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DNA structure
Uni of Notts, Structure Function & Analysis of Genes, year 2, topic 1
| Term | Definition |
|---|---|
| Why DNA is rarely left handed | Made with D-deoxyribose sugar, forms right handed chirality. It is more energetically favourable with torsional strains of base stacking. Cellular machinery is adapted to fit right handed helix |
| B-DNA | Canon Watson & Crick right handed double helix, 10.5 bases, planar base bonding, flexible structure. Most common form of DNA |
| A-DNA | Dehydrated right handed form, much more compact & slightly wider, 11 bases per turn, similar to double stranded RNA, forms in DNA-RNA hybrids. Good for desiccated or protein bound DNA |
| Z-DNA | Left handed with zigzagging backbone, formed in high salt concentrations & with many GC bonds. 12 bases per turn. Changes local topology to relieve torsion & be recognised by proteins. Very rare |
| Axial rise | Distance between adjacent base pairs, usually 3.4A |
| Convenience of measuring in angstrom (A) | Redundant due to being 1/10 of a nm but good for molecular biology since is roughly the distance of a covalent bond |
| Structural variation of DNA: Causes | Base stacking - π-π interactions between aromatic rings Sugar puckering - Out of plane distortions from ribose sugars Backbone torsion angles - 6 different angles (α, β, γ, δ, ε, ζ) Environmental - hydration, ions, temperature, other molecules |
| Structural variation of DNA: Sugar puckering | Different naturally occurring conformations of pentose sugars, 2 exist: C2'-endo - C2 sticks up in the same plane as C5, lengthens sugar-phosphate bond, B-DNA C3'-endo - Same as C2'-end but it's C3, shortens sugar phosphate distance, A-DNA & RNA |
| Structural variation of DNA: Base stacking | π-π interactions - delocalised electrons & partial charges create powerful complimentary dispersion forces reducing repulsion Hydrophobic interactions - Water exclusion from aromatic bases pushes them inwards, protecting the DNA from nucleophilic water |
| Structural variation of DNA: Backbone angles | Dihedral angles of DNA structure. 6 between adjacent phosphate-sugars (α, β, γ, δ, ε, ζ) & 1 for glycosidic bond angle (χ). Backbone torsion affects helical pitch (tightness of helix) & χ interacts with sugar puckering to decide DNA form |
| Why the canon DNA structures aren't perfectly representative of real life DNA | Canon structures are based on an average taken from DNA in lots of different conditions. Each sequence & external condition will distort DNA in different ways. Dynamic molecule |
| How proteins recognise bases | The electron donors, electron acceptors, & non-polar groups on bases form hydrogen bonds or hydrophobic interactions with complimentary side chains on amino acids causing protein binding |
| How DNA is bent & the purpose of bending | Energetically costly but using basic proteins to bond ionically with the phosphates & form hydrogen bonds will open up the grooves to allow factors to bind & initiate cellular processes |
| Plectosomes | Supercoils of DNA wrapping around each other to form a super structure to relieve torsion during replication & transcription. Difficult to separate without breaking a strand |
| Benefits of positive supercoiling | Makes the DNA more compact & structurally stable |
| Benefits of negative supercoiling | Makes DNA easier to separate for replication & transcription |
| Linking Number (LK) equation & explaination | LK = Tw + Wr LK = Constant showing the degree of supercoiling in a closed system (such as plasmids or between nucleosomes) Tw = Twists. How many times each strand wraps around the other Wr = Writhes. How many times the helices cross |
| Toroidal (or solenoidal) writhes | The DNA spirals in larger loops, typically around protein cores such as histones in chromatin. Each is called a toroidal node |
| Plectoneme writhes | The double helix twists together like ropes into a quadruple helix |
| Gyrase | Tetrameric protein, adds negative supercoils at -0.03/3% density (unwinds 3 turns every 100 turns) by double breaking & fixing DNA ahead of the replication fork. Only in prokaryotes |
| DNA topology & links to LK | The physical geometry of DNA & how it affects biological functioning LK = 0 - DNA is relaxed (ideal energy conformation) LK>0 - positively supercoiled LK<0 - negatively supercoiled |
| Link between protein binding, DNA bending, & topology in genetic regulation | Proteins bind to grooves on DNA causing it to distort which bends & changes topology which affects what genes are exposed and therefore translated |
Created by:
Denny12
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