The Art of Protein Synthesis

This amazing artwork shows a process that takes place in the cells of all living things: the production of
proteins. This process is called protein synthesis, and it actually consists of two processes —
transcription and translation. In eukaryotic cells, transcription takes place in the nucleus. During
transcription, DNA is used as a template to make a molecule of messenger RNA (mRNA). The molecule
of mRNA then leaves the nucleus and goes to a ribosome in the cytoplasm, where translation occurs.
During translation, the genetic code in mRNA is read and used to make a protein. These two processes
are summed up by the central dogma of molecular biology: DNA → RNA → Protein.

Transcription
Transcription is the first part of the central dogma of molecular biology: DNA → RNA. It is the transfer of
genetic instructions in DNA to mRNA. During transcription, a strand of mRNA is made to complement a
strand of DNA. You can see how this happens in the diagram below.

Overview of Transcription. Transcription uses the sequence of bases in a strand of DNA to make a complementary strand of
mRNA. Triplets are groups of three successive nucleotide bases in DNA. Codons are complementary groups of bases in mRNA.

Steps of Transcription
Transcription takes place in three steps: initiation, elongation, and termination. The steps are illustrated
in the figure below.

Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase binds to a region
of a gene called the promoter. This signals the DNA to unwind so the enzyme can “read” the bases in
one of the DNA strands. The enzyme is ready to make a strand of mRNA with a complementary
sequence of bases.
Elongation is the addition of nucleotides to the mRNA strand.
Termination is the ending of transcription. The mRNA strand is complete, and it detaches from DNA.

Steps of Transcription. Transcription occurs in three steps: initiation, elongation, and termination.

Processing mRNA
In eukaryotes, the new mRNA is not yet ready for translation. At this stage, it is called pre-mRNA, and it
must go through more processing before it leaves the nucleus as mature mRNA. The processing may
include splicing, editing, and polyadenylation. These processes modify the mRNA in various ways. Such
modifications allow a single gene to be used to make more than one protein.

Splicing removes introns from mRNA, as shown in the diagram below. Introns are regions that do not
code for the protein. The remaining mRNA consists only of regions called exons that do code for the
protein. The ribonucleoproteins in the diagram are small proteins in the nucleus that contain RNA and
are needed for the splicing process.
Editing changes some of the nucleotides in mRNA. For example, a human protein called APOB, which
helps transport lipids in the blood, has two different forms because of editing. One form is smaller than
the other because editing adds an earlier stop signal in mRNA.
Polyadenylation adds a “tail” to the mRNA. The tail consists of a string of As (adenine bases). It signals
the end of mRNA. It is also involved in exporting mRNA from the nucleus, and it protects mRNA from
enzymes that might break it down.

Splicing. Splicing removes introns from mRNA.

Translation
Translation is the second part of the central dogma of molecular biology: RNA → Protein. It is the
process in which the genetic code in mRNA is read to make a protein. Translation is illustrated in the
diagram below. After mRNA leaves the nucleus, it moves to a ribosome, which consists of rRNA and
proteins. The ribosome reads the sequence of codons in mRNA, and molecules of tRNA bring amino
acids to the ribosome in the correct sequence.

To understand the role of tRNA, you need to know more about its structure. Each tRNA molecule has an
anticodon for the amino acid it carries. An anticodon is complementary to the codon for an amino acid.
For example, the amino acid lysine has the codon AAG, so the anticodon is UUC. Therefore, lysine would
be carried by a tRNA molecule with the anticodon UUC. Wherever the codon AAG appears in mRNA, a
UUC anticodon of tRNA temporarily binds. While bound to mRNA, tRNA gives up its amino acid. With the
help of rRNA, bonds form between the amino acids as they are brought one by one to the ribosome,
creating a polypeptide chain. The chain of amino acids keeps growing until a stop codon is reached.
Translation. Translation of the codons in mRNA to a chain of amino acids occurs at a ribosome. Find the
different types of RNA in the diagram. What are their roles in translation?

What Happens Next?

After a polypeptide chain is synthesized, it may undergo additional processes. For example, it may
assume a folded shape due to interactions between its amino acids. It may also bind with other
polypeptides or with different types of molecules, such as lipids or carbohydrates. Many proteins travel
to the Golgi apparatus within the cytoplasm to be modified for the specific job they will do.

Summary
- Protein synthesis is the process in which cells make proteins. It occurs in two stages:
transcription and translation.
- Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It includes
three steps: initiation, elongation, and termination. After the mRNA is processed, it carries the
instructions to a ribosome in the cytoplasm.
- Translation occurs at the ribosome, which consists of rRNA and proteins. In translation, the
instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the
ribosome. Then, rRNA helps bonds form between the amino acids, producing a polypeptide
chain.
- After a polypeptide chain is synthesized, it may undergo additional processing to form the
finished protein.
 After Watson and Crick came up with their hypothesis the scientific world was now curious to
know how it could be replicated.

They put forth a hypothesis that the DNA replicates in a semiconservative manner. That is, both
strands separate and each serves as a template for the synthesis of new strands. 

Template in literal terms means a pattern used as a sample to make something.

However, the scientific world was not ready to accept this fact easily.

So there were three theories put forth which hinted at the replication process of the DNA double
helix.

One was called conservative model, the other word was the Dispersive model. And the last was
the semiconservative model.

Theories of DNA replication

 Conservative model
 Dispersive model
 Semiconservative model

Let’s first understand what each method had to say. 

The first model in the list is the conservative model.

1. Conservative model
 This model suggested that two DNA strands separate and serve as templates for
replication. But soon after replication, the strands joined back to form the original
parent DNA, while the new synthesised strands joined to form a completely new
DNA. Thus, we get a newly synthesised DNA molecule. And we also get the
original parent DNA molecule back, which is conserved. Hence the name
conservative replication. 

Now comes the next one, this was called Dispersive model of replication. As the name
suggests, Dispersive means to disperse or scatter.

2. Dispersive model
 Well, according to this model the DNA which is about to replicate breaks into
small fragments. The new strands get synthesised in between. As a result, we
get a hybrid of both new and old strands together. The old parental strands
appear to be dispersed. In the newly synthesised one. Hence, this method is
named as Dispersive. 

Now comes the last model, It was called the semiconservative model of replication. 
3. Semiconservative model
  The model suggested that two strands of DNA unwind and serve as templates for
neewer strands. As a result, the replicated DNA is contained one old and one
new strands. Hence the name semiconservative. Nevertheless, this model was
not accepted initially when put forth by Watson and Crick. 

However, one of the most amazing experiments in biology named the Meselson and Stahl
experiment helped crack this mystery. 

MeselsonStahl Experiment

Two geneticists Matthew Meselson and Franklin Stahl  carried out an experiment around
1958. In the DNA of the bacterium Escherichia Coli analysed each for the presence of DNA.
The result helped them understand that the replication of DNA in E.coli is indeed
semiconservative. This is how DNA replication takes place in almost all organisms. 

Now, let me introduce you to one more interesting term. It’s called the Central Dogma. Well it’s
an important term, and an equally interesting concept in biology. 

Central Dogma

The Central Dogma in Molecular Biology is used to explain the flow of genetic
information.

 And what does that mean? We all know that DNA governs life. But any idea how this
mechanism works? Let’s understand this with the help of the Central dogma. 

In a cell the DNA from the nucleus replicates to make a copy of itself. 

This is what we’re aware of and do we know what the functional segment of DNA is?

It’s a gene. It’s the segment of DNA that codes for a particular character,
 the part of DNA which acts as a Gene gets copied in the form of a single strand. 

This is called mRNA(messenger RNA) is a single stranded copy of DNA. It comes out
of the nucleus in the cytoplasm and then, the enzyme machinery reads the code hidden in the
mRNA and synthesises proteins accordingly. 

This complete process of mRNA synthesis from the DNA followed by the synthesis of proteins
from the mRNA is called as Central dogma. 

In other words this simplest process by which proteins are synthesised from the code of the
DNA molecule is the Central Dogma of life. This is how it’s usually summarised. 

Did you know that these two steps have a scientific name?

The process in which the mRNA is synthesised from the DNA strand is called transcription. And
the process in which proteins are synthesised from the code of mRNA is called translation. 
DNA
 Central Dogma of Life

DNA makes copies of itself by the process of replication. Post replication in every cell
the code of the DNA is cracked and transcribed into a messenger RNA. This mRNA is then read
and the code is translated into proteins. This interesting concept is nothing but the central
dogma. 

We know that the replication process is semiconservative in nature. So now our focus will be on
the two processes, namely transcription and translation. Let’s begin with the transcription first.
As we can see here,

Transcription - the process in which mRNA is synthesized based on the parent DNA template,
is called transcription.

The part or segment of a particular protein is called gene. 

So how are proteins made from the sequence of base pairs in the gene? Let’s go in the reverse
direction now. 

Proteins are a specific sequence of amino acids. 

So the various amino acids come together in a specific series to form a chain that makes up the
proteins. Now to get the amino acids in a series we need a set of instructions. These are
present in the form of mRNA where does the mRNA come from? It is synthesized in a special
template. Can you guess what this template is? The template is a gene. So a segment of the
DNA that encodes for proteins is copied first. The copy is in the form of mRNA. 
This process of making mRNA is called transcription. 

Why is this process is needed?

If there is no transcription then how will mRNA be synthesized. And if that’s not done,
then how will the proteins be made? Hence, transcription is vital. But it’s not as easy as it
seems. There are several enzymes and sub steps involved in the process. We are
referring to the steps like opening of the DNA double helix at a specific point.
Assembling the set of enzymes gathering of nucleotides and so on. After all these steps,
an mRNA is formed. The mRNA is like an exact copy of the DNA sequence that coats
 the proteins. The only difference between the two, is that mRNA is single stranded and
the base thymine is replaced by uracil. Now that the mRNA is ready. It’s all set to enter
the cytoplasm.

 The is where the next step begins. It’s the translation process. Let’s have a look at this
interesting process in the upcoming part.

EXAMPLE: Imagine you’re appearing for an exam, but the paper presented to you is in a
language that you don’t understand. You are prepared for the exam but interpretation of the
question is a problem. WHAT CAN BE DONE? SOME HELP FROM A TRANSLATOR WOULD
WORK WONDERS RIGHT? So translation is the simplest way to solve this problem. Clearly a
wise move would be to decode the unrecognisable language and then attempt the exam. 

Now imagine this cell to be in a similar situation. Let’s assume that this cell encounters a set of
instructions for performing a task. But the instructions are written in a coded language. So all it
needs to d is to translate this language and then perform the task. 

Translation means converting something into a simpler understandable form. 

The code hidden in the mRNA molecule is being translated. The process of transcription helps
in copying the code written on the DNA. that means it forms mRNA. Now the mRNA comes out
of the nucleus through the nuclear pore and enters the cytoplasm. Here the process of
translation begins. 

To begin with let’s find out the directionality of this mRNA molecule. 

This is the 5 prime end of the mRNA and this is the 3 prime end. 

And how do we know this? Are we randomly stating this? 

No it’s not random. Wee can recognize these ends with the help of specific markers. The three
prime end has a continuous series of the “A” nucleotides. This region is called the poly A tail.
The 5 prime end on the other hand has a cep of methyl group. Thus, this end is said to be
methylated. 

But why is the directionality needed?

Well, it’s extremely important. The assembly that carries out transcription binds to the mRNA
near the 5 prime end. 

So how does the assembly know that this is the prime end? 
The easiest way to recognize the 5 prime end is by the presence of this methyl cap. This is how
the assembly understands to bind near the 5 prime end and not to the poly A tail. 

Now what exactly i this assembly that we’re referring to?

Well, that’s the ribosome unit. Two unit of ribosomes, one small and one large, form an
assembly that helps in the process. 

Ribosomes are basically a complex assembly which acts like a molecular machine for protein
synthesis. 

Remember the small dots attached to the surface of the rough endoplasmic reticulum? Wee
find them in the diagram of a typical cell. These are nothing but ribosomes. 

So the ribosomes are usually made up of two subunits; a smaller and a larger one. 

The smaller subunit binds to the mRNA at the initiation site. Once this is done the larger subunit
binds and completes the assembly. Now the other type of RNA called tRNA steps in to get the
remaining work done. At the end a chain of amino acids is formed and released from the
ribosomal unit. 

So doen’t this chain of amino acids look familiar? 

It’s our protein.The chain is further modified to achieve a proper configuration so that the
protein becomes functional. 

This is how the translation process works. 

The code of mRNA is translated and the protein chain is synthesized out of it. The process of
transcription and translation together are called as gene expression.

The code of a gene is transcribed first and then translated into the form of proteins. 

There is an extremely important thing to note here.

 Whatever we’ve talked so far is all about the processes in eukaryotes. Such high level of
organization is found only in eukaryotes.

But we know what eukaryotes are right? 

Eukaryotic cell  - A cell with a well defined nucleus and a highly organised system.
Prokaryotic cell - cells which lack or proper membrane bound nucleus and organization. They
do not undergo such complex and sophisticated process. So their replication process in
prokaryotes is slightly different.

CODON ANTICODON