matches sequence of RNA transcript
that encodes protein
- double helix
- forms base pairs with DNA, resulting in heteromeric
double helix
- cannot form 2’, 3’ cyclic diesters. These are compounds - can be hydrolyzed by alkali to 2’, 3’ cyclic diesters of
that cannot be formed from alkali-treated DNA because the mononucleotides.
of the absence of 2’ hydroxyl group
DNA Grooves
- found parallel to phosphodiester bonds
- proteins can interact specifically with exposed atoms of nucleotides (via specific hydrophobic and ionic interactions)
- able to recognize and bind to specific nucleotide without disrupting base pairing
▪ Major Groove
▪ Minor Groove
Relaxed and Supercoiled forms
- ends of DNA molecule join to create a closed circle (relaxed / supercoiled form) with no covalently free ends
- does not destroy polarity, but eliminates all free 3’ and 5’ hydroxyl and phosphoryl groups
- supercoils – when a closed circle is twisted around its own axis -> energy requiring process -> torsional stress (supercoils = stress)
- Negative supercoils – twisted in opposite direction -> underwound
- Energy in underwound DNA is stored in the supercoils
- Transition to another form is facilitated by underwinding -> strand separation (prerequisite for DNA replication and transcription)
- Supercoiled DNA – preferred form
- Topoisomerase – enzymes that catalyze topologic changes; relax or insert supercoils using ATP
3. Structural features of DNA as to
3.1. Dominant form -> B DNA
3.2. Differentiate between B and Z atoms
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