Biochemistry 2/e - Garrett & Grisham
Chapter 11
Nucleotides and Nucleic Acids
to accompany
Biochemistry, 2/e
by
Reginald Garrett and Charles Grisham
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Biochemistry 2/e - Garrett & Grisham
Outline
• 11.1 Nitrogenous Bases
• 11.2 The Pentoses of Nucleotides and NA
• 11.3 Nucleosides are Formed by Joining a
Nitrogenous Base to a Sugar
• 11.4 Nucleotides - Nucleoside Phosphates
• 11.5 Nucleic Acids are Polynucleotides
• 11.6 Classes of Nucleic Acids
• 11.7 Hydrolysis of Nucleic Acids
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Biochemistry 2/e - Garrett & Grisham
Information Transfer in Cells
See Figure 11.1
• Information encoded in a DNA molecule
is transcribed via synthesis of an RNA
molecule
• The sequence of the RNA molecule is
"read" and is translated into the
sequence of amino acids in a protein.
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
11.1 Nitrogenous Bases
Know the basic structures
• Pyrimidines
– Cytosine (DNA, RNA)
– Uracil (RNA)
– Thymine (DNA)
• Purines
– Adenine (DNA, RNA)
– Guanine (DNA, RNA)
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Properties of Pyrimidines and
Purines
• Keto-enol tautomerism
• Acid/base dissociations
• Strong absorbance of UV light
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
11.2 Pentoses of Nucleotides
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Know these structures too
D-ribose (in RNA)
2-deoxy-D-ribose (in DNA)
The difference - 2'-OH vs 2'-H
This difference affects secondary
structure and stability
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
11.3 Nucleosides
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Linkage of a base to a sugar
Base is linked via a glycosidic bond
The carbon of the glycosidic bond is anomeric
Named by adding -idine to the root name of a
pyrimidine or -osine to the root name of a
purine
Conformation can be syn or anti
Sugars make nucleosides more water-soluble
than free bases
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
11.4 Nucleotides
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Nucleoside phosphates
Know the nomenclature
"Nucleotide phosphate" is redundant!
Most nucleotides are ribonucleotides
Nucleotides are polyprotic acids
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Functions of Nucleotides
• Nucleoside 5'-triphosphates are carriers of
energy
• Bases serve as recognition units
• Cyclic nucleotides are signal molecules and
regulators of cellular metabolism and
reproduction
• ATP is central to energy metabolism
• GTP drives protein synthesis
• CTP drives lipid synthesis
• UTP drives carbohydrate metabolism
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
11.5 Nucleic Acids Polynucleotides
• Polymers linked 3' to 5' by
phosphodiester bridges
• Ribonucleic acid and deoxyribonucleic
acid
• Know the shorthand notations
• Sequence is always read 5' to 3'
• In terms of genetic information, this
corresponds to "N to C" in proteins
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Biochemistry 2/e - Garrett & Grisham
11.6 Classes of Nucleic Acids
• DNA - one type, one purpose
• RNA - 3 (or 4) types, 3 (or 4) purposes
– ribosomal RNA - the basis of structure and
function of ribosomes
– messenger RNA - carries the message
– transfer RNA - carries the amino acids
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
The DNA Double Helix
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Stabilized by hydrogen bonds!
"Base pairs" arise from hydrogen bonds
Erwin Chargaff had the pairing data, but
didn't understand its implications
Rosalind Franklin's X-ray fiber diffraction
data was crucial
Francis Crick knew it was a helix
James Watson figured out the H-bonds
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
The Structure of DNA
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An antiparallel double helix
Diameter of 2 nm
Length of 1.6 million nm (E. coli)
Compact and folded (E. coli cell is only
2000 nm long)
Eukaryotic DNA wrapped around histone
proteins to form nucleosomes
Base pairs: A-T, G-C
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Messenger RNA
Transcription product of DNA
• In prokaryotes, a single mRNA contains
the information for synthesis of many
proteins
• In eukaryotes, a single mRNA codes for
just one protein, but structure is
composed of introns and exons
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Eukaryotic mRNA
• DNA is transcribed to produce
heterogeneous nuclear RNA
– mixed introns and exons with poly A
– intron - intervening sequence
– exon - coding sequence
– poly A tail - stability?
• Splicing produces final mRNA without
introns
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Biochemistry 2/e - Garrett & Grisham
Ribosomal RNA
• Ribosomes are about 2/3 RNA, 1/3
protein
• rRNA serves as a scaffold for ribosomal
proteins
• 23S rRNA in E. coli is the peptidyl
transferase!
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Transfer RNA
• Small polynucleotide chains - 73 to 94
residues each
• Several bases usually methylated
• Each a.a. has at least one unique tRNA
which carries the a.a. to the ribosome
• 3'-terminal sequence is always CCA-a.a.
• Aminoacyl tRNA molecules are the
substrates of protein synthesis
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Biochemistry 2/e - Garrett & Grisham
DNA & RNA Differences?
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Why does DNA contain thymine?
Cytosine spontaneously deaminates to
form uracil
Repair enzymes recognize these
"mutations" and replace these Us with Cs
But how would the repair enzymes
distinguish natural U from mutant U?
Nature solves this dilemma by using
thymine (5-methyl-U) in place of uracil
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
DNA & RNA Differences?
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Why is DNA 2'-deoxy and RNA is not?
Vicinal -OH groups (2' and 3') in RNA
make it more susceptible to hydrolysis
DNA, lacking 2'-OH is more stable
This makes sense - the genetic material
must be more stable
RNA is designed to be used and then
broken down
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Biochemistry 2/e - Garrett & Grisham
Hydrolysis of Nucleic Acids
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RNA is resistant to dilute acid
DNA is depurinated by dilute acid
DNA is not susceptible to base
RNA is hydrolyzed by dilute base
See Figure 11.29 for mechanism
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Restriction Enzymes
• Bacteria have learned to "restrict" the
possibility of attack from foreign DNA by
means of "restriction enzymes"
• Type II and III restriction enzymes cleave
DNA chains at selected sites
• Enzymes may recognize 4, 6 or more
bases in selecting sites for cleavage
• An enzyme that recognizes a 6-base
sequence is a "six-cutter"
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Biochemistry 2/e - Garrett & Grisham
Type II Restriction Enzymes
• No ATP requirement
• Recognition sites in dsDNA usually
have a 2-fold axis of symmetry
• Cleavage can leave staggered or
"sticky" ends or can produce "blunt”
ends
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Biochemistry 2/e - Garrett & Grisham
Type II Restriction Enzymes
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Names use 3-letter italicized code:
1st letter - genus; 2nd,3rd - species
Following letter denotes strain
EcoRI is the first restriction enzyme
found in the R strain of E. coli
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Biochemistry 2/e - Garrett & Grisham
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