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Chapter 28
Biomolecules: Heterocycles and Nucleic
Acids
Based on McMurry’s Organic Chemistry,
6th edition
Heterocycles
• Cyclic organic compounds are carbocycles or heterocycles
– Carbocycle rings contain only carbon atoms
– Heterocycle rings atoms in addition to carbon (N,S,O are common)
• Heterocycles include many important natural materials as
well as pharmaceuticals
28.1 Five-Membered Unsaturated
Heterocycles
• Pyrrole, furan, and thiophene are common fivemembered unsaturated heterocycles
• Each has two double bonds and N, O, or S
Pyrrole
• Commercially from coal tar or by treatment of
furan with ammonia over an alumina catalyst
at 400°C.
Furan
• Made commercially by extrusion of CO from
furfural, which is produced from sugars
Thiophene
• From coal tar or by cyclization of butane or
butadiene with sulfur at 600°C
Unusual Reactivity
• Pyrrole is an amine but it is not basic
• Pyrrole, furan, and thiophene are conjugated
dienes but they undergo electrophilic
substitution (rather than addition)
28.2 Structures of Pyrrole, Furan,
and Thiophene
• Pyrrole, furan, and thiophene are aromatic
(Six  electrons in a cyclic conjugated system
of overlapping p orbitals)
• In pyrrole  electrons come from C atoms and
lone pair on sp2-N
Why Pyrrole is Not a Base
• The nitrogen lone pair is a part of the aromatic sextet,
protonation on nitrogen destroys the aromaticity,
giving its conjugate acid a very low pKa (0.4)
• The carbon atoms of pyrrole are more electron-rich
and more nucleophilic than typical double-bond
carbons (see comparison with cyclopentadiene)
28.3 Electrophilic Substitution Reactions of
Pyrrole, Furan, and Thiophene
• The heterocycles are more reactive toward
electrophiles than benzene
Position of Substitution
• Electrophilic substitution normally occurs at C2, the
position next to the heteroatom, giving more stable
intermediate
28.4 Pyridine, a Six-Membered
Heterocycle
• Nitrogen-containing heterocyclic analog of benzene
• Lone pair of electrons on N not part occupies an sp2
orbital in the plane of the ring and is not involved in
bonding (Figure 28.3).
Electronic structure of pyridine
• Pyridine is a stronger base than pyrrole but a weaker
base than alkylamines
• The sp2-hybridized N holds the lone-pair electrons
more tightly than the sp3-hybridized nitrogen in an
alkylamine
28.5 Electrophilic Substitution of
Pyridine
• The pyridine ring undergoes electrophilic aromatic
substitution reactions with great difficulty, under
drastic conditions
Low Reactivity of Pyridine
• Complex between ring nitrogen and incoming
electrophile deactivates ring with positive charge
• Electron-withdrawing nitrogen atom deactivates
causes a dipole making positively polarized C’s poor
Lewis bases
28.6 Nucleophilic Substitution of
Pyridine
• 2- and 4-substituted (but not 3-substituted)
halopyridines readily undergo nucleophilic aromatic
substitution
Mechanism of Nucleophilic
Substitution on Pyridine
• Reaction occurs by addition of the nucleophile to the
C=N bond, followed by loss of halide ion
Addition-Elimination
• Addition favored by ability of the electronegative
nitrogen to stabilize the anionic intermediate
• Leaving group is then expelled
28.7 Fused-Ring Heterocycles
• Quinoline, isoquinoline, and indole are fused-ring
heterocycles, containing both a benzene ring and a
heterocyclic aromatic ring
Quinoline and Isoquinoline
• Quinoline and isoquinoline have pyridine-like nitrogen
atoms, and undergo electrophilic substitutions
• Reaction is on the benzene ring rather than on the
pyridine ring
Indole
• Has pyrrole-like nitrogen (nonbasic)
• Undergoes electrophilic substitution at C3 of the
electron-rich pyrrole
Purine and Pyrimidine
• Pyrimidine contains two pyridine-like nitrogens in a
six-membered aromatic ring
• Purine has 4 N’s in a fused-ring structure. Three are
basic like pyridine-like and one is like that in pyrrole
28.8 Nucleic Acids and Nucleotides
• Deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA), are the chemical carriers of genetic information
• Nucleic acids are biopolymers made of nucleotides,
aldopentoses linked to a purine or pyrimidine and a
phosphate
Sugars in DNA and RNA
• RNA is derived from ribose
• DNA is from 2-deoxyribose
– (the ' is used to refer to positions on the sugar portion of a
nucleotide)
Heterocycles in DNA and RNA
• Adenine, guanine, cytosine and thymine are in DNA
• RNA contains uracil rather than thymine
Nucleotides
• In DNA and RNA the heterocycle is bonded to C1 of
the sugar and the phosphate is bonded to C5 (and
connected to 3’ of the next unit)
The Deoxyribonucleotides
The Ribonucleotides
28.9 Structure of Nucleic Acids
• Nucleotides join together in DNA and RNA by as
phosphate between the 5-on one nucleotide and the 3
on another
• One end of the nucleic acid polymer has a free
hydroxyl at C3 (the 3 end), and the other end has a
phosphate at C5 (the 5 end).
Generalized Structure of DNA
Nucleic Acid Sequences
• Differences arise from the sequence of bases
on the individual nucleotides
Describing a Sequence
• Chain is described from 5 end, identifying the bases in
order of occurrence, using the abbreviations A for
adenosine, G for guanosine, C for cytidine, and T for
thymine (or U for uracil in RNA)
• A typical sequence is written as TAGGCT
28.10 Base Pairing in DNA: The
Watson–Crick Model
• In 1953 Watson and Crick noted that DNA consists of
two polynucleotide strands, running in opposite
directions and coiled around each other in a double
helix
• Strands are held together by hydrogen bonds between
specific pairs of bases
• Adenine (A) and thymine (T) form strong hydrogen
bonds to each other but not to C or G
• (G) and cytosine (C) form strong hydrogen bonds to
each other but not to A or T
H-Bonds in DNA
• The G-C base pair involves three H-bonds
A-T Base Pairing
• Involves two H-bonds
The Difference in the Strands
• The strands of DNA are complementary
because of H-bonding
• Whenever a G occurs in one strand, a C occurs
opposite it in the other strand
• When an A occurs in one strand, a T occurs in
the other
Grooves
• The strands of the DNA
double helix create two
continuous grooves (major
and minor)
• The sugar–phosphate
backbone runs along the
outside of the helix, and the
amine bases hydrogen bond
to one another on the inside
• The major groove is slightly
deeper than the minor groove,
and both are lined by
potential hydrogen bond
donors and acceptors.
28.11 Nucleic Acids and
Heredity
• Processes in the transfer of genetic information:
• Replication: identical copies of DNA are made
• Transcription: genetic messages are read and carried out of
the cell nucleus to the ribosomes, where protein synthesis
occurs.
• Translation: genetic messages are decoded to make proteins.
28.12 Replication of DNA
• Begins with a partial unwinding of the double helix,
exposing the recognition site on the bases
• Activated forms of the complementary nucleotides (A
with T and G with C) associate two new strands begin
to grow
The Replication Process
• Addition takes place 5  3, catalyzed by DNA
polymerase
• Each nucleotide is joined as a 5-nucleoside
triphosphate that adds a nucleotide to the free 3hydroxyl group of the growing chain
28.13 Structure and Synthesis of
RNA: Transcription
• RNA contains ribose rather than deoxyribose and
uracil rather than thymine
• There are three major kinds of RNA - each of which
serves a specific function
• They are much smaller molecules than DNA and are
usually single-stranded
Messenger RNA (mRNA)
• Its sequence is copied from genetic DNA
• It travels to ribsosomes, small granular particles in the
cytoplasm of a cell where protein synthesis takes place
Ribosomal RNA (rRNA)
• Ribosomes are a complex of proteins and rRNA
• The synthesis of proteins from amino acids and ATP
occurs in the ribosome
• The rRNA provides both structure and catalysis
Transfer RNA (tRNA)
• Transports amino acids to the ribosomes where they
are joined together to make proteins
• There is a specific tRNA for each amino acid
• Recognition of the tRNA at the anti-codon
communicates which amino acid is attached
Transcription Process
• Several turns of the DNA double helix unwind,
exposing the bases of the two strands
• Ribonucleotides line up in the proper order by
hydrogen bonding to their complementary bases on
DNA
• Bonds form in the 5  3 direction,
Transcription of RNA from DNA
• Only one of the two DNA strands is transcribed into
mRNA
• The strand that contains the gene is the coding or
sense strand
• The strand that gets transcribed is the template or
antisense strand
• The RNA molecule produced during transcription is a
copy of the coding strand (with U in place of T)
Mechanism of Transcription
• DNA contains promoter sites that are 10 to 35 base
pairs upstream from the beginning of the coding
region and signal the beginning of a gene
• There are other base sequences near the end of the
gene that signal a stop
• Genes are not necessarily continuous, beginning gene
in a section of DNA (an exon) and then resume farther
down the chain in another exon, with an intron between
that is removed from the mRNA
28.14 RNA and Protein
Biosynthesis: Translation
• RNA directs biosynthesis of peptides and proteins
which is catalyzed by mRNA in ribosomes, where
mRNA acts as a template to pass on the genetic
information transcribed from DNA
• The ribonucleotide sequence in mRNA forms a
message that determines the order in which different
amino acid residues are to be joined
• Codons are sequences of three ribonucleotides that
specify a particular amino acid
• For example, UUC on mRNA is a codon that directs
incorporation of phenylalanine into the growing protein
Codon Assignments of Base
Triplets
The Parts of Transfer RNA
• There are 61 different tRNAs, one for each of the 61
codons that specifies an amino acid
• tRNA has 70-100 ribonucleotides and is bonded to a
specific amino acid by an ester linkage through the 3
hydroxyl on ribose at the 3 end of the tRNA
• Each tRNA has a segment called an anticodon, a
sequence of three ribonucleotides complementary to
the codon sequence
The Structure of tRNA
Processing Aminoacyl tRNA
• As each codon on mRNA is read, tRNAs bring amino
acids as esters for transfer to the growing peptide
• When synthesis of the proper protein is completed, a
"stop" codon signals the end and the protein is
released from the ribosome
28.15 DNA Sequencing
• The order of the bases along DNA contains the genetic
inheritance.
• Determination of the sequence is based on chemical
reactions rather than physical analysis
• DNA is cleaved at specific sequences by restriction
endonucleases
• For example, the restriction enzyme AluI cleaves
between G and C in the four-base sequence AG-CT
Note that the sequence is identical to that of its
complement, (3)-TC-GA-(5)
• Other restriction enzymes produce other cuts
permitting partially overlapping sequences of small
pieces to be produced for analysis
Analytical Methods
• The Maxam–Gilbert method uses organic chemistry to
cleave phosphate linkages at with specificity for the
adjoining heterocycle
• The Sanger dideoxy method uses enzymatic reactions
• The Sanger method is now widely used and automated,
even in the sequencing of genomes
The Sanger Dideoxy Method
• The fragment to be sequenced is combined with:
– A small piece of DNA (primer), whose sequence is
complementary to that on the 3 end of the restriction
fragment
– The four 2-deoxyribonucleoside triphosphates (dNTPs)
The Dideoxy Nucleotides
• The solution also contains small amounts of the four
2,3-dideoxyribonucleoside triphosphates (ddNTPs)
• Each is modified with a different fluorescent dye
molecule
The Dideoxy Method - Growing the and
Stopping the Copied Chains
• DNA polymerase is added and a strand of DNA
complementary to the restriction fragment begins to
grow from the end of the primer
• Whenever a dideoxyribonucleotide is incorporated,
chain extension cannot continue
Dideoxy Method - Analysis
• The product is a mixture of dideoxy-terminated DNA
fragments with fluorescent tags
• These are separated according to weight by
electrophoresis and identified by their specific
fluorescence
28.16 DNA Synthesis
• DNA synthesizers use a solid-phase method starting
with an attached, protected nucleotide
• Subsequent protected nucleotides are added and
coupled
• After the final nucleotide has been added, the
protecting groups are removed and the synthetic DNA
is cleaved from the solid support
• The bases are protected from reacting
DNA Synthesis: Attachment
• Attachment of a protected deoxynucleoside to a
polymeric or silicate support as an ester of the 3 OH
group of the deoxynucleoside
• The 5 OH group on the sugar is protected as its pdimethoxytrityl (DMT) ether
DNA Synthesis: DMT Removal
• Removal of the DMT protecting group by treatment
with a moderately weak acid
DNA Synthesis: Coupling
• The polymer-bound (protected) deoxynucleoside
reacts with a protected deoxynucleoside containing a
phosphoramidite group at its 3 position, catalyzed by
tetrazole, a reactive heterocycle
DNA Synthesis: Oxidation and
Cycling
• Phosphite is oxidized to phosphate by I2
• The cycle is repeated until the sequence is complete
DNA Synthesis: Clean-up
• All protecting groups are removed and the product is
released from the support by treatment with aqueous
NH3
28.17 The Polymerase Chain
Reaction (PCR)
• Copies DNA molecules by unwinding the double helix
and copying each strand using enzymes
• The new double helices are unwound and copied
again
• The enzyme is selected to be fast, accurate and heatstable (to survive the unwinding)
• Each cycle doubles the amount of material
• This is exponential template-driven organic synthesis
PCR: Heating and Reaction
• The subject DNA is heated (to separate strands) with
– Taq polymerase (enyzme) and Mg2+
– Deoxynucleotide triphosphates
– Two, oligonucleotide primers, each complementary to the
sequence at the end of one of the target DNA segments
PCR: Annealing and Growing
• Temperature is reduced to 37 to 50°C,
allowing the primers to form H-bonds to their
complementary sequence at the end of each
target strand
PCR: Taq Polymerase
• The temperature is then raised to 72°C, and Taq
polymerase catalyzes the addition of further
nucleotides to the two primed DNA strands
PCR: Growing More Chains
• Repeating the denature–anneal–synthesize cycle a
second time yields four DNA copies, a third time yields
eight copies, in an exponential series.
• PCR has been automated, and 30 or so cycles can be
carried out in an hour