UNIT 3: Molecular Genetics
Chapter 5: The Structure and Function
of DNA
Chapter 6: Gene Expression
Chapter 7: Genetic Research and
Biotechnology
UNIT 3 Chapter 6: Gene Expression
Chapter 6: Gene Expression
How does a gene determine the expression of a trait?
Gene expression is a process. Information from a gene’s
DNA sequence is used to synthesize (make) a protein. The
information flows from the gene’s DNA sequence to RNA to
protein during the process.
Therefore, an altered or deleted
nucleotide pair will change the
DNA sequence of a gene and affect
its product, just as a missed note
will change the musical structure
of a scale.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
6.1 The Transfer of Information
from DNA
Early studies in genetics showed a relationship between
the inheritance of a gene and the expression of a trait. A
question that resulted from this discovery was “How does
a gene determine a trait?”
In the early 1900s, researchers began to investigate the
relationship between genes and proteins. The researchers
suggested that proteins were the molecules involved in
inheritance, since they carry out several key cellular
functions.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Establishing a Link between
Genes and Protein
In 1902, Archibald Garrod published a study linking genes
and proteins.
Garrod investigated the disease alcaptonuria. This disease
causes a patient’s urine to turn black when it is exposed to air.
This colour change is due to the build-up of homogentisic
acid, an intermediate molecule produced during the
catabolism of the amino acid phenylalanine. He reached the
conclusions shown on the next slide.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Establishing a Link between
Genes and Protein
•
The build-up of homogentisic acid was due to a defective
enzyme in the metabolic pathway that breaks down
phenylalanine.
•
Alcaptonuria was an inherited disease caused by a
recessive inheritance factor. Having this factor would
result in the production of the defective enzyme. This
conclusion laid the foundations for demonstrating a link
between genes and proteins.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
One-Gene/One-Enzyme Hypothesis
In 1941, George Beadle and Edward Tatum looked for
experimental evidence of the relationship between genes and
proteins. They used the bread mold Neurospora crassa to
investigate whether one gene controlled the production of one
enzyme or multiple enzymes. Normal, wild-type N. crassa
can grow on minimal medium.
Mutant strains of N. crassa were created by exposing wildtype strains to X rays to cause changes in genes. The mutant
strains that required minimal medium supplemented with the
amino acid arginine were isolated. These mutants were
known as arg mutants, since they required arginine to grow.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.1
One-Gene/One-Enzyme Hypothesis
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.1
One-Gene/One-Enzyme Hypothesis
Beadle and Tatum wanted to identify which arg mutants
affected particular steps in the arginine synthesis pathway.
They hypothesized that a defective gene would produce a
defective enzyme. A defective enzyme in one of the steps of
the pathway would mean that the intermediate compound it
produced would not be synthesized.
The arg mutants were grown in media supplemented with
intermediates of the arginine synthesis pathway. Using this
method, Beadle and Tatum isolated mutant strains that were
defective at a specific step.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.1
One-Gene/One-Enzyme Hypothesis
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.1
One-Gene/One-Polypeptide Hypothesis
Beadle and Tatum concluded that one gene codes for one
enzyme. This relationship was updated to the one-gene/onepolypeptide hypothesis, since not all proteins are enzymes.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Finding a Messenger between
DNA and Proteins
In 1953, Frederick Sanger showed that each protein had a
specific amino acid sequence.
In 1961, François Jacob and Jacques Monod hypothesized that
a special type of RNA, called messenger RNA (mRNA), is
synthesized from DNA.
Messenger RNA is complementary to DNA and provides the
amino acid sequence information for protein synthesis.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
The Genetic Code
The genetic code is a set of rules for determining how genetic
information in the form of a nucleotide sequence is converted to
an amino acid sequence of a protein.
Researchers identified four nucleotides in RNA (A, U, G, and C)
and 20 amino acids. Mathematically, there could not be a oneto-one relationship between nucleotides and amino acids, nor
could there be just two nucleotides per amino acid.
The triplet hypothesis states that the genetic code consists of a
combination of three nucleotides, called a codon. Each codon
would code for an amino acid. This hypothesis was supported by
work done by Francis Crick and Sydney Brenner, which showed
that the code is read in triplets.
Continued…
UNIT 3 Chapter 6: Gene Expression
The Genetic Code
Section 6.1
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Determining the Genetic Code
Between 1961 and 1965, researchers compared artificially
synthesized RNA of known nucleotide sequences with the amino
acid sequences of polypeptides, determining the MRNA codons and
their corresponding animo acids.
*AUG is an initiator codon.
It also codes for the amino
acid methionine.
** UAA, UAG, and UGA
are terminator codons.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Summarizing the Genetic Code
The genetic code has three important characteristics. It is:
•
•
•
redundant: more than one codon can code for the same
amino acid
continuous: the code is read as a series of three-letter codons
universal: almost all organisms build proteins with the same
genetic code. For example,
a codon in a fruit fly codes
for the same amino acid as
in a human.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Gene Expression
Gene expression refers to the transfer of genetic information
from DNA to RNA to protein. This theory is called the
central dogma of genetics.
UNIT 3 Chapter 6: Gene Expression
Section 6.1
Gene Expression
The two steps in gene expression are transcription and translation.
•
•
In transcription, a DNA sequence serves as a template for
the synthesis of RNA.
In translation, an mRNA sequence serves as a template for
the synthesis of a protein.
Transcription of a DNA template produces an
RNA molecule that is a copy of the genetic
information. The nucleotide sequence of this
RNA molecule is then translated using the
genetic code so that the protein coded for by the
gene is produced.
UNIT 3 Chapter 6: Gene Expression
Section 6.1 Review
Section 6.1
UNIT 3 Chapter 6: Gene Expression
Section 6.2
6.2 Transcription: Synthesizing
RNA from DNA
Transcription is the first step in gene expression and involves the
production of an RNA molecule from a DNA template.
RNA is a single-stranded
polymer of nucleotides.
Recall that RNA contains
the nucleotides A (adenine),
U (uracil), G (guanine),
and C (cytosine).
UNIT 3 Chapter 6: Gene Expression
RNA
There are different RNA molecules, which are classified
according to the functions they perform.
Section 6.2
UNIT 3 Chapter 6: Gene Expression
Section 6.2
The Molecular Events of Transcription
As in the replication of DNA, there are three defined stages
in transcription:
•
•
•
initiation
elongation
termination
Transcription in prokaryotes and eukaryotes is similar. The
main difference is that there are more proteins involved in
eukaryotic transcription.
UNIT 3 Chapter 6: Gene Expression
Section 6.2
Initiation Phase of Transcription: Part I
The correct transcription start site is selected and the
transcription machinery, composed of a large protein-DNA
complex, is assembled.
For each gene, only one strand of DNA is transcribed. This
strand is called the antisense strand or template strand. The
strand that is not transcribed is called the sense strand or coding
strand. This strand has the same sequence as the mRNA that is
produced, with thymines instead of uracils.
UNIT 3 Chapter 6: Gene Expression
Section 6.2
Initiation Phase of Transcription: Part II
RNA polymerases are a group of enzymes that catalyze the
synthesis of RNA. Transcription begins when an RNA
polymerase complex binds to a promoter region on the DNA.
This region has a specific sequence of nucleotides that allows
the RNA polymerase to bind to the correct strand in the correct
orientation.
Once the RNA polymerase complex is bound to the DNA, it
unwinds and opens a section of the double helix.
The promoter region
in E. coli is composed
of two specifically
positioned nucleotide
sequence elements.
Both of these are
required for the RNA
polymerase complex
to correctly bind to the
DNA template.
UNIT 3 Chapter 6: Gene Expression
Elongation Phase of Transcription
The RNA polymerase complex moves in
the 5′ to 3′ direction to synthesize an
mRNA molecule that is complementary
to the antisense strand. In the mRNA
strand, T is replaced by U.
Hundreds of mRNA molecules can be
synthesized simultaneously as long as
the RNA polymerase complex has
moved from the promoter region,
allowing another RNA polymerase
complex to bind.
Continued…
Section 6.2
UNIT 3 Chapter 6: Gene Expression
Elongation Phase of Transcription
The synthesis of many mRNA molecules
can occur at one time.
Section 6.2
UNIT 3 Chapter 6: Gene Expression
Section 6.2
Termination Phase of Transcription
Specific nucleotide sequences in
the DNA template serve as a
signal to stop transcription.
When the RNA polymerase
complex reaches this signal, it
detaches from the DNA strand.
The new mRNA strand is
released from the transcription
assembly, and the DNA double
helix reforms.
UNIT 3 Chapter 6: Gene Expression
Section 6.2
mRNA Modifications in Eukaryotes: Part I
In prokaryotes, transcription and translation can occur
simultaneously. In eukaryotes, mRNA must undergo
modifications before it crosses the nuclear membrane to the
cytoplasm. Once the modified mRNA enters the cytoplasm, it
can undergo translation. There are three modifications that
convert precursor mRNA (pre-mRNA) to mature mRNA.
Addition of a 5′ cap of modified G nucleotides
The cap is recognized by protein synthesis machinery.
Addition of a 3′ poly-A tail
The tail is a series of A nucleotides that makes the mRNA
more stable in the cytoplasm.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.2
mRNA Modifications in Eukaryotes: Part I
All eukaryotic mRNAs undergo modification on
their ends. (A) A derivative of guanine is added to
the 5′ end. (B) A series of nucleotides containing
the base adenine are added to the 3′ end.
UNIT 3 Chapter 6: Gene Expression
Section 6.2
mRNA Modifications in Eukaryotes: Part II
Removal of Introns
Introns (non-coding regions) are removed and exons (coding
regions) are joined together. This process, called splicing, is
performed by snRNA and snRNP proteins, which form a large
spliceosome complex. In some cases, only certain exons are used to
form a mature RNA, allowing for one gene to code for more than
one protein.
UNIT 3 Chapter 6: Gene Expression
Section 6.2 Review
Section 6.2
UNIT 3 Chapter 6: Gene Expression
Section 6.3
6.3 Translation: Synthesizing
Proteins from mRNA
Translation, the second stage of gene expression, involves
translating the nucleic acid code of mRNA into the amino acid
code of a protein. Translation occurs in the cytoplasm.
The following table provides an overview of the major
components involved in translation.
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Transfer RNA
Transfer RNA (tRNA) molecules are composed of three
stem-loops and a single-stranded region, all of which fold
into a three-dimensional shape.
Each tRNA molecule has two functional regions:
•
•
the anticodon loop, which is a sequence of three
nucleotides that is complementary to an mRNA codon
the acceptor stem, which is a single-stranded region
where an amino acid is attached. The aminoacyl-tRNA
synthetase enzymes attach the correct amino acid to a
tRNA. There are 20 different enzymes, one for each of
the 20 amino acids.
Continued…
UNIT 3 Chapter 6: Gene Expression
Transfer RNA
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Ribosomes
Ribosomes are cytoplasmic structures made up of proteins and
ribosomal RNAs (rRNAs). The molecules involved in
translation (mRNA, tRNA, translation factors) are assembled
on ribosomes.
Each ribosome is comprised of two sub-units—one is small
and one is large. There are three binding sites for tRNA and
one binding site for mRNA. These binding sites allow
complementary base pairing between tRNA anticodons and
mRNA codons.
A complex of multiple ribosomes, called a polyribosome, can
be attached to and translate a single mRNA at the same time.
Continued…
UNIT 3 Chapter 6: Gene Expression
Ribosomes
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.3
The Molecular Events of Translation
Translation is one of the most energy-consuming
processes in a cell because many protein and nucleic acid
components must be synthesized and assembled; again,
these processes occur during three phases:
•
•
•
initiation
elongation
termination
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Initiation Phase of Translation
The components of translation (translation factors, mRNA,
tRNA, ribosomes) assemble during the initiation phase.
The small ribosomal sub-unit attaches to the mRNA near
the start codon (AUG). The initiator tRNA with the
anticodon UAC binds to the start codon. In eukaryotes, this
tRNA carries the amino acid methionine; in prokaryotes, it
carries a derivative of methionine. The large ribosomal
sub-unit attaches to form an active ribosome.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Initiation Phase of Translation
The start codon sets the
reading frame for the
gene. The reading
frame establishes how
subsequent codons in the
sequence will be read to
produce an amino acid
sequence.
Continued…
UNIT 3 Chapter 6: Gene Expression
Initiation Phase of Translation
There are three binding sites for tRNAs:
• The P (peptide) site of the ribosome
contains the tRNA that carries the
growing polypeptide.
• The A (amino) site holds the RNA
with the next amino acid.
• The E site is the exit site.
During initiation, the initiator tRNA
binds to the P site.
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Enlongation Phase of Translation
Protein synthesis occurs during elongation. One amino acid is
added at a time to the growing polypeptide chain.
Elongation factors join to facilitate the growth of the
polypeptide. Amino acids are joined by peptide bonds.
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Termination Phase of Translation
Termination begins when a stop codon on the mRNA
is reached.
The polypeptide and the translation machinery are
separated when a protein, called a release factor,
cleaves the polypeptide from the last tRNA.
The polypeptide is released and can fold into its
three-dimensional shape to carry out cellular functions.
UNIT 3 Chapter 6: Gene Expression
Section 6.3
A Review of Gene Expression
Continued…
UNIT 3 Chapter 6: Gene Expression
A Review of Gene Expression
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.3
DNA Mutations and Effects of Mutagens
Gene expression can be affected by errors that occur during
DNA replication. Some errors are repaired, but others can
become mutations, which are changes in the nucleotide
sequence of a cell’s DNA. Mutations in reproductive cells
can affect the next generation; mutations in somatic cells
can affect daughter cells.
Mutations can be neutral or harmful. In rarer cases, they are
beneficial. These mutations are important in terms of
species change and adaptation.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.3
DNA Mutations and Effects of Mutagens
All cells undergo spontaneous mutation. Substances or
events that increase the rate of mutation are called mutagens.
Mutations are grouped into two categories:
•
•
single-gene mutations
chromosome mutations
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Single-Gene Mutations
Single-gene mutations involve changes in the nucleotide
sequence of one gene.
Single-gene mutations can be categorized according to how
they affect the nucleotide sequence of DNA:
•
•
Point mutations result from a change in a single base
pair within a DNA sequence. It can involve the
substitution, addition, or deletion of one nucleotide. A
substitution may not affect the protein due to the
redundancy built into the genetic code.
Frameshift mutations result from the insertion or
deletion of nucleotides not divisible by three. This
causes a change in the reading frame.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Single-Gene Mutations
A frameshift mutation results in
alteration of the reading frame
due to the insertion or deletion
of one (or more) nucleotides.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Single-Gene Mutations
Single-gene mutations may also be categorized according to
how they affect the amino acid sequence of a protein.
•
•
•
Silent mutations do not change the amino acid sequence
of a protein.
Missense mutations change the amino acid sequence and
are usually harmful. Occasionally they produce a protein
that helps with survival.
Nonsense mutations are usually harmful since they
shorten a protein by introducing an early stop codon.
Continued…
UNIT 3 Chapter 6: Gene Expression
Single-Gene Mutations
A nucleotide substitution can cause silent,
missense, or nonsense mutations.
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Chromosome Mutations
Chromosome mutations involve changes in chromosomes
and many genes. These mutations include:
•
•
•
deletion or duplication of portions of chromosomes
inversions (a chromosome segment is broken and reinserted in the opposite direction)
translocations (a section of one chromosome is broken
and fused to another chromosome)
Continued…
UNIT 3 Chapter 6: Gene Expression
Chromosome Mutations
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Causes of Mutations
Mutations may be spontaneous or induced. Spontaneous
mutations may be caused by:
• the result of normal molecular interactions
• incorrect base pairing by DNA polymerase during
replication
• transposition, in which specific DNA sequences (called
transposons) move within and between chromosomes
Barbara McClintock was the first individual to
study transposons. In 1983, she was awarded the
Nobel Prize in physiology or medicine for the
discovery of the process of transposition.
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.3
Causes of Mutations
Induced mutations may be caused by:
• physical mutagens, an event or substance such as highenergy radiation (X rays and UV rays). These mutagens
physically change the structure of DNA. For example, UV
radiation distorts the DNA molecule at adjacent
C and T bases, causing replication interference.
•
chemical mutagens, such as nitrites and chemicals
in cigarette smoke. These mutagens are molecules
that can enter the nucleus of a cell and induce mutations by
reacting with DNA. Some mutagens have a structure similar
to DNA nucleotides and can incorporate into a DNA strand,
causing incorrect base pairing during replication.
UNIT 3 Chapter 6: Gene Expression
Section 6.3
DNA Repair
Recall from Chapter 5 that DNA polymerases and mismatch
repair mechanisms help to repair replication errors.
Two additional types of DNA repair mechanisms are:
•
•
specific repair mechanisms, such as photorepair, which
can be tailored to fix certain types of damage
non-specific repair mechanisms, such as excision
repair, which can correct different forms of damage
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.3
DNA
Repair
Photorepair is a specific mechanism to repair damage to
DNA caused by exposure to UV radiation. A photolyase
enzyme recognizes the damage, binds to the dimer, and
uses visible light to cleave the dimer.
Excision repair is a non-specific
mechanism of DNA repair because it
can fix a variety of damage.
UNIT 3 Chapter 6: Gene Expression
Section 6.3 Review
Section 6.3
UNIT 3 Chapter 6: Gene Expression
Section 6.4
6.4 Regulation of Gene Expression
Gene regulation refers to control of the level of gene
expression. Regulation involves whether a gene is
active or inactive. It also determines the level of activity
and the amount of protein that is available.
Constitutive (housekeeping) genes are always active
because they are essential for cell survival. However,
most genes are regulated so that they are only expressed
when needed.
UNIT 3 Chapter 6: Gene Expression
Section 6.4
Regulation of Gene Expression in
Prokaryotes
Regulation of gene expression in prokaryotes occurs at three
different levels:
• transcription
• translation
• after a protein has been synthesized
The most common regulation is during initiation of
transcription. In prokaryotes, genes are clustered in a region
under the control of a single promoter. The region is called
an operon. One mRNA strand, called a polycistronic
mRNA, is synthesized for multiple genes in the same
metabolic pathway.
UNIT 3 Chapter 6: Gene Expression
Section 6.4
The lac Operon
The genes that encode the enzymes needed to break down
the sugar lactose are found in the lac operon on the E. coli
chromosome.
The coding region contains genes for three enzymes that
break down lactose. The regulatory region contains the
following components:
•
•
•
promoter: involved in transcription of the lactosemetabolizing enzymes
operator: a DNA sequence to which a protein (a
repressor) binds to inhibit transcription initiation
CAP binding site: a DNA sequence to which CAP
(catabolite activator protein) binds to increase the rate
of transcription
UNIT 3 Chapter 6: Gene Expression
Section 6.4
Activating the lac Operon
In the absence of lactose, the lac repressor protein binds to
the operator, preventing RNA polymerase from binding to
the promoter to initiate transcription.
In the presence of lactose, a derivative called allolactose is
made. Allolactose binds to the repressor so it can no longer
can bind to the operator. Transcription of the genes can
therefore occur. The binding of the CAP activator protein
can further enhance transcription levels.
The lac operon contains three genes (Z, Y,
and A) needed for the breakdown of
lactose in E. coli. All three genes are
under the control of one promoter.
Therefore, they undergo the same level of
regulation. When lactose is not present,
the lac repressor inhibits transcription.
UNIT 3 Chapter 6: Gene Expression
Section 6.4
The trp Operon
The lac operon is an inducible operon; this means that
transcription is induced when lactose is present. The trp
(tryptophan) operon, however, is normally active until a
repressor turns it off.
The trp operon is similar to the lac operon. It contains:
•
•
a coding region with five genes for enzymes required for
tryptophan synthesis
a regulatory region with a promoter and an operator
Continued…
UNIT 3 Chapter 6: Gene Expression
Section 6.4
The trp Operon
Under normal conditions, tryptophan must be synthesized,
and therefore the repressor is not bound to the operator and
transcription occurs.
When tryptophan levels are high, tryptophan binds to a
repressor protein, which then binds to the operator to reduce
transcription activity.
The trp operon contains
five genes that are
involved in the synthesis
of tryptophan. This
operon is normally
transcribed until the cell
has sufficient tryptophan.
Then the trp repressor
binds to the promoter and
inhibits transcription.
UNIT 3 Chapter 6: Gene Expression
Regulation of Gene
Expression in Eukaryotes
There are five levels of gene
regulation in eukaryotes:
•
•
•
•
•
pre-transcriptional
transcriptional
post-transcriptional
translational
post-translational
Regulation of eukaryotic gene expression occurs
at multiple stages of protein production. The
regulation points occur in both the nucleus and
the cytoplasm.
Section 6.4
UNIT 3 Chapter 6: Gene Expression
Section 6.4
Pre-transcriptional and Transcriptional Control
Pre-transcriptional gene regulation:
• The cell can loosen the nucleosome structure by chemical
modification or the use of an enzyme complex called
chromatin remodeling complexes. This allows increased
access to the DNA for proteins involved in transcription
initiation.
Transcriptional gene regulation:
• Transcription factors must interact with the promoter for
RNA polymerase to initiate transcription.
• Certain activator proteins also enhance transcription by binding
to transcription factors, RNA polymerase, and DNA sequences
called enhancers.
Continued…
UNIT 3 Chapter 6: Gene Expression
Pre-transcriptional and
Transcriptional Control
Section 6.4
UNIT 3 Chapter 6: Gene Expression
Section 6.4
Post-transcriptional and
Translational Control
Post-transcriptional and translational gene regulation:
•
•
•
Alternative splicing of the mRNA produces different
protein products.
If the 5′ cap or the 3′ poly-A tail are not added, the
mRNA is degraded and is not available for translation.
RNA interference can occur where micro RNA
(miRNA) or small interfering RNA (siRNA) molecules
can cleave mRNA or interfere with translation.
UNIT 3 Chapter 6: Gene Expression
Section 6.4
Post-translational Control
Post-translational gene regulation:
• Modifications can be made to some polypeptides to
make them functional. Cleaving and re-bonding of
amino acids or the addition of a phosphate group can
occur to make a protein functional.
• The amount of time during which a protein is
functional can be altered by adding ubiquitin to a
molecule to encourage degradation.
UNIT 3 Chapter 6: Gene Expression
Section 6.4 Review
Section 6.4
UNIT 3 Canadian Research in Action
STSE
Dr. Sachdev Sidhu and his team work in the field of synthetic
antibody research at the University of Toronto. His lab is
currently working to develop a large number of antibodies
that target proteins associated with cancer. These antibodies
will likely play a key role in determining how the products of
certain genes function under normal and cancerous conditions.