Download Where are we heading? Unit 3:

Unit 3:
Unit 3: Introduction
Where are we heading?
Unit 1: What is cancer and why should we care?
Unit 2: What does it mean to be a 'normal' cell?
Unit 3: How do normal cells become cancerous?
Unit 4: How does cancer make us sick?
Unit 5: How is cancer diagnosed and treated?
______________________________________
In Unit 3 we'll zoom in on how cell function is
disrupted in cancer.
Lesson 3.1 will give you the opportunity to apply your understanding
about DNA replication and protein synthesis to an investigation of
how DNA is organized, and how mutations can affect gene function.
Lesson 3.2 examines how DNA mutations affect protein synthesis and
how this may promote development of cancer. Lesson 3.3 investigates the internal clock that allows a cell to age normally, and how
this clock is disrupted in cancer. Lesson 3.4 explores how cancer
cells become immortal by cheating normal cell death. Lesson 3.5
grapples with the idea that each cancer cell evolves independently,
so that each tumor has different characteristics.
79
LESSON 3.1 WORKBOOK
What is in our DNA sequence?
DEFINITIONS OF TERMS
For a complete list of defined
terms, see the Glossary.
Gene expression – the process
by which information from
a gene-coding region of DNA is
used to make a protein.
Somatic cells – All cells that
aren’t eggs or sperm
Autosome – one of 22 chromosomes in human DNA that is
found in females and males
Zygote – Fertilized egg
Wo r k b o o k
Lesson 3.1
The previous Unit described the regulatory mechanisms that keep normal cells
normal. We learned that these mechanisms occur through the activity of proteins,
which are encoded in our genomic DNA. Tumors and cancer occur when DNA is
mutated so that those regulatory proteins can no longer control cellular behavior.
This lesson explains how genomic DNA is organized, and how that organization
can dynamically regulate gene expression to impact cell behavior.
What is in our DNA sequence?
We have learned in other modules, as well as in Unit 2, how the activity of the proteins a cell synthesizes
determines that cell’s behavior. So to understand cell behavior we need to understand those proteins and
how they work. Each protein is encoded by a DNA sequence called a gene. The gene’s DNA sequence is
first transcribed into an RNA sequence, and then the RNA sequence is then translated into an amino acid
sequence that forms a protein. As the protein matures it folds into a characteristic 3-dimensional shape that
permits it to perform its function. For example receptor proteins always contain a binding ‘pocket’ where
their specific ligand can fit. Generating proteins from gene sequences is also known as gene expression
and altering gene expression, for instance following DNA mutation, can have serious effects on cell behavior. For example, as we learned in Unit 1, proto-oncogenes are genes that normally make sure that cell
proliferation is tailored to tissue requirements. However, when proto-oncogenes mutate to form oncogenes,
proliferation is no longer regulated and tumors form. Understanding how DNA is organized will give us a
better idea of how and when the important functional mutations to genes occur.
Most somatic cells have 23 pairs of chromosomes. 22 pairs of chromosomes are found in both male and
female cells, these chromosomes are called autosomes, while the 23rd pair, called sex chromosomes,
can take one of two forms. Female cells usually have the XY form, whereas males usually have YY. Germ
cells (eggs and sperm) only have one of each chromosome rather than a pair, because they fuse together
during fertilization to produce the zygote which then has 23 pairs of chromosomes.
MC Questions:
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
1. True or false: Gene expression refers
to generating proteins from DNA.
aa. True.
bb. False.
________________________________
________________________________
________________________________
________________________________
2. Which of the following does the
genome contain?
aa. Autosomes;
bb. Introns;
cc. Exons;
dd. All the above.
________________________________
________________________________
________________________________
80
LESSON READINGS
DEFINITIONS OF TERMS
Genome – The complete sequence
of all the chromosomes
Exons – the nucleotide sequence
of a gene that codes for protein
sequence.
Introns – Parts of a gene between
exons that do not contain sequence
necessary for protein coding, and
are removed prior to translation.
Non-coding DNA – DNA sequences that do not make protein. They
may make RNA molecules that are
necessary for gene expression.
Transposon – a segment of DNA
that is capable of moving into
another position in a genome.
Retrotransposon – a segment of
DNA that is capable of copying itself
into RNA and undergoing reverse
transcription to form a new DNA
segment that can move into another
position in the genome.
Wo r k b o o k
Lesson 3.1
Human chromosomes contain 32 billion
nucleotides. All of these nucleotides together
make the human genome. Figure 1 shows
how the genome is divided into various types
of functions. When the human genome was
first fully sequenced in 2001, it was clear that
only a very small proportion, maybe 2%,
contains DNA that actually codes for genes.
People found this very surprising because at
the time it was not at all obvious what the rest
of the genome was for. For a long time the
remaining 98% was dismissed as ‘junk’ DNA
Figure 1: Genes compose only 2% of all the
that we had somehow acquired during evoluDNA sequence in our genome. The majority
tion, but that had no functional significance. In
of sequence is composed of retrotransposons,
DNA transposons, and noncoding DNA.
fact, the non-protein encoding DNA sequence
turns out not to be ‘junk’ at all; instead it is
composed of important sequences that can
regulate how and when gene expression occurs. The DNA sequences that directly code for amino acids
are called exons (called genes in Figure 1). Interspersed within exons are sequences called introns.
Introns are non-coding DNA that play important roles in regulating how exons are expressed. Yet
other non-coding DNA sequences (the green wedge in Figure 1) can be transcribed into RNA but are
not translated into protein. Some of these RNA sequences, like transfer RNA (tRNA) or microRNAs help
protein translation. Another large component are regulatory sequences that also affect gene expression
without making RNA. Finally a major chunk of non-coding DNA sequences are called DNA transposons
and retrotransposons. These sequences can actually jump around the genome from one location to
another. Obviously, if they land in a gene sequence they can affect gene expression. Thus even though
most of the genome does not code for protein directly it does play an indirect role in regulating protein
expression.
Genome organization: gene sequences.
As we learned in Lesson 2.4, DNA is packaged around histones, with the tightness of the packaging
determining whether or not DNA will be transcribed. We learned in Lesson 2.5 DNA can be transcribed
when it is loosely packed and that it is transcribed when a transcription factor binds to a promoter
sequence (also known as a regulatory sequence) a stretch of non-coding DNA located just in front of
the coding sequence. When the transcription factor is bound to the regulatory sequence, RNA polymerase can bind to the coding sequence of the DNA and transcribe the gene into RNA. Up to now we
only learned about transcription factors that promote gene expression, but inhibitory transcription factors
MC Questions:
3. Which of the following DNA
sequences are most prevalent in the
genome?
aa. Genes;
bb. Introns;
cc. Non-coding DNA;
dd. Retrotransposons.
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
4. True or false: Most of our DNA
contains sequence involved in
protein expression.
aa. True.
bb. False.
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
81
LESSON READINGS
also exist. When they bind to the regulatory sequence, they block it and prevent gene expression. Regulatory sequences therefore play multiple roles to stimulate and inhibit gene expression some of which are
extremely complex
DEFINITIONS OF TERMS
Transcription factor – Protein
that binds to a DNA sequence
at the start of a gene and either
promotes or inhibits transcription.
Each gene is composed of two regions – the region that codes for the amino acids in the protein, called
the exon, and non-coding regions interspersed among the exons called introns. As a result the DNA
sequence of a gene in the genome is often considerably longer than the sequence of the protein that will
result at the end of translation (remember that each amino acid is coded for by three nucleotides). The
progression from DNA to RNA to protein is illustrated graphically in Figure 2, which represents the gene
sequence for a protein with 10 exons, each colored differently. We can see how, in the DNA sequence,
each exon is separated from another by a log stretch of non-coding introns (represented by the dotted
line). Both the exons (colored) and the introns (black line) are transcribed into RNA, but when the RNA is
translated into protein the introns are removed, so that the protein is now a single molecule composed of
the different introns. The process of removing the introns from RNA as it is translated into protein is called
splicing. As a result the size of the protein is much smaller than the size of the RNA and much, much
smaller than the size of the gene.
Regulatory sequence – a segment of DNA that is responsible
for increasing or decreasing the
expression of specific genes in
the cell.
Figure 2: Genes are composed of short coding sequences called
exons, which are separated by longer, non-coding sequences called
introns. When a gene is transcribed into RNA, both introns and
exons are included in the sequence. Introns are removed from
mRNA sequence, leaving only exon sequence to make proteins.
Wo r k b o o k
Lesson 3.1
What is the purpose of introns and exons? Dividing the protein up into chunks like this provides an
opportunity to create protein diversity. Sometimes when an intron is removed an exon will be removed
along with it. For example a protein without the yellow exon could potentially be very different from the
protein with it, if the yellow exon provided the protein with an important function – for example the ability to
respond to signals from the environment.
MC Questions:
5. What is the best description of
regulatory sequence?
aa. DNA sequence encoding
proteins that regulate cell
behavior;
bb. DNA sequence that regulates
gene expression;
cc. DNA sequence that regulates
cell cycle;
dd. DNA sequence that regulates
translation.
6. Which of the following best
describes the purpose of splicing?
aa. Removal of intron DNA
sequence to allow for translation
of exon sequence;
bb. Removal of intron RNA
sequence to allow for translation
of exon sequence;
cc. Removal of exon DNA sequence
to allow for translation of intron
sequence;
dd. Removal of exon RNA sequence
to allow for translation of intron
sequence.
82
LESSON READINGS
Introns perform two important functions in a gene: First, having large stretches of intron DNA can act as
a kind of ‘insulation’ for the coding sequences in the exon. If most of the DNA in a gene is not involved in
coding for protein, random mutations to the gene are less likely to affect an important region, even if the
gene is unfolded ready for transcription and therefore vulnerable to carcinogens. Second it has recently
been discovered that introns actually contain regulatory sequences that can control how much RNA is
transcribed from the gene, therefore regulating protein levels. This can be
Non-gene sequences in the genome
DEFINITIONS OF TERMS
Transposable element – the
collective term for transposons
and retrotransposons, or any
DNA sequence that can change
its position within a genome.
Reverse transcriptase – the
enzyme responsible for copying
an RNA template into a doublestranded DNA sequence. This
is used in retroviruses and in
retrotransposons.
Wo r k b o o k
Lesson 3.1
Maybe surprisingly, over half of the genome sequence is not fixed in place. Instead it is composed of
moveable segments of DNA collectively called transposable elements. These moveable elements are
divided into two groups DNA transposons and retrotransposons that move around differently. DNA transposons can actually cut themselves out of the genomic DNA and paste themselves into another region
– not surprisingly this is called ‘cut and paste’ because the DNA sequence is no longer in its usual place.
On the other hand retrotransposons are transcribed into RNA and then re-converted back into DNA
by an enzyme called reverse transcriptase. You may remember from the ID module that reverse
transcriptase is essential to the
replication cycle of HIV. Reverse
transcriptase, which is encoded
within the retrotransposon
sequence itself is able to convert
single-strand RNA sequences into
double-stranded DNA sequences,
which can then insert themselves
somewhere else in the DNA. In
the case of retrotransposons there
are therefore now 2 copies in
the genome – one in the original
location and the second somewhere
else in the genome.
Genomic DNA is clearly a dynamic
flexible molecule rather than an
inert sequence. The moveable
sequences of DNA allows for
diversity. Having DNA that can
move around can disrupt gene
Figure 3: Transposon movement occurs through
a “cut and paste” manner, where the transposon is
removed from the original DNA sequence and inserts
into a new location. Retrotransposons move through
a “copy and paste” method, where the RNA copy of
the retrotransposon is converted into DNA, which
then inserts into another site of DNA.
MC Questions:
7. Which of the following is a useful
function of introns? (Circle all
correct)
aa. Promoting cell survival.
bb. Providing diversity of gene
expression.
cc. Regulating gene expression.
dd. Spacing of exon sequence.
8. True or false: Transposable elements
do not express proteins.
aa. True.
bb. False.
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
________________________________
83
LESSON READINGS
expression when they insert inappropriately into genes. Having reverse transcriptase could lead to
duplication of actual genes if the reverse transcriptase transcribed and then inserted them somewhere
else. This could clearly be a problem if that gene is a proto-oncogene, and in fact there are several
examples of proto-oncogenes to which this has happened.
DEFINITIONS OF TERMS
Epigenetic silencing – the
silencing of expression of certain
regions of DNA through modification of its DNA sequence.
Wo r k b o o k
Lesson 3.1
Fortunately, most transposable elements are tightly wrapped around histones, which inhibits their function
in the same way that tight wrapping prevents gene expression. In the case of transposable elements,
this is called epigenetic silencing. However, as we learned in Unit 2 if tumor formation disrupts the
packaging of DNA it can also stop the epigenetic silencing of genes involved in transposon/retrotransposon movement. As a result the activity of transposons and retrotransposons is increased significantly in
cancer, which, as we will see in the next lesson, increases the chance that genes important for keeping
cells normal will become mutated.
MC Questions:
9. How do transposable elements
affect gene expression? (Circle all
correct.)
aa. Disrupt a gene sequence by
insertion.
bb. Induce epigenetic silencing of
genes.
cc. Reverse transcription of gene
RNA sequences.
dd. Decrease length of introns.
10. Which of the following
explains why there are
more retrotransposons than
transposons in our genome?
aa. Retrotransposons use a “copy
and paste” strategy to move.
bb. Retrotransposons use a “cut
and paste” strategy to move.
cc. Retrotransposons are
normally highly active in the
cell.
dd. Transposons are more
inactive in the cell than
retrotransposons.
84
STUDENT RESPONSES
Describe 2-3 reasons why the 98% of our DNA that does not encode proteins should not be called 'junk' DNA. _____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
____________________________________________________________________________________________________
Remember to identify your
sources
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
_____________________________________________________________________________________________________
Wo r k b o o k
Lesson 3.1
_____________________________________________________________________________________________________
___________________________________________________________________________________________
85
TERMS
TERM
For a complete list of defined
terms, see the Glossary.
Wo r k b o o k
Lesson 3.1
DEFINITION
Autosome
One of 22 chromosomes in human DNA that is found in females and males
Complementary A sequence of DNA or RNA that contains the appropriate sequence of nucleotides to pair with another
strand of DNA or RNA.
Diploid
Any cell that has a pair of chromosomes, or two sets of chromosomal DNA.
Epigenetic silencing
The silencing of expression of certain regions of DNA through modification of its DNA sequence.
Exons
The nucleotide sequence of a gene that codes for protein sequence.
Gene expression
The process by which information from a gene coding region of DNA is used to make a protein.
Genome
The complete sequence of all the chromosomes
Haploid
Any cell that only has a single set chromosomal DNA.
Introns
Parts of a gene between exons that do not contain sequence necessary for protein coding, and are
removed prior to translation.
Meiosis
The process of cell division in sexually reproducing organisms that reduces the number of chromosomes
from diploid to haploid.
Non-coding DNA
DNA sequences that do not make protein. They may make RNA molecules that are necessary for gene
expression.
Regulatory sequence
A segment of DNA that is responsible for increasing or decreasing the expression of specific genes in the
cell.
Retrotransposon
A segment of DNA that is capable of copying itself into RNA and undergoing reverse transcription to form a
new DNA segment that can move into another position in the genome.
Reverse transcriptase
The enzyme responsible for copying an RNA template into a double-stranded DNA sequence. This is used
in retroviruses and in retrotransposons.
Somatic cells
All cells that aren’t eggs or sperm
Transcription factor
Protein that binds to a DNA sequence at the start of a gene and either promotes or inhibits transcription.
86
TERMS
TERM
DEFINITION
Transposable element
The collective term for transposons and retrotransposons, or any DNA sequence that can change its position within a genome.
Transposon
A segment of DNA that is capable of moving into another position in a genome.
Zygote
Fertilized egg
For a complete list of defined
terms, see the Glossary.
Wo r k b o o k
Lesson 3.1
87