Nucleic Acids

1
Nucleic Acids
Nucleic Acids are very long, thread-like
polymers, made up of a linear array of monomers
called nucleotides. Nucleic acids vary in size
in nature tRNA molecules contain as few as 80
nucleotides Eukaryotic chromosomes contain as
many as 100,000,000 nucleotides.
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Nucleotide Structure
All nucleotides contain three components 1. A
nitrogen heterocyclic base 2. A pentose sugar 3.
A phosphate residue
3
Ribose is present as a ring form in aqueous
solution
4
Ribofuranose rings in nucleotides can exist in
four conformations
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Chemical Structure of DNA vs RNA
Ribonucleotides have a 2-OH Deoxyribonucleotides
have a 2-H
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Bases are classified as Pyrimidines or Purines
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Structure of Nucleotide Bases
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DNA and RNA
DNA deoxyribonucleic acid nucleic acid that
stores genetic information found in the nucleus
of a mammalian cell. RNA ribonucleic acid 3
types of RNA in a cell Ribosomal RNAs (rRNA) are
components of ribosomes Messenger RNAs (mRNA)
carry genetic information Transfer RNAs (tRNA)
are adapter molecules in translation
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The nucleus contains the cells DNA (genome)
Nucleus
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RNA is synthesized in the nucleus andexported to
the cytoplasm
Nucleus
Cytoplasm
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Deoxyribonucleotides found in DNA
dT
dC
dG
dA
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Ribonucleotides found in RNA

C
U
G
A
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Nucleotides arelinked byphosphodiesterbonds
5 End
3 End
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DNA is double stranded
Bases form a specific hydrogen bond pattern
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Properties of a DNA double helix
The strands of DNA are antiparallel The strands
are complimentary There are Hydrogen bond
forces There are base stacking
interactions There are 10 base pairs per turn
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DNA is a Double-Helix
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Three-dimensional structure of B DNA
NMR solution structure of a 12 nucleotide
fragment of DNA 5- C G C G A A T T C G C G 3
3- G C G C T T A A G C G C 5 Total of 32
hydrogen bonds. Reading Assignment Tjandra et
al Journal of the American Chemical Society
(2000) 122, 6190
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Cellular Processes
replication
DNA
transcription
RNA (mRNA)
translation
Proteins
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RNA and Transcription
DNA is in the nucleus Proteins are synthesized
on ribosomes in the cytoplasm RNA carries the
genetic information from the nucleus to the
cytoplasm This RNA is called messenger RNA (mRNA)
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RNA Structure
Transcription of a DNA molecule results in a
mRNA molecule that is single-stranded. RNA
molecules do not have a regular structure like
DNA. The structures of RNA molecules are complex
and unique. RNA molecules can base pair with
complementary DNA or RNA sequences. G pairs
with C, A pairs with U, and G pairs with U.
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RNA structures have many hairpins and loops
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Structure of RNA Hairpin
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RNase P M1 RNA
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Phenylalanine tRNA
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Hammerhead ribozyme
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A self-splicing intron from mRNA
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History of Nucleic Acids
1869 German biochemist Friedrich Miescher
discovered nuclein from nuclei of white blood
cells. 1889 The term nucleic acid was first
used by Richard Altmann 1920s the
tetranucleotide hypothesis is introduced
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The tetranucleotide hypothesis
Up to 1940 researchers were convinced that
hydrolysis of nucleic acids yielded the four
bases in equal amounts. Nucleic acid was
postulated to contain one of each of the four
nucleotides, the tetranucleotide
hypothesis. Takahashi (1932) proposed a structure
of nucleotide bases connected by phosphodiester
linkages.
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History of Nucleic Acids
1869 German biochemist Friedrich Miescher
discovered nuclein from nuclei of white blood
cells. 1889 The term nucleic acid was first
used by Richard Altmann 1920s the
tetranucleotide hypothesis is introduced 1938
First X-ray diffraction pattern of DNA is
published. The pattern indicates a helical
structure.
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X-ray diffraction of DNA
31
History of Nucleic Acids
1869 German biochemist Friedrich Miescher
discovered nuclein from nuclei of white blood
cells. 1889 The term nucleic acid was first
used by Richard Altmann 1920s the
tetranucleotide hypothesis is introduced 1938
Astbury and Bell publish first X-ray diffraction
pattern of DNA, indicated periodicity 1944
Avery, MacLeod, and McCarty demonstrate DNA
could transform cells. Some doubt remained.
Supporters of the tetranucleotide hypothesis did
not believe nucleic acid was variable enough to
be a molecule of heredity and store
genetic information.
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The Avery, MacLeod, and McCarty Experiment
Mice injected with virulent bacteria die
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The Avery, MacLeod, and McCarty Experiment
Mice injected with nonvirulent bacteria live
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The Avery, MacLeod, and McCarty Experiment
Mice injected with heat-killed virulent bacteria
live
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The Avery, MacLeod, and McCarty Experiment
Mice injected with a mixture of nonvirulent
bacteria andheat-killed virulent bacteria die
36
The Avery, MacLeod, and McCarty Experiment
Mice injected with a mixture of nonvirulent
bacteria andDNA from heat-killed virulent
bacteria die
37
History of Nucleic Acids
1869 German biochemist Friedrich Miescher
discovered nuclein from nuclei of white blood
cells. 1889 The term nucleic acid was first
used by Richard Altmann 1920s the
tetranucleotide hypothesis is introduced 1938
Astbury and Bell publish first X-ray diffraction
pattern of DNA, indicated periodicity 1944
Avery, MacLeod, and McCarty demonstrate DNA
could transform cells. Some doubt
remained. Late 1940s Erwin Chargaff used paper
chromatography for separation of DNA
hydrolysates. Amount of adenine is equal to
amount of thymine and amount of guanine is equal
to amount of cytosine. 1952 Hershey and Chase
confirm DNA is a molecule of heredity.
38
The Hershey-Chase experiment
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The Hershey-Chase experiment
40
History of Nucleic Acids
1869 German biochemist Friedrich Miescher
discovered nuclein from nuclei of white blood
cells. 1889 The term nucleic acid was first
used by Richard Altmann 1920s the
tetranucleotide hypothesis is introduced 1938
Astbury and Bell publish first X-ray diffraction
pattern of DNA, indicated periodicity 1944
Avery, MacLeod, and McCarty demonstrate DNA
could transform cells. Some doubt
remained. Late 1940s Erwin Chargaff used paper
chromatography for separation of DNA
hydrolysates. Amount of adenine is equal to
amount of thymine and amount of guanine is equal
to amount of cytosine. 1952 Hershey and Chase
confirm DNA is a molecule of heredity. 1951
Furberg published the crystal structure of a
nucleoside (cytidine) 1953 Watson and Crick
determine the structure of DNA
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History of Nucleic Acids
1953 Watson and Crick determine the structure
of DNA (Nature 1953) 1958 Francis Crick
proposes the central dogma of molecular
biology Kornberg purifies DNA polymerase I
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History of Nucleic Acids
1953 Watson and Crick determine the structure
of DNA 1958 Francis Crick proposes the central
dogma of molecular biology Kornberg purifies
DNA polymerase I 1969 Entire genetic code
determined
43
History of Nucleic Acids
1953 Watson and Crick determine the structure
of DNA 1958 Francis Crick proposes the central
dogma of molecular biology Kornberg purifies
DNA polymerase I 1969 Entire genetic code
determined 1972 First recombinant DNA molecules
constructed Lambda phage DNA inserted into SV40
virus Restriction enzyme EcoRI used to create a
recombinant plasmid containing penicillin and
tetracycline resistance
44
History of Nucleic Acids
1953 Watson and Crick determine the structure
of DNA 1958 Francis Crick proposes the central
dogma of molecular biology Kornberg purifies
DNA polymerase I 1969 Entire genetic code
determined 1972 First recombinant DNA molecules
constructed Lambda phage DNA inserted into SV40
virus Restriction enzyme EcoRI used to create a
recombinant plasmid containing penicillin and
tetracycline resistance 1982 Tetrahymena
ribosomal RNA splicing shown to be
self-splicing 1986 RNA is shown to act as an
enzyme
45
History of Nucleic Acids
1953 Watson and Crick determine the structure
of DNA 1958 Francis Crick proposes the central
dogma of molecular biology Kornberg purifies
DNA polymerase I 1969 Entire genetic code
determined 1972 First recombinant DNA molecules
constructed Lambda phage DNA inserted into SV40
virus Restriction enzyme EcoRI used to create a
recombinant plasmid containing penicillin and
tetracycline resistance 1982 Tetrahymena
ribosomal RNA splicing shown to be
self-splicing 1986 RNA is shown to act as an
enzyme The polymerase chain reaction (PCR) was
developed by Kari Mullis at Cetus Corporation.
46
History of Nucleic Acids
1953 Watson and Crick determine the structure
of DNA 1958 Francis Crick proposes the central
dogma of molecular biology Kornberg purifies
DNA polymerase I 1969 Entire genetic code
determined 1972 First recombinant DNA molecules
constructed Lambda phage DNA inserted into SV40
virus Restriction enzyme EcoRI used to create a
recombinant plasmid containing penicillin and
tetracycline resistance 1982 Tetrahymena
ribosomal RNA splicing shown to be
self-splicing 1986 RNA is shown to act as an
enzyme The polymerase chain reaction (PCR) was
developed by Kari Mullis at Cetus
Corporation. 1995 First complete genome
sequenced of the bacterium Haemophilus
influenzae at TIGR 2001 Human genome sequenced
by NIH and Celera Genomics
47
Reading Assignment
Lehninger Principles of Biochemistry Chapter
10 Nucleotides and Nucleic Acids Stryer
Biochemistry Chapter 5 DNA, RNA, and the Flow
of Genetic Information and A structure for
deoxyribose nucleic acid Watson and Crick Nature
April 2, 1953
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Classroom Exercise
Two groups Each construct a tetranucleotide 5-G
ATC-3
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Classroom Exercise
Two groups Each construct a tetranucleotide 5-GA
TC-3 these nucleic acids are complementary. Next
, groups get together and form hydrogen bonds
between bases