H2 Biology – Problem Set

[Nucleic Acids and Gene Expression]

Name: Class: Date:

CORE IDEA 2: GENETICS AND INHERITANCE

NUCLEIC ACIDS AND GENE EXPRESSION

Multiple Choice Questions (MCQ)

1 B 6 A 11 D 16 C
2 D 7 A 12 C 17 A
3 B 8 C 13 B 18 A
4 D 9 B 14 B 19 C
5 D 10 C 15 C 20 C

1. The table shows the percentages of nitrogenous bases in four samples of nucleic
acids. Which base is adenine?

bases
sample (A) (B) (C) (D) uracil

1 19 31 30 19 Nil
2 27 23 24 26 Nil
3 25 25 Nil 25 25
4 17 32 33 18 Nil
C is thymine

2. The following are found in nucleic acids:

1 2 3 4 5
PHOSPHATE RIBOSE DEOXYRIBOSE PURINE PYRIMIDINE

Which two are linked by hydrogen bonds in DNA?

(A) 1 and 3
(B) 2 and 5
(C) 3 and 4
(D) 4 and 5
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[Nucleic Acids and Gene Expression]

3. Which of the following describes the structure of DNA?

Polynucleotide chains Number of base pairs

per complete turn of
(A) parallel helix 5
(B) anti-parallel 10
(C) parallel 15
(D) anti-parallel 20

4. Which statement correctly describes messenger RNA (mRNA)?

(A) mRNA binds amino acids for incorporation into proteins.

(B) mRNA contains the five-carbon sugar deoxyribose.
(C) mRNA is a double stranded helix.
(D) mRNA binds the anticodon of tRNA.

5. The diagram shows the structure of a nucleotide.

One type of polynucleotide consists of a single strand, twisted into a clover leaf
shape. What is the type of pentose of this molecule and the bonding between the
nucleotides?

pentose bonding between nucleotides

(A) deoxyribose between positions 1 and 3
(B) deoxyribose between positions 2 and 3
(C) ribose between positions 4 and 4
(D) ribose between positions 2 and 3
tRNA structure, 5-3 representation
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[Nucleic Acids and Gene Expression]

6.

(A)

7. In this diagram of the process of DNA replication at a replication fork, the

components labeled (i) to (iv) are the:

(i) (ii) (iii) (iv)

(A) Template DNA Leading Okazaki RNA primer

strand fragment
(B) Template DNA Okazaki Leading RNA primer
fragment strand
RNA primer Leading Okazaki Template DNA
(C)
strand fragment
Leading strand Okazaki RNA primer Template DNA
(D)
fragment
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[Nucleic Acids and Gene Expression]

8. A culture of bacteria had all its DNA labelled with the heavy isotope of nitrogen, 15N.
The culture was then allowed to reproduce using nucleotides containing normal 14N.
The DNA was examined using a centrifuge after one generation and again after two
generations.

The diagram below shows the position of the DNA band at Z in the centrifuge tube when
the DNA was first labelled.

In which pattern would the DNA be found after the first and after division?

After first division After second division

(A) Half at X and half at Y Quarter at X and at Z and half at Y
(B) Half at X and half at Z Quarter at X and at Z and half at Y
(C) All at Y Half at X and half at Y
(D) All at Z Half at Y and half at Z

9.

(B)
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[Nucleic Acids and Gene Expression]

10.

(C)

11. In which of the following actions does RNA polymerase differ from DNA polymerase?

(A) RNA polymerase uses RNA as a template, and DNA polymerase uses a DNA
template.
(B) RNA polymerase binds to single-stranded DNA, and DNA polymerase binds to
double-stranded DNA.
(C) RNA polymerase does not need to separate the two strands of DNA in order to
synthesize an RNA copy, whereas DNA polymerase must unwind the double
helix before it can replicate the DNA.
(D) RNA polymerase can initiate RNA synthesis, but DNA polymerase requires a
primer to initiate DNA synthesis.
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[Nucleic Acids and Gene Expression]

12.

(C)

13.

(B)

14.

(B)
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[Nucleic Acids and Gene Expression]

15.

(C)

16.

(C)

17.

(A)
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[Nucleic Acids and Gene Expression]

18. Which of the following types of mutation, resulting in an error in the mRNA just after
the AUG start of translation, is likely to have the most serious effect on the polypeptide
product?
(A) a deletion of 2 nucleotides

(B) a deletion of a codon

(C) a substitution of the third nucleotide in an ACC codon
(D) an insertion of a codon

19.

(C)
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[Nucleic Acids and Gene Expression]

20.

(C)
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[Nucleic Acids and Gene Expression]

Structured Questions (SQ)

Question 1 (N98/P3/Q1)
Table 1.1 shows the relative amounts of the bases Adenine, Thymine, Guanine and
Cytosine in DNA from different organisms.
Table 1.1
Source Adenine Thymine Guanine Cytosine

Bacterium 23.8 23.1 26.8 26.3

Maize 26.8 27.2 22.8 23.2
Fruit fly 30.7 29.5 19.6 20.2
Chicken 28.0 28.4 22.0 21.6
Human 29.3 30.0 20.7 20.0

(a) Explain the importance of the ratios of A to T and G to C to the structure of DNA.
Due to complementary base pairing, the ratio of A:T and C:G is approximately 1:1 ;

A purine is paired with a pyrimidine which provides the same width of 2nm throughout
the double helix, thus contributing towards stability of DNA;

Hydrogen bonds hold two strands together which contributes towards the stability of
the double helix ;

Each strand serves as a template for semi-conservative replication, allowing [3]

accurate copying of genetic information;
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[Nucleic Acids and Gene Expression]

(b) In the space below draw, and label fully, a short length of a DNA molecule. [4]

5’ 3’
D
D

D
D

D
D Correct labeling of:
§ deoxyribose
§ phosphate group
D
§ hydrogen bonding
D between bases
§ phosphodiester bond
D § nucleotide
Legend:
D § anti-parallel strands
D § correct number of bonds
- deoxyribose
between A and T, C and
D G.
P
- phosphate group D
3’ 5’

The bacteriophage virus X-174 has single-stranded DNA with the four bases present in the
following relative amounts.
Adenine Thymine Guanine Cytosine
24.0 31.2 23.3 21.5

(c) Suggest why the ratios of A to T and G to C for the virus do not correspond to the ratio
found in living organisms.

The ratios deviate from 1 : 1 because no base pairing occurs in single-stranded

viral DNA. [1]

[Total: 8]
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

Question 2 (N05/P2/Q3)
Fig. 3.1 is a diagram showing DNA replication.

(a) Name two molecules required for DNA replication that are not shown in Fig. 3.1.

§ DNA helicase or DNA ligase or Deoxyribonucleotides or ATP or Single-strand DNA

binding proteins or RNA primers or DNA primase or DNA topoisomerase

Any two [2]

(b) Explain how Fig. 3.1 shows semi-conservative replication.

§ Each strand of the parental DNA double helix is used as a template

§ The new DNA molecule / helix (not strands) contains one parental strand and [2]
one newly synthesised daughter strand,

(c) Describe how the two original strands determine the structure of the two newly
synthesised strands.

§ The exposed sequence of bases on each unwound DNA strand determines the
sequence of the newly synthesised strands as DNA polymerase adds free DNA
nucleotides by complementary base pairing,

§ where adenine base pairs with thymine and cytosine base pairs with guanine. [2]
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[Nucleic Acids and Gene Expression]

(d) The DNA molecule is described as having anti-parallel strands. Describe the evidence
visible in Fig. 3.1 and Fig. 3.2 that DNA has anti-parallel strands.

Figure 3.1 shows that one DNA strand runs in the 5’ to 3’ direction while its
complementary strand runs in the 3’ to 5’ direction.

Figure 3.2 shows a phosphate group attached to carbon 5 of deoxyribose on one [2]
strand and an OH group attached to carbon 3 of deoxyribose on its
complementary strand.

[Total: 8]
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

Question 3 (N97/P3/Q4)
DNA replicates semi-conservatively by the two strands separating and forming templates for
the synthesis of two new strands.

(a) In addition to the template provided by the DNA, state three other factors that are
required for DNA replication.

1. Deoxyribonucleotides / Deoxyribonucleoside Triphosphates (dNTPs)

2. DNA polymerase (III and I)

3. Helicase or ATP or DNA ligase or RNA primers or DNA primase [3]

Bacterial cells have a single loop of DNA. Fig 4.1 shows the site of initiation of replication of
bacterial DNA, with each arrow representing the direction of replication.

Fig 4.1

(b) Suggest why replication only occurs in a 5’ to 3’ direction.

§ The enzyme DNA polymerase III has an active site which is complementary only to
the 3’ OH end, hence it can only add new dNTPs to a free 3’ OH end of the growing
strand / primer;

§ The DNA polymerase can only catalyse the formation of phosphodiester bonds [2]
between the 5’ phosphate group of new dNTPs and the 3’ OH end of the growing
strand, synthesising the new strand in the 5’ to 3’ direction;

Replication of bacterial DNA with a single replication site takes approximately 20 minutes.
Replication of an average human chromosome with a single replication site would take
approximately 800 hours. However, in actively dividing cells in humans, the process takes
only twelve hours.

(c)(i) Explain why replication of human chromosomes would take so long with a single
replication site.

§ Human chromosomes have longer DNA molecules with more bases;

§ Human DNA are coiled around histone proteins to form chromatins, and they [2]
will need to be uncoiled before helicase can unwind the double helix;
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(c)(ii) Suggest how replication is speeded up in human chromosomes.

§ There are many Origins of replication. (OR)

§ More enzymes are involved to catalyse the replication process. [1]

[Total: 8]
Question 4 (N06/P2/Q3)
DNA makes RNA, RNA makes protein.

(a) State where in an animal cell and by what process RNA and protein molecules are
made.

RNA molecules

location nucleus

process transcription [2]

protein molecules

location Free ribosomes in the cytoplasm / bound ribosomes on the rough

endoplasmic reticulum;

process Translation ; [2]

(b) In addition to RNA, state three other molecules that are required for protein synthesis to
proceed.
1. ATP / GTP ;

2. Aminoacyl tRNA synthetase ;

3. peptidyl transferase / amino acids / initiation factors / elongation factors/ [3]

release factors ;

Any 3 of the above

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[Nucleic Acids and Gene Expression]

Fig. 3.1 shows the molecule of RNA and four of the twenty one protein molecules that make
up the small subunit of a ribosome. The individual molecules are shown separated so they
can be seen clearly.

(c) Describe in what ways the helical structures that are shown in Fig. 3.1 in both RNA and
protein molecules differ.

The helical structure in RNA folds back on itself resulting in sections of clearly visible
double helix while in protein, helical structure is formed by single helix called alpha
helix found in the secondary structure of proteins;

The helical structure in RNA is maintained by hydrogen bonds between

complementary base pairing of different strands, while the helical structure in proteins
is maintained by hydrogen bonds within one strand;

The helical structure in RNA is larger with 10 nucleotides forming one turn of the helix
(the length of each turn is 3.4nm), while the helical structure in proteins is smaller with
3.6 amino acids forming one turn of the helix (the length of each turn is 0.54nm);

[3]

[Total: 10]
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[Nucleic Acids and Gene Expression]

Question 5 (N01/P3/Q3)
Fig 3.1 shows a diagram of a ribosome synthesizing a protein – translation.
growing
polypeptide
tRNA
molecules

mRNA

Fig 3.1

(a) Explain how the tRNA binds to the mRNA.

§ Each tRNA carries an anticodon made up of three bases.

§ The anticodon binds to its corresponding codon on the mRNA by hydrogen bonding
via complementary base pairing,

§ where cytosine base pairs with guanine and adenine base pairs with uracil, [2]
and vice versa.

(b) List three ways in which transcription differs from translation.

Features Transcription Translation

Site of synthesis Occurs in the nucleus. Occurs in the cytoplasm on

(in eukaryotic cells) ribosomes.

Template used DNA is used as a template. mRNA is used as a template.

Product formed RNA (mRNA, rRNA, tRNA) are Polypeptides are synthesised.
synthesised.

Monomers used The basic units are The basic units are amino
ribonucleotides. acids.

Key enzymes involved RNA Polymerase Peptidyl transferase

Linkages between Ribonucleotides are linked by Amino acids are linked by

monomers phosphodiester bonds. peptide bonds.
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[Nucleic Acids and Gene Expression]

(c) Describe the main features of ribosome structure.

§ Each ribosome is approximately 20 to 30 nm in size, and.

§ In eukaryotes, made up of a large (60S) and small (40S) ribosomal subunit.

§ Each subunit is a complex of ribosomal RNA and ribosomal proteins.

§ Each ribosomal large unit has three binding sites, a peptidyl-tRNA, aminoacyl-
tRNA and exit site, which holds tRNA molecules during translation.

§ Each ribosomal small unit has an mRNA binding site. [3]

(d) State where in the cells ribosomes are made.

rRNA is synthesised in the nucleolus and ribosomal subunits are assembled in [1]
the nucleolus also. The functional ribosomes are formed in cytoplasm.

[Total: 9]
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[Nucleic Acids and Gene Expression]

Question 6 (N08/P2/Q2)
Sickle cell anaemia is most commonly caused by the haemoglobin variant HbS. In HbS the
amino acid valine takes the place of glutamic acid at the sixth amino acid position of the beta
globin polypeptide chain. Table 1.1 and 1.2 shows the details of this change.

Position of amino acid 3 4 5 6 7 8 9

DNA bases CTG ACT CCT GAG GAG AAG TCT
Amino acid Leu Thr Pro Glu Glu Lys Ser
Table 1.1 Beta globin sequence in normal adult haemoglobin (HbA).

Position of amino acid 3 4 5 6 7 8 9

DNA bases CTG ACT CCT GTG GAG AAG TCT
Amino acid Leu Thr Pro Val Glu Lys Ser
Table 1.2 Beta globin sequence in mutant adult haemoglobin (HbS)

(a) State the type of mutation responsible for this change in the amino acid sequence.
Substitution – missense mutation
[1]

(b) Explain the significance of the change in amino acid to the properties of haemoglobin.

Change in codon results in replacement of glutamic acid with valine.

Valine is hydrophobic whereas glutamic acid is hydrophilic.

This substitution causes a decrease in solubility of deoxygenated haemoglobin

molecules, which precipitate out of solution to form rigid fibres.

[3]

(c) Describe the effects of this haemoglobin change in the organism.

Such haemoglobin is inefficient in carrying oxygen.

The sickle-shaped red blood cells may obstruct blood vessels and interfere with
circulation. Such deprivation of oxygen causes damage to organs, especially kidneys
and bone.

The red blood cells, being more fragile, haemolyse easily, leading to anaemia.

In addition, these red blood cells accumulate in the spleen for destruction, [3]
resulting in an enlarged spleen.

[Total: 7]
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

Question 7 (N07/P2/Q4)
Li-Fraumeni syndrome is a rare inherited cancer syndrome caused by mutations in a tumour
suppressor gene on chromosome 17, known as p53. Mutations in p53 confer an increased
risk for early onset breast cancer, childhood sarcoma, osteosarcoma, brain tumours,
leukaemia and adrenocortical carcinoma.

(a) State the meaning of the term gene mutation.

change in DNA / nucleotide sequence / base sequence that makes up a gene ;

examples of gene mutation include base-pair substitution / base-pair insertion /

deletion ;

(these) mutations result in a change in the codon in mRNA;

Which may alters the amino acid sequence of the protein ;

and the phenotype of the organism might be affected ; [3]

(b) Explain how a mutation in the p53 gene could affect the structure of its product.

if addition / deletion had occurred, this would result in a frameshift of the codons,
causing extensive missense or nonsense mutation downstream of the point of
mutation ;

proteins coded for would no longer be synthesized / would be of a different 3D

structure

alternatively, if substitution (missense) occurrs, this would results in an amino acid

being changed ;

and the presence of a different R group would change the 3D / tertiary structure [3]
of the protein ;

Fig. 4.1 shows the protein produced by the normal p53 gene (p53 protein) attached to DNA.
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

(c) Suggest why the p53 protein only binds to certain parts of the DNA molecule.

p53 protein has a binding site which has a specific shape ;

that is complementary to the shape of part of the DNA molecule ;

the different shapes of the DNA is determined by the different sequences of bases [3]
on DNA ;

Fig. 4.2 shows the structure of the core domain of the p53 protein with the six most
frequently mutated amino acids marked.

(d) Suggest why some mutations of the p53 gene have no effect on the activity of the p53
protein.

the genetic code is degenerate , which means that some amino acids are coded for by
more than one codon / triplet bases, therefore, some mutations that alter a codon /
triplet bases may not necessarily change the amino acid encoded (silent mutation) ;

Missense mutation results in a change in an amino acid with very similar properties as
the original amino acid hence it does not change the overall shape of p53;

Missense mutation results in a change in an amino acid may occur in a region [3]
away from binding site (and this may not change the overall shape or the binding
properties of p53);

[Total: 12]
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

Free Response Questions (FRQ)

Question 1: N21/P3/Q4a
Describe the molecular structure of DNA. [15]

Question 2: N04/P2/Q7
Outline the differences in structure between amino acids and nucleotides [6]

Question 3: J01/P3/Q10
a. Describe the main features of replication of DNA [8]
b. Explain using a named example, how a gene mutation may affect the phenotype of an
organism. [8]

Question 4: J97/P3/Q8
a. Outline the main features of the genetic code. [4]
b. Outline the main events of transcription [7]
c. Describe briefly how proteins are synthesized after mRNA has been produced [7]
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

Question 1: N21/P3/Q4a
Describe the molecular structure of DNA. [15]

• DNA is a polymer of nucleotides;

• Nucleotides structure consist of deoxyribose, phosphate, nitrogenous base;
• Types of nitrogenous bases: adenine, guanine, thymine, cytosine;
• Nucleotides are joined together by phosphodiester bonds to form polynucleotides;
• The backbone of a strand of polynucleotide is formed by the deoxyribose and
phosphate;
• Each strand of polynucleotide has a 5’ end and a 3’ end;
• The 5’ end refers to the end with a phosphate group attached to the 5th carbon of
deoxyribose;
• The 3’ end refers to the end with an -OH group attached to the 3rd carbon of deoxyribose;
• The phosphodiester bond is formed between the 3’ end of one nucleotide and the 5’ end
of the next nucleotide;
• DNA in living organisms (prokaryotes and eukaryotes) consists of two strands of
polynucleotides;
• DNA in viruses can be single-stranded or double-stranded;
• In double-stranded DNA, the two strands run anti-parallel to each other;
• The polynucleotides in a dsDNA are held together by hydrogen bonds via
complementary base-pairing;
• Adenine forms two hydrogen bonds with guanine;
• Cytosine forms three hydrogen bonds with thymine;
• The double-stranded DNA forms a double-helix structure;
• The double-helix has a major and minor groove;
• Appropriate labelled diagram;
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[Nucleic Acids and Gene Expression]

Question 2: N04/P2/Q7
Outline the differences in structure between amino acids and nucleotides [6]
No Points for Amino acids Nucleotides
.
comparison

1 Groups All amino acids have four All nucleotides have a phosphate group, a
present in different groups attached to pentose sugar and a nitrogenous base.
monomer a central (a) carbon – a
hydrogen atom, an amino
group (NH3+), a carboxyl
group (COO-) and a unique
side chain or R group.

2 Unique Each amino acid has a Each nucleotide has one of the following 5
group that unique side chain or R nitrogenous bases:
gives rise group associated with it –
to different adenine (A)
(a) electrically charged guanine (G)
monomers
hydrophilic side chain, cytosine (C)
thymine (T) and
(b) polar but uncharged Uracil (U)
side chain (hydrophilic)

(c) non-polar hydrophobic Adenine and guanine are purines while cytosine,
side chain thymine and uracil are pyrimidines.

(d) special hydrophobic R

groups in cysteine, glycine
and proline
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[Nucleic Acids and Gene Expression]

3 Number of 20 different essential amino 5 different nucleotides:

different acids
monomers dATP
dTTP
dCTP
dGTP and
rUTP

The DNA sequence is made up of 4 different

nucleotides: dATP, dTTP, dCTP and dGTP
whereas

RNA sequence is made up of rATP, rCTP, rGTP

and rUTP.

4 Charge Can be of any charge: Negatively charged due to the presence of

positively or negatively phosphate gp / phosphoric acid in the nucleotide
charged or uncharged
(depending on R groups of
amino acids that make up
protein)

5 Type of Covalent bonds between all Covalent bonds between phosphate group,
bonds 4 groups associated with nitrogenous base and pentose sugar in nucleotide.
present the central carbon of an
within amino acid.
monomer

6 Type of Peptide bond formed Phosphodiester bond links the sugar and
bonds between the amino and phosphate group of 2 adjacent nucleotides, while
present carboxyl groups of 2 hydrogen bonds can be formed between the
between adjacent amino acids. bases of complementary nucleotides.
monomers

6 Importanc R groups are important in The sequence of nitrogenous bases is important in

e of unique determining the three- determining the sequence in DNA and RNA.
group in dimensional structure and
monomer function of the proteins.

7 Type of Building blocks of proteins Building blocks of DNA and RNA.

polymer / polypeptides
that arises
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[Nucleic Acids and Gene Expression]

Question 3: J01/P3/Q10
(a) Describe the main features of replication of DNA [8]

§ First, an enzyme helicase unwinds the DNA double helix by breaking the hydrogen
bonds between bases.
§ Single-strand binding proteins stabilize the unwound strands so they can act as the
template for DNA synthesis.
§ DNA polymerase III is the enzyme that catalyses polynucleotide synthesis but it cannot
initiate DNA replication.
§ An enzyme primase synthesises RNA primers so that DNA Pol III can add
deoxyribonucleotides to a pre-existing 3’ end.
§ Therefore, replication occurs in a 5’ à 3’ direction as DNA Pol III can only add
nucleotides to the 3’ end of the growing strand.
§ DNA Pol III attaches free nucleotides to the new strand in a sequence complementary to
the parent strand, base pairing occurs between adenine and thymine, cytosine and
guanine.
§ Only one strand, called the leading strand is synthesized continuously.
§ The other strand, called the lagging strand, undergoes discontinuous replication.
§ Short fragments, called Okazaki fragments are synthesized in the lagging strand.
§ DNA polymerase I (DNA Pol I) will hydrolyse the RNA primers and replace them with
deoxyribonucleotides.
§ DNA ligase seals the gap by catalysing the formation of a phosphodiester bond between
the 3’-OH of one nucleotide with the 5’-phosphate of the adjacent nucleotide.
§ DNA replication is semi-conservative, as each new DNA molecule contains one original
parental strand and one newly synthesised strand.

(b) Explain using a named example, how a gene mutation may affect the phenotype of an
organism. [8]

§ A gene mutation is a change in the nucleotide sequence of the DNA molecule.

§ There are two categories of point mutations: base pair insertion / deletion and base pair
substitution.
§ As genes encode specific sequences of amino acids, a change in the DNA sequence will
cause a change in the amino acid it encodes, in turn affecting the protein formed and
the phenotype of an organism.
§ An example of gene mutation affecting the phenotype of an organism is sickle cell
disease in humans.
§ Sickle cell disease is due to a single base substitution; in which thymine is replaced by
adenine in the DNA base sequence.
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

§ This causes one of the codons on the mRNA to change from GAA to GUA.
§ This changes the amino acid sequence / primary structure of the polypeptide chain.
§ This results in the beta-globin chain having a valine residue instead of a glutamic acid
residue.
§ The abnormal hemoglobin tends to crystallize under low oxygen conditions, causing the
red blood cells (RBCs) to become sickle-shaped, which tends to block blood capillaries
and may prevent normal blood flow.

§ Sufferers of sickle cell disease are anaemic as their RBCs carry less oxygen.

Question 4: J97/P3/Q8

(a) Outline the main features of the genetic code. [4]

§ The genetic code is made up of triplet bases, known as a codon.

§ Each codon specifies one amino acid.
§ The genetic code is almost universal, as the same codons encode the same amino acids
in almost all organisms.
§ It is degenerate as there is usually more than one codon that encodes a specific amino
acid. [e.g. glycine is encoded by 4 different codons.]
§ The genetic code is non-overlapping, meaning that successive triplets / codons are read
in order, without skipping any nucleotides.
§ The genetic code is punctuated with a start codon AUG, and three stop codons that do
not encode amino acids, i.e. UAA, UGA and UAG signal the termination of polypeptide
synthesis.

(b) Outline the main events of transcription [7]

§ In prokaryotes, RNA polymerase recognises and binds to the promoter region / Pribnow
Box to initiate transcription.
§ Binding of RNA polymerase causes the DNA double helix to unwind, as hydrogen bonds
between the bases are broken.
§ One DNA strand acts as the template strand for the synthesis of a RNA molecule.
§ Complementary base pairing occurs between RNA nucleotides and bases on the DNA
template.
§ Adenine in DNA base pairs with uracil in RNA, and thymine in DNA base pairs with
adenine in RNA. Cytosine in DNA base pairs with guanine in RNA and vice versa.
§ Incoming ribonucleotides are added to the 3’ –OH end and RNA polymerase catalyses
the formation of phosphodiester bonds between ribonucleotides.
§ RNA is synthesised in the 5’ to 3’ direction.
§ Transcription stops when RNA polymerase reaches the terminator sequence.
 H2 Biology – Problem Set
[Nucleic Acids and Gene Expression]

Note: In eukaryotes, transcription factors (TFs) bind to the promoter on DNA first, so as to mediate
binding of RNA polymerase to initiate transcription.

(c) Describe briefly how proteins are synthesized after mRNA has been produced [7]

§ The translation of mRNA into proteins involves 4 stages: amino acid activation,
initiation, elongation and termination.

§ During amino acid activation, amino-acyl tRNA synthetase catalyses the attachment of
a specific amino acid to the 3’ end of a specific tRNA.
§ During the initiation stage, the small ribosomal subunit recognizes and binds to the 5’
end of the mRNA.
§ The anticodon of the initiator tRNA (carrying methionine) attaches to the start codon
(AUG) on the mRNA by complementary base-pairing.
§ The large ribosomal subunit then binds to the small ribosomal subunit to complete the
translation initiation complex.
§ The ribosome can cover only two codons on the mRNA at one time.
§ In the elongation stage, the mRNA codon in the aminoacyl (A) site of the ribosome forms
hydrogen bonds with the anticodon of a second aminoacyl-tRNA complex.
§ The first amino acid (methionine) is transferred to the aminoacyl-tRNA at the A site,
forming a peptidyl-tRNA.
§ Peptidyl transferase catalyses the formation of a peptide bond between the two amino
acids.
§ The tRNA that was in the P site is moved to the exit (E) site and then leaves the ribosome.
§ The tRNA in the A site carrying the growing polypeptide chain is translocated to the P
site.
§ Translocation ensures that the mRNA is read in a 5’ to 3’ direction, codon by codon.
§ The elongation process is repeated to assemble amino acids in the correct order as
dictated by the template mRNA.
§ Termination occurs when a stop codon (UGA, UAG and UAA) on the mRNA is read.
§ A release factor binds and a molecule of water is added to hydrolyse the polypeptide
chain from the tRNA.
§ After translation, the polypeptide spontaneously coils and folds into its three-
dimensional shape.
§ The protein may then undergo post-translational modification in the ER / Golgi
apparatus to become a functional protein.