Protein biosynthesis

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Protein biosynthesis is the process in
which cells build protein. The term is sometimes used to
refer only to protein translation, but more often it refers
to a multi-step process, beginning with transcription and
ending with translation:
Table of contents
1 Transcription 
2 Translation 
3 Events following biosynthesis 
4 External link
Transcription
In transcription, the double-stranded DNA is copied into
single-stranded mRNA(messenger RNA) by
the enzyme RNA polymerase. In eukaryotes, the RNA is
likely to be modified after transcription by splicing.
Finally, the RNA is inserted into ribosomes. As it is often
used, the term protein synthesis typically excludes
transcription and describes only the subsequent step of
translation (see below).
Translation
Protein synthesis consists of a number of stages
including: preparing tRNAmolecules for use by
the ribosome; attaching the ribosome molecule to
themRNA; and
the initiation, elongation and termination phases of
translation.
Transfer RNA (tRNA) is a small RNA chain (74-93
nucleotides), which is responsible for carrying amino
acids in to the prokaryotic ribosome, which in turn links
them together to form a protein. It has sites for amino-
acid attachment and codon (a particular sequence of 3
bases) recognition. The codon recognition is different for
each tRNA and is determined by the anticodon region,
which contains the complementary bases to the ones
encountered on the mRNA. Each tRNA molecule binds
only one type of amino acid, but because the genetic
code is degenerate, more than one codon exists for each
amino acid.
Amino acids must be attached to the tRNA. This is
achieved by enzymes termedamino acyl tRNA
synthetases. There exists a different synthetase for each
amino acid. This enzyme catalyses the binding of the
amino acid with ATP. PP is released to form an amino
acid-AMP complex. A tRNA molecule is then substituted
for the AMP to form an activated tRNA-amino acid
molecule. The binding of ATP gives energy to the
molecule which is used later on in the energy
intensive elongation phase of translation.
The ribosome used in prokaryote protein synthesis
consists of 50S and 30S subunits, which are made up of
protein and ribosomal RNA (rRNA). A ribosome can
concurrently hold three tRNA molecules in its aminoacyl
(A), peptidyl (P) and exit (E) sites.
Initiation of translation involves the 30S ribosomal
subunit binding to the 'start' codon on the mRNA, which
indicates where the mRNA starts coding for the protein.
This codon is AUG, which in prokaryotes codes for the
modified amino acid N-Formyl Methionine (f-Met). F-Met
has had an amino group replaced by a carboxyl, so it can
not form a peptide bond � this is not wanted as it is at
the end of the protein chain. The ribosome subunit is able
to bind in the correct orientation to the RNA by base
pairing to a series of codons known as the Shine-
Dalgarno sequence, located 8-13 nucleotides before the
start site.
F-Met base pairs to the start codon and sits in the P site
of the ribosome. The 50S subunit then forms a complex
with the 30S and elongation proceeds. A new activated
tRNA enters the A site of the ribosome and base pairs
with the mRNA. The enzyme peptidyl transferase forms a
peptide bond between the adjacent amino acids. As this
happens, the amino acid on the P site leaves its tRNA and
joins the tRNA at the A site. The ribosome them moves in
relation to the mRNA shifting the tRNA at the A site on to
the P whilst releasing the empty tRNA, this process is
known as translocation.
This procedure repeats until the ribosome encounters one
of three possible stop codons, where termination occurs.
This stalls protein growth, and release factors, proteins
which mimic tRNA, enter the A site and release the
protein in to the cytoplasm.
Synthesis of proteins can take place extremely quickly.
This is aided by multiple ribosomes being able to attach
themselves to one mRNA chain, thus allowing multiple
proteins to be constructed at once. An mRNA chain with
multiple ribosomes is called a polysome. Also, as
prokaryotes have no nucleus transcription can occur at
the same time as translation. This is not possible in
eukaryotes as translation occurs in the cytoplasm,
whereas transcription occurs in the nucleus.
Events following biosynthesis
During and after its synthesis, a polypeptide chain begins
to coil and foldspontaneously to form a three-dimensional
molecule with secondary and tertiary structures. Folding
is sometimes assisted by chaperone proteins[?].
Post-translational modification[?] then attaches to the
protein any of a number of biologically-
relevant functional groups, such as acetate or phosphate,
or various lipids or carbohydrates. Enzymes may also
remove one or more amino acids from the leading
(amino) end of the polypeptide chain, leacing a protein
made up by two polypeptide chains connected
by disulfide bridges. In other cases, two or more
polypeptides that are synthesized separately may join to
vecome the subunits of a protien with quaternary
structure.
What is protein synthesis?
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Image Credit:

http://www2.estrellamountain.edu
Proteins are important in building cells. They are chains of amino
acids which are joined together to form different kinds of protein
molecules depending on the various types of amino acids that join
to form the proteins. The production of protein by an individual
cell is called asprotein synthesis.  So the information on the
sequence of amino acids that need to join in a specific order to
form the right protein molecule for each of these proteins is stored
in the gene which is in the DNA of the cell. Protein
synthesis usually takes place in two major steps. The first step is
Transcription which involves the creation of mRNA from the
DNA.The second step involves the polymerization of amino acids
to form polypeptides which is proteins as defined by the mRNA.
This second step is called as Translation.
Content

What is Transcription?

What is Translation?

What is aminoacylation of tRNA?

How is protein synthesized?

What is Transcription?

The process of copying of the genetic information from one strand

of DNA into RNA is termed as transcription. This is the first step
required for protein synthesis. Transcription is also based on
the complementarity of the strand. Also, only one strand of the
DNA is converted into RNA. One transcription unit consists of 3
regions: A promoter, the Structural Gene and a Terminator. The
promoter is located towards the 5’ end and defines the template
and coding strand. The terminator is towards the 3’ end defining
the end of transcription process. TheRNA is transcribed in 5' to
3’ direction by RNA polymerase.

What is Translation?

The process of polymerization of amino acids to form

a polypeptide is called as Translation. It is the second and final
step of protein synthesis. The order into which the amino acids
are arranged is defined by the bases in mRNA (messenger).
Ribosome is the cellular factory responsible for the protein
synthesis. The ribosome consists of structural RNAs and about
80 different proteins. It is in inactive stage and exists as two
subunits, one large and other small. The synthesis
of protein begins when the small subunit encounters an mRNA.
The ribosome also acts as a catalyst for the formation
of peptide bonds.

What is aminoacylation of tRNA?

The amino acids are joined to form proteins by peptide bonds.

The formation of peptide bonds requires a good amount of
energy. Therefore, in the first phase of translation for protein
synthesis, the amino acids are activated in the presence of ATP
and linked to their cognate tRNA (transfer RNA). This process is
called as charging of the tRNA or aminoacylation of tRNA. If
two such charged tRNA are brought close enough, the formation
of peptide bond between them is favored energetically. This
function occurs inside the ribosome, as it contains two sites for
subsequent amino acids to bind to and thus be close enough for
bonding.

How is protein synthesized?

For initiation of the translation process, the ribosome binds to the

mRNA at the start codon recognized by the initiator tRNA. The
ribosome then proceeds to the elongation phase of protein
synthesis. During this stage, the complexes formed by amino
acids are linked to tRNA, sub sequentially to bind to the
appropriate codon in mRNA by forming complimentary base pairs
with the tRNA anticodon. The ribosome moves from codon to
codon along the mRNA. Amino acids are added one by
one, translated into polypeptide sequences dictated by the DNA
and represented by mRNA. At the end, release factor binds to the
stop codon, thus terminating the translation stage and
completing the protein synthesis process. The
complete polypeptide is released from the ribosome.

Protein biosynthesis
From Wikipedia, the free encyclopedia
RNA is transcribed in the nucleus; once completely processed, it
is transported to the cytoplasm andtranslated by
the ribosome (shown in very pale grey behind the tRNA).
Protein biosynthesis is the process whereby
biological cells generate new proteins; it is balanced by the loss of
cellular proteins via degradation or export. Translation, the
assembly of amino acids by ribosomes, is an essential part of the
biosynthetic pathway, along with generation of messenger
RNA (mRNA), aminoacylation of transfer RNA (tRNA), co-
translational transport, and post-translational modification.
Protein biosynthesis is strictly regulated at multiple steps. They
are principally during transcription (phenomena of RNA synthesis
from DNA template) and translation (phenomena of amino acid
assembly from RNA).
The cistron DNA is transcribed into a variety
of RNA intermediates. The last version is used as a template in
synthesis of apolypeptide chain. Protein will often be synthesized
directly from genes by translating mRNA. When a protein must be
available on short notice or in large quantities, a protein
precursor is produced. A proprotein is an inactive protein
containing one or more inhibitory peptides that can be activated
 when the inhibitory sequence is removed
by proteolysis duringposttranslational modification. A preprotein is
a form that contains a signal sequence (an N-terminal signal
peptide) that specifies its insertion into or through membranes,
i.e., targets them for secretion.[1] The signal peptide is cleaved off
in theendoplasmic reticulum.[1] Preproproteins have both
sequences (inhibitory and signal) still present.
In protein synthesis, a succession of tRNA RNA molecules
charged with appropriate amino acids are brought together with
an mRNA molecule and matched up by base-pairing through the
anti-codons of the tRNA with successive codons of the mRNA.
The amino acids are then linked together to extend the growing
protein chain, and the tRNAs, no longer carrying amino acids, are
released. This whole complex of processes is carried out by
the ribosome, formed of two main chains of RNA, called
ribosomal RNA (rRNA), and more than 50 different proteins. The
ribosome latches onto the end of an mRNA molecule and moves
along it, capturing loaded tRNA molecules and joining together
their amino acids to form a new protein chain.[2]
Protein biosynthesis, although very similar, is different
for prokaryotes and eukaryotes.
Contents
[hide]

 1 Transcription
 2 Translation
 3 Events following protein translation
 4 See also
 5 References
 6 External links
Transcription[edit]
Main article: Transcription (genetics)

Diagram showing the process of transcription

In transcription an mRNA chain is generated, with one strand of
the DNA double helix in the genome as a template. This strand is
called the template strand. Transcription can be divided into 3
stages: initiation, elongation, and termination, each regulated by a
large number of proteins such as transcription
factors andcoactivators that ensure that the correct gene is
transcribed.
Transcription occurs in the cell nucleus, where the DNA is held.
The DNA structure of the cell is made up of two helixes made up
of sugar and phosphate held together by hydrogen bonds
between the bases of opposite strands. The sugar and the
phosphate in each strand are joined together by
strongerphosphodiester covalent bonds. The DNA is "unzipped"
(disruption of hydrogen bonds between different single strands)
by the enzyme helicase, leaving the single nucleotide chain open
to be copied. RNA polymerase reads the DNA strand from the 3-
prime (3') end to the 5-prime (5') end, while it synthesizes a single
strand of messenger RNA in the 5'-to-3' direction. The general
RNA structure is very similar to the DNA structure, but in RNA the
nucleotide uracil takes the place that thymine occupies in DNA.
The single strand of mRNA leaves the nucleus through nuclear
pores, and migrates into the cytoplasm.
The first product of transcription differs in prokaryotic cells from
that of eukaryotic cells, as in prokaryotic cells the product is
mRNA, which needs no post-transcriptional modification,
whereas, in eukaryotic cells, the first product is called primary
transcript, that needs post-transcriptional modification (capping
with 7-methyl-guanosine, tailing with a poly A tail) to give hnRNA
(heterophil nuclear RNA). hnRNA then undergoes splicing
of introns (noncoding parts of the gene) via spliceosomes to
produce the final mRNA.
Translation[edit]
Main article: Translation (biology)
Diagram showing the process of translation

Diagram showing the translation of mRNA and the synthesis of

proteins by a ribosome
The synthesis of proteins from RNA is known as translation. In
eukaryotes, translation occurs in thecytoplasm, where
the ribosomes are located. Ribosomes are made of a small and
large subunit that surround the mRNA. In translation, messenger
RNA (mRNA) is decoded to produce a
specific polypeptideaccording to the rules specified by the
trinucleotide genetic code. This uses an mRNA sequence as a
template to guide the synthesis of a chain of amino acids that
form a protein. Translation proceeds in four phases: activation,
initiation, elongation, and termination (all describing the growth of
the amino acid chain, or polypeptide that is the product of
translation).
In activation, the correct amino acid (AA) is joined to the
correct transfer RNA (tRNA). While this is not, in the technical
sense, a step in translation, it is required for translation to
proceed. The AA 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, it is termed "charged". Initiation involves the small
subunit of the ribosome binding to 5' end of mRNA with the help
ofinitiation factors (IF), other proteins that assist the process.
Elongation occurs when the next aminoacyl-tRNA (charged tRNA)
in line binds to the ribosome along with GTP and an elongation
factor. Termination of the polypeptide happens when the A site of
the ribosome faces a stop codon (UAA, UAG, or UGA). When this
happens, no tRNA can recognize it, but releasing factor can
recognize nonsense codons and causes the release of the
polypeptide chain. The capacity of disabling or inhibiting
translation in protein biosynthesis is used by
some antibiotics such
as anisomycin, cycloheximide, chloramphenicol, tetracycline, stre
ptomycin,erythromycin, puromycin, etc.
Events following protein translation[edit]
Main articles: Posttranslational modification and Protein folding
The events following biosynthesis include post-translational
modification and protein folding. During and after synthesis,
polypeptide chains often fold to assume, so called,
native secondary and tertiary structures. This is known as protein
folding.

Protein Synthesis

Edited Notes by Leigh Eisenman, Megan Hjermstad

Transcription

Nucleotides are added to the 3' end of RNA using information in

DNA as instructions. Only one strand of DNA is used to
synthesize RNA in transcription, the other has redundant
information because it is complimentary. In the vast majority of
cases there is no overlap between the two strands. However, it is
possible to have coding regions in both directions. This is rare
and dangerous because a single mutation can knock out two
genes at the same time.

Translation

mRNA contains information needed to synthesize proteins.

Protein synthesis begins at a start signal at the 5' end of the
mRNA and continues along the coding sequence towards 3' end
until it reaches a stop signal. There might be extra information, or
untranslated regions at the ends of the mRNA (called flanking
sequences) that don't code for protein. The extra sequence at the
5' end is called a leader sequence and the extra sequence at the
3' end is called a trailer sequence. In eukaryotes, the ends
contain control elements which contain signals (for example, to
degrade or stabalize) which regulate the amount of translation.
The mRNA might be thousands of nucleotides long.
In eukaryones there are only single coding regions on each RNA
strand, but in prokaryotes more than one coding region can be
present on the same mRNA. This is called polycistronic
mRNA because on a single mRNA there are multiple coding
sequences which will produce different proteins. The different
coding regions will likely be related in function. Separate initiation
and termination signals are needed to translate each coding
region. A cistron is the gene in a prokaryotic organism that codes
for a specific protein.

The main objective of translation is to convert the genetic

information in the mRNA into a functional protein. The terms:
proteins, peptides and polypeptides are used interchangeably and
may be confusing. A protein is made up of one or more
polypeptide chain.

There are many components functioning in

translation. Ribosomes contain about 80 proteins and 3-5
ribosomal RNAs (rRNAs) which interact to form a specific
structure. The ribosomes are the "factory" for protein synthesis.
They are responsibile for initiation at the correct site, accurate
elongation, and termination of protein synthesis. The ribosome
reads information along the mRNA, coordinates bringing the
amino acids together and guides assembly into proteins.

tRNA finds amino acids and carries them to the ribosome. 

tRNAs have the same general Yeast Phenylalanine-tRNA

cloverleaf shape with base- You need a CHIME plugin to
paired arms, but with one view this interactve image
variable side arm and a
different anti-codon sequence. If you have CHIME installed
tRNA has the unique ability to and still cannot see the image
recognize a specific codon (3 above, try going to this tRNA
letter chunk). Different tRNAs
exist for each codon. The tRNA tutorial.
has a site for the attachment of an amino acid. At the bottom of
the tRNA there is an anti-codon that can base pair with a codon
on the mRNA. The tRNA aligns with the codon and brings the
appropriate amino acid to the translation machinery. The amino
acid it carries can be used to add to a growing polypeptide chain.
For example: the codon used to add alanine can only base pair
with the alanine tRNA. Otherwise the wrong amino acid would be
incorporated, such as lysine. 1/100-1,000 times a mistake is
made. The genetic information in the anti-codon gets priority, so
the if the tRNA carries the wrong amino acid, that incorrect amino
acid will be added to the growing polypeptide chain because the
tRNA is recognized during transcription only by its anti-codon, not
the amino acid it carries. Certain (perscription) drugs change the
rate of error and make a faulty protein (purposely).

mRNA is the source of coding information for protein synthesis

and contains start and stop signals for translation. Initiation
factors help the ribosome, initiator tRNA, and other components
assemble at the correct location on the mRNA and ensure that
protein synthesis starts in the correct reading frame. Elongation
factors are responsible for moving the ribosome along the mRNA
and for maintaining the correct reading frame. In addition, they
facilitate the removal of "used" tRNAs and bringing in of "new"
tRNAs. Termination factors recognize the stop codons and
release proteins and ribosomes. The energy source for these
processes is ATPor GTPwhich are synthesized in
the mitochondria.

The correct reading frame is needed for translation to produce the

correct protein. The cell has a mechanism for reading a sequence
of nucleotides in groups of 3 (called codons). Mutations in
elongation factors may cause ribosome to shift incorrectly (more
or fewer than three nucleotides). This leads to the synthesis of
wrong or useless proteins. For example compare to a sequence
of letters in the english alphabet:
sorexthebigreddogranandsatfortheboy

This sequence can be read as:

s ore xth ebi gre ddo gra nan dsa tfo rth ebo y
so rex the big red dog ran and sat for the boy
sor ext heb igr edd ogr ana nds atf ort heb oy

Only one of these is in the correct reading frame and therefore

makes sense. The other two are nonsense. The same situation
holds for reading a mRNA in the cell.

99.9% of initiation starts at an AUG codon. A special initiator

tRNAmet carrying the amino acid methionine interacts with a
ribosome that is in a special state at an AUG codon (no tRNA is
previously bound to ribosome). A different tRNAmet is responsible
for interacting with the ribosome during elongation.

Figure 3.7; p68 illustrates translation. There are two tRNA binding
sites on ribosomes. The process occurs on ribosomes. tRNA is
"charged" with an amino acid it is supposed to carry by an
enzyme that recognizes both the amino acid and the correct
tRNA. This enzyme recognizes tRNA by length of the variable
arm in addition to the tRNA sequence. The charged tRNA is
brought to the ribosome with its amino acid attached and aligns
with the mRNA by matching its anticodon with the next codon on
the mRNA.

The ribosome joins adjacent amino acids together to assemble

the protein chain. The amino acid on the newly arrived tRNA is
joined to the growing end of the polypeptide chain through
apeptide bond. The enzyme that does the joining is
called peptidyl synthetase and is part of the ribosome. After
donating its amino acid the tRNA is released from the ribosome.
The ribosome then translocates (moves) to the next codon. A
new tRNA brings in the new amino acid and the process is
continued. When a stop codon is reached, the process ceases
andtermination factors cause the release of the completed
polypeptide chain and the other protein synthesizing components.

Figure 3.8; p69 is a polysome (polyribosome) drawing. In this

case, multiple ribosomes are attached to the same mRNA, each
making a new protein. Many identical peptides can be made from
the same mRNA in a short time.

In prokaryotes, translation and transcription can occur

simultaneously. Ribosomes can actually bind to the RNA that is
still being transcribed and simultaneously can begin protein
synthesis. This shows there is a direct connection between the
two processes. (This isn't possible in eukaryotes because RNA
synthesis occurs in the nucleus and proteins are synthesized in
the cytoplasm).

RNAase is an enzyme which digests RNA, breaking it down into

nucleotides. Constant translation actually protects the RNA in
bacteria from RNAase. Ribosomes protect RNA by fitting around
it like a sleeve fits around an arm. mRNAs which are more
actively translated in the cell are more stable because they have
more ribosomes bound to them, protecting them from RNAases.
A typical prokaryotic cell has a period of 20 minutes between
divisions. The cell has to change in response to its environment.
For example, a bacterial cell living in the presence of lactose has
to change to respond to a different energy source when the
lactose is gone. So the old mRNAs need to be degraded, and
replaced with new mRNAs.

In polycistronic translation there are multiple cycles of start and

stop for each mRNA and coordinately regulated genes. However,
when some RNA viruses infect procaryotic cells, some RNA
genes are not translated immediately. This is because
the AUGstart codon of one of the genes is basepaired to another
region on the RNA - and is therefore unavailable to the
ribosomes. The only way this start codon can be used is when the
base pairing is disrupted, usually as the result of translating the
complementary region of the RNA (the regions that is base paired
to the AUGin question). It is the movement of the ribosomes along
the mRNA that disprupts regions of intrastrand base pairing

Eukaryotes often need to synthesize proteins that are secreted

from the cell. The beginning of the growing protein chain binds to
the endoplasmic reticululum to start the process of
secretion.The newlys synthesized protein is released into the
lumen of the endoplasmic reticulum, where it is modified by
enzymes. The protein eventually travels through the Golgi
complex where it is modified further. The protein is then
packaged in vesicles from the Golgi and transported to the cell
surface, where the vesicles fuse with the cell surfact to release
the protein contents.

This pathway was elucidated by a pulse-chase experiment. This

experiment allowed the proteins to be tracked through the cell to
the outside of the cell. Cells are placed in a medium of radioactive
amino acids for about five minutes. This labels all proteins
synthesized during that time period. This is the "pulse" phase of
the experiment. The cells are then removed from the radioactive
medium, placed into a non-radioactive medium and monitored.
The slide is coated with photographic emulsion at different times
during the "chase" period. In parallel cultures, cells are viewed
after zero, five, ten and twenty minutes. This is referred to as
chasing the radioactivity. At first the radioactive material will be in
the endoplasmic reticulum. It will then move to the Golgi. Next
vesicles will start to be radioactive, and finally the radioactivity will
be secreted by the vesicles outside the cell.

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