SURVEY OF
BIOCHEMISTRY
Nucleic Acids
Week #1
CHEM 3511 - Summer 2008
1
What are nucleic acids?
• Building blocks of genetic material that a cell uses
to direct cellular functions and heredity
• 3 Components: Sugar Moiety
HOH2C
OH
O
HO
OH
O
OH
HO
Ribose (in RNA)
Week #1
HOH2C
Deoxyribose (in DNA)
CHEM 3511 - Summer 2008
2
Ring Numbering in Ribose
HOH2C 5’
OH
O
4’
1’
3’
HO
Week #1
HOH2C
DNA lacks the
2’-OH group
2’
OH
CHEM 3511 - Summer 2008
3
What are nucleic acids?
• Building blocks of genetic material that a cell uses
to direct cellular functions and heredity
• 3 Components: Phosphate Moiety
O
O
HO
P
OH
O
P
O
OH
O-
Phosphoric Acid
Phosphate Group
Week #1
CHEM 3511 - Summer 2008
4
What are nucleic acids?
• Building blocks of genetic material that a cell uses
to direct cellular functions and heredity
• 3 Components: 5 Nitrogenous Bases
O
NH2
PURINES
N
N
HN
N
N
Adenine
A
Week #1
N
Guanine
G
H2N
N
N
R
R
CHEM 3511 - Summer 2008
5
What are nucleic acids?
• Building blocks of genetic material that a cell uses
to direct cellular functions and heredity
• 3 Components: 5 Nitrogenous Bases
Cytosine
C
NH2
Thymine
T
CH3
HN
HN
N
O
N
O
N
PYRIMIDINES
Week #1
O
O
CHEM 3511 - Summer 2008
O
N
Uracil
U
6
Ring Numbering in Bases
NH2
Adenine
A
N
N
6
5
1
8
2
4
3
N
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7
CHEM 3511 - Summer 2008
9
N
R
7
Ring Numbering in Bases
NH2
Cytosine
C
N3
4
5
2
6
1
O
Week #1
N
CHEM 3511 - Summer 2008
8
Nomenclature
Base
Nucleoside
Nucleotide
Adenine
A
Adenosine
Adenosine
Monophosphate
Guanine
G
Guanosine
Guanosine
Monophosphate
Etc.
Study Table 3-1 for more details…
Week #1
CHEM 3511 - Summer 2008
9
How do nucleotides link?
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CHEM 3511 - Summer 2008
10
Base Pairing
Carbon
Nitrogen
Oxygen
Hydrogen
Week #1
CHEM 3511 - Summer 2008
11
Base Pairing
Carbon
Nitrogen
Oxygen
Hydrogen
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CHEM 3511 - Summer 2008
12
How Does RNA Differ from DNA?
• Ribose vs. Deoxyribose
• Bases and Base Pairing
– T in DNA vs. U in RNA
– A-T in DNA vs. A-U in RNA
• 3D Structure
• Role
Week #1
CHEM 3511 - Summer 2008
13
Protein Data Bank
http://www.rcsb.org/pdb/home/home.do
Week #1
CHEM 3511 - Summer 2008
14
Protein Data Bank
Download PDB file to Desktop
Use Freeware to View Contents
 RasMol
 PyMol
 Swiss PDB Viewer
 Protein Explorer
Week #1
CHEM 3511 - Summer 2008
15
Software for Viewing Structures
• Rasmol
– http://www.rasmol.org
• Pymol
– http://pymol.sourceforge.net
• SwissPDB Viewer
– http://www.expasy.ch/spdbv/
• Protein Explorer
– http://www.umass.edu/microbio/chime/pe
_beta/pe/protexpl/frntdoo2.htm
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CHEM 3511 - Summer 2008
16
DNA Double Helix
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CHEM 3511 - Summer 2008
17
DNA Structural Features
• Handedness
• Anti-parallel strands
• Major and minor grooves
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CHEM 3511 - Summer 2008
18
Different Conformations of DNA
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CHEM 3511 - Summer 2008
19
DNA has incredible flexibility!
CataboliteActivator
Protein (CAP)
+ DNA
Yale (1991)
Week #1
CHEM 3511 - Summer 2008
20
DNA has incredible flexibility!
DNA
Octahedron
Ned Seeman
NYU
International Society for Nanoscale Science, Computation, and Engineering
Week #1
CHEM 3511 - Summer 2008
21
More on Friday…
• Limitations to DNA Flexibility
• Supercoiling and Topoisomerases
• RNA Structure
• Nucleic Acid Function
• Recombinant DNA Technology
• Potentially PRS questions…
Week #1
CHEM 3511 - Summer 2008
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