BIOCHEMISTRY: NUCLEIC ACID
found in both DNA and RNA
• 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
TYPES OF NUCLEIC ACID
• 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
NUCLEOTIDES: STRUCTURAL BUILDING BLOCKS
FOR 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
Pentose Sugars
• The structural difference between ribose and
pentose 2′ - deoxyribose occurs at carbon 2′
o —OH group is present in ribose
o —H atom is present in 2′-deoxyribose
• Ribose is present in RNA
• 2′-deoxyribose is present in DNA
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
– Uracil is found only in RNA
– Thymine is found only in DNA
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–)
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 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
• 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 Figure 22.6 - Comparison of the General Primary
• Formed by the addition of a phosphate group to a Structures of Nucleic Acids and Proteins
nucleoside
• Characteristics of phosphate addition
- The phosphate is attached to C5′ position
- Water is released

Figure 22.7 - The DNA Double Helix

Table 22.1 - The Building Blocks of DNA and RNA

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 DNA Sequence
thymine • Two polynucleotide strands are coiled around each
Primary Nucleic Acid Structure other in a spiral
• A sequence - Bases on each strand extend inwardly toward
that each other
contains - They are connected by hydrogen bonds
nucleotides - They run in opposite directions
linked to a • 5′-to-3′ direction
nucleic acid • 3′-to-5′ direction
• Primary Base Pairing
structure
depends on • A pyrimidine is always paired with a purine
the – Fits inside the DNA double strand
sequence – Hydrogen bonding is most favored in A–T and G–C
of bases pairs
present – A–T and G–C pairing is termed complementary
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
• 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
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
OVERVIEW OF PROTEIN SYNTHESIS
• DNA molecules control the synthesis of proteins
• Phases of protein synthesis
- Transcription
- Translation
RIBONUCLEIC ACIDS
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
TRANSCRIPTION: RNA SYNTHESIS
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: 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
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
Practice Exercise
Sections A, C, and E of the following base sequence
section of a DNA template strand are exons, and
sections B and D are introns.
a. What is the structure of the hnRNA transcribed from
this template?
b. What is the structure of the mRNA obtained by
splicing the hnRNA?
Answers:
a. 3′ GCG–GCA–UCA–ACC–GGG–CCU–CCU 5’
b. 3’ GCG–ACC–CCU–CCU 5’
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
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
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
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
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
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
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
o Resistance to the harmful effects of pesticides
o Protection from insects Figure 22.33 (a) - Basic Steps of the Polymerase Chain
▪ Plants produce pesticides Reaction
o 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 Figure 22.33 (b) - Basic Steps of the Polymerase Chain
– Cells with identical DNA that have Reaction
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

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