Replication, Transcription & Translation

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16.1 The DNA Double Helix

Our current understanding of the structure of DNA is based on the model proposed
initially by James Watson and Francis Crick in 1953 (Figure 1).

Figure 1 The Three-Dimensional Structure of DNA—A Double Helix

The sugar–phosphate backbone lies on the outside of the helix and the bases lie on the
inside, perpendicular to the axis of the helix. The two strands of DNA run in opposite directions;
that is, one strand runs from the 5' end to the 3' end, while the other runs from the 3' end to the
5' end.
The double helix is stabilized by hydrogen bonding between the bases of the two DNA
strands as shown in Figure 2. A purine base on one strand always hydrogen bonds with a
pyrimidine base on the other strand. Two bases hydrogen bond together in a predictable
manner, forming complementary base pairs.

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Figure 2 Hydrogen Bonding in the DNA Double Helix

Because of this consistent pairing of bases, knowing the sequence of one strand of DNA
allows us to write the sequence of the other strand, as shown in Sample Problem 16.1.

Sample Problem 16.1

Predicting Base Sequence of a Complementary DNA Strand

Write the sequence of the complementary strand of the following portion of a DNA molecule:
5'–TAGGCTA–3'

The complementary strand runs in the opposite direction, from the 3' to the 5' end. Use base
pairing to determine the corresponding sequence on the complementary strand: A pairs with T
and C pairs with G.

Problem 1

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The enormously large DNA molecules that compose the human genome—the total
DNA content of an individual—pack tightly into the nucleus of the cell. The double-stranded
DNA helices wind around a core of protein molecules called histones to form a chain of
nucleosomes, as shown in Figure 3. The chain of nucleosomes winds into a supercoiled fiber
called chromatin, which composes each of the 23 pairs of chromosomes in humans.

Figure 3 The Structure of a Chromosome

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In the previous module, we learned that the genetic information of an organism is

stored in the sequence of bases of its DNA molecules. How is this information transferred
from one generation to another? How, too, is the information stored in DNA molecules used to
direct the synthesis of proteins?

To answer these questions we must understand three key processes.

16.2 Replication

During replication, the strands of DNA separate and each serves as a template for a new
strand. Thus, the original DNA molecule forms two DNA molecules, each of which contains
one strand from the parent DNA and one new strand. This process is called semiconservative
replication. The sequence of both strands of the daughter DNA molecules exactly matches the
sequence in the parent DNA.

The first step in replication is the unwinding of the DNA helix to expose the bases on
each strand. Unwinding occurs at many places simultaneously along the helix, creating

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“bubbles” where replication can occur. The point at which unwinding occurs is called the
replication fork. Unwinding breaks the hydrogen bonds that hold the two strands of the double
helix together. Once bases have been exposed on the unwound strands of DNA, the enzyme
DNA polymerase catalyzes the replication process using the four nucleoside triphosphates
(derived from the bases A, T, G, and C) that are available in the nucleus. Three features are key
and each is illustrated in Figure 4.

Figure 4 DNA Replication

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Since replication proceeds in only one direction—that is, from the 3' end to the 5' end of
the template—the two new strands of DNA must be synthesized by somewhat different
techniques. One strand, called the leading strand, grows continuously. Since its sequence is
complementary to the template, its nucleotide sequence grows in the 5' to 3' direction. The other
strand, called the lagging strand, is synthesized in small fragments, which are then joined
together by a DNA ligase enzyme. The end result is two new strands of DNA, one in each of the
daughter DNA molecules, both with complementary base pairs joining the two DNA strands
together.

Sample Problem 16.2

Predicting Base Sequence of a New DNA Segment

What is the sequence of a newly synthesized DNA segment if the template strand has the
sequence 3'–TGCACC–5'?

The newly synthesized strand runs in the opposite direction, from the 5' end to the 3' end in this
example. Use base pairing to determine the corresponding sequence on the new strand: A pairs
with T and C pairs with G.

Problem 2

16.3 RNA

While RNA is also composed of nucleotides, there are important differences between
DNA and RNA. In RNA: The sugar is ribose. U (uracil) replaces T (thymine) as one of the
bases. RNA is single stranded.

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RNA molecules are much smaller than DNA molecules. Although RNA contains a
single strand, the chain can fold back on itself, forming loops, and intermolecular hydrogen
bonding between paired bases on a single strand can form helical regions. When base pairing
occurs within an RNA molecule (or between RNA and DNA), C and G form base pairs, and A
and U form base pairs.

There are three different types of RNA molecules.

tRNAs have two important sites. The 3' end, called the acceptor stem, always contains
the nucleotides ACC and has a free OH group that binds a specific amino acid. Each tRNA also
contains a sequence of three nucleotides called an anticodon, which is complementary to three
bases in an mRNA molecule, and identifies what amino acid must be added to a growing
polypeptide chain.
tRNA molecules are often drawn in the cloverleaf fashion shown in Figure 5. The
acceptor stem and anticodon region are labeled. Folding creates regions of the tRNA in which
nearby complementary bases hydrogen bond to each other.

Figure 5 Transfer RNA (tRNA) – Cloverleaf Representation

17.1 Transcription

The conversion of the information in DNA to the synthesis of proteins begins with
transcription— that is, the synthesis of messenger RNA from DNA.

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RNA synthesis begins in the same manner as DNA replication: the double helix of DNA
unwinds (Figure 6). Since RNA is single stranded, however, only one strand of DNA is needed
for RNA synthesis.

Figure 6 Transcription

Each mRNA molecule corresponds to a small segment of a DNA molecule. Transcription

begins at a particular sequence of bases on the DNA template using an RNA polymerase
enzyme, and proceeds from the 3' end to the 5' end of the template strand. Complementary base
pairing determines what RNA nucleotides are added to the growing RNA chain: C pairs with
G, T pairs with A, and A pairs with U. Thus, the RNA chain grows from the 5' to 3' direction.
Transcription is completed when a particular sequence of bases on the DNA template is
reached. The new mRNA molecule is released and the double helix of the DNA molecule re-
forms.
In bacteria, the new mRNA molecule is ready for protein synthesis immediately after it
is prepared. In humans, the mRNA molecule first formed is modified before it is ready for
protein synthesis. Portions of the mRNA molecule are removed and pieces of mRNA are spliced
together by mechanisms that will not be discussed here.

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Sample Problem 17.1

Predicting Base Sequence of an Informational Strand of DNA

If a portion of the template strand of a DNA molecule has the sequence 3'–CTAGGATAC–5',
what is the sequence of the mRNA molecule produced from this template? What is the sequence
of the informational strand of this segment of the DNA molecule?

mRNA has a base sequence that is complementary to the template from which it is prepared.
mRNA has a base sequence that is identical to the informational strand of DNA, except that it
contains the base U instead of T.

Problem 3

Problem 4

17.2 The Genetic Code

Once the genetic information of DNA has been transcribed in a messenger RNA
molecule, RNA can direct the synthesis of an individual protein. How can RNA, which is

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composed of only four different nucleotides, direct the synthesis of polypeptides that are
formed from 20 different amino acids? The answer lies in the genetic code.

For example, the codon UAC in an mRNA molecule codes for the amino acid serine, and
the codon UGC codes for the amino acid cysteine. The same genetic code occurs in almost all
organisms, from bacteria to whales to humans.

Given four different nucleotides (A, C, G, and U), there are 64 different ways to combine
them into groups of three, so there are 64 different codons. Sixty-one codons code for specific
amino acids, so many amino acids correspond to more than one codon, as shown in Table 2. For
example, the codons GGU, GGC, GGA, and GGG all code for the amino acid glycine. Three
codons—UAA, UAG, and UGA—do not correspond to any amino acids; they are called stop
codons because they signal the termination of protein synthesis.

Table 2 The Genetic Code

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Codons are written from the 5' to 3' end of mRNA. The 5' end of the mRNA molecule
codes for the N-terminal amino acid in a protein, and the 3' end of the mRNA molecule codes
for the C-terminal amino acid. Sample Problem 17.2 illustrates the conversion of a sequence of
bases in mRNA to a sequence of amino acids in a peptide.

Sample Problem 17.2

Using the Genetic Code and mRNA Codons to Predict Amino Acid Sequences

Derive the amino acid sequence that is coded for by the following mRNA sequence.
5' CAU AAA ACG GUG UUA AUA 3'

Use the Genetic Code table to identify the codons that correspond to each amino acid. Codons
are written from the 5' to 3' end of an mRNA molecule and correspond to a peptide written
from the N-terminal to C-terminal end.

Problem 5

Problem 6

Problem 7

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17.3 Translation & Protein Synthesis

The translation of the information in messenger RNA to protein synthesis occurs in the
ribosomes. Each type of RNA plays a role in protein synthesis.

Each individual tRNA contains an anticodon of three nucleotides that is complementary

to the codon in mRNA and identifies individual amino acids. For example, a codon of UCA in
mRNA corresponds to an anticodon of AGU in a tRNA molecule, which identifies serine as the
amino acid. Other examples are shown in Table 3.

Table 3 Relating Codons, Anticodons, and Amino Acids

Problem 8

There are three stages in translation: initiation, elongation, and termination.

[1] INITIATION
Translation begins when an mRNA molecule binds to the smaller subunit of the
ribosome and a tRNA molecule carries the first amino acid of the peptide chain to the binding
site. Translation always begins at the codon AUG, which codes for the amino acid methionine.
The arriving tRNA contains an anticodon with the complementary base sequence UAC. The
large and small subunits of the ribosome combine to form a tight complex where protein
synthesis takes place.

[2] ELONGATION
The next tRNA molecule containing an anticodon for the second codon binds to mRNA,
delivering its amino acid, and a peptide bond forms between the two amino acids. The first
tRNA molecule, which has delivered its amino acid and is no longer needed, dissociates from

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the complex. The ribosome shifts to the next codon along the mRNA strand and the process
continues when a new tRNA molecule binds to the mRNA. Protein synthesis always occurs on
two adjacent sites of the ribosome.

[3] TERMINATION
Translation continues until a stop codon is reached. There is no tRNA that contains an
anticodon complementary to any of the three stop codons (UAA, UAG, and UGA), so protein
synthesis ends and the protein is released from the ribosome. Often the first amino acid in the
chain, methionine, is not needed in the final protein and so it is removed after protein synthesis
is complete.

Figure 7 depicts the main features of translation.

Figure 7 Translation—The Synthesis of Proteins from RNA

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Figure 8 shows a representative segment of DNA, and the mRNA, tRNA, and amino acid
sequences that correspond to it.

Figure 8 Comparing the Sequence of DNA, mRNA, tRNA, and a Polypeptide

Sample Problem 17.3

Predicting tRNA Anticodons from the mRNA Sequence

What sequence of amino acids would be formed from the following mRNA sequence:
5' CAA AAG ACG UAC CGA 3'? List the anticodons contained in each of the needed tRNA
molecules.

Use the Genetic Code table to determine the amino acid that is coded for by each codon. The
anticodons contain complementary bases to the codons: A pairs with U, and C pairs with G.

Problem 9

Sample Problem 17.4

Predicting the Polypetide from the DNA Template Strand

What polypeptide would be synthesized from the following template strand of DNA:
3' CGG TGT CTT TTA 5'?

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To determine what polypeptide is synthesized from a DNA template, two steps are needed.
First use the DNA sequence to determine the transcribed mRNA sequence: C pairs with G, T
pairs with A, and A (on DNA) pairs with U (on mRNA). Then use the codons in the Genetic
Code table to determine what amino acids are coded for by a given codon in mRNA.

Problem 10

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