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DNA/RNA Basics
Based on slides presented by Dr. DeJoung at the University of Texas at Dallas
84
Biochemistry
10/12/2011

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Cards

Term
Sentence to remember nucleoside structures
Definition
U Can Take An Intelligent Guess
Term
Structure for Cytidine
Definition
[image]
Term
Structure for Uridine
Definition
[image]
Term
Structure for Adenosine
Definition
[image]
Term
Structure for Guanosine
Definition
[image]
Term
Structure for Inosine
Definition
[image]
Term
Structure for Hypoxanthine
Definition
[image]
Term
What is attached to the 5'C end of a nucleoside?
Definition
Phosphate
Term
What is attached to the 3' end of a nucleoside?
Definition
Phosphate
Term
What is another name for AMP?
Definition
adenylic acid
Term
Keto-enol tautomerization
Definition
[image]
Term
At what absorbance do nucleotides tend to absorb light?
Definition
260nm with a 280nm shoulder
Term
What happens to the UV absorbance if a sample of nucleotides is contaminated with proteins?
Definition
Energy decreases, wavelength increases... therefore increased 280nm:260nm ratio
Term
How many degrees of rotational freedom do nucleotides have?
Definition
6 (phosphodiester) + 1 glycosidic = 7
Term
Furanose C1 connects to which atom of purines? or pyrimidines?
Definition

purines - N9

pyrimidines - N1

Term
In relation to 5'C and base up, endo conformation is means _____
Definition
C2 or C3 is up
Term

In relation to 5'C and base up, exo conformation is _____

Definition
both C2 and C3 are down
Term
Syn and Anti
Definition
Ways to describe the conformations of the C1 to N1 (pyrimidines) or N9 (purines) bond
Term
Upstream
Definition
towards the 5'-side
Term
Downstream
Definition
Towards the 3'-side
Term
5' -> 3' corresponds to ______ in proteins
Definition
N terminal to C terminal
Term
What's the difference in the structure of DNA and RNA?
Definition
DNA has a H on the 2'C. RNA has an -OH at this C.
Term
5 causes for DNA stability
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

Term
Chargaff's Rules
Definition
A=T and G=C
Term
How many H bonds do A and T share? G and C? Which are more stable?
Definition

A and T: 2 H bonds

G and C: 3 H bonds

G and C are more stable

Term
Which ring positions from H bonds for A and T?
Definition

A (1 and 6)

T (3 and 4)

Term

Which ring positions from H bonds for G and C?

Definition

C (2, 3, 4)

G (1, 2, 6)

Term
Propellor twist
Definition

 involves rotation around a different 

axis, namely an axis perpendicular to the helix axi

Term
3 examples of intercalating agents
Definition
 ethidium bromide, acridine orange, and actinomycin D
Term
B-form: pitch and bp per turn
Definition

pitch: 3.4nm

10bp per turn

Term
Where is A-DNA observed?
Definition
RNA-RNA and RNA-DNA chains, and in dehydrated DNA-DNA chains
Term
A DNA: pitch and bp per turn
Definition

pitch: 2.46nm

11bp per turn

Term
Z-form: 2 facts
Definition

1. left handed

2. may occur in G-C rich regions of DNA

Term
B-DNA: Approximate rise per base pair
Definition
3.32A
Term
B-DNA: pitch per turn
Definition
33.2A
Term
B-DNA: bp per turn
Definition
10
Term
B-DNA: diameter
Definition
23.7A
Term
B-DNA: handedness
Definition
right handed
Term
B-DNA: rotation per base pair
Definition
36 degrees
Term
Overall length of human genome
Definition
haploid: 3.4 billion base pairs
Term
Cruciform and Hairpin
Definition
2 other structures (other than double and single strands) that DNA can form
Term
Triple stranded DNA
Definition
formed when a double strand partially binds with another double strand
Term
Hoogsteen base pairs
Definition
T(3,4):A(6,7) and C+(3,4):G(6,7)
Term
G-quadruplexes
Definition
cyclic arrays of four G residues united through Hoogsteen base pairing
Term
Are minor groove binding proteins more or less specific than major groove binding proteins?
Definition
less specific - fewer binding spots
Term
What temperature begins denaturing DNA?
Definition
80C
Term
hyperchromic shift
Definition
An increase in UV absorbance by 30-40% as DNA is denatured: reflects the unwinding and strand separation of double stranded DNA
Term
Change in absorbance when denatured
Definition
stacked base pairs absorb less light. Therefore an increase in absorbance will be observed.
Term
renaturation or annealing
Definition
lowering temp of DNA to reform base pairs
Term
Nucleation
Definition
Rate determining step in reannealing DNA. Involved annealing the 1st annealed base pair
Term
All DNA isolated from cells is found to be _________ supercoiled.
Definition
negatively
Term
average superhelical density
Definition
about -0.05,
which means that there is on average 1 negative supercoil every 200 bp
Term
writhe
Definition
total number of positive crossings - total number of negative crossings
Term
L (linking number) =
Definition
Twist (T) + Writhe (W)
Term
negative supercoil favors _________.
Definition
unwinding
Term
Topoisomerase II (DNA gyrase)
Definition
uses
ATP to introduce negative supercoils into DNA
Term
Topoisomerase I
Definition
relaxes supercoiled DNA back to the unsupercoiled relaxed state
Term
Histones
Definition
H1, H2A, H2B, H3, H4 - DNA wraps around these
Term
H2A, H2B, H3 and H4
Definition
2*each forms an octamer that DNA helix is wound around
Term
H1
Definition
"linker" histone
Term
thickness of "beads on a string"
Definition
10nm
Term
Solenoid diameter
Definition
30nm
Term
Loops
Definition
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
Term
Chromosome
Definition
stacked minibands of diameter 840nm
Term
DNA tweezers: open position
Definition
S1 and S2 forms outside, Q forms inside of V
Term
DNA tweezers: closed
Definition
F binds to S1 and S2 ends, closing tweezers
Term
DNA tweezers: reopening
Definition
R strand binds to F's foothold removing it from tweezers and releases as waste
Term
RNA pseudoknot
Definition
singlestranded region of RNA folds to base-pair with a hairpin loop
Term
unusual base pairing in RNA
Definition
G-U
Term
How many nucleotides in a tRNA?
Definition
73-94 nucleotides
Term
"L-shaped"
Definition
Phenylalanine tRNA
Term
CCA
Definition
3'-terminal sequence on tRNA for aa attachment
Term
Tertiary structure in tRNA arises
from...
Definition
...base-pairing interactions between bases in the D loop with bases in the variable and TψC loops
Term
Prokaryotic ribosomal subunit RNA
Definition
23S, 16S, 5S
Term
Eukaryotic ribosomal RNA
Definition
28S, 18S, 5.8S, 5S
Term
Riboswitches
Definition
conserved regions of mRNAs, usually at the 5‟-end, that reversibly bind specific metabolites and coenzymes and act as gene expression regulators
Term
aptamer
Definition
oligonucleic acid or peptide molecules that bind to a specific target molecule
Term
TPP
Definition
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
Term
The ________ in RNA make it more susceptible to chemical hydrolysis
Definition
vicinal -OH groups (2' and 3')
Term
RNA and DNA effects in dilute acid
Definition
RNA - resistant
DNA - depurination
Term
RNA and DNA effects in dilute base
Definition
RNA - hydrolyzed
DNA - denatured
Term
Alkaline hydrolysis of RNA
Definition
Nucleophilic attack by OH- on P atom leads to 5'-phosphodiester cleavage
Term
a side hydrolysis leaves ___________
Definition
5'-phosphate products
Term
b-side hydrolysis yields ________
Definition
3'-phosphate products