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| Sentence to remember nucleoside structures |
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| U Can Take An Intelligent Guess |
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| Structure for Hypoxanthine |
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| What is attached to the 5'C end of a nucleoside? |
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| What is attached to the 3' end of a nucleoside? |
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| What is another name for AMP? |
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| Keto-enol tautomerization |
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| At what absorbance do nucleotides tend to absorb light? |
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| 260nm with a 280nm shoulder |
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| What happens to the UV absorbance if a sample of nucleotides is contaminated with proteins? |
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| Energy decreases, wavelength increases... therefore increased 280nm:260nm ratio |
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| How many degrees of rotational freedom do nucleotides have? |
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| 6 (phosphodiester) + 1 glycosidic = 7 |
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| Furanose C1 connects to which atom of purines? or pyrimidines? |
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Definition
purines - N9
pyrimidines - N1 |
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| In relation to 5'C and base up, endo conformation is means _____ |
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In relation to 5'C and base up, exo conformation is _____
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| Ways to describe the conformations of the C1 to N1 (pyrimidines) or N9 (purines) bond |
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| 5' -> 3' corresponds to ______ in proteins |
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| What's the difference in the structure of DNA and RNA? |
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| DNA has a H on the 2'C. RNA has an -OH at this C. |
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| 5 causes for DNA stability |
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Definition
1. Phosphodiester linkages between nucleotides
2. Hydrogen bonds between base pairs
3. Electrostatic interactions –repulsion of phosphate groups, which makes them most stable on the helix exterior
4. Salt and water interactions with helix surface
5. Base pair stacking interaction |
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| How many H bonds do A and T share? G and C? Which are more stable? |
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A and T: 2 H bonds
G and C: 3 H bonds
G and C are more stable |
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| Which ring positions from H bonds for A and T? |
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Which ring positions from H bonds for G and C?
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involves rotation around a different
axis, namely an axis perpendicular to the helix axi |
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| 3 examples of intercalating agents |
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| ethidium bromide, acridine orange, and actinomycin D |
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| B-form: pitch and bp per turn |
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pitch: 3.4nm
10bp per turn |
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| RNA-RNA and RNA-DNA chains, and in dehydrated DNA-DNA chains |
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| A DNA: pitch and bp per turn |
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pitch: 2.46nm
11bp per turn |
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1. left handed
2. may occur in G-C rich regions of DNA |
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| B-DNA: Approximate rise per base pair |
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| B-DNA: rotation per base pair |
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| Overall length of human genome |
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| haploid: 3.4 billion base pairs |
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| 2 other structures (other than double and single strands) that DNA can form |
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| formed when a double strand partially binds with another double strand |
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| T(3,4):A(6,7) and C+(3,4):G(6,7) |
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| cyclic arrays of four G residues united through Hoogsteen base pairing |
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| Are minor groove binding proteins more or less specific than major groove binding proteins? |
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| less specific - fewer binding spots |
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| What temperature begins denaturing DNA? |
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| An increase in UV absorbance by 30-40% as DNA is denatured: reflects the unwinding and strand separation of double stranded DNA |
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| Change in absorbance when denatured |
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| stacked base pairs absorb less light. Therefore an increase in absorbance will be observed. |
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| renaturation or annealing |
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| lowering temp of DNA to reform base pairs |
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| Rate determining step in reannealing DNA. Involved annealing the 1st annealed base pair |
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| All DNA isolated from cells is found to be _________ supercoiled. |
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Definition
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| average superhelical density |
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Definition
about -0.05,
which means that there is on average 1 negative supercoil every 200 bp |
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| total number of positive crossings - total number of negative crossings |
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| negative supercoil favors _________. |
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| Topoisomerase II (DNA gyrase) |
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uses
ATP to introduce negative supercoils into DNA |
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| relaxes supercoiled DNA back to the unsupercoiled relaxed state |
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| H1, H2A, H2B, H3, H4 - DNA wraps around these |
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| 2*each forms an octamer that DNA helix is wound around |
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| thickness of "beads on a string" |
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250 nm (50 turns per loop)
30 nm filament forms long DNA loops of variable
length, each containing on average between 60,000 and 150,000 bp |
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| stacked minibands of diameter 840nm |
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| DNA tweezers: open position |
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| S1 and S2 forms outside, Q forms inside of V |
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| F binds to S1 and S2 ends, closing tweezers |
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| R strand binds to F's foothold removing it from tweezers and releases as waste |
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| singlestranded region of RNA folds to base-pair with a hairpin loop |
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| unusual base pairing in RNA |
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| How many nucleotides in a tRNA? |
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| 3'-terminal sequence on tRNA for aa attachment |
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Tertiary structure in tRNA arises
from... |
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| ...base-pairing interactions between bases in the D loop with bases in the variable and TψC loops |
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| Prokaryotic ribosomal subunit RNA |
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| conserved regions of mRNAs, usually at the 5‟-end, that reversibly bind specific metabolites and coenzymes and act as gene expression regulators |
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| oligonucleic acid or peptide molecules that bind to a specific target molecule |
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in presence of high [], 1st splicing site is spliced leading to uORF translation.
In presence of low[], 3' splice site is made available for NMT1 translation. Thanks to TPP aptamer |
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| The ________ in RNA make it more susceptible to chemical hydrolysis |
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| vicinal -OH groups (2' and 3') |
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| RNA and DNA effects in dilute acid |
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RNA - resistant
DNA - depurination |
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| RNA and DNA effects in dilute base |
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RNA - hydrolyzed
DNA - denatured |
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| Alkaline hydrolysis of RNA |
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Definition
| Nucleophilic attack by OH- on P atom leads to 5'-phosphodiester cleavage |
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| a side hydrolysis leaves ___________ |
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| b-side hydrolysis yields ________ |
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