Cantos, Aldwin Robert L.

Sec.

1. Define Replication, Transcription, and Translation

Replication

DNA replication is the process by which a double-stranded DNA molecule is

copied to produce two identical DNA molecules. Replication is an essential process
because, whenever a cell divides, the two new daughter cells must contain the same
genetic information, or DNA, as the parent cell.

The replication process relies on the fact that each strand of DNA can serve as a
template for duplication. DNA replication initiates at specific points, called origins, where
the DNA double helix is unwound. A short segment of RNA, called a primer, is then
synthesized and acts as a starting point for new DNA synthesis. An enzyme called DNA
polymerase next begins replicating the DNA by matching bases to the original strand.
Once synthesis is complete, the RNA primers are replaced with DNA, and any gaps
between newly synthesized DNA segments are sealed together with enzymes.

DNA replication is a crucial process; therefore, to ensure that mistakes, or

mutations, are not introduced, the cell proofreads the newly synthesized DNA. Once the
DNA in a cell is replicated, the cell can divide into two cells, each of which has an
identical copy of the original DNA.

Transcription

Transcription is the process by which the information in a strand of DNA is copied

into a new molecule of messenger RNA (mRNA). DNA safely and stably stores genetic
material in the nuclei of cells as a reference, or template. Meanwhile, mRNA is
comparable to a copy from a reference book because it carries the same information as
DNA but is not used for long-term storage and can freely exit the nucleus. Although the
mRNA contains the same information, it is not an identical copy of the DNA segment,
because its sequence is complementary to the DNA template.

Transcription is carried out by an enzyme called RNA polymerase and a number

of accessory proteins called transcription factors. Transcription factors can bind to
specific DNA sequences called enhancer and promoter sequences in order to recruit
RNA polymerase to an appropriate transcription site. Together, the transcription factors
and RNA polymerase form a complex called the transcription initiation complex. This
complex initiates transcription, and the RNA polymerase begins mRNA synthesis by
matching complementary bases to the original DNA strand. The mRNA molecule is
elongated and, once the strand is completely synthesized, transcription is terminated.
The newly formed mRNA copies of the gene then serve as blueprints for protein
synthesis during the process of translation
Translation

Translation is the process by which a protein is synthesized from the information

contained in a molecule of messenger RNA (mRNA). During translation, an mRNA
sequence is read using the genetic code, which is a set of rules that defines how an
mRNA sequence is to be translated into the 20-letter code of amino acids, which are the
building blocks of proteins. The genetic code is a set of three-letter combinations of
nucleotides called codons, each of which corresponds with a specific amino acid or stop
signal. Translation occurs in a structure called the ribosome, which is a factory for the
synthesis of proteins. The ribosome has a small and a large subunit and is a complex
molecule composed of several ribosomal RNA molecules and a number of proteins.
Translation of an mRNA molecule by the ribosome occurs in three stages: initiation,
elongation, and termination. During initiation, the small ribosomal subunit binds to the
start of the mRNA sequence. Then a transfer RNA (tRNA) molecule carrying the amino
acid methionine binds to what is called the start codon of the mRNA sequence. The
start codon in all mRNA molecules has the sequence AUG and codes for methionine.
Next, the large ribosomal subunit binds to form the complete initiation complex. During
the elongation stage, the ribosome continues to translate each codon in turn. Each
corresponding amino acid is added to the growing chain and linked via a bond called a
peptide bond. Elongation continues until all of the codons are read. Lastly, termination
occurs when the ribosome reaches a stop codon (UAA, UAG, and UGA). Since there
are no tRNA molecules that can recognize these codons, the ribosome recognizes that
translation is complete. The new protein is then released, and the translation complex
comes apart.

2. Enumerate the steps of replication, transcription, and translation

Transcription involves four steps:

1. Initiation. The DNA molecule unwinds and separates to form a small open
complex. RNA polymerase binds to the promoter of the template strand.

2. Elongation. RNA polymerase moves along the template strand, synthesising an

mRNA molecule. In prokaryotes RNA polymerase is a holoenzyme consisting of
a number of subunits, including a sigma factor (transcription factor) that
recognises the promoter. In eukaryotes there are three RNA polymerases: I, II
and III. The process includes a proofreading mechanism.

3. Termination. In prokaryotes there are two ways in which transcription is

terminated. In Rho-dependent termination, a protein factor called "Rho" is
responsible for disrupting the complex involving the template strand, RNA
polymerase and RNA molecule. In Rho-independent termination, a loop forms at
the end of the RNA molecule, causing it to detach itself. Termination in
 eukaryotes is more complicated, involving the addition of additional adenine
nucleotides at the 3' of the RNA transcript (a process referred to as
polyadenylation).

4. Processing. After transcription the RNA molecule is processed in a number of

ways: introns are removed and the exons are spliced together to form a mature
mRNA molecule consisting of a single protein-coding sequence. RNA synthesis
involves the normal base pairing rules, but the base thymine is replaced with the
base uracil.

Translation involves four steps:

1. Initiation. The small subunit of the ribosome binds at the 5' end of the mRNA
molecule and moves in a 3' direction until it meets a start codon (AUG). It then
forms a complex with the large unit of the ribosome complex and an initiation
tRNA molecule.

2. Elongation. Subsequent codons on the mRNA molecule determine which tRNA

molecule linked to an amino acid binds to the mRNA. An enzyme peptidyl
transferase links the amino acids together using peptide bonds. The process
continues, producing a chain of amino acids as the ribosome moves along the
mRNA molecule.

3. Termination. Translation in terminated when the ribosomal complex reached

one or more stop codons (UAA, UAG, UGA). The ribosomal complex in
eukaryotes is larger and more complicated than in prokaryotes. In addition, the
processes of transcription and translation are divided in eukaryotes between the
nucleus (transcription) and the cytoplasm (translation), which provides more
opportunities for the regulation of gene expression.

4. Post-translation processing of the protein

Replication involves 4 steps

Step 1: Replication Fork Formation

Before DNA can be replicated, the double stranded molecule must be “unzipped”
into two single strands. DNA has four bases called adenine (A), thymine (T), cytosine
(C) and guanine (G) that form pairs between the two strands. Adenine only pairs with
thymine and cytosine only binds with guanine. In order to unwind DNA, these
interactions between base pairs must be broken. This is performed by an enzyme
known as DNA helicase. DNA helicase disrupts the hydrogen bonding between base
pairs to separate the strands into a Y shape known as the replication fork. This area will
be the template for replication to begin.

DNA is directional in both strands, signified by a 5' and 3' end. This notation
signifies which side group is attached the DNA backbone. The 5' end has a phosphate
(P) group attached, while the 3' end has a hydroxyl (OH) group attached. This
directionality is important for replication as it only progresses in the 5' to 3' direction.
However, the replication fork is bi-directional; one strand is oriented in the 3' to 5'
direction (leading strand) while the other is oriented 5' to 3' (lagging strand). The two
sides are therefore replicated with two different processes to accommodate the
directional difference.3. Research on the three-base-sequence and their corresponding
code

Replication Begins

Step 2: Primer Binding

The leading strand is the simplest to replicate. Once the DNA strands have been
separated, a short piece of RNA called a primer binds to the 3' end of the strand. The
primer always binds as the starting point for replication. Primers are generated by the
enzyme DNA primase

Step 3: Elongation

Enzymes known as DNA polymerases are responsible creating the new strand
by a process called elongation. There are five different known types of DNA
polymerases in bacteria and human cells. In bacteria such as E. coli, polymerase III is
the main replication enzyme, while polymerase I, II, IV and V are responsible for error
checking and repair. DNA polymerase III binds to the strand at the site of the primer and
begins adding new base pairs complementary to the strand during replication. In
eukaryotic cells, polymerases alpha, delta, and epsilon are the primary polymerases
involved in DNA replication. Because replication proceeds in the 5' to 3' direction on the
leading strand, the newly formed strand is continuous.

The lagging strand begins replication by binding with multiple primers. Each
primer is only several bases apart. DNA polymerase then adds pieces of DNA, called
Okazaki fragments, to the strand between primers. This process of replication is
discontinuous as the newly created fragments are disjointed.

Step 4: Termination

Once both the continuous and discontinuous strands are formed, an enzyme
called exonuclease removes all RNA primers from the original strands. These primers
are then replaced with appropriate bases. Another exonuclease “proofreads” the newly
formed DNA to check, remove and replace any errors. Another enzyme called DNA
ligase joins Okazaki fragments together forming a single unified strand. The ends of the
linear DNA present a problem as DNA polymerase can only add nucleotides in the 5′ to
3′ direction. The ends of the parent strands consist of repeated DNA sequences called
telomeres. Telomeres act as protective caps at the end of chromosomes to prevent
nearby chromosomes from fusing. A special type of DNA polymerase enzyme called
telomerase catalyzes the synthesis of telomere sequences at the ends of the DNA.
Once completed, the parent strand and its complementary DNA strand coils into the
familiar double helix shape. In the end, replication produces two DNA molecules, each
with one strand from the parent molecule and one new strand.

3. Research on the three-base-sequence and their corresponding code

References:
 https://www.thoughtco.com/dna-replication-3981005
 https://www2.le.ac.uk/projects/vgec/highereducation/topics/geneexpression-
regulation
 https://www.khanacademy.org/science/biology/gene-expression-central-
dogma/transcription-of-dna-into-rna/a/stages-of-transcription
 http://www.macmillanhighered.com/BrainHoney/Resource/6716/digital_first_cont
ent/trunk/test/hillis2e/hillis2e_ch10_4.html