SIM Biochemistry ULO9

College of Health Sciences Education
3rd Floor, DPT Building

Matina Campus, Davao City
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Big Picture in Focus: ULO9. Demonstrate knowledge on structures,

functions, synthesis, and levels of organization of nucleic acids; as
well as understanding of the central dogma in the transfer of genetic
information and mutations.
Metalanguage
The most essential terms and concepts below are defined, for you to have a better understanding of this
section in the course. You are advised to frequently refer to these definitions to help you understand the succeeding
topics.
1. Nucleic acids – Nucleic acids are polymeric molecules in which the repeating units are nucleotides. Cells contain
two kinds of nucleic acids – deoxyribonucleic acids (DNA) and ribonucleic acids (RNA). The major biochemical
functions of DNA and RNA are, respectively, transfer of genetic information and synthesis of proteins.
2. Nucleic acid building blocks – Three types of subunits are present in a nucleic acid. They are (1) a pentose sugar
(ribose or deoxyribose), (2) a nitrogen-containing base (either a purine or a pyrimidine derivative), and (3) a
phosphate group. The nitrogen-containing bases are of five types: adenine (A), guanine (G), cytosine (C), thymine
(T), and uracil (U).
3. Nucleosides and nucleotides – A nucleoside is a compound formed from a pentose sugar and a purine or
pyrimidine base derivative. A nucleotide is a nucleoside to which a phosphate group has been added (bonded to the
sugar). Nucleotides are the monomers for nucleic acid polymers.
4. Primary nucleic acid structure – The “backbone” of a nucleic acid molecule is a constant alternating sequence of
sugar and phosphate groups. Each sugar unit has a nitrogen-containing base attached to it.
5. Complementary bases – Complementary bases are specific pairs of bases in nucleic acid structures that hydrogen-
bond to each other.
6. Secondary DNA structure – A DNA molecule exists as two polynucleotide chains coiled around each other in
double-helix arrangement. The double helix is held together by hydrogen bonding between complementary pairs of
bases. Only two base-pairing combinations occur: A with T and C with G.
7. DNA replication – DNA replication occurs when the two strands of a parent DNA double helix separate and act as
templates for the synthesis of new chains using the principle of complementary base pairing.
8. Chromosome – A chromosome is a structure that consists of an individual DNA molecule bound to a group of
proteins.
9. Transcription – Transcription is the process in which the genetic information encoded in the base sequence of
DNA is copied into hnRNA/mRNA molecules.
10. Translation – Translation is the stage of protein synthesis in which the codons in mRNA are translated into amino
acid sequences of new proteins. Translation involves interactions between the codons of mRNA and the anticodons
of tRNA.
Reference textbook: Stoker, H. S. (2017). Biochemistry 3rd Edition. C & E Publishing Inc. Quezon City. 1
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11. Gene – A gene is a portion of a DNA molecule that contains the base sequences needed for the production of a
specific hnRNA/mRNA molecule. Genes are segmented, with portions called exons that contain genetic information
and portions called introns that do not convey genetic information.
12. Genetic code – The genetic code consists of all the mRNA codons that specify either a particular amino acid or
the termination of protein synthesis.
Essential Knowledge
Nucleic Acids
Types of Nucleic Acids

• The Swiss physiologist Friedrich Miescher (1844-1895) discovered nucleic acids in 1869 while studying the
nuclei of white blood cells.
• The fact that they were initially found in cell nuclei and are acidic accounts for the name nucleic acid.
• It is now known that nucleic acids are found throughout a cell, not just in the nucleus.
• Of all biomolecules, it is only the nucleic acids that have the remarkable property of replicating itself, thus
nature chose these molecules to serve as the repository and transmitter of genetic information in every
cell and organism.
• The genome or total DNA of a cell acts like a molecular file where the program for an organism’s activities
(maintenance, development, growth, reproduction, and even death) are encoded.
• Cells in an organism are exact replicas.
• Cells have information on how to make new cells.
• Molecules responsible for such information are nucleic acids.
• The nucleic acids (DNA in particular) are the “informational molecules”; into their primary structure is
encoded a set of directions that ultimately governs the metabolic activities of the living cell.
• Two types of Nucleic Acids:
• DNA: Deoxyribonucleic Acid: found within cell nucleus
– storage and transfer of genetic information
– passed from one cell to other during cell division
• RNA: Ribonucleic Acid: occurs in all parts of cell
– primary function is to synthesize the proteins
• Gene is a segment of DNA which specifies the chain of amino acids that comprises the protein molecule
– most human genes are 1000–3500 nucleotide units long
– genome: all of the genetic material (the total DNA) contained in the chromosomes of an organism
– human genome is about 20,000–25,000 genes
• The genetic message is transcribed by mRNA and translated by tRNA and rRNA into thousands of different
proteins.
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Nucleotide Building Blocks

• Nucleic Acids: polymers in which repeating unit is nucleotide
• A nucleotide has three components:
– pentose sugar – a monosaccharide
– phosphate group (PO43-)
– heterocyclic base
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Nucleoside Formation
• Nucleoside: formed from condensation reaction between a five-carbon monosaccharide and a purine or
pyrimidine base derivative.
– The N9 of a purine or N1 of a pyrimidine base is attached to C1’ position of sugar (beta-conformation)
in an N-C-glycosidic linkage.
• Nomenclature:
– For pyrimidine bases – suffix -idine is used (cytidine, thymidine, uridine)
– For purine bases – suffix -osine is used (adenosine, guanosine)
– Prefix “-deoxy” is used to indicate deoxyribose present (e.g.: deoxythymidine)
Nucleotide Formation
• Phosphate group is added to a nucleoside.
– Attached to C5’ position through a phosphoester bond.
– Condensation reaction (H2O released).
– Named by appending 5’- monophosphate to nucleoside name.
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Nucleotide Nomenclature
Primary Nucleic Acid Structure
Primary Structure
• The nucleotides of a polynucleotide chain are linked to one another in 3’,5’- phosphodiester bonds.
• Phosphoric acid forms a phosphate ester to connect the 3’-hydroxyl group of one pentose to the 5’-carbon
on another pentose.
• 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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Polynucleotides and the Nucleic acids

• A ribonucleic acid (RNA) is a polynucleotide 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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• 5’ end has free phosphate group and 3’ end has a free OH group.
• The sequence of bases is read from 5’ to 3’.
• The next nucleotide binds at the 3’ end.
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The DNA Double Helix

• DNA, a high mol.wt., double-stranded polynucleotide that occurs almost exclusively in the nucleus of the
cell.
• Primary function is storage and transfer of genetic information which is used (indirectly) to control many
functions of a living cell.
• Genetic information is encoded in the primary structure of the DNA.
• The primary structure of DNA is the sequence of nucleotides in the chain.
• The base content of DNA displays three sets of equivalent pairs:
A + G = T + C (pu / pyr ratio = 1)
A=T
G=C
• The structure of the four bases permit hydrogen bonding between specific base pairs: Adenine always
pairs with Thymine and Guanine with Cytosine.
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• The proof of this base-pairing came when Watson and Crick proved by x-ray diffraction that the DNA
structure was a double helix whose chains were complementary and antiparallel.
• Complementary → means that A binds to T and C to G between the chains.
- The sequence of bases on one strand automatically determines the sequence of bases on the other
strand.
- Antiparallel → means that each end of the helix contains the 5’ end of one strand and the 3’ end
of the other, so that the chains travel in opposite directions.
- Only when the 2 strands are antiparallel can the base pairs form the H-bonds that hold them
together.
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• The double helical secondary structure of DNA is stabilized by a number of factors:

• Chargaff’s rule of base pairing: (A=T and G=C) or (%A = %T and %C = %G)
– example: human DNA contains 30% adenine, 30% thymine, 20% guanine and 20% cytosine
• Stacking interaction of the hydrogen-bonded bases (the purines and pyrimidine rings) at the center
• Hydrophobic interior (bases) and hydrophilic exterior (sugar-phosphate backbone) ; contact with bases
through spiral grooves : major and minor grooves.
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• The sugar-phosphate backbone of the two strands spiral around the outside of the helix like the handrails
on a spiral staircase.
• The nitrogenous bases extend into the center at right angles to the acids of the helix as if they are the steps
of the spiral staircase.
Denaturation of DNA
• The loss of helical structure due to disruption of H–bonds is called denaturation or melting, where the
double strands separate into single strands.
• This can be due to extremes of pH, heat, or chemicals that disrupt H-bonds.
• DNAs which are G-C rich denature at a higher temperature (T m) than those which are A-T rich.
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Conformations of DNA
• DNA can assume different conformations because deoxyribose is flexible and the C–N-glycosidic linkage
rotates.
• B-DNA – the common form as described by Watson and Crick model.

• A-DNA – when DNA becomes partially dehydrated it assumes the A-form; observed when DNA is extracted
with solvents such as ethanol.
• Z-DNA – named for its “zigzag” conformation; DNA segments with alternating purine and pyrimidine bases
(esp. CGCGCG) are most likely to adopt a Z configuration; regions of DNA rich in GC repeats are often
regulatory, binding specific proteins that initiate or block transcription.
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Types of DNA Sequences

1. Exons – the coding sequences; interrupted by noncoding sequences
2. Introns – the noncoding sequences; from 10 to 10,000 bases long
3. Palindrome or inverted repeats
• a DNA sequence that contains the same information whether it is read forward or backward; e.g. “MADAM,
MADAM”
• tendency to form hairpin loop and a snapback (cruciform)
• perfect palindrome forms with exact base pairs; quasi palindrome, when not all will form hairpin loop
4. Cruciform (or snapback)
• as their name implies, are crosslike structures
• when a DNA sequence contains a palindrome
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HGP from 1990, completed in 2003
1. There are approximately 22,300 protein-coding genes in human beings, the same range as in other
mammals.
2. The human genome has significantly more segmental duplications (nearly identical, repeated sections of
DNA) than had been previously suspected.
3. At the time when the draft sequence was published fewer than 7% of protein families appeared to be
vertebrate specific.
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What is the main purpose of the Human Genome Project?

The main goals of the Human Genome Project were to provide a complete and accurate sequence of the 3 billion
DNA base pairs that make up the human genome and to find all of the estimated 20,000 to 25,000 human genes.
Why is it important to study the human genome?

The Human Genome Project (HGP) is an international thirteen-year project that began on October 1990. It
is important because it uses information from DNA to develop new ways to treat, cure, or even prevent the
thousands of diseases that afflict humankind.
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The Central Dogma
The central dogma of biology provides the basic framework for how genetic information flows from a DNA sequence
to a protein product inside cells. This process of genetic information flowing from DNA to RNA to protein is called
gene expression.
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Replication of DNA Molecules

• Process by which DNA molecules produce exact duplicates of themselves.
• The two strands of the DNA double helix unwind, the separated strands serve as templates for the
formation of new DNA strands.
• Free nucleotides pair with the complementary bases on the separated strands of DNA.
• When the process is completed two identical molecules of DNA are formed.
• The newly synthesized DNA has one new DNA strand and old DNA strand.
• Two daughter DNA molecules are produced from one parent DNA molecule, with each daughter DNA
molecule containing one parent DNA strand and one newly formed DNA strand.
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• DNA replication is semiconservative and mostly bidirectional.

• First step is the separation of the strands
– accomplished by helicase, which breaks the H-bonds between base pairs
– positive supercoiling results when H-bonds are broken, this is relieved by topoisomerase
– when supercoiling is relieved, single-strand binding protein binds to the separated strands to keep
them apart
– primase catalyzes synthesis of a 10-12 base piece of RNA to “prime” the DNA replication
• DNA polymerase “reads” the parental strand or template, catalyzing the polymerization of a
complementary daughter strand; the enzyme checks the correct base pairing and catalyzes the formation
of phosphodiester linkages.
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• There are different mechanisms for replication of the two strands.

• DNA polymerase enzyme can function only in the 5’ -to- 3’ direction which can be offered only by the
3’strand.
1) The 3’ strand is called the leading strand because it is replicated in a continuous process in the
direction of the unwinding;
2) The 5’ strand is the lagging strand, it is replicated in a discontinuous mechanism and grows in
segments (Okazaki fragments) in the opposite direction; the segments are later connected by DNA
ligase.
In the Leading Strand:

• The DNA Polymerase, using dNTP’s and Mg2+, cause the replication by base-pairing the 3’strand with free
nucleotide units.
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In the Lagging Strand:

• The enzyme primase (using NTP’s and Mg2+) puts primers on the lagging strand by forming short RNA
strands through base-pairing of the 5’strand.
• DNA Polymerase recognize, then lengthen the primers using dNTP’s.
• The primers are then removed by nucleotidase and further lengthening is done by DNA Polymerase resulting
to an OKAZAKI STRAND.
• The Okazaki strands are then linked together and sealed using the enzyme ligase leading to the formation
of a NEW STRAND.
DNA replication usually occurs at multiple sites within a molecule (origin of replication) and the replication is
bidirectional from these sites.
• Multiple-site replication enables rapid DNA synthesis.
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Two conditions must be satisfied for replication to take place with high fidelity and accuracy:
a) normal electronic characteristics
b) normal base sequence
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Overview of Protein Synthesis

• Protein synthesis is directly under the direction of DNA.
• The expression of the information contained in the DNA is fundamental to the growth, development, and
maintenance of all organisms.
• Proteins are responsible for the formation of skin, hair, enzymes, hormones, and so on.
• Protein synthesis can be divided into two phases.
– Transcription – a process by which DNA directs the synthesis of mRNA molecules.
– Translation – a process in which mRNA is deciphered to synthesize a protein molecule.
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Ribonucleic Acids
Differences Between RNA and DNA Molecules

• The sugar unit in the backbone of RNA is ribose; it is deoxyribose in DNA.
• The base thymine found in DNA is replaced by uracil in RNA.
• RNA is a single-stranded molecule; DNA is double-stranded (double helix).
• A hairpin loop is produced when single-stranded RNA doubles back on itself and
complementary base pairing occurs.
• RNA molecules are much smaller than DNA molecules, ranging from 75
nucleotides to a few thousand nucleotides.
Types of RNA Molecules

• RNA functions primarily in the synthesis of proteins, the molecules that carry out essential cellular
functions.
• Heterogeneous nuclear RNA (hnRNA).
– formed directly by DNA transcription.
• Messenger RNA (mRNA) - carries instructions for protein synthesis (genetic information) from DNA.
• Small nuclear RNA (snRNA) - facilitates the conversion of hnRNA to mRNA.
• Ribosomal RNA (rRNA) - combines with specific proteins to form ribosomes - the physical site for protein
synthesis.
• Transfer RNA (tRNA) - delivers amino acids to the sites for protein synthesis.
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Transcription: RNA Synthesis

• Once the mRNA is formed and released from DNA, it moves into the cytoplasm and combines with rRNA in
ribosomes where protein synthesis occurs.
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The Genetic Code

• In translation, the base sequence in mRNA determines the amino acid sequence of the protein synthesized.
• The base sequence of an mRNA molecule involves only 4 different bases - A, C, G, and U
• The code is a triplet code since it involves 3 bases per coding unit.
• The coding unit is called a codon.
• The genetic code is a series of base triplets in mRNA called codons that code for a particular amino acid.
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• The genetic code is highly degenerate:

– Many amino acids are designated by more than one codon.
– Arg, Leu, and Ser are represented by six codons.
– Most other amino acids are represented by two codons.
– Met and Trp have only a single codon.
– Codons that specify the same amino acid are called synonyms.
• There is a pattern to the arrangement of synonyms in the genetic code table.
– All synonyms for an amino acid fall within a single box unless there are more than four synonyms.
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• The genetic code is almost universal:

– With minor exceptions the code is the same in all organisms.
– The same codon specifies the same amino acid whether the cell is a bacterial cell, a plant cell, or
a human cell.
• An initiation codon exists:
– The existence of “stop” or termination codons (UAG, UAA, and UGA) suggests the existence of
“start” codons.
– The codon - coding for the amino acid methionine (AUG) functions as initiation codon.
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Anticodons and tRNA Molecules

• During protein synthesis amino acids do not directly interact with the codons of an mRNA molecule.
• tRNA molecules as intermediates deliver the amino acids to mRNA.
• Two important features of tRNA
– the 3’ end is where an amino acid is covalently bonded to the tRNA.
– the loop opposite to the open end is the site for a sequence of three bases called an anticodon.
• Anticodon - a three-nucleotide sequence on a tRNA molecule that is complementary to a codon on an
mRNA molecule.
• Codon-anticodon interaction is antiparallel.
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Translation: Protein Synthesis

• Translation – a process in which mRNA codons are deciphered to synthesize a protein molecule.
• Ribosome – an rRNA–protein complex that serves as the site, or “workbench” for protein synthesis:
• Ribosomal RNA (rRNA)
– constitutes about 60% of the ribosomes (40% protein)
– structurally composed of two spherical particles of unequal size: the smaller has affinity for mRNA;
the larger has an attraction for tRNA ;
– has two sites to bind tRNA
o P-site binds to the growing peptide
o A-site binds the aminoacyl tRNA
Five 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. Peptidyl transferase links the A site and P site amino acids
via a peptide bond.
• Termination: The polypeptide continues to grow via translocation until all necessary amino acids are in
place and bonded to each other. The process stops when a stop codon is encountered.
• Post-translational processing: Gives the protein the final form it needs to be fully functional.
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Regulation of Protein Synthesis

• Since protein is not synthesized continuously but only as needed, the DNA must normally be in a “repressed”
state.
• A repressor, which is a polypeptide, binds to small segment of the DNA called the operator site.
• As long as the repressor is bonded to the operator site of the DNA, no mRNA is produced and protein
synthesis is inhibited.
• When a particular protein is needed, an inducer is formed.
• The inducer combines with the repressor changing its shape so that it can no longer bind to the DNA.
• Once the repressor is removed from the DNA, synthesis of mRNA and hence, protein can begin.
• When sufficient protein has been synthesized, the inducer is removed and the repressor once again binds
the DNA, stopping protein synthesis.
Antibiotics Inhibit Bacterial Protein Synthesis

• Several antibiotics stop bacterial infections by interfering with the synthesis of proteins needed by the
bacteria. Some antibiotics act only on bacterial cells by binding to the ribosomes in bacteria, but do not act
on human cells.
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Mutations
Replication, transcription, and translation occur with very high accuracy and fidelity (normal base sequence and
normal electronic character) except under conditions of spontaneous and induced 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.
• Such changes have a profound effect on an organism.
Spontaneous Mutations
1. Point Mutations
• substitution of a single nucleotide for another caused by tautomeric base-mispairs due to the ease by which
rare tautomers are formed.
• C is the most mutable base due to the very small energy difference between its two tautomers.
• In nature, there are more A-T pairs than G-C pairs to protect us from the effect of spontaneous mutation.
A. Transition (C-A* ; G-T* ; C *- A mispair)

- a purine base is changed to another purine; a pyrimidine base to another pyrimidine
B. Transversion (A-A* mispair)

- a purine base is changed to pyrimidine; a pyrimidine base changed to purine
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2. Frameshift Mutation
• leads to a change in the reading frame.
A. Insertion
B. Deletion
• In an insertion or deletion mutation, one or more nucleotides are added to or deleted from the DNA
sequence.
• Then a frameshift occurs which leads to a misreading of all the codons following the base change.
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Mutagens
• Although a number of structural features of nucleic acids promote stabilization of base sequences, reactivity
with some physical and chemical agents can alter the electronic characteristics of the bases and other
structural units.
• Consequently, nucleic acid functions would be affected.
• A mutagen is a substance or agent that causes a change in the structure of a gene:
– Physical agents : heat, Ultraviolet, ionizing radiation (X-ray, gamma rays)
– Chemical agents :HNO2 can convert cytosine to uracil
o Nitrites, nitrates, and nitrosamines – can form nitrous acid in cells
• Under normal conditions mutations are repaired by repair enzymes.
Induced Mutations – Physical Agents

• UV radiation
• Absorbed primarily by the pyrimidine bases.
– UV light causes covalent linkage of adjacent pyrimidine bases forming cyclobutane pyrimidine
dimer.
– When T is irradiated with UV, excitation of pi electrons to antibonding MO’s will result in the
formation of T diradicals. Coupling of T diradicals may result in the formation of thymine
cyclobutane dimers.
– Failure to repair this defect can lead to xeroderma pigmentosum; people who suffer from this
genetic skin disorder are very sensitive to UV light and develop multiple skin cancers.
– No purine dimers since purines are more thermodynamically stable than pyrimidines.
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• Heat mutagenesis
– characterized by transmigration of N – C glycosidic bonds producing neoguanosine crosslinks
• Ionizing radiation
– More often when a plant or animal is irradiated most of the energy is deposited in the aqueous
phase. Less often will a primary ionization occur in an organic molecule.
– A portion of damage to the living system results from reactive particles that are formed in the
water phase and diffuse to an organic molecule in the cell causing secondary reactions (free
radicals are implicated in radiation damage).
Induced Mutations – Chemical Agents

• Intercalating agents (PAH), alkylating agents, heavy metal ions, etc.
• One notorious source of numerous mutagens is cigarette smoke.
• It contains PAH, nitrosamines, hydrazines, pyrolysates, alkoxy free radicals, superoxide anion radicals, Cd2+,
etc.
• Other notorious sources are: cured foods; burnt portion of broiled fish and meat; moldy peanuts and
cereals; pesticides;
• Polluted air (epoxides, SO2, ozone, Pb2+, ethylene dibromide, etc.).
• Laboratory chemicals (benzene has been linked to leukemia, CHCl3, CCl4, etc.).
• Intercalating agents
– With polycyclic planar structures, like PAH, e.g. benzo(a)pyrene, interpose
between the strands within the grove of DNA.
– Inhibit its replication/transcription, or cause deletions.
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• Alkylating agents
– Have electrophilic sites or may be metabolized to electrophiles which can interact with alkylating sites
at DNA; include PAH, nitrosamines, aflatoxins, aromatic amines, epoxides, nitrogen mustard,
nitrosoureas, etc.
– Bases in DNA are nucleophiles and as such are strongly attracted to electrophilic compounds.
• N7- alkylation leads to apurinic sites (positivity of R is relayed to C8 & N9 thereby enhancing the dipositivity
of the N-C – glycosidic bond & render it more less stable)
• O6- alkylation leads to base mispairs
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Chemical Mutagens
(a) HNO2 (nitrous acid) converts cytosine to uracil and adenine to hypoxanthine.
(b) Nitrosoamines, organic compounds that react to form nitrous acid, also lead to the oxidative deamination of A
and C.
(c) Hydroxylamine (NH2OH) reacts with cytosine, converting it to a derivative that base-pairs with adenine instead
of guanine. The result is a C-G to T-A transition.
(d) Alkylation of G residues to give O6- methylguanine, which base-pairs with T.
(e) Alkylating agents include nitrosoamines, nitrosoguanidines, nitrosoureas, alkyl sulfates, and nitrogen mustards.
Note that nitrosoamines are mutagenic in two ways: they can react to yield HNO 2 or they can act as alkylating
agents.
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When DNA is Hit by a Mutagen
Some Chemical and Environmental Carcinogens
Carcinogen Tumor occurrence
Asbestos Lung, respiratory tract

Arsenic Skin, lung
Cadmium Prostate, kidneys
Chromium Lung
Nickel Lung, sinuses
Aflatoxin Liver
Nitrites Stomach
Aniline dyes Bladder
Vinyl chloride Liver
Benzene Leukemia
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DNA Repair Mechanisms

• DNA is the only macromolecule that is repaired rather than degraded.
• The repair processes are very efficient with fewer than 1 out of 1,000 accidental changes resulting in
mutations.
• The rest are corrected through various repair mechanisms before, during, or after replication.
A) Photoreactivation Repair
• Uses an enzyme photolyase, which binds the T-T cyclobutane dimer & in the presence of visible light
changes the cyclobutane ring back into individual pyrimidine bases.
B) Excision Repair
• Mutations are excised by a series of enzymes that remove incorrect bases and replace them with the
correct ones.
• Base excision repair – involves a battery of enzymes called DNA glycosylases each of which recognizes a
single type of altered base in DNA and catalyzes its hydrolytic removal from the deoxyribose sugar (e.g.,
removing deaminated cytosine, deaminated adenine, alkylated bases, etc.)
• Nucleotide excision repair
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Nucleic Acids and Viruses
Viruses
• Viruses: Tiny disease causing agents with outer protein envelope and inner nucleic acid core.
• They cannot reproduce outside their host cells (living organisms).
• Invade their host cells to reproduce and in the process disrupt the normal cell’s operation.
• Virus invade bacteria, plants animals, and humans.
– Many human diseases are of viral origin, e. g. Common cold, smallpox, rabies, influenza, hepatitis, and
AIDS.
Human Cancers Caused by Oncogenic Viruses
Recombinant DNA and Genetic Engineering

• Recombinant DNA: DNA molecules that have been synthesized by splicing a sequence of segment DNA
(usually a gene) from one organism to the DNA of another organism.
• Genetic Engineering (Biotechnology): A process in which an organism is intentionally changed at the
molecular (DNA) level so that it exhibits different traits.
Benefits
• First genetically engineered organism are bacteria (1973) and Mice (1974).
• Insulin producing bacteria - commercialized in 1982.
– Bacteria act as protein factories
• Many plants have now been genetically engineered and numerous beneficial situations have been created.
– Disease resistance – increased crop yield
– Drought resistance – consumption of less water
– Predator resistance – less insecticide use
– Frost resistance – resist changes in temps below freezing
– Deterioration resistance – long shelf-life
• Transformed cell can reproduce a large number of identical cells–clones:
– Clones are the cells that have descended from a single cell and have identical DNA
• Given bacteria grow very fast, within few hours 1000s of clones will be produced.
• Each clone can synthesize the protein directed by foreign gene it carries.
Telefax: (082)
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Telefax: (082)
Phone No.: (082)300-5456/300-0647 Local 117
The Polymerase Chain Reaction

• The polymerase chain reaction (PCR): A method for rapidly producing multiple copies of a DNA nucleotide
sequence (gene).
• This method allows to produce billions of copies of a specific gene in a few hours.
• PCR is very easy to carryout and the requirements are:
– Source of gene to be copied
– Thermostable DNA polymerase
– Deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP)
– A set of two oligonucleotides with complementary sequence to the gene (primers)
– Thermostable plastic container and
– Source of heat
-END-
GOOD JOB!
Telefax: (082)
Phone No.: (082)300-5456/300-0647 Local 117
Keywords Index
Nucleic Acid Chromosome Cytosine Exon
DNA Nucleotide Thymine Intron
RNA Nucleoside Uracil Palindrome
Gene Adenine DNA Double Helix Cruciform
Genome Guanine Chargaff’s Rule Human Genome Project
Central Dogma Replication Transcription Translation
Leading Strand Lagging Strand hnRNA mRNA
snRNA rRNA tRNA Genetic Code
Codon Anticodon Mutation Mutagen
Carcinogen Virus Recombinant DNA Genetic Engineering
Clone Polymerase Chain Reaction Biotechnology DNA Repair

SIM Biochemistry ULO9

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SIM Biochemistry ULO9

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College of Health Sciences Education

3rd Floor, DPT Building

Big Picture in Focus: ULO9. Demonstrate knowledge on structures,

Types of Nucleic Acids

Nucleotide Building Blocks

Primary Nucleic Acid Structure

Polynucleotides and the Nucleic acids

The DNA Double Helix

• The double helical secondary structure of DNA is stabilized by a number of factors:

• B-DNA – the common form as described by Watson and Crick model.

Types of DNA Sequences

HGP from 1990, completed in 2003

What is the main purpose of the Human Genome Project?

Why is it important to study the human genome?

The Central Dogma

Replication of DNA Molecules

• DNA replication is semiconservative and mostly bidirectional.

• There are different mechanisms for replication of the two strands.

In the Leading Strand:

In the Lagging Strand:

Overview of Protein Synthesis

Differences Between RNA and DNA Molecules

Types of RNA Molecules

Transcription: RNA Synthesis

The Genetic Code

• The genetic code is highly degenerate:

• The genetic code is almost universal:

Anticodons and tRNA Molecules

Translation: Protein Synthesis

Five Steps of Translation Process

Regulation of Protein Synthesis

Antibiotics Inhibit Bacterial Protein Synthesis

• An error in base sequence reproduced during DNA replication

A. Transition (C-A* ; G-T* ; C *- A mispair)

B. Transversion (A-A* mispair)

Induced Mutations – Physical Agents

Induced Mutations – Chemical Agents

When DNA is Hit by a Mutagen

Some Chemical and Environmental Carcinogens

Carcinogen Tumor occurrence

Asbestos Lung, respiratory tract

DNA Repair Mechanisms

Nucleic Acids and Viruses

Human Cancers Caused by Oncogenic Viruses

Recombinant DNA and Genetic Engineering

The Polymerase Chain Reaction

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