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protein synthesis
introduction
The process oftranslationin biology is decoding
Message in a polypeptide product. In other words, a message written in the chemical language of nucleotides is "translated" into the chemical language of amino acids. amino acids
linked by covalent bonds (called peptide bonds) between
and carboxy terminals of adjacent amino acids. The process of decoding and "binding"
through a ribonucleoprotein complex calledribosomesand can
Chains of amino acids ranging in length from tens to more than 1,000.
The resulting proteins are so important to the cell that their synthesis consumes more energy from the cell than any other metabolic process. Like DNA replication and transcription, translation is a complex molecular process that we can tackle with the Energy Story and Design Challenge sections. The description of the overall process or steps requires consideration of the matter and energy before and after the process and how this is important.
and the energy transferred during the process. From the perspective of the Design Challenge, we can - even before addressing what is or
about translation: try to figure out some basic questions that we need to answer about this process.
Let's start by considering the basic problem. We have one strand of RNA (called
) and lots of amino
and we need to design a machine that somehow:
(a) decode the chemical language of nucleotides into the language of amino acids,
(b) connect amino acids together in a very specific way,
(c) complete this process with reasonable accuracy and
(d) do so at a reasonable speed. Reasonable
through natural selection.
As before, we can identify subproblems.
(a) How does our molecular machine determine where and when to work?
(b) How does the molecular machine coordinate decoding and bond formation?
(c) Where does the energy for this process come from and how much?
(d) How does the machine know where to stop?
More questions and functional issues/challenges will come up as we dig deeper.
The point, as always, is that even if we don't know any details about translation, we can use our imagination, curiosity, and common sense to find some requirements for the process that we need to learn more about. It is crucial to understand these questions as context for what follows.
A peptide bond connects the carboxy terminus of one amino acid to the amino terminus of another, expelling a water molecule. The R1y R. S.2The designation refers to the side chain of the two amino acids.
assignment:
Machines for protein synthesis
The components involved in the process.
Many molecules and macromolecules contribute to the translation process. However, the exact composition of the "players" in this process can vary from species to species; For example, ribosomes can contain different numbers
Reminder: amino acids
Remember that the basic structure of amino acids
The 20 most common amino acids.
assignment:
ribosomes
AribosomesIt is a complex macromolecule composed of structural and catalytic molecules.
and many different polypeptides. If we try to think about the energy balance in the cell, we find that the ribosomes themselves are not "free." already before
, a cell must invest energy to build each of its ribosomes. InE. coliThere are between 10,000 and 70,000 ribosomes in each cell.
Ribosomes exist in the cytoplasm of bacteria and archaea, and in the cytoplasm and rough endoplasmic reticulum of eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which are more like bacterial ribosomes (and have similar sensitivity to drugs) than ribosomes outside their outer membranes in the cytoplasm. Ribosomes dissociate into large and small subunits when not synthesizing proteins and reassociate during translation initiation. InE. coli, we describe the small subunit as 30S and the large subunit as 50S. Mammalian ribosomes have a small 40S subunit and a large 60S subunit. The small subunit connects the
pattern while the large subunit binds sequentially
. Many ribosomes can translate an individual at the same time
Molecule, each ribosome synthesizes protein in the same direction: reading the
from 5' to 3' and synthesizing the polypeptide from the N-terminus to the C-terminus.
/Structure-poly-ribosome
Apolysomy.
ARNt
of genes Depending on the species from 40 to 60 species
They exist in the cytoplasm. Serve as adapter, specific
joins sequences in
Template and add the corresponding amino acid to the polypeptide chain. For this reason,
they are the molecules that actually "translate" the language of RNA into the language of proteins.
Of the 64 possible
codon- or triplet combinations of A, U, G and C, three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also codes for translation initiation. Each
anticodoncan be paired with one of the bases
Add codons and an amino acid or
Translation, according to the genetic code. For example, if the CUA sequence occurred in
Model in the appropriate reading frame that would fire one
expresses the complementary sequence GAU, the
to the amino acid leucine.
Aminoacyl-tRNA Synthasene
The process of
The mechanism of protein synthesis.
As with transcription, we can divide protein synthesis into three phases: initiation, elongation, and termination. The translation process is similar in bacteria, archaea, and eukaryotes.
Introduction to translation
bacterialcontra eukaryote Introduction
emE. coli
, a sequence upstream of the first codon called AUGShine-Dalgarno episode(AGGAGG), interact with a
Molecule. This interaction anchors the 30S ribosomal subunit in place in the
Model. Pause for a moment to appreciate the repetition of a mechanism that you have encountered before. Here, a protein complex is induced to associate, in the correct register, with a nucleic acid polymer.
Alignment of two antiparallel strands of complementary nucleotides. We have also seen this in the function of telomerase.
Instead of binding to the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-
Cap at the 5' end of
. A cap-binding protein (CBP) aids in movement of the ribosome into the 5' cap. Arriving at the border, the initiation complex continues along it.
in the 5' to 3' direction, looking for the AUG start codon.
since the first AGO, but this is not always the case. RespectivelyReglas Cossack, the nucleotides around the AUG
if it is the correct start codon. Kozak's rules state that the following consensus sequence should appear around the AUG of vertebrate genes: 5'-
-3'. OR (Purinabfall)
a site that can be A or G, but not C or U. In essence, the closer the sequence is to this consensus, the more efficient the translation.
Possible NB discussion
point it out
Compare and contrast translation initiation with transcription: how are these processes alike and how are they different?
translation stretch
During translational stretching, the
The model provides specificity. As the ribosome progresses
, each
the codon goes into 'see', and
. Se
were not present in the elongation complex, the ribosome would bind
nonspecific Again, consider using base pairing between two antiparallel strands of complementary nucleotides to record and keep track of our molecular machinery, and in this case, also to do the job of "translating" between the language of nucleotides and amino acids.
The large ribosomal subunit consists of three compartments:
The site connects the entrance fee
(
with specific amino acids attached), binds to the charged P site
containing amino acids that have formed bonds with the growing polypeptide chain but have not yet dissociated from their counterparts
, and the E site that publishes
so they can
with another free amino acid.
The stretch continues with the load.
Possible NB discussionpoint it out
Tetracycline is an antibiotic on the World Health Organization's List of Essential Medicines. It alleviates the infection by blocking the A site on the bacterial ribosome. Another antibiotic, chloramphenicol, blocks peptidyl transfer. Describe the immediate and long-term effects of these two antibiotics. What other strategies can you think of to combat the infection specifically at the translation level?
the genetic code
To summarize what we know to this point, the process of cellular transcription produces messenger RNA (
), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). translation of
The template converts nucleotide-based genetic information into a protein product. protein sequences
20 common amino acids; Therefore, we can say that the protein alphabet
20 letters We define each amino acid by a sequence of three nucleotides called a triplet.A code. The relationship between a nucleotide codon and its corresponding amino acid
ogenetic code. Given the different number of “letters” in the
and protein "alphabets" mean that there are
64 (4 × 4 × 4)
codons; therefore, one amino acid must be used (20 total)
Von
ein Kodon.
Three of the 64 codons
Protein synthesis and release of the polypeptide from the translation machinery. these triplets
stop codons. Another codon, AUG, also has a special function.
specifying the amino acid methionine, also serves asstart codonfor
Translation.
by the AUG start codon near the 5' end of the
. The genetic code is universal. With few exceptions, virtually all species use the same genetic code for protein synthesis, providing strong evidence that all life on Earth shares a common origin.
redundant, clearly
The information in the genetic code is redundant. Multiple codons code for the same amino acid. For example, using the graph above, you can find 4 different codons that code for valine, likewise there are 2 codons that code for leucine, etc. But the code is clear, that is, if
end of translation
Translation termination occurs when a stop codon (UAA, UAG, or UGA)
Coupling between transcription and translation
As mentioned above, bacteria and archaea do not need to transport their RNA transcripts across a bound membrane.
protein separation
em
a design challenge for protein synthesis, we can also pose the question/problem of how do proteins go where
go. We know that some proteins
to the plasma membrane, which others require in eukaryotic cells
to various organelles, some proteins, such as hormones or nutrient-binding proteins,
are secreted by cells while others need it
Parts of the cytosol to perform structural functions. How did this happen?
As we discovered various mechanisms, the details of this process
in one or two short paragraphs. However, we can mention some key elements that are common to all mechanisms. First, a specific "tag" is required that can provide molecular information about where the protein of interest is located.
for. This tag usually consists of a short chain of amino acids, called a signal peptide, which can encode information about where the protein should end up. The second necessary component of the protein classification machinery must be a system for reading and classifying proteins. This is often the case in bacterial and archaeal systems.
Proteins that can identify the signal peptide during translation, bind to it, and direct the synthesis of nascent proteins to the plasma membrane. Inevitably, in eukaryotic systems, sorting is more complex, involving a rather sophisticated set of mechanisms for signal recognition, protein modification, and vesicle transport between organelles or membranes. These biochemical steps
in the endoplasmic reticulum and later in the Golgi apparatus where the proteins are "ennobled".
and packaged in vesicles destined for different parts of the cell.
. The key for all students is to understand the problem and get an overview of the general requirements that cells have adopted to solve the problem.
post-translational protein modification
After
summary section
The players in the translation include the