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Chapter 10
Nucleotides and Nucleic
Acids
Biochemistry
by
Reginald Garrett and Charles Grisham
Garrett and Grisham, Biochemistry, Third Edition
Essential Question
• What are the structures of the nucleotides?
How are nucleotides joined together to form
nucleic acids? How is information stored in
nucleic acids? What are the biological
functions of nucleotides and nucleic acids?
Garrett and Grisham, Biochemistry, Third Edition
Outline
• What Is the Structure and Chemistry of
Nitrogenous Bases?
• What Are Nucleosides?
• What Is the Structure and Chemistry of
Nucleotides?
• What Are Nucleic Acids?
• What Are the Different Classes of Nucleic Acids?
• Are Nucleic Acids Susceptible to Hydrolysis?
Garrett and Grisham, Biochemistry, Third Edition
Information Transfer in Cells
See Figure 10.1
• 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.
Garrett and Grisham, Biochemistry, Third Edition
Figure 10.1 The
fundamental process of
information transfer in
cells. Information encoded
in the nucleotide sequence
of DNA is transcribed
through synthesis of an
RNA molecule whose
sequence is dictated by
the DNA sequence.
As the sequence of this
RNA is read (as groups of
three consecutive
nucleotides) by the protein
synthesis machinery, it is
translated
into 10.1
the
Figure
sequence of amino acids
in a protein.
This information transfer
system is encapsulated in
the dogma:
DNA  RNA  protein.
Garrett and Grisham, Biochemistry, Third Edition
10.1 – What is the Structure and
Chemistry of Nitrogenous Bases?
Know the basic structures
• Pyrimidines
– Cytosine (DNA, RNA)
– Uracil (RNA)
– Thymine (DNA)
• Purines
– Adenine (DNA, RNA)
– Guanine (DNA, RNA)
Garrett and Grisham, Biochemistry, Third Edition
Figure 10.2 (a) The pyrimidine ring system; by convention, atoms are
numbered as indicated. (b) The purine ring system, atoms numbered
as shown.
Garrett and Grisham, Biochemistry, Third Edition
Properties of Pyrimidines and
Purines
• Keto-enol tautomerism
• Acid/base dissociations
• Strong absorbance of UV light
Garrett and Grisham, Biochemistry, Third Edition
10.2 – What Are Nucleosides?
Know these structures too
• Nucleosides are compounds formed when a
base is linked to a sugar. The sugars are
pentoses.
• D-ribose (in RNA)
• 2-deoxy-D-ribose (in DNA)
• The difference - 2'-OH vs 2'-H
• This difference affects secondary structure and
stability.
Garrett and Grisham, Biochemistry, Third Edition
Figure 10.9 Furanose structures—ribose and deoxyribose.
Garrett and Grisham, Biochemistry, Third Edition
10.2 – What Are Nucleosides?
• 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.
• Nucleosides are relatively stable in alkali, but
purine nucleosides are easily hydrolyzed in acid
to yield the free base and pentose.
Garrett and Grisham, Biochemistry, Third Edition
Figure 10.10 b-Glycosidic bonds link nitrogenous bases and sugars to form
nucleosides. Garrett and Grisham, Biochemistry, Third Edition
Figure 10.11 The common ribonucleosides—cytidine, uridine, adenosine,
and guanosine. Also, inosine drawn in anti conformation.
Garrett and Grisham, Biochemistry, Third Edition
Adenosine: a nucleoside with
physiological activity
High [Ado] promotes sleepiness. Caffeine blocks the
interaction of extracellular Ado with its neuronal receptors.
Garrett and Grisham, Biochemistry, Third Edition
p. 134
10.3 – What Is the Structure and
Chemistry of Nucleotides?
Nucleoside phosphates
• Know the nomenclature
• "Nucleotide phosphate" is redundant!
• Most nucleotides are ribonucleotides
• Nucleotides are polyprotic acids.
Garrett and Grisham, Biochemistry, Third Edition
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.
Garrett and Grisham, Biochemistry, Third Edition
10.4 - What Are Nucleic Acids?
• 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.
• The base sequence of a nucleic acid is its
distinctive characteristic.
• pGpApCpU, GpApCpUp, pGpApCpUp, GACU,
dGACT
Garrett and Grisham, Biochemistry, Third Edition
10.5 - What Are the Different
Classes of Nucleic Acids?
• DNA - one type, one purpose:
- a single DNA molecules in virus and bacteria
- Eukaryotic cells have many diploid chromosomes
mainly in nucleus, but also mitochondria and
chloroplasts.
• 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
– Small nuclear RNA
– Small non-coding RNAs
Garrett and Grisham, Biochemistry, Third Edition
The DNA Double Helix
Stabilized by hydrogen bonds!
• DNA: Genetic material: Typically double
stranded
• dsDNA: Strands antiparallel
• Interchain H bonds form base pairs.
• Chargaff’s rules: A=T, G=C, Purines =
Pyrimidines
• X-ray diffraction of Franklin and Wilkins
and model building of Watson and Crick
Garrett and Grisham, Biochemistry, Third Edition
The DNA Double Helix
• "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.
Garrett and Grisham, Biochemistry, Third Edition
The sequence of bases in one
strand is complementary to the
sequence of bases in the other
strand.
Figure 10.21 Replication of DNA gives identical
progeny molecules because base pairing is the
mechanism determining the nucleotide sequence
synthesized within each of the new strands during
replication.
Garrett and Grisham, Biochemistry, Third Edition
The information in DNA is
encoded in digital form.
DNA contains two kinds of information:
• The base sequences of genes that encode
the amino acid sequences of proteins and
the nucleotide sequences of functional RNA
(rRNA and tRNA).
• The gene regulatory networks that control
the expression of protein-encoding (and
functional RNA-encoding) genes.
Garrett and Grisham, Biochemistry, Third Edition
The Structure of DNA
An antiparallel double helix
• diameter of 2 nm
• circular in prokaryotic cells.
• length of 1.6 million nm (E. coli)
• Compact and folded (E. coli cell is only 2000 nm
long)
• The linear eukaryotic DNA is wrapped around
histone proteins to form nucleosomes.
• Base pairs: A-T, G-C
Garrett and Grisham, Biochemistry, Third Edition
RNA: Typically single stranded: Produced
during transcription
• mRNA: Carries information encoded in genes to direct protein
synthesis on ribosomes
– Derive from heterogeneous nuclear RNA (hnRNA)
– RNA processed by splicing (removal of introns and joining of
exons), capping (5’ end), and polyA tail addition (3’ end)
• rRNA: Components of ribosome: Protein synthesis
– Small subunit of ribosome: Single rRNA
– Large subunit of ribosome: Large subunit rRNA, 5S rRNA,
and in eukaryotes 5.8S rRNA
• tRNA: Carriers of activated amino acids used by ribosome for
protein synthesis
• snRNA: Small nuclear RNAs
• siRNAs: Small interfering RNAs: Degrade mRNAs
• miRNAs: Bind to mRNA and block translation
• snoRNAs: Required for certain RNA modification
Garrett and Grisham, Biochemistry, Third Edition
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.
Garrett and Grisham, Biochemistry, Third Edition
Eukaryotic mRNA
• DNA is transcribed to produce heterogeneous
nuclear RNA (hrRNA).
– mixed introns and exons with poly A
– intron - intervening sequence
– exon - coding sequence
– poly A tail - stability?
• Splicing produces final mRNA without introns.
Garrett and Grisham, Biochemistry, Third Edition
Ribosomal RNA
• Ribosomes are about 2/3 RNA, 1/3 protein.
• rRNA serves as a scaffold for ribosomal
proteins. rRNA has a characteristic secondary
structure due to many intramolecular H-bonds.
• 23S rRNA in E. coli is the peptidyl transferase!
Garrett and Grisham, Biochemistry, Third Edition
Ribosomal RNA
• rRNA: Components of ribosome:
Protein synthesis
–Small subunit of ribosome:
Single rRNA
–Large subunit of ribosome:
Large subunit rRNA, 5S rRNA,
and in eukaryotes 5.8S rRNA
Garrett and Grisham, Biochemistry, Third Edition
Transfer RNA
• Small polynucleotide chains - 73 to 94
residues each
• Several bases are usually methylated.
• Carriers of activated amino acids used by
ribosome for protein synthesis.
• 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.
Garrett and Grisham, Biochemistry, Third Edition
Structure of a tRNA molecule
Garrett and Grisham, Biochemistry, Third Edition
Small RNAs
Altering gene expression in response to
stressful environmental situations
• snRNA: Small nuclear RNAs: Important in
converting hnRNA to mature mRNA.
• siRNAs: Small interfering RNAs: Degrade
mRNAs — post-transcriptional gene silencing
• miRNAs: micro RNAs: Bind to mRNA and
block translation
• snoRNAs: small nucleolar RNAs: Required for
certain RNA modifications
Garrett and Grisham, Biochemistry, Third Edition
DNA & RNA Differences?
Why does DNA contain thymine?
• Cytosine spontaneously deaminates to form
uracil.
• Repair enzymes recognize these "mutations"
and replace these uracils with cytosines.
• 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.
Garrett and Grisham, Biochemistry, Third Edition
DNA & RNA Differences?
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.
Garrett and Grisham, Biochemistry, Third Edition
Hydrolysis of Nucleic Acids
•
•
•
•
•
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 10.29 for mechanism.
Garrett and Grisham, Biochemistry, Third Edition
Peptide Nucleic Acids (PNAs) are
synthetic mimics of DNA and RNA
• Poor substrates for proteases
• Neutral charge; facilitate
penetration into negatively
charged cell membranes.
p.331
Garrett and Grisham, Biochemistry, Third Edition
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“.
Garrett and Grisham, Biochemistry, Third Edition
Type II Restriction Enzymes
• No ATP requirement.
• Recognition sites in dsDNA have a 2-fold axis
of symmetry.
• Cleavage can leave staggered or "sticky"
ends or can produce "blunt” ends.
• 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.
Garrett and Grisham, Biochemistry, Third Edition