NUCL EIC A CIDS
Nucleic acids are involved in the storage and transfer of genetic information in all living organisms,
including the simplest viruses. There are 2 types of nucleic acid in cells, Deoxyribonucleic acid (DNA)
and Ribonucleic acid (RNA). Nucleic acids are so named because DNA was 1st isolated from nuclei, but
both DNA and RNA also occur in other parts of the cell, e.g. DNA is also found in mitochondria and
chloroplasts, whilst RNA is also found in the cytoplasm, particularly at the ribosomes.
Both DNA and RNA are polymers, the monomeric units being called nucleotides. DNA and RNA are
therefore polynucleotides.
THERE ARE FIVE DIFFERENT NITROGEN-CONTAINING ORGANIC BASES PRESENT IN NUCLEIC ACIDS:
 adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U).
 A, T, C and G are found in DNA.
 A, U, C and G are found in RNA (uracil replaces thymine here).
THE NITROGENOUS BASES BELONG TO TWO DIFFERENT CHEMICAL FAMILIES.
 Adenine and guanine are purine bases and have a double-ringed structure.
 Cytosine, thymine and uracil are pyrimidine bases and have a single-ringed structure
The combination of a sugar and a base forms a compound called a nucleoside. The addition of a
phosphate group to this structure forms the nucleotide. Different nucleotides are formed according to the
sugar and bases used. Cells continuously produce nucleotides and these form a "pool" from which
nucleotides can be used up as required for manufacturing DNA, RNA or a variety of other substances.
DISTINGUISH BETWEEN THE FOLLOWING TERMS:
Nucleotide and Polynucleotide
Purine and Pyrimidine bases
Structure of DNA
1 DNA is a double stranded molecule. It consists of two polynucleotide chains held together by
interactions between pairs of bases projecting towards each other from each strand. The interactions
involve H-bonding between base pairs.
2. The two polynucleotide chains in a molecule of DNA are not identical but are complementary. The
bases always pair up in a specific fashion; adenine always pairs with thymine, cytosine always pairs
with guanine. i.e. a purine base pairs with a pyrimidine base.
There are several pieces of evidence that support this:
a) In any molecule of DNA, the ratio of A:T is always 1:1, and the ratio of C:G is similarly always 1:1.
However, the ratio of A or T to C or G is variable between different molecules of DNA.
b) Hydrogen bonding can only occur between A and T and between C and G.
c) Base pairing between a purine (double-ringed) and a pyrimidine (single-ringed) allows a constant base
pair length. It therefore follows that the distance between the two polynucleotide chains will also be
constant throughout the length of the molecule.
The double-stranded molecule is coiled up into a helical structure with ten nucleotides per turn of the
helix.
Structure of RNA
RNA is a single-stranded polynucleotide. There are three different types of RNA in the cells, each with
a particular structure and function.
1.Messenger RNA (mRNA)
They are single-stranded and are made up of hundreds to several thousand nucleotides. mRNA is made
in the nucleus from coded instructions in the DNA and then passes into the cytoplasm where it is involved
in the process of protein synthesis on the ribosomes.
2.Transfer RNA (tRNA)
They are single strands of 75-90 nucleotides wound up to form an overall "clover-leaf" shape. All cells
have at least twenty different kinds of tRNA. They interact with mRNA during protein synthesis on the
ribosomes. Two important features of the tRNA molecules are:
a) they possess an `anticodon' loop through which they can interact with molecules of mRNA.
b) at the opposite end of the molecule they possess an amino acid binding site. The amino acids carried
by tRNA molecules eventually form polypeptide chains during protein synthesis.
3.Ribosomal RNA (rRNA)
This is made inside the nucleus within the nucleoli and is a major component of ribosomes. The precise
configuration of rRNA is unknown but they are very large molecules containing thousands of nucleotides.
DNA REPLICATION
A major requirement of genetic material is that it should be able to replicate so that its messages can be
passed on from cell to cell as an organism develops and also from one generation to the next. It is also
vital that during replication, identical copies of DNA are made so that the correct genetic messages are
passed on.
DNA replication takes place during interphase of the cell cycle, so that by the time nuclear division starts,
two identical copies of each DNA molecule are already present for distribution into daughter cells.
Two models of DNA replication have been proposed.
Conservative mechanism
Generation 1
Generation 2
Make drawings to predict
the molecules formed in
Generation 3
This model suggests that an entire new helix is synthesised along the original molecule. Therefore the
parental molecule is "conserved".
Semi-conservative mechanism
This model suggests that the DNA double helix gradually "unzips" to expose the bases of each strand.
New nucleotides align themselves in a complementary fashion against the bases of each parental strand.
These nucleotides are joined by an enzyme (DNA POLYMERASE) to make new polynucleotides.
Therefore in the two new double helices, one strand is the original parental strand, whilst the other is
newly made; i.e.. only half the parental molecule is conserved in each daughter molecule.
Semi-conservative mechanism
Generation 1
Make drawings to predict
the molecules formed in
Generation 3
Generation 2
The following experiment carried out by Meselsohn and Stahl (1957) identified the correct model.
The bacterium E.coli was transferred from a growth medium containing normal nitrogen 14N, to a medium
containing the heavy isotope of nitrogen 15N. They were grown on this medium for a sufficient number of
generations so that all the nitrogenous bases in their DNA contained this heavy isotope. Light and heavy
DNA can easily be distinguished by special centrifugation techniques where heavy DNA sediments to
form a band lower down the centrifuge tube than light DNA. The bacteria that had been grown in 15N
medium were then transferred back to 14N medium and grown for one generation. A sample of cells was
taken, the DNA extracted and centrifuged to see if it was light or heavy. It was found that neither type
was present. Instead an intermediate band was formed. The cells were left to grow on 14N medium for a
second generation and the DNA samples as before. This time, two bands were seen, light and
intermediate.
Results of the Meselsohn and Stahl experiment
Cells grown
in 14N
Cells transferred from `B' and
grown in 14N for
Cells grown
in 15N
1
2
generations
Light DNA
Intermediate DNA
Heavy DNA
A
B
C
D
INTERPRET THESE RESULTS AND STATE WHICH MODEL OF DNA REPLICATION IS CORRECT.
THE GENETIC CODE
DNA is the hereditary material responsible for all the characteristics of an organism and it controls all the
activities of a cell. It is able to do this as it carries messages which control the synthesis of proteins. An
important class of proteins is the enzymes which control chemical reactions within the cell, including the
synthesis and breakdown of other classes of molecule. Therefore, by controlling which proteins are
made at a particular time in a particular type of cell, DNA is able to control all the characteristics of a
cell.
Proteins are made up of amino acids. There are about 20 different types of amino acids commonly found
in proteins. The precise number and sequence of amino acids makes up the primary structure of a
polypeptide chain. A functional protein may consist of a single, or several polypeptide chains.
DNA must therefore carry a coded message that determines not only the number and types of amino acids
that appear in a polypeptide, but also their precise sequence in the chain.
The code for primary structure cannot be carried in the sugar-phosphate backbone of DNA since this
structure is identical in all DNA molecules. The only part of DNA that varies between different
molecules is the base sequence. Therefore, the sequence of bases in DNA must determine the sequence of
amino acids in a polypeptide chain. The length of DNA that codes for a polypeptide chain is called a gene
and it can be thousands of nucleotides long.
 The code cannot be as simple as 1 base coding for 1 amino acid as this would allow for the coding of
only 4 amino acids.
 If the bases are read together in pairs, this would allow for only 16 different combinations i.e.. 16
different amino acids.
 Each amino acid is in fact coded for by a sequence of 3 consecutive nucleotide bases in the DNA
chain. This is called the triplet base hypothesis and each triplet of bases is called a codon. The
maximum number of combinations this allows is 64, but since there are only 20 common amino acids,
some are coded for by more than one triplet codon. The genetic codon is thus described as degenerate.
The genetic code is usually represented in the form of RNA that would be complementary to the DNA in
the gene. This is because it is messenger RNA that is directly involved in protein synthesis and not the
genes themselves.
Some of the triplet codons do not code for any amino acid. These are called non-sense codons and they
act as signals to terminate the synthesis of the polypeptide chain i.e.. they act as "full stops" and are called
termination codons. Some other triplets code for modified amino acids that act as signals to start the
synthesis of the protein chain and these are called initiation codons.
The Genetic Code
Each triplet of bases represents a sequence in mRNA. Each sequence codes for the amino acid shown.
2nd base of codon
U
U
C
A
G
C
A
G
UUU
UUC
UUA
UUG
Phe
Phe
Leu
Leu
UCU
UCC
UCA
UCG
Ser
Ser
Ser
Ser
UAU
UAC
UAA
UAG
Tyr
Tyr
*Term
*Term
UGU Cys
UGC Cys
UGA *Term
UGG Try
U
C
A
G
CUU
CUC
CUA
CUG
Leu
Leu
Leu
Leu
CCU
CCC
CCA
CCG
Pro
Pro
Pro
Pro
CAU
CAC
CAA
CAG
His
His
Gln
Gln
CGU
CGC
CGA
CGG
Arg
Arg
Arg
Arg
U
C
A
G
AUU
AUC
AUA
AUG
Ile
Ile
Ile
Met
*Init
ACU
ACC
ACA
ACG
Thr
Thr
Thr
Thr
AAU
AAC
AAA
AAG
Asn
Asn
Lys
Lys
AGU
AGC
AGA
AGG
Ser
Ser
Arg
Arg
U
C
A
G
GUU
GUC
GUA
GUG
Val
Val
Val
Val
*Init
GCU
GCC
GCA
GCG
Ala
Ala
Ala
Ala
GAU
GAC
GAA
GAG
Asp
Asp
Glu
Glu
GGU
GGC
GGA
GGG
Gly
Gly
Gly
Gly
U
C
A
G
AMINO ACIDS
Phe = phenylalanine
Ile = isoleucine
Ser = serine
Thr = threonine
His = histidine
Cys = cysteine
Try = tryptophan
Arg = arginine
Gly = glycine
Val = valine
Leu = leucine
Met = methionine
Pro = proline
Ala = alanine
Tyr = tyrosine
Gln = glutamine
Asn = asparagine
Lys = lysine
Asp = aspartic acid
Glu = glutamic acid
TRIPLETS MARKED:
* Init = initiation of polypeptide
*Term = termination of polypeptide
PROTEIN SYNTHESIS
Transcription
This is the first stage in protein synthesis. The genetic information required for protein synthesis is
contained in DNA which remains in the nucleus. Protein synthesis however, occurs at the ribosomes in
the cytoplasm (rough endoplasmic reticulum). Therefore, a messenger molecule (mRNA) is made, which
carries the required genetic information from the nucleus to the ribosomes. The process by which mRNA
is made is called transcription (or DNA-dependent RNA synthesis.)
The DNA double helix unwinds in that part which carries the code for the required protein (the gene).
One of the strands then acts as a template (pattern) for the production of mRNA.
mRNA synthesis occurs in 3 stages:
mRNA synthesis involves the association of the enzyme RNA polymerase with the DNA template.
Therefore, mRNA carries an identical genetic message to the gene, but in a complementary nucleotide
sequence.
The mRNA then passes through pores in the nuclear membrane to the ribosomes where one end of the
molecule becomes attached to a ribosome.
The information carried by mRNA must now be decoded to form a protein.
Translation
This is the process by which the genetic information in mRNA directs the synthesis of a polypeptide by
controlling the order of insertion of amino acids into the growing polypeptide (i.e.. it determines the
protein's primary structure). It occurs in four stages:
This involves a species of RNA called transfer (t) RNA. Its function is to decode the message carried by
mRNA by correctly positioning amino acids into the growing polypeptide chain according to the sequence
of nucleotides in mRNA. Each cell contains about 60 different types of tRNA it is single stranded, 70-90
nucleotides long, and portions of the molecule are wound up into a double helix to give a clover-leaf
shape.
Each tRNA molecule possesses three important features:
1
An anticodon site, which consists of a triplet of unpaired bases. The sequence
of bases in this site varies from molecule to molecule and there is an anticodon
sequence that is complementary to each codon sequence found on mRNA.
2
An attachment site at the free end of the molecule that can bind a specific amino acid.
3
A recognition site that enables the correct amino acid to bind to each tRNA molecule.
The particular amino acid that binds to each tRNA molecule is somehow determined by the anticodon
sequence. The actual amino acid is that which would be specified by the nucleotide sequence
complementary to the anticodon, i.e. the codon on mRNA.
E.g..
the codon UCU specifies the amino acid serine. Thus the tRNA molecule that
could recognise and bind serine would carry the anticodon AGA.
However, before the correct amino acid can be bound to tRNA, it must first undergo an initial activation
step. Twenty amino acids are commonly involved in protein synthesis. Each amino acid of the common
20, has its own specific activation enzyme which forms a complex with its specific amino acid. Energy is
required for this and is provided by ATP. The activated amino acid is then accepted by a specific tRNA
molecule to form a complex called an amino acyl tRNA.
Consider a sequence of mRNA to be translated:
AUGAAACGGUUA
mRNA
codons
for:
*met
lys
arg
leu
amino acids
*met = methionine (initiation)
arg = arginine
lys = lysine
leu = leucine
1
An mRNA molecule attaches to a ribosome. A tRNA molecule with an attached a.a. bearing the
anticodon to the codon AUG and a modified amino acid (a modified molecule of the amino acid
methionine) is positioned on the ribosome. This marks the initiation of the polypeptide chain. (also
energy is required.) The ribosome is now ready to receive the tRNA with attached a.a. specified by the
next codon, AAA, i.e.. the tRNA with attached a.a bearing the anticodon UUU.
2
A peptide linkage is now formed between the two adjacent amino acids. The amino acid becomes
detached from its tRNA, and a dipeptide is now attached to the tRNA which is still at the ribosome.
3
The next tRNA molecule (bearing the anticodon GCC and the amino acid arginine) is positioned.
Energy is required for the selection and binding of tRNA molecules. Once again, a peptide linkage is
formed between the amino acids and in this way, the peptide increases in length.
4
These steps are repeated until the entire sequence of codons on mRNA have been "read".
Termination of protein synthesis occurs when a termination codon (UAA,UAG or UGA) is reached and
the newly synthesised polypeptide is released from the final tRNA molecule.
Following completion, the polypeptide may undergo modification before it becomes a functional protein
In eukaryotic cells, the polypeptide is released into cavity of the RER for transport through the cell.
Often several ribosomes "read" simultaneously along the same messenger so that several polypeptides can
be made from the same mRNA. A chain of ribosomes attached to the same mRNA is called a polysome.
Protein synthesis is an energy consuming process. Energy, in the form of ATP is required for:
chain initiation
amino acid activation
translocation
selection and binding of amino acyl tRNAs to the A site
The role of nucleic acids in the storage and transfer of genetic information can be summarised as follows:
transcription
translation
DNA

RNA

Proteins
 Metabolic reactions and their regulation
SOME SAMPLE QUESTIONS:
Nucleic acids
1
Distinguish between the following:
nucleotide and polynucleotide
(2)
2
List FIVE differences between DNA and RNA.
(5)
3
The following is the sequence of bases in one of the two strands of
part of a DNA molecule.
CAGGTACTG
(a)
4
What will be sequence of bases in the complementary strand?
(1)
The following sequence of bases in DNA codes for the formation of
a short peptide chain:
TACTTTAGAGGACCAGTAATT
(a)
(b)
6
Show the sequence of bases you would expect to find in the
corresponding messenger RNA molecule.
(1)
What will be the resulting sequence of amino acids in the
finished peptide chain? (use code table in h/o)
(1)
Lysozyme is a protein made up of 129 amino acids.
(a)
(b)
(c)
How many DNA nucleotides are needed to encode for this
chain of amino acids?
(1)
A complete turn of the DNA double helix contains 10 pairs
of bases and is 3.4 nm long. What length of DNA molecule
is occupied by the gene for lysozyme?
(1)
How many turns of the DNA double helix does this represent?
(1)