6nucleic Acids PDF

Chapter 22
Nucleic Acids
Chapter 22
Table of Contents
22.1 Types of Nucleic Acids
22.2 Nucleotides: Building Blocks of Nucleic Acids
22.3 Primary Nucleic Acid Structure
22.4 The DNA Double Helix
22.5 Replication of DNA Molecules
22.6 Overview of Protein Synthesis
22.7 Ribonucleic Acids
22.8 Transcription: RNA Synthesis
22.9 The Genetic Code
22.10 Anticodons and tRNA Molecules
22.11 Translation: Protein Synthesis
22.12 Mutations
22.13 Nucleic Acids and Viruses
22.14 Recombinant DNA and Genetic Engineering
22.15 The Polymerase Chain Reaction
22.16 DNA Sequencing
Copyright © Cengage Learning. All rights reserved 2
Section 22.1
Types of Nucleic Acids
• Cells in an organism are exact replicas

• Cells have 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 a polymer in which the monomer units are
nucleotides.
• 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
Return to TOC

Section 22.2
Nucleotides: Building Blocks of Nucleic Acids
• Nucleic Acids: Polymers in which repeating unit is

nucleotide
• A Nucleotide has three components:
– Pentose Sugar: Monosaccharide
– Phosphate Group (PO43-)
– Heterocyclic Base
Return to TOC

Section 22.2
Pentose Sugar
• Ribose is present in RNA and 2-deoxyribose is present
in DNA
• Structural difference:
– a —OH group present on carbon 2’ in ribose
– a —H atom in 2-deoxyribose
• RNA and DNA differ in the identity of the sugar unit in
their nucleotides.
Return to TOC

Section 22.2
Nitrogen-Containing Heterocyclic Bases

• There are a total five bases (four of them in most of DNA
and RNAs)
• Three pyrimidine derivatives - thymine (T), cytosine (C),
and uracil (U)
• Two purine derivatives - adenine (A) and guanine (G)
• 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.
Return to TOC

Section 22.2
Nitrogenous Bases
Return to TOC
Section 22.2
Phosphate
• 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-)
Return to TOC

Section 22.2
Complementarity of bases
DNA RNA
Adenine Uracil**
• The different bases in the
nucleotides which make up Thymine* Adenine
DNA and RNA are: Guanine Cytosine
– Adenine Cytosine Guanine
– Guanine Table showing complementarity of base pairs

* Present only in DNA
**Present only in RNA
– Cytosine
– Thymine (DNA only)
– Uracil (RNA only)
• Chemical structure only allows
bases to bind with specific
other bases due to chemical
structure From: Elliott WH & Elliott DC. (1997) Biochemistry and Molecular Biology. New York: Oxford University Press. P245.
Return to TOC
Section 22.2
Nucleotide Formation
• The formation of a nucleotide from sugar, base, and
phosphate is visualized below.
– Phosphate attached to C-5’ and base is attached to
C-1’ position of pentose
Return to TOC

Section 22.2
Nucleotide Nomenclature
Return to TOC

Section 22.3
Primary Nucleic Acid Structure
• Sugar-phosphate groups are referred to as nucleic acid

backbone - Found in all nucleic acids
• Sugars are different in DNA and RNA
Return to TOC

Section 22.3
Primary 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.
Return to TOC

Section 22.3
Primary Structure
• Structure: Sequence of
nucleotides in DNA or
RNA
• Primary structure is due
to changes in the bases
• Phosphodiester bond at
3’ and 5’ position
• 5’ end has free
phosphate and 3’ end
has a free OH group
• Sequence of bases read
from 5’ to 3’ Return to TOC

Section 22.3
Comparison of the General Primary Structures of Nucleic Acids
and Proteins
• Backbone: -Phosphate-Sugar- Nucleic acids
• Backbone: -Peptide bonds - Proteins
Return to TOC

Section 22.4
The DNA Double Helix
• Nucleic acids have secondary and tertiary structure

• 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)
– Example: Human DNA contains 30% adenine, 30%
thymine, 20% guanine and 20% cytocine
Return to TOC

Section 22.4
• DNA Sequence: the sequence of bases on one polynucleotide is

complementary to the other polynucleotide
• Complementary bases are pairs of bases in a nucleic acid structure
that can hydrogen-bond to each other.
• 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’
Return to TOC

Section 22.4
Base Pairing
• One small and one large base can fit inside the DNA
strands:
– Hydrogen bonding is stronger with A-T and G-C
– A-T and G-C are called complementary bases
Return to TOC

Section 22.4
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’
Return to TOC

Section 22.5
Replication of DNA Molecules
• Replication: Process by which DNA molecules produce

exact duplicates of themselves
• Old strands act as templates for the synthesis of new
strands
• DNA polymerase checks the correct base pairing and
catalyzes the formation of phosphodiester linkages
• The newly synthesized DNA has one new DNA strand
and old DNA strand
Return to TOC

Section 22.5
• DNA polymerase enzyme can only function in the 5’-to-3’ direction

• Therefore one strand (top; leading strand ) grows continuously in the
direction of unwinding
• The lagging strand grows in segments (Okazaki fragments) in the
opposite direction
• The segments are latter connected by DNA ligase
• DNA replication usually occurs at multiple sites within a molecule
(origin of replication)
• DNA replication is bidirectional from these sites (replication forks)
• Multiple-site replication enables rapid DNA synthesis
Return to TOC

Section 22.5
Chromosomes
• Upon DNA replication the large DNA molecules interacts with
histone proteins to fold long DNA molecules.
• The histone–DNA complexes are called chromosomes:
– A chromosome is about 15% by mass DNA and 85% by mass
protein.
– Cells of different kinds of organisms have different numbers of
chromosomes.
– Example: Number of chromosomes in a human cell 46, a
mosquito 6, a frog 26, a dog 78, and a turkey 82
• Chromosomes occur in matched (homologous) pairs.
• Example: The 46 chromosomes of a human cell constitute 23
homologous pairs
Return to TOC

Section 22.6
Overview of Protein Synthesis
• Protein synthesis is directly under the direction of DNA

• 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 isdeciphered
to synthesize a protein molecule
Transcription Translation
DNA RNA Protein
Return to TOC

Section 22.7
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)
• RNA molecules are much smaller than DNA molecules,
ranging from 75 nucleotides to a few thousand
nucleotides
Return to TOC

Section 22.7
Ribonucleic Acids
Types of RNA Molecules

• Heterogeneous nuclear RNA (hnRNA): Formed directly by DNA
transcription.
• Post-transcription processing converts the hnRNA to mRNA
• Messenger RNA: Carries instructions for protein synthesis (genetic
information) from DNA
– The molecular mass of mRNA varies with the length of the
protein
• Small nuclear RNA: Facilitates the conversion of hnRNA to mRNA.
– Contains from 100 to 200 nucleotides
• Ribosomal RNA (rRNA): Combines with specific proteins to form
ribosomes - the physical site for protein synthesis
Ribosomes have molecular masses on the order of 3 million
Return to TOC

Section 22.7
Ribonucleic Acids
Types of RNA Molecules

• Transfer RNA (tRNA): Delivers amino acids to the sites
for protein synthesis
– tRNAs are the smallest (75–90 nucleotide units)
Return to TOC

Section 22.8
Transcription: RNA Synthesis
Transcription
• Transcription: A process by which DNA directs the
synthesis of mRNA molecules
– Two-step process - (1) synthesis of hnRNA and (2)
editing to yield mRNA molecule
• Gene: A segment of a DNA base sequence responsible
for the production of a specific hnRNA/mRNA 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
Return to TOC

Section 22.8
Steps in the Transcription Process

• Unwinding of DNA double helix to expose some bases
(a gene):
– The unwinding process is governed by RNA
polymerase
• Alignment of free ribonucleotides along the exposed
DNA strand (template) forming new base pairs
• RNA polymerase catalyzes the linkage of
ribonucleotides one by one to form mRNA molecule
• Transcription ends 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 Return to TOC

Section 22.8
Post-Transcription Processing: Formation of mRNA

• Involves conversion of hnRNA to mRNA
• Splicing: Excision of introns and joining of exons
– Exon - a gene segment that codes for genetic
information
– Intron – a DNA segments that interrupt a genetic
message
• The splicing process is driven by snRNA
• Alternative splicing - A process by which several different
protein variants are produced from a single gene
– The process involves excision of one or more exons
Return to TOC

Section 22.8
Transcriptome
• Transcriptome: All of the mRNA molecules that can be
generated from the genetic material in a genome.
– Transcriptome is different from a genome
– Responsible for the biochemical complexity created
by splice variants obtained by hnRNA.
Return to TOC

Section 22.9
The Genetic Code
• The base sequence in a 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 specifi c 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 (or stop signals)
– 3 of the 64 codons are termination codons (―stop‖ signals)
Return to TOC

Section 22.9
The Genetic Code
DNA
• DNA contains genetic
information
• Gene - segment of
DNA on a chromosome
that codes for a
particular protein
• Coding contained in
sequence of bases (on
mRNA) which code for
a particular amino acid
(i.e. genetic code)
• Genetic code universal
in all organisms
– Mitochondrial DNA
slightly different
From: Elliott WH & Elliott DC. (1997) Biochemistry and Molecular Biology. New York: Oxford University Press. P294.
Return to TOC
Section 22.9
The Genetic Code
Characteristics of Genetic Code

• The genetic code is highly degenerate:
– Many amino acids are designated by more than one codon.
– Arg, Leu, and Ser - represented by six codons.
– Most other amino acids - 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 in unless there
are more than four synonyms
– The significance of the ―single box‖ pattern - the first two bases are the
same
– For example, the four synonyms for Proline - CCU, CCC, CCA, and
CCG.
Return to TOC

Section 22.9
The Genetic Code
Characteristics of Genetic Code

• 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 corn plant cell, or
a human cell.
• An initiation codon exists:
– The existence of ―stop‖ codons (UAG, UAA, and
UGA) suggests the existence of ―start‖ codons.
– The codon - coding for the amino acid methionine
(AUG) functions as initiation codon.
Return to TOC

Section 22.9
The Genetic Code
Practice Exercise
Answers:
a. 3’ GCG–GCA–UCA–ACC–GGG–CCU–CCU 5’
b. 3’ GCG–ACC–CCU–CCU 5’
Return to TOC

Section 22.10
Anticodons and tRNA Molecules
• During protein synthesis amino acids do not directly

interact with the codons of an mRNA molecule.
• tRNA molecules as intermediaries 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 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. Return to TOC

Section 22.11
Translation: Protein Synthesis
• 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:
– Contains 4 rRNA molecules and ~80 proteins -
packed into two rRNA-protein subunits (one small and
one large)
– ~65% rRNA and 35% protein by mass
– A ribosome’s active site – Large subunit
– Ribosome is a RNA catalyst
– The mRNA binds to the small subunit of the
ribosome. Return to TOC

Section 22.11
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.
• 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
Return to TOC

Section 22.11
Efficiency of mRNA Utilization

• Polysome (polyribosome): complex of mRNA and several
ribosomes
• 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.
• In the process – several ribosomes bind to a single
mRNA - polysomes.
Return to TOC

Section 22.12
Mutations
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.
Return to TOC

Section 22.12
Mutations
Mutagens
• Mutations are caused by mutagens
• A mutagen is a substance or agent that causes a change in the
structure of a gene:
– Radiation and chemical agents are two important types of
mutagens
– Ultraviolet, X-ray, radioactivity and cosmic radiation are
mutagenic –cause cancers
– Chemical agents can also have mutagenic effects
• E.g., HNO2 can convert cytosine to uracil
• Nitrites, nitrates, and nitrosamines – can form nitrous acid in
cells
• Under normal conditions mutations are repaired by repair enzymes
Return to TOC

Section 22.13
Nucleic Acids and Viruses
Viruses
• Viruses: Tiny disease causing agents with outer protein
envelope and inner nucleic acid core
• They can not 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
Return to TOC

Section 22.13
Vaccines
• Inactive virus or bacterial envelope
• Antibodies produced against inactive viral or bacterial
envelopes will kill the active bacteria and viruses
Return to TOC

Section 22.13
Viruses
• Viruses attach to the host cell on the outside cell surface
and proteins of virus envelope catalyze the breakdown of
the cell membrane and forms a hole
• Viruses then inject their DNA or RNA into the host cell
• The viral genome is replicated, proteins coding for the
viral envelope are produced in hundreds of copies.
• Hundreds of new viruses are produced using the host
cell replicated genome and proteins in short time
Return to TOC

Section 22.14
Recombinant DNA and Genetic Engineering
• 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):
– The study of biochemical techniques that allow the
transfer of a ―foreign‖ gene to a host organism and
produce the protein associated with the added gene
– Bacterial strains such as E. coli inserted with circular
plasmids, and/or yeast cells carrying vectors
containing foreign genes are used for this purpose
– Plasmids (double stranded DNA) replicate
independently in bacteria or yeast Return to TOC

Section 22.14
Recombinant DNA Production using a Bacterial Plasmid

• Dissolution of cells:
– E. coli cells of a specific strain containing the plasmid of interest are treated with
chemicals to dissolve their membranes and release the cellular contents
• Isolation of plasmid fraction:
– The cellular contents are fractionated to obtain plasmids
• Cleavage of plasmid DNA:
– Restriction enzymes are used to cleave the double-stranded DNA
• Gene removal from another organism:
– Using the same restriction enzyme the gene of interest is removed from a
chromosome of another organism
• Gene–plasmid splicing:
– The gene (from Step 4) and the opened plasmid (from Step 3) are mixed in the
presence of the enzyme DNA ligase to splice them together.
• Uptake of recombinant DNA:
– The recombinant DNA prepared in stept 5 are transferred to a live E. coli culture
where they can be replicated, trasncribed and translated.
Return to TOC

Section 22.14
• 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
Return to TOC

Section 22.15
The Polymerase Chain Reaction
• The polymerase chain reaction (PCR) is 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
– Thermostabel 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
Return to TOC

Section 22.16
DNA Sequencing
• DNA sequencing is a method by which the base

sequence in a DNA molecule (or a portion of it) is
determined.
• Discovered in 1977 by Fredrick Sanger
• Concept in DNA sequencing:
• Selective interruption of polynucleotide synthesis using
2’,3’-dideoxyribonucleotide triphosphates (ddNTPs).
Return to TOC

Section 22.16
DNA Sequencing
• This interruption of synthesis leads to the formation of

every possible nucleotide site mixture.
• These nucleotides are labeled using radioactive dNTP
during their synthesis.
• The radiolablled nucleotides are then separated on a gel
by electrophoresis
Return to TOC

Section 22.16
DNA Sequencing
Basic steps involved in DNA sequencing

• Step 1: Cleavage of DNA using restriction enzymes:
Restriction enzymes are used to cleave the large DNA
molecule into smaller fragments (100–200 base pairs).
• Step 2: Separation into individual components: The
mixture of small DNA fragments generated by the
restriction enzymes is separated into individual
components via gel electrophoresis techniques.
• Step 3: Separation into single strands: A given DNA
fragment is separated into its two strands by chemical
methods to use it as a template in step 4.
Return to TOC

Section 22.16
DNA Sequencing
Basic steps involved in DNA sequencing
Return to TOC

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Chapter 22

• Cells in an organism are exact replicas

Copyright © Cengage Learning. All rights reserved 3

• Nucleic Acids: Polymers in which repeating unit is

Copyright © Cengage Learning. All rights reserved 4

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Nitrogen-Containing Heterocyclic Bases

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DNA and RNA are: Guanine Cytosine

– Adenine Cytosine Guanine

– Guanine Table showing complementarity of base pairs

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• Sugar-phosphate groups are referred to as nucleic acid

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• Nucleic acids have secondary and tertiary structure

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• DNA Sequence: the sequence of bases on one polynucleotide is

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• Predict the sequence of bases in the DNA strand

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• Replication: Process by which DNA molecules produce

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• DNA polymerase enzyme can only function in the 5’-to-3’ direction

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• Protein synthesis is directly under the direction of DNA

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Differences Between RNA and DNA Molecules

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Types of RNA Molecules

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Types of RNA Molecules

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Steps in the Transcription Process

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Post-Transcription Processing: Formation of mRNA

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• The base sequence in a mRNA determines the amino acid

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Characteristics of Genetic Code

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Characteristics of Genetic Code

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• During protein synthesis amino acids do not directly

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• Translation – a process in which mRNA codons are

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Five Steps of Translation Process

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Efficiency of mRNA Utilization