Biochemistry

CHAPTER 5:
Nucleic Acid
ROLINA MORADA-CABALLERO, R.N
 LEARNING OUTCOME

5.1 Distinguish between

deoxyribonucleic acids
and ribonucleic acids in
terms of biochemical
functions and in terms
of where they are found
within.
5.1 Types of Nucleic Acids

• 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
• 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
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5.2 Be familiar with the chemical

composition of nucleotides, the
structural building blocks for nucleic
acids.
Nucleic Acids

• They are polymers in which the repeating unit is

a nucleotide
– Components of a nucleotide
• Pentose sugar
• Phosphate group (PO43-)
• Heterocyclic base
Nucleic Acids
A block structural diagram of nucleotides
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
Nucleic Acids
The sugar unit of a nucleotide is either the pentose ribose or the
pentose 2′-deoxyribose.
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
Five nitrogen-containing heterocyclic bases are
nucleotide components.
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–)
Phosphate
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5.3 Distinguish between the

terms Nucleoside and
nucleotide; known names
and abbreviations for the
eight nucleotides that are
found in nucleic acids.
 5.3 Nucleotide Formation

• Nucleotides are formed from a sugar, a base, and

a phosphate
• It is a two-step process
– The pentose sugar and nitrogenous base react
to form a nucleoside
– The nucleoside reacts with a phosphate group
to form a nucleotide
• 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
• 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
• 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
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5.4 Know the common

differing structural
characteristics of
primary structure for
DNA and RNA
molecules.
5.4 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
• A sequence that contains nucleotides
linked to a nucleic acid
• Primary structure depends on the
sequence of bases present
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5.5 Be familiar with the double

Helix secondary structure feature
associated with DBA molecule;
be familiar with the concept of
complementary base pairing and
the rules associated with such
pairing.
5.5 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
– Amounts of C and G were always equal
– Human DNA contains:
• 30% adenine
• 30% thymine
• 20% guanine
• 20% cytosine
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
• 5′-to-3′ direction
• 3′-to-5′ direction
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
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5.6 Describe the various steps
involved in the process of DNA
replication; be familiar with
terminology and enzymes
associated with DNA
replication.
• 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
• 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
 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
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5.7 Be able to give overview

summary for protein
synthesis.
5.7 Overview of Protein Synthesis

• DNA molecules control the synthesis of proteins

• Phases of protein synthesis
– Transcription
– Translation
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5.8 Be familiar with the major

differences between DNA
molecules and RNA molecules; be
familiar with the characteristics of
and functions for the five major
types of RNA molecules.
5.8 Ribonucleic Acids
Differences Between RNA and DNA Molecules

DNA Molecule RNA Molecule

• Ribose is the basic
• Deoxyribose is the
sugar unit
basic sugar unit
• Thymine is replaced
• Thymine is present
by uracil
• It is a double-stranded
• It is a single-stranded
helix
unit
• Molecules are bigger
• Molecules are smaller
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
• Transfer RNA (tRNA): Delivers amino acids to sites
for protein synthesis
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5. 9 Be familiar with how DNA,

genes, hnRNA, snRNA, and
mRNA are involved in the
process of transcription;
distinguish between exons and
introns and how the process of
splicing relates to these
entities.
 5.9 Transcription: RNA Synthesis
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
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
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
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
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5.10 Understand the relationship

between codons and the genetic
code, know important
characteristics of the genetic code.
 5.10 The Genetic Code
• 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
Characteristics of 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
• 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
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5. 11 Be familiar with the

relationships between (1)
anticodons and tRNAs and (2)
anticodons and codons.
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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5.12 Be familiar with how
ribosomes, mRNA, rRNA,
rRNA, are involved in the
process of translations; be
familiar with the five general
steps of the translation part of
the 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
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
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5.13 Know the characteristics for

both point and frameshift
mutations; be familiar with
common types of mutagens.
5.13 Mutations

• 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
Two common types of mutations are:

A point mutation is a mutation in which one base

in a DNA base sequence is replaced with another
base.
A frameshift mutation is a mutation that inserts
or deletes a base in a DNA molecule base
sequence.

Such a change affects not only the base triplet

located at the insertion or deletion point but
also all triplets that follow in the sequence.
Mutagens
• A mutagen is a substance or agent that causes a
change in the structure of a gene
• Types
– Radiation
• Ultraviolet light, X-rays, and radioactivity
– Chemical agents
• HNO2
• Repair enzymes present in the body are able to
identify and replace altered bases
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5.14 Describe a common
method by which a virus
infects a cell; describe
how a vaccine works.
 5.14 Nucleic Acids and Viruses
Viruses
• Minute disease-causing agents with an outer
coat of protein
• They can reproduce only by invading host cells
– 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
• 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
• 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
 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
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5.15 Be familiar with the

procedures by which
recombinant DNA is
produced; be able to give
examples of important end
products obtained using
genetic engineering
techniques
 5.15 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
• 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
• 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
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5.16 Be familiar with the

nature of the polymerase
chain reactions and what
is accomplishes.
5.16 The Polymerase Chain Reaction

• A method for rapidly producing

multiple copies of a DNA nucleotide
sequence
• 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 Chain Reaction
Figure 22.33 (b) - Basic Steps of the Polymerase Chain
Reaction