Al Wadi International School BIOLOGY 9700-2016

Nucleic acids have roles in the storage and retrieval of genetic information and in
the use of this information to synthesise polypeptides. DNA is an extremely stable
molecule that cells replicate with extreme accuracy. The genetic code is used by
cells for assembling amino acids in correct sequences to make polypeptides. In
eukaryotes this involves the processes of transcription in the nucleus to produce
short-lived molecules of messenger RNA followed by translation in the
cytoplasm.

6.1 STRUCTURE AND REPLICATION OF DNA:

Understanding the structure of nucleic acids allows an
understanding of their role in the storage of genetic information and
how that information is used in the synthesis of proteins.

a) Describe the structure of nucleotides, including the

phosphorylated nucleotide ATP (structural formulae are not
required)

Structure of Nucleotide:

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are two types of
nucleic acids. These are polynucleotides, i.e. polymers built up from basic
units of monomers called nucleotides. Each nucleotide has three parts; a
pentose sugar, a phosphate and an organic nitrogenous base. Note that
both DNA and RNA contain phosphate and nitrogen.

Sugar: It has five

carbon atoms; therefore
it is a pentose. There
are two types of nucleic
acids, depending on the
pentose they contain.
Those containing ribose
(C5H10O5) are called
ribonucleic acids or
RNA and those
containing deoxyribose
(C5H10O5) are called deoxyribose nucleic acids or DNA.

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Nitrogenous base: Each nucleic acid contains four different bases, two
derived from purine and two from pyrimidine. The nitrogen in the rings gives
the molecules their basic nature. 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. Thymine is chemically very similar to uracil.
Purines have two rings and pyrimidines have one ring in their structure.

Phosphate: Phosphoric acid gives nucleic acids their acid character, and it
joins the adjacent nucleic acids by means of phosphodiester bond.

The nitrogen containing bases are commonly represented by their initial letters A,
G, T, U and C.
The nucleotide as monomers can be joined together to form a polymer
(polymerisation). The phosphate group of one nucleotide is joined with a
phosphodiester bond to a pentose sugar of another by a condensation
reaction.

Joining up of nucleotides forms a polynucleotide chain with a sugar

phosphate backbone. The bases stick out to the side. As there are different
types of nucleotides, the bases can be in any order along the chain.

The Structure of ATP

ATP, adenosine triphosphate, is often called the energy currency of the cell.
Reactions that take place within a cell require small amounts of energy, certainly
not all the energy that is contained in a single glucose molecule. Therefore, cells
convert energy to little energy packets of ATP that can be used to power small
reactions. ATP is very similar to one of the bases in DNA, adenine. It is thought
that ATP was probably one of the earliest molecules formed on primitive earth
when life first began. ATP is an adenine with three phosphate groups attached to
it. The phosphate groups give ATP its energy. In your cells there is always a pool of
two molecules. There is a pool of ATP, the triphosphate. The "T" stands for those
three phosphate groups. There is also a pool of ADP, the "D" stands for "di," or two
phosphate groups. ATP can be broken down to ADP if a water molecule is inserted

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between the last two phosphates. This is hydrolysis. A water molecule is used to
break a chemical bond, releasing energy. When ATP is converted to ADP, it is an
exothermic reaction, and a phosphate is released at the same time. This ADP can
be converted back to ATP, by adding a phosphate and storing energy in that
chemical bond, through dehydration synthesis, where water is released. As ATP is
used to power cellular work, ADP is produced, and then it is "recharged" with more
energy, regenerating ATP.

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b) describe the structure of RNA and DNA and explain the importance
of base pairing and the different hydrogen bonding between bases
(include reference to adenine and guanine as purines and to cytosine,
thymine and uracil as pyrimidines. Structural formulae for bases are
not required but the recognition that purines have a double ring
structure and pyrimidines have a single ring structure should be
included)

The structure of RNA

RNA (ribonucleic acid) is a nucleic acid built up from four types of RNA nucleotides
each with a different base. The larger purine bases are adenine and guanine. The
smaller pyrimidine bases are uracil and cytosine. This is similar to DNA except
that the base uracil replaces thymine and the pentose sugar ribose replaces
deoxyribose.

RNA nucleotides are polymerized to produce single polynucleotide chains.

RNA is normally single stranded, unlike DNA. Certain forms of RNA do assume
complex structure, notably transfer RNA (tRNA) and ribosomal RNA (rRNA).
Another form is messenger RNA (mRNA).

Messenger RNA (mRNA) is formed in the nucleus. It has a single chain

twisted into a helix whose length and base sequence vary. As it carries
information specifying amino acid sequences of proteins from DNA to
ribosomes, it has a short life.

Transfer RNA (tRNA) has a single

chain folded into a clover leaf shape.
There are many different types of
tRNA. The structure is always similar
except for the three bases of the
anticodon which determine which
amino acid attaches. tRNA is also
involved in protein synthesis. The
function of tRNA is to transfer amino
acids from the cytoplasms amino
acid pool to a ribosome.

Ribosomal RNA (rRNA) is made

in the nucleus and forms over half
the mass of ribosomes. It plays
structural and catalytic (rybozyme) role in ribosome.

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The structure of DNA

The double Helix

The two strands are twisted to form a double helix. The helical arrangement and
the hydrogen bonds between the bases help to make the DNA molecule very stable.
This is very important for DNAs function as a store of genetic information. The
DNA will tend to stay unchanged for the lifetime of the cell.
By being double stranded with the base attached to each other, the bases and their
specific sequence are protected from most damage. Damage (mutation) is fairly
rare.

Each chain forms a right-

handed helical spiral and
two chains coil around
each other to form a double
helix. The chains run in
opposite directions, they
are antiparallel. Each
chain has a sugar-
phosphate backbone with
bases which project at
right-angles and hydrogen
bond with the bases of the
opposite chains across the
double helix. Each strand
has a 5end, where the
carbon -5 of the pentose
sugar is nearest to the end,
and a 3end, where the
carbon -3 of the pentose
sugar is nearest to the end.
The 5end of one strand lies
next to the 3end of the
other strand.

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COMPLEMENTARY BASE PAIRING IN DNA:

DNA consists of two polynucleotide chains or strands linked by hydrogen bonds
between the bases.
The base adenine (A) can only pair with thymine (T) as they both form two
hydrogen bonds. Cytosine (C) can only pair with guanine (G) as they form three
hydrogen bonds.

The double helix structure of DNA

This specific or complementary base pairing is essential to the

understanding of the function of DNA and RNA, in particular the functions of DNA
replication and protein synthesis.
The precise order and sequence of the different bases along a strand varies. It is
this sequence of bases which forms the genetic information stored by the DNA.
The relative amounts of bases in DNA
Because of specific base pairing the relative amounts of bases A and T will always
be the same, as will the amounts of C and G. For instance, if a sample of DNA has
10% of base A it must also have 10% of base T. Wherever there is an A it will be
attached to a T.
However, because each species is genetically different with a unique sequence of
bases, the total amounts of A added to T will always be different to C plus G. This
means that species X may have 10% A, 10% T, 40% C, 40% G buts species Y has
15% A, 15% T, 35 % C, and 35% G.

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Functions of DNA

DNA is a genetic material as it is inherited and contains the coded information for
protein synthesis.
DNA contains coded information in form of genes. The precise order and
sequence of the different bases along a strand of DNA varies. It is this sequence
which forms the genetic information or genetic code stored by the DNA. By
controlling which proteins (particularly enzymes) are made, genes determine the
characteristics and development of organisms.

c) Describe the semi-conservative replication of DNA during

interphase

DNA Replication
DNA has the only set of genetic instructions in a cell. These instructions are
different for each species. When new cells are made in cell division each new cell
must receive an exact copy of the instructions to function properly. Replication is
also essential for inheritance. The DNA has to copy itself accurately to allow
offspring to inherit genes from parents.
DNA replication is semi conservative. The two strands unzip and each strand
acts as a template for the formation of a new strand. Each new DNA molecule
contains one of the old strands and one new strand. The old molecule is semi
conserved (half conserved).

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The important points about DNA replication are as follows:

The two strands of DNA are

separated by the enzyme
helicase. This breaks the
hydrogen bonds between
the bases, causing the strands
to separate from one end.
Replication is semi
conservative.
Each strand now acts as a
template for the formation of
a new strand.
Free DNA nucleotides join up
to the exposed bases by
specific base pairing.
Adenine pairs with thymine
and cytosine pairs with
guanine due to the number of
hydrogen bonds each can
form.
For the new 5 to 3 strand the
enzyme DNA polymerase
then catalyses the joining of
the separate nucleotides all in
one go to make complete new
strand.
For the new 5 to 3 strand the
enzyme DNA polymerase produces short segments of strand but these
sections are joined by the enzyme DNA ligase to make the complete new
strand.
Specific base pairing has ensured that two identical copies of the original DNA
have been formed.

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DNA Replication

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Genetic Code

DNA stores information as sequences of bases. This information acts as

instructions to synthesize proteins. The base sequence acts as a language or code,
which spells out which amino acids will be used to make a protein.

A triplet Code
The genetic code is a triplet code. Twenty different amino acids are used to make
proteins. The genetic code must be able to code for all 20. A triplet code of three
bases per amino acid produces sixty four possible combinations, more than
enough.

Three bases, read from the

inside outward,
show the amino acid encoded
by the triplet.
For example, the triplet CAC
encodes the
amino acid histidine (His)

A degenerate Code:

There are 64 different triplets of DNA bases and only 20 different amino acids
which mean there is excess capacity in the genetic code. The code is referred to as
degenerate code because some amino acids are coded for by more than one
triplet of DNA bases. Also, some triplets act as a full stop to end the series of triplet
words, e.g. TAA.
One important implication of degeneracy is that a mutation which substitutes one
DNA base for another may not alter the amino acid coded for. The mutation may
have no effect on the protein produced.

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6.2 PROTEIN SYNTHESIS:

The genetic code specifies the amino acids that are assembled to
make polypeptides. The way that DNA codes for polypeptides is
central to our understanding of how cells and organisms function.

a) State that a polypeptide is coded for by a gene and that a gene is a

sequence of nucleotides that forms part of a DNA molecule

Gene:
Gene is a sequence of nucleotides that forms part of a DNA molecule and a
polypeptide is coded for by a gene

b) state that a gene mutation is a change in the sequence of

nucleotides that may result in an altered polypeptide

GENE MUTATION:
It is a change in the sequence of nucleotides that may result in an altered
polypeptide

c) Describe the way in which the nucleotide sequence codes for the
amino acid sequence in a polypeptide with reference to the nucleotide
sequence for HbA (normal) and HbS (sickle cell) alleles of the gene
for the -globin polypeptide

Sickle Cell Anemia

Sickle cell anemia is the most common form of sickle cell disease (SCD). SCD is a
serious disorder in which the body makes sickle-shaped red blood cells. Sickle-
shaped means that the red blood cells are shaped like a crescent.

Normal red blood cells are disc-shaped and look like doughnuts without holes in
the center. They move easily through the blood vessels. Red blood cells contain an
iron-rich protein called hemoglobin. This protein carries oxygen from the lungs to
the rest of the body.

Sickle cells contain abnormal hemoglobin called sickle hemoglobin or hemoglobin

S. Sickle hemoglobin causes the cells to develop a sickle, or crescent, shape.

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Sickle cells are stiff and

sticky. They tend to block
blood flow in the blood
vessels of the limbs and
organs. Blocked blood flow
can cause pain, serious
infections, and organ
damage.

Cause

The sickle cell mutation

reflects a single change in the
amino acid building blocks of
the oxygen-transport protein,
hemoglobin. This protein,
which is the component that
gives red cells their color, has
two subunits. The alpha
subunit is normal in people
with sickle cell disease. The
beta subunit has the amino
acid valine at position 6
instead of the glutamic acid
that is normally present. The
alteration is the basis of all
the problems that occur in
people with sickle cell
disease.

Figure A shows normal red blood cells

flowing freely in a blood vessel. The
inset image shows a cross-section of a
normal red blood cell with normal
hemoglobin.
Figure B shows abnormal, sickled red
blood cells blocking blood flow in a
blood vessel. The inset image shows a
cross-section of a sickle cell with
abnormal (sickle) hemoglobin forming
abnormal strands.

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d) Describe how the information in DNA is used during

transcription and translation to construct polypeptides,
including the role of messenger RNA (mRNA), transfer RNA
(tRNA) and the ribosomes

Protein Synthesis
Protein synthesis occurs in all cells at the ribosomes and involves the assembly
of amino acids in the correct order into polypeptide chains as directed by the
genetic code on the DNA. Polypeptides are then later modified into proteins.
In eukaryotic cells the DNA is found in the nucleus but protein synthesis occurs
at ribosomes, which are in the cytoplasm. Transporting the DNA instructions
to the cytoplasm would risk damage to the vital DNA. Instead the instructions
are copied from the DNA to messenger RNA (mRNA), which takes the message
to the ribosomes where the mRNA directs the synthesis of the particular
polypeptide.

Stages in Protein Synthesis

Stage 1. Transcription

At the site of one gene the two

strands of DNA unwind and the
hydrogen bonds between the
bases are broken. This is
catalyzed by the by the enzyme
RNA polymerase.
One of the DNA strands, the
coding strand, acts as a template
for the copying of a
complementary strand of
messenger RNA (mRNA). Free
RNA nucleotides attach to the
exposed DNA bases on the coding
strand by complementary base
pairing, e.g. the base cytosine will
only join with the base guanine.
The RNA nucleotides now join up
to make a strand. This is also
catalyzed by RNA polymerase.
Each sequence of three bases on the mRNA is called a codon and it
codes from one amino acid. The DNA base sequence of the gene has been copied
to a complementary sequence of bases on the mRNA.

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Stage 2: mRNA carries information to ribosomes

The completed strand of mRNA now leaves the nucleus via a nuclear pore ad enters
the cytoplasm. Carrying the instructions (the message) from the DNA, the mRNA
moves to a ribosome.
In the nucleus, the bases on the two strands of DNA now rejoin and the DNA
molecule rewinds. This protects the gene, as the bases are no longer exposed.
Stage 3: Amino acid activation

There are many different types of

transfer RNA (tRNA). Each tRNA
becomes attached to a particular
amino acid. This attachment requires
energy from ATP. Each tRNA has a
different sequence of three bases
called the anticodon. It is the
anticodon which determines which
amino acid joins to the tRNA.

Stage 4: Translation
After attachment, the ribosome
moves along the mRNA strand
reading the information of the
codons. At the ribosome the mRNA
strand and the tRNAs are brought
close together. Each codon of mRNA
bases attracts a tRNA with the
complementary anticodon due to
specific base pairing. As each tRNA
carries a particular amino acid, this
results in the building up of amino
acids in a specific sequence.
Peptide bonds form between the
amino acids, joining them up into a
polypeptide chain. The sequence of
amino acids in the polypeptide
represents the primary structure of
the protein. The tRNAs now become
detached from the amino acids and
leave the ribosome to collect another
amino acid. Messenger RNA is

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relatively short lived but it may be used a number of times before it is broken down.
This avoids synthesizing excess protein.
The sequence of bases on the mRNA has been translated into a specific sequence
of amino acids. The sequence of amino acids is determined by the sequence of
mRNA, which in turn was determined originally, by the DNA base sequence of the
gene.

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Stage 5: Functional protein produced

The completed polypeptide is processed by the rough endoplasmic reticulum

and the Golgi apparatus to produce the final functional protein, for example an
enzyme.

Enzymes control cell activities, so by controlling protein synthesis DNA controls

the structure, function and development of organism.

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Comparison between transcription, translation and replication

It is very important to be able to clearly distinguish between the processes of

transcription, translation and replication of DNA.

In transcription a specific sequence of bases on DNA acts as a template for the

formation of a strand of mRNA by complementary base pairing.

The information of the DNA triplets is transcribed into a specific sequence of

mRNA codons. It occurs in the nucleus.

In translation tRNAs carrying particular amino acids join with mRNA,

determined by a matching of tRNA anticodon with mRNA codons. This causes
the amino acids to link up in a particular sequence to form a specific polypeptide.
It occurs at ribosomes in the cytoplasm.

Process Transcription Translation Replication

mRNA copied from DNA Yes No No
Occurs at ribosomes No Yes No
DNA copied from DNA No No Yes
Catalysed by RNA polymerase Yes No No
Catalysed by DNA polymerase No No Yes
Involves joining with tRNA No Yes No
Involves producing codons Yes No No
Assembles amino acids into No
No Yes
polypeptides
Occurs in nucleus Yes No Yes
Involves joining of codons with No Yes No
anticodon
Occurs in cytoplasm No Yes No
All of the DNA unzips No No Yes

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