Protein Synthesis

November 2019
by Kasra
Introduction 1
Protein synthesis, also known as gene expression is the process in which proteins are produced
from polypeptide chains released after translation. Protein synthesis is significant in sustaining
cell life as it provides the cell with numerous proteins with varying functions. For instance, in
humans, proteins are responsible for building and repairing tissues and muscle, production of
hormone, enzymes, maintaining immune functions and are a source of energy. Protein
synthesis consists of numerous stages which can be summarised in to 3 stages. Transcription
occurs in the nucleus, which results in the production of a complementary copy called mRNA
from ordinary double-stranded DNA which is needed for translation. Simultaneously with
transcription, splicing occurs in order to create a functioning sequence in mRNA from pre-mRNA
produced in transcription. Translation occurs after transcription in the cytoplasm where mRNA
is translated by rRNA and directs tRNA to direct the corresponding amino acid to the mRNA
strand in order to produce the polypeptide chain. (Campbell, 2019) The last stage of protein
synthesis is the folding of the polypeptide chain and attachment of chemical groups based on
the amino acid sequence. Transcription and Translation are broken down in to 3 major phases,
initiation, elongation and termination. (Campbell, 2019) Transcription begins by initiation where
the RNA polymerase binds to the promoter region of a DNA strand, signalling the double helix to
unwind in order for the reading of base pairs to initiate. Elongation is the process in which the
complementary strand is formed and nucleotides are added to mRNA. Further in elongation,
Thymine is replaced by Uracil which is bound to Adenine for energy efficiency. Termination
occurs when the RNA Polymerase encounters the terminator region of the DNA and the pre-
mRNA is complete.(Campbell, 2019) Almost simultaneously or after transcription, splicing
occurs where introns(non-coding section) are cut from exons(coding sections) in the nucleotide
sequence by an enzyme called, Spliceosome. (Campbell, 2019) Translation leads to the
formation of a polypeptide chain in primary structure. The polypeptide is then folded and goes
through primary, secondary and tertiary structures and ultimately leads to the synthesis of a
certain protein in its quaternary structure. (Khan Academy, 2015)

The following flowchart DNA

illustrates the major phases
of polypeptide synthesis
and protein folding in Transcription
Eukaryotes.
pre-mRNA

Splicing

mRNA

Cytoplasm
rRNA tRNA
(ribosomal) (transfer)

Translation

Protein
2
Polypeptide Synthesis
Transcription
Transcription is the first stage in the process of polypeptide synthesis and takes place in the
nucleus of a cell. The purpose of transcription is in order to produce an mRNA strand from a
functional double stranded DNA which is utilised in the second stage of polypeptide synthesis.
The RNA copy carries the information which is used to synthesise a polypeptide. Transcription
can be divided in to three stages, initiation, elongation and termination. Transcription begins
when the main enzyme in transcription, RNA Polymerase binds to the promoter region of a
double stranded DNA. The double stranded DNA is then pulled apart by the polymerase,
providing a complementary replica single strand. Transcription continues in it's second phase,
elongation where the RNA polymerase reads the strand and creates an RNA strand from the
complementary nucleotides. The RNA strand is an identical replica with the exception that
Thymine is replaced by Uracil for energy efficiency. At last, transcription concludes in the
termination stage. Termination occurs when the RNA polymerase come across the terminator
region of the DNA, signalling that the transcription is complete and that the pre-mRNA strand
can be released. (Campbell, 2019)

Splicing
Simultaneously or straight after transcription is complete, the pre-mRNA strand has to go
through splicing in order to be a usable mRNA. Splicing cuts out introns(non-coding segments)
and attaches exons(coding segments) in order to create a usable mRNA strand. Splicing is a
significantly important stage of transcription since if an mRNA consists of both introns and
exons, the sequence will be out of order and unusable.

mRNA, rRNA & tRNA

mRNA(messenger), rRNA(ribosomal) and tRNA(transfer) are the three types of ribonucleic acid
with various functions in the process of polypeptide synthesis. mRNA is the product of
transcription and is used to produce proteins from genes. rRNA along with amino acids form the
ribosome of the cell which carry out translation of the mRNA where the mRNA sequence is
read. tRNA is responsible for the transfer of amino acids to the ribosome where they are
attached to the strand according to the codon sequence.

Translation
Translation is the second stage in polypeptide synthesis and occurs in the cytoplasm of the cell
within the ribosome complex. Translation is responsible for reading the mRNA strand produced
by transcription and attach an amino acid based on the codon sequence. Similar to
transcription, translation also is divided in to initiation, elongation and termination. Translation
begins with initiation where the small ribosomal subunit(40S) attaches to the mRNA strand and
tRNA transports methionine and binds it to the strand with the codon AUG at the start. Initiation
is completed when the large subunit(60S) attaches to the strand. During elongation, each codon
binds with the corresponding amino acid and the chain is held in place by peptide bonds.
Translation is over when the rRNA comes across a terminator codon
(UAA, UGA, UAG). After translation, the newly synthesis polypeptide
strand is then released from the ribosome. A protein is complete when
the polypeptide chain folds and goes through primary, secondary, tertiary
fig. 1 flowchart of amino acid to
and quaternary structures.(fig.1 & 6) protein
Protein Folding 3
Prior to the polypeptide chain being a fully functional protein, the chain has to fold and have
modifications added. The polypeptide chain is the primary structure of a protein which includes
numerous amino acids held in place by peptide bonds. The polypeptide chain begins to fold in
two various structures, the alpha helix and the beta sheet. The beta sheet and alpha helix form
the secondary structure of protein. Once the R-groups between the amino acids begin to
interact, the tertiary structure forms, folding the alpha helix on to the beta sheet. The protein is
complete in it's quaternary structure which consists of multiple polypeptide chains in their tertiary
structure held in place by hydrogen or disulfide bonds. Often, protein folding is assisted by
chaperones which offer the protein an ideal environment to fold in, restricting the possibility of a
random folding occurring.

Model Overview
The A1 Model is a
representation of the
process of
synthesising a
protein from a double
stranded DNA to a
fully functional
protein, also known
as gene expression.
The model illustrates
the processes of
transcription,
splicing, translation,
protein synthesis and
protein folding.

Transcription
The process of transcription is displayed by the model in
four stages. In stage 1, the RNA polymerase(white pipe-
cleaner) attaches to the promoter region(purple pipe-
cleaner) and begins initiation. In stage 2, the polymerase
then pulls the strands apart. In stage 3, the promoter region
begins producing a complementary strand representing
elongation. In stage 4, the polymerase reaches a
terminator region and transcription is finished after the pre-
mRNA is released. (fig. 2)

fig. 2 Transcription
as seen in the
model.
4 Splicing
Splicing in the model is represented by an array of pipe-cleaners and is divided in to two stages.
During stage 1, the pre-mRNA is inclusive of both exons and introns post-transcription. In order
for mRNA to be usable by translation, a functional genetic sequence is required. The green
pipe-cleaners are representative of exons and dark blue pipe-cleaner is representative of an
intron. During stage 2, the spliceosome(enzyme responsible for splicing) attaches to the intron
and the intron is then removed. Further, the exons are reconnected and splicing is over when all
introns are cut out. (fig. 3)

fig. 3 splicing
as seen in
model.

Translation
Translation in the model is divided in to three stages(by white
pipe cleaners) according to regular gene expression, initiation,
elongation and termination. During Stage 1 initiation begins
when the small ribosomal subunit(40s)(pink pipe cleaner)
attaches to the mRNA strand followed by the large ribosomal
subunit(60s)(curved pink pipe cleaner). In stage 2, elongation
starts when the rRNA reads and translates the sequence.
Further, the tRNA metabolite brings in the corresponding fig. 4 Translation as
amino acid and binds with the RNA.(as seen by the T-shaped seen in the model.

white pipe cleaner(tRNA) and black pom pom(amino acid))

Translation is finished during termination and the ribosomal
subunits detach and polypeptide chain is released. (fig. 4)

fig. 5 polypeptide chain as seen

in the model.
Protein Folding
Protein folding in the model begins when the polypeptide chain is
released from the ribosome after translation.(fig. 5) Protein
folding continues when the polypeptide chain starts to fold as
seen in the primary structure. Further, the strand folds in two
ways in the secondary structure based on the amino acid
sequencing during secondary structure forming an alpha helix
and a beta pleated sheet. In tertiary structure, the helix and beta
join together to form a functional protein with R-groups. In
quaternary structure, the protein is fully functional and consists of
multiple polypeptide chains.

fig. 6 different structures of protein

Model Analysis
5
Representation of Material
The model has been produced using two pieces of foam boards adding up to a generic A1 piece
of paper. Pipe cleaners and coloured paper along with craft pom poms have been used to
represent each phase and component involved in the process of gene expression. The table
below illustrates what each material represents.
6
Model Evaluation
The model produced includes all 3 stages of the process of gene expression including
transcription, translation and protein folding. Each phase of the process is done to a somewhat
thorough and detailed extent with annotations throughout. Overall, the model is mostly accurate
as it illustrates all stages to a thorough and identical level with corresponding materials that are
used to represent each component during each stage of gene expression. For instance, during
transcription the dsDNA is constructed, clearly showing each base pair with corresponding
colours and the sugar phosphate backbone.

However, the model does not possess a continuous flow, showing each stage of gene
expression in chronological order. This limits the accuracy and readability of the model as the
viewer will possibly not be able to follow along. In order to limit this issue, each stage has been
annotated with red numbers. However, this issue can be resolved through the rearrangement of
each stage so that the stages are placed in chronological order. The model is also overly linear,
lacking three-dimensional structures which restrict the overall accuracy of the process since
gene expression and protein folding consist of three-dimensional structures. This could be
improved using external 3D structures which link back to the corresponding stages of gene
expression. Further, during the unwinding of dsDNA, the RNA polymerase is only visible in the
detailed process. The addition of the polymerase to the dsDNA can increase the accuracy of the
model.