REPLICATION

Cells, like these prokaryotic E. coli cells, replicate themselves quickly and efficiently. Part
of the process of asexual reproduction is the ability of cells to make identical copies of their DNA
before cell division occurs. Prokaryotic cells that reproduce by binary fission rely on the fast,
accurate process of DNA replication to ensure future generations of cells will have the same
genetic instructions as the parent cell. The structure of DNA aids in the speed and accuracy of
replication. Double stranded DNA is a polymer of two strands of nucleotides which are hydrogen
bonded to each other to form a double helix. Nucleotides are molecules that consist of a
deoxyribose sugar, a phosphate, and one of four nitrogenous bases. The phosphodiester backbones
consist of alternating sugar and phosphate groups. The nitrogenous bases include cytosine,
thymine, adenine, and guanine. Cytosine forms three hydrogen bonds with guanine and thymine
forms two hydrogen bonds with adenine. This referred to as complementary base pairing. The
double helix will have one strand oriented in a 5’ – 3’ direction relative to the hydroxyl group pf
the deoxyribose sugar, and the other strand oriented in a 3’ – 5’ direction. This shows the
antiparallel nature of the DNA strands. The complementary base pairing in the structure of DNA
allows replication to be executed in a semi-conservative manner. Each strand of the DNA molecule
is used as a template in the creation of a new double strand.
Replication begins with double stranded DNA being separated and each original strand,
called parent strand, is used as a template for the complementary base pairing of the nucleotides
to make two new molecules. DNA replication occurs in the 5’ – 3’ direction, adding new
nucleotides to the 3’ end of the newly forming strand. DNA replication will begin at a specific area
of the molecule called the origin of replication. The origin of replication denotes the area of active
replication called the replication fork. In order to understand how complex eukaryotic organisms
replicate DNA, scientists first studied replication in prokaryotic models, like E. coli. A number
enzymes are needed for replication to proceed once the replication fork is established. Helicase
separates the strands of the double helix and single stranded binding proteins stabilize the newly
single stranded regions. DNA gyrase is used to make sure the double stranded areas outside the
replication fork do not supercoil. Once the replication for is stable, DNA polymerase catalyze the
addition of new nucleotides to the growing daughter strand. Other proteins, such as beta clamps
and clam loader, help hold the DNA polymerase in place on the DNA. Short sequences of RNA,
called primers, have to be paired to the template strands by the enzyme primase because DNA
polymerase cannot begin to add nucleotides without a primer. Replication of both strands occur at
the same time, one using continuous synthesis and the other, discontinuous. Continuous synthesis
occurs on the 3’ – 5’ oriented parent strand, referred to as the leading strand. New nucleotides are
added to the 3’ end moving continuously towards the expanding replication fork. Discontinuous
synthesis occurs on the parent strand that is oriented 5’ – 3’, called the lagging strand, and is
completed in segments called Okazaki fragments. Replication on this strand uses primase to add
primers ahead of the 5’ end of the lagging strand. DNA polymerase III then adds short sequences
of nucleotides, the Okazaki fragments, to the primer filling in the gap. As helix is opened further,
this process repeats until the entire strand is replicated. DNA polymerase I replaces the RNA
primers with DNA nucleotides and DNA ligase is used to ensure bonding between the fragments
and the replace nucleotides. Once both the leading and lagging strands have completed their
replication, two identical copies of the DNA molecule result.
The process of DNA replication allows actively dividing bacterial cells to make sure all
daughter cells have the same genetic instructions as the parent cell allowing them to function in
the same manner. Thus bacterial populations can grow, increasing the number if individuals in a
colony.
TRANSCRIPTION AND TRANSLATION
In order for our bodies to function, we need to supply them with a variety of nutrients we
get from out diet. Our bodies cannot use the food as it is when it enters our digestive system. The
process if chemical digestion uses different proteins and enzymes to break down the food particles
into useable nutrients our cells can absorb. And where are the instructions to manufacture these
and all the different types of proteins we need to stay alive? The instructions to make proteins are
contained in our DNA. DNA contains genes. A gene is a continuous string of nucleotides
containing a region that codes for and RNA molecule. This region begins with a promoter and
ends in a terminator. Genes also contain regulatory sequences that can be found near the promoter
or at a more distant location. For some genes, the encoded RNA is used to synthesize a protein, in
a process called gene expression. For these genes, expression can be divided in to two processes:
transcription and translation.
In eukaryotic cells, transcription occurs in the nucleus, where DNA is used as a template
to make messenger RNA. Then in translation, which occurs in the in the cytoplasm of the cell, the
information contained in the messenger RNA is used to make a polypeptide. During transcription,
the DNA in the gene is used as a template to make a messenger RNA strand with the help of the
enzyme RNA polymerase. This process occurs in three stages: initiation, elongation, and
termination. During INITIATION, the promoter region of the gene functions as a recognition site
for RNA polymerase to bind. This is where the majority of gene expression is controlled, by either
permitting or blocking access to this site by the RNA polymerase. Binding causes the DNA double
helix to unwind and open. Then during ELONGATION, the RNA polymerase slides along the
template DNA strand. As the complementary bases pair up, the RNA polymerase links nucleotides
to the 3’ end of the growing RNA molecule. Once the RNA polymerase reaches the terminator
(TERMINATION) portion of the gene, the messenger transcript is complete and the RNA
polymerase, the DNA strand and the messenger RNA transcript dissociate from each other. The
strand of messenger RNA that is made during transcription includes regions called exons that code
for a protein, and non-coding sections called introns. In order for the messenger RNA to be used
in translation, the non-coding introns need to be removed and modifications such as a 5’ cap and
3’ poly-A tail are added. This process is called intron splicing and is performed by a complex made
up of proteins and RNA called spliceosome. This complex removes the intron segments and joins
the adjacent exons to produce a mature messenger RNA strand that can leave the nucleus through
a nuclear pore and enter the cytoplasm to being translation.
How is the information in the mature messenger RNA strand translated into a protein? The
nitrogenous bases are grouped into three letter codes called codons. The genetic code includes 64
codons. Most codon codes for specific amino acids. There are four special codons: one that codes
for “start” and three that code for “stop”. Translation begins with the messenger RNA strand
binding to the small ribosomal subunit upstream to start the codon. Each amino acid is brought to
the ribosome by a specific transfer RNA molecule. The type of amino acid is determined by the
anticodon sequence of the transfer RNA. Complementary base pairing occurs between the codon
of the messenger RNA and the anticodon of the transfer RNA. After the initiator transfer RNA
molecule binds to the start codon, the large ribosomal subunit binds to form the translation complex
and initiation is complete. In the large ribosomal subunit, there are three distinct regions, called
the E, P, and A sites. During elongation, individual amino acids are brought to the mRNA strand
by a transfer RNA molecule through complementary base pairing of the codons and anticodons.
Each anticodon of a transfer RNA molecule corresponds to a particular amino acid. A charged
transfer RNA molecule binds to the A site and a peptide bond forms between its amino acid and
the once attached to the transfer RNA molecule at the P site. The complex slides down one codon
to the right where the now uncharged transfer RNA exits from the E site and the A site is open to
accept the next transfer RNA molecule. Elongation will continue until a stop codon is reached. A
release factor binds to the A site at a stop codon and the polypeptide is released from the transfer
RNA in the P site. The entire complex dissociated and can reassemble to begin the process again
at initiation. The purpose of translation is to produce polypeptide quickly and accurately. After
dissociation, the polypeptide may need to be modified before it is ready to function. Modifications
take place in different organelles for different proteins. In order for a digestive enzyme to be
secreted into the stomach on intestines, the polypeptide is translated into the endoplasmic
reticulum, modified as is passes through the Golgi, then secreted using a vesicle through the plasma
membrane of the cell into the lumen of the digestive tract.
Proteins are needed for most physiological functions of the body to occur properly, such
as breaking down food particles in digestion, and the process of transcription and translation make
the production of proteins possible.