Chapter Seventeen
Nucleic Acids
Nucleic acids comprise the genetic machinery of living cells.
They are polymers composed of nucleotide monomer units.
They were first discovered by F. Miescher in 1869, but their
importance was not recognized for nearly a century.
There are two types of nucleic acids: deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA). They contain
ribose and deoxyribose sugars, respectively.
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Nucleotides: The Building Blocks
of Nucleic Acids
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Nucleotides are three-component molecules containing:
(1) a phosphate group,
(2) a pentose sugar (deoxyribose or ribose),
(3) a heterocyclic nitrogen-containing base
(a purine or a pyrimidine).
Base
Phosphate
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Sugar
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The Pentose Sugars
The only difference is that an OH group is bound to
carbon 2’ in ribose, and this is replaced by an H in
deoxyribose.
RNA has ribose as its sugar, DNA uses deoxyribose.
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The Nitrogenous Bases
There are two basic forms: Purines and Pyrimidines:
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The Nitrogenous Bases
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The Phosphate Group
Phosphoric acid is H3PO4
OOH
|
O==P—OH
|
OH
Phosphoric Acid
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O|
O==P—OH
|
OIonized form at
pH = 7
16a–8
Nucleotide Formation
Nucleotides are formed from their subunits by (you
guessed it!) condensation reactions, splitting out waters.
Both the phosphate-sugar reaction and the sugar-base
reaction split out water molecules.
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Nucleotide Nomenclature
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Primary Structure of Nucleic Acids
The backbone of a nucleic acid is composed of sugarphosphate bonds. The bases stick off of the sugar units
and their sequence forms the primary structure.
Only four types of bases appear in any nucleic acid.
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The Structure of a Nucleic Acid
Note the 3’ and 5’
ends.The primary
structure has a
direction.
The links are 3,5’
“phosphodiester”
links. Each phosphate
link has a -1 charge.
By convention, the
strand is read from the
5’ to the 3’ end. Here
TGCA.
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The Double Helix
In 1953 in James D. Watson
and Francis Crick figured
out the structure of DNA—
it turned out to be a double
helix.
They published their results
in the journal Nature.
Watson later wrote a
controversial book called
The Double Helix.
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There Were Clues Earlier
￭ One clue was that in DNA the percentage of the base
adenine was always the same as that of the base
thymine, and the percentage of guanine was always the
same as that of the base cytosine: that is,
%A = %T and %G = %C
￭ Also, experiments indicated that nucleic acids were
the genetic materials in viruses.
￭ But these clues were largely ignored while most
workers focused on proteins as the supposed genetic
material.
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The Two Strands Of DNA are
Complementary
“A” hydrogen bonds to “T”, and “G” hydrogen bonds
to “C,” so one strand is complementary to the other.
Example:
Strand 1:
Strand 2:
AGTCAATGCC
TCAGTTACGG
Remember: We start on strand 1 at the 5’ end and go
from there.
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Replication of DNA
In this process DNA molecules produce exact
duplicates of themselves. The strands separate and
acquire new strands. Enzymes direct the process.
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Chromosomes and Genes
A chromosome is a DNA molecule bound to a group of
proteins. Typically a chromosome is about 15% DNA
and 85% protein.
Humans have 46 chromosomes in each cell; dogs have
78, frogs 26, mosquitos 6.
Chromosomes come in matched pairs: so humans have
23 pairs, one from the father, the other from the mother,
in each pair.
Each chromosome houses a large number of genes.
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Protein Synthesis
The Central Dogma: Information flows from DNA to RNA
to proteins:
Information
DNA → RNA → Proteins
The DNA → RNA step is called transcription. In this step
DNA passes on the code for a protein to RNA.
The RNA → Proteins step is called translation. In this
step (which is actually composed of several steps) the
codes in the RNA are used as blueprints in protein
synthesis.
Note that RNA molecules are usually single-stranded,
whereas DNA is double-stranded. RNA molecules also
tend to be much smaller than DNA molecules.
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The Structure of a Cell
■ All higher organisms have “eukaryotic” cells that
have a nucleus.
Schematic of a
eukaryotic cell
Mitochondria
are the main
energyproducing
organelles
Ribosomes (the small dots) are the
organelles where proteins are
manufactured.
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Ribonucleic Acids
There are several important types of RNA molecules:
Messenger RNA – mRNA molecules carry the codes for
proteins from the DNA (in the nucleus) to the ribosomes
(which are structures in the cell outside the nucleus).
Primary transcript RNA – ptRNA is the “raw material” for
messenger RNA. It will be edited to produce mRNA
Ribosomal RNA – The ribosomes are structures in the cell
where the actual synthesis of proteins occurs. They
consist of RNA and protein. This RNA is designated rRNA.
Transfer RNA – tRNA molecules transfer specific amino
acids to the ribosomes, where the amino acids are joined
into proteins.
Other RNAs – A number of other types of small RNAs play
special genetic roles, such as regulating gene expression.
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The Genetic Code
A gene is a segment of DNA that carries the code for the
structure of a protein (or sometimes an RNA molecule).
A gene usually consists of a DNA sequence of about 10003500 nucleotides.
The human genome (the entire genetic code on 46
chromosomes) apparently contains about 20-22,000 genes.
The “code” consists of three-nucleotide sequences
(codons) that stand for individual amino acids. For example,
the DNA sequence G-U-C (starting, remember, from the 5’
end) represents the amino acid valene.
Other coding sequences are:
UUC – phenylalanine
CCA – proline
UCA – serene
AGA – argenine
And
so forth: See Table 17.2 for a full list.
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Additional Comments on the Code
• The code is almost universal: that is, it used by
almost all organisms: plants, microbes, and humans.
• The code contains start and stop signals.
• With four different “letters” (A,T,G,C), a threeletter sequence has 43 = 4x4x4 = 64 possibilities.

A given amino acid may be specified by several
sequences. For example, the sequences UCU, UCC,
UCA, and UCG all specify the amino acid serine.
(The code is thus said to be “degenerate”, i.e., not
having a single, unique sequence for each amino
acid.)
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Transcription of the Code from DNA to RNA
Four steps:
1. A portion of the DNA sequence unwinds and exposes a
gene. This is governed by the enzyme RNA polymerase.
2. Free ribonucleotides align along one of the exposed DNA
strands. They pair up with complementary bases on the
DNA.
3. RNA polymerase links up these ribonuceotides.
4. Transcription ends when the enzyme encounters a “stop”
signal in the DNA sequence. This produces “primary
transcript RNA”, ptRNA.
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Editing of the ptRNA: Formation of mRNA
But the RNA sequence (ptRNA) is not quite ready to be
used for protein formation – it must be edited. In the
editing some parts (introns) are spliced out. Exons are
kept and joined.
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Some Additional Details
• Splicing means that a single gene can yield several
protein codes, depending on how it is spliced. This is
called alternative splicing.
• Both the exons and introns of a gene are initially
transcribed to form ptRNA. Then the ptRNA is spliced to
form the mRNA for a given protein. Enzymes direct the
splicing.
• The Human Genome Project (which produced a rough
sequence for the human genome) was completed in 2001
with the sequencing of about 3 billion nucleotides and
about 22,000 genes. Two groups were responsible for it: an
NIH group led by Francis Collins and a private group
(Celera Genomics) led by J. Craig Venter.
• Now many additional organisms have had their genomes
sequenced.
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Transfer RNA
Transfer RNA (tRNA) molecules pick up amino acids and
transfer them to the ribosomes, where they are aligned and
linked up to form proteins. tRNAs attach amino acids at
one end and have a recognition portion (anticodon) that
pairs up with a complementary sequence on the mRNA that
codes for that amino acid.
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Translation: Protein Synthesis
■ Protein synthesis occurs on the ribosomes, which are cell
organelles. The synthetic process requires a number of
ingredients:
■ Ribosomes are the sites, or “factories”, where proteins
are synthesized. They are comprised of subunits containing
about 65% RNA and 35% protein.
■ Messenger RNA molecules act like messengers, bringing
the code, or blueprint, for a protein (the “message”) from
the DNA gene to the ribosomes.
■ Transfer RNA molecules pick up amino acids and carry
them to the ribosomes. There they line them up using their
anticodons. Thus they act like workers who gather and
assemble the parts.
■ Enzymes act like managers and workers to control and
operate the manufacturing process.
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■ Enzymes direct the process, and the polypeptide
continues to grow as more amino acids are added.
■ Growth continues until a “stop” codon is encountered.
■ Finally, the polypeptide is cleaved from the tRNAs by
hydrolysis.
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■ Protein synthesis
involves a number of
different stages.
■ Normally,some
additional processing of
the protein takes place
after it separates
from the ribosome.
■ A single mRNA
molecule can code for
the production
of a large number of
Identical protein
molecules.
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￭ Translation of the mRNA
code into protein.
￭ tRNAs bring in amino
acids and put them in their
proper places on the mRNA.
￭ The process continues
until the entire protein
sequence is formed.
￭ The yellow glob is the
enzyme that directs the
operation.
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Comments on “Junk DNA”
￭ For a long time it was thought that large portions of
the genome contained useless, or “junk”, sequences
of nucleotides.
￭ Now it is realized that these supposed junk regions
actually code for different kinds of RNA molecules
that help regulate the expression of genes.
￭ Apparently the resulting differences in gene
expression are very important in determining
differences between different individuals and
different species, e.g., between humans and
chimpanzees.
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EPIGENETICS
■ This term refers to effects that go beyond, or fall outside,
effects caused by the genetic code itself. Thus
epigenetic means ”beyond the genetic code.”
■ Genetics is not destiny. Epigenetic effects account for
why identical twins, with the same genetic code, are not
completely identical. For example, why does one gets a
disease and the other doesn’t.
■ Many epigenetic effects come from the environment.
■ Selective methylation of biomolecules can have dramatic
effects, turning genes on or off.
■ Histones are proteins that surround the DNA of the
genetic code. These proteins can “hide” parts of the
code and prevent genes from being expressed.
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Genetic Engineering
• In general genetic engineering involves placing a gene
from one organism into another organism.
• Example: Bacteria have been genetically altered to
produce human insulin, and this can be used to treat
diabetics.
• The bacteria can be grown in large numbers and the
insulin is harvested for medical use.
• Special enzymes are used to extract and insert the
desired genes.
• In some cases genes can be artificially constructed for
such purposes.
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Misfolded Proteins
■ Just as misguided people can cause problems, so also
can misfolded proteins.
■ Disease-causing misfolded proteins are called prions
(pronounced “PREE-ons’). They are believed responsible
for the following diseases:
Sheep – scrapies
Cattle – mad cow disease
Humans – human variant Creutzfeld-Jacob disease (and
perhaps Alzheimer’s disease, Parkinson’s disease)
■ Stanley Prusiner (UCSF) won the 1997 Nobel Prize for
first suggesting that misfolded proteins were responsible
for disease. This was, and is, a very controversial idea.
■ A tribe of cannibals in New Guinea honored their dead
by eating their brains—and developed a neurological
disease
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What you absolutely must understand from Chapter 17
■ Understand that nucleic acids form the genetic machinery of
cells, and that they are polymers of nucleotide monomers.
■ Understand that there are two types of nucleic acids: RNAs
and DNAs.
■ Understand that nucleotides have three parts: a pentose
sugar, a phosphate group, and a nitrogen-containing base.
■ Be able to distinguish ribose from deoxyribose.
■ Be able to distinguish a purine from a pyrimidine.
■ Know that T, C, and U are pyrimidines, and A and G are
purines.
■ Know that DNA contains deoxyribose with A, T, G, and C,
whereas RNA contains ribose with A, U, G,and C.
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What you must know (cont.)
■ Know that the nucleotides are called adenosine, guanosine,
etc.
■ Understand that the pentose sugars of nucleotides are
joined to both phosphate and base units by means of
condensation reactions. Know what a condensation reaction
is and what its reverse reaction is called.
■ Appreciate what the “primary structure” of a nucleic acid
refers to, and that it has a 5’ and a 3’ end. Be able to contrast
this primary structure with that of a protein. (What types of
links are involved in each? What types of side groups?)
■ Understand that the secondary structure of DNA is a double
helix, with two strands wrapped around each other in a spiral,
with the bases inside, and held together by hydrogen bonds
between the bases. Know what bases bond to each other in
this way.
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What you must know (cont.)
■ Know who first determined the DNA structure and when.
Appreciate that they relied on X-ray diffraction studies to
find the structure.
■ Appreciate why the fact that the % G = % C in DNA was
an important clue for the structure determination.
■ Appreciate that there are three hydrogen bonds between
G and C, and just two between A and T.
■ Understand the process by which DNA replicates itself
so that two identical copies are made.
■ Understand the terms gene, genome, and chromosome.
Know how many chromosomes humans have.
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What you must know (cont.)
■ Understand the general idea of the “Central Dogma” (even
though some exceptions are now known).
■ Understand the different types of RNA (rRNA, ptRNA,
mRNA, tRNA) present in a cell and what their roles in protein
synthesis are.
■ Understand the general process by which proteins are
made in a cell: where it happens and how it happens.
■ Understand the basic idea of the genetic code —that each
amino acid is coded for by a sequence of three nucleotides
(a codon). Appreciate that the human genome has about 3
billion nucleotides and 22,000 genes.
■ Understand the idea of splicing of ptRNA, and how it
allows a single gene to yield several different mRNAs that
code for several different proteins.
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What you must know (cont.)
■ Appreciate that an amino acid may be represented in the
code by several different codons.
■ Understand the basic structure of a tRNA molecule and how
its attachment site and anticodon region contribute to its
action. Appreciate that it forms an ester link to its amino
acid, and that this link is later hydrolyzed.
■ Appreciate that protein formation on the ribosome is ended
when a stop condon is encountered. Also understand that
the whole process is controlled by several enzymes.
■ Understand that a single messenger RNA can be used
repeatedly as the blueprint for a number of identical proteins.
■ Understand that genetic engineering generally involves the
transfer of a gene from one organism into the genome of
another organism.
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To Do List
• Read chapter 17!!
• Do additional problems
• Do practice test T/F
• Do practice test MC
• Review Lecture notes for
Chapter Seventeen
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