Nucleic Acids

Nucleic Acids
 Nucleic acid is an important class of macromolecules found
in all cells and viruses. The functions of nucleic acids have
to do with the storage and expression of genetic information.
Deoxyribonucleic acid (DNA) encodes the information the
cell needs to make proteins.

There are two types of nucleic acids:

- deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
 These are polymers consisting of long chains of monomers called nucleotides
 A nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate
group:
 Nitrogen Bases
 The nitrogen bases in nucleotides consist of two general
types:
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C), thymine (T) and Uracil (U)
 Nucleosides and Nucleotides
 A nucleoside consists of a nitrogen base linked by a
glycosidic bond to C1’ of a ribose or deoxyribose
 Nucleosides are named by changing the the nitrogen
base ending to -osine for purines and –idine for
pyrimidines
 A nucleotide is a nucleoside that forms a phosphate
ester with the C5’ OH group of ribose or deoxyribose
 Nucleotides are named using the name of the
nucleoside followed by 5’-monophosphate
 Primary Structure of Nucleic Acids
 The primary structure of a nucleic acid is the nucleotide
sequence
 The nucleotides in nucleic acids are joined by phosphodiester
bonds
 The 3’-OH group of the sugar in one nucleotide forms an ester
bond to the phosphate group on the 5’-carbon of the sugar of
the next nucleotide
 Reading Primary Structure

 A nucleic acid polymer has a

free 5’-phosphate group at
one end and a free 3’-OH
group at the other end
 The sequence is read from
the free 5’-end using the
letters of the bases
 This example reads
5’—A—C—G—T—3’
 Example of RNA Primary Structure
 In RNA, A, C, G, and U are linked by 3’-5’
ester bonds between ribose and phosphate
 Example of DNA Primary Structure
 In DNA, A, C, G, and T are linked by 3’-5’ ester
bonds between deoxyribose and phosphate
 Secondary Structure: DNA Double Helix

 In DNA there are two strands of nucleotides that wind

together in a double helix
- the strands run in opposite directions
- the bases are are arranged in step-like pairs
- the base pairs are held together by hydrogen
bonding
 The pairing of the bases from the two strands is very
specific
 The complimentary base pairs are A-T and G-C
- two hydrogen bonds form between A and T
- three hydrogen bonds form between G and C
 Each pair consists of a purine and a pyrimidine, so
they are the same width, keeping the two strands at
equal distances from each other
Base Pairing in the DNA Double Helix
 DNA Replication
 When a eukaryotic cell divides, the process is called
mitosis
- the cell splits into two identical daughter cells
- the DNA must be replicated so that each daughter cell
has a copy
 DNA replication involves several processes:
- first, the DNA must be unwound, separating the two
strands
- the single strands then act as templates for synthesis of
the new strands, which are complimentary in sequence
- bases are added one at a time until two new DNA
strands that exactly duplicate the original DNA are
produced
 The process is called semi-conservative replication
because one strand of each daughter DNA comes from the
parent DNA and one strand is new
 The energy for the synthesis comes from hydrolysis of
phosphate groups as the phosphodiester bonds form
between the bases
Semi-Conservative DNA Replication
 Direction of Replication
 The enzyme helicase unwinds several sections of parent
DNA
 At each open DNA section, called a replication fork,
DNA polymerase catalyzes the formation of 5’-
3’ester bonds of the leading strand
 The lagging strand, which grows in the 3’-5’
direction, is synthesized in short sections called
Okazaki fragments
 The Okazaki fragments are joined by DNA ligase to give
a single 3’-5’ DNA strand
 Ribonucleic Acid (RNA)
 RNA is much more abundant than DNA
 There are several important differences between RNA
and DNA:
- the pentose sugar in RNA is ribose, in DNA it’s
deoxyribose
- in RNA, uracil replaces the base thymine (U pairs with
A)
- RNA is single stranded while DNA is double stranded
- RNA molecules are much smaller than DNA molecules
 There are three main types of RNA:
- ribosomal (rRNA), messenger (mRNA) and transfer
(tRNA)
 Ribosomal RNA and Messenger RNA
 Ribosomes are the sites of protein synthesis
- they consist of ribosomal DNA (65%) and proteins
(35%)
- they have two subunits, a large one and a small one
 Messenger RNA carries the genetic code to the
ribosomes
- they are strands of RNA that are complementary to the
DNA of the gene for the protein to be synthesized
 Transfer RNA
 Transfer RNA translates the genetic code from the
messenger RNA and brings specific amino acids to the
ribosome for protein synthesis
 Each amino acid is recognized by one or more specific tRNA
 tRNA has a tertiary structure that is L-shaped
- one end attaches to the amino acid and the other binds to
the mRNA by a 3-base complimentary sequence
 Protein Synthesis
 Steps in protein synthesis are
- the transfer of information from DNA to
DNA(Replication)
- transfer of information from DNA to RNA(transcription)
- transfer of information from DNA to protein(translation)
 Transcription takes place in the nucleus, while translation
takes place in the cytoplasm
 Genetic information is transcribed to form mRNA much the
same way it is replicated during cell division
 Transcription
 Several steps occur during transcription:
- a section of DNA containing the gene unwinds
- one strand of DNA is copied starting at the
initiation point, which has the sequence TATAAA
- an mRNA is synthesized using complementary
base pairing with uracil (U) replacing thymine
(T)
- the newly formed mRNA moves out of the
nucleus to ribosomes in the cytoplasm and the
DNA re-winds
 RNA Polymerase
 During transcription, RNA polymerase moves
along the DNA template in the 3’-5’direction to
synthesize the corresponding mRNA
 The mRNA is released at the termination point
 Processing of mRNA
 Genes in the DNA of eukaryotes contain
exons that code for proteins along with
introns that do not
 Because the initial mRNA, called a pre-RNA,
includes the noncoding introns, it must be
processed before it can be read by the tRNA
 While the mRNA is still in the nucleus, the
introns are removed from the pre-RNA
 The exons that remain are joined to form the
mRNA that leaves the nucleus with the
information for the synthesis of protein
mRNA Codons and Associated Amino
Acids
 Reading the Genetic Code

 Suppose we want to determine the amino acids

coded for in the following section of a mRNA

5’—CCU —AGC—GGA—CUU—3’

 According to the genetic code, the amino acids for

these codons are:

CCU = Proline AGC = Serine

GGA = Glycine CUU = Leucine

 The mRNA section codes for the amino acid

sequence of Pro—Ser—Gly—Leu
 Predicting base sequence in a
complementary DNA strand

Practice Exercise:
 Predict the sequence of bases in the DNA
strand that is complementary to the single
DNA strand

5’ C-G-A-A-T-C-C-T-A 3’
 Predicting base sequence in a
complementary DNA strand

 Predict the sequence of bases in the DNA strand

that is complementary to the single DNA strand

Given: 5’ C-G-A-A-T-C-C-T-A 3’
Complementary strand:
3’ G-C-T-T-A-G-G-A-T 5’
 Determining Relationships Among DNA
Base Sequences, mRNA Base Sequences,
Codons, Anticodons, and Amino Acids
 A DNA template strand is read as follows:

3’ ACGAACCGATAGGGA 5’
Determine each of the ff. using this base sequence.
a) The base sequence in the DNA informational strand.
b) The codons present in the mRNA transcribed from the DNA
template strand.
c) The tRNA anticodons that interact with the mRNA codons
d) The amino acids that the tRNA molecules carry
e) The structure of the peptide formed from the overall
translation process.
 Translation and tRNA Activation
 Once the DNA has been
transcribed to mRNA, the
codons must be tranlated to
the amino acid sequence of
the protein
 The first step in
translation is activation of
the tRNA
 Each tRNA has a triplet
called an anticodon that
complements a codon on
mRNA
 A synthetase uses ATP
hydrolysis to attach an
amino acid to a specific
tRNA
 Initiation and Translocation
 Initiation of protein synthesis occurs when a mRNA
attaches to a ribosome
 On the mRNA, the start codon (AUG) binds to a tRNA
with methionine
 The second codon attaches to a tRNA with the next
amino acid
 A peptide bond forms between the adjacent amino
acids at the first and second codons
 The first tRNA detaches from the ribosome and the
ribosome shifts to the adjacent codon on the mRNA
(this process is called translocation)
 A third codon can now attach where the second one
was before translocation
 Elongation
 attachment of first amino acid carrying t-RNA to a
binding site of the ribosome. At t-RNA and its
amino acid attach to A binding site.
 Peptide bond formation bet. Methionine and amino
acid carried at A binding site. Polypeptide chain is
now met.
 Ribosomes moves in the 3’ direction down the
mRNA by 3 bases or 1 codon shifting tRNA and
polypeptide chain to P binding site. A binding site
is open and vacant tRNA is the E binding site.
 tRNA is ejected from E binding site and elation
step1-4 is repeated until stop codon is
encountered
 Termination
 After a polypeptide with all the amino acids for a
protein is synthesized, the ribosome reaches the
the “stop” codon: UGA, UAA, or UAG
 There is no tRNA with an anticodon for the
“stop” codons
 Therefore, protein synthesis ends (termination)
 The polypeptide is released from the ribosome and
the protein can take on it’s 3-D structure
(some proteins begin folding while still being
synthesized, while others do not fold up until after
being released from the ribosome)
Nature of Genetic Code
1. Consists of triplet of bases (Pu/Py)
e.g. AUG;GUG = initiation codon or start
codon.
UAA; UAG; UGA = stop codon or
termination codon
GCA; AGG; CGA = Arginine
AAA; AAG = Lysine
2. Universality – all living systems have the same code for a
particular a.a. (fish, animals, plants have the same code).

3. Codon degeneracy – one a.a. can have more than one code.
(refer to the a.a. chart).

Flosy NOW arriving.

Flosy NOT arriving.

Mutation- misreading of the code.

- It is the “typographical error”that occur when DNA
molecules, affected by physical or chemical mutagens, are
replicated.
- can cause damage in the a.a. side sequence which may
affect on the functioning of the organism.
e.g. replacement of the glutamic acid side chain by valine in
the hemoglobin molecules result in sickle cell anemia.
2PSY02
Mutation – micro lesions which involve the replacement of one base pair by another
(substitution).
Substitutions are divided into two subclasses:
1. Transition – is a replacement of a purine by another purine base or a pyrimidine
by another pyrimidine base.
Ex: A  G; T C
2. Transversion - is a replacement of a purine by a pyrimidine or a pyrimidine by a
purine base.
Ex. A  C
T  G
T  G
A  C
Frameshift mutation – is another type of microlesion mutation which involves a loss or
addition of one or few base pairs.
Addition of one base +
TAC TA+ CTA CTA CTA Frameshift
Addition of one base +
TAC TAC TAC TAC TAC Normal
Deletion of one base –
TAC+ ACT ACT ACT Frameshift

TAC TAC TAC TAC TAC Normal

2PSY02
 Which of the following changes is a transition base substitution?
a. Adenine is replaced by thymine.
b. Cytosine is replaced by adenine.
c. Guanine is replaced by adenine.
d. Three nucleotide pairs are inserted into DNA.
Concept Check 1
Which of the following changes is a transition
base substitution?

a. Adenine is replaced by thymine.

b. Cytosine is replaced by adenine.
c. Guanine is replaced by adenine.
d. Three nucleotide pairs are inserted into DNA.
TYPES OF MUTATION
1. Somatic vs. gametic mutation
The consequences of mutations depend upon the
individual where it occurs. Some mutations occur in
regular body cells. These are somatic mutations. This
mutation would not be passed into subsequent
generations.
For example: too much exposure to the sun can cause
skin cancer. This type of mutation is felt only by the
individual due to too much exposure to the sun

Some mutations occur in the cells that produce gametes,

and therefore they are called gametic mutations. These
mutations, in contrast to the somatic mutations, will be
passed into the next generation because they occur in the
cells that produce the next generation.
2. Spontaneous and Induced Mutations
Some mutations arise from natural errors in DNA replications ( as a
result of unknown chemical reactions). Occurrence of this type of
mutation varies from species to species. Humans have higher
spontaneous rate, probably due to higher complexity of human
replication.
Induced mutation is caused by agents in the environment. The
agents are called mutagens.
TYPES of mutagens:
1>Physical mutagens
a) Heat and high pressure: Constant exposure to extreme
heat and high pressure can cause damage to the skin thus
resulting in skin cancer.
b)UV radiation : DNA absorbs primarily by the pyrimidine bases
thymine and cytosine. When thymine is irradiated with UV light,
excitations of pi electrons will result in the formation of thymine
diradicals. Coupling of thymine diradicals result in the formation
of thymine cyclobutane dimer. When these dimers are formed, the
interaction between bases are cleaved. This may lead short, at
some points, or may proceed, incorrectly, with an altered base
sequence.
On with subsequent replications, this aletered strand could
replicate itself and produce molecules with a wrong base
sequence in both strands. Defective strands, if not repaired, may
also lead to mistakes in transcription of genetic message to m-
RNA.
Because of the effects of UV radiation, this erves as a molecular basis for the
following:
1. UV rays can kill bacteria.
2. UV rays can temporarily delay cell division.
3. UV rays can delay synthesis of proteins in the cell.
4. UV rays can produce mutation.

C) IR (Ionizing radiation) – consists of electromagnetic radiation such as x-rays,

gamma rays, or highly energetic particles such as electrons, alpha particles, and
radioactivity. In terms of its effect on the cell, this is more potent than UV
radiation.
Thymine is more sensitive to IR, forming free radicals altering DNA molecule and
interfering with the coding of the genetic information. It can also trigger the
formation of other free radicals.
Adenine is also affected, resulting to its oxidation
Single strand breaks are also produced by IR. Electrons can be knocked off frm
the suga-phosphate backbone of the nucleic acids.
Cytosine can also undergo free radical addition at 5-6 position, forming immune
tautomers. This will result in the conversion of C  U.

2>Chemical mutagens
2>Chemical mutagens
• Inorganic Mutagens
• A) Pb – an antiknock agent to increase the efficiency of the engine.
It has a strong affinity for ligands such as phosphate groups. The
interaction increases the positivity of phosphorous atoms and
therefore can be easily hydrolyzed. It induces the hydrolysis of t-
RNA and prevents its interaction with t-RNA in the ribosome due to
conformation changes
• B) Nitrous acid – is produced from nitrogen oxides in polluted air in
the presence of water and also used as food preservatives in the
form of nitrites. This reacts with the amino group of A, G, and C.
This A will react with nitrous acid can convert A to hypoxanthine,
affecting base pair with cytosine rather than thymine.
• C) Sulfur dioxide – is used as preservative for fruits and
vegetables to prevent browning reactions. SO2 is a throat and lung
irritant. However, SO2 reacts with water to form bisulfite ion which
is very reactive at 5-6 position of cytosine. With this reversible
reaction, C is converted to U, thus affecting base-pairing with DNA.
2>Chemical mutagens
• Organic Mutagens

• A) Benzopyrene – is a polycyclic aromatic

hydrocarbon found in cigarette smoke and
auto engine exhaust. Being planar, it has
the capacity to intercalate in every two
base-pairs of DNA, thereby affecting
replication.

• B) Ethylene dibromide- a very good

alkylating agent, reacts with G which may
lead to two apurinic sites because alkylation
not only results in weakening of H bonds
between G-C base-pairs but also weakens
the N-C glycosidic bonds. In such cases,
hydrolysis of the bonds can easily take
place.
2>Chemical mutagens
• Organic Mutagens
• C) Formaldehyde – is an organic compound found in auto engine
exhaust, textile markets and is used as preservative. This compound
reacts readily with the free amino group of A and less readily with the
amino group of C and G. This is expected because A is in a less stable
H-bonded base-pair the G-C base pair with 3 H-bond. The reaction is
one of the nucleophilic additions to the positive carbonyl carbon of
formaldehyde. It provides methylene bridge between two adenine
molecules that are properly oriented forming bis-adenosine
derivatives.
• D)Caffeine-is one of the food pollutants found in coffee, tea, cocoa,
and cola drinks.
• This has a similar structure to the pu basesand, therefore, has
chromosome breaking effects because it interferes with the bases
through its pi electron cloud, blocking the precise orientation of
bases during repair.
• Another effect of caffeine is its tendency to be inserted in the
apurinic site bec. Its structure is similar to Pu base. When this
happens, base-pairing is affected and, consequently, replication
and transcription are also affected.

• E) Drug mutagens (antibiotics)

2>Chemical mutagens
• Organic Mutagens
• E) Drug mutagens (antibiotics)- It is known that a number of
drugs interact with nucleic acids. For example, amino acridine,
which has antibacterial properties, interacts with DNA by
intercalation.

• Other drugs which interact with the nucleic acid are some
antibiotics. For example, actinomycins bind with DNA, thereby
interfering with the normal functions. These interactions with DNA
and RNA both interfere in the transcription process, through
intercalation and H-bond interaction.