Nucleic Acid

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NUCLEIC ACID

The Molecules of Heredity


• Each cell of our bodies contains thousands of different
proteins.
• How do cells know which proteins to synthesize out of
the extremely large number of possible amino acid
sequences?
• From the end of the 19th century, biologists suspected
that the transmission of hereditary information took
place in the nucleus, more specifically in structures
called chromosomes.
• The hereditary information was thought to reside in
genes within the chromosomes.
• Chemical analysis of nuclei showed chromosomes are
made up largely of proteins called histones and nucleic
acids.

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The Molecules of Heredity
• By the 1940s, it became clear that deoxyribonucleic
acids (DNA) carry the hereditary information.
• Other work in the 1940s demonstrated that each gene
controls the manufacture of one protein.
• Thus the expression of a gene in terms of an enzyme
protein led to the study of protein synthesis and its
control.

3
NUCLEIC ACIDS
- are molecules that store the patterns of life and
these patterns are passed from one generation
to the next.
- a polymer in which the monomer units are
nucleotides
- nucleotides joined together by phosphodiester
bonds
- found in cells as nucleoproteins

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Nucleosides – a combination of N-base (heterocyclic base or amine
base) and pentose sugar

Nucleotides – building blocks of nucleic acid composed of N-base


and pentose sugar and phosphate or phosphoric acid
Three Components of Nucleotide

1. Pentose Sugar: Monosaccharide


2. N-bases – heterocyclic amines derived from purine and
pyrimidine
3. Phosphate Group (PO43-)

Base

Phosphate Sugar

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SUGARS

RNA DNA
Nitrogen-Containing Heterocyclic Bases

1. Purine Bases
adenine (A) and guanine (G)

2. Pyrimidine Bases
thymine (T), cytosine (C), and uracil (U)

• Adenine (A), guanine (G), and cytosine (C) are found


in both DNA and RNA.
• Uracil (U): found only in RNA
• Thymine (T) found only in DNA.

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Purine/Pyrimidine Bases

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Phosphate
- third component of a nucleotide, is
derived from phosphoric acid (H3PO4)

• Under cellular pH conditions, the phosphoric


acid is fully dissociated to give a hydrogen
phosphate ion (HPO42-)

✓ DNA and RNA are called nucleic acids because


of the phosphate group, and every residue in a
DNA or RNA molecule is negatively-charged at
physiological pH.
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Nucleoside Formation
• Nucleoside: A two-subunit molecule in which a
pentose sugar is bonded to a nitrogen-containing
heterocyclic base
• Characteristics
• The base is attached to C1′ position of the sugar (β-
configuration)
• It is a condensation reaction

sugar

sugar

+
amine base

amine base

nucleoside
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Nucleotide Formation
- a nucleic acid constituent consisting of a sugar residue
bonded to both a heterocyclic purine or pyrimidine base
and to a phosphate group
sugar sugar H3PO4

+ H3PO4

amine base amine base

nucleoside nucleotide

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Two Types of Nucleic Acids:

1. DNA: Deoxyribonucleic Acid:


- Found within cell nucleus
– Storage and transfer of genetic information
– Passed from one cell to other during cell division

2. RNA: Ribonucleic Acid: Occurs in all parts of cell


– Primary function is to synthesize the proteins

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The Building Blocks of DNA and RNA

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Nucleotides
adenosine 5’-triphosphate (ATP) serves as a common
currency into which energy gained from food is
converted and stored.
anhydride ester N H2
N
O O N
O
-
O- P-O- P-O- P-O-CH 2 O N N
-
O O- O- H H
H H
HO OH
AMP
ADP
Adenos ine 5'-triphosphate
(ATP)

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Differences between DNA and RNA

DNA RNA
Structure Double stranded Single stranded

Sugar deoxyribose ribose

N-bases A, G, C, T A, G, C, U

Function Stores genetic Transmit genetic


information information
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STRUCTURAL ORGANIZATION
OF THE DNA

❖ primary
❖ secondary

❖ tertiary
❖ quaternary

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DNA—Primary (1°) Structure

For nucleic acids, primary structure is the sequence of


nucleotides, beginning with the nucleotide that has the
free 5’ terminus.

• The strand is read from the 5’end to the 3’end.


• Thus, the sequence AGT means that adenine (A) is the base at
the 5’ terminus and thymine (T) is the base at the 3’ terminus.

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Primary Nucleic Acid Structure

• A ribonucleic acid (RNA) is a nucleotide polymer in which


each of the monomers contains ribose, a phosphate group,
and one of the heterocyclic bases adenine, cytosine, guanine,
or uracil

• A deoxyribonucleic acid (DNA) is a nucleotide polymer in


which each of the monomers contains deoxyribose, a
phosphate group, and one of the heterocyclic bases adenine,
cytosine, guanine, or thymine

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PRIMARY LEVEL of
DNA structure

- Describes the sequence and relative


contents or % composition of the
DNA molecule

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PRIMARY LEVEL of
DNA structure

❖ 2 important features of all polynucleotides

a. A polynucleotide has a sense of


directionality

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5’ end

Unreacted
phosphate

Unreacted OH

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Primary Structure
• Structure: Sequence of
nucleotides in DNA or
RNA

• 5’ end has free


phosphate and 3’ end
has a free OH group

• Sequence of bases read


from 5’ to 3’
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PRIMARY LEVEL of DNA/RNA Structure
PRIMARY LEVEL of
DNA structure

b. A polynucleotide has individuality,


determined by the sequence of its
bases (the nucleotide sequence)

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Structure of DNA and RNA

Schematic diagram of a nucleic


acid molecule. The four
bases of each nucleic acid
are arranged in various
specific sequences.

base sequence is read


from the 5’ end to the
3’ end

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• Sugar-phosphate groups are referred to as nucleic
acid backbone - Found in all nucleic acids
• Sugars are different in DNA and RNA

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Comparison of the General Primary Structures of
Nucleic Acids and Proteins

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DNA—2° Structure
Secondary structure: The ordered arrangement of nucleic acid
strands.
• The double helix model of DNA 2° structure was proposed by
James Watson and Francis Crick in 1953.

Double helix: A type of 2° structure of DNA in which two


polynucleotide strands are coiled around each other in a screw-
like fashion.

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DNA Double Helix

• The secondary structure involves two


polynucleotide chains coiled around each
other in a helical fashion
• The poly nucleotides run anti-parallel
(opposite directions) to each other, i.e., 5’ -
3’ and 3’ - 5’
• The bases are located at the center and
hydrogen bonded (A=T and GΞC)
• Base composition: %A = %T and %C = %G)
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Base Pairing

A and T pair by
forming two
hydrogen bonds.

G and C pair by
forming three
hydrogen bonds.

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DNA Sequence: the sequence of bases on one
polynucleotide is complementary to the other
polynucleotide

• Complementary DNA strands are strands of DNA in a


double helix with base pairing such that each base is
located opposite its complementary base.

• Example :
• List of bases in sequential order in the direction from the 5’ end to 3’
end of the segment:

• 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’

• Complementary strand of this sequence will be:


3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’
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Practice Exercise

• Predict the sequence of bases in the DNA strand


complementary to the single DNA strand shown below:

5’ A–A–T–G–C–A–G–C–T 3’
Answer:
3’ T–T–A–C–G–T–C–G–A 5’

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TERTIARY LEVEL of
DNA structure

- The 3-D structure that involves a


higher-order folding of elements of
regular secondary structure

- The supercoiling of the DNA

HISTONES – small proteins that participate


in forming the nucleosomal structure of
the chromatin
Superstructure of Chromosomes
DNA is coiled around proteins called histones.
• Histones are rich in the basic amino acids Lys and Arg,
whose side chains have a positive charge.
• The negatively-charged DNA molecules and positively-
charged histones attract one another and form units
called nucleosomes.
Nucleosome: A core of eight histone molecules around
which the DNA helix is wrapped.
• Nucleosomes are further condensed into chromatin.
• Chromatin fibers are organized into loops, and the
loops into the bands that provide the superstructure of
chromosomes.

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QUATERNARY LEVEL
of DNA structure

- Involves the interaction of the DNA


with other macromolecules,
specifically proteins.
- This organizational structure allows
long stretches of DNA to be tightly
packed in a space of about 2 µm in
diameter
Localization of the DNA
• Genome – the total genetic information contained in a cell,
an organism or virus.

• Prokaryotes
• In the nucleoid region of the cytoplasm.
• Their DNA is circular loop.

• Eukaryotes
• In certain subcellular components: mitochondria,
chloroplasts, nucleus
• Most of the DNA of an organism is found in the nucleus,
and occur as structures known as chromosomes.
THE CENTRAL DOGMA
OF GENETICS

- Summarizes the mechanisms for


transfer of genetic information

I DNA RNA Proteins


IIa IIb

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Information Transfer in Cell

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Information Copying:
REPLICATION

FEATURES:
1. Both strands are replicated.
2. There is a start, but no stop signals.
3. Primers are needed before polymerization
can occur.
4. Polymerization is catalyzed by DNA
polymerases. Direction of synthesis is
5’ → 3’.
5. Mode of replication is semi-conservative.
Information Copying:
REPLICATION

• The process begins with the unwinding of the DNA double


helix, facilitated by enzymes called helicases.
• Then an RNA primase begins to synthesize RNA primers at
the replication fork.
• This is the starting point for the DNA polymerases to start
copying the parent DNA strand.
• The DNA polymerases copy the DNA strand by making
complementary strands to these by base pairing.
• Adenine pairs with thymine and guanine pairs with
cytosine.
REPLICATION
- Process by which DNA molecules produce exact
duplicates of themselves

• Old strands act as templates for the synthesis of new


strands

• The newly synthesized DNA has one new DNA strand


and old DNA strand

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Continuous-Growing Strands and Okazaki Fragments

- During replication process, the strands separate


- Each can then act as a template for the synthesis of a new complimentary strand

Replication fork – point at which DNA double helix is unwinding

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Sample Replication Process

DNA informational: 5’ A–A–T–G–C–A–G–C–T 3’


DNA template strand: 3’ T–T–A–C–G–T–C–G–A 5’

DNA Replication Process


https://www.youtube.com/watch?v=TNKWgcFPHqw
Overview of Protein Synthesis
Proteins are responsible for the formation of skin, hair,
enzymes, hormones, and so on

Protein synthesis can be divided into two phases.


1. Transcription – A process by which DNA directs the
synthesis of mRNA molecules
2. Translation – a process in which mRNA is deciphered
to synthesize a protein molecule
Transcription Translation
DNA RNA Protein

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Types of RNA Molecules
1. Heterogeneous nuclear RNA (hnRNA)
- Formed directly by DNA transcription.
- Post-transcription processing converts the hnRNA to mRNA
2. Messenger RNA (mRNA)
- Carries instructions for protein synthesis (genetic information)
from DNA
3. Small nuclear RNA (snRNA)
- facilitates the conversion of hnRNA to mRNA.
4. Ribosomal RNA (rRNA)
- Combines with specific proteins to form ribosomes - the physical
site for protein synthesis
5. Transfer RNA (tRNA)
- delivers amino acids to the sites for protein synthesis

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53
RNA

❖ messenger RNA (mRNA)

❖ ribosomal RNA (rRNA)

❖ transfer RNA (tRNA)

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Messenger RNA
- The product of DNA transcription
-Carries instructions for protein
synthesis from DNA
-It contains a sequence of three
bases specifying for an amino acid.
This sequence is called a codon.

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Messenger RNA

- The mRNA is single-stranded and


has a random conformation

codon

3'

5'

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• The base sequence in mRNA determines the amino acid
sequence for the protein synthesized.
• The base sequence of an mRNA molecule involves only 4
different bases - A, C, G, and U
Codon: A three-nucleotide sequence in an mRNA molecule that
codes for a specific amino acid
• Based on all possible combination of bases A, G, C, U”
there are 64 possible codes
Genetic code: The assignment of the 64 mRNA codons to specific
amino acids
• 3 of the 64 codons are termination codons (“stop” signals)
Gene: A segment of a DNA base sequence responsible for the
production of a specific hnRNA/mRNA molecule

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Characteristics of Genetic Code
• The genetic code is almost universal:

The same codon specifies the same amino acid whether


the cell is a bacterial cell, a corn plant cell, or a human cell.

The codon - coding for the amino acid methionine


(AUG) functions as initiation codon.
“Stop” codons (UAG, UAA, and UGA)
- terminate protein synthesis

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Transfer RNA

-The only RNA with a specific shape


2 – D structure: cloverleaf
3 – D structure: L-shaped

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• During protein synthesis, amino acids do not directly
interact with the codons of an mRNA molecule
• tRNA molecules act as intermediaries to deliver amino acids to
mRNA
• Two important features of the tRNA structure
• The 3′ end of tRNA is where an amino acid is covalently bonded
to the tRNA
• The loop opposite to the open end of tRNA, called the
anticodon, comprises seven unpaired bases
• Three unpaired bases constitute the anticodon
• A three-nucleotide sequence on a tRNA molecule
that is complementary to a codon on an mRNA
molecule

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Reserved.
Transfer RNA

-The adaptor molecule that


recognizes the codon in mRNA and
transfers the amino acid
corresponding to the codon

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Transfer RNA

-Contains the
anticodon loop
~ a sequence of
three bases
complementary
to the codon

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Sample Replication Process

DNA informational: 5’ A–A–T–G–C–A–G–C–T 3’


DNA template strand: 3’ T–T–A–C–G–T–C–G–A 5’

mRNA: 5’ A- A- U- G-C-A- G -C -U 3’

Amino Acid Seq.:


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tRNA
– Each tRNA is specific for only one amino acid.
– Each cell carries at least 20 specific enzymes, each specific
for one amino acid.
– Each enzyme recognizes only one tRNA.
– The enzyme bonds the activated amino acid to the 3’
terminal -OH group of the appropriate tRNA by an ester
bond.
– At the opposite end of the tRNA molecule is a codon
recognition site.
– The codon recognition site is a sequence of three bases
called an anticodon.
– This triplet of bases aligns itself in a complementary
fashion to the codon triplet on mRNA.
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Ribosomal RNA

-Allows the binding of mRNA in the


ribosomes

-rRNA complexes with proteins to


form structures called ribosomes, the
site of protein biosynthesis

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TRANSLATION – a process in which mRNA codons are
deciphered to synthesize a protein molecule

Ribosome – an rRNA–protein complex - serves as the


site of protein synthesis:
• The mRNA binds to the small subunit of the ribosome.

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Steps of Translation Process
Activation of tRNA: addition of specific amino acids to the 3’-OH group of
tRNA.
Initiation of protein synthesis: Begins with binding of mRNA to small
ribosomal subunit such that its first codon (initiating codon AUG) occupies
a site called the P site (peptidyl site)
Elongation: Adjacent to the P site in an mRNA–ribosome complex is A site
(aminoacyl site) and the next tRNA with the appropriate anticodon binds to
it.
Termination: The polypeptide continues to grow via translocation until all
necessary amino acids are in place and bonded to each other.
Post-translational processing – gives the protein the final form it needs
to be fully functional

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DNA to Protein

https://www.youtube.com/watch?v=gG7uCskUOrA
Mutation
• An error in base sequence reproduced during DNA
replication
• Errors in genetic information is passed on during
transcription.
• The altered information can cause changes in amino
acid sequence during protein synthesis and thereby
alter protein function
-Involves a change in shape, structure or nucleotide
sequence of the DNA

• Such changes have a profound effect on an organism.


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MUTATIONS OF THE DNA

➢ The knowledge of the genetic


mechanism give insights to the problem
of genetic disorders.
➢ Genetic disorders are now known to
be a result of alterations of DNA
sequences which correspondingly
results in alterations of amino acid
sequence of the protein product.
MUTATIONS OF THE DNA

Protein equation:

amino acid
DNA sequence conformation function
sequence
MUTATION

• Any alteration in gene sequence


• Involves a change in shape, structure
or nucleotide sequence of the DNA
• The change may be spontaneous or
induced by agents called mutagens
• May be lethal to the organism or it
may lead to a branching in the
evolutionary tree or specie diversity
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POINT MUTATIONS

• Can be a change in a single base, or


addition or removal of one or more
nucleotides in the DNA
• Single base changes are of two types:
▪ transitions – involves a change of a
purine to another purine OR a pyrimidine
to another pyrimidine
▪ transversions – involves a change of a
purine to a pyrimidine and vice versa
POINT MUTATIONS
• May have no effect on the amino acid sequence of the
protein. This is most likely if the substituted base is
in the third codon.
• However, if there are deletions or additions, the effect
may be lethal to an organism since this shifts the
reading frame of the codons.
• Deletion mutation alters the function of the affected
protein. Deletion mutation leads to congenital
anomalies or birth defects and significant intellectual
and physical disability.
• Thus, additions or deletions are also referred to as
frameshift mutations.
SPONTANEOUS MUTATIONS

• Can occur when the bases convert to their


rare tautomeric forms just as when the bases
are being copied during replication or
transcription.
• Tautomers – structural isomers that differ
in the location of their hydrogens and
double bonds.
• In most instances however, mutations are
induced by physical and chemical agents.
MUTATIONS may be
due to
1. Physical agents
▪ ultraviolet and ionizing radiation
2. Chemical agents
▪ alkylating agents
▪ deaminating agents
▪ intercalating agents
3. Viral agents
▪ oncogenes
Mutagens
◼ Mutations are caused by mutagens.
◼ Mutagen: a chemical or physical agents

that causes a base change or mutation


in DNA.
Physical Agents
◼ Radiations such as Ultraviolet, X-ray,

radioactivity and cosmic radiation are


mutagenic –cause cancers
◼ The base which is most affected by UV

radiation is the base thymine.


◼ For thymine, the major product is the

thymine-thymine cyclobutane dimer. 87


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Mutagens
◼ Chemical/Environmental Substances
Alkylating agents
◼ The largest class of potential mutagens present in man’s
environment.Are produced by N-nitrosamines, which are found in
cigarette smoke. They are metabolized by liver enzymes to form
alkylating agents.
◼ Guanine is the most reactive of all bases toward nearly all
alkylating agents, and this results in an “apurinic site” in the DNA, a
location in DNA (also in RNA but much less likely) that has neither
a purine nor a pyrimidine base, either spontaneously or due
to DNA damage.
◼ During replication, an apurinic site may be ignored, resulting in
deletion in the daughter strand.
Mutagens

▪ Chemical/Environmental Substances
Deaminating Agents
▪ Obtained from sodium nitrite, which is used as a
preservative, color enhancer and fixative in bacon,
smoked fish, tocino etc. When ingested, it is
converted to nitrous acid in acidic conditions.
▪ Nitrous acid is a deaminating agent and removes
amino groups from adenine, guanine, cytosine. This
may result in point mutations.
Mutagens
▪ Chemical/Environmental Substances
Intercalating agents
▪ Their structures can interact with the bases of the DNA. They have
flat structures, similar to the DNA bases, thus they can intercalate or
insert in the DNA molecule.
▪ These substances do not chemically modify DNA, but they physically
bind to it, becoming inserted in the DNA sequence.
▪ Intercalating agents include the following:
• Benzopyrene – automotive exhaust and cigarette smoke
• Benzene – an organic solvent
• Aflatoxin – a metabolic product of molds in peanuts, oils and
grains
Viruses
◼ Tiny disease causing agents with outer protein envelope and
inner nucleic acid core
◼ Some viruses contain oncogenes (cancer-causing genes)
which can be activated once they insert their DNA in their
host’s genome. As a consequence, the sequence of the
bases in the host DNA may be altered, resulting in altered
protein product or activation of certain destructive genes.
◼ Virus invade bacteria, plants animals, and humans:
◼ Many human diseases are of viral origin, e. g. Common

cold, smallpox, rabies, influenza, hepatitis, and AIDS


Vaccines

◼ Inactive virus or bacterial envelope


◼ Antibodies produced against inactive viral
or bacterial envelopes will kill the active
bacteria and viruses
REPAIR MECHANISMS

1. Enzymes
2. Free-radical scavengers/
antioxidants
3. Dark repair mechanism
Repair Mechanisms

• Since the cell is prone to mutation by exposure


to mutagenic agents, it is also endowed with a
variety of defense and repair mechanism to
protect its DNA from damage

1. Enzymes
2. Free-radical scavengers/antioxidants
3. Dark repair mechanism
Repair Mechanisms

Enzymes
• Cells are equipped with enzymes that can repair
damage in the structure of their DNA.
Eg. A photoreactivating enzyme, photolyase, monomerizes
the thymine-thymine cyclobutane dimer
Eg. DNA glycosylases recognize altered bases and
catalyze their hydrolytic removal from DNA
Repair Mechanisms

Free radical scavengers or Antioxidants


• Removes harmful free radicals created by ionizing
radiations or chemical agents.
Include the following molecules or substances found in cells:
• Glutathione and metallothionein produced by cells
• Enzymes such as catalase, peroxidases and superoxide
dismutase
• Vitamins C, A and E
Repair Mechanisms

Dark repair mechanism


▪ Light-independent mechanism for the removal of
damaged DNA.
• Includes excision repair – removes the thymine-
thymine dimer and replaces it with an priginal DNA
strand
• Post-replication repair and proofreading mechanism
during replication
Other Functions of
Nucleotides
1. Nucleotides carry chemical energy in cells. Nucleotide
triphosphates, such as ATP, GTP, UTP and so on, are
utilized to drive chemical reactions in the cell. ATP is the
most widely used.
2. Nucleotides are components of many enzyme
cofactors, such as NAD+ , FAD and coenzyme A.
3. Some nucleotides are intermediates in cellular
communication. Cyclic AMP (cAMP) serves regulatory
functions outside the cell, such as in glycogen
metabolism.
Applications in Medicine

◼ Development of antibiotic drugs as inhibitors of genetic


mechanisms:
◼ Puromycin – a structural analogue of the amino acyl tRNA. It

can be mistaken as amino acyl tRNA and can be incorporated


into peptide chains. This causes premature termination of
protein synthesis.
◼ Streptomycin – causes cell death by binding to the small

subunit (30S) of the prokaryotic ribosomes, thus preventing the


binding of mRNA.
◼ Chloramphenicol – binds with the 50S subunit of the

prokaryotic ribosomes blocking the action of peptidyl


transferase and preventing the attachment of the mRNA-30S
complex
99
to the large subunit.
Applications in Medicine

Gene therapy
◼ Treatment of a genetic disease by introduction of a gene

for a missing protein.


◼ Most successful case as of 2007 is the treatment of

adenosine deaminase (ADA), an enzyme involved in


purine metabolism.
◼ The absence of the gene for ADA affects DNA

synthesis in the lymphocytes, and this leads to a


condition known as severe combined immune
deficiency (SCID) or the “bubble bloy syndrome”.
Individuals with this disease are prone to infection.
Applications in Medicine

Gene therapy
◼ The goal of planned therapy is to take bone marrow cells

from affected individuals, introduce the gene for


adenosine deaminase from cells using a virus as a
vector, and then reintroduce the bone marrow cells in the
body, where they will produced the desired enzyme.

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