Singapore Junior Biology Olympiad 2018

CHROMOSOMES, DNA AND GENES

 Chromatin fibres are structures found in the nucleus in which genetic material in the form of
deoxyribonucleic acid (DNA) molecule is organised.

 In eukaryotic cells, the DNA molecule is associated with proteins called histones. DNA is wound
around 8 histone protein molecules to form a nucleosome. The string of nucleosomes coils to
form the chromatin fibre.

 When a cell prepares for

nuclear division, the chromatin
coils and folds up (condenses)
to form thick chromosomes.

 A gene is a small segment of

DNA in a chromosome which
codes for a polypeptide. A gene
can be regarded as a unit of
inheritance.
chromatin fibre

chromosome

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NUCLEIC ACIDS

 Nucleic acids are essential for life. They form the genetic material of all living organisms.

 Two types of nucleic acids are found in living cells, namely deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).

 Nucleic acids are made up of basic units called nucleotides. These are arranged to form extremely
long molecules called polynucleotides.

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 EVIDENCE THAT DNA CAN TRANSFORM BACTERIA (GRIFFITH’S EXPERIMENT)

Living S Heat-
strain Living R
killed S
strain Heat-killed S
t i
strain +
living R
i

Living S strain
in blood sample
of dead mouse

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HERSHEY‐CHASE EXPERIMENT

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Results of the investigation showed that:

1. Radioactive sulfur (35S) was found predominantly in the supernatant.
2. Radioactive phosphorus (32P) was found predominantly in the cell fraction, from which a new
generation of infective phage can be isolated.
Conclusion: Phage DNA entered bacterial cells, but phage proteins did not. Hershey and Chase
concluded that DNA, not protein, functions as the genetic material of phage T2.

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 STRUCTURE OF NUCLEOTIDES

 A nucleotide consists of three components: a pentose (5‐carbon) sugar, phosphoric acid and a
nitrogenous base.

 DNA contains the 5‐carbon sugar deoxyribose and RNA contains ribose instead.

 Phosphoric acid gives nucleic acids its acidic property.

 Nucleic acids contain four different bases which can be categorised into purines and pyrimidines.
Purines have two rings and pyrimidines have one ring in their structure.

 The two purines are adenine (A) and guanine (G).

 The two pyrimidines are thymine (T) and cytosine (C) in DNA, with uracil (U) in place of thymine
in RNA.

STRUCTURE OF DNA

 The DNA molecule consists of two polynucleotide chains twisted around each other to form a
double helix, thus it is a double‐stranded molecule.

 Each strand has a sugar phosphate backbone with bases that project at right angles.

 The adjacent nucleotides within a strand are held together by strong covalent phosphodiester
bonds.

 The 5’ end of a polynucleotide chain ends with a phosphate group attached to carbon atom 5 of
the sugar. The 3’ end of the chain ends with the –OH group on carbon atom 3 of the sugar.

 The two strands run in opposite directions, i.e. they are antiparallel. One strand runs in the 5’ to
3’ direction while the other strand runs in the 3’ to 5’ direction.

 The two strands are held together by hydrogen bonds between nitrogenous bases of opposite
strands.

 A purine always pairs with a pyrimidine. Adenine forms two hydrogen bonds with thymine, while
guanine forms three hydrogen bonds with cytosine. This is known as complementary base‐
pairing. Within a DNA molecule, the ratio of A to T is 1; the ratio of G to C is also 1.

 The width between the two sugar‐phosphate backbones of a DNA molecule is constant at 2 nm.
One complete turn of the DNA double helix has 10 base pairs and spans a distance of 3.4 nm.

 The sugar‐phosphate backbones of both strands lie on the outside of the DNA molecule, with the
nitrogenous bases occupying the centre of the molecule.

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DNA double helix

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 DNA REPLICATION

Models of DNA replication

Generation 0

Generation 1

Generation 2

In the conservative model, the parental DNA strands direct the synthesis of an entirely new double‐
stranded DNA molecule, such that after one generation, both parental strands are conserved. This is
repeated in the second round.

In the semi‐conservative model, the parental DNA strands separate and each acts as a template to
synthesise a new DNA strand. After one generation, each daughter molecule comprises one parental
and one newly synthesised strand.

In the dispersive model, segments of the two parental DNA strands are distributed more or less
randomly between two daughter molecules.

The Meselson‐Stahl Experiment

In 1958, Matthew Meselson and Franklin Stahl tested the hypothesis of DNA replication.

1. They cultured bacteria in a medium containing 15N. 15N is a heavy isotope of nitrogen, so the DNA
synthesised is of higher density. Bacterial DNA was isolated at generation 0.

2. Then they transferred the bacteria to medium containing 14N, and bacterial DNA was isolated at
generation 1, 2, and so on.

3. To separate DNA based on density, DNA was mixed with caesium chloride and centrifuged at very
high speeds (50,000 rpm) in an ultracentrifuge for many hours. A linear gradient of CsCl with the
lightest density at the top and the heaviest density at the bottom is formed. As the CsCl gradient
forms, the DNA comes to equilibrium in the gradient where its density equals the density of the
surrounding CsCl.

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 (14N / 15N)

The first replication in the 14N medium produced a band of hybrid (15N – 14N) DNA. This result
eliminated the conservative model. The second replication produced both light and hybrid DNA in a
ratio of 1:1. Thus Meselson and Stahl concluded that DNA replication is semiconservative.

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Synthesis of leading strand and lagging strand of DNA during semi‐conservative replication of DNA

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 STRUCTURE OF RNA

 RNA is normally single‐stranded, with the exception of the RNA is some viruses.

 It is structurally similar to a single strand of DNA, except for the following:

(a) The sugar ribose is found, instead of deoxyribose.

(b) The nitrogenous base uracil is found, instead of thymine.

 There are three types of RNA, namely messenger RNA (mRNA), ribosomal RNA (rRNA) and
transfer RNA (tRNA).

COMPARISON BETWEEN DNA AND RNA

Similarity between DNA and RNA: Both act as genetic material (RNA more common in viruses).

Table showing differences between DNA and RNA

Features DNA RNA

Basic unit Deoxyribonucleotide Ribonucleotide
Pentose sugar Deoxyribose Ribose
Nitrogenous Adenine, guanine, cytosine, thymine Adenine, guanine, cytosine, uracil
bases
Ratio of bases A : T = 1 : 1 and G : C = 1 : 1 A : U  1 : 1 and G : C  1 : 1
No. of strands Double‐stranded Single‐stranded
No. of types One type Three types (mRNA, rRNA, tRNA)
Size Relatively larger molecule Smaller molecule
Location Mostly in nucleus, with small amounts Mostly in cytoplasm, although
in chloroplasts and mitochondria synthesised in nucleus
Amount Constant in all cells of a species Varies from cell to cell according to
(exceptions: twice in dividing cells and level of protein synthesis
half in gametes)

IMPORTANCE OF HYDROGEN BONDING AND COMPLEMENTARY BASE‐PAIRING IN DNA

 In order to function as a hereditary material, the structure of DNA has to allow for its own
replication prior to nuclear and cell division.

 During DNA replication, the strands unwind and separate.

 Both strands act as templates to which the complementary set of nucleotides will attach by base‐
pairing and hydrogen bonding. Each daughter cell inherits a DNA molecule consisting of one old
and one new strand. This is called semi‐conservative replication of DNA.

 The original DNA molecule will give rise to two copies of DNA with identical base sequence.

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 Semi‐conservative DNA replication

The two strands of the parent DNA

molecule unwind.

Each parental strand acts as a template to

synthesise a complementary strand.

Two identical daughter DNA molecules are

formed.

CONCEPT OF A GENE

 There are many genes along the length of the DNA molecule.

 A gene is a specific sequence of nucleotides along a DNA molecule that codes for a specific
sequence of amino acids in a polypeptide chain.

 DNA controls the activity of the cell as it contains genetic information for the manufacture of
proteins such as enzymes. The particular range of enzymes within a cell determines what type of
cell it becomes.

CENTRAL DOGMA OF MOLECULAR BIOLOGY

 The flow of genetic information from DNA

through RNA to protein is known as the Central
Dogma of Molecular Biology.

 The genetic information for the manufacture of

enzymes and other proteins are located in the
DNA which is found in the nucleus.

 Synthesis of proteins occurs in the cytoplasm at the ribosomes. Genetic information on the DNA
is transmitted from the nucleus to cytoplasm in the form of messenger RNA (mRNA) molecule.

 Two processes are involved:

(a) Genetic information in the form of base sequence of a gene is transferred in the process
called transcription onto an mRNA molecule which exits the nucleus into the cytoplasm.

(b) In the cytoplasm, the ribosome interacts with mRNA and tRNA molecules to translate the
information in the mRNA in the form of base sequence into an amino acid sequence of a
polypeptide. This process is called translation.

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 THE GENETIC CODE

 The sequence of bases in the DNA is a code for the sequence of amino acids in protein.

 Features of the genetic code:

(a) The genetic code is a triplet code. Three bases in DNA code for one amino acid in a protein.
The DNA code for a protein is first copied into mRNA which is complementary to the DNA.
The complementary triplets in the mRNA are referred to as codons. Each codon is three
bases long and is the code for one amino acid.

(b) The code is degenerate, i.e. a given amino acid may be coded for by more than one codon.

(c) The code is non‐overlapping. An mRNA sequence beginning AUGAGCGCA is not read
AUG/UGA/GAG… (an overlap of two bases) or AUG/GAG/GCG… (an overlap of one base).

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 TRANSCRIPTION

 Transcription is the synthesis of RNA under the direction of DNA. The sequence of bases in the
DNA template is transcribed onto a complementary sequence of bases in an mRNA molecule.
This occurs in the nucleus.

 The sequence of events in transcription:

1) The enzyme RNA polymerase binds to a region of the DNA near the beginning of the gene to
be transcribed. This region is called the promoter. This binding causes the DNA double helix
to unwind.

In prokaryotes, the RNA polymerase recognises and binds to the promoter. In eukaryotes, a
protein called transcription factor first binds to a crucial promoter DNA sequence known as a
TATA box before RNA polymerase can bind to the promoter. The assembly of transcription
factors and RNA polymerase bound to the promoter is called the transcription initiation
complex.

2) One of the exposed strands of DNA is used as a template for transcription.

3) Free ribonucleotides which are complementary to the bases in DNA are matched with the
DNA template by complementary base‐pairing.
 Adenine in the DNA pairs with uracil.
 Thymine in the DNA pairs with adenine.
 Guanine in the DNA pairs with cytosine.
 Cytosine in the DNA pairs with guanine.

4) Transcription proceeds until shortly after the RNA polymerase transcribes a DNA sequence
called a terminator. The transcribed terminator (RNA sequence) functions as the actual
termination signal. In a prokaryotic cell, transcription usually stops right at the end of the
termination signal. However in a eukaryotic cell, the polymerase continues past the
termination signal (AAUAAA sequence in the pre‐mRNA) to a point about 10‐35 nucleotides
further before the pre‐mRNA is cut free from the enzyme. The newly formed mRNA is
released and the DNA rewinds.

5) Enzymes in the eukaryotic nucleus modify pre‐mRNA in various ways before the mature
mRNA leaves the nucleus through pores in the nuclear envelope.

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 Transcription

Modification of mRNA in eukaryotes

 The 5’ end of a pre‐mRNA molecule is capped off with a modified form of a guanine (G)
nucleotide. The 5’ cap helps protect the mRNA from degradation by hydrolytic enzymes and it
serves as an attachment sign for ribosomes in the cytoplasm.

 The 3’ end of the pre‐mRNA, a poly(A) tail consisting of 30‐200 adenine nucleotides is added. The
poly(A) tail inhibits degradation of the mRNA, helps the ribosome attach to it and facilitate the
export of mRNA from the nucleus.

 RNA splicing occurs in which noncoding segments that lie between coding regions are removed.
Noncoding segments (intervening sequences) are called introns and coding regions (which are
eventually expressed or translated into amino acid sequences) are called exons.

 How is mRNA splicing carried out? Short nucleotide sequences at the end of introns are splice
sites which are recognised by small nuclear ribonucleoproteins or snRNPs.
 Several different snRNPs join with additional proteins to form a spliceosome, which interacts
with the splice sites at the ends of an intron and cuts at specific points to release the intron,
and immediately joins two exons that flank the intron.

RNA processing in
eukaryotes

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 ROLES OF DIFFERENT TYPES OF RNA

 There are three types of RNA which are all involved in protein synthesis. These are messenger
RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).

 All three types are synthesised directly on DNA, and the amount of RNA in each cell is directly
related to the amount of protein synthesis.

Messenger RNA (mRNA)

 This constitutes about 5% of total RNA of a cell. It is synthesised from a DNA template during
transcription. The base sequence of the mRNA is complementary to that of the DNA template it
was transcribed from. It conveys the message from the nucleus to the ribosomes in the
cytoplasm.

 The triplets of bases on the mRNA are called codons. Each codon codes for one amino acid.

Ribosomal RNA (rRNA)

 This constitutes 80% of total RNA of a cell. The nucleolus in the nucleus is responsible for the
synthesis of rRNA.

 rRNA leaves the nucleus via pores in the nuclear envelope and combines with proteins to form
the ribosome.

Transfer RNA (tRNA)

 This constitutes 15% of total RNA of a cell.

 The tRNA molecule folds upon itself and is

held in shape by hydrogen bonds between
complementary base‐pairs at certain regions.

 One of the ends binds to an amino acid

specific to the tRNA molecule.

 The anticodon is made up of a specific triplet

base sequence at a region of the folded tRNA
molecule.

a transfer RNA molecule

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 TRANSLATION

 Translation is the process by which a sequence of bases in a messenger RNA molecule codes for a
sequence of amino acids in a polypeptide.

 It occurs on ribosomes in the cytoplasm. Ribosomes are made of protein and rRNA. In eukaryotic
cells, the ribosome is made up of a small (40S) and a large (60S) subunit.

 The sequence of events in translation:

1) The first two mRNA codons (a total of 6 bases) enter the ribosome.

2) The first codon binds to the tRNA molecule having the complementary anticodon and which
is carrying the first amino acid (usually methionine) of the polypeptide being synthesised.

3) The second codon attracts the second tRNA molecule with the complementary anticodon
and the second amino acid specific to the tRNA.

4) A peptide bond forms between the first and second amino acids.

5) The mRNA then shifts its

position on the ribosome by
one codon. The first tRNA
molecule leaves the ribosome.
A new tRNA molecule specified
by the third codon of the mRNA
moves into the ribosome.

6) This continues until a stop

codon on the mRNA is
encountered. At this point the
polypeptide chain, with its
amino acid sequence as
determined by the DNA, leaves
the ribosome.

 Some tRNAs have anticodons that

can recognize two or more different
codons. This is possible due to the
relaxation of base‐pairing rules,
known as wobble, in the third
position of an mRNA codon. For
example, the base U of a tRNA
anticodon can pair with either A or
G in the third position of an mRNA
codon.

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 The structure of the ribosome reflects its function of bringing mRNA together with amino acid‐
bearing tRNA molecules. It possesses the following:

 A binding site for mRNA

 3 binding sites for tRNA
1. The P site (peptidyl‐tRNA site) holds the tRNA carrying the growing polypeptide chain
2. The A site (aminoacyl‐tRNA site) holds the tRNA carrying the next amino acid to be
added to the polypeptide chain
3. The E site (exit site) where discharged tRNAs leave the ribosomes

Codon recognition: An
incoming aminoacyl tRNA
(tRNA bound to an amino
acid) binds to the codon in
Ribosome is ready for the the A site of the ribosome.
next aminoacyl tRNA.

Translocation: The tRNA in the Peptide bond formation: The

A site is translocated to the P ribosome, functioning as a
site, taking the mRNA along ribozyme, catalyses the
with it. The tRNA in the P site formation of a peptide bond
moves to the E site and is between the new amino acid
released from the ribosome. and the carboxyl end of the
The mRNA shifts its position on growing polypeptide.
the ribosome by one codon.

 A single mRNA is used to make many copies of a polypeptide simultaneously. Once a ribosome
moves past the initiation codon, a second ribosome can attach to the mRNA, and thus several
ribosomes (polyribosomes) may be found on the same mRNA.

 During and after its synthesis, a polypeptide chain begins to coil and fold, forming a functional
protein of specific three‐dimensional conformation.

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 Post‐translational modifications may occur:

 Chemical modification of certain amino acids by the attachment of sugars, lipids or phosphate
groups

 Enzymatic removal of one or more amino acids from the amino end of the polypeptide chain

 Enzymatic cleavage of a single polypeptide chain into two or more pieces

MUTATIONS

 Genes are usually passed on from one generation to the next unchanged. Whenever
chromosomes are duplicated prior to cell division, the DNA is copied accurately by the
biochemical machinery of the cell.

 A gene mutation is a change in the structure of the gene (nucleotide sequence of DNA) due to
erroneous copying of DNA or in the presence of mutagenic agents such as ultraviolet light; alpha,
beta and gamma radiations and chemicals such as mustard gas, nitrous acid and acridine orange.

 If a gene mutation involves a change in only one base, it is called a point mutation. An alteration
in the sequence of nucleotides in a gene may change the sequence of amino acids in a
polypeptide.

 Deletion or insertion of a nucleotide often results in the production of a non‐functional protein as

ribosomes read incorrect triplets from the point of deletion or insertion. This is known as a
frame‐shift mutation.

 The effect of substituting a nucleotide may not necessarily alter the amino acid residue of a
polypeptide. This is because the genetic code is degenerate.

 Mutations occur rarely, randomly and spontaneously and may be inheritable if it occurs in the
germline cells in the gonads that give rise to gametes.

 Examples of gene mutations:

 Albinism is a condition characterized by pink skin and white hair. Albinos are unable to make
the black pigment melanin because they lack the functional enzyme required for its synthesis.

 Sickle‐cell anaemia is a result of a gene mutation that alters the DNA sequence coding for
haemoglobin, resulting in abnormal haemoglobin and sickle‐shaped red blood cells which are
unable to transport oxygen efficiently and often get stuck in blood vessels. Haemoglobin
consists of two  and two  polypeptide subunits. Patients with sickle‐cell disease have a
mutation in the ‐globin gene on chromosome 11. As a result, haemoglobin molecules do not
form properly.

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