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SCI 118: CELL AND MOLECULAR BIOLOGY

CHAPTER 9: PROTEIN SYNTHESIS
Learning Objectives:
1. Define Protein Synthesis
2. Describe the process of protein synthesis
3. Differentiate translation and transcription

Protein synthesis is the creation of proteins. In biological systems, it is carried out inside the cell. Protein
synthesis is the creation of proteins by cells that uses DNA, RNA, and various enzymes.

Protein synthesis, as the name implies, is the process by which every cell produces specific proteins in its
ribosome. In this process, polypeptide chains are formed from varying amounts of 20 different amino acids. It is
one of the fundamental biological processes in both prokaryotes and eukaryotes. This is a vital process, as the
proteins formed take part in every major cellular activities, ranging from catalysis to forming various structural
elements of the cell.

In 1958, Francis Crick proposed a theory called central dogma to describe the flow of genetic information from
DNA to RNA to protein. According to this framework, protein is formed from RNA via translation, which in turn,
is formed from DNA through transcription.

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DNA → RNA → Protein
i. DNA → RNA (Transcription)

ii. RNA → Protein (Translation)

Where and When does Protein Synthesis Take Place

In both prokaryotes and eukaryotes, protein synthesis occurs in the ribosome. That’s why the ribosome is called
the ‘protein factory’ of the cell.

However, in eukaryotes, the ribosomes remain scattered in the cytoplasm and are also attached to
the Endoplasmic reticulum (RER). So, generally, it is said that, in eukaryotes, the process occurs in the cytoplasm
and RER.
On the other hand, in prokaryotes, the ribosomes are scattered throughout the cell cytoplasm. So, commonly, it is
said that, in prokaryotes, it takes place in the cytoplasm.

Process: How does it Work

The process of protein synthesis occurs in two steps: transcription and translation. In the first step, DNA is used
as a template to make a messenger RNA molecule (mRNA). The mRNA thus formed, exits the nucleus through
a nuclear pore and travels to the ribosome for the next step, translation. Upon reaching the ribosome, the genetic
code in mRNA is read and used for polypeptide synthesis.

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Below is a flowchart of the overall process:

a. Blueprints for RNA and Proteins

DNA contains the genetic code of the cell, a code that controls the cell’s structure and function. However, the
DNA itself is just the information, a detailed blueprint, not the active agents that carry out the plan. The plan is
carried out by the molecules that are coded for by the DNA. So, the code in the DNA leads to the creation of
worker molecules, and these worker molecules act according to the plan in the DNA and based on signals
received by the cell. The actions of the worker molecules lead to the particular structure and function of the cell.
Thus, the code in the DNA ultimately controls the structure and function of the cell.

Two types of worker molecules are encoded by the DNA:

✓ RNA molecules of several types are involved in the synthesis of proteins.
Some RNA molecules act as information carriers, while others have enzymatic activity and catalyze reactions
during protein synthesis. RNA molecules that act as enzymes are called ribozymes.
✓ Proteins are the main worker molecules of the cell. They perform a wide range of cellular functions including
catalysis (enzymes), structural support (cytoskeleton), signaling (receptors), transport (membrane proteins
and cytoskeleton), and cellular identity (membrane proteins).

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The basis of life in its simplest form consists of four components: DNA, RNA, proteins and lipids. DNA and
RNA are nucleic acids (DNA = Deoxyribonucleic Acid / RNA = Ribonucleic Acid) and are found in the cells
of all living organisms. The tasks of nucleic acids are to store and transmit genetic information.
Proteins belong to the so-called macromolecules. The blueprint for protein molecules is stored in the cell nucleus
in the form of DNA. To produce proteins, the blueprint in the DNA is first copied into another macromolecule,
the RNA. The RNA is exported from the cell nucleus to the sites of protein synthesis, the ribosomes. Ribosomes
read the RNA sequence and produce new protein molecules according to the blueprint.

b. Transcription

Now, let us discuss these two steps of protein synthesis in detail:

1) Transcription: The First Step of Protein Synthesis

Transcription is the first part of the central dogma of

molecular biology: DNA-RNA. In this process, a
single-stranded mRNA molecule is transcribed from a
double-stranded DNA molecule. The mRNA thus
formed is used as a template for the next step,
translation. Transcription is the first step in gene
expression, in which information from a gene is used to
construct a functional product such as a protein. The
goal of transcription is to make a RNA copy of a
gene's DNA sequence. For a protein-coding gene, the RNA copy, or transcript, carries the information needed
to build a polypeptide (protein or protein subunit). Eukaryotic transcripts need to go through some processing
steps before translation into proteins.

Make a Copy, Please: Transcription

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The code in DNA is copied into RNA by a process called transcription. During transcription, the double helix of
DNA is opened, and one strand of DNA is used as a pattern for the construction of an RNA molecule. Several
types of RNA molecules perform different jobs in the cell. The RNA molecules either do a job directly for the
cell, or, as in the case of mRNA, the mRNA molecules serve as a copy of important information. Because protein
synthesis is so important to the life of a cell, it’s usually a big topic in molecular and cellular biology. Biology
professors place lots of emphasis on the flow of information from DNA to mRNA to protein. With all this
emphasis on the central dogma, you can easily forget that other kinds of RNA exist besides mRNA and that
transcription makes all kinds of RNA. So, when you think about transcription, remember that this process can
make several different types of RNA, but that only mRNA goes on to serve as the blueprint for a protein during
the process of translation.

Locating the file

Genes may make up only a small percentage of the total DNA of a cell. In humans, for example, only about 2
percent of DNA contains the codes for protein. Scientists are still figuring out the functions of the other 98 percent,
although much of it seems to be involved in regulating how the information in the DNA is used. When a cell
needs to build a protein, it recognizes the genes for proteins among all that other DNA. Cells recognize genes for
proteins by their promoters, unique sequences of DNA that are located at the beginning of genes.

Marking the end

Just like promoter sequences mark the

beginning of genes, transcription
terminators mark the ends of genes.
Transcription terminators are sequences in
the DNA that trigger RNA polymerases to
release the DNA and stop transcribing. A
transcription terminator may contain a code
that creates a piece of RNA that folds back
on itself, forming a hairpin loop. This lumpy
piece of RNA essentially knocks RNA
polymerase loose from the DNA, ending
transcription of this gene.

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Finishing Touches: RNA Processing in Eukaryotes

After eukaryotic genes for proteins are transcribed, they’re not quite ready to be translated. In fact, the RNA that
is made from protein-encoding genes in eukaryotes is called a pre-mRNA or primary RNA transcript to indicate
that the transcript isn’t yet finished.

One issue that needs to be dealt with before translation is that eukaryotic genes for proteins don’t just contain the
code for the protein. The code for the protein contains short stretches of nucleotides, called introns, that break up
the code (see Figure 18-2). The introns must be removed from the prem RNA before the mRNA is translated. The
portions of the pre-mRNA that do contain the information for the protein are called exons. The exons remain in
the finished mRNA and are expressed in the final protein. To remember the difference between exons and introns,
think “Exons are expressed; introns interrupt.”

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The three steps of transcription are: initiation, elongation, and termination.

i) Initiation
Initiation is the beginning of transcription. The process of
transcription begins when the enzyme RNA polymerase binds to a
region of a gene called the promoter sequence with the assistance
of certain transcription factors. Due to this binding, the double-
stranded DNA starts to unwind at the promoter region, forming a
transcription bubble. Among the two strands of DNA, one that is
used as a template to produce mRNA is called the template,
noncoding, or antisense strand. On the other hand, the other one is
called the coding or sense strand.

ii) Elongation
Elongation is the addition of nucleotides to the mRNA
strand. After the opening of DNA, the attached RNA
polymerase moves along the template strand of the
DNA, creating complementary base pairing of that
strand to form mRNA. As a result of this, an mRNA
transcript containing a copy of the coding strand of
DNA is formed. The only exception is, in the mRNA,
the nitrogenous base thymine gets replaced by uracil.
The sugar-phosphate backbone forms through RNA
polymerase.

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iii) Termination

Termination is the ending of transcription. Once the mRNA strand is complete, the hydrogen bonds between the
RNA-DNA helix break. As a result, the mRNA detaches from the DNA and undergoes further processing.

c. Translation
2) Translation: The Second Step of Protein Synthesis

Translation, the next major step of protein synthesis is the process in which the genetic code in mRNA is read to
make the amino acids, which are linked together in a particular order based on the genetic code, forming protein.

Similar to transcription, translation also occurs in three stages: initiation, elongation, and termination.

Making a Protein: Translation

When a cell needs to build a protein, RNA polymerase reads the code for the protein in the DNA and copies it
into a molecule of mRNA. The mRNA is then shipped out of the nucleus and into the cytoplasm where ribosomes
and tRNAs use the code in the mRNA to build the protein. When the protein is finished, it will be available to do
its job for the cell.

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The code in mRNA is written in the pattern of the four nucleotides — C, G, A, and U — that occur in the strand.
The length of the strand, the proportion of each nucleotide in the strand, and the order of the nucleotides can all
be different from one mRNA molecule to another. For example, the mRNA that contains the code for the protein
insulin would be quite different from the mRNA that contains the code for the protein collagen. Insulin and
collagen are unique in shape and function — insulin is a globular signaling protein and collagen is a fibrous
structural protein, so their primary structure, the sequence of amino acids in the protein, is also unique. The
differences in the code in the mRNA molecules is what determines the differences in the primary structure of the
protein.

Below are the three steps of Translation:

i) Initiation
After the mature mRNA leaves the nucleus, it travels to a ribosome. The 5′ methylated cap of the mRNA,
containing the strat codon binds to the small ribosomal subunit of the ribosome consisting rRNA. Next, a tRNA
containing anticodons complementary to the start codon on the mRNA attaches to the ribosome. These mRNA,
ribosome, and tRNA together form an initiation complex. The ribosome reads the sequence of codons in
mRNA, and tRNA bring amino acids to the ribosome in the proper sequence. It begins when the small subunit
of the ribosome binds to the ribosomal binding site on the mRNA. Then, the aminoacyl tRNA that carries
methionine binds by its anticodon to the start codon. Finally, the large subunit of the ribosome binds to the
small subunit and mRNA. At the end of initiation, the ribosome is complete, and the first tRNA is positioned in
the P site of the ribosome. The second codon in the mRNA is positioned in the A site of the ribosome.

ii) Elongation
Once the initiation complex is formed, the large ribosomal subunit of ribosome binds to this complex, releasing
initiation factors (IFs). The large subunit of the ribosome has three sites for tRNA binding; A site, P site, and E
site. The A (amino acid) site is the region, where the complementary anticodons of aminoacyl-tRNA (tRNA
with amino acid) pairs up with the mRNA codon. This ensures that correct amino acid is added to the growing
polypeptide chain at the P (polypeptide) site. Once this transfer is complete, the tRNA leaves the ribosome at
the E (exit) site and returns to the cytoplasm to bind another amino acid. The whole process gets repeated
continuously and the polypeptide chain gets elongated. The rRNA binds the newly formed amino acids via
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peptide bond, forming the polypeptide chains. It occurs as amino acids are brought together and joined to form a
polypeptide chain.

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Elongation has several steps, which repeat until the polypeptide chain is complete:

a. An aminoacyl tRNA enters the A site of the ribosome. The tRNA that enters the A site has the
complementary anticodon to the codon in the A site. As the two tRNA molecules are side by side in the
P and A sites of the ribosome, their amino acids are next to each other.

b. The ribosome catalyzes bond formation between the two adjacent amino acids. The amino acid carried
by the tRNA in the P site is attached to the amino acid carried by the tRNA in the A site. The growing
protein chain is temporarily held by the tRNA in the A site.

c. The ribosome and mRNA slide relative to each other. You can think of this step, called translocation,
like the movement of fabric through a sewing machine. The tRNA that was in the P site is pushed into
the E site, whereas the tRNA that was in the A site is pushed into the P site. This places a new codon in
the A site and the growing polypeptide chain in the P site. The tRNA in the E site exits the ribosome,
and the A site is available for a new aminoacyl tRNA to enter, and the steps of elongation repeat.

iii) Termination
The 3′ poly A tail of the mRNA holds a stop codon that signals to end the elongation stage. A specialized protein
called release factor gets attached to the tail o mRNA, causing the entire initiation complex along with the
polypeptide chain to break down. As a result, all the components are released.

The ribosome will translate the mRNA molecule until it reaches a termination codon on the mRNA. When this
happens, the growing protein called a polypeptide chain is released from the tRNA molecule and the ribosome
splits back into large and small subunits.

The newly formed polypeptide chain undergoes several modifications before becoming a fully functioning
protein. Proteins have a variety of functions. Some will be used in the cell membrane, while others will remain in
the cytoplasm or be transported out of the cell. Many copies of a protein can be made from one mRNA molecule.
This is because several ribosomes can translate the same mRNA molecule at the same time. These clusters of
ribosomes that translate a single mRNA sequence are called polyribosomes or polysomes.

Termination of translation begins when a stop codon enters the A site of the ribosome. Stop codons aren’t
recognized by aminoacyl tRNAs. Instead, the stop codon is recognized by an enzyme called release factor.
Release factor enters the ribosome and catalyzes the breaking of the bond between the growing polypeptide

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chain and the tRNA that holds it. Release factor releases the polypeptide chain from the ribosome so that it can
go out into the cell and be converted into a finished protein.

What is a Genetic Code?

The genetic code can be defined as the set of certain rules
using which the living cells translate the information encoded
within genetic material (DNA or mRNA sequences).
The ribosomes are responsible to accomplish the process of
translation. They link the amino acids in an mRNA-specified
(messenger RNA) order using tRNA (transfer RNA )
molecules to carry amino acids and to read the mRNA three
nucleotides at a time.

Genetic Code Table

The complete set of relationships among amino
acids and codons is said to be a genetic code which is often
summarized in a table.

It can be seen that many amino acids are shown in the table by more than one codon. For example, there are six
ways to write leucine in mRNA language.

Note: A codon is a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA
molecule.

A key point of the genetic code is its universal nature. This indicates that virtually all species with minor
exceptions use the genetic code for protein synthesis.

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In other words, genetic code is defined as the nucleotide sequence of the base on DNA which is translated into a
sequence of amino acids of the protein to be synthesized.

Properties of Genetic Code

• Triplet code
• Non-ambiguous and Universal
• Degenerate code
• Nonoverlapping code
• Commaless
• Start and Stop Codons
• Polarity
These properties of genetic code are explained below.

Triplet code
A codon or a code word is defined as a group of bases that specify an amino acid. There is strong evidence, which
proves that a sequence of three nucleotides codes for an amino acid in the protein, i.e., the code is a triplet.

The four bases of nucleotide i.e, (A, G, C, and U) are used to produce three-base codons. The 64 codons involve
sense codons (that specify amino acids). Hence, there are 64 codons for 20 amino acids since every codon for one
amino acid means that there exist more than code for the same amino acid.

Commaless code
No room for punctuation in between which indicates that every codon is adjacent to the previous one without any
nucleotides between them.

Nonoverlapping code
The code is read sequentially in a group of three and a nucleotide which becomes a part of triplet never becomes
part of the next triplet.

For example

5’-UCU-3’ codes for Serine

5’-AUG-3’ codes for methionine

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Polarity
Each triplet is read from 5’ → 3’ direction and the beginning base is 5’ followed by the base in the middle then
the last base which is 3’. This implies that the codons have a fixed polarity and if the codon is read in the reverse
direction, the base sequence of the codon would reverse and would specify two different proteins.

Degenerate code
Every amino acid except tryptophan (UGG) and methionine (AUG) is coded by various codons, i.e, a few codons
are synonyms and this aspect is known as the degeneracy of genetic code. For instance, UGA codes for tryptophan
in yeast mitochondria.

Start and Stop Codons

Generally, AUG codon is the initiating or start codon. The polypeptide chain starts either with eukaryotes
(methionine) or prokaryotes (N- formylmethionine).

On the other hand, UAG, UAA and UGA are called as termination codons or stop codons. These are not read by
any tRNA molecules and they never code for any amino acids.

Non-ambiguous and Universal

The genetic code is non-ambiguous which means a specific codon will only code for a particular amino acid.
Also, the same genetic code is seen valid for all the organisms i.e. they are universal.

Exceptions to the Code

The genetic code is universal since similar codons are assigned to identical amino acids along with similar START
and STOP signals in the majority of genes in microorganisms and plants. However, a few exceptions have been
discovered and most of these include assigning one or two of the STOP codons to an amino acid.

Apart from this, both the codons GUG and AUG may code for methionine as a starting codon, although GUG is
meant for valine. This breaks the property of non-ambiguousness. Thus, it can be said that few codes often differs
from the universal code or non-ambiguous code.

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` References:
https://www.sciencefacts.net/protein-synthesis.html
https://www.biologyonline.com/dictionary/protein-synthesis
https://molecool.ch/en/rna-knowledge/detail/the-blueprint-of-life
Molecular & Cell Biology for Dummies by Rene Fester Kratz, PhD
https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/transcription-and-rna-
processing/a/overview-of-transcription

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