NUCLEIC ACIDS

Nucleic Acids
• Discovered by Friedrich Miescher in 1869
• Building blocks: Nucleotides
• Of two types: DNA (deoxyribonucleic acid) and
RNA (ribonucleic acid)
 Nucleotide
• Is a three sub-unit molecule in which a
pentose sugar is bonded to both a phosphate
group and a nitrogen-containing heterocyclic
base.
 Pentose sugar
• Sugar unit of a nucleotide which could either
be a ribose or a deoxyribose
RIBOSE DEOXYRIBOSE

CH2OH OH CH2OH
O O OH

C C C C

H H H H H H H H
C C C C

OH OH OH H
Phosphate group
Nitrogen-containing heterocyclic base
 Nucleotide Formation
1. Formation of the NUCLEOSIDE (pentose sugar
and nitrogen-containing heterocyclic base)
2. Nucleoside react with a phosphate group to
form a nucleotide
 NUCLEOSIDES
• Eight nucleosides are associated with NA
chemistry
RNA NUCLEOSIDES DNA NUCLEOSIDES

Ribose-adenine Deoxyribose-adenine

Ribose-cytosine Deoxyribose-cytosine

Ribose-guanine Deoxyribose-guanine

Ribose-uracil Deoxyribose-thymine
 NUCLEOSIDES
• Are named as derivatives of the base that they
contain; and the bases’ name is modified
using a suffix
– For Pyrimidine bases: the suffix “idine” is used
• Cytidine, Uridine, Thymidine
– For Purine bases: the suffix “osine” is used
• Guanosine and Adenosine
 Nucleotide Nomenclature
• All the names end with “5-monophosphate”
• Preceding is the name of the base present in a
modified form (Cytidine, Uridine, Thymidine,
Guanosine and Adenosine)
– The prefix “deoxy” signifies that the sugar present
is a deoxyribose
– No prefix is used for ribose sugar-containg
nucleotides
 Primary Nucleic Acid Structure
P
• The Sugar Phosphate Backbone
– The nucleotides are all oriented in P

the same direction.

P
– Bonded by 3’,5’-phosphodiester
bond.
P

P
 Primary Nucleic Acid Structure
P
G
• Bases are attached to C-1
P
of the pentose sugar. C

P
C

P
A

P
T

P
T
 The DNA Double Helix
• Established by James Watson and Francis Crick
• The model was based on important pieces of
information obtained by other workers:
– Chargaff’s Rule
• A=T ; C=G
– X-ray diffraction photographs
The DNA Double Helix
 The DNA Double Helix
• The sister strands of the DNA molecule
run in opposite directions (antiparallel)
• They are joined by the bases
• Each base is paired with a specific
partner:
A is always paired with T
G is always paired with C
(Purine with Pyrimidine)
• Thus the sister strands are
complementary but not identical
• The bases are joined by hydrogen bonds,
individually weak but collectively strong.
 DNA REPLICATION
• A biochemical process by which DNA
molecules produce exact duplicates of
themselves
 DNA REPLICATION
• Under the enzyme DNA helicase, the double helix
unwinds. They pair with free individual nucleotides
present in the cell’s nucleus. The pairing occurs
one at a time.
• After a free nucleotide has formed H-bonds with
the base of the old strand, DNA polymerase
verifies that the base pairing is correct then
catalyzes the formation of phosphodiester linkage
between the nucleotide and the growing strand.
 DNA REPLICATION
• The DNA polymerase then slides down the
strand to the next unpaired base of the
template. The same process is repeated.
 Drugs that inhibit DNA synthesis
• Antimetabolites:
– 6-Mercaptopurine
• Resembles adenine
– Thioguanine
• Resembles guanine
– 5-Fluorouracil
• Structure is close to thymine (methyluracil)
– Methotrexate
• Non-base analog
• Inhibits the conversion of folic acid to a needed derivative for
nucleotide synthesis
 Overview of Protein Synthesis
• Is under the direction of DNA molecule
• Divided into two phases:
– Transcription
– Translation
transcription translation

DNA RNA PROTEIN

 Ribonucleic acids
• Four major differences between DNA and RNA
– Sugar unit of RNA is ribose
– The base Thymine is replaced by Uracil
– RNA is a single stranded molecule
– RNA are much smaller (ranging from 75 NT to a
few thousand NT
 Types of RNA
• Heterogeneous nuclear RNA(hnRNA)
o Formed directly by DNA transcription
• Messenger RNA(mRNA)
o Carries instructions for protein synthesis to the
site of protein synthesis
• Small nuclear RNA(snRNA)
o Facilitates the conversion of hnRNA to mRNA
o Contains from 100-200 NT
 Types of RNA
• Ribosomal RNA(rRNA)
o Combines with specific proteins to form
ribosomes
o Physical sites for protein synthesis
• Transfer RNA(tRNA)
o Delivers amino acids to the sites for protein
synthesis
o Smallest of the RNA (75-90 NT)
 TRANSCRIPTION
• Process by which DNA directs the synthesis of
hnRNA/mRNA molecules that carry the coded
information needed for protein synthesis
Gene- a segment of DNA strand that contains the
base sequence for the production of a specific
hnRNA/mRNA molecule
 STEPS in TRANSCRIPTION
• A portion of DNA unwinds, exposing
some bases (governed by the
enzyme RNA polymerase)
• Free ribonucleotides align with the
exposed strands of DNA bases
• RNA polymerase is involved in the
linkage of ribonucleotides
• Transcription ends with when RNA
polymerase encounters a sequence
of bases that is read as a stop signal.
• The hnRNA is released and the DNA
rewinds to re-form the double helix
 Post Transcription Processing:
Formation of mRNA
• Portions of hnRNA are
deleted and the
retained parts are
spliced together
• Leads to the concept of
EXONS and INTRONS
– Exons- a gene segment
that conveys genetic
information
– Introns- a gene segment
that does not convey
genetic information
 Splicing
• Is the process of removing introns from an
hnRNA molecule and joining the remaining
exons to form an mRNA molecule
– Carried out by Spilceosome
 The Genetic Code
• The assignment of the 64 mRNA codons to
specific amino acids.
• Codon- a three-nucleotide sequence in an
mRNA molecule that codes for a specific acid
The Genetic Code Features
 Anticodons and tRNA molecule
• At least one type of
tRNA molecule exists
for each of the 20
amino acids found in
proteins. (amino acyl
tRNA synthetase)
• All tRNA have the
same general shape
(clover leaf)
 Two features of tRNA
• The 3’ end of the clover leaf
structure is where an amino
acid becomes covalently
bonded to the tRNA molecule
through an ester bond
• The loop opposite the open
end is consist of an anticodon
– Anticodon is a three-nucleotide
sequence on a tRNA molecule
that is complementary to a
codon on a mRNA molecule
 TRANSLATION
• Is the process by which mRNA codons are
deciphered and a particular protein molecule
is synthesized
– Ribosome: is an rRNA-protein complex that serves
as the site for the translation phase of protein
synthesis
• Has two subunits
• Large subunit is the active site
• mRNA involved in the translation phase binds to the
small subunit
 Steps in TRANSLATION
• Activation of tRNA
• Initiation
• Elongation
• Termination
• Post-translation processing
 Activation of tRNA
– An amino acid interacts
with an activator
molecule to form a
highly-energetic
complex
– The complex then
reacts with the
appropriate tRNA
molecule to produce
an activated tRNA
molecule
 Initiation
• Begins when the mRNA attaches itself to the
surface of the SRS with the initiating codon
occupies a site called the P-site(peptidyl site)
• The activated tRNA with an anticodon
complementary to the codon attaches itself
through complementary base pairing.
• The resulting complex interacts with LRS to
complete the initiation complex
 Elongation
• Next to the P-site is the second binding site called
the A-site(aminoacyl site)
• The activated tRNA would then bind to the
exposed mRNA codon
• The enzyme peptidyl transferase effects the linking
of the P-site to the A-site to form a dipeptide.
• Such peptide bond formation leaves the tRNA at
the P-site empty
• The ribosome shifts along the mRNA
 Termination
• Appearance in the mRNA codon sequence of
one of the three stop codons terminates the
process
• The polypeptide is then cleaved from the
tRNA through hydrolysis
 Post-Translational Processing
• Modification of protein
• Gives the protein its final form
M

x
 Antibiotics that Inhibit Bacterial Protein
Synthesis
• Streptomycin
– Binds to 30s subunit in prokaryotes
– Causes the mRNA codons to be read incorrectly
– Inhibits chain elongation
• Chloramphenicol
– Inhibits peptidyl transferase in the LRS (50s)
• Erythromycin
– Binds to LRS (50s) and inhibits translocation
• Terramycin
– Blocks A-site, prevents the attachment of AA-carrying tRNA
• Tetracycline
– Binds to SRS (30s) and inhibits binding of incoming tRNA
 Assignment
• Read about mutation and its types: Silent,
Missense and Non-sense