NUCLEIC ACIDS and PROTEIN SYNTHESIS

Natural Science Department

Ateneo de Zamboanga University
Roselita O. Natividad

• life depends upon directed reactions brought about by specific protein

catalysts called enzymes
• but without nucleic acids these enzymes and other proteins cannot be
made in the living cell because all biological processes are dependent on
information
• the complexity of living processes must require a large amount of
information and this information must be stored and then retrieved in an
orderly and precise manner
• DNA is known as the central information storage molecule. It embodies
the heredity message of each organism
• considered to be macromolecular polymers that occurs in living things
• their chemical composition is best understood in terms of their hydrolysis
products
• complete hydrolysis yields a mixture of heterocyclic amines, a five-carbon
sugar and phosphoric acid
• partial hydrolysis yields nucleotides and nucleosides

Components of Nucleic Acids

• the two types of nucleic acids, RNA and the DNA, are found in the cells,
each has its own role in the transmission of hereditary information
• are polymers
• the building blocks of nucleic acids are the nucleotides
• a nucleotide is composed of a base, sugar, and a phosphate
 The Bases
• the bases consist of two groups: the purines and the pyrimidines
• the purines are adenine and guanine while the pyrimidines are cytosine,
thymine, and uracil
• uracil is found only in RNA and thymine is found only in DNA, the rest are
found in both
• thus, DNA and RNA contain four bases each; the bases for DNA are
adenine, guanine, cytosine and thymine while that of RNA are adenine,
guanine, cytosine and uracil
 The sugars
• the sugar component of RNA is ribose while that of DNA is deoxyribose
 The Phosphate
• the third component of nucleic acid is phosphoric acid

In Summary
nucleoside = base + sugar
nucleotide = base + sugar + phosphoric acid
nucleic acid = a chain of nucleotides
The Structure of DNA and RNA

Primary Structure
• nucleic acids are polymers of nucleotides
• the structure can be divided into two parts: the backbone and the side
chain
• the backbone of DNA consists of alternating deoxyribose and phosphate
groups while the side chain consists of the bases

• the primary structure of RNA is the same except that each sugar is ribose
and that uracil is present instead of thymine

• thus, the backbone of both the DNA and RNA chains has two ends: a
3’- OH end and a 5’- OH end. These two ends have roles similar to those
of the C-terminal and N-terminal ends in proteins
• the backbone, which is hydrophilic, provides the structural stability of the
DNA and RNA
• the bases that are linked, one to each sugar unit, are the side chains, and
they carry all the information necessary for protein synthesis
• in addition, hydrogen bonding between complementary bases promotes
stability as well as provides a mechanism for accurate pairings between
bases
• the order of bases provides the primary structure of DNA
• therefore, the writing of the sequence of bases start with the nucleotide
that has the free 5’-OH terminal and ends with the nucleotide that has the
3’-OH terminal
DNA
• a high molar mass that occurs almost exclusively in the nucleus
• just as the order of the amino acid residues of protein side chains
determines the primary structure of the protein, the order of the bases
provides the primary structure of DNA
• the two polynucleotides that form the double helix runs in opposite
direction and which are intimately associated with one another by means
of hydrogen bonding
• the antiparallel orientation of the two polynucleotide strands allows H-
bonds to form between the nitrogenous bases that are oriented toward
the helix interior
• the intermolecular hydrogen bonding accounts for the secondary
structure and is the primary force holding the two strands of the molecule
together
• the two strands are oriented toward each other in such a way that the
bases projecting from each other in close proximity
• the strands are right handed complementing each other about the same
axis so that they form the double helix
• the double helix chains run in opposite direction at 5’ and 3’ – OH terminal
• the bases project inward in such a way that the purine of one strand
always pairs with a pyrimidine of the other
• the bases purines adenine and guanine always pairs with the pyrimidines
thymine and cytosine respectively
• such pairing rules demand that the base sequence of one chain be
completely determined by the base sequence of the other
• therefore, the entire action of DNA – and of the hereditary mechanism –
depends on the fact that, wherever there is an adenine on one strand of
the helix, there must be a thymine on the other strand because that is
the only base that fits and forms strong hydrogen bond, and similarly for
G and C
• thus, the entire heredity mechanism rests on these slender hydrogen
bonds
DNA Replication
• the DNA in the chromosomes carries out two functions: it reproduces
itself and it supplies the information necessary to make all the proteins in
the body
• the base sequence of the gene carries the information necessary to
produce one protein molecule
• genetic information is transmitted from one cell to the next when cell
division occurs
• this can occur at either end or at the middle
• the duplication that starts at the middle is the common pathway
• special molecule called unwinding proteins attach themselves to one DNA
strand and cause the separation of the double helix
• Crick and Watson proposed that during replication the two strands uncoil,
and each strand acts as template
• the key to the process is that only thymine can fit opposite adenine and
only cytosine opposite guanine
• while the bases of the newly arrived nucleotides are hydrogen bonded to
their partners, enzyme called polymerases join the nucleotide back bones
• if the unwinding begins at the middle, the synthesis of new DNA
molecules on the old templates continue in both direction until the whole
molecule is duplicated
 RNA
• single stranded nucleic acid
• the sugar is ribose
• contains the base uracil instead of thymine
• hydrolytic analysis indicates that it does not obey Chargaff rules, that is
the purine: pyrimidine are not in the 1 : 1 base ratio unlike that of the DNA
• the absence of the hydrogen bonding results in an irregular and relatively
unpredictable structure
• three types are known to exist: mRNA, tRNA and rRNA

mRNA
• messenger RNA
• carries the genetic information from the DNA
• consists of a chain of nucleotides whose sequence is exactly
complementary to that of one of the strands of the DNA
• not very stable; synthesize as needed and then degraded
 tRNA
• transfer RNA
• relatively small molecules containing from 73 to 93 nucleotides per chain
• There is at least one different tRNA molecule for each 20 amino acids from
which the body makes its proteins
• L – shaped or can be represented as a clover leaf in two dimensions
 rRNA
• ribosomal RNA
• found in ribosomes which are small spherical bodies located in the cells
but outside the nuclei
• consists of about 35% protein and 65% of a type of RNA called ribosomal
RNA
• large molecules with molecular weights of up to 1 million

Transmission of Information
• the information contained in DNA molecules is transferred to RNA
molecules and then from RNA molecules the information is expressed in
the structure of proteins which involves two steps; the transcription
followed by the translation

replication transcription translation

DNA  DNA  mRNA  Protein
Transcription
• the information is found inside the nucleus and the amino acids are
assembled outside the nucleus
• thus the information must be carried out of the nucleus and into the site
where the amino acids are located
• this is done by transcribing the information from the DNA and onto the
messenger RNA which then carries the message from the nucleus to the
site of protein synthesis
• the DNA strand determines the sequence of amino acids along the protein
chain then the information contained in the DNA must be conveyed from
the nucleus to the site of protein synthesis through mRNA. This is done by
what is known as transcription
• the mRNA is made from a DNA template that contains a base sequence
that is complementary to that of the DNA upon whose surface it was
synthesized. Once it is formed, the mRNA diffuses to the ribosomes
carrying with it the genetic instructions
• each group of three bases along the mRNA strand now specifies a
particular amino acid, and the sequence of these triplet groups dictates
the sequence of the amino acids in the protein. This triplet code is known
as codon
• the copying of information is done with the help of the enzyme RNA
polymerase which catalyzes the synthesis of RNA
• the DNA double helix begins to unwind at a point near the gene that is to
be transcribed
• on the DNA strand there is always a sequence of bases that the RNA
polymerase recognizes as the initiation signal and the termination signal
• between these two signals the enzyme zips up the complementary bases
by combining each ribose to the next phosphate
• once the mRNA has been synthesized it moves away from the DNA
template, which then rewinds to the original double-helix form
The Role of RNA in Translation
• translation is the process by which the genetic information preserved in
the DNA and transcribed into the mRNA is converted to the language of
proteins
• the substance required for the translation phase of protein synthesis are
mRNA, tRNA, amino acids, ribosomes, and a number of different enzymes
• the synthesis of proteins take place on the ribosomes. These spheres
dissociate into two parts – a larger body and a smaller body . Each of
these bodies contains rRNA and some polypeptide chains that act as
enzymes speeding up the synthesis
(The Role of RNA in Translation)
• as the mRNA is being made on the DNA template, the 5’ end of the mRNA
coming off this assembly is first attached to the smaller ribosomal body
and later joined by the larger body. Together they form a unit on which the
mRNA is stretched. Once the mRNA is attached to the ribosome in this
way, the 20 amino acids are brought to the site, each carried by its own
particular tRNA
• the tRNA contained important segments: the site to which enzymes attach
the amino acids and the recognition site
• each tRNA is specific for one amino acid only
• the recognition site contains the sequence of three bases called anticodon
which is located at the opposite end of the molecule

Translation and Protein Synthesis

• there are four major stages in protein synthesis: activation, initiation,
elongation and termination
 Activation

• the amino acid is first activated by reacting with ATP

• the activated amino acid is then attached to its own particular tRNA with
the aid of an enzyme that is specific for that particular amino acid and
tRNA
a.a. + ATP  a.a.–AMP + Pi

a.a–AMP + tRNA  a.a.- tRNA + AMP

• the specific recognition by an enzyme aminoacyl-tRNA synthetase, of its

proper tRNA and amino acid is often referred to as second genetic code

• this step is very important because once the amino acid is on the
tRNA, there is no way of checking for the correct pairing
• so the aminoacyl-tRNA synthetase have to get it right
 Initiation

• this stage consists of three steps: (a) the mRNA which carries the
information attaches itself to the smaller body ribosome; (b) the
anticodon of the first tRNA which is always methionine, binds to the codon
of the mRNA that represents the initial signal; (c) the larger body
ribosome now combines with the small body
• The large body carries two binding sites: the P site where the growing
peptide chain will bind and the A site, the one right next to it and where
the incoming tRNA will bring the next amino acid
• when the large body attaches itself to the small body , it does so in such a
way that the P site is right where the methionine tRNA already is
• then, elongation begins
 Elongation

• at this point the A site is vacant and each of the 20 tRNA can come in and
try to fit itself in
• but only one of the 20 carries exactly the right anticodon that corresponds
to the next codon on the mRNA
• the binding of the tRNA to the A site takes place with the aid of proteins
called elongation factors
• once at the A site, the new amino acid is linked to the first in a peptide
bond by the enzyme transferase
• the empty tRNA remains on the P site
• on the next phase of elongation, the whole ribosome moves one codon
along the mRNA
(Elongation)

• with this move the dipeptide is translocated from the A site to

the P site while the empty tRNA dissociates and goes back to
the tRNA pool to pick up another amino acid
• this elongation steps is repeated until the last amino acid is
attached
 Termination

• after the translocation, the next codon reads ”STOPS”

• releasing factors then cleave the polypeptide chain from the last tRNA and
the tRNA itself is released from the P site
• the whole mRNA is then released from the ribosome and the ribosome
dissociates into its constituent subunits
• three releasing factors are involved
Posttranslational Modification

• as the polypeptide emerges from the ribosome, it begins to

unfold into its final three-dimensional shape
• the polypeptide undergoes a series of modifying reactions to
prepare the molecule for its functional role
• several cleavage reactions may occur during the modification
and this include the removal of fMet residue