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Reginald H. Garrett
Charles M. Grisham
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Chapter 10
Nucleotides and Nucleic Acids
Reginald Garrett & Charles Grisham • University of Virginia
Outline
• What are the structure and chemistry of nitrogenous
bases?
• What are nucleosides?
• What are the structure and chemistry of nucleotides?
• What are nucleic acids?
• What are the different classes of nucleic Acids?
• Are nucleic acids susceptible to hydrolysis?
Information Transfer in Cells
The fundamental
process of information
transfer in cells.
10.1 What Are 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)
10.1 What Are the Structure and
Chemistry of Nitrogenous Bases?
(a) The pyrimidine ring system; by convention, atoms are
numbered as indicated.
(b) The purine ring system; atoms numbered as shown.
10.1 What Are the Structure and
Chemistry of Nitrogenous Bases?
The common pyrimidine bases – cytosine, uracil, and
thymine – in the tautomeric forms predominant at pH
7.
10.1 What Are the Structure and
Chemistry of Nitrogenous Bases?
The common purine bases – adenine and guanine – in the
tautomeric forms predominant at pH 7.
10.1 What Are the Structure and
Chemistry of Nitrogenous Bases?
Other naturally occurring purine
derivatives – hypoxanthine, xanthine,
and uric acid.
The Properties of Pyrimidines and Purines Can
Be Traced to Their Electron-Rich Nature
10.2 What Are Nucleosides?
Structures to Know
• Nucleosides are compounds formed when a
base is linked to a sugar via a glycosidic bond
• 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
10.2 What Are Nucleosides?
10.2 What Are Nucleosides?
• The base is linked to the sugar 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
• Sugars make nucleosides more water-soluble than
free bases
10.2 What Are Nucleosides?
The common ribonucleosides.
10.3 What Is the Structure and Chemistry
of Nucleotides?
Nucleotides are nucleoside phosphates
• Know the nomenclature
• "Nucleotide phosphate" is redundant!
• Most nucleotides are ribonucleotides
• Nucleotides are polyprotic acids
10.3 What Is the Structure and Chemistry
of Nucleotides?
Structures of the four common ribonucleotides – AMP, GMP,
CMP, and UMP. Also shown: 3’-AMP.
10.3 What Is the Structure and Chemistry
of Nucleotides?
Figure 10.12 The cyclic nucleotide cAMP.
10.3 What Is the Structure and Chemistry
of Nucleotides?
Nucleoside 5'-Triphosphates Are Carriers
of Chemical Energy
• Nucleoside 5'-triphosphates are indispensable
agents in metabolism because their phosphoric
anhydride bonds are a source of chemical 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
Nucleoside 5'-Triphosphates Are Carriers
of Chemical Energy
Nucleoside 5'-Triphosphates Are Carriers
of Chemical Energy
Figure 10.14 Phosphoryl, pyrophosphoryl, and
nucleotidyl group transfer, the major biochemical
reactions of nucleotides. Nucleotidyl group transfer is
shown here.
10.4 What Are Nucleic Acids?
• Nucleic acids are linear polymers of nucleotides
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
10.4 What Are Nucleic Acids?
3',5'-Phosphodiester bridges
link nucleotides together to
form polynucleotide chains.
The 5'-ends of the chains are
at the top; the 3'-ends are at
the bottom. RNA is shown
here.
10.4 What Are Nucleic Acids?
3’,5’-phosphodiester bridges
link nucleotides together to
form polynucleotide chains.
The 5’-ends of the chains are
at the top; the 3’-ends are at
the bottom. DNA is shown
here.
10.5 What Are the Different 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 for
protein synthesis
• transfer RNA - carries the amino acids for
protein synthesis
• Others:
• Small nuclear RNA
• Small non-coding RNAs
10.5 What Are the Different Classes of
Nucleic Acids?
The antiparallel nature of
the DNA double helix. The
two chains have opposite
orientations.
The DNA Double Helix
The double helix is stabilized by hydrogen bonds
• "Base pairs" arise from hydrogen bonds
A-T; G-C
• Erwin Chargaff had the pairing data, but didn't
understand its implications
• Rosalind Franklin's X-ray fiber diffraction data
was crucial
• Francis Crick showed that it was a helix
• James Watson figured out the H bonds
The Base Pairs Postulated by Watson
The Structure of DNA
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
The Structure of DNA
Replication of DNA gives identical
progeny molecules because base
pairing is the mechanism that
determines the nucleotide
sequence of each newly
synthesized strand.
Messenger RNA Carries the Sequence
Information for Synthesis of a Protein
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
Messenger RNA Carries the Sequence
Information for Synthesis of a Protein
Transcription and translation of mRNA molecules in
prokaryotic versus eukaryotic cells.
In prokaryotes, a single mRNA molecule may contain the
information for the synthesis of several polypeptide
chains within its nucleotide sequence.
Messenger RNA Carries the Sequence
Information for Synthesis of a Protein
Transcription and translation of mRNA molecules in prokaryotic
versus eukaryotic cells.
Eukaryotic mRNAs encode only one polypeptide but are more
complex.
Eukaryotic mRNA
• DNA is transcribed to produce heterogeneous
nuclear RNA (hnRNA)
• mixed introns and exons with poly A
• intron = intervening sequence
• exon = coding sequence
• poly A tail - stability?
• Splicing produces final mRNA without introns
Ribosomal RNA Provides the Structural
and Functional Foundation for Ribosomes
• Ribosomes are about 2/3 RNA, 1/3 protein
• rRNA serves as a scaffold for ribosomal proteins
• The different species of rRNA are referred to
according to their sedimentation coefficients
• rRNAs typically contain certain modified
nucleotides, including pseudouridine and
ribothymidylic acid
• Briefly: the genetic information in the nucleotide
sequence of mRNA is translated into the amino
acid sequence of a polypeptide chain by
ribosomes
Ribosomal RNA Provides the Structural
and Functional Foundation for Ribosomes
Ribosomal RNA has a complex
secondary structure due to
many intrastrand H bonds. The
gray line here traces a
polynucleotide chain consisting
of more than 1000 nucleotides.
Aligned regions represent Hbonded complementary base
sequences.
Ribosomal RNA Provides the Structural
and Functional Foundation for Ribosomes
The organization and composition of ribosomes.
Transfer RNAs Carry Amino Acids to
Ribosomes for Use in Protein Synthesis
• 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-3′-OH. The
a.a. is attached in ester linkage to this 3′-OH.
• Aminoacyl tRNA molecules are the substrates
of protein synthesis
Transfer RNAs Carry Amino Acids to
Ribosomes for Use in Protein Synthesis
Transfer RNA also has a
complex secondary
structure due to many
intrastrand hydrogen
bonds. The black lines
represent base-paired
nucleotides in the
sequence.
The Chemical Differences Between DNA
and RNA Have Biological Significance
• Two fundamental chemical differences distinguish
DNA from RNA:
• DNA contains 2-deoxyribose instead of ribose
• DNA contains thymine instead of uracil
The Chemical Differences Between DNA
and RNA Have Biological Significance
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
The Chemical Differences Between DNA
and RNA Have Biological Significance
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
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"
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
Type II Restriction Enzymes
•
•
•
•
Names use 3-letter italicized code:
1st letter - genus; 2nd,3rd - species
Following letter denotes strain
EcoRI is the first restriction enzyme isolated from
the R strain of E. coli
Cleavage Sequences of Restriction
Endonucleases
Restriction Mapping of DNA
Problems
• End of Chapter problems 1-14