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Biology 30
Protein Synthesis
General Outcome C3: Students will explain classical genetics at the molecular level.
A. The Genetic Code
Polypeptides are long chains of amino acids. As polypeptides grow longer, or are
attached together, they are called proteins. The sequence of amino acids in a polypeptide
determines the characteristics and nature of the protein. Therefore, by ordering the
sequence of amino acids, the DNA controls the kinds of proteins, which are built by the
cell.
The language is composed of series of nucleotides to represent information.
DNA has only four kinds of nucleotides, but must code for 20 different amino acids used
to build polypeptides. Just as a specific series of dots and dashes is used to represent one
letter in Morse code, a specific series of nucleotides is used as the code for each amino
acid. This series of nucleotides is called a codon. A gene, which is the “blueprint” for a
polypeptide, is a long series of codons. The number of codons in different genes varies
depending upon the size of the polypeptide chain to be built.
Proteins are large, complex molecules made up of many amino acids joined together.
Proteins can be classified into two common types:
1. Functional Proteins – may be enzymes, antibodies, or hormones. Enzymes are
needed to lower the activation energy required for chemical reactions to occur
inside the cells of organisms. Without the thousands of specific enzymes life
wouldn’t be possible. Antibodies defend the body against foreign substances, and
hormones help control many processes in organisms.
2. Structural Proteins – include muscles, parts of the cell membranes, hair,
tendons, and ligaments.
How many nucleotides are there in each codon?
If there were only one, there could only be four codes, representing only four different
amino acids.
How many different codons can be made if there are two nucleotides in each, for
example, AA, AT, AC, AG, and so on? Will this be enough to represent all 20 amino
acids?
Since it is only possible to make 16 different codons if two nucleotides are used for each
(4x4=16), there must be at least three nucleotides in each codon. This means that there
are 64 possible combinations (4x4x4).
A series of biochemical studies in the early 1960’s confirmed this number, and also
established the specific nucleotide composition of each codon.
Proteins are found in every living cell. It is used as building blocks for all parts of the cell
(membranes, organelles, nucleic acids). Cells are responsible for producing their own
proteins. The blueprint for the protein is contained in the nucleus (DNA) and the protein
is manufactured in the ribosome.
By linking defective enzymes (protein molecules) to genetic mutations scientists Beadle
& Tatum came up with the “one gene-one enzyme” gene theory. Each protein is
specific to that gene and to that organism.
Beadle and Tatum set out to provide experimental proof of the connection between genes
and enzymes. They hypothesized that if there really was a one-to-one relationship
between genes and specific enzymes, it should be possible to create genetic mutants that
are unable to carry out specific enzymatic reactions. To test this theory, they exposed
spores of Neurospora crassa (a bread mold) to X-rays or UV radiation and studied the
resulting mutations. The mutant molds had a variety of special nutritional needs. Unlike
their normal counterparts, they could not live without the addition of particular vitamins
or amino acids to their food. For example, normal Neurospora requires only one vitamin
(biotin), but mutants were created that also required thiamine or choline.
Genetic analysis showed that each mutant differed from the original, normal type by only
one gene. Biochemical studies showed that the mutants seemed to be blocked at certain
steps in the normal metabolic pathways. Their cells contained large accumulations of the
substance synthesized just prior to the blockage point
As Beadle and Tatum had predicted, they were able to create single gene mutations that
incapacitated specific enzymes, so that the molds with these mutations required an
external supply of the substance that the enzyme normally produced, and the substance
that the enzyme normally used, piled up in the cell. These results led them to the one
gene/one enzyme hypothesis, which states that each gene is responsible for directing the
building of a single, specific enzyme.
B. Manufacture of Proteins
Nucleus of cell
Chromosomes – parts of the cell which carry hereditary information.
DNA – DNA molecules make up chromosomes. The DNA molecules transfer the
information that determines the composition of proteins.
Gene – portion of the DNA molecule which contains the set of instructions for
manufacturing a specific protein.
Codons – long series of codons makes up a gene.
3 nucleotides – adenine, thymine, cytosine, and guanine.
Amino acid – 3 nucleotides (codon) on the mRNA specify for a specific amino acid
transported to ribosomes by tRNA (note: some amino acids can be specified by more than
one codon).
Polypeptide – amino acids linked together via peptide bonds to form a polypeptide called
a protein.
Protein
C. RNA – ribonucleic acid
Like DNA, RNA is a polynucleotide chain containing only four different types of
nucleotides. However, there are four major differences between these two molecules:
1. RNA is a single stranded molecule.
2. DNA has a ribose sugar that lacks one oxygen atom (the meaning of the name
“deoxyribose”), compared to RNA’s “ribose” which has a full complement of
oxygen.
3. In RNA the nitrogen base uracil (U) – (a single ring pyrimidines) replaces the
thymine found in DNA.
 What is the RNA strand corresponding to the DNA strand below?
 ACC GTC CCT CAT AGT CGT AAT CGT ACC GTT ACC GAC

4. RNA may be found in the nucleus or the cytoplasm, but DNA never leaves the
nucleus.
D. Types of RNA
There are three types of RNA
1. mRNA – messenger RNA – copies a portion of the DNA and takes it to the
ribosome where the message will be read.
2. tRNA – transfer RNA – picks up amino
acids and takes them to the ribosome to
create the polypeptide. Figure to the right.
3. rRNA – ribosomal RNA - located in the
ribosome. The function of the rRNA is to
provide a mechanism for decoding mRNA
into amino acids and to interact with the
tRNA’s during translation.
E. Protein Synthesis
Protein synthesis involves two processes:
1. Transcription
2. Translation
There can be thousands of
amino acids in a single
protein chain. The
sequence of amino acids
determines the type of
protein. It is a very
sensitive process, if even
one amino acid is out of
sequence it can affect the
entire protein. For example,
sickle cell anemia occurs
because the amino acid
valine is substituted for the
amino acid glutamic acid.
1. Transcription
Since DNA cannot leave the nucleus, a copy of a gene must be made. One strand of the
DNA is copied onto RNA.
Transcription can be divided into three distinct phases.
a. Initiation
 RNA polymerase binds to the segment to be transcribed and opens the double
helix.
 RNA binds to a region in front of a gene termed the promoter. This indicates
which strand to transcribe and where RNA polymerase should start.
b. Elongation
 The formation of mRNA by RNA polymerase
 This is similar to DNA replication, except the mRNA contains uracil instead of
thymine.
c. Termination
 RNA polymerase stops transcribing a gene when it reaches the termination
sequence of bases.
 Transcription stops and the mRNA strand peels off the DNA and moves to a
ribosome in the cytoplasm.
 After the copy is released, the DNA zips back up.
Characteristics of the Genetic Code
mRNA Codon Table
First
base
U
UUU
U
phenylalanine
UUC
phenylalanine
UUA leucine
UUG leucine
CUU leucine
C
CUC leucine
CUA leucine
CUG leucine
AUU isoleucine
A
AUC isoleucine
AUA isoleucine
AUG methionine*
Second base
C
UCU serine
UCC serine
UCA serine
UCG serine
A
UAU tyrosine
UAC tyrosine
UAA stop**
UAG stop**
Third
base
G
UGU cysteine
UGC cysteine
UGA stop**
UGG
tryptophan
CCU proline
CAU histidine
CGU arginine
CCC proline
CAC histidine
CGC arginine
CCA proline
CAA glutamine CGA arginine
CCG proline
CAG glutamine CGG arginine
ACU
AAU
AGU serine
threonine
asparagine
AGC serine
ACC
AAC
AGA arginine
threonine
asparagine
AGG arginine
ACA
AAA lysine
threonine
AAG lysine
ACG
threonine
GUU valine
GCU alanine
GAU aspartate GGU glycine
G
GUC valine
GCC alanine
GAC aspartate GGC glycine
GUA valine
GCA alanine
GAA glutamate GGA glycine
GUG valine
GCG alanine
GAG glutamate GGG glycine
* AUG is an initiator codon. It also codes for the amino acid methionine.
** UAA, UAG, and UGA are terminator codons.
The general characteristics of the genetic code can be summarized as follows:
1. All 64 possible codons have a specific meaning. Three of the 64 codons act the
same way that a period does at the end of a sentence. UAA, UAG, and UGA on
the mRNA cause the assembly process to stop and the newly formed polypeptide
to be released. The remaining 61 codons each designate a specific amino acid.
Obviously, several codons must code for the same amino acid. However, each
codon only corresponds to one amino acid. For example, both UUU and UUC
code for phenylalanine; yet both correspond only to phenylalanine, and not to any
other amino acids.
2. Codons, which correspond to the same amino acid, are very similar, usually
sharing the same first two nucleotides.
3. The codon AUG has a dual function. It codes for an amino acid, but also signals
where a translation sequence should start.
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Summary
The copy of the genetic blueprint made during transcription is called mRNA (messenger
ribonucleic acid).
The mRNA carries the information from the nucleus to the ribosomes, where it directs
the manufacture of a polypeptide by the cell’s machinery.
As an analogy, consider a reference library where books can be used but not borrowed.
These books could represent the DNA. When specific information is needed,
photocopies can be made and taken out. In the cell, the equivalent of the photocopying
process makes the messenger RNA as a copy of the DNA. Just as one normally
photocopies only a few pages of a book, the mRNA copy represents only a small segment
of the genetic information contained in the DNA.
A) DNA codons
ATG TCA CCG AAG CGT
TAC AGT GGC TTC GCA
TRANSCRIPTION
B) mRNA codons
AUG UCA CCG AAG CGU
A short segment of DNA is shown in (A). Each DNA codon consists of three
nucleotide pairs. For transcription, one strand of the DNA will serve as a template to
make messenger RNA (mRNA) – (b). The segment of mRNA corresponds to the
DNA segment above.
Transcription in Reverse
Key enzymes in DNA replication
Enzyme group
Function
helicase
cleaves and unwinds short sections of DNA ahead of the replication fork
primase
synthesizes an RNA primer to begin the elongation process
DNA polymerase adds new nucleotides to the 3’ OH group of an existing nucleotide strand;
dismantles the RNA primer; proofreads base pairing
DNA ligase
splices together Okazaki fragments in the lagging strand
Amino acid abbreviations
Amino acid
Three-letter
abbreviation
ala
arg
asn
asp
cys
glu
gln
gly
his
ile
Amino acid
Three-letter
abbreviation
leu
lys
met
phe
pro
ser
thr
trp
tyr
val
alanine
leucine
arginine
lysine
asparagine
methionine
aspartate
phenylalanine
cysteine
proline
glutamate
serine
glutamine
threonine
glycine
tryptophan
histidine
tyrosine
isoleucine
valine
Procedure
1. The illustration shows an imaginary polypeptide produced by a
bacterial cell. Using the tables above, draw one possible nucleotide
sequence for the DNA molecule that contains the gene for this
polypeptide.
2. Translation
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

This is the actual reading of the code and the construction of the protein. For a
cell to synthesize a particular polypeptide, it must assemble the amino acid
building blocks in a specific sequence. This sequence determines the molecules
overall structure and shape, and therefore, its characteristics.
The sequence of codons on the mRNA directs the assembly of the polypeptide,
and ensures that the component amino acids are brought together in the proper
sequence. The message carried by the mRNA is rewritten in the sequence of
amino acids found in the newly constructed polypeptide.
This process is called translation, and consists of three distinct stages.
a) Initiation
 The ribosome binds to the mRNA at the start codon.
 The start (initiator) codon AUG codes for methionine, meaning that all
polypeptides begin with the amino acid methionine (Met).
b) Elongation
 A molecule of transfer RNA (tRNA) serves as an amino acid carrier. Each tRNA
molecule has a site where it can bond to one specific amino acid (A site).
 It also has a triplet sequence of nucleotides, called an anticodon, which is
complimentary to one particular codon found on the mRNA. This site on the
mRNA is called the P site.
 As the tRNA molecule carries an amino acid to the mRNA on the ribosome, it
will only deliver its cargo to one specific address (P site). This address is the
codon, which matches the complimentary sequence of bases on the anticodon.
 A peptide bond will form between the two amino acids.
 The ribosome will move down one codon, so that the second codon on the mRNA
can be read. The corresponding tRNA will be sent out to carry the appropriate
amino acid back to the ribosome.
c) Termination
The ribosome reaches a stop codon (UAA, UAG, UGA).
These codons do not code for an amino acid, which causes the protein synthesis to stop,
releasing the finished protein.
The mRNA may be read hundreds of times forming many copies of the same protein.
Summary
1. Messenger RNA is formed in the nucleus (transcription). It is a sequence of
nucleotides which is complementary to a section of the DNA strand.
2. The mRNA leaves the nucleus and becomes associated with a ribosome. The
ribosome is the site of polypeptide synthesis. The ribosome consists of ribosomal
RNA (rRNA), and many different proteins. The rRNA serves as a framework for
the ribosomal proteins. Together, these molecules play an important role in
binding the mRNA and tRNA molecules.
3. In the cytoplasm there is a pool of amino acids. Each kind of amino acid is linked
to one specific enzyme for each amino acid. ATP supplies the energy.
4. Each tRNA molecule carries its amino acid to the ribosome. The anticodon of the
tree specific nucleotides on the tRNA determines where on the mRNA it will fit.
If the mRNA codon reads AAG, what must the anticodon read?
5. As the amino acids are brought together on the ribosome in sequence, a peptide
bond forms between adjacent amino acid molecules.
6. The tRNA molecule is released into the cytoplasm. It is now free to pick up
another of the same kind of amino acid.
7. When the mRNA codon reads “stop” (UAG, UAA, or UGA), the polypeptide is
released. The mRNA is also released from the ribosome.
A) DNA codons
ATG TCA CCG AAG CGT
TAC AGT GGC TTC GCA
TRANSCRIPTION
B) mRNA codons
AUG UCA CCG AAG CGU
TRANSLATION
C) Protein
MET SER PRO LYS ARG
A short segment of DNA is shown in (A). Each DNA codon consists of three
nucleotide pairs. For transcription, one strand of the DNA will serve as a template to
make messenger RNA (mRNA) – (b). The segment of mRNA corresponds to the
DNA segment above. (C) – The segment of protein corresponds to the codons in the
mRNA, and consequently, to the information in the DNA. Each specific amino acid
is indicated by its short form, eg., LYS = lystine
Simulating Protein Synthesis
Experimental Plan
1. As a group, list the steps that are involved in transcription and translation. For each
step, note the structures, molecules, and events involved.
2. Discuss how you might simulate transcription and translation in your classroom. Your
simulation could take any form. For example, you could prepare an interactive
computer program, write and perform a play, a story or construct a physical model.
3. Once you have agreed on a plan, list the materials and equipment you will need to
carry out your simulation. Assign responsibilities to each member of your group.
Then assemble your materials and prepare your simulation.
Data and Observations
4. Present your simulation to the class. Record any comments you receive from your
classmates.
Transcription and Translation Worksheet
Answer the following questions in the space provided.
1. Name the amino acids that correspond with the following mRNA codons:
a) AGA ________________________
b) GCC_________________________
c) CUU ________________________
d) UGA ________________________
2. A geneticist isolates a strand of DNA containing the following nucleotide sequence:
TACGGTCACATGATT
a) Provide the nucleotide sequence of the mRNA strand transcribed from this
sequence.
_____________________________________________________________________
b) What is the amino acid sequence of the polypeptide produced from this strand of
mRNA?
_____________________________________________________________________
c) What is the nucleotide sequence of the tRNA anticodon that codes for the first
amino acid in the polypeptide?
____________________________________________________________________
3. The same geneticist then isolates the following polypeptide: met-lys-his-trp.
a) What amino acids make up this polypeptide?
_____________________________________________________________________
b) How many different nucleotide sequences could code for this polypeptide? List these
sequences.
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
c) Which important characteristic of the genetic code is illustrated in b)? How does
this characteristic reduce the number of amino acids that are incorrectly translated?
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
F. Sorting and Analyzing DNA
Gel electrophoresis is
used to separate
molecules according to
their mass and charge. It
is used to separate
fragments produced by
using restriction
enzymes. A solution that
contains DNA fragments
is applied to one end of
the gel. An electric
current is then passed
through the gel. One end
of the gel will develop a
positive electric charge,
the other a negative
electric charge.
DNA will be attracted to
the positive charge as it is
negatively charged.
Smaller fragments move
more frequently.
Fragments will separate
into a pattern of bands, a
DNA fingerprint.
Different samples that display similar DNA fragments provided evidence of inheritance.
This is used in crime scene investigation and paternity cases.
G. DNA Fingerprinting
A DNA fingerprint is a pattern of DNA fragments that results when DNA undergoes a
process known as gel electrophoresis. A solution containing DNA fragments is applied at
one end of a gel, and an electric current is passed through it, causing a positive electric
charge to develop at one end of the gel and a negative electric charge to form at the other.
DNA has a negative charge, and the fragments thus move toward the gel’s positive end.
Smaller fragments move more quickly than larger ones. As a result, the fragments
separate into a pattern of bands, a DNA fingerprint.
Once a DNA fingerprint has been created, scientists identify fragments of DNA that
contain sequences that are unique to an individual. These sequences are known as
VNTRs, or variable number tandem repeats. They contain 20-100 base pairs and are
found in the non-coding regions of human DNA. VNTRs are inherited from parents. This
means that some of your VNTRs came from your mother and some from your father.
Your pattern of VNTRs will be unique to you, however.
As a result of this unique pattern, DNA fingerprinting can be used to identify an
individual. How is this done? While DNA fingerprinting cannot distinguish an individual
directly, it can do so through means of comparison. For example, a DNA fingerprint can
help determine if two DNA samples are from the same person. This is useful in solving
crimes in which DNA evidence, such as hair, blood, or skin tissue, has been found at the
scene. If the DNA fingerprint of a suspect matches the DNA fingerprint found at the
crime scene, this indicates that the individual was likely to have been at the scene of the
crime. It’s important to note that DNA fingerprinting is not foolproof. It can only
determine that there is an extremely high probability that the DNA run though the gel
belongs to a certain person. Technical errors can occur in the lab. The margin for error
increases if the DNA sample is very small. Also, until recently, strict lab standards for
DNA testing were not universal.
DNA fingerprinting can also help determine the paternity or maternity of a child, as you
will learn in Thought Lab 18.5: Reading a DNA Fingerprint. As indicated, a person’s
VNTRs are inherited from both parents. By comparing a child’s DNA fingerprint with
those of the adults, the child’s parent(s) can be identified. The following diagram shows
the results of a gel electrophoresis analysis of one child and four different sets of parents.
Use these DNA fingerprints to complete Thought Lab 18.5.
The following diagram shows the results of a gel electrophoresis analysis of one child
and four different sets of parents. Use these DNA fingerprints to answer the Analysis
questions and identify the child’s biological parents.
Analysis
1. Which parental DNA matches the child’s DNA? How do you know?
2. Try to determine the percentage of the father’s DNA that matches the child’s DNA.
Can you do the same for the mother’s DNA? Explain why or why not.
3. Describe other situations in which DNA fingerprinting might be useful.
H. Tracing Ancestry
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
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The cytoplasm in a zygote is donated by the ovum.
The sperm contributes essentially no cytoplasm, therefore no cytoplasmic
organelles.
The DNA in the nuclei of your cells is made from equal combinations from your
parents, your mitochondrial DNA (mtDNA) is genetically identical to your
mothers mtDNA.
Both mtDNA and chloroplast DNA is independent of the nuclei DNA.
If two people have identical mtDNA sequences, they likely share a relatively
recent maternal ancestor.
By comparing mtDNA of different living people, scientists can deduce lineage
patterns that reveal prehistoric relationships among human populations.
As well, as evolutionary paths of animals and plant species can be determined.
Detection
Amniocentesis
Chorionic Villi Sampling
I. Mutations

If genetic information is to be transmitted accurately from one cell generation to
the next, then DNA replication must be accurate. If there is a mistake in the
process, the sequence of nitrogen bases in the DNA may be altered. This is a
mutation. Since every cell carries a full complement of genetic material, a
mutation can occur in any cell in the body. However, only mutations, which occur
in reproductive cells can be passed on to the next generation.

Mutations are rare, random events. The likelihood of a specific gene mutation
occurring is one in a million per generation. However, if one considers the total
number of individuals in a population, and the fact that each individual has about
35,000 genes, there is a good chance that mutations do occur in each generation.

A low rate of mutation is desirable since it can introduce new characteristics and
traits into a population. Too high a rate is potentially harmful because most
detectable mutations are harmful rather than beneficial to the organism.

Mutations, which alter a single gene, are commonly called point mutations. A
much larger alteration, which visibly affects the structure and/or number of
chromosomes, is classified as a chromosomal mutation.
Point Mutations
There are two main kinds of point mutations: nitrogen base pair substitution and
frameshift mutations.
Base Pair Substitution
 In a base pair substitution, only a single base pair is affected. For example, a
single G-C pair might be replaced by an A-T pair. If the change is in the third
position of the codon, it might not alter the genetic message at all. However, it
may change the code and call for a completely different amino acid. This may
change the character of the polypeptide chain, sometimes with serious
implications.
 The nitrogen base pair mutation may also change a codon to code for a stop in the
translation process. This would in effect tell the cell machinery to stop building a
polypeptide before it was complete. As a result, the polypeptide would lack some
or all of its ability to function properly since it would lack part of its structure.
Point Mutations are categorized into the following:
a) Silent mutation – a change in base pairs that does not result in a change in an
amino acid. i.e., cysteine UGU to UGC
b) Missense mutation – a change in base sequence which results in altering the
codon leading to a different amino acid. i.e., sickle cell anemia
c) Nonsense mutation – a change in base sequence that causes a stop codon to
replace an amino acid codon. Results in a fragmented polypeptide which is often
lethal to the cell.
Frameshift Mutation
This mutation occurs when one or more nitrogen base pairs are added or deleted from the
DNA strand. As you know, the DNA information is read from a starting point in groups
or “frames” of three. There is nothing to identify each specific codon so accuracy is
important. The cell machinery simply reads the information in groups of threes. If a base
is added or deleted, all the codons from that point are affected. This mutation causes a
shift in the frames of three, and the cell machinery will now read a completely different
code.
Chromosomal Mutations
Mutation of large segments of DNA and is seen at the chromosomal level.
a) Translocation – the relocation of groups
of base pairs from one part of the genome to
another . This often occurs between
nonhomologous chromosomes. This is
believed to be the cause of some types of
leukemia.
b) Inversion – section of the chromosome has reversed its orientation in the
chromosome. Hunters Syndrome a rare
sex-linked hereditary disorder that varies
widely in its severity but is generally
characterized by some degree of
dwarfism, mental retardation, and
deafness, is caused by inversion
mutations.
What Causes Mutations?
Mutations may arise from either a spontaneous mutation or exposure to a mutagenic
agent.
Spontaneous Mutation – occurs under normal conditions. Often caused by mispairing
mistakes in which a “wrong’ nucleotide is added during the process of replication.
Malfunction of DNA polymerase I and DNA polymerase II.
Mutagenic Agents – occur under artificial conditions, such as exposure to mutagens
(agents that increase the natural rate of mutations). Examples include UV radiation, Xrays, and chemicals such as mustard gas.
Mutations Worksheet
Answer the following questions in the space provided.
1. Fill in the blanks with the appropriate terms.
A permanent change in the genetic material of an organisms is called a
a)_______________. Permanent genetic changes that occur in body cells are called
b) _________________________, while those that occur in reproductive cells are
called c) __________________________. Body cell mutations are a key cause of d)
__________________. A substance that increases the rate of mutation is called a e)
_____________________. When a substance causes physical changes in the structure
of DNA, it is called a f) __________________________________. Mutations can
also be caused by g) _________________________, which enter the nucleus of a cell
and
h) ____________ mutations by reacting chemically with the DNA.
2. Consider the following nucleotide sequence in a strand of mRNA:
GUU-CAU-UUG-CUC-CCG-AAG
val – his – leu – leu – pro – lys
a) The second uracil base in the first leucine in the polypeptide is substituted with an
adenine base, resulting in the replacement of the codon UUG with the codon UAG.
What type of mutation results from this substitution? Explain your reasoning.
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
b) The uracil base in the codon for histidine is substituted with a cytosine base. What
type of mutation results from this substitution? Explain.
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
c) The first cytosine base in the second leucine is deleted. Write the nucleotide and
amino acid sequences that occur as a result of this mutation. What type of mutation(s)
may result from this deletion?
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
_____________________________________________________________________
Thought Lab – Investigating Cancer Genes
Procedure
1. Study the graphs. Write a brief summary of the relationships shown in the graph.
2. Record your ideas about the molecular reactions that may be occurring based on what
you have learned in this chapter.
3. Conduct research to describe one of the molecular reactions that might contribute to
the relationship you see in the graph. You may find the following keywords helpful to
guide your research:
A. oncogenes
B. tumour-suppressor genes
C. stability genes
D. p53 gene
J. Prevention of Cancer
Smoking
Smoking and second-hand smoke inhalation are the most preventable causes of cancer in
Canada. Cigarette smoke is linked to the development of numerous cancers. (This is
discussed in the handout FAQ—Tobacco and Cancer in greater detail.) 80 carcinogens
are found in cigarette smoke, along with many other toxic compounds. These carcinogens
are chemical mutagens. They cause cancer by entering the nucleus of a cell and inducing
mutations by reacting chemically with the DNA. A chemical mutagen may act by
inserting itself into the DNA molecule in a manner that causes a nucleotide substitution
or a frameshift mutation. Other chemical mutagens have a structure that is similar to the
structure of ordinary nucleotides but with different base pairing properties. When these
mutagens are incorporated into a DNA strand, they can cause incorrect nucleotides to be
inserted during DNA replication. Over time, these mutations can result in cancer.
Diet and Exercise
A healthy diet and regular exercise have a big influence on the risk of developing cancer.
Next to stopping smoking, eating a healthy diet, maintaining a healthy weight, and
getting enough exercise are the most important lifestyle habits a person can maintain to
reduce the incidence of cancer. Overweight individuals have a higher risk of developing
certain cancers, including breast, colon, kidney, esophageal, and endometrial (referring to
the lining of the uterus) cancers. Additionally, people who carry excess body weight
produce more insulin and estrogen, hormones that have been linked to accelerated tumour
growth. Increasing physical activity and decreasing portion size are two good ways to
maintain a healthy weight. The food choices an individual makes can also reduce his or
her cancer risk. With regards to cancer prevention, studies have shown that eating at least
5 servings of fruits and vegetables a day reduces the risk of many cancers, including
cancers of the lung and digestive system. Research has shown that brightly coloured
fruits and vegetables have a particularly high level of cancer-fighting nutrients.
Consumption of red and processed meats is linked to an increased risk of cancer.
Sun Exposure
Ultraviolet (UV) radiation is a known physical mutagen. Physical mutagens cause
physical changes
in the structure of DNA. They tear through DNA molecules, causing random changes that
range from point mutations to the loss of large portions of chromosomes. The resulting
mutations can lead to tumour formation. Increased risk of skin cancers, such as the highly
curable basal and squamous cell (types of skin cells) cancers, as well as the more
dangerous melanoma, is indisputably linked to exposure to UV radiation, both from the
sun and artificial tanning. The best way to reduce this risk is to limit sun exposure to
short periods of time when the sun is less intense and to “practice safe sun” by wearing
sunscreen and protective clothing. X-ray radiation is an even more powerful physical
mutagen than UV radiation, and exposure to these rays should be limited if possible.
Environment
Today’s society is home to many carcinogens. These include chemical mutagens, such as
many chemical additives, environmental pollutants, drugs, and hormonal treatments;
physical mutagens, including most forms of radiation; and even infectious diseases, such
as bacteria, viruses, and parasites. Infectious disease may increase cancer risk by
compromising the immune system, causing long-term inflammation in the body, or by
directly interfering with the body’s DNA. While some infectious diseases have been
found to play a role in the development of cancer, it is important to bear in mind that
most people who get these infections do not go on to develop cancer. Certain varieties of
HPV (human papilloma virus) have been linked to cervical cancer, the second most
common cancer in women, as well as cancer of the penis, vagina, and anus, among
others. A vaccine that prevents four of the most common forms of HPV (two-high risk
types and two low-risk types) has been available in Canada since 2006. While the vaccine
has been shown to provide protection against these four forms of the virus, it will not
treat a pre-existing infection.
Early Detection
A last, but important, means of preventing cancer is early detection. In some cancers,
such as cervical cancer, pre-cancerous cells can be easily detected. Prompt treatment in
cases of early detection can often stop tumour formation. Even in cases where cancer has
already developed, early detection can significantly increase the cure rate or future life
expectancy of an individual.
K. Restriction Endonucleases
L. Cohen-Boyer Experiment
1973 was the year in which genetic engineering was born. In this year, the American
researchers Stanley Cohen and Herbert Boyer created the first genetically engineered
organism. This organism, known as a chimera, consisted of a bacterium that contained
DNA from an unrelated species, Xenopus laevis, the African clawed toad. To create this
chimera, Cohen and Boyer first isolated a bacteria plasmid known as pSC101 (so named
as it was the 101st plasmid isolated by Stanley Cohen). A plasmid is a double stranded,
circular molecule of DNA that replicates on its own, independently of the bacterial
chromosomal DNA. Plasmid pSC101 contains a derivative of an R factor, a factor that
codes for antibiotic resistance in bacteria, in this case to tetracycline. In general, R factors
are very large and can be cleaved at many sites by restriction enzymes. Plasmid pSC101
contains a derivative of an R factor, which has only 9000 base pairs, and is cleaved in
only one site by the restriction endonuclease EcoRI. When cleaved, the plasmid opens at
this specific site to form a linear piece of double stranded DNA with sticky ends on both
ends. Another gene that is cut by restriction endonuclease EcoRI may then bind to these
sticky ends and be added to the plasmid.
Over 30 years ago, Cohen and Boyer
created their chimera in just this
way. The scientists isolated a gene
from Xenopus laevis that coded for
the production of rRNA. This gene
was cleaved with restriction
endonuclease EcoRI and inserted
into plasmid pSC101. The plasmid
now contained the amphibian gene
for rRNA production and the
bacterial gene for tetracycline
resistance. Bacteria were then
exposed to both the recombinant
plasmid and to tetracycline. Those
bacteria that displayed tetracycline
resistance had taken up the plasmid.
The following figure illustrates the
Cohen-Boyer experiment. In the
figure, the amphibian gene coding
for the production of rRNA is shown
in black and the bacterial gene, tetR,
which confers resistance to the
antibiotic tetracycline, is shown in white. The restriction endonuclease EcoR1 and DNA
ligase were used to splice (insert) a gene from the toad into the plasmid pSC101.
Thought Lab – Recreating the First Chimera
In genetic engineering, a chimera is a
genetically engineered organism that
contains DNA from unrelated species. The
first chimera was created in 1973 by the
American team of Stanley Cohen and
Herbert Boyer. Bacteria were then exposed
to the recombinant plasmid. Those bacteria
that displayed tetracycline resistance had
taken up the plasmid.
In Cohen and Boyer’s experiment, the
amphibian gene coded for the production of
rRNA. The bacterial gene tetR conferred
resistance to the antibiotic tetracycline. They
used the restriction endonuclease EcoR1 and
DNA ligase to splice (insert) a gene from a
toad into a molecule of bacterial DNA
plasmid pSC101.
Procedure
1. Study the illustration of the Cohen-Boyer experiment. Make a list of the materials that
the researchers used.
2. Develop a plan to simulate the experiment. Show how you will use materials in your
classroom to represent the materials that Cohen and Boyer used. Then perform your
simulation.
Analysis
1. How did your simulation illustrate the action of an endonuclease and a ligase? In
what ways was your simulation effective? What were its limitations?
2. The Cohen-Boyer experiment was important because it created a colony of bacterial
cells that were resistant to the antibiotic tetracycline and produced amphibian rRNA.
What other bacterial phenotypes would have resulted from this experiment? What
would each phenotype indicate about events at the molecular level?
3. a) Give one example of how you might use this technology for a social or industrial
purpose.
b) What environmental, social, or ethical issues would your experiment raise? Make a
list of these issues, and discuss them with other students in your class.