Fatma Kamal Ahmed
H31/131164/2018
Protein synthesis
Proteins are important components in every living cell, eukaryotic and prokaryotic. They
form the basis for most biological processes including the process of protein synthesis itself.
This process starts with transcription where a messenger RNA is formed that undergoes
modification before it is transported to ribosomes (on RER or free) to begin the process of
translation to form a polypeptide that undergoes modification before being integrated in a
protein.
Initiation
In order for transcription to occur, RNA polymerase needs to bind to DNA so that it
synthesizes the mRNA. Thus, for regulation purposes, promoters work to initiate the
synthesis process following careful mechanisms.
These promoters are regions in the DNA sequence located close to the transcription genes.
They contain sequences for proteins that control the rate of transcription of the genetic
information from DNA to mRNA and are known as transcription factors. Promoters also
contain sequences that are able to bind specific transcription factors to regulate
transcription. These are called response elements.
The transcription factors have specific sequences of nucleotides that bind to specific
promoters hence regulating gene expression. These sequences can be activators or
repressors. In eukaryotes, seven different factors are required to allow the binding of RNA
polymerase to the promoter.
There are other regulatory regions that work with promoters to direct gene transcription.
These are enhancers, silencers, and boundary elements or insulators.
Transcription
Transcription is the process where a gene in DNA is copied into mRNA. This is similar to the
process of DNA replication where DNA polymerase binds to DNA causing the enzyme
helicase to unwind the DNA strand. However, in transcription, the transcription factors
allow RNA polymerase to bind to the DNA strand after which the enzyme creates a
transcription bubble to unwind the molecule by breaking the hydrogen bonds between the
complementary nucleobases hence exposing the sequence of a gene that codes for a
specific protein.
Following this, RNA nucleotides in the nucleus move towards the unzipped DNA molecule
and complementary base pair with only one strand in the molecule. Where there is an
adenine nucleobase, an uracil nucleobase will pair and where there’s a thymine nucleobase
an adenine bae will pair with it. The same pairing happens between guanine and cytosine.
Fatma Kamal Ahmed
H31/131164/2018
After complementary base pairing, the nucleobases must be bonded together and this
condensation reaction to form phosphodiester bonds is catalyzed by the enzyme RNA
polymerase previously mentioned after it had bound to the promoter region and the RNA
sugar-phosphate backbone is formed. From that point the enzyme moves along the DNA
strand template to synthesize RNA until it reaches a terminator sequence wherein the
hydrogen bonds of RNA-DNA helix break, freeing the newly synthesized RNA strand.
The termination process involves cleavage of the new transcript followed by templateindependent addition of adenines at its new 3’end in a process called polyadenylation.
Posttranscriptional modification
This is the process in eukaryotic cells where primary transcript RNA is converted into
mature RNA. Here it is the conversion of precursor messenger RNA into mature messenger
RNA (mRNA) that occurs prior to protein translation. The process includes three major
steps: addition of a 5' cap, addition of a 3' poly-adenylation tail, and splicing.
Capping of the pre-mRNA involves the addition of 7-methylguanosine(m7G) to the 5'
end. The cap protects the 5' end of the primary RNA transcript from attack
by ribonucleases that have specificity to the 3'5' phosphodiester bonds.
The pre-mRNA processing at the 3' end of the RNA molecule involves cleavage of its 3' end
and then the addition of about 250 adenine residues to form a poly(A) tail. As the poly(A)
tail is synthesised, it binds multiple copies of poly(A) binding protein, which protects the 3'
end from ribonuclease digestion.
RNA splicing is the process by which introns, regions of RNA that do not code for proteins,
are removed from the pre-mRNA and the remaining exons connected to re-form a single
continuous molecule.
Translation
In translation, messenger RNA (mRNA) is decoded in a ribosome to produce a specific amino
acid chain, or polypeptide. The polypeptide later folds into an active protein and performs
its functions in the cell. The ribosome facilitates decoding by inducing the binding
of complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific
amino acids that are chained together into a polypeptide as the mRNA passes through and
is "read" by the ribosome.
The basic process of translation is the addition of one amino acid at a time to the end of the
polypeptide being formed. This process takes place inside the ribosome. A ribosome is
made up of two subunits, a small 40S subunit and a large 60S subunit. These subunits come
together before translation of mRNA into a protein to provide a location for translation to
be carried out and a polypeptide to be produced.
Fatma Kamal Ahmed
H31/131164/2018
The choice of amino acid type to be added is determined by the genetic code on
the mRNA molecule. Each amino acid added is matched to a three-nucleotide subsequence
of the mRNA. For each such triplet possible, the corresponding amino acid is accepted. The
successive amino acids added to the chain are matched to successive nucleotide triplets in
the mRNA. In this way, the code of nucleotides in the template mRNA chain determines the
sequence of amino acids in the generated polypeptide.
The ribosome molecules translate this code to a specific sequence of amino acids. The
ribosome is a multi-subunit structure containing rRNA and proteins. It is the "factory" where
amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (75-90
nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid
attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary
to the mRNA triplet that codes for their cargo amino acid.
Aminoacyl tRNA synthetases (enzymes) catalyse the bonding between specific tRNAs and
the amino acids that their anticodon sequences call for. The product of this reaction is
an aminoacyl-tRNA.
The correct amino acid is covalently bonded to the correct transfer RNA (tRNA) by amino
acyl transferases. The amino acid is joined by its carboxyl group to the 3' OH of the tRNA by
an ester bond. When the tRNA has an amino acid linked to it, the tRNA is termed "charged".
Initiation involves the small subunit of the ribosome binding to the 5' end of mRNA with the
help of initiation factors (IF).
The process of translation is highly regulated in prokaryotic and eukaryotic organisms.
Regulation of translation can impact the global rate of protein synthesis which is closely
coupled to the metabolic and proliferative state of a cell.
Termination of the polypeptide happens when the A site of the ribosome faces a stop codon
(UAA, UAG, or UGA) on the mRNA. tRNA usually cannot recognize or bind to stop codons.
Instead, the stop codon induces the binding of a release factor protein that prompts the
disassembly of the entire ribosome/mRNA complex and the hydrolysis and the release of
the polypeptide chain from the ribosome.
Posttranslational modification
This is the covalent and generally enzymatic modification of proteins following protein
biosynthesis. PTMs are important components in cell signalling, as for example when
prohormones are converted to hormones.
Post-translational modifications can occur on the amino acid side chains or at the
protein's C- or N- termini. They can extend the chemical repertoire of the 20
standard amino acids by modifying an existing functional group or introducing a new one
such as phosphate. Phosphorylation is a very common mechanism for regulating the activity
of enzymes and is the most common post-translational modification.
Fatma Kamal Ahmed
H31/131164/2018
Many eukaryotic proteins also have carbohydrate molecules attached to them in a process
called glycosylation, which can promote protein folding and improve stability as well as
serving regulatory functions.
Attachment of lipid molecules, known as lipidation, often targets a protein or part of a
protein attached to the cell membrane.
Identification of destination and tagging
Protein tags are peptide sequences genetically grafted onto a recombinant protein. Often
these tags are removable by chemical agents or by enzymatic means, such as proteolysis
or intein splicing. They are attached to proteins for various purposes.
 Affinity tags are appended to proteins so that they can be purified from their crude
biological source using an affinity technique.
 Solubilization tags are used to assist in the proper folding in proteins and keep them
from precipitating.
 Chromatography tags are used to alter chromatographic properties of the protein to
afford different resolution across a particular separation technique.
 Epitope tags are short peptide sequences which are chosen because highaffinity antibodies can be reliably produced in many different species.
 Fluorescence tags are used to give visual readout on a protein.
 Protein tags may allow specific enzymatic modification or chemical modification.
Fate of proteins
The fate of proteins is protein catabolism. Protein catabolism is the process by which
proteins are broken down to their amino acids. This is also called proteolysis. This can be
followed by further amino acid degradation.