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Core Topic 2: DNA and Genomics
Core Topic 4: Organisation & Control of Eukaryotic Genome
Name:

Class:

Date:

MULTIPLE CHOICE QUESTIONS

Qn

Answer

Qn

Answer

Qn

Answer

ACJC 2014/11

ACJC 2014/12

ACJC 2014/13

TJC 2014/14

10

TJC 2014/18

TJC 2014/19

Which correctly describes the structure and role of a type of nucleic acid?
A

double stranded, partly base paired, unpaired bases to bind to a ribosome

single stranded, base sequence acts as a template for RNA synthesis

double stranded, base sequence acts as a template for DNA synthesis

single stranded, partly base paired, binds to tRNA

The list shows the stages in the cellular synthesis of proteins.

1 movement of mRNA from nucleus to cytoplasm
2 linking of adjacent amino acid molecules
3 transcription of mRNA from a DNA template
4 formation of the polypeptide chain
5 attachment of the mRNA strand to a ribosome
Which sequence is correct?
A

13254

15342

31524

34125

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If there were 34 amino acids and DNA only contained two types of nitrogen bases, what is the
minimum number of bases per codon that could code for proteins?
A

Below is a part of the DNA genetic code for six amino acids.
CGG codes for alanine
TTT
codes for lysine
GCG codes for arginine
AAA
codes for phenylalanine
CCA
codes for glycine
CAA
codes for valine
A length of DNA codes for the sequence of amino acids shown below.
arginine - glycine - phenylalanine - valine - alanine
The diagram shows an mRNA molecule that was transcribed from the DNA.

Which mRNA triplet contains a single transcription error?

A

the first

the second

the third

the fourth

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A mutation of a gene coding for an ion pump in cell surface membranes results in the
substitution of one amino acid, arginine, by another, histidine.
The DNA triplet codes for the two amino acids are shown.
arginine
GCA
histidine
GTA
GCG
GTG
GCT
GCC
TCT
TCC
Which mutation has occurred in the DNA?

addition of an extra nucleotide

replacement of a nucleotide with a purine base by one with a different purine base

replacement of a nucleotide with a purine base by one with a pyrimidine base

replacement of a nucleotide with a pyrimidine base by one with a different pyrimidine base

Which of the listed features are characteristic of a eukaryotic genome?

1 circular DNA
2 DNA associated with histone
3 DNA may be transferred to new cells by mitosis
A

1 only

2 only

1 and 3

2 and 3

One stage during protein synthesis in eukaryotic cells involves preliminary mRNA. known as
pre-mRNA. The pre-mRNA is made up of exons and introns.
What describes the next stage in the process?
A

All the exons are removed, so that the introns can be translated.

All the introns are removed, so that the exons can be translated.

Some of the introns and exons are removed, so that the remaining exons and
introns can be translated.

All the exons and introns are translated.

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When a person undergoes a stressful experience, their immune system can be depressed and
they become more susceptible to infection. Some of the elements involved in this chain of
events are shown in the diagram below.

Which combination correctly shows the genes that have transcription-enhancing factors bound
to their control elements during the above sequence of events?

gene for ACTH

gene for TCF

gene for
interleukin 2

Four different genes are regulated in different ways.

Gene 1 undergoes tissue-specific patterns of alternative splicing.
Gene 2 is part of a group of structural genes controlled by the same regulatory sequences.
Gene 3 is in some circumstances subject to methylation.
Gene 4 codes for a repressor protein which acts at an operator site close by.
Which row of the table correctly identifies which genes are prokaryotic and which are
eukaryotic?
prokaryotic

eukaryotic

1 and 2

3 and 4

1 and 3

2 and 4

2 and 3

1 and 4

2 and 4

1 and 3

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10

Structured Questions (Answer all questions. Write your answers in the spaces provided.)
1

In the Meselson-Stahl density-gradient experiment, it was shown that DNA replicates semiconservatively.
(a) Describe how the experiment was carried out.
Culture bacteria Escherichia coli, in ammonium chloride medium;
With 15N isotope and allow to grow for a many generations;
Transfer bacteria to medium containing 14N and allow bacteria to grow for one generation /
20 minutes, two generations ;
Extract DNA from a sample of bacteria from each generation and centrifuge DNA in caesium
chloride;
[4]
(b) Draw bands on Fig. 1.1 to indicate the position of DNA band relative to the DNA standards
composed entirely of 15N and 14N DNA. Indicate the relative amounts by the thickness of
the band.

After one generation

After two generation

Fig. 1.1
[2]
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(c) List four ways in which DNA replication differs from transcription.
Replication

Transcription

Template

Involves both strands of DNA

Involves only the template strand

Parts of template
copied

Entire DNA molecule is replicated

Only short segments of DNA is

transcribed to form RNA

Enzymes
involved

DNA polymerase, RNA primase, RNA polymerase

DNA helicase, DNA topoisomerase,
DNA ligase

Product

Double-stranded DNA

Single-stranded RNA, which can

exist as rRNA, mRNA or tRNA

Pyrimidine bases Thymine and Cytosine (must spell Uracil and Cytosine (must spell out),
used
out), Adenine base pairs with Uracil base pairs with Adenine of
Thymine
DNA or another RNA molecule
Monomers
added

Deoxyribonucleotides
/ Ribonucleotides / ribonucleosides
deoxyribonucleoside triphosphates
triphosphate

[4]
(d) Explain the importance of base pairing in DNA replication.
Complementary nucleotides bind via hydrogen bonding between A = T, G C (spell out);
Ensures stability of DNA by maintaining a constant width / diameter of 2nm;
Accept: allow for proofreading + elaboration
[2]
[Total: 12]
2

Table 2.1 shows three amino acids and the DNA base sequence that codes for them.
(a) Complete Table 2.1 by stating the sequence of mRNA bases that code for each amino
acid.

AGC
UAU
UGU
Table 2.1
[1]

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(b) Fig. 2.1 shows the tRNA molecule that would bring serine to the ribosome.
Y

Z
Fig. 2.1
(i) Write the letter Y on the diagram to show where serine would attach.
[1]
(ii) Write the letter Z on the diagram to show where the anticodon would be.
[1]
(iii) Explain the role of the anticodon in protein synthesis.
Binds to codon on mRNA via complementary base pairing A = U, G C using hydrogen
bonds;
Thus allows correct amino acid to be brought into Acceptor site of ribosome during
translation;
[2]
(c) The base sequences on the DNA of homologous chromosomes are almost the same, even
though they may have different alleles in many positions.
Explain why the DNA base sequence of homologous chromosomes is almost the same.
Homologous chromosomes contain the same genes at the same gene loci;
Alleles usually possess small differences in nucleotide base sequence due to point
mutations;

[2]
[Total: 7]

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H1 2007/P2/Q2
3

In 1958, an experiment was carried out to investigate the way in which DNA replicates.
Escherichia coli bacteria were grown in a medium containing 15NH4Cl. After very many
generations all the bacterial DNA contained 15N and was described as 'heavy'.
(a) (i) Name the parts of a DNA nucleotide that do not contain nitrogen.
Deoxyribose and phosphate group;
[1]
(ii) Suggest why bacteria were used in this experiment.
Bacteria reproduce quickly and many generations can be studied in a short time;
[1]
(b) The bacteria were then transferred to a medium containing 14NH4Cl. Some of the bacteria
were removed as soon as they had reproduced once (first generation). Further samples
were removed after the 2nd and 3rd generations.
The bacterial DNA was then extracted from each sample, placed in a solution of caesium
chloride and spun in a centrifuge. The percentage of 15N (heavy) DNA in each sample was
then calculated.
From your knowledge of DNA replication, complete Table 2.1, below.
Table 2.1
generation

%15N in each sample

50

25

12.5

[2]
(c) Explain why DNA replication is said to be 'semi-conservative'.
Parent DNA molecule separate into 2 single stranded DNA by breaking hydrogen bonds
between nitrogenous base;
Each parental strand act as a template to synthesise daughter strands;
Each new DNA molecule consists of a parental strand and a newly synthesised strand;

[3]
[Total: 7]

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H1 2007/P2/Q3
4

Fig. 2.1 shows a section of DNA containing one gene.

Fig. 2.1
(a) (i) State one way in which the structure of this gene indicates that it is from a eukaryote.
The gene contains introns;

[1]
(ii) Using the same diagrammatic format as Fig. 2.1, show what the pre-mRNA and mRNA
will be for this gene.
pre-mRNA

5 UTR

3 UTR

mRNA

5 UTR

5 methylguanosine cap

3 UTR

AAAAAAAAA
3 poly A tail

[3]

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(b) Sometimes, a single nucleotide in the DNA sequence is replaced by a different nucleotide.
This is called a substitution.
Explain one possible consequence of each of the following changes, on the structure of
the resulting protein.
a substitution at P.
Substitution of one base pair for another at P (DNA) will change a triplet / codon in the
mRNA;
The amino acid coded for by codon may be changed;
Since an amino acid is changed, different bonds may formed resulting in different 3dimensional structure / tertiary structure from original protein;
OR
Substitution of one base pair for another at P (DNA) will change a triplet / codon in the
mRNA;
The amino acid coded for by codon may remain the same;
Due to the degeneracy of the genetic code, where more than one codon codes for the
same amino acid;
Since an amino acid is same, tertiary structure from original protein;
[3]
a substitution at Q.
Q is within the intron sequence and introns will be removed during splicing / post
transcriptional modification ;
No change in the structure of final protein since it is translated from mature mRNA;

[2]
[Total: 9]

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N2009/H1/P2/Q3
5

(a) Describe how DNA is packaged in eukaryotic cells.

Linear double stranded DNA which is negatively charged;
winds around an octamer of positively charged histone proteins to form a nucleosome;
Nucleosomes are joined added by linker DNA to give rise to a beads-on-string structure;
Further coiling of nucleosomes to form solenoid structure, which is appears as 30nn
chromatin fibre;
Further folding of the 30nm fibres into looped domains (300nm) which are held by nonhistone proteins / scaffolding proteins.
Further compaction of looped domains to 700nm fibres which form the chromosomes /
heterochromatin;
[5]
(b) The ends of each DNA molecule are lengths of DNA called telomeres. In humans,
telomeres are made up of the base sequence TTAGGG, which is repeated up to 400 times.
In some cells, each time a DNA molecule is replicated, the last 150 - 200 bases are not
copied. The telomeres therefore get shorter with each DNA replication until they become
too short for DNA replication to take place.
Calculate the maximum number of replications that can occur with the DNA that contains
400 TTAGGG repeats.
Show your working.

400 x 6 = 2400 ;
2400 divided by 150;
= 16;
@15; (it would be unlikely for the DNA molecule to replicate if there were no spare bases
available)

..[3]

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(c) In the body, only cells such as embryonic stem cells that need to divide regularly express
telomerase. Other somatic cells do not normally express telomerase.
Most cancer cells which are continually dividing contain an enzyme, telomerase, which
maintains the length of the telomere.
Suggest how these cancers could be treated.
Using an inhibitor for telomerase enzyme;
Inhibitor binds permanently to the active site of enzyme preventing telomerase from
maintain the length of telomere;
@ (Gene switching) A repressor that binds to silencer controlling expression of
telomerase gene
Prevents the formation of transcription initiation complex / RNA polymerase can no longer
binds to promoter;
[2]
[Total: 10]
6

The diagram shows a duplicated eukaryotic chromosome.

Fig 2.1
(a) Describe the functions of:
(i) Centromere
site of attachment for two sister chromatids of a metaphase chromosome;
involved in chromosomal movement during mitosis and meiosis;
Function as spindle-fibre attachment sites on chromosomes via kinetochore;
Required for separation of homologous pair of chromosomes to opposite poles during
anaphase I of meiosis /
separation of sister chromatids during anaphase of mitosis and anaphase II of meiosis;
[2]

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(ii) Telomere
Telomeres prevent the ends of chromosomes from being degraded by exonucleases;
Telomeres protect important genes near the telomeres by merely delaying the
degradation of genes;
Telomeres prevent ends of different chromosomes from accidentally fusing with each
other;
Telomeres provide a counting mechanism for the number of cell division a cell has
undergone and prevents unlimited proliferation of cells in adult tissue;
[2]
(b) Describe the unique structural features of telomeres.
Telomere is non-coding DNA in nature ( does not contain genes ) but consists of tandem
repeats of a short nucleotide sequence. E.g. TTAGGG;
The 3 single-stranded overhang folds back and forms a T-loop, hiding the singlestranded DNA overhang;
The overhang hybridises with an earlier repeat of the same complementary sequence in
the opposite strand;
Telomere capping proteins bind at the T-loop juncture to maintain the stability of this
structure hence preventing degradation by exonucleases;
[3]
(c) In yeast, protozoa and other single-celled organisms, telomerase is active and these cells
can potentially divide forever. Explain briefly how telomerase carries out its function.
Telomerase functions as a reverse transcriptase, an enzyme which synthesizes a
double-stranded single stranded DNA from a single-stranded RNA template;
Telomerase binds to telomere via complementary base pairing between 3 overhang of
the telomere and the RNA component of the enzyme;
The 3 overhang is extended using the telomerase RNA as a template. DNA nucleotides
complementary to the telomerase RNA are added;
The telomerase translocates towards the 3 end of the newly added sequence for further
extension;
The extended 3 end is used as a template for addition of primers and DNA polymerase
synthesises a strand complementary to the 3 overhang;

[3]

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(d) When chromosomes are broken by exposure to high-energy radiation such as X-rays, the
resulting broken ends exhibit a pronounced tendency to stick to each other and fuse.
Suggest why this might have occurred.
The broken ends resulting from irradiation will not contain telomeres;
Thus free ends are subjected to the activities of enzymes like exonucleases and ligases,
which modify the ends;
The ends can regain stability by fusing with broken ends of other DNA fragments;
[3]
[Total 13]
7

Figure 3.1 shows an eukaryotic cell undergoing protein synthesis.

Fig 3.1
(a) State the four stages in which protein synthesis is regulated.
1. Chemical and structural modification of chromatin/DNA;
2. Transcription;
3. Post-transcriptional modification;
4. Transport of RNA from nucleus to cytoplasm;
5. Translation;
6. Post-translational modifications; (any 4)
[2]
(b) Transcription and translation are coupled in prokaryotes. Describe why this is not the case
in eukaryotes.
Eukaryotes have nuclear envelope which compartmentalises the two processes and
prevents them from happening simultaneously;
[1]
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(c) State how the pre-mRNA is modified to produce the mature mRNA
Capping of the 5 end of pre-mRNA with methyl group to ( prevent degradation by 5
exonucleases and allow binding to large ribosomal subunit);
Splicing which is the removal of intron and the subsequent ligation of exons to
produce a mature mRNA;
Addition of poly(A) tail to the 3 end of pre-mRNA (to prevent degradation by 3
exonucleases and facilitates the transport of mRNA from the nucleus);
[3]
[Total 6]
8

In Drosophila, expression of the yellow gene is needed for the formation of dark pigment in
many different tissues; without this expression, a tissue appears yellow in colour.
In the wings, the expression of the yellow gene is controlled by an enhancer located upstream
of the genes transcription initiation site. In the tarsal claws, expression is controlled by an
enhancer located within the genes only intron.
(a) Explain the role of an enhancer.
Enhancers are regulatory sequences on DNA which activators bind to;
increases interaction between promoter and RNA polymerase, hence increasing
the rate of transcription;
It occurs by looping the DNA, which further stabilizes the transcription initiation
complex through protein-protein interaction;

[2]
(b) Suppose that by genetic engineering, the wing enhancer is placed within the intron and the
claw enhancer is placed upstream of the transcription initiation site. Suggest and explain
the phenotype exhibited by a fly that carried this modified yellow gene in place of its
natural yellow gene.
Darkly pigmented wings and claws;
Enhancers can function in different positions, either in introns or upstream of a gene;
[2]

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Figure 4.1 shows alternative splicing of a pre-mRNA generating divergent forms of the protein.

Fig 4.1
(c) With reference to Figure 4.1, describe how introns regulate gene expression.
They are interspersed between the exons in pre-mRNA;
Action of spliceosome results in excision of different introns, giving rise to different
mature mRNA sequences;
Some combinations of exons results in the mature mRNAs that are degraded while
other combinations of exons are translated to synthesize proteins that are of different
forms;
Resulting in differential gene expression, which gives rise to proteins of different
functions in different specialised tissues;
[4]
[Total 8]

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A cell uses its genes selectively. This process allows for the different kinds of cells needed to
make up different organs like the brain and liver. Some genes stay active all the time to
produce proteins needed for basic cell functions. Others are turned on when necessary.
Examples of such genes include proto-oncogenes and tumour suppressor genes, both of
which regulate cell division. Mutation of these genes may lead to cancer.
(a) Define the following terms:
(i) Cancer
Cancer is a result of alterations within specific genes;
Cells proliferate uncontrollably resulting in cell masses known as tumour and is
capable of spreading throughout the body / metastasize;
[2]
(ii) Mutation
Describes any changes in the nucleotide sequence of DNA
Can either be acquired or inherited;
State the 3 types of gene mutation (addition, substitution and deletion) + an effect
[2]
(b) Explain how mutation of a named tumour suppressor gene may result in cancer.
p53 tumour suppressor gene encode protein involved in apoptosis of DNA-damaged
cells;
When it is mutated, these cells with DNA damage cannot be repaired nor undergo
apoptosis;
i.e. loss-of-function mutation;
and hence damaged cells continue to grow and proliferate uncontrollably to give rise to
tumour and may eventually spread to result in cancer;
[4]
[Total 8]

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10 PPC2A NJC 2010/P2/4

(a)

Cisplatin is a novel compound isolated from a tree bark. It has been observed to slow
down the rate of DNA synthesis in euglena (a kind of unicellular organism). Inside cells,
each cisplatin molecule forms two chemical bonds with a DNA molecule. Fig. 4.1 shows
part of a DNA molecule with cisplatin attached.

Fig. 4.1

i) Name the structures A and B in Fig. 4.1

A: Phosphate Group
B: Deoxyribose ( Reject : Pentose sugar / 5- carbon sugar)
(ii) Give one advantage of DNA molecules having two strands each.

[1]
[1]

1. Greater Stability of the DNA molecules by having numerous H-bonds between the
base pairs strengthens the double helical structure.
2. Protects/shields the hydrophobic nitrogeneous bases from the hydrophilic medium.
3. Each strand of DNA can act as a template for DNA replication and for error correction /
proof reading
(iii) Suggest how cisplatin slows down the rate of DNA synthesis in euglena. [2]
Prevent the DNA helicase from unzipping the double strand DNA /Prevents strands
separating / helix/ or DNA unwinding / unzipping/ prevents H bonds from breaking

Prevents DNA Replication/ being copied from taking place

Blocks complementary base pairing/ hydrogen bonds

Blocks DNA polymerase;

[Any 2 ]

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A group of researchers went on to find out how DNA replication could differ in euglena.
This was done by allowing the cells to grow in a medium that contains nutrients enriched
in heavy isotopes of nitrogen and carbon for several generations ( 15N and 13C, in place
of the naturally abundant 14N and 12C). Starting cells will only have nucleic acids
incorporated with the heavy isotopes.
These cells were then transferred to a normal, light medium containing 14N and 12C
nutrients. Finally, amount of DNA from cells that had grown for different number of
generations in the light medium were then determined by density centrifugation.
Fig. 4.2 shows four graphs of amount of DNA against its density for the different groups
of cells.

Fig. 4.2
(i) Explain whether the results shown in Fig. 4.2 are in agreement with your expectations.
DNA isolated from starting cells has a heavy density. After one generation in
normal, light medium, the DNA has uniformly shifted to medium density:

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The synthesis of the new DNA molecule from light nucleotides results in hybrid
DNA molecules that contain one heavy parental strand and one light newly
synthesized strand.

Agreement with semi-conservative mode of DNA replication;

After another round of replication in light medium, two forms of DNA appear in
about equal proportions: one form is again a hybrid of a light and a heavy strand
and has medium density, while the other form is composed of two light strands
and has a low density.

In the 3rd generation, more light DNA molecules are formed, and the proportion of
light DNA molecule to medium density DNA molecule is 3:1
[ Any 2 points]

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Another group of researchers investigated the rate at which the flagella of euglena grew
in three different types of media.
Medium 1: Contains actinomycin D, which prevents transcription by binding to guanine in
DNA.
Medium 2: Contains puromycin, which prevents translation by attaching to ribosomes.
Medium 3 (Control) : Contains neither actinomycin D nor puromycin
Fig. 4.3 shows the experimental results obtained.

Fig. 4.3
(i) with reference to Fig 4.3, describe how the rate of growth of flagella was affected by
puromycin.
Overall increase from 0 min till 20 th min (quote value from graph)
Decrease in the rate of growth , not much affected in first 20/30 min / lower peak than
control;
then decrease / much lower (than control) for sample with puromycin;
[2]
(ii) state two pieces of evidence that suggest the use of pre-existing mRNA and proteins in
euglena for the growth of flagella.

Actinomycin D has no effect on growth of flagella even though mRNA production /

transcription of mRNA is prevented (accept reference to Expt 1)

(Re) growth little affected by puromycin at first; protein synthesis was affected so it is
most likely to be using proteins already present in the cell.

[2]

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[Total: 10]

11 PPC2A ACJC 2011/P2/3

1

Fig. 3.1 outlines the production of a protein in a eukaryotic cell.

2
A

structure C

Fig. 3.1
(a) Identify structures A and B.
A

(mature) mRNA;

(80S) ribosome; @ m
A! small ribosomal unit

[1]

(b) Explain how the structure of C is adapted to its function.

1. Has 3 CCA sequence;
2. Allows attachment of amino acid;
3. Has anti-codon;
4. Complementary to codon on mRNA;
5. Brings correct amino acid to ribosome;
6. Ref. to tRNA has specific 3D conformation / tertiary structure;
7. Allows binding to P / A sites in ribosome OR binding to aminoacyl tRNA synthetase
(for amino acid attachment); @ m
[2]

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(c) Starting from the position of the ribosome as shown in stage II in Fig. 3.1, outline the steps that
occur to produce the complete polypeptide.
1. Peptidyl transferase catalyses formation of peptide bond between amino acids;
2. Ribosome moves along mRNA in 5' to 3' direction / downstream;
3. Ref. to amino acids are carried by specific tRNAs to ribosomes / aminoacyl tRNA
recruited to ribosome;
4. Anti-codon of tRNA binds with codon of mRNA by complementary base pairing;
5. Until stop codon reached / ribosome moves towards stop codon;
6. Release factor binds;
7. Polypeptide released;
@ m, max 3
[3]

The unfolded protein response (UPR) is a cellular stress response that is triggered by an
accumulation of unfolded or misfolded proteins. One of the primary aims of the UPR is to stop
protein translation. During the UPR, a kinase known as PERK is activated and acts on the protein
eIF2. The normal function of eIF2 is to bind to a tRNA with the UAC anticodon and bring it to the
ribosome.
(d) (i)

Using the information provided, suggest the role of eIF2 in translation.

1. Initiates translation / translation initiation factor;
2. Brings tRNA with anticodon UAC to the start codon (to ribosome);
@ 1m

[2]

(i) Hence suggest how activation of the UPR stops translation.

1. PERK phosphorylates eIF2;
2. (Inactivated) eIF2 does not bind to tRNA with UAC anticodon / recruit tRNA with
UAC anticodon / starting amino acid to ribosome; @ 1m
[2]
(ii) Apart from the mechanism in (d)(ii), describe one other method by which translation can be
stopped.
1. Binding of repressor protein to 5 UTR;
2. Prevents ribosome from binding to mRNA; OR
3. Degradation of 3 poly(A) tail;
4. Triggers (removal of 5 cap and subsequent) degradation of mRNA; OR
5. Prevent binding of CPEB (cytoplasmic polyadenylation element binding protein) to
CPE (cytoplasmic polyadenylation element) in 3 UTR;
6. Prevents extension/elongation of (short) 3 poly(A) tail;
7. Add inhibitor to aminoacyl tRNA synthetase;
8. Prevents formation of aminoacyl tRNAs / amino acid activation / charging of [1]
tRNA; @ m
(e) Misfolded proteins are eventually degraded in the cytoplasm. Describe how this degradation
occurs.
1. Protein is ubiquinated / ubiquitin is added to the protein;
2. Degraded by proteasome; R! protease @ m
R! degradation by lysosome (usually for proteins taken in by endocytosis)

[1]

[Total: 12]
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12 PPC2A IJC 2011/P2/2

2

Fig. 2 shows the sequence of bases in a section of the DNA template strand coding for
the first seven amino acids of a polypeptide chain.
3 ' T AC AAG G T CG T CT TT GT C AAA 5 '
Fig. 2
(a)(i)

List the corresponding codons in the mRNA transcribed from the template in
Fig. 2.
AUG UUC CAG CAG AAA CAG UUU
[1]

(ii)

Methionine is coded by the initiation codon. On Fig. 2, label, the 3' and 5' end
of the DNA template strand.
[1]

The polypeptide was hydrolysed to release the first seven amino acids. It contained
four different amino acids. The number of each type obtained is shown in the Table 2.
Table 2

(b)

Use the base sequence shown in Fig. 2 to work out the order of amino acids in
the polypeptide.
[1]
met

(c)(i)

phe

gln

gln

lys

gln

phe

Explain why single base deletions in the DNA sequence is more likely to
produce non-functional proteins than single base substitutions.
1. deletion cause frameshift mutation;
2. all aas downstream of mutation ; nonsense mutation
3. substitution usually cause missense / in 1 aa;
4. or silent mutation if sub occurs at 3 rd base as mutation leads to degenerate
codes due to wobble base phenomenon;
5. in aa seq more drastic / more R grps / folding in del, thus prot
more likely to have vastly diff 3D conformation leading to lost in fn;
[2]

(ii)

Describe the effect of a transition mutation at base position 6.

1. G A sub
2. AAG AAA / UUC UUU
3. results in degenerate code;
4. still code for phe / no in aa, silent mutation;

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(d)

H2 Biology
Revision Tutorial

Explain how the structure of the ribosome is suited to perform its function.
1. small s.u. with recog / binding site for initiation tRNA;
2. binding site for 5' end of mRNA to initiate translation;
3. large s.u. with P site to bind tRNA with growing polypep chain;
4. with A site to bind incoming tRNA ;
5. with E site to allow tRNA exit;
6. with peptidyl transferase to catalyse peptide bond;
7. binding site for translation factors / GTP / release factor etc.

[3]
[Total: 10]

13 PPC2A RI 2011/P2/2
The main function of a chromosome is to act as a template for the synthesis of RNA molecules,
since only in this way does the genetic information stored in chromosomes become directly useful
to the cell. RNA synthesis is a highly selective process.

(a) Explain what is meant by the term template. [3]

Template here refers to one of the DNA (strand/polynucleotide) of a DNA molecule;
The DNA template has a specific sequence of nucleotides which determines the sequence of
nucleotides in the RNA molecule; (idea of transferring code from DNA RNA)
Resultant RNA molecule has a sequence complementary to that of the DNA;
This is possible because of complementary base pairing, where Adenine in DNA pairs with Uracil
in RNA, Thymine on DNA with Adenine in RNA and Guanine pairs with Cytosine) through weak
hydrogen bonds;

Fig. 2.1 is a section through the rough endoplasmic reticulum representing the synthesis of
proteins.

Fig 2.1

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(b) Describe and explain the role in protein synthesis of

(i) structure A;[3]
Identify mRNA;
carries the information of a gene (from DNA) in the nucleus to the ribosome;
Information from the DNA is conveyed as triplet bases of codons in the mRNA that codes
for a specific sequence of amino acids in the polypeptide;
(ii) structure B.[3]
Identify ribosome;
Role in translation where it allows anti-codon on amino acyl tRNA to be matched with
corresponding codons on mRNA through complementary base pairing;
The ribosome covers two codons where two adjacent tRNAs with their attached amino
acids are aligned side by side; or if student make reference to details on the function of A,
P and E site in the process of translation
Peptidyl transferase on the large subunit of ribosome catalyses the formation of peptide
bonds that links the adjacent amino acids together to form a specific sequence of amino
acids in a polypeptide chain;
(c) Explain why mutations in the coding region for C can still result in identical polypeptide C? [2]
Degeneracy of the code where the same amino acid can be coded for by more than one
codon;
Variations/mutations in the third base of the codon inconsequential;

(d) C is an insulin receptor. Outline the route taken by protein C after it is synthesized in the rough
endoplasmic reticulum. [2]
Protein C inserted into the membrane of the rough endoplasmic reticulum;
[1] for pt. 2 or 3
Vesicles with protein embedded in membrane bud off and move to Golgi apparatus;
Vesicles bud off and vesicle membrane fuse with the plasma/cell surface membrane and
receptor is presented to the exterior of the cell;
[Total: 13]

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14 PPC2A RI 2011/P2/4
Over-expression of the HER2 (human epidermal growth factor receptor 2) gene is often associated with
the development of breast cancer. One of the mechanisms causing the over-expression is
illustrated in Fig. 4.1.

HER2

Fig. 4.1

(a) Name the process that has occurred. [1]

Gene amplification;

(b) Explain how the above process can result in over-expression of HER2. [3]
a) Lack of telomeres resulting in fusion of ends of sister chromatids by complementary
base pairing.
b) (during anaphase) breakage of chromatid resulting in 2 copies of HER2 gene on one
chromosome
c) Increase in number of/more copies of HER2 gene;
d) More mRNA molecules resulting in more HER2 proteins produced;
(c) Explain how chromosomal translocation can also result in over-expression of the HER2 gene. [3]
a) HER2 gene translocated such that it falls under the control of an enhancer; @ active
promoter
b) Activator binds to enhancer;
c) Bind to other transcription factors/RNA polymerase to promote assembly of
transcription initiation complex/histone acetylase/chromatin remodeling complex;
d) Increase frequency/level of transcription;

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(d) A similar mechanism exists to increase the expression of rRNA genes in oocytes of the South
African clawed toad.

Fig. 4.2

With reference to Fig. 4.2, describe the process of replication. [4]

a) One strand of a double-stranded DNA is nicked/cut at a site;
b) (DNA polymerase) adds nucleotides to the free 3OH end to synthesise a
complementary DNA strand;
c) Using the un-nicked/intact strand as a template;
d) 5 end of the nicked strand is displaced as synthesis/strand elongation proceeds;
e) Displaced strand can be used as a template and replicated discontinuously;

(e) Explain why such a mechanism is necessary in the oocytes. [2]

a)
b)
c)
d)

Increase in copy number of rRNA genes;

Large number of ribosomes required for protein synthesis;
For rapid growth of the embryo;
Existing number of genes cannot be transcribed rapidly enough to meet demand
OR
e) More proteins can be produced in a shorter time;
[Total: 12m]

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Free Response Questions

1 (a)
(b)

Outline the differences in structure between amino acids and nucleotides.

[6]

Describe the main features of the genetic code.

[4]

PPC2A RI11/P2/Q9

PPC2A SAJC11/P2/Q9

Features

Amino acids

Nucleotides

Components

Amino acids comprise a central

carbon atom bonded to:

Nucleotides comprise of:

amino group (-NH2),

phosphate group and

carboxyl group (-COOH) and

nitrogenous base.

a R group ;

Types
of There are 20 different amino acids
amino acid.
due to the different R groups

a pentose sugar,

There are four different nucleotides

AT(U)CG in each nucleic acid (DNA
& RNA);
due to different nitrogenous bases ;

Classification R groups are classified by polar

of
variable and non-polar ;
groups

Nitrogeneous bases are classified

by purines and pyrimidines based
on the number of rings ;

Elements
present

Nucleotides contain element

phosphorus in phosphate group ;

Amino acids contain element

sulphur in some amino acids (e.g.
cysteine)

Note: As there are 2 different of pentose sugars and 4 different nitrogenous bases in
nucleic acids, there are 8 different nucleotides. 4 different nucleotides present in DNA and
4 different nucleotides in RNA.
(b)
Genetic code is a triplet code three consecutive nucleotide bases on a genetic sequence code
for an amino acid;
Degenerate more than one codon can code for the same amino acid;
Non-overlapping successive triplets are read in order with no overlapping nucleotide bases;
Universal same triplet code codes for the same amino acid in all organisms;
Unpunctuated no gaps between adjacent codons;
Unambiguous no codon specifies for more than one amino acid;

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(a) Describe the structure and function of centromeres. [7]

Structure
a) constricted regions on chromosomes
b) comprise of largely / entirely of repetitive non-coding DNA
c) in humans, centromere region is made up of tandemly repeating units (OR of 170 base
pairs known as -satellite DNA)
d) special DNA sequence in centromeric region is important for kinetochore protein
recognition/ binding [Reject: protein]
Function
e) allow sister chromatids to adhere to each other (with the help of proteins cohesins)
f) allow spindle fibres to attach at kinetochores on centromere
so that sister chromatids OR homologous chromosomes can be separated to
opposite poles.
g) during anaphase of mitosis OR anaphase II of meiosis
centromeres divide (R: split)
h) when spindle fibres shorten (R: contract)
sister chromatids are pulled to opposite poles (R: ends/sides) with centromeres
leading
(b)

a)

Outline the differences between prokaryotic transcriptional control of gene expression with
the eukaryotic model. [7]
Point of
comparison
Critical elements /
short sequences
required for
promoter (to recruit
transcription
factors)
different
sequences /
different locations

Prokaryotes

Eukaryote

-10 sequences / -10 site /

Pribnow box/ TATAAT
AND
-35 sequences / -35 site /
TTGACA

At -25 site / TATA box/

TATAA
AND
At -75 site / CAAT box/
GGCCAATCT
AND
At -90 site / GC box/
GGGCGG

b) Similarity of critical
elements to
consensus
sequence

Major control in transcriptional

regulation; if critical elements
have sequences close to
consensus strong promoter

Minor control
[Reject: consensus
sequence does not exist]

c)

General transcription factors

bind to promoter

General transcription
factors bind to promoter
Specific transcription
factors bind to enhancers
and silencers

d) Sigma factor

Controlling availability of
different sigma factors
determines which genes are
transcribed.

Not present

e)

Allows bacteria to
coordinately regulate a group
of genes that encode gene

Not present/ not significant

Type of
transcription
factors

Operon

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Revision Tutorial

products with related

functions.
f)

Enhancer

Absent/ not significant

Major control; increase

efficiency of transcription

g) Silencer

Absent/ not significant

Major control; decrease

efficiency of transcription

h) Accessibility of
RNA polymerase to
promoter

Absent/ not significant

Eg:
Acetylation / methylation /
chromatin remodeling
complex

(c) Outline the significance of post-translational modifications of eukaryotic proteins. [6]

a) Cleavage and/or covalent modification
Give 1 suitable example - glycosylation, disulfide bond formation, attachment of
prosthetic groups etc. is required.
b) Form functional protein - newly synthesized proteins need to be modified for proper
assembly / functioning
c) Regulate - control cellular activity / influence biological activity
d) Eg: phosphorylation/dephosphorylation may activate/inactivate (ORA) proteins
e) Degrade proteins allows control of protein activities OR prevent aberrant activities
so that proteins will not stay too long in cytoplasm and still be active
f) E.g. Proteins are linked to ubiquitin that will target a protein for degradation.
g) (Save/recycle resources) - proteins not needed can be hydrolysed to amino acids, to
be used for synthesis of new proteins
h) (Heterogeneity) - many different proteins modified from one polypeptide serve
different function so smaller no of proteins/ small genome needed
i)

(Localisation) direct proteins to particular locations inside and outside cell

j)

Eg: modifications at terminus of amino acid chain help target proteins for
transporting to final destination in the cell / move across membranes/ tag proteins to
be incorporated in various cellular and organelle membranes

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9(a) Compare the structure and organisation of prokaryotic and eukaryotic chromosome.
[6]
For every comparison:
mark for correct comparison
mark for correct information

1. Genome size
2. Gene length

3. Chromosome
structure
4. Packaging of
DNA

5. Introns

6. Regulatory
sequences

Prokayotic chromosome
Smaller genomes,
0.6 Mb to 10 Mb
Shorter gene sequences
/ more compact genetic
organisation
Circular DNA molecule.
Does not form chromatin.
(Prokaryotic DNA is organized
into a DNA-protein complex
called the nucleoid.
Coding sequence proceeds from
start to finish without interruption
by introns.
Small amount of non-coding
DNA consists mainly of regulatory
sequences, such as promoters)

Eukaryotic chromosome
Large genomes, being less than
10 Mb 100,000 Mb
Longer gene sequences
/ presence of more intergenic
spaces
Linear DNA, each contained in a
different chromosome.
Eukaryotic DNA is complexed
with histones and other proteins
to form chromatin.
Presence of introns within genes.

More complex regulatory

sequences (eg. enhancers and
silencers)

Others (max 3)
7. Chromosome
number
8. Location

Single chromosome
/ Haploid
Chromosome found in the
nucleoid region of the cytoplasm

9. Repetitive
sequences
10. Coding and noncoding DNA

Few repetitive DNA sequences.

11. Presence and

absence of
operons
12. Origins of
replication
13. Telomeres
14. Centromere

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Most of DNA are coding

sequences (codes for protein,
tRNA, or rRNA.
Two or more genes may be
expressed and regulated as a
unit (genomes arranged in
operons / polycistronic genes)
One
Absent
Absent

Many chromosomes
/ Diploid or polyploid
Chromosomes are enclosed
within a double-membrane bound
nucleus
Many highly repetitive DNA
sequences
Most of DNA are non-coding.

Absence of operons /
monocistronic genes

Many
Present
Present

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9(b) Outline the differences between prokaryotic control of gene expression with the
eukaryotic model. [8]
For every comparison:
mark for correct comparison
mark for correct information
Chromosomal Level (max 2)
Prokaryotes
1. Prokaryotic DNA not organised into
chromatin / not associated with
histones

Eukaryotes
Eukaryotic DNA is complexed with histones
and other proteins to form chromatin /
associated with histones

2.

DNA and histone modification cannot

occur

DNA and histone modification can occur,

resulting in conversion between euchromatin
and heterochromatin

3.

DNA sequences, eg. promoters and

operators, serve as the on/off switch

Structure of chromatin euchromatin, ready

to be transcribed, or heterochromatin and not
available is the major on/off switch for gene
regulation
/ Ease of transcription DNA made
accessible to RNA polymerase and other
regulatory proteins

Transcriptional Level (max 2)

Prokaryotes
4. One RNA polymerase consisting of five
subunits
/ All RNAs synthesized by the same
RNA polymerase;

Eukaryotes
Three different RNA polymerases, each
containing 10 or more subunits;
/ Three different classes of RNA each
synthesized by a different RNA polymerase
(i.e. mRNA, tRNA, rRNA)

5.

Simple regulatory sequence:

Transcriptional regulatory protein /
Regulator protein binds to DNA-binding
sites upstream of the cluster of
structural genes to regulate initiation of
transcription.

Complex regulatory sequence:

More extensive interaction between upstream
DNA sequences and protein factors involved
to stimulate and initiate transcription. In
addition to promoters, enhancers and
silencers control rate of transcription.

6.

Related genes are transcribed together

as operons
/ only 1 promoter
/ polycistronic mRNA

No operon
/ each gene has own promoter
/ monocistronic mRNA

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Post-transcriptional Level (max 2)

Prokaryotes
7. Translation is often coupled to
transcription
/ Transcription and translation take
place in the same cellular compartment
simultaneously.

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Eukaryotes
No direct coupling of transcription and
translation
/ mRNA must pass across nuclear envelope
before translation in the cytoplasm. RNA
transcript is not free to associate with
ribosomes prior to the completion of
transcription.

8.

Primary transcripts are the actual

mRNAs
/ no post-transcriptional modification

Primary transcripts undergo processing to

produce mature mRNAs methylated
guanosine cap at the 5 end, poly-A tail at the
3 end, splicing

9.

Lower stability of transcript

/ degradation within seconds or
minutes
/ mRNAs shorter half life to rapidly
respond to environmental changes

Higher stability of transcript

/ prevent transcript degradation
/ mRNAs longer half-life remaining much
longer to orchestrate protein synthesis prior
to their degradation by nucleases in the cell

Translational level (max 2)

Prokaryotes
10. Control at this level is unlikely; due to
simultaneous transcription and
translation

Eukaryotes
Control at translational level:
phosphorylation of ribosomal translation
initiation factors
/ negative translational control through
regulatory proteins
/ cytoplasmic elongation of poly (A) tails
/ mRNA degradation
/ RNA interference and microRNA

11. mRNAs have multiple ribosome binding mRNAs have only one start site
sites
/ direct synthesis of only one kind of
/ direct the synthesis of several
polypeptide
different polypeptides

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Post-translational Level (max 2)

Prokaryotes
12. no/minimal post-translational
modifications occur
13.

14.
15.
16.

17.

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Eukaryotes
Post-translational modifications determine
the functional abilities of the protein
Proteolysis: Processing eukaryotic
polypeptides to yield functional protein
molecules e.g. cleavage of pro-insulin to
form the active insulin hormone
Chemical modification of proteins to yield
functional protein molecules
Phosphorylation of proteins to increase or
decrease its function
Transportation of proteins to target
destinations in the cell where it functions is
mediated by signal sequences at N-terminus
of some proteins. Once transported to
destination, signal sequence is enzymatically
removed from the proteins
Ubiquitination marks protein for degradation,
ref to ubiquitin & proteasome

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9(c) Describe the development of cancer as a multi-step process.

1
2
3
4
5

H2 Biology
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[6]

loss of function mutation of tumour suppressor gene

mutant tumour suppressor alleles are usually recessive
/ mutations must knock out both alleles in a cells genome to produce abnormal protein
loss of arrest of cell division to allow more time for the cell to repair its DNA / loss of ability for
DNA repair / loss of apoptosis

gain of function mutation of proto-oncogene

oncogenes behave as dominant alleles
/ only need one mutated allele to produce abnormal protein
lead to stimulation of the cell cycle / cell keeps dividing

accumulation of many mutations

8
9

activation of telomerase gene

telomerase enzyme prevents the shortening of the chromosome ends / cell can continue to
divide indefinitely

10 angiogenesis / formation of new network of blood vessels to the cancer cells

11 blood vessels provide the cancer cells oxygen and nutrients for growth and to remove any
waste products

12 loss of contact inhibition / density-dependence (and cells do not stop dividing)

13 loss of ability to differentiate
14 formation of benign tumour
15 cells in the tumour no longer exhibit anchorage dependence / loss of cell adhesion
16 metastasis / break loose and may enter the bloodstream / invade other tissues form secondary
tumors
17 tumour is considered malignant

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