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NUCLEOTIDES and NUCLEIC ACIDS
Nucleotides - variety of roles
___________________ store/release energy
Structural component of ________________
Involved in cell _______________________
___________ of the nucleic acids: ______________
____ - _________________________ of most organisms
____ - involved in ______________________________
-__________ (tRNA) - _________________ to ribosome
-__________(mRNA) - intermediate that __________ for
protein sequences from DNA ______________________
-__________ (rRNA) - makes up most of the _________
One nucleotide consists of 3 covalently linked parts:
1. _______________________ (P)
2. ______________ (S) - put primes on numbers
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3. _______________________ (B) (heterocyclic amine)
5 types (4 types each in DNA and RNA)
1. ________(A) - in ________________________
2. ________ (G)
- in ________________________
3. ________ (C) - in ________________________
4. ________ (T) - in ________________________
5. _________(U) - in ________________________
Two groups:
________________ - _________
_________________ - __________
Note numbering. Numbering the same for the bases.
No primes on numbers to distinguish from sugar ring
atoms.
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The 3 parts (P, S and B) join covalently.
________________ - _______________ only
Bond joining sugar and base - ________________ bond.
_____ of sugar to ____ (purines) or ___(pyrimidines)
Nucleoside Nomenclature
with ribose
with deoxyribose
Adenosine
Deoxyadenosine
Guanosine
Deoxyguanosine
Cytidine
Deoxycytidine
Uridine
N/A
N/A
Thymidine (deoxythymidine)
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__________________ - ____________
(in this order)
Bond joining sugar and base - ________________ bond.
Nucleotide Nomenclature (Two ways )
1. - ____________ suffix
2. Start with the nucleoside name
Add suffix to indicate number and position of
phosphate(s)
Phosphates most often on 3' or 5' position
- Prefixes mono-, di-, tri- for number of phosphates
Example: Adenosine- 5'-triphosphate (ATP)
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First way
with ribose
with deoxyribose
Adenylate
Deoxyadenosylate
Guanosylate
Deoxyguanosylate
Cytidylate
Deoxycytidylate
Uridylate
N/A
N/A
Thymidylate (deoxythymidylate)
Second way Examples
Adenosine-5'-monophosphate
Adenosine-3'-monophosphate
Adenosine-5'-diphosphate
Deoxyadenosine-5'-monophosphate
Deoxyadenosine-3'-monophosphate
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Abbreviations
5'-phosphates
A, T, C, G, U
dA, dT, dC, dG, dU
pA, pT, pC, pG, pU
pdA, pdT, pdC, pdG, pdU
ATP = pppA
ADP = ppA
AMP = pA
3'-phosphates
Ap, Tp, Cp, Gp, Up
dAp, dTp, dCp, dGp, dUp
Nucleotide monomers link by phosphate ester
(phosphodiester) bonds
_________ end
P-S-B
P-S-B
P-S-B
P-S-B
_________ end
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Oligonucleotides (dinucleotides, trinucleotides, etc.)
Polynucleotides
 __ structure is the ______ of the nitrogenous _____
 like proteins one end is distinct from the other
 __(five prime) ___ - the end where the 5' carbon of
the sugar does not lead to another nucleotide
 __ (three prime) ___- the end where the 3' carbon of
the sugar does not lead to another nucleotide
 By convention the sequence is given in the
_____________direction
____________________________
Chargaff studied base composition of DNA's from many
organisms.
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Results: for all species:
____________
____________
Written as a Sum:
_________________________
% ______ =
%_________
________________________________ - proposed the
structure of DNA
(X-ray crystallographic data from __________________)
Chargaff's rules lead to Watson-Crick _______________
__ and __ are ______________
2 Hydrogen bonds
__ and __ are complementary - in ________
__ and __ are complementary
3 Hydrogen bonds
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DNA structure
2 polynucleotide strands associate by base-pairing
P-S-A
T-S- P
P-S-T
A-S- P
P-S-G
C-S- P
P-S-C
G-S- P
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Double-stranded structure is twisted into a ____________
Properties of the DNA double-helix:
 Strands are ___________________________
 Strands are ________________ - on goes 3' 5' the
other is 5'3'
 Helix is ________________________
 Two _____________ run along the helix - good sites
for protein binding because of access to bases (and
hence the sequence)
o ____________groove
o ____________ groove
 ______________________ - repeats throughout
structure
 Pitch - _________nm
 Rise per base pair - _________ nm
 About ______base pairs per _________
 Width of helix - _________nm
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Some forces that stabilize the helix:
1. _________________ effects: Purines and Pyrimidines
are buried in center of helix
2. _____________ interactions: Planes of rings have 
clouds, van der Waals' contacts
3. Hydrogen bonds: Between complementary bases
4. _________________ Interactions: _______ ions help
decrease repulsion between neighboring phosphates
There are 3 forms of DNA:
 B-DNA
o ___________________ form
o ________-handed helix
o predominant form _______________________
o ______________ approximately ___________ to
helix axis
 ___DNA
o __________ form
o _____________-handed helix
o planes of bases not perpendicular to helix axis
o ________________ than B-DNA
o ________________ than B-DNA
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 __-DNA
o rare, some sequences have it
o ____-handed helix
o _______________________ than B-DNA
o ____________________
DNA can also be _____________.
Ends are joined.
May twist up on itself: _________________ -depends on
twists introduced before ends joined.
Circular DNA can be:
 supercoiled
 ____________ (no extra twisting; can be induced by a
break, "_______", in just one of the DNA strands)
Circular DNA's can be ________________ by:
 __________ treatment, _____ light, ______ breaks
(flow through pipettes, etc.)
____________________ - change degree of supercoiling




Cleave one or both strands (backbone)
Under or overwind by rotating strands
Rejoin ends to increase or decrease supercoiling
Important in DNA replication and in transcription
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____________: small circular extrachromosomal DNA's
in bacteria (not part of the regular, necessary genetic
material)
Often carriers of __________________________ genes.
Can be passed between bacteria by conjugation. Take all
of your antibiotics!
Can be used in the laboratory to ___________________.
Example: Bacteria can now produce human insulin.
(Insulin previously isolated from pigs)
Denaturation
DNA denaturation - complete _____________ and
_____________ of the 2 strands
Requires breaking of H-bonds between base-pairs
2 common ways to denature DNA:
 _________- MELTING
 ________________________ (e.g. urea)
UV Absorbance - peak at ____________________
(Recall proteins have a peak at 280 nm from
aromatic amino acids.)
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Abbreviations: ___DNA = double-stranded DNA
Double-stranded DNA is thermodynamically more stable
than the separated strands (under physiological
conditions)
___DNA = single-stranded DNA (denatured)
Compare spectra
Melting: absorbance increases - _______________ effect
Reverse:
Annealing: absorbance decreases - _____________effect
Change is due to differences in electronic environment in
the  clouds of the aromatic bases and the stacking
interactions.
• __________ point (Tm) - temperature at which 1/2
of the DNA has become single-stranded
• Melting curves monitor the Absorbance at 260nm
Tm depends on ___________________________ of DNA
GC pairs: more H-bonds (3)
AT pairs (2) H-bonds
Rule of thumb: _________________________________