T2M3: Translation
Requirements for translation:
The process of translation requires many cellular components that
include initiation, elongation, & release factor proteins, transfer RNA,
& the correct matching of transfer RNA & amino acids, which is
facilitated by aminoacyl tRNA synthetase enzymes along with
ribosomal RNA & ribosomal proteins which make up the assembled
ribosome which makes up the assembled protein.
tRNA molecules are able to transfer amino acids from a pool of
cytoplasmically situated amino acids to a growing polypeptide str& in
a ribosome. Since each type of tRNA is not identical, it can translate
a specific mRNA codon into a specific amino acid. The structure of
tRNA allows for specificity in translation.
Structure of tRNA:
Each tRNA molecule is made of a single RNA str&
ranging between 70-90 nucleotides in length.
There is a large degree of complementarity along
many stretches of a tRNA molecule. & this often
results in many stretches of hydrogen bonding
between complementary nucleotide bases. This
allows for the formation of four double-helical
segments & three characteristic loops. This 2d
structure is represented as a "cloverleaf"
The tRNA can also fold upon itself into a roughly
L-shaped 3d structure.
An anticodon region of the tRNA molecule is a
specific nucleotide triplet that forms complementary
base pairs with a specific mRNA codon that codes
for a specific amino acid. These anticodons are
conventionally written in the 3’->5’ direction &
align properly with mRNA codons in the 5’->3’ direction.
At the 3’ end of the tRNA molecule, there is a protruding amino
acid attachment site that is made up of a single-str&ed CCA
nucleotide sequence. The terminal A is the actual point of
attachment for an amino acid tRNA activation.
How does tRNA activation take place?
The activation of tRNA molecules
with specific amino acids is carried
out by a family of enzymes called
aminoacyl tRNA synthetases. Each
aminoacyl tRNA synthetase is
specific to the type of tRNA &
corresponding amino acid that it will bind to.
The active site, of these enzymes, recognizes the anticodon end of the
tRNA & the region of amino acid attachment site. This leads to the
existence of 20 aminoacyl tRNA synthetases, one for each amino acid.
Once bound to the active site, these enzymes can catalyze the covalent
attachment of the tRNA molecule to its amino acid using the energy
from ATP hydrolysis. This leads to a charged tRNA molecule, or an
aminoacyl tRNA being released from the enzyme, which can now
deliver its specific amino acids to a growing polypeptide chain on a
ribosome.
For proper translation to occur, the
tRNA anticodon should correctly pair
with the appropriate mRNA codon.
While matching the correct amino acid
to the tRNA is done by aminoacyl
tRNA synthetase, base pairing between
a codon in mRNA & an anticodon in
tRNA largely contribute to the 1°
sequence of amino acids.
AUG codon in mRNA codes for methionine which signals for protein
translation machinery to begin translating the mRNA at that point.
There are actually only ~45 tRNA molecules meaning that some
tRNA molecules are maybe able to bind to more than one codon, due
to the chemical nature of codon-anticodon pairing interactions.
While the first base (or 5’ end) of the codon will bind with the last
base (or 3’ end of the anticodon), there is greater flexibility for base
pairing between the third nucleotide of a codon & the corresponding
base of a tRNA anticodon. This flexibility is often referred to as
wobble & is what also helps explain the redundancy of the genetic
code.
Translation requires the assembly of ribosomes & associated
molecular components along a transcribed messenger RNA str&.
As an mRNA molecule is shuffled through a ribosome, specific
mRNA codons are translated into amino acids one by one. These
amino acids are attached one by one to a growing polypeptide chain
until translation is terminated.
The process of translation:
1) Initiation:
In eukaryotes, the initiation of translation occurs when a translation
initiation complex forms towards the 5’ cap of the mRNA & then scans
the mRNA until an AUG start codon is encountered.
Since prokaryotes have no 5’ caps, the translation initiation complex
will assemble at one or more ribosome binding sites called ShineDalgarno sequences.
These sequences tend to be located a few bases upstream of the
translation start codon AUG.
The really unique ability for translation to occur along multiple
regions of a polycistronic mRNA sequence, allows prokaryotes to
have specific open reading frames for more than one protein along a
single mRNA str&. Translation of this type of polycistronic mRNA
in prokaryotes can occur because prokaryotes can have functionally
related genes grouped together along the prokaryotic DNA & these
genes are often transcribed as a single unit from one promoter.
The difference between monocistronic (in eukaryotes) & polycistronic
(in prokaryotes) mRNA is that the former generates a specific
protein while the latter generates a number of functionally relevant
proteins.
In both prokaryotes & eukaryotes,
the large & small subunits of the
ribosome will assemble to form
a functional ribosome only when
they are
attached to an mRNA molecule. In fact, initiation of the translation
will require the assembly of various components, that include the two
ribosomal subunits, the mRNA that requires translation, the charged
tRNA methionine, & initiation factors that will help with assembling
the initiation complex.
At the start of translation in eukaryotes, initiation factors will bind
to the 5’ cap of the messenger RNA. This allows for the recruitment
of the small ribosomal subunit. At the same time, other initiation
factors will bind to the transfer RNA that is charged with
methionine.
This partially assembled initiation complex will then move along the
mRNA in a 5’ to 3’ direction until an AUG (start codon) is
encountered.
When this occurs, the large subunit of ribosome is able to bind to
the rest of the initiation complex using energy released from GTP
hydrolysis, the next charged tRNA molecule can then join ribosome.
2) Elongation:
Once the ribosomal translation
complex is completely
assembled, the initiation factors
are released.
All polypeptides are synthesized from the amino end to the carboxyl
end. Methionine is the first amino acid that is found at the amino
end of a polypeptide. However, unlike all other incoming charged
tRNAs, at the start of translation, methionine will be at the P site
(peptidyl site) of the ribosome.
As translation continues, & the ribosome scans the mRNA, each
subsequently charged tRNA enters & binds within the aminoacyl (A
site) of the large ribosomal unit prior to each amino acid being
incorporated into the growing polypeptide chain. This is done as the
sequence of mRNA coding for amino acids is read by the ribosome
in successive, non-overlapping groups of 3 nucleotides.
Each incoming charged tRNA is delivered with a GTP-bound
elongation factor. When correct codon-anticodon pairing has been
made, GTP is hydrolyzed & aminoacyl end of tRNA is released from
the elongation factor.
Following binding of charged
aminoacyl tRNA, there is a
conformational change that is
induced in the ribosomal RNA that
allows for a peptidyl-transferase
reaction to occur. It involves
formation of condensation rxn. as
peptide bond & transfer of growing
polypeptide chain onto tRNA that
is in the A-site.
The ribosome will then continue to translocate along the length of
the mRNA molecule. This is enabled by the binding of GTP-bound
elongation factors that cause the deacylated tRNA to move from the
P-site to the exit (or E-site). The subsequent aminoacyl-tRNA to enter
the A site will then allow for the release of the deacylated tRNA
from the E site.
3) Termination:
Once the ribosome reaches stop codon
on the mRNA sequence, GTP-bound
release factors will bind to A-site &
catalyze the hydrolysis of the bond
between terminal amino acid in the
polypeptide & tRNA in the P-site.
Further GTP hydrolysis will also enable the dissociation of the
translation complex, including the ribosomal subunits & any
remaining bound tRNA.
Overview of Translation:
Eukaryotic translation begins when initiation factors bind to the 5’
cap of the messenger RNA. This recruits the small ribosomal
subunit along with the methionine-charged transfer RNA.
The partially assembled initiation complex then moves along the
mRNA in a 5’ to 3’ direction until the start codon is encountered.
When this occurs, the large subunit of the ribosome is able to bind
to the rest of the initiation complex using the energy released from
GTP hydrolysis & continue to scan the mRNA molecule.
Subsequently charged tRNA molecules can then join the ribosome at
the aminoacyl site & induce a conformational change that allows for
the formation of condensation reactions as peptide bonds, between
each amino acid that is added to the growing polypeptide chain.
With each peptide bond formed, deacylated tRNA move from the Psite to the E site. The subsequent aminoacyl-tRNA to enter the A site
will then allow for the release of deacylated tRNA from the E site.
The process of translation is then terminated once the ribosome
reaches a stop codon on the mRNA sequence, with GTP-bound release
factors now being able to bind to the A-site & catalyzing the
dissociation of the translation complex, including the ribosomal
subunits & any remaining bound tRNA.
Q) What is the max. number of charged tRNAs that can be present
within the ribosome at any given time?
Answer: Two tRNAs. Although ribosomes have three sites for binding
tRNA molecules, ribosomes bind no more than two tRNA molecules at
any given time. The tRNA in the P site holds the peptide chain, then
passes it to the tRNA originally in the A site as a new peptide bond
forms. The first tRNA exits the E site of the ribosome before a new tRNA
enters the A site.
One gene - One enzyme hypothesis: (Beadle - Tatum experiment)
Early work on the filamentous fungus bread mold Neurospora
crassa in the 1940s by George Beadle & Edward Tatum established
the relationship between genes & proteins. This is referred to as the
“one-gene-one-enzyme” hypothesis.
This hypothesis is based on the fact that Neurospora can grow well
on minimal medium (that is growth medium that contains only some
simple sugars, inorganic salts & some essential growth vitamins), & as
a result, Neurospora must have some enzymes produced by a specific
gene that convert these simple substances into the amino acids &
vitamins that are needed for growth.
In particular, its found that bread mold cells grow well on a growth
medium that lacks the amino acid arginine, presumably because
Neurospora is able to synthesize its own arginine.
The synthesis of arginine can occur through a metabolic pathway in
a series of steps. Along this metabolic pathway, the transition
between steps requires specific enzymes that catalyze the formation
of each subsequent intermediate compound between the precursor &
synthesized arginine.
The precursor compound can lead to the synthesis of Ornithine,
Citrulline & finally Arginine through the action of Enzymes 1, 2 & 3
respectively.
One gene - One enzyme hypothesis: (Srb - Horowitz experiment)
Adrian Srb & Norman Horowitz further tested
the one gene-one enzyme hypothesis.
They performed a genetic screen on radiationtreated Neurospora to determine whether there
are specific genes that produced each of the 3
enzymes that are needed for arginine synthesis.
They were aware that treating Neurospora cells
with radiation would lead to potential
mutations in bread mold DNA. Hence they
decided to conduct the genetic screen by raising
colonies of radiation-treated cells on a medium
that was supplemented with nothing else or had
ornithine, citrulline or arginine added to the
growth medium.
When growing the radiation-treated Neurospora on medium that
was supplemented with arginine, Srb & Horowitz observed that
there was continual growth of the Neurospora fungus. This was a
positive control & certainly indicated that with supplemented
arginine, the Neurospora fungus was still able to undergo growth.
However, when the radiation-treated Neurospora cells were placed
on non-supplemented medium, there was no growth. This led Srb &
Horowitz to believe that the radiation must have produced mutations
in the genes that encode the necessary enzymes for the production of
arginine by the Neurospora cells.
When examining the
Neurospora cells that
were placed in
Ornithine-only or
citrulline-only media, it
was found that there
was inhibition in growth.
Results from this study indicated that Srb & Horowitz had identified
3 mutants: arg1, arg 2 & arg3, representing mutant Neurospora that
had mutations for enzyme 1, 2 & 3 respectively that are needed for
the production of arginine.
This experiment convinced most researchers of the accuracy of the
one gene, one enzyme hypothesis, & future research after Srb &
Horowitz further identified that genes do not only code for enzymes
in an organism, but rather that genes dictate the structures of all
proteins, each produced by a specific gene product. As a result, this
hypothesis is now more often referred to as the one gene-one
polypeptide hypothesis.
Exception to one gene-one polypeptide hypothesis: (Human Proteome)
The human proteome represents the full number of proteins that
are expressed by all the hereditary information in our DNA (also
referred to as our genome). When the human genome was sequenced,
20-25,000 protein-encoding genes were identified.
This astonished many researchers & provided evidence that more
than one protein can possibly be produced from a single gene.
While alternative splicing of genes & other mechanisms contribute to
the diverse number of mRNA transcripts, there is added complexity
that exists from genome to proteome. Specifically, post-translational
modifications of proteins that are translated from the same DNA
allow for the production of diverse proteins that will have very
specific roles.