Cellular nucleic acids and their ratios + roles
RNA: mRNA, microRNA
DNA: genetic storage
RNA»DNA
Chemical composition of nucleic acids
3 + examples + where bonded + nucleoside/nucleotide
Pentose
> Ribose
> Deoxyribose
Base:
> bond to C1’
> Purine or Pyrimidine
Phosphodiester linkage
Nucleoside: Pentose + Base
Nucleotide: Pentose + Base + Phosphate link
> 3’5’ Polynucleotides (shows where phosphodiester linkage is)
Torsional Angles in Polynucleotides
6 backbone torsion angles
> from P3 to P5’
4 Torsional angles of ribose ring
> RNA/DNA
1 Torsion angle around glycosidic bond
Protein torsional angles throwback/reminder
3 backbone torsional angles
> omega = fixed at 180
> variable nu. of side chain torsional angles
Bases:
2 groups + location of NH bond + Double bond order of substituents?
Purines: A/G
> with NH bond on C9
Pyrimidine: T/U and G
> diff between T>U is one extra methyl group attached to C
> NH bond on C1
Amino substituents:
50% double bond
C=O
80% double bond
Bases Tautomerisation
what happens?
how many times?
undergo keto-enol tautomerisation
> NH-C=O -> N=C-OH
rare in free DNA
> stabilised in base paired/folded RNA
Bases deamination property
what happens?
most common bond change?
how many times?
they spontaneously deaminate
most common: C->U
N=C-NH2 -> NH-C=O bond
100-500x per cell per day
Bases pKa values
outside typical range
= limited use as catalysts
2’Deoxyribose in DNA
property?
conformations? (2+1)
nucleoside conformations + preferences (2+2)
ribose = non planar = relieves contacts between substituents
Two conformations:
> Envelope: 1 atom out of plane
> Twisted: 2 atoms OOP
= rarely PURE, it’s usually swap between both
Nucleoside conformations:
C2’-endo: Purines
C3’-endo: Pyrimidine
> rapid equilibrium
> in polynucleotide the conformation is locked
Ribose in RNA
property?
nucleoside conformation? (1+1)
more rigid
Nucleoside conformation:
Strictly C3’-endo!!
> avoids clashes between O2’ and C6 (of both Pyr and Pur)
Glycosidic Bond
bond interchange?
purine and pyrimidine pref
undergo rapid syn-anti interchange
Pyrimidine: pref. anti (C3’-endo)
Purines: both anti and syn
> C2’-endo: either
> C3’-endo: anti
Standard Base pairing
3+1 + bond distance?
+ bond energy?
about base pairs? 2?
- H-bond mediated
- Watson-Crick B.P
- C1’-C1’ = 0.5 Angstrom
> asymmetry with respect to c1 = Major and minor grooves
G-C: -5.8kcal/mol (3H-Bonds)
A-T: -4.3kcal/mol (2H-Bonds)
Base pairs:
Flexible
16 parameters to describe + many forms? idk
Do other types of base pairing occur?
Yea, other types of base pairing do occur, however watson-cricks is just the most dominant form
> not the only tho !
DNA helical structures
DNA = polymorphic
> exists in many diff forms
DNA helical structure depends on…5
Salt conc.
Presence or Absence of cations (Mg2+)
Org. solvents?
Sequence
Humidity
RNA structures in comparison?
+ DNA-RNA hybrids structure?
RNA only occurs in 2 closely related forms
> depends on SALT conc
DNA-RNA hybrids
> restricted to RNA form !!
B-DNA Double helix
conditions? (2+2)
properties?
helix type, diameter, bp/turn, twist, pitch, rise, groove + ribose properties
Standard DNA conformation
> moderate salt
> presence of counter ions
Conserved spine of hydration = Stability
Bent up to 20 degrees
Properties:
> Right handed helix
> Diameter: 2.0nm
> 10 bp/turn = Twist of 36 degrees (360/10)
> Pitch: 3.4nm = Rise: 0.34
Major groove: wide
Minor groove: narrow
Ribose: C2’-endo
A-DNA Double helix
conditions? (3)
properties?
helix type, diameter, bp/turn, twist, pitch, rise, groove + ribose properties
> Low salt conditions
Absence of cations
= More rigid
Properties:
> Right handed helix
> Diameter: 2.6nm (inc)
> 11.6 bp/turn = Twist of 31 degrees
> Pitch: 3.4 nm = Rise: 0.29nm (same)
Major groove: narrow
Minor groove: wide
Ribose: C3’-endo
Z-DNA Helix
conditions? (4)
properties?
helix type, diameter, bp/turn, twist, pitch, rise, glycosidic bond ! + ribose properties
About:
> Alt. purine, pyrimidine seq. (seq. dependant)
> Repeat unit: Purine, Pyrimidine dimers
> very high salt
> presence of organic solvents
role = transcriptional activation
Properties:
> Left handed helix
> Diameter: 1.8nm (dec)
> 12 bp/turn (6 dimers) = Twist of 60 degrees
> Pitch: 4.4nm = Rise: 0.74 (for dimers) (inc)
Ribose: C2’endo for pyrimidine C3’endo for purines
Glycosidic bond: anti (pyr) and syn (pur)
G-Quadruplexes
what are they (2)
depend on ?
> DNA with G-Rich seq.
form quadruplex structures of guanine bases
> depend on counter ions !!!
does DNA have a higher ordered structure?
Yes, when they are in cells
> 3D packed into loops of 30nm fibres !!
DNA higher order structure
nucleosome histone
> 200 nucleotide pairs of DNA
+ linker DNA
30nm wide!!!
How to separate octameric histone core from nucleotide DNA (2)
and what are the results? (2)
- Nuclease digests linker DNA
-> Released nucleosome core - Disassociation
= Octameric Histone core + 147 Nucleotide pair DNA double helix
RNA structure
2 + 2
ONLY occures in A-form helices
> 2’OH enforces C3’endo conformation
= lower structural variability compared to DNA
A’-RNA
> low humidity high salt
> only observed for RNA and RNA/DNA hybrids
can also adopt complex folds!
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T1: intro8
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T2: Visualizing and Accessing Structural Biology Data5
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3.1: Methods Overview7
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3.3: Electron Microscopy20
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3.4: Volume Data Visualization4
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3.5: NMR spectroscopy15
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3.2: X-ray Crystallography18
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links2
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4 and 560
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6:Structure-Function Relationship36
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7: Structure-Sequence Relationship41
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8: Membrane proteins47
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9: The Respiratory Chain42
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10: Protein Filaments & Cytoskeleton47
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11: DNA & RNA Structure30
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12: DNA to RNA (Transcription)25
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13: ribosome42
