Guided Summary

Y6 2015

A. CORE SYLLABUS

(4) Organisation of Prokaryotic and Eukaryotic Genome (I)

Learning outcome 4 (a)
Compare the structure and organization of prokaryotic and eukaryotic chromosomes.
Key words:
Double-stranded DNA, encodes gene products, Genes, Promoter, association with histone, level of
condensation, nucleoid, Nucleus, Origin of replication, Introns, Exons, Enhancers, Silencers,
Centromere, Telomere, genes organized into operons
Similarities:
1. Prokaryotic and eukaryotic chromosomes are both made of double stranded DNA* and
encodes gene products essential for the function of the organism;
2. They genetic information they carry are organized into genes* where each gene is controlled
by a promoter* upstream;
Differences:
Pt of comparison
1. Size and
appearance of
chromosome
2. Association with
histones
3. Level of
condensation
4. Location
5. Origin of replication
6. Presence of noncoding sequences

Prokaryote
Prokaryotes have a single,
small chromosome

Eukaryote
Eukaryotes have multiple, large
chromosomes;

Prokaryotic chromosomes are

not associated with proteins

Eukaryotic chromosomes are

associated with histone*
proteins;
Eukaryotic chromosomes have a
very high level of condensation
forming multiple levels of coiling;
Eukaryotic chromosomes are
found in the nucleus*;
Eukaryotic chromosomes have
multiple origin of replications*;
Non-coding sequences are very
common in eukaryote
chromosomes making up to 98%
of the DNA;
Eukaryote chromosomes have
introns* interspersed between
coding exons*;
Besides promoters, enhancers*
as well as silencers* are
involved in gene-regulation in
eukaryotes;
There is one centromere* per
chromosome while the ends of
the chromosome has telomeres*;
Operons* are rare in eukaryotic
chromosomes;

Prokaryotic chromosomes have

a low level of condensation
forming supercoiled loops
Prokaryotic chromosomes are
found in the nucleoid region
Prokaryotic chromosomes have
a single origin of replication*
Non-coding sequences are not
common in prokaryote
chromosome

7. Presence of introns

Prokaryote chromosomes do
not have introns*

8. Gene regulatory
elements

Promoters* regulate the

expression of genes in
prokaryotes

9. Repeated
sequences

Repeated sequences are rare

in prokaryotes

10. Operons

Related genes are often

organized into operons*;

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Guided Summary

Y6 2015

Comments:
Please make sure that the sentences in each cell under prokaryotes and eukaryotes columns are complete sentences.
You can also write in continuous prose instead of a table if you are fluent enough and have a clear idea about what your
point of comparison is. Prokaryotes is . while eukaryotes ise.g.
Prokaryotes have a single, small chromosome while eukaryotes have multiple, large chromosomes;

Learning outcome 4 (b)

Describe the structure and function of introns, promoters, enhancers and silencers.
Key words:
Non-coding sequences, exons, coding sequences, splicing, introns excised, alternative splicing,
combinations of exons, pre-mRNA, mature mRNA, upstream of transcriptions start site, RNA
polymerase, critical elements, consensus sequence, frequency of initiation of transcription, pribnow
box, TATA box, enhancer regulatory element, specific transcription factors, activators, transcription
initiation complex, looping of DNA, silencer, repressor
Introns:
Structure
1. Introns are non-coding sequences found within a gene;
2. They are interspersed between exons* which are coding sequences;
3. During splicing*, introns are excised out while exons are joined together;
Function
4. Having introns allow alternative splicing* to take place where different segments of DNA are
spliced out while combining different combinations of exons;
5. Resulting in a single pre-mRNA* yielding multiple mature mRNAs or one gene yielding
multiple proteins;
Promoters:
Structure
1. Promoters are non-coding sequences found just upstream of the transcription start site of a
gene;
Function
2. They serve as recognition sites for the binding of RNA polymerase*;
3. The closer the sequences of the critical elements* resemble the consensus sequence, the
stronger the promoter and the higher the frequency of initiating transcription;
4. E.g. Pribnow box* of prokaryotes and TATA box* of eukaryotes;
Enhancers:
Structure
1. Enhancers are non-coding regulatory elements that has an influence on the expression of a
gene far away from them;
Function
2. They bind to specific transcription factors called activators* which increases the frequency of
transcription;
3. by promoting the assembly of the transcription initiation complex* as they cause the looping
of DNA that brings the activators, RNA polymerase and general transcription factors together
at the promoter;
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Guided Summary

Y6 2015

Silencers:
Structure
1. Silencers are non-coding regulatory elements that has an influence on the expression of a
gene far away from them;
Function
2. They bind to specific transcription factors called repressors* which decreases the frequency
of transcription;
3. by preventing the assembly of the transcription initiation complex*;
Comments:
For each item, please address both structure and function.

Learning outcome 4 (c)

Describe the role of telomeres and centromeres.
Key words:
Non-coding DNA, without loss of genetic information, protect and stabilize terminal ends of
chromosomes, chromosome breaks, apoptosis, fusion of chromosome ends, base pair with the
template on telomerase, proper alignment of telomerase, allows for its own extension, constricted
region along the chromosome, sister chromatids to adhere, allow attachment of kinetochore proteins,
spindle fibers, alignment of chromosomes, separation of chromosomes.

Telomeres:
1. Telomeres are non-coding tandemly repeating DNA sequences at the terminals of linear
chromosomes;
2. Allow successive rounds of DNA replication and consequent shortening of daughter
chromosome molecules without (loss of genetic information/erosion of genes);
3. By forming a loop with the 3 overhang, they protect and stabilize terminal ends of
chromosome;
4. which prevents the ends of chromosomes from being recognized as chromosome breaks
which can lead to (cell death/apoptosis);
or prevent fusion of ends of different chromosomes;
5. Possess an overhang which base pairs with the template on telomerase so as to ensure
proper alignment of telomerase;
6. hence allows for its own extension in a repeated manner;
Centromere:
7. Centromeres are non-coding, tandemly repeating DNA sequences found on a constricted
region along the chromosome;
8. They allow sister chromatids to adhere to each other and also allow attachment of
kinetochore proteins* which in turn attach to spindle fibers;
9. This is important in enabling alignment of chromosomes along the metaphase plate and also
separation of chromosomes during anaphase;

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Guided Summary

Y6 2015

Learning outcome 4 (d)

Describe the process and significance of gene amplification in xenopus oocyte.
Key words:
Upregulation of gene expression, increases gene copy number, increases templates for transcription,
rapid demand, cannot be met by transcription and translation of a single gene, rRNA gene cluster,
ribosomes, protein synthesis, rapid growth of oocyte, extrachromosomal circular DNA, rolling circle
mechanism, nick, free 3 end for continuous strand synthesis, recircularises, template used to form
complementary strand.
Significance:
1. Gene amplification allows the upregulation of gene expression by increasing the gene copy
number of a specific gene(s) and hence the templates used in transcription;
2. This is to meet the rapid demand for ribosomes that cannot be met by transcription and
translation of a single gene;
3. The gene amplified in Xenopus oocyte is the rRNA gene cluster* as these genes code for an
important component of ribosomes;
4. that are important in protein synthesis during the rapid growth of the oocyte;
Process:
5. The genomic chromosome give rise to extrachromosomal circular DNA* carrying the rRNA
gene cluster;
6. From this first ring many more copies of circular DNA is synthesized through the rolling circle
mechanism*;
7. A nick occurs in one strand of the circular DNA, and using the free 3 end, continuous DNA
synthesis occurs while the 5 end is displaced;
8. Another nick is made to release the displaced strand that recircularises and act as a template
to form the complementary strand;

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Guided Summary

Y6 2015

(4) Organisation of Prokaryotic and Eukaryotic Genome (II)

Learning outcome 4 (e)

Describe the eukaryotic processing of pre-mRNA in terms of intron splicing, polyadenylation and 5
capping.
Key words:
introns excised, exons joined together, spliceosomes, adenosine monophosphates, 3 end, poly-A
polymerase, 3 poly-A tail, 7 methyl-guanosine, 5 end
Intron splicing:
1. Splicing is a process whereby introns* are excised and exons* are joined together and is
carried out by spliceosomes*.
2. Spliceosomes recognize the points of excision at the intron-exon boundaries.
Polyadenylation:
3. Polyadenylation is a process whereby multiple adenosine monophosphates are added to the 3
end* the pre-mRNA by poly-A polymerase*, forming a 3 poly-A tail*;
5 capping:
4. 7 methyl-guanosine is added to the 5 end* of the pre-mRNA.

Learning outcome 4 (f)

Define control elements and explain how control elements (e.g. promoter, silencer and enhancers)
and other factors (e.g. transcription factors, repressors, histone modification and DNA methylation)
influence transcription.
Key words:
non-coding DNA sequences, transcription factors, promoter, silencer, enhancer, upstream of
the transcription start site, general transcription factors, usually located far away from a gene,
specific transcription factors, activators, repressors
Promoter, binding of RNA polymerase, critical elements, consensus sequence, stronger the
promoter, higher the frequency of initiating transcription, pribnow box, TATA box
silencers, specific transcription factors, repressors, decreases frequency of transcription,
looping of DNA, prevent assembly, general transcription factors, RNA polymerase, promoter,
transcription initiation complex is not formed
enhancer, specific transcription factors, activators, increases frequency of transcription,
looping of DNA, promote assembly, general transcription factors, RNA polymerase,
promoter, transcription initiation complex is formed
Control elements:
(what are control elements?)
6. Control elements are non-coding DNA sequences that transcription factors* bind to
regulate transcription;
7. Control elements include promoter*, silencer* and enhancer*.
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Guided Summary

Y6 2015

8. A promoter usually lies upstream of the transcription start site* and binds to general
transcription factors*;
9. Enhancer and silencer are usually located far away from a gene and bind to specific
transcription factors* called activators* and repressors* respectively;
(how do control elements influence transcription?)
Promoter:
10. Promoter* serve as the recognition site for the binding of RNA polymerase*;
11. The closer the resemblance between the sequences of the critical elements* in the
promoter and the consensus sequence, the stronger the promoter and the higher the
frequency of initiating transcription;
12. e.g. Pribnow box* of prokaryotes and TATA box* of eukaryotes;
Silencer (only eukaryotes):
13. Silencers* bind to specific transcription factors called repressors* which decreases the
frequency of transcription;
14. Looping of spacer DNA* allows repressors bound at silencers to
15. Prevent assembly of general transcription factors* and RNA polymerase* at the
promoter* and the transcription initiation complex* is not formed.
Enhancer (only eukaryotes):
16. Enhancers* bind to specific transcription factors called activators* which increases the
frequency of transcription;
17. Looping of spacer DNA* allows activators bound at the enhancers to
18. promote assembly of general transcription factors* and RNA polymerase* at the
promoter* and the transcription initiation complex* is formed.

Key words:
Acetylation, deacetylation, histones, decondensation, condensation, chromatin, histone
acetylases, add acetyl groups, removes positive charges on histones, removes positive
charges on histones, decreases the electrostatic interactions, negatively charged DNA,
adding acetyl groups, general transcription factors, RNA polymerase, bind the promoter, form
the transcription initiation complex, remove acetyl groups, restores positive charges on
histones, increasing the electrostatic interactions, negatively charged DNA, positively
charged histones, prevents binding, general transcription factors, RNA polymerase,
promoter, transcription initiation complex is not formed.
DNA methylation, addition of methyl group, cytosine, condensation of chromatin, prevent
transcription, blocking binding, general transcription factors, RNA polymerase, promoter,
preventing the formation, transcription initiation complex, recruiting DNA-binding proteins,
condense chromatin
Other factors:
(how do other factors influence transcription?)
Transcription factors:
19. (refer to above section how do control elements influence transcription?)
Histone modification:
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Guided Summary

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20. Acetylation* and deacetylation* of histones* can result in decondensation and

condensation of chromatin* respectively;
21. Histone acetylases* add acetyl groups to lysine residues on histones and removes
positive charges on histones*;
22. This thereby decreases the electrostatic interactions between negatively charged DNA*
and the histones;
23. This allows general transcription factors* and RNA polymerase* to bind the promoter*
to form the transcription initiation complex*, to allow transcription to occur;
24. Histone deacetylases* remove acetyl groups from histones and restores positive charges
on histones*;
25. This increases the electrostatic interactions between negatively charged DNA* and the
positively charged histones*;
26. This prevents binding of general transcription factors* and RNA polymerase* to the
promoter* and the transcription initiation complex* is not formed, and transcription is
prevented.
DNA methylation:
27. DNA methylases* adds methyl group to selected cytosine* nucleotides in e.g. a CG
sequence;
28. This blocks binding of general transcription factors* and RNA polymerase* to the
promoter*, preventing the formation of the transcription initiation complex* and
transcription does not occur;
or
29. This recruits DNA-binding proteins (e.g. repressors, histone deacetylases, repressive
chromatin remodeling complexes) to condense chromatin;
30. such that general transcription factors* and RNA polymerase* to cannot bind the
promoter* to form the transcription initiation complex*, transcription does not occur;

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Guided Summary

Y6 2015

Learning outcome 4 (g)

State the various ways in which gene expression may be controlled at translational (e.g. half life of
RNA, 5 capping, initiation of translation) and post-translational level (e.g. biochemical modification
and protein degradation).
Learning outcome 4 (h)
Outline the differences between prokaryotic control of gene expression with the eukaryotic model.

Genomic level

Prokaryotic
None prokaryotes (in general) dont rely on modifying chromosomal structures to control gene
expression.

Eukaryotic
(1) Organisation of chromosome
What happens to expression of gene X if it is found in a region of chromosome called
heterochromatin or euchromatin?
Heterochromatin* = DNA winds more tightly around histones
prevents access of general transcription factors* and RNA polymerase* to promoter
of gene, transcription initiation complex* not formed at promoter*
inactive gene expression / no transcription
Euchromatin* = DNA winds less tightly around histones
promotes access of general transcription factors* and RNA polymerase* to promoter
of gene, transcription initiation complex* formed at promoter*
active gene expression / transcription
What is X chromosome inactivation?
1 of 2 X chromosomes in mammals like female humans is compacted to become Barr
body.
Describe what happens to expression of gene X if it is found on a chromosome that
undergoes X chromosome inactivation.
Compact structure of Barr body prevents access of RNA polymerase, and general
transcription factors to promoter of gene
inactive gene expression / no transcription
(2) DNA methylation
What is DNA methylation?
Addition of a methyl group to selected cytosine* (C) nucleotides
Describe what happens to expression of gene X when it is methylated.
General transcription factors* and RNA polymerase* cannot bind to promoter,
transcription initiation complex* is not formed at promoter*
no gene expression
(3) Chromatin remodelling complex
What is chromatin remodelling complex?
A complex of proteins capable of altering structure of nucleosomes
Describe what happens to expression of a gene when chromatin remodelling complex
causes DNA to bind more tightly/loosely to histones.
When DNA is more tightly coiled around histones, general transcription factors* and
RNA polymerase* cannot bind promoter* and transcription initiation complex* is not
formed.
no transcription
When DNA is less tightly coiled around histones, general transcription factors* and RNA
polymerase* can bind promoter* and transcription initiation complex* is formed.
transcription can occur
Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Guided Summary

Y6 2015
(4) Histone deacetylation / acetylation
What is histone deacetylation?
- Removal of acetyl groups from lysine residues of histones by histone deacetylases*
Describe what happens to expression of gene X when histones are deacetylated.
- Removal of acetyl groups restores positive charge of histones*, increasing the
electrostatic interactions between negatively charged DNA* and histones
- Prevent binding of general transcription factors* and RNA polymerase*, transcription
initiation complex* is not formed at promoter* of gene.
- Transcription prevented.

What is histone acetylation?

Addition of acetyl groups to lysine residues of histones by histone acetylases*
Describe what happens to expression of gene X when histones are acetylated.
Addition of acetyl groups removes positive charge of histones*, decreasing the
electrostatic interactions between negatively charged DNA* and histones
Allow binding of general transcription factors* and RNA polymerase*, transcription
initiation complex* is formed at promoter* of gene.
Gene is expressed / transncribed

(5) Gene amplification

Define gene amplification.
Describe what happens to expression of gene X when the region it is contained in,
undergoes gene amplification.
Replication of a specific gene to create more copies of that gene.
Gene of interest exists in high copy number, so increased copies of its mRNA and protein
formed.

Transcriptional
level

Prokaryotic
Eukaryotic
What is transcription?
(Must include terms: DNA, mRNA, tRNA, rRNA, transcribed, RNA polymerase)
Transcription is a process in which base sequence of a gene (DNA) is used as a template to
direct synthesis of RNA (mRNA, tRNA, rRNA). Need RNA polymerase (enzyme) and
transcription factors (proteins).
Where does transcription take place?
Prokaryotes: Nucleoid
Eukaryotes: Nucleus
What does transcriptional control mean?
Controlling when and how often a gene is transcribed to form mRNA.

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Guided Summary

Y6 2015
Transcriptional control is the most important part
of control of gene expression for prokaryotes.
(1) Promoter
- What is a promoter?
Promoter = DNA sequence where RNA
polymerase*
bind
to
start/initiate
transcription.
- What are the critical elements?
Critical elements = short DNA sequences
located within the promoter & consists of:
-10 sequence (aka Pribnow box)
-35 sequence
- What is the role of the -10 and -35
sequences in regulating frequency of
gene expression?
The more similar the -10 and -35
sequences are to the consensus
sequences*, the stronger the promoter*,
the higher frequency of transcription /
gene expression.
(2) Sigma factor
- What are sigma factors?
Sigma factor = a subunit of RNA
polymerase that recognises the -10 & -35
sequences in prokaryotic promoters.
Sigma factor + core RNA polymerase =
RNA polymerase holoenzyme
Sigma factor binds to core RNA
polymerase to form the RNA polymerase
holoenzyme which scans along the DNA
for the -10 and -35 sequences.
- How do sigma factors regulate frequency
of transcription?
Different
sigma
factors
recognise
different promoters.
Availability of sigma factors will determine
which genes are transcribed and the
frequency of transcription (e.g. high
levels of sigma factor that recognises
promoter of gene X high transcription
frequency of gene X).
(3) Operon
- What is an operon?
Genes with related functions are
grouped together. Expression of these
genes are controlled by one common
promoter* and transcribed into a
single, polycistronic mRNA*.
- What is the advantage of grouping
genes that code for gene products with
related functions together?
Since expression of the genes in the
operon are controlled by one promoter,
all the genes in the operon are turned
on and off together, hence more
efficient.

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

(A) Promoter
- What is a promoter?
Promoter = DNA sequence where RNA
polymerase* and general transcription
factors* bind to form the transcription
initiation complex* to start/initiate
transcription.
- What are the critical elements?
Critical elements = short DNA sequences
located within the promoter & consists of:
TATA box at -25 site
CAAT and GC boxes
- What is the role of the TATA box, CAAT
& GC boxes in regulating frequency of
gene expression?
- TATA box determines the precise
location of the transcription start site
- CAAT & GC boxes help to recruit
general transcription factors* and
RNA polymerase* to promoter for
assembly
of
the
transcription
initiation complex*.
The greater the similarity between
the critical elements and the
consensus
sequences*,
the
stronger the promoter*, the higher
frequency of transcription / gene
expression.
(B) Enhancers / Silencers
What are enhancers & silencers?
Enhancer = DNA sequence that bind to
specific transcription factors* called
activators* to increase transcription
frequency.
Silencer = DNA sequence that bind to
specific transcription factors* called
repressors* to prevent transcription.
Where are enhancers & silencers
located?
Usually far from a gene - thousands of
nucleotides upstream / downstream of the
gene, but can also be found within intron.
Describe how do enhancers influence the
expression of a gene.
- Activators* bind to enhancer*
- Spacer DNA bends and allows
activators bound to enhancer
- to promote binding of general
transcription factors* and RNA
polymerase* to promoter* to form the
transcription initiation complex*.
- Bound activator may recruit histone
acetylases* or chromatin remodelling
complexes* to increase accessibility to
promoter.

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(4) Operator & Repressor
- How do repressors influence frequency
of transcription of genes?
Repressor* (protein) bind to operator*
(in lac and trp operon) prevent
binding of RNA polymerase* to
promoter* no transcription / basal
level of transcription.
(5) CAP binding site & CAP
- How does Catabolite Activator Protein
(CAP)
influence
frequency
of
transcription of genes?
CAP* (protein) bind to CAP binding
site* (in promoter of lac operon)
increases affinity of RNA polymerase*
for promoter* higher frequency of
transcription.

Posttranscriptional
level

Describe how do silencers influence the

expression of a gene.
- Repressors* bind to silencer*
- Spacer DNA bends and allows
repressors bound at silencer region
- to
prevent
binding
of
general
transcription factors* and RNA
polymerase*
and
transcription
initiation complex* is not formed at
promoter*.
- Bound repressor may recruit histone
deacetylases* (HDACs) or repressive
chromatin remodelling complexes* to
decrease accessibility to promoter, or
interfere with action of activators bound
to enhancer.

None prokaryotes (in general) dont modify As opposed to prokaryotes, transcription and
mRNA after transcription. mRNA is used directly translation do not occur concurrently. Why?
for translation.
Presence of nuclear envelope* in
Often, both transcription and translation happen
eukaryotes prevents transcription and
at the same time. As the mRNA is being
translation from taking place concurrently
synthesised, ribosomes begin binding to mRNA In eukaryotes, pre-mRNA* is formed from
to synthesise polypeptides.
transcription and needs to undergo posttranscriptional modification* to form
mature mRNA* before translation can take
place.
Post-transcriptional modification of mRNA
What is the order of the 3 modifications?
(a) capping at 5 end
(b) splicing of pre-mRNA
(c) adding a poly-A tail to the 3 end
(polyadenylation)
Where do these modifications take place in
the cell?
Nucleus
For each of the 3 modifications:
Describe
each
modification
and
its
significance to gene regulation
(a) Capping at 5 end of pre-mRNA
Add a 7-methyl guanosine (modified
guanosine) to 5 end of pre-mRNA.
Significance?
helps cell to recognise mRNA from other
RNAs for splicing & polyadenylation
helps mRNA to exit from nucleus to
cytoplasm for translation
protects
pre-mRNA
from
rapid
degradation by cellular ribonucleases.
Increases half life of mRNA.
recognised by translation initiation
factors* which then help small

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ribosomal subunit bind to mRNA so that
translation can occur
(b) Splicing of pre-mRNA
Process where introns* are excised,
exons*
are
joined
together
by
spliceosome*.
Significance?
- cut out non-coding introns or else a
protein will not be properly made.
- Alternative splicing*; all introns*
excised, different combination of exons*
are joined together to give different
mature mRNA*
allows 1 gene to code for different
polypeptides.
(c) Polyadenylation at 3 end of pre-mRNA
Process
of
adding
adenosine
monophosphates to 3 end* of pre-mRNA
by poly-A polymerase*.
Significance?
- Slow down degradation of mRNA by
ribonucleases. Enhances half-life /
stability of mRNA.
- a signal to direct export of mature
mRNA from nucleus to cytoplasm.
- works with 5 cap* to regulate mRNA
translational efficiency.

Translational level

What is translation?
Process by which mRNA is used by ribosomes as a template to synthesise polypeptides.
Where does translation occur?
Free ribosomes in cytoplasm or ribosomes on rough endoplasmic reticulum.
What is a polycistronic mRNA?
A single mRNA codes for several different
polypeptides. Contains multiple start and stop
codons in a single mRNA. Only prokaryotes
produce polycistronic mRNA.
(1) Half life of mRNA
What does an mRNA with a short half life
mean?
Short half life = mRNA is rapidly degraded
by ribonucleases, cant get that many
polypeptides translated from it.
Describe the 2 ways to control mRNA half
life.
Prokaryotic mRNAs inherently have a
relatively short half-life as compared to
eukaryotes due to lack of 5 cap* & 3
poly-A tail*.
Anti-sense RNA* binds to the mRNA*,
block translation / target the mRNA for
degradation shorten half life of mRNA.

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

Note:
eukaryotic
mRNAs
are
monocistronic and not polycistronic.

usually

(1) Half life of mRNA

What does an mRNA with a short half life
mean?
Short half life = mRNA is rapidly degraded by
ribonucleases,
cant
get
that
many
polypeptides translated from it.

Describe the ways to control mRNA half life.

Half-life/ stability is influenced by factors such
as length of 3 poly-A tail* and presence of 5
cap*.

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(2) Start of translation
Describe the 2 ways to control translation
initiation on an mRNA.
- A repressor* protein binds at/near to
Shine-Dalgarno sequence*, prevents
binding of small ribosomal subunit,
ribosomes cannot assemble properly
translation fails.
- Anti-sense RNA* binds to the mRNA*,
prevents binding of small ribosomal
subunit, ribosomes cannot assemble
properly
translation fails.

Post-translational
level

(2) Start of translation

Describe the 2 ways to control translation
initiation on an mRNA.
Translation can be blocked by a repressor*
protein that binds to these parts on an mRNA:
5 cap* and/or its vicinity i.e. 5 untranslated
region* (5 UTR), and 3 untranslated
region* (3 UTR).

What does post-translational control mean? Has the polypeptide been made?
Controlling proteins that are already present in the cell by activating or inhibiting their functions, or
regulating their levels
None prokaryotes (in general) dont depend
on modifying proteins to control their activities.

Briefly describe what these post-translational

modifications are, and how they control the
gene expression levels:
(1) Covalent modifications
Newly synthesised protein go through
changes (e.g. glycosylation*, disulfide
bond* formation, cleavage*) to form the
functional protein.
(2) Phosphorylation / Dephosphorylation
Newly synthesised protein go through
phosphorylation*
(add
phosphate
group) or dephosphorylation* (remove
phosphate group) so that they can
become active/inactive respectively.
(3) Protein degradation
Proteins no longer needed will be
degraded by proteasomes*. Ubiquitin*,
will be added to such proteins, and
proteasomes will recognise and degrade
such proteins.

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Learning Outcomes
4 (i) Describe the functions of common proto-oncogenes and tumour suppressor genes (limited to ras and p53) and
explain how loss of function mutation and gain of function mutation can contribute to cancer.

Define

Explain consequences of
mutation

proto-oncogenes
Normal cellular genes that code for products
that stimulate normal cell growth and
proliferation.

tumour suppressor genes

Normal cellular genes which code for
products which inhibit cell division and help
prevent uncontrolled cell division.

Proteins coded by proto-oncogenes are

involved in stimulating normal cell division,
and signaling pathways.
e.g. growth factors, growth factor receptors,
growth
signal
transduction
factors,
transcription factors

Products of tumour suppressor genes

activate cell cycle arrest, DNA repair and/or
apoptosis (programmed cell death).

When proto-oncogenes mutate, they are

known as oncogenes*.
Mutation results in an increase in activity or
increased amount of a proto-oncogenes
protein product.
Since proto-oncogenes regulate cell division,
any extra gene products coded by protooncogenes will cause uncontrolled/excessive
cell division.

Explain how mutation

can be brought about

(a) Substitution mutation such that the protooncogene protein

coded for is
hyperactive or more resistant to
degradation
e.g.: a regulatory protein (such as growth
factor encoded by proto-oncogene)

Mutation results in a non-functional tumour

suppressor genes protein product.
Since tumour suppressor genes help inhibit
cell division (while repairing a mutation), any
missing gene products from them will cause
cell division to continue without repairing
DNA/without going into apoptosis.
Any mutations that cause gene product
coded by tumour suppressor gene to be nonfunctional.
e.g.: point mutations (i.e. substitution /
addition / deletion mutation)

(b) Gene amplification unexpectedly making

many copies of a chromosomal region
containing that proto-oncogene.
leads to excessive production of protooncogene protein
(c) Chromosomal movement
such
that
unusual exchange of chromosomes causes
a proto-oncogene to be placed under the
control of an enhancer
leads to increased transcription and
more gene products from proto-oncogene
Virus genome that integrate into human
genome may carry its own enhancer
leads to increased transcription and
more gene products from proto-oncogene

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

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Y6 2015
Ras gene

State if gene is a protooncogene or tumour

suppressor gene
Describe role of these
gene products

Proto-oncogene

Ras gene codes for ras proteins which are

signal transducers.
Activated ras proteins transduce signals
when growth factor binds to receptor to
downstream signaling processes. This
activates cell division.

Link consequences of
their mutation to cancer

p53 gene
Tumour suppressor gene

p53 gene codes for a specific transcription

factor (p53) that binds to DNA to promote
synthesis of cell cycle-inhibiting proteins
p53 protein can activate genes that are involved
in stopping cell division, repairing DNA and
starting apoptosis.

Mutation results in a ras protein that is

active all the time.
This leads to increased cell division even
when growth factor doesnt bind to the
receptor. Uncontrolled cell division leads to
cancer.

Mutation results in a p53 protein that is not

active or whose amount cannot be increased.
This leads to continued cell division even when
DNA is not repaired, accumulating mutations
(characteristic of cancer).

Gain-in-function mutation
A mutation that causes a gene to be
expressed in a place/ at a time when it is
not normally expressed, or the gene
product is hyperactive.

Loss-in-function mutation
A mutation that causes a gene product to nonfunctional

Type of genes the

mutation affects
Number of alleles that
has to be mutated in
order to be cancerous

Proto-oncogene

Tumour suppressor gene

One allele need to be mutated

- mutation in just one copy is enough to
give extra gene products / hyperactive
gene products that cause the cell cycle to
escape normal control.

Both alleles need to be mutated

- if only one allele is mutated, there is still
another allele that still codes for functional
tumour suppressor gene products to inhibit cell
division.

Characteristics of gene
products from mutation

Gene products of mutated protooncogenes become hyperactive / resistant

to degradation, or are produced in
excessive amounts

Gene products of mutated tumour-suppressor

genes are defective / non-functional.

Effect on cell cycle

Overstimulate cell cycle

Cant stop cell cycle to repair damages.

Cells with accumulated mutations keep dividing.

Description

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

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Guided Summary

Y6 2015

Learning Outcomes
4 (j) Describe the development of cancer as a multi-step process.
Definition:
Cancer is a group of diseases characterised by uncontrolled cell division and spread of abnormal cells.

Multi-step development of cancer

The development of cancer requires the accumulation of mutations* in the genes which control regulatory

checkpoints* of the cell cycle in a single cell

This

will disrupt the normal cell cycle*, thus causing the cell to undergo excessive cell growth and
proliferation

A gain-in-function* mutation is a dominant mutation where mutation in just one copy/allele of a proto-

oncogene* will result in its overexpression which will result in the production of excessive amounts of growth
factors, or production of hyperactive/degradation-resistant growth factors, leading to cell proliferation
A loss-of- function* mutation is a recessive mutation where mutations in both copies/alleles of a tumour

suppressor gene* will disrupt their ability to inhibit cell cycle, enable DNA repair and promote apoptosis
Upregulation/activation of the genes coding for telomerase* result in telomeres being lengthened and the

cell can thus dividing indefinitely as the chromosomes are prevented from shortening with each DNA
replication cycle.
Loss of contact inhibition* will enable the cells to grow into a tumour/mass of cells.
Angiogenesis* must occur within the tumour so that the blood vessels formed can transport oxygen and

nutrients for its growth.

Finally the cells must have the ability to metastasise*. i.e leave the primary site and spread to other tissues

in different parts of the body via the blood stream and form tumours there.
The above mutations should occur for cancer to develop.
As it takes years to accumulate these mutations, developing cancer increases with age.

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

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Guided Summary

Y6 2015

Characteristics
Cell division
Contact inhibition
Ability to differentiate
Susceptibility to
apoptosis
Ability to adhere to other
cells
Ability to stimulate
growth of blood vessels

Pre-requisite
before cancer
occurs
All changes must
occur in a single cell
Mutations are not be
repaired
Cells with mutations
are not be killed
Regulatory
checkpoints must be
disrupted

Normal cells
Controlled cell proliferation
Contact inhibition
monolayer of cells
Can differentiate
Undergoes apoptosis

Cancerous cells
Excessive cell proliferation
No contact inhibition
multiple layer of cells
Undifferentiated
Not susceptible to apoptosis

Cell adhesion
formation of tissues and organs
No new blood vessels

Can detach from surrounding cells

Stimulates growth of new blood vessels within
tumours

Description

Cancer begins with a single cell which undergoes uncontrolled cell division
All changes such as getting genetic mutations, not repairing those mutations must all
happen to that same, single cell first.
Cells naturally contain proof-reading mechanisms to check, and to correct genetic
mutations.
Cells with genetic damages that cant be repaired are induced to die (so that damaging
mutations are eliminated)
Regulatory checkpoints in cell cycle prevent a cell from deteriorating into a cancerous
one.
For a cell to become cancerous, the genes at each checkpoint have to be mutated such
that they are unable to carry out their normal functions.

Last updated by Ms. Emeline Choo, Mr. WY Ngan, Mr Ariff Chan

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