Nucleic Acids

Nucleic Acids
Stoker Chapter 22
Lippincott Chapters 30, 31 and
32
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1
Reserved.
2 Introduction
– Cells in an organism are capable of replicating

– Cells possess information on how to make new
cells
– Molecules responsible for such information are
nucleic acids
– Found in nucleus and are acidic in nature
– A nucleic acid is an unbranched polymer in
which the monomer units are nucleotides
Both DNA and RNA are unbranched polymers.
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3
Types of Nucelic
Acids
– Deoxyribonucleic acid (DNA)

– Found within the cell nucleus
– Stores and transfers genetic information
– Passed from existing cells to new cells
during cell division
– Ribonucleic Acid (RNA)
– Occurs in all parts of a cell
– Primary function is the synthesis of
proteins

4
Nucleic Acids
– They are polymers in which the repeating unit is a

nucleotide
– Components of a nucleotide
– Pentose sugar
– Phosphate group (PO43-)
– Heterocyclic base Base
Phosphate Sugar
5 Pentose Sugars
– The structural difference between

ribose and pentose 2′ -
deoxyribose occurs at carbon 2′
– —OH group is present in ribose
– —H atom is present in 2′-
deoxyribose
– Ribose is present in RNA
– 2′-deoxyribose is present in DNA

•6 Nitrogen-Containing
Heterocyclic Bases
– They are five in total

– Three pyrimidine derivatives -
Thymine (T), cytosine (C), and uracil
(U)
– Two purine derivatives - Adenine
(A) and guanine (G)
• Adenine, guanine, and cytosine
are found in both DNA and RNA
• Uracil is found only in RNA
• Thymine is found only in DNA

7
Phosphate – The third component of a nucleotide

– Derived from phosphoric acid (H3PO4)
– Loses two hydrogen atoms, resulting in
formation of a hydrogen phosphate ion
(HPO42–)

8 Nucleotide Formation
– Nucleotides are formed from a

sugar, a base, and a phosphate
– It is a two-step process
Nucleoside is a substance that

– The pentose sugar and
does not contain a phosphate nitrogenous base react to form
group. Sugar and base pa lang
yung meron. a nucleoside
– The nucleoside reacts with a
phosphate group to form a
nucleotide

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

9
10 Nucleoside Formation
– There are 8 nucleosides associated with nucleic acid chemistry

– Four RNA nucleosides
– Four DNA nucleosides
– Nomenclature
– For pyrimidine bases, the suffix -idine is used
– Cytidine, thymidine,
– For purine bases, the suffix -osine is used
– Adenosine, guanosine
– Prefix deoxy- is used to indicate deoxyribose present
– Deoxythymidine

Nucleotide
Formation
– Formed by the addition of a phosphate group

to a nucleoside
– Characteristics of phosphate addition
– The phosphate is attached to C5′ position
– Water is released Dehydration

11
Table 22.1 - The Building Blocks of DNA and
RNA

12 Reserved.
13
Primary – A ribonucleic acid (RNA) is a

nucleotide polymer in which each of
Nucleic Acid the monomers contains ribose, a
Structure 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

Primary
Nucleic Acid
Structure
– A sequence that
contains nucleotides
linked to a nucleic acid
– Primary structure
depends on the
sequence of bases
present

14
Figure 22.6 - Comparison of the General Primary
Structures of Nucleic Acids and Proteins

15 Reserved.
16 The DNA Double Helix
– In addition to primary structures, nucleic acids also have secondary

and tertiary structures
– Amounts of A,T,G, and C present in DNA molecules helped determine
the three-dimensional structure of the DNA molecules
– Amounts of A and T were always equal
In a normal DNA double helix, the adenine and thymine is always equal.
– Amounts of C and G were always equal
– Human DNA contains:
– 30% adenine
– 30% thymine
– 20% guanine
– 20% cytosine

Figure
22.7 -
The DNA
Double
Helix
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Reserved.
18 DNA Sequence
– Two polynucleotide strands are coiled around

each other in a spiral
– Bases on each strand extend inwardly toward each
other
– They are connected by hydrogen bonds
– They run in opposite directions Also called anti-parallelism
– 5′-to-3′ direction
– 3′-to-5′ direction

19
Base Pairing
– A pyrimidine is always paired with a purine

– Fits inside the DNA double strand
– Hydrogen bonding is most favored in A–T
and G–C pairs
– A–T and G–C pairing is termed
complementary

20 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′

21
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′

22 Base Pairing
– Hydrogen Bonding Interactions Weak
– Base-Stacking Interactions (like

stack of coins) Makes it look like they’re strong

23 Replication of DNA Molecules
– DNA replication: The biochemical process by which DNA molecules

produce exact duplicates of themselves
– The strands of DNA are used as templates
– DNA polymerase ensures correct base pairing and catalyzes the
formation of phosphodiester linkages
– Components of a new DNA strand
– One new DNA strand
– Daughter strand
– One old DNA strand
– Parent strand

24 The Replication Process in Finer
Detail
– DNA polymerase enzyme can operate on a forming DNA daughter strand only in
the 5′-to-3′ direction
– One strand grows continuously in the 5′-to-3′ direction
– The other strand grows in segments in the opposite direction
– Okazaki fragments
– The segments are connected by DNA ligase
– DNA replication usually occurs at multiple sites within the molecule
– Bidirectional replication occurs at these sites
– Multiple-site replication enables rapid replication of large molecules

Figure 22.1 - Continuous-Growing Strands and
Okazaki Fragments

25 Reserved.
26 Chromosomes
– They are formed by the interaction of newly-replicated

DNA molecules with histones
– A chromosome is about 15% by mass DNA and 85% by
mass protein
– Cells of different kinds of organisms have different
numbers of chromosomes
– They occur in matched (homologous) pairs
‒ Example - The 46 chromosomes of a human cell constitute 23
homologous pairs

27
Overview of Protein Synthesis
– DNA molecules control the synthesis of proteins

– Phases of protein synthesis
– Transcription
– Translation
Transcription Translation
DNA RNA Protein

28
Differences Between RNA
and DNA Molecules
– DNA Molecule – RNA Molecule
– Deoxyribose is the basic – Ribose is the basic sugar

sugar unit unit
– Thymine is present – Thymine is replaced by

uracil
– It is a double-stranded
helix – It is a single-stranded unit
– Molecules are bigger – Molecules are smaller

29 Types of RNA Molecules
– Heterogenous nuclear RNA (hnRNA): Formed by DNA

transcription
– Messenger RNA (mRNA): Carries instructions for protein
synthesis
– Small nuclear RNA (snRNA): Facilitates the conversion of
hnRNA to mRNA
– Ribosomal RNA (rRNA): Combines with specific proteins to
form ribosomes

Types of RNA Molecules
Transfer RNA (tRNA): Delivers amino acids to sites for protein synthesis

30 Reserved.
•31 Transcription
– Transcription: The process by which DNA directs the synthesis of

hnRNA/mRNA molecules by a two-step process
– hnRNA is synthesized
– hnRNA is edited to yield mRNA
– Gene: A segment of a DNA strand responsible for the production
of a specific hnRNA/mRNA molecule
– Most human genes comprise 1000–3500 nucleotide units
– Genome: All of the genetic material contained in the
chromosomes of an organism

32 Steps in the Transcription
Process
– Unwinding of DNA double helix to expose a sequence

of bases
– Governed by RNA polymerase
– Alignment of free ribonucleotides along an exposed
DNA strand, forming new base pairs
– Influence of RNA polymerase in the linkage of
ribonucleotides
– Cessation of transcription when the RNA polymerase
enzyme encounters a stop signal on the DNA
template
– The newly formed RNA molecule and the RNA
polymerase enzyme are released

33 Steps in the
Transcription Process
– The strand of DNA used for hnRNA/mRNA

synthesis is called the template strand. It is
copied proceeding in the 3’ to 5’ direction.
– The other DNA strand (the non-template strand)
is called the informational strand.
– The informational strand, although not involved
in RNA synthesis, gives the base sequence
present in the hnRNA strand being synthesized
(with the exception of U replacing T).

34
Post-Transcription
Processing: Formation of
mRNA
– Involves post-transcription processing of hnRNA
– Splicing: Excision of introns and joining of exons
– Exon: A gene segment that conveys codes for
genetic information
– Intron: A DNA segment that does not convey
genetic information
– snRNA is involved

Alternative
splicing
– Alternative splicing: A
process of producing
several different
proteins from a single
gene
– Involves splicing of
an hnRNA molecule
with multiple exons

35
36 Transcriptome
– All of the mRNA molecules that can be

generated from the genetic material in a genome
– It is different from a genome
– Acknowledges the biochemical complexity
created by splice variants obtained by hnRNA

The Genetic Code
37
– The base sequence in mRNA determines the amino acid

sequence in the synthesis of protein
– The base sequence of an mRNA molecule involves 4
different bases - A, C, G, and U
– Codon: A three-nucleotide sequence in an mRNA
molecule that codes for a specific amino acid
– 64 codons in total
– Genetic code: The assignment of the 64 mRNA codons
to specific amino acids
– 3 of the 64 codons are termination codons

•3 Characteristics of
8
Genetic Code
– The genetic code is highly degenerate

– Many amino acids are designated by more
than one codon
– Met and Trp possess a single codon
– There is a pattern to the arrangement of
synonyms in the genetic code table
– All synonyms for an amino acid fall within
a single category unless there are more
than four synonyms

39
Characteristics of
Genetic Code
– The genetic code is almost universal

– There are minor exceptions
– An initiation codon exists
– Suggested by the existence of “stop”
codons
– AUG is an initiator of protein synthesis

Anticodons and tRNA Molecules
– 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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Translation: Protein Synthesis
– Translation: The process in which mRNA codons are deciphered and a specific protein molecule is
synthesized
– Ribosome: An rRNA–protein complex that is the site for the translation phase of protein synthesis
– Characteristics of ribosome structures
• They contain four rRNA molecules and 80 proteins in two subunits
• Each subunit possesses 65% rRNA and 35% protein
• The active site is located in the ribosomal subunit
• rRNA is the active site
• The predominance of rRNA at the active site gives it the impression of a ribozyme
• The mRNA binds to the small subunit of the ribosome

Five Steps of Translation
– Activation of tRNA
– Accomplished in two steps
– Initiation
– tRNA attaches itself to the P site of a small ribosomal unit
– Elongation
– Another tRNA attaches itself to the A site
– A dipeptide is formed under the influence of peptidyl transferase
– Termination
– The polypeptide continues to grow via translocation till a stop codon is encountered
– Post-translational processing
– The protein is rendered fully functional

43 Efficiency of mRNA
Utilization
– Many ribosomes can move

simultaneously along a single
mRNA molecule
– The multiple use of mRNA
molecules reduces the amount of
resources and energy that the cell
expends to synthesize needed
protein
– Polyribosome: A complex of an
mRNA and several ribosomes

44 Mutation
– An error in base sequence in a gene that is

reproduced during DNA replication
– Altered genetic information is passed on during
transcription
– Altered information can cause changes in amino
acid sequence during protein synthesis
– Changes can cause a profound effect on the
organism

A mutagen is a substance or
agent that causes a change in the
structure of a gene
45
Mutagens
Radiation
Types •Ultraviolet light, X-

rays, and radioactivity
Chemical agents
HNO2
Repair enzymes present in the

body are able to identify and
replace altered bases
Viruses
Viruses are categorized depending on the type of nucleic acid present
– Minute disease-causing agents with an outer coat of

protein
– They can reproduce only by invading host cells
Which means outside the body, viruses are actually dead.
– Host cells are caused to produce more viruses
– Host cells’ normal function is disrupted
– They attack bacteria, plants, animals, and humans
– Many human diseases are of viral origin

46
47
– They attach themselves to the host cell on
the external surface
– An enzyme present in the external structure
of the virus catalyzes the breakdown of the
cell membrane and forms a hole
Viruses – They then inject their DNA or RNA into the
host cell
– The viral nucleic acid is replicated
– Hundreds of new viruses are produced
using the host cell within 30 minutes

48 Vaccine
– A preparation containing an inactive or weakened form of a

virus
– Antibodies produced against inactive viral or bacterial
envelopes also kill naturally occurring viruses or bacteria

•49 Recombinant DNA and Genetic
Engineering
– Genetic engineering: The process by which an organism is

intentionally changed at the molecular (DNA) level so that
it exhibits different traits
– Recombinant DNA: DNA possessing genetic material from
two different organisms

50 Recombinant DNA and Genetic
Engineering
– First genetically engineered organisms were

bacteria (1973) and mice (1974)
– Insulin-producing bacteria were
commercialized in 1982
– Many plants have now been genetically
engineered
– Resistance to the harmful effects of
pesticides
– Protection from insects
– Plants produce pesticides
– Increased crop production

Principles and Procedures of Genetic
Engineering
– E.coli cells containing recombinant DNA are obtained using the

following steps
– Cell membrane dissolution
– Isolation of plasmid fraction
– Cleavage of plasmid DNA
– Gene removal from another organism
– Gene-plasmid splicing
– Uptake of recombinant DNA

52 Principles and Procedures of
Genetic Engineering
– Transformed cell can reproduce a large

number of identical cells called clones
– Cells with identical DNA that have
descended from a single cell
– Thousands of clones can be produced
from a single bacteria within a short
time
– Each clone can synthesize the protein
directed by foreign gene it carries

Figure 22.30
- Production
of
Recombinant
DNA

53 Reserved.
A method for rapidly
producing multiple copies of 54
a DNA nucleotide sequence
The
Polymerase
Chain
Reaction
This method allows to
produce billions of copies of a
DNA sequence in a few hours

Figure 22.33 (a) - Basic Steps of the Polymerase
55 Chain Reaction

Figure 22.33 (b) - Basic Steps of the Polymerase Chain
56
Reaction

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Nucleic Acids

Copyright ©2016 Cengage Learning. All Rights

– Cells in an organism are capable of replicating

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Deoxyribonucleic acid (DNA)

Copyright ©2016 Cengage Learning. All Rights Reserved.

– They are polymers in which the repeating unit is a

– The structural difference between

Copyright ©2016 Cengage Learning. All Rights Reserved.

– They are five in total

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Phosphate – The third component of a nucleotide

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Nucleotides are formed from a

Nucleoside is a substance that

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Nucleoside: A two-subunit molecule in which

Copyright ©2016 Cengage Learning. All Rights Reserved.

– There are 8 nucleosides associated with nucleic acid chemistry

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Formed by the addition of a phosphate group

Copyright ©2016 Cengage Learning. All Rights Reserved.

Copyright ©2016 Cengage Learning. All Rights

Primary – A ribonucleic acid (RNA) is a

Copyright ©2016 Cengage Learning. All Rights Reserved.

Copyright ©2016 Cengage Learning. All Rights Reserved.

Copyright ©2016 Cengage Learning. All Rights

– In addition to primary structures, nucleic acids also have secondary

Copyright ©2016 Cengage Learning. All Rights Reserved.

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– Two polynucleotide strands are coiled around

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– A pyrimidine is always paired with a purine

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Predict the sequence of bases in

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Predict the sequence of bases in the DNA strand

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– Hydrogen Bonding Interactions Weak

– Base-Stacking Interactions (like

Copyright ©2016 Cengage Learning. All Rights Reserved.

– DNA replication: The biochemical process by which DNA molecules

Copyright ©2016 Cengage Learning. All Rights Reserved.

Copyright ©2016 Cengage Learning. All Rights Reserved.

Copyright ©2016 Cengage Learning. All Rights

– They are formed by the interaction of newly-replicated

Copyright ©2016 Cengage Learning. All Rights Reserved.

– DNA molecules control the synthesis of proteins

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Deoxyribose is the basic – Ribose is the basic sugar

– Thymine is present – Thymine is replaced by

– Molecules are bigger – Molecules are smaller

Copyright ©2016 Cengage Learning. All Rights Reserved.

– Heterogenous nuclear RNA (hnRNA): Formed by DNA

Copyright ©2016 Cengage Learning. All Rights Reserved.

Copyright ©2016 Cengage Learning. All Rights

– Transcription: The process by which DNA directs the synthesis of