Department of Physics

Assignment on Cracking the Central Dogma: From

Functional Proteins to DNA Transcription and Translation

Course Code: PHY441 (Biophysics-I)

Submitted to:
Dr Mohammad Delawar Hossain
Professor, Department of Physics
Shahjalal University of Science and Technology

Submitted by:
Mahabubur Rahman
2019132082
4th year, 1st semester
2019-20
Date of Submission: 22/02/24
Introduction: The Central Dogma of biology

The complex interactions between different biomolecules are essential to the

functioning of living organisms. The "central dogma" of molecular biology
mostly revolves around the roles of proteins, RNA, and DNA. Established by
Francis Crick in 1958, this fundamental idea delineates the one-way flow of
genetic information from DNA, the genetic blueprint, to RNA, the
intermediary molecule, and finally to proteins, the multifunctional molecular
workhorses of the cell. Deciphering the mechanisms controlling biological
processes, from development and growth to cellular function and illness,
requires an understanding of this fundamental concept.

DNA, RNA, and Proteins

DNA: The inherited blueprint

The genetic instructions necessary for the
growth, operation, and reproduction of an
organism are encoded in deoxyribonucleic
acid, or DNA. It is a double-stranded
molecule made up of nucleotides, each of
which has a nitrogenous base—adenine (A),
thymine (T), cytosine (C), or guanine (G)—
along with a sugar and phosphate group.
Similar to how letters make words in a
language, the arrangement of these bases
encodes genetic information. Figure: DNA double helix

RNA: The Middleman Communicator

As the messenger molecule, ribonucleic acid (RNA) transports genetic
information from DNA to the ribosomes, the site of protein synthesis. RNA
differs slightly from DNA in that it is a single-stranded molecule with uracil
(U) in place of thymine.
There are several types of RNA:
● Messenger RNA (mRNA): Carries the
genetic code from DNA to the ribosomes.
● Transfer RNA (tRNA): Decodes the
genetic code and delivers specific amino
acids to the ribosomes during protein
synthesis.
● Ribosomal RNA (rRNA): Forms the
structural core of ribosomes, essential for
protein synthesis.

Figure - RNA Strands

Figure - Types of RNA

Proteins: The Workhorses of Molecular

The workhorses of the cell, proteins perform a wide range of tasks such as
transport, communication, catalysis, and structural support. They consist of
lengthy sequences of amino acids joined by peptide bonds. Each protein's
distinct structure and function are determined by the order and sequence of
its amino acids.
The Central Dogma: A One-Way Journey of Information

The central dogma outlines the unidirectional flow of genetic information:

● Transcription: Transcription is the process by which mRNA is
synthesized using DNA as a template. The DNA sequence is
translated into a corresponding mRNA molecule by enzymes.
● Translation: The genetic information is transported by mRNA to the
ribosomes, where it is translated into a sequence of proteins. When
mRNA codons are decoded, tRNA molecules transfer the
corresponding amino acids to the ribosome so that proteins can be
assembled.
● Protein Function: Freshly generated proteins perform their intended
roles inside the cell, impacting different physiological functions.

Figure: Schematic diagram of The Central Dogma

Cracking the Blueprint of Life: Steps of the Central Dogma

Transcription: Cracking the Blueprint

The first act in this drama is transcription, which is essential to understanding
the message encoded in DNA and converting it into working proteins. A
particular DNA segment acts as a template for the creation of a
complementary RNA molecule during this process.
The Stage: The nucleus
The nucleus, the cell's control center, houses the blueprint of life – the
double-stranded DNA molecule.

The Players: RNA polymerase and Ribonucleotides

● RNA polymerase: This particular enzyme serves as the conductor,
unraveling the DNA helix to reveal the template, a single strand that
may be copied.
● Ribonucleotides: The actors in the play are these RNA building units,
which each carry one of the four nitrogenous bases (adenine, guanine,
cytosine, and uracil).

Figure - Steps of Transcription: Initiation, Elongation and Termination

The Act: Initiation, Elongation, and Termination
Three separate segments comprise the transcription journey, each focusing
on a specific aspect of the task.

Act I: Initiation
RNA polymerase recognizes specific promoter sequences on the DNA,
marking the start of a gene. Assisted by other proteins, it assembles
and binds to the promoter, initiating the unwinding of the DNA strand.

Act II: Elongation

RNA polymerase starts its reading journey as the DNA unravels. It links
complementary ribonucleotides after painstakingly reading the
exposed template strand base by base to create messenger RNA
(mRNA). This procedure is similar to careful copying, in which every
base in DNA is matched to a particular base in the newly created
mRNA.

Act III: Termination

Certain DNA sequences indicate that a gene has ended. When RNA
polymerase detects these cues, it stops its activity and releases the
freshly created mRNA molecule. A last bow is made by the polymerase
as the DNA helix rewinds.

The Significance: Why Transcription Stages Matter

The process of transcription plays a crucial role in connecting the genetic
code found in DNA with the cytoplasmic machinery responsible for protein
synthesis. With its message now transcribed, the mRNA molecule leaves the
nucleus and makes its way to the ribosomes, where the information it
contains is translated into proteins—the adaptable players that do all of the
vital tasks for the cell. The instructions contained in DNA are not accessible
without this first transcription process, which prevents the cell and organism
from operating.
Translation: From Code to Action
The theory highlights the one-way flow of information from DNA to proteins,
but it's important to recognize that the last stage, translation, is a complex
and multifaceted process.

The Stage: The Ribosome

Ribosomal RNA (rRNA) and proteins make up the ribosome, a
macromolecular apparatus on which the translation process takes place.
Depending on the destination of the protein, ribosomes might be seen
floating freely in the cytoplasm or attached to the endoplasmic reticulum. The
appearance of messenger RNA (mRNA), the traveling emissary bearing the
genetic code that has been transcribed, sets the scene.

The Players: mRNA, tRNA, and Amino Acids

The protagonist, mRNA, acts as the script; its sequence determines the order
of amino acids in the developing protein. The supporting cast, transfer RNA
(tRNA) molecules, are in charge of converting the mRNA codons into the
appropriate amino acids. Every tRNA has an associated amino acid and a
unique anticodon that is complementary to a particular codon on the mRNA.
Consider them as translators, helping to move information between the
language of amino acids and the language of nucleotides.

Figure - Steps of translation: Initiation, Elongation and Termination

The Act: Initiation, Elongation, and Termination
The process of translation unfolds in three clear phases, each highlighting
different challenges and decisions.

Act I: Initiation
The first tRNA containing the initiator amino acid (methionine) is
recruited by the ribosome as it forms around the start codon (AUG) of
the mRNA. Now is the time for the synthesis of proteins.

Act II: Elongation

The ribosome cycles through three key steps:
● Decoding: In order to guarantee proper amino acid incorporation,
the tRNA anticodon attaches itself to the complementary codon
on the mRNA.
● Peptide Bond Formation: The newly delivered amino acid and
the expanding polypeptide chain on the preceding tRNA combine
to form a peptide bond through the action of the ribosome.
● Translocation: While the mRNA and the tRNA carrying the
expanding polypeptide chain travel one codon forward, placing
the subsequent codon for decoding, the tRNA in the decoding
site (A site) moves to the exit site (E site). One amino acid at a
time, the protein is constructed by this exquisite dancing, which
is continued until a stop codon is found.

Act III: Termination

No tRNA with a complimentary anticodon exists when the ribosome
comes into contact with a stop codon (UAA, UAG, or UGA). The freshly
generated protein is released and the ribosome disassembles when
release factors attach to the stop codon. An accomplished translation
performance comes to an end.
The significance: The Bridge between Code and Action
The intervening act in the life script that is translation has great importance.
It converts the genetic code into proteins, which are the backbones of the
cell. Without it, the blueprint is mute and unable to drive reactions, move
molecules, or develop muscles. It's a dynamic stage that is controlled to
generate the appropriate protein at the appropriate moment, enabling cells
to adjust and perform. The core of life is revealed in this complex dance
between code and action, where knowledge is converted into action and
shapes all living things.

Beyond the Script: Post-translational Modifications

The recently created protein might not be prepared for its grand finale.
Numerous proteins go through post-translational changes that adjust their
structure and function, such as phosphorylation, glycosylation, or the
creation of disulfide bonds. These alterations ensure that the wide range of
participants in the cell can carry out their responsibilities flawlessly by adding
another level of intricacy to the protein symphony..

Conclusion

The core dogma of biology is an illuminated guide that reveals the

information flow within living cells, not a strict set of laws. Consider it the
script for the great theater of life, in which the blueprint for existence is held
by DNA, the jealously guarded scriptwriter. The ribosome, the devoted stage
director, will subsequently be able to transform this screenplay into mRNA,
a mobile messenger, and put it into action.