Nucleic Acids

1
Proteins are large, organic molecules which play a fundamental role in
metabolic activities including nutrition, respiration, transport, sensitivity,
co-ordination and reproduction.
The characteristics of cells and organisms are determined by the particular
proteins which are present. The synthesis of these proteins involves two
types of nucleic acid; DNA and RNA. DNA is contained within the nucleus
of a cell and carries the code to determine which particular proteins are
made. Various forms of RNA then carry this information to the cytoplasm
of the cell and assemble the protein. To understand protein synthesis, you
must first have an understanding of DNA and RNA.
Nucleic acids
DNA and RNA are both nucleic acids. Nucleic acids are macromolecules
(large molecules) made up of chains of individual units called nucleotides.
Each nucleotide is made up of 3 parts (Fig 1):
Fig 1. Diagrammatic representation of a nucleotide
Phosphate
Pentose
Sugar
Base
1. A phosphate group (H
3
PO
4
), which is the same in all nucleotides.
2. A pentose (5 carbon atoms) sugar. This sugar can either be ribose
sugar (C
5
H
10
O
5
) or deoxyribose sugar (C
5
H
10
O
4
)
3. One of five nitrogenous bases. These bases are divided into two
types, depending on their structure (Fig 2):
(a) Purines - Bases made up of one six-sided ring and one five-sided
ring.
(b) Pyrimidines - Bases made up of a single six-sided ring. The details
of these rings is given in Table 1.
The three components of nucleotides are joined together by condensation
reactions (through the removal of water). Individual nucleotides are then
joined together by similar condensation reactions between the phosphate
group of one nucleotide and the pentose sugar of another (Fig 3). This
linkage of nucleotides forms long chains, called polynucleotides, which
make up nucleic acids.
A purine
eg. adenine
A pyrimidine
eg. thymine
Ring structure
Purine (double)
Pyrimidine
(single)
Base
Adenine
Guanine
Cytosine
Thymine
Uracil
Nucleic acid
DNA/RNA
DNA/RNA
DNA/RNA
DNA
RNA
Symbol
A
G
C
T
U
Table 1. Nitrogenous bases in nucleic acids
From Fig 3, it can be seen that polynucleotides have a backbone of
phosphate and sugar, with the nitrogenous bases projecting inwards.
Fig 3. Formation of a polynucleotide
Nucleotides are linked as follows
................
................
................
................
................
................
................
................
................
................
................
................
................
................
P
S A
P
S T
P
S G
P
S T
P
S G
P
S T
P
S A
P
S C
P
S A
P
S C
P
S A
P
S T
Fig 2. The ring structure of pyrimidines and purines
Exam hint - Not all Examination Boards require candidates to be
able to recognise purines and pyrimidines but all expect candidates
to know that purines are larger molecules than pyrimidines and that A
and G are purines etc.
NH
2
C
N C
C H-C
N
N
N
H
C-H
O
C
C-CH
3
C-H
N
H
H-N
O-C
hydrogen bond
Nucleic Acids
2
Comparing DNA & RNA
DNA and RNA are both vital in protein synthesis. Table 2 summarises the
similarities and differences between these two macromolecules:
G
A
C
T
A
G
C
T
G
A
T
C
C
G
G
A
C
T
A
G
C
T
G
A
T
C
G
A
C
T
A
G
C
T
G
A
T
C
4. DNA polymerase continues to move along the DNA, exposing the
bases for free nucleotides to come into and bond. Once these new
nucleotides are in place they bond together (phosphate to deoxyribose
sugar) forming a new strand of DNA.
DNA
Formed in nucleus
Predominantly found in nucleus
Double strand of nucleotides -
coiled into a double helix. The
two strands are linked by
hydrogen bonding between the
bases (Fig 3): Cytosine with
Guanine, Adenine with Thymine
Pentose sugar present -
Deoxyribose
Bases present: Cytosine,
Guanine, Adenine, Thymine
Larger molecule
One basic form
Ratio of 1:1 for adenine:thymine,
and cytosine:guanine
Table 2. Comparison of DNA and RNA
RNA
Formed in nucleus
Found throughout the cell
Single strand of nucleotides
which can be folded into
different shapes
Pentose sugar present - Ribose
Bases present: Cytosine,
Guanine, Adenine, Uracil
Smaller molecule
Three main forms: messenger
RNA, transfer RNA, ribosomal
RNA
Ratio of adenine:thymine, and
cytosine:guanine variable
1. A portion of the DNA double helix about to be replicated
G
A
C
T
A
G
C
T
G
A
T
C
G
A
C
T
A
G
C
T
G
A
T
C
Movement
of DNA
polymerase
2. Replication has started. The enzyme DNA polymerase moves along
the DNA double helix unwinding it and unzipping it by breaking the
hydrogen bonds between the nitrogenous bases.
3. Free nucleotides in the nucleoplasm of the nucleus are attracted to
the exposed complementary bases and form new hydrogen bonds with
them.
Fig 4. Replication of DNA
To summarise, DNA and RNA are both made up of nucleotides. In DNA,
there are two nucleotide strands which are wound around each other at
approximately every ten bases. Thus DNA forms a helix. The strands are
anti-parallel - i.e. they run in opposite directions to each other. The two
strands of nucleotides which make up the DNA double helix are held
together by the hydrogen bonding between nitrogenous bases. This paring
is always as follows:
Adenine with Thymine (A-T)
Cytosine with Guanine (C-G)
The different structures of the bases result in two hydrogen bonds being
formed A to T (A=T), and three hydrogen bonds between C to G (CG).
The bonding of the nitrogenous bases ensures that purines always bond
with pyrimidines, and more specifically, A to T and C to G. The precise
nature of this bonding is biologically important for two reasons:
1. The structure of DNA remains exact and regular. This is vital since
DNA carries the heredity material for an individual.
2. DNA can exist as a very long sequence of bases, with an enormous
variety in order, to carry the large amount of genetic information for an
individual.
DNA Replication
The replication of DNA takes place shortly before cell division, during a
phase of the cell cycle called interphase. DNA replication is said to be
semi-conservative. This means that when two new double helixes of
DNA are produced, one of the strands of each helix is from the original
(parental) DNA strand and the other is new. The sequence of diagrams in
Fig 4 illustrate the replication of DNA.
Exam hint - Do not confuse thymine with thiamine.
5. Replication is now complete, forming two identical strands of DNA
which are exact copies of the original strand. This method is said to be
semi-conservative, since each strand retains half of the original DNA
material.
Nucleic Acids
3
Evidence for semi-conservative DNA replication
The evidence for semi-conservative DNA replication came from
experiments by Matthew Meselsohn and Franklin Stahl, two
scientists at the California Institute of Technology, using the bacterium
Escherichia coli. Matthew and Franklin experiments can be explained
in the following series of steps:
1. E. coli were cultured in a growth medium containing nitrogen in
the form of the isotope
15
N (known as heavy nitrogen).
2. By leaving the E. coli in the culture for a long enough period of
time, all DNA in the E. coli became made up of heavy nitrogen.
This meant that the molecular weight of the DNA in these E. coli
was measurably greater.
3. The E. coli containing the heavy nitrogen were then placed into
a medium containing normal nitrogen (
14
N), so that any new DNA
manufactured would be from this normal nitrogen.
4. The E. coli was allowed to divide once and the first generation
cells were then collected.
5. When the DNA was extracted from these cells and the relative
weight determined using a centrifugation technique, the molecular
weight of the DNA was found to be intermediate between heavy
and light types. This confirmed that the DNA was made up of one
original (heavy) strand of DNA and one new (light) strand of
DNA - Semi-conservative replication.
Practice Questions
1. Define the following terms:
(a) DNA double helix (3 marks)
(b) complementary base pairing (3 marks)
(c) semi-conservative replication of DNA (2 marks)
2. (a) Read through the following account of DNA replication, then
find the most appropriate word or words to complete the
account.
During DNA replication, the enzyme binds
to the DNA double .This causes the DNA to
and breaks the
bonds between the nucleotides. These nucleotides are bound together at
bases. The base adenine binds with
and binds with
guanine. Free nucleotides found in the bind
with the exposed bases producing two strands of DNA. The process is
said to be because in both of the two DNA
strands produced, one sequence of nucleotides is new and the other is
from the DNA. (10 marks)
(b) When a sample of DNA is extracted from the nucleus of a cell,
chemical analysis showed that 38% of the bases were adenine. What
percentage of the bases are guanine (3 marks)
3. DNA and RNA are major molecules involved in the transfer of
hereditary material and protein synthesis.
(a) To which group of molecules do DNA and RNA belong?
(1 mark)
(b) DNA and RNA are both composed of nucleotide sub-units.
Describe the structure of a nucleotide. (3 marks)
(c) State four similarities and four differences between a DNA
molecule and an RNA molecule (8 marks)
Answers
Marking points are shown by semicolons
1. (a) Two strands of nucleotide;
held together by hydrogen bonding;
coiled or twisted around each other (approximately every 10
bases).
(b) hydrogen bonding between pairs of organic bases;
(projecting from the sugar-phosphate backbone of nucleic
acids);
pairing occurs between adenine-thymine, guanine-cytosine in
DNA;
pairing between adenine-uracil, guanine-cytosine in RNA.
(Any 3)
(c) Half of the original parent molecule is retained/conserved;
half is composed of new nucleotide molecules.
2. (a) DNA polymerase;
helix;
unwind;
hydrogen;
nitrogenous/exposed;
thymine;
cytosine;
nucleoplasm/nucleus;
semi-conservative;
parental/original.
(b) 38% adenine, 38% thymine;
remaining 24% is cytosine and guanine (50% each);
12% guanine.
3. (a) nucleic acids.
(b) phosphate;
ribose/5C sugar;
nitrogenous base;
components joined by condensations reactions
(c) (see Table 2)