Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 1

Biological Science Canadian 2nd Edition

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Chapter 16 – Transcription, RNA Processing, and Translation

Learning Objectives: Students should be able to …

• Relate the structure of RNA polymerase to its function in transcription.
• Describe the steps in initiation, elongation, and termination of
transcription and translation.
• Explain how RNA is processed in eukaryotes.
• Relate the structure of ribosomes and tRNA to their functions in
translation.

Lecture Outline
Proteins are the stuff of life and play many roles.
• Proteins control most cell processes like chemical reactions and also
give cells their structure and shape.
• Cell function is dependent on protein function.
• If one or more proteins do not work correctly, the cell may become
abnormal and die.
• Proteins are synthesized in a two-step process: transcription of genes
into messenger RNAs and translation of messenger mRNAs into
proteins.
I. An Overview of Transcription
A. RNA polymerase enzyme
1. This enzyme is responsible for synthesizing RNA from DNA.
2. The enzyme uses only one of the DNA strands as a template.
a. This is called the template strand.
b. The other strand is called the nontemplate or coding strand.
c. The coding strand matches the mRNA sequence, except that it
has thymine where the mRNA has uracil.
B. Characteristics of RNA polymerase

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 2

1. RNA polymerase reads the DNA template and synthesizes a

complementary RNA strand. (Fig. 16.1)
2. It builds RNA in the 5' → 3' direction by reading the DNA template.
3. It does not require a primer to begin RNA synthesis.
4. Bacteria have one RNA polymerase; eukaryotes have three distinct
types: pol I, pol II, and pol III. (Table 16.1)
a. RNA polymerase I transcribes genes that code for ribosomal
RNAs.
b. RNA polymerase II transcribes genes that code for proteins; thus,
it synthesizes mRNAs.
c. RNA polymerase III transcribes genes that code for tRNAs and
other small RNAs.
C. Initiation: How does transcription begin?
1. In bacteria, a sigma protein binds to RNA polymerase before
transcription begins.
a. RNA polymerase + sigma = holoenzyme.
b. RNA polymerase is the core enzyme. (Fig. 16.2a)
2. David Pribnow studied promoters.
a. Sigma binds tightly to specific regions of DNA called promoters.
b. Pribnow analyzed the base sequence of promoters
(1) Promoters are 40−50 base pairs long.
(2) They have a series of bases similar or identical to TATAAT,
known as the –10 box
(3) The –10 box is 10 base pairs upstream from where
transcription will start (the +1 site).
(4) Another conserved sequence, TTGACA, occurs in the same
promoters about 35 bases upstream of the start site; it is
called the –35 box.
(5) In eukaryotic cells, most promoters include a unique
sequence called the TATA box, centred about 30 base pairs
upstream from the transcription initiation site.
c. Researchers found that sigma is required to facilitate RNA
polymerase binding to DNA.
d. The holoenzyme binds to DNA at specific locations called
promoters.
e. Promoters are sites on the DNA template where transcription
begins.
f. Sigma appeared to be responsible for guiding RNA polymerase
to promoters.
3. The role of sigma subunits and basal transcription factors
a. Transcription begins when sigma binds to the –35 and the –10
boxes. (Fig. 16.2b)
b. Bacteria have several different types of sigma proteins that each
bind to different promoters, determining which genes are
transcribed at a given time.
c. Eukaryotic basal transcription factors

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 3

(1) Analogous to sigma proteins in prokaryotes.

(2) Involve many proteins
(3) Not part of a holoenzyme
(4) Bind to the appropriate region of DNA
(5) Followed by RNA polymerase binding
4. Events inside the holoenzyme
a. After sigma binds to a promoter for a bacterial gene, the DNA
double helix opens.
b. The template strand is threaded through a channel in RNA
polymerase that leads to the active site. (Fig. 16.3, steps 1 + 2)
c. Ribonucleoside triphosphates (NTPs) enter another channel in
RNA polymerase, move to the active site, and are incorporated
into the mRNA when they are complementary to the template
strand.
d. Sigma is released once RNA synthesis is under way.
D. Elongation and termination
1. Elongation
a. RNA polymerase moves in the 3' → 5' direction along the
template DNA strand
b. In the interior of the enzyme, a group of amino acids called the
rudder helps steer the template and non-template strands
through channels inside enzyme. (Fig. 16.3, step 3)
c. RNA polymerase catalyzes the addition of the nucleotide to the
3' end of the growing RNA molecule at a rate of about 50
nucleotides per second.
d. It inserts a uracil whenever it encounters adenine in the
template DNA.
e. A group of amino acids called the enzyme’s zipper helps
separate the new strand from the template strand.
f. An enzyme’s structure is correlated with its function.
(1) Double-stranded DNA goes into and out of one groove.
(2) NTPs enter another channel.
(3) The growing RNA structure exits through the rear.
2. Termination
a. Specific sequences in template DNA act as termination sites.
(1) In bacteria, the bases in the transcriptional termination
sequence form complementary base pairs.
(2) This results in a hairpin structure, which causes the RNA
strand to separate from the RNA polymerase, terminating
transcription. (Fig. 16.4)
b. RNA polymerase and the mRNA strand are released from the
DNA template.
3. Students should be able to draw the RNA polymerase
holoenzyme; label sigma and the RNA polymerase core
enzyme and describe their function; and diagram the
initiation, elongation, and termination phases of transcription.

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 4

II. RNA Processing in Eukaryotes

A. The unexpected discovery of eukaryotic genes in pieces
1. In prokaryotes, when transcription of mRNA is complete, the
mRNA is ready to be converted into a protein.
2. In eukaryotes, pre-mRNA is produced by transcription, and this
must be processed before translation can occur.
3. Eukaryotic genes have intervening sequences called introns.
a. The protein-coding region of eukaryotic genes is interrupted by
stretches of noncoding DNA.
b. Noncoding sequences must be disposed of to make a functional
mRNA.
c. Eukaryotic gene organization is very different from that in
prokaryotes.
4. Phillip Sharp and colleagues detected noncoding regions in genes.
a. They mixed together mRNA and DNA.
b. Then they incubated the mixture under conditions that promote
hybridization of the mRNA to its DNA template.
c. Following hybridization, they used electron microscopy to
observe the molecules in the solution.
d. Result: All of the mRNA was paired to DNA, but some of the
DNA looped out and was unpaired to the mRNA. (Fig. 16.5a)
e. Conclusion: The template DNA had stretches of nucleotides
that were not present in the mRNA, so they could not hybridize
and consequently looped out away from the mRNA. A 1:1 ratio
of nucleotides did not exist between the DNA and the mRNA.
(Fig. 16.5b)
5. Walter Gilbert called the expressed portions of genes (translated
regions) exons and the intervening portions introns.
B. RNA splicing
1. Eukaryotic genes are first transcribed into a primary transcript that
contains both introns and exons. (Fig. 16.6a)
2. Intron splicing (removing the extra sequences) occurs inside the
nucleus.
3. Intron splicing is catalyzed by a complex of proteins and small
RNAs (snRNPs⎯that is, small nuclear ribonucleoprotein particles,
or “snurps”). (Fig. 16.6b, step 1)
a. snRNPs assemble on the primary mRNA transcript, forming a
spliceosome. (Fig. 16.6b, step 2),
b. The intron forms a loop that breaks when a specific adenine
nucleotide in the intron RNA attacks the 5' end of the intron.
c. The spliceosome mediates breakage of the intron at its 5' end,
and a loop forms. (Fig. 16.6b, step 3)
d. The loop is excised, and a phosphodiester bond links the exons
on either side. (Fig. 16.6b, step 4)
e. The excised intron is usually degraded to ribonucleotide
monophosphates.

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 5

C. Adding caps and tails to transcripts

1. A cap of 7-methylguanylate-P-P-P is attached to the 5' end of each
mRNA. (Fig. 16.7)
a. It serves as a recognition signal for the translational machinery.
b. It protects the transcript from degradation.
2. A tail, consisting of 100−250 adenines (“poly(A) tail”), is added to
the 3' end of mRNA.
3. The coding sequence is flanked at the 5’ and 3’ ends by sequences
that are not destined for translation, known as untranslated
sequences (UTRs).
4. Caps and tails protect mRNAs from degradation by ribonucleases
and increase the efficiency of translation.
5. Similarities and differences between eukaryotic and prokaryotic
transcription are summarized in Table 16.2.

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III. An Introduction to Translation

A. Ribosomes are the site of protein synthesis.
1. Translation is the conversion of a sequence of nucleotides in an
mRNA into a sequence of amino acids in a protein.
2. Cells that synthesize lots of protein have lots of ribosomes, and
vice versa. Based on this correlation, researchers proposed that
ribosomes are the site of protein synthesis.
3. Roy Britten and colleagues tested ribosomes as the site of protein
synthesis.
a. They conducted a pulse-chase experiment with 35S to label
proteins and track their locations at various times during and
after translation.
b. Results:
(1) Immediately after giving the pulse, the researchers found
radioactivity in ribosomes.
(2) Two minutes later, they found radioactivity only in free
proteins.
c. Conclusion: Protein synthesis occurs at the ribosome, and then
the protein is released from the ribosome.
B. Comparing translation in bacteria and eukaryotes
1. Electron microscopy of Escherichia coli DNA being transcribed
shows that:
a. Ribosomes attach to mRNA even before transcription is
complete, while the mRNA is still linked to DNA.
b. Ribosomes translate mRNA as it is being synthesized by RNA
polymerase; transcription and translation occur simultaneously
in bacteria. (Fig. 16.8a, b)
c. Multiple ribosomes attach to each mRNA, forming a
polyribosome.
d. Transcription and translation are physically connected because
there is no nuclear membrane.
2. In eukaryotes:
a. mRNAs are released from DNA in the nucleus.
b. mRNAs are processed before leaving the nucleus.
c. mRNAs become associated with ribosomes in the cytoplasm;
transcription and translation are separate processes in
eukaryotes. (Fig. 16.9)
C. How does an mRNA triplet specify an amino acid?
1. Hereditary instructions are contained in sequences of nucleotides,
which are then converted into a sequence of amino acids.
2. Early hypothesis: Nucleotides of an mRNA codon chemically
combine with amino acid side chains through shape or charge
interactions. (Fig. 16.10a)
3. Crick proposed an alternate hypothesis: Adapter molecules hold
amino acids in place while interacting with an mRNA codon. He
predicted the existence of transfer RNA molecules. (Fig. 16.10b)

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IV. The Structure and Function of Transfer RNA

A. Requirements for translation
1. Ribosomes provide the machinery.
2. mRNAs contribute the message.
3. Amino acids are the building blocks.
4. ATP and GTP provide energy.
5. tRNA is important.
a. A tRNA that becomes covalently linked to an amino acid is
called an aminoacyl tRNA.
b. The addition of amino acids to tRNAs (charging a tRNA) is
catalyzed by aminoacyl tRNA synthetases. (Fig. 16.11)
c. Each of the 20 amino acids has a different aminoacyl tRNA
synthetase and one or more tRNAs.
d. Amino acids are transferred from aminoacyl tRNAs to proteins
synthesized in ribosomes. (Fig. 16.12)
B. What do tRNAs look like?
1. Sequencing revealed that tRNAs are 75−85 nucleotides long.
2. Secondary structure was inferred from the nucleotide sequence.
(Fig. 16.13)
a. Hydrogen bonding occurs between complementary bases in
different parts of the tRNA molecule.
(1) Short, double-stranded regions form.
(2) The tRNA assumes a cloverleaf shape of stems and loops.
Stems are double-stranded; loops are single-stranded
regions.
b. All tRNAs have the sequence CCA at their 3' end; it is a binding
site for an amino acid.
c. One of the loops has a triplet of bases that varies in each tRNA;
this is the anticodon (i.e., the nucleotides that form base pairs
with an mRNA codon).
3. X-ray crystallography shows tertiary structure—the 3-D
arrangement of atoms.
a. The tRNA cloverleaf folds over, producing an L-shaped
structure.
b. Each tRNA has a distinct anticodon and amino acid.
c. The anticodon and amino acid attachment sites are separated
by a precise distance.
d. Students should be able to make a rough sketch of a tRNA
with and without an amino acid attached, and explain the
relationship between the anticodon of a tRNA and a codon
in an mRNA.
C. How many tRNAs are there?
1. There are 61 different mRNA codons but only about 40 tRNAs.
2. How can an mRNA codon for which there is no tRNA be
translated?
3. Crick’s wobble hypothesis:

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 8

a. Many amino acids are specified by more than one codon.

b. Codons for the same amino acid tend to differ only in the third
position.
(1) Example: Codons 5'-CAA-3' and 5'-CAG-3' code for
glutamine.
(2) A tRNA with the anticodon 3'-GUU-5' can pair with either 5'-
CAA-3' or 5'-CAG-3'.
(3) The third codon position is the wobble position.
V. The Structure and Function of Ribosomes
A. Characteristics of protein synthesis
1. The sequence of bases in an RNA message is translated into a
sequence of amino acids in a polypeptide.
2. The conversion of each mRNA codon begins when the anticodon
of an aminoacyl tRNA binds to the codon.
3. The conversion is complete when a peptide bond forms between
the tRNA’s amino acid and the growing polypeptide.
4. Conversion occurs inside a ribosome, which is composed of two
subunits. (Fig. 16.14)
a. There is a larger 50S subunit and a smaller 30S subunit.
b. Both subunits are composed of multiple RNA molecules and
numerous proteins.
c. The small subunit holds the mRNA in place during translation.
d. The large subunit is where peptide bond formation takes place.
e. The large ribosomal subunit has three tRNA binding sites. (Fig.
16.14a)
(1) During translation, the acceptor or aminoacyl (A) site holds
the tRNA with an amino acid that is about to be added to
the polypeptide.
(2) The peptidyl (P) site holds the tRNA that is holding the
growing polypeptide chain.
(3) The exit (E) site holds the empty tRNA that is about to be
released.
5. Three-step sequence of protein synthesis: (Fig. 16.15)
a. Aminoacyl tRNA diffuses into the A site; its anticodon binds to a
mRNA codon
b. A peptide bond forms between the amino acid on the aminoacyl
tRNA in the A site and the growing polypeptide (held by a tRNA)
in the P site.
c. The ribosome moves ahead, and all the tRNAs move one
position down the mRNA. The tRNA in the E site exits, the
tRNA in the P site moves to the E site, and the tRNA in the A
site moves to the P site.
6. The polypeptide has grown by one amino acid.
7. The process occurs up to 20 times per second in bacteria and
about 2 times per second in eukaryotes.

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8. Protein synthesis begins at the amino end (N-terminus) of the

protein and proceeds to the carboxy end (C-terminus).
B. Initiating translation
1. In bacteria, the 30S ribosomal subunit binds to a sequence on
mRNA about six nucleotides upstream from an AUG start codon.
2. The sequence to which the 30S subunit binds is the Shine-
Dalgarno sequence and contains all or part of 5-AGGAGGU-3.
3. The initial interaction is mediated by initiation factors. In
eukaryotes, initiation factors bind to the 5 cap on mRNA.
4. An aminoacyl tRNA with N-formylmethionine (f-Met) binds to the
AUG codon. (Fig. 16.15, step 2) In eukaryotes, the first amino acid
is normal methionine.
5. Initiation is complete when the large ribosomal subunit binds and
the tRNA-bearing f-Met occupies the P site.
C. Elongation: extending the polypeptide (Fig. 16.16)
1. After the ribosome subunits join, a new aminoacyl tRNA binds to
the mRNA codon in the A site of the ribosome (aminoacyl site).
This reaction requires GTP.
2. A peptide bond forms between the carboxyl end of the N-
formylmethionine amino acid in the P site and the amino end of the
amino acid in the A site.
3. Is the ribosome an enzyme or a ribozyme?
a. The active site of the ribosome is composed of rRNA, so the
ribosome is a ribozyme.
b. The observation that protein synthesis is catalyzed by RNA
provides support for the RNA world hypothesis: Life began with
RNA molecules.
4. Moving down the mRNA
a. The tRNA in the P site moves to the E site (exit site).
b. The new peptidyl tRNA moves from the A site to the P site.
c. The empty tRNA is ejected from the E site.
d. Translocation requires energy in the form of GTP and
assistance from elongation factors.
e. Translocation of the mRNA occurs, moving it through the
ribosome in the 5 → 3 direction.
5. The three-part cycle of elongation (arrival of aminoacyl tRNA,
peptide bond formation, translocation) repeats over and over.
6. Once elongation is under way, additional ribosomes can bind to the
translational start site and begin translating.
D. Terminating translation (Fig. 16.17)
1. Three stop codons are included in the genetic code: UAA, UAG,
and UGA.
2. The ribosome reaches any one of these codons on an mRNA.
a. Then release factor proteins enter the A site.
b. The completed polypeptide is released from the tRNA in the P
site.

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 10

c. The ribosome separates from the mRNA.

d. The two ribosomal subunits dissociate from each other, allowing
subunits to attach to the start codon of another message so that
translation can begin again.
E. Canadian Research 16.1: RNA synthesis in mitochondria
1. The mitochondria of Drosophila melanogaster produce five primary
RNA molecules that are cleaved at specific sites to make 11
mRNAs, 22 tRNAs and 2 tRNAs.
2. These mitochondria make 13 of the thousand proteins they require
to function.
F. Post-translational modifications
1. Folding
a. Protein shape is critical to function.
b. How does folding occur to produce the 3-D structure of an
active enzyme?
c. Thermodynamic hypothesis: Proteins fold into their most stable
energetic state.
d. Molecular chaperones facilitate protein folding.
2. Chemical modifications
a. Many proteins go through the ER and Golgi apparatus and have
sugar and/or lipid groups added.
b. Many proteins have phosphate groups added or removed
during their lifetimes. The addition or removal of this large
negatively charged group changes a protein’s structure and
thus changes its function.

Chapter Vocabulary

transcription TATA box

RNA polymerase I (pol I) basal transcription factor
RNA polymerase II (pol II) nucleoside triphosphate (NTP)
RNA polymerase III (pol III) initiation phase of transcription
template strand elongation phase of transcription
nontemplate or coding strand rudder
initiation zipper
sigma protein termination phase of transcription
holoenzyme hairpin structure
core enzyme transcription termination signal
promoters exon
downstream intron
upstream primary RNA transcript
TATAAT RNA splicing
–10 box precursor or pre-mRNA
TTGACA mature mRNA
–35 box

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 11

small nuclear ribonucleoprotein aminoacyl (A) site

(snRNP) exit (E) site
spliceosome peptidyl (P) site
5' cap (7-methylguanylate-P-P-P) wobble hypothesis
3' poly(A) tail translation initiation
untranslated region (UTR) Shine-Dalgarno
pulse-chase experiment sequence/ribosome binding site
translation translation initiation factors
ribosome AUG codon
polyribosome ribosomal RNA N-formylmethionine (f-Met)
(rRNA) translation elongation
messenger RNA (mRNA) translation elongation factors
transfer RNA (tRNA) GTP
aminoacyl tRNA peptide bond formation
aminoacyl tRNA synthetase ribozyme
peptidyl tRNA translocation
codon translation termination
anticodon release factors
CCA sequence stop codon
X-ray crystallography post-translational modification
ribosome protein folding
large (50S) subunit molecular chaperones
small (30S) subunit phosphorylation

Lecture Activities

What Makes a Firefly Glow?

Estimated duration of activity: 5–10 minutes
The website http://learn.genetics.utah.edu/content/begin/dna/firefly/
has a fun and interesting review of transcription and translation in the
context of the question What makes a firefly glow? If your classroom is
computer equipped, this would be a nice website to go through with your
students as a review.

An In-Class Demonstration: Translation

Estimated duration of activity: 15 minutes
This activity is especially suited to large lecture classes, particularly if there
is enough space at the front of the room to assemble sizable groups of
students. (You can scale down the activity presented here for smaller
classes or smaller rooms.)
This activity involves turning students into ribosomes, messenger
RNAs, protein factors, ribozymes, aminoacyl tRNAs, and aminoacyl
synthetases. You can assemble some relatively simple, inexpensive
identification labels in advance (suggestions follow), and you can get a large

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 12

number of students in the class directly involved in acting out the process of
translation. This activity may seem elementary to you, but students will
welcome the break from lecture and appreciate the chance to visualize a
complex biological process. If you don’t have time to put the activity
together, assign it to a teaching assistant and have the TA direct the activity
during class.
Procedure:
1. Have 24 students come to the front of the room to form an mRNA
molecule. The 24 students should form a long, straight line facing the rest
of the class. Start with the first student on the far left side (stage left) and
proceed to the right.
a. Give student 1 a card to hold up that says 5.
b. Leave student 2 unlabelled (this person is part of the mRNA 5' leader
sequence).
c. Give students 3, 4, 5, and 6 each a label to wear that is marked SD
(Shine-Dalgarno sequence).
d. Leave students 7 and 8 unlabelled (they are the rest of the 5' leader
sequence).
e. Label students 9, 10, and 11 as A, U, and G (respectively) to mark
them as the AUG codon, which specifies methionine.
f. Label students 12, 13, and 14 as C, C, and A (respectively) to mark
them as the CCA codon, which specifies proline.
g. Label students 15, 16, and 17 as G, C, and A (respectively) to mark
them as the GCA codon, which specifies alanine.
h. Label students 18, 19, and 20 as U, G, and A (respectively) to mark
them as the UGA stop codon.
i. Leave students 21, 22, and 23 unlabelled (they are the 3' trailer
sequence of the mRNA).
j. Give student 24 a card to hold up that says 3.
2. Next, have nine students come to the front of the room to form the 30S
subunit of the ribosome. These students should form a group in front of
the 5' end of the mRNA molecule (between the mRNA and the audience).
a. Three of the nine students will be the E site (label each with an E).
Have them stand at the extreme 5' end.
b. Three students will be the P site (label each with a P). Have them
stand just to the right of the E site.
c. Three students will be the A site (label each with an A). Have them
stand just to the right of the P site.
3. Have the 30S subunit students link arms and, as a group, bind to the
Shine-Dalgarno sequence in the 5' leader of the mRNA.
a. They can be assisted by a couple of students labelled IF (initiation
factor).
b. The 30S subunit students should pause at the Shine-Dalgarno
sequence and then spread out across the front of the mRNA so that
the three 30S students labelled P are positioned in front of the three
mRNA students labelled AUG.

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4. Off to one side of the mRNA, some students may be labelled as various
transfer RNAs and others as aminoacyl synthetases. Each of them will
hold a card specifying a single amino acid.
a. The aminoacyl synthetase (labelled Met aa-synth) should give a card
that says MET to the person labelled tRNA-met.
b. The tRNA-met student, who is now holding the MET card, should go
behind the mRNA molecule, directly behind the students labelled
AUG.
c. The tRNA-met student may be assisted in positioning by one or more
IFs.
5. Now, assemble a group of 11 students behind the mRNA molecule and
the tRNA-met student.
a. Student 1 closest to the 5' end of the mRNA should be unlabelled.
b. The next three students will be the E site.
c. The next three students will be the P site.
d. The next student will be labelled as the 23S ribozyme.
e. The next three students will be the A site.
f. One student at the 3' end will be unlabelled.
g. Have the students link arms in order and then line up so that the 50S
E site students are directly aligned with the 30S E site students, and
so forth. At this point, the ribosome is completely assembled on the
mRNA, and the tRNA-met student is positioned between the 30S and
50S P-site students.
6. Next, a person labelled tRNA-pro should pick up a card labelled PRO
from the appropriate aa-synth and go to the A site of the mRNA
molecule.
7. The individual on the 50S ribosome who is labelled 23S ribozyme then
forms a peptide bond between the card labelled MET and the card
labelled PRO (staple the cards together or have the ribozyme string them
together through previously punched holes in the cards).
8. After the peptide bond forms, the cards are handed to the person labelled
tRNA-pro.
9. Translocation: All of the mRNA students link arms and each takes three
steps to the left (i.e., in the direction of the 5' end).
a. The tRNA students should stay with the AUG and CCA sites on the
mRNA.
b. Students labelled EF (elongation factor) can assist the mRNA
movement.
c. When translocation is complete, the tRNA-met student should be in
the E site of the ribosome, and the tRNA-pro student (holding the
MET-PRO peptide) should be located in the P site.
10. The tRNA-met student now leaves the E site.
11. A student labelled tRNA-ala now picks up the ALA card from the
appropriate synthetase, enters the A site, and binds to the GCA codon,
where the ribozyme can form a peptide bond.
12. Repeat steps 7–10, until the UGA stop codon is positioned at the A site.

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a. Students labelled RF (release factor) enter the A site, instead of a

tRNA.
b. Release the completed peptide (of three amino acids) from the tRNA
at the A site.
c. Last, the 50S ribosome subunit students all link arms and move as a
group away from the mRNA, as do the 30S students, to complete one
round of translation.

Suggestions for labels:

• Make the labels large (use 8.5-by-11-inch paper). Design them to be
attached to the person’s chest using safety pins, tape, or some other
rapid, easy method.
• For the cards that represent amino acids, use paper or stiffer cardboard,
keeping in mind that they’ll need to be quickly and easily linked together.
• Use different colours of papers to designate different items. All the labels
for students who will be part of the mRNA could be on red paper, the
amino acid cards could all be orange, the 30S ribosome labels could be
green, the 50S blue, and so on.
• All labels and cards may be photocopied onto coloured paper from a
master sheet, or printed from a computer with coloured letters on white
paper or black letters on coloured paper.
For the procedure as outlined in steps 1–12, you’ll need the following labels
and cards:
a. Labels designed to go on a person’s chest
18 red labels for the mRNA students:
• 4 marked SD
• 3—each one marked with either A, U, or G
• 3—each one marked with either C, C, or A
• 3—each one marked with either G, C, or A
• 3—each one marked with either U, G, or A
• 2 unmarked red labels for the leader and trailer students
9 green labels for the 30S students:
• 3 marked E
• 3 marked P
• 3 marked A
11 blue labels for the 50S students:
• 2 unmarked
• 3 marked E
• 3 marked P
• 3 marked A
3 purple labels for the tRNA students:
• 1 marked tRNA-met
• 1 marked tRNA-pro
• 1 marked tRNA-ala
3 white labels for the aminoacyl synthetase students:
• 1 marked MET aa synth

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• 1 marked PRO aa synth

• 1 marked ALA aa synth
Optional: Labels marked IF, EF, and RF (for initiation, elongation, and
release factors), if you choose to have students perform these roles.
b. Cards to represent amino acids
• 1 marked MET
• 1 marked PRO
• 1 marked ALA
c. Cards for either end of the mRNA molecule
• 1 marked 5'
• 1 marked 3'

Discussion Ideas

Identifying the Products of Translation

Estimated duration of activity: 15 minutes
Students have difficulty recognizing which molecules involved in translation
are also the products of protein synthesis. For example, many students
think that amino acids – but not the enzymes involved in protein synthesis –
are produced by translation. Ask your students to discuss which of the
following molecules are the products of translation. Tell them to include
molecules that are subject to further modification after their initial synthesis.
• The amino acid glycine
• Ribosomal proteins
• Transfer RNA
• The digestive enzyme pepsin
• RNA polymerase
• Ribozymes

Understanding Prions
Estimated duration of activity: 45–60 minutes
Because the central focus of this chapter is the link between nucleic acids
and proteins, this might be a good time to consider the differences between
molecules that are catalysts (proteins and RNA) and templates (DNA and
RNA). Prions are unusual molecules because they seem to be able to
perform both functions. How are prions different? Where do they fit in? You
may want to pose these questions to the whole class, to small groups, as
challenge questions for pairs of students, or as thought problems to prepare
for a general discussion.
Question 1: What makes DNA and RNA good templates?
Possible answers:
• DNA and RNA can act as blueprints for new synthesis from monomers.
• When DNA double strands open and beginning primers are established,
synthesis proceeds in a predictable way, making a complementary copy
of each existing strand.

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 16

• The start complex that includes RNA polymerase binds to the promoter
region of a gene in the DNA sequence, and the RNA molecule is
synthesized to be complementary to the DNA strand that follows the
promoter position.
• DNA and RNA have very predictable structures under ordinary
conditions.
Question 2: Why are proteins considered poor templates?
Possible answers:
• Proteins cannot act as blueprints for new synthesis from monomers.
• Proteins do not have complementary pieces that can act as a template.
• Proteins have complex, three-dimensional structures that can vary
drastically even under physiological conditions.
• Proteins do not have a means to regularly transmit their blueprints
through generations.
Question 3: Why are proteins the best catalysts?
Possible answers:
• Proteins have the ability to change three-dimensional shapes drastically,
often with very small differences in their primary structure.
• Proteins have many variable “R” groups in their amino acids to bind to
other molecules in order for changes to occur.
Question 4: What do prions do?
Possible answers:
• Prions are normal proteins in cells. Mutated or misfolded forms exist, and
they apparently can cause normal forms to assume the mutated shape
without intervention of a nucleic acid like RNA or DNA. (You could quiz
students about how they could test this—treating suspensions with
DNase or RNase to see whether the mutated prions still change normal
ones.)
• Cases have now been documented that somehow, these mutated prion
forms present in food can affect normal prions in the brains of those
species exposed.
• Prions seem to act as infectious agents but have no known nucleic acid.
Question 5: Are these prions like catalysts or templates?
Possible answers:
• Prions do not seem to be able to act as templates to form entirely new
molecules using only monomers.
• Prions change shape like other proteins that act as catalysts. The prions
are misfolded compared to the normal protein.
• Prions or some information related to them survive the digestive system,
absorption, and migration through the body to get to the site where they
do damage. The protein that has changed shape is partially protease
resistant.
• The host does not mount an immune response, which suggests that no
virus is associated with the protein.
• Some explanation needs to be found for how the first change in the
normal protein took place. The ability to change shape might be possible,

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 Freeman, Biological Science, 2Ce, Chapter 16 Instructor Guide − 17

at least due to the flexibility of shape for proteins. After all, they are good
catalysts.
• Although the differently folded proteins of the infectious particles are
called “mutant”, are they? Families with inherited forms of the human
disease all have mutations in their normal protein gene.
• In England and France, these infectious agents have apparently crossed
the species barrier from cattle and sheep to humans. This makes them
even more mysterious. This transmission is different from the inherited
type; presumably, some sort of agent is transmitted.
To emphasize the importance of in vitro experiments to biological
research, and to focus on the differences between transcription and
translation, you can present the following challenge question to the class.
You can also make a connection to DNA replication, which was discussed in
Chapter 14, by asking the question given in part c.
Question 6: How is a cell-free transcription system different from a cell-free
translation system?
a. What purified components would you need to combine to achieve
transcription in vitro?
Answer: Template DNA that contains one or more genes (with their
promoters)
Ribonucleotides—ATP, GTP, CTP, and UTP
RNA polymerase enzyme
If the gene is prokaryotic—a cell fraction that contains sigma
factors
If the gene is eukaryotic—a nuclear extract that contains
transcription factors
b. What purified components would you need to combine to achieve
translation in vitro?
Answer: Ribosomes
Messenger RNA
Amino acids (all 20)
GTP and ATP to provide energy
A cell fraction that contains aminoacyl tRNAs, aminoacyl
synthetases, initiation factors, elongation factors, and
termination factors
c. How is an in vitro DNA replication system different from transcription and
translation systems? What components would be needed to achieve
replication in vitro?
Answer: Template DNA
Deoxyribonucleotides—dATP, dGTP, dCTP, and dTTP
DNA polymerase
A protein fraction from bacterial cells that contains helicases,
topoisomerases, single-stranded binding proteins, and primase

© 2014 Pearson Canada, Inc.