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By Librada M. Rubio
Function
The important functions of DNA include the storage of genetic information,
expression of genetic information through synthesis of specific proteins, self-replication
that provides the means by which genetic information can be transmitted from cell to cell,
and change by mutation to provide variability among organisms.
Structure
DNA is one of the nucleic acids present in the cell. It is made up of nucleotides
composed of nitrogen base, sugar and phosphate group. The nitrogen bases are of two
types: the pyrimidines with six-membered and single-ringed structure and the purines,
with nine-membered and double-ringed structure. The pyrimidine bases are the thymine
(T) and cytosine (C), while the purines are the adenine (A) and guanine (G) . The pentose
sugar is the deoxyribose that has one less oxygen than ribose sugar present in the other
type of nucleic acid, the ribulonucleic acid, or RNA.
To form a strand of DNA or a polynucleotide , the nucleotides are joined, in
which the phosphate attached to the 5’ carbon of one sugar is linked to the hydroxyl
group attached to the 3’ carbon of the next sugar in line. The chemical bonds by which
the sugar components of adjacent nucleotides are linked through the phosphate groups are
called phosphodiester bonds. The 5’-3’-5’-3’ orientation of these linkages continues
through out the chain, which typically consists of millions of nucleotides. The terminal
groups of each polynucleotide chain are a 5’-phosphate at one end and a 3’-hydroxyl (3’-
OH) group at the other (Fig.1). The asymmetry of the ends of a DNA strand is the
chemical basis of its polarity: one end of the strand is the 5’ end whereas the other end is
the 3’ end.
The structure of DNA is double helix as described by James Watson and Francis
Crick. This can be liken to the shape of a ladder that has been twisted. The
phosphate/sugar attachments are on the outside uprights of the ladder, while the attached
bases, between the two nucleotide strands, can be considered the rungs of the ladder. Two
strands of sugar and phosphate backbone are twisted and connected to alternating bases.
There are ten bases per helical turn in each strand, or ten base pairs per turn of the double
helix. The paired bases are planar, parallel to one another, and perpendicular to the long
axis of the double helix (Fig. 2)
Watson and Crick established that the strands of their proposed double helix are
antiparallel, that is their C-5’ to C-3’ orientations run in opposite direction, and exact
complements of one another, such that the rungs of the ladder always consist of either A
= T or G = C. Adenine and guanine are held by double hydrogen bonds while guanine
and cytosine triple hydrogen bonds (Fig. 3). According to Erwin Chargaff in a DNA
molecule, the amount of adenine equals the amount of thymine, and the amount of
cytosine equals the amount of guanine. Using Chargaff’s data, Watson and Crick
proposed the concept of complementary base pairing of adenine and thymine and
cytosine and guanine. This complementarity serves as basis for the replication of DNA,
the expression of hereditary characteristics that involves the transcription of DNA into
RNA, and the transmission of genetic information from generation to the next.
Replication
Replication is one of the major functions of the DNA that makes it ideal to serve
as the genetic material. The rapidity and accuracy at which new copies of DNA are
produced from old DNA ensure the distribution of chromosomes and the transmission of
genetic information from parent to daughter cells during division. This replication
process happens in the cell during the S phase of the interphase of the cell cycle. The new
synthesized DNA molecules separate during the anaphase stage of mitotic phase or M
phase.
The mode of DNA replication is called semiconservative replication because each
parental DNA strand serves as template or pattern for a new strand, and as each new
strand is formed, it is hydrogen-bonded to its parental template. As replication proceeds,
the parental double helix unwind and then rewinds again into new double helices, each of
which contains one originally parental strand and one newly formed daughter strand (Fig.
4).
The position along the molecule at which DNA replication begins is called a
replication origin, and the region in which the parental strands unwind is a replication
fork. The process of generating new replication fork is initiation.
During replication, helix unwinding protein (HUP) or helicase is responsible for
the unwinding of the parental strands to create two template strands. Helix-destabilizing
proteins or single-strand-binding proteins then bind to each of the single stranded DNA at
the replication fork and is responsible for preventing the separated strands from
reannealing. Helix-relaxing protein or DNA gyrase functions to relax the tension of
supercoiled twists created in unwinding the parental double helix without rotation.
Complementary free nucleotide monomers in the nucleus are added to the
template strands by an enzyme called DNA polymerase
Because the double strands of the DNA are antiparallel, or run in opposite
direction: one strands runs from 5’ to 3’ direction while the other from 3’ to 5’ direction,
replication is bidirectional at each origin. The strand that terminates in a free 3’ -end or
the direction is 5’ to 3’, is synthesized continuously and this is referred to as the leading
strand. This is because the DNA polymerase can only make new DNA in 5’ to 3’
direction. The other strand, which is antiparallel and terminates in a free- 5’-end, is
synthesized discontinuously and is referred to as the lagging strand (Fig. 5 16.13) The
replication in the lagging strand is discontinuous because it has to wait for the other
strand to unwind. Short strands of nucleotides are formed in the lagging strand due to
discontinuous replication. These short strands of nucleotides or small precursor fragments
are called Okazaki fragments, named after its discoverer, Reiji Okazaki. The Okazaki
fragments ultimately joined to a continuous strand of DNA. Then the DNA ligase closes
the nick by creating a phosphodiester bond between a 3’-OH end and a 5’-P end so the
nucleotides are linearly attached. After the synthesis of the two new DNA molecules,
they recoil or rewind again into new double helices. Then DNA polymerase also
proofreads the newly synthesized DNA molecules to remove the undesirable nucleotides
DNA replication has multiple origins to ensure that the chromosomal DNA is
replicated within the necessary time period. It requires numerous proteins to act as
enzymes for rapid and accurate copying of DNA .
The process of DNA replication can be summarized as follows:
1. the double helix DNA uncoils.
2. the two strands unzip by breaking the weak hydrogen bonds between nitrogen
bases.
3. free nucleotides in the nucleoplasm attach themselves to the separated strands
of nucleotides through their complementary nitrogen bases.
4. sugars and phosphate of nucleotides link.
5. the newly formed DNA molecules recoil to become double helices.
Making Proteins from DNA- the way of expressing inherited traits
DNA has the code of instruction for the expression of inherited traits. A certain
inherited trait cannot be expressed if the right protein is not made. The direction in which
genetic information flows is from the DNA to RNA to proteins. This idea was first
proposed by Francis Crick in 1958 which he called the central dogma of Molecular
Genetics, which can be represented in a flow diagram as follows:
Transcription Translation
The diagram shows that the DNA, as a genetic material, can replicate itself. The
DNA at the same time supervises the expression of hereditary traits as it is transcribed
into RNA which in turn is translated into protein. This central dogma is, simply, that
DNA codes for the production of RNA, RNA codes for the production of protein, and
protein does not code for the production of protein, RNA, or DNA. So for the trait
controlled by a certain gene is expressed, another type of nucleic acid is required for the
synthesis of protein and this the RNA or ribonucleic acid.
Table 1 shows the how DNA and RNA differ while Table 2 gives the 3 types of RNA and
their corresponding function.
RNA can base-pair with a single-stranded DNA, and this pairing obeys the same
hydrogen-bonding rules as in DNA, except the adenine pairs with uracil (U) instead of
thymine. RNA can also base-pair with itself.
Genetic information is stored in the DNA contained in the nucleus. How does the
genetic information get out from the nucleus and reach the cytoplasm, particularly the
ribosome, the workbench of protein synthesis? According to the messenger hypothesis
developed by Crick and his colleagues, RNA molecule forms as a complementary copy
of one DNA strand of a particular gene. The process by which this RNA forms is called
transcription. During transcription the information contained in the DNA is exactly
copied by the messenger RNA, or mRNA. This mRNA, then travels from the nucleus to
the ribosome in the cytoplasm, where it serves as a template for the synthesis of proteins.
What is the relationship between a specific nucleotide sequence in DNA and a
specific amino acid sequence in a protein? Based on the adapter hypothesis also
proposed by Crick, there must be an adapter molecule that can bind a specific amino acid
at one end and recognize a sequence of nucleotides with another region. This adapter
molecule is another type of RNA and identified now as the transfer RNA, or tRNA.
Transfer RNA has a cloverleaf shape. One of the tRNA loops has a portion containing a
sequence of three nucleotides that can form weak hydrogen bonds with the nitrogen bases
of a complementary portion of mRNA. It is the ability of tRNA to form weak hydrogen
bonds with both mRNA and amino acid which makes it an ideal agent for translating the
coded genetic message in nucleotide sequences into a particular amino acid sequence
expressed in proteins. Because tRNA recognizes the genetic message of mRNA and
simultaneously carries specific amino acids, tRNA’s can translate the language of DNA
into the language of proteins. The tRNA adapters line up on the mRNA so that the amino
acids are in the proper sequence for a growing polypeptide chain – a process called
translation. Therefore, a specific nucleotide sequence in DNA is actually a code for a
specific amino acid sequence in a protein.
Based on the central dogma, a given gene is transcribed to produce a messenger
RNA (mRNA) complementary to one of the DNA strands, and that transfer RNA
(tRNA) molecules translate the sequence of bases in the mRNA into the appropriate
sequence of amino acids to form specific protein.
The Genetic Code
The genetic code is written in the language of nucleic acids. It is passed on from
one cell to another, from one generation to the next when chromosomes are distributed
from the parent cell to the daughter cells. Chromosomes are chemically made up of
proteins and the nucleic acid DNA. The genetic code, therefore, is stored in the DNA and
maybe expressed when copied into messenger RNAs.
Messenger RNA is a single strand of linearly arranged nucleotides. The
nucleotides are read in threes. Each triplet code made up of a particular sequence of
nitrogen bases is called a codon. The codon has its complement in an anticodon found in
one of the three loops of the cloverleaf-shaped tRNA. A transfer RNA has an attachment
site for a particular type of amino acid. Proteins are made up of linearly arranged amino
acids. Each amino acid that will form the protein molecule to be synthesized is
determined by the triplet code or codon on the mRNA.
The genetic code chart may be used to determine the triplet code(s) for each
amino acid. The complete genetic code is shown in Table 3. It can be noticed that there
are many more codons than there are different amino acids in proteins. Combinations of
the four available “letters” (the bases) give 64 (43) different three-letter codons, yet only
61 codons encode only 20 amino acids. AUG which a code for methionine, is also the
start codon that initiates translation. The three of the codons, (UAA,UAG, UGA) are
stop codons, or chain terminators; when the translation machinery reaches one of these
codons, translation stops, and the polypeptide is released from the translation complex.
These three codons do not determine specific amino acid. It can also be noticed that one
amino acid may be represented by more than one codon. This only shows that the genetic
code is redundant. The redundancy is not evenly divided among amino acids. For
instance, methionine and tryptophan are represented by only one codon each, while
leucine is represented by six different codons.
The genetic code appears to be nearly universal, applying to all species on our
planet. Thus the code must be an ancient one that has been maintained intact throughout
the evolution of living things. Exceptions are known: within mitochondria and
chloroplasts, the code differs slightly from that in prokaryotes and in the nuclei of
eukaryotic cell; in one group of protists, UAA and UAG code for glutamine rather than
functioning as stop codons.
Genes provide the instructions for making specific proteins. But gene does not
build a protein directly. The bridge between DNA and protein synthesis is RNA. The
flow of genetic information from DNA to RNA to protein involves two main stages: the
transcription and translation.
Transcription
Transcription is the synthesis of RNA under the direction of DNA. The particular
type of RNA that transcribes or copies the gene’s protein-building instruction from the
DNA is the messenger RNA because it carries at the same time a genetic message from
the DNA to protein-synthesizing machinery of the cell, the ribosome. The enzyme
responsible for transcription is RNA polymerase. It can add nucleotides only to the 3’ end
of the growing polymer. Hence an RNA molecule elongates in its 5’ to 3’ direction.
Transcription has three stages: initiation, elongation, and termination of the RNA
chain (Fig.6)
Translation
Translation is the actual synthesis of a polypeptide or protein which occurs under
the direction of mRNA. Another type of RNA is involved in this process and it is the
transfer RNA (tRNA). It translates or interprets the base sequence of mRNA into amino
acid sequence of a protein at the same time transfers the amino acids from the
cytoplasm’s amino acid pool to the ribosome, complex particles that facilitate the orderly
linking of amino acids into polypeptide chains. The ribosome adds each amino acid
brought to it by tRNA to the growing end of a polypeptide chain (Fig. 9).
Just like the other types of RNA, tRNA molecules are also transcribed from
DNA templates and travel from the nucleus to the cytoplasm where translation occurs. A
molecule of tRNA is composed of a single strand that is only about 80 nucleotides long
(compared to hundreds of nucleotides for most mRNA molecules). The tRNA molecule
folds back upon itself and forms a cloverleaf-shaped (Fig. 10). The tRNA actually twists
and folds into a compact 3-dimensional structure that is roughly L-shaped. The loop
protruding from one end of one L includes anticodon, the specialized base triplet that
binds to a specific mRNA codon. From the other end of the L-shaped tRNA molecule
protrudes its 3’ end, which is the attachment site for the amino acid. Thus, the structure of
the tRNA molecule fits to its function. Aminoacyl-tRNA synthetase is the enzyme that
binds a particular amino acid to the correct tRNA.
Translation happens in the ribosomes. These organelles facilitate the specific
coupling of tRNA anticodons with mRNA codons during protein synthesis. A ribosome
is composed of two subunits, the large and the small subunits (Fig. 11). These ribosomal
subunits are constructed of proteins and another type of RNA molecules called ribosomal
RNA (rRNA). These subunits are made in the nucleolus and are exported to the
cytoplasm. The ribosome has a binding site for mRNA and another three binding sites for
tRNA. These are the P site (peptidyl-tRNA site) that holds the tRNA carrying the
growing polypeptide chain; the A site (aminoacyl-tRNA site) that holds the tRNA
carrying thenext amino acid to be added to the chain; and lastly the E site (exit site) that
releases tRNA that has unloaded amino acid.
Translation, or synthesis of a polypeptide chain, is also divided into three stages
which are analogous to those of transcription). These are initiation, elongation, and
termination. These All three stages require enzymes that aid mRNA, tRNA, and
ribosomes in the translation process. Energy is also needed for chain initiation and
elongation.
Initiation
The initiation stage of translation brings together mRNA, a tRNA carrying the
first amino acid, the methionine, of the polypeptide, and the two subunits of a ribosome
(Fig.12). The small ribosomal subunit attaches to the leader segment at the 5’ end of the
mRNA. The initiation codon AUG signals the start of translation. The initiator tRNA,
that carries the amino acid methionine, attaches the initiation codon.
The union of initiation mRNA codon, initiator tRNA, and a small ribosomal
subunit is followed by the attachment of a large ribosomal subunit, completing a
translation initiation complex. At the completion of the initiation process, the initiator
tRNA sits in the P site of the ribosome, and the vacant A site is ready for the next
aminoacyl tRNA (tRNA carrying specific amino acid).The synthesis of a polypeptide is
initiated at its amino end. Initiation factors are proteins involved during initiation stage of
translation.
Elongation
During this stage of translation, amino acids are added one by one to the first
amino acid. Each addition involves the participation of several protein called elongation
factors and occurs in a three-step cycle (Fig. 13). These are:
1. Codon recognition
The mRNA codon in the A site of the ribosome forms hydrogen bonds with the
anticodon of an incoming molecule of tRNA carrying appropriate amino acid. An
elongation factor ushers the tRNA into A site. This step requires from the
hydrolysis of guanosine triphosphate (GTP).
2. Peptide bond formation
An rRNA molecule of the large ribosomal subunit, functioning as a ribozyme,
catalyses the formation of a peptide bond that joins the polypeptide extending
from the P site to the newly arrived amino acid in the A site. In this step, the
polypeptide separates from the tRNA to which it was attached and connects to
the amino acid carried by the tRNA in the A site.
3. Translocation
The tRNA in the A site, now attached to the growing polypeptide, is translocated
to the P site. As the tRNA moves, its anticodon remains hydrogen-bonded to the
mRNA codon; the mRNA moves along with it and brings the next codon to be
translated into the A site. Meanwhile, the tRNA that was in the P site moves to the
E (exit) site and from there leaves the ribosome. This translocation step also
requires energy from the hydrolysis of a GTP.The mRNA moves through the
ribosome in one direction only, 5’ end first; this is the same as the ribosome
moving 5’ → 3’ on the mRNA. The ribosome and the mRNA move relative to
each other, unidirectionally, codon by codon.
Termination
The final stage of translation is termination (Fig.14). Elongation continues until a
stop codon reaches the A site of the ribosome. These special base triplets – UAG,
UGA, and UUA – do not code for amino acids (as already mentioned) but instead
act as signals to stop translation. A protein called a release factor binds directly to
the stop codon in the A site. The release factor causes the addition of a water
molecule instead of an amino acid to the polypeptide chain. This reaction
hydrolyses the completed polypeptide from the tRNA that is in the P site , freeing
the polypeptide from the ribosome.
This free polypeptide chain begins to coil and fold spontaneously,
forming a functional protein of specific conformation to express the trait
controlled by a certain gene.
The signals that start and stop transcription and translation are shown in
Table 4.
Table 4. Signals that Start and Stop Transcription and translation
Stage Transcription Translation
Initiation Promoter sequence in DNA AUG start codon
Termination Terminator sequence in UAA, UAG, or UGA stop codon in
DNA mRNA
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