S2023_Bis2A_Singer_Translation (2023)

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    protein synthesis


    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

    are linearly linked

    linked by covalent bonds (called peptide bonds) between


    and carboxy terminals of adjacent amino acids. The process of decoding and "binding"

    is catalyzed

    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

    It's not understood

    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

    it is defined

    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:marc t. Facciotti (Taller Original).

    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 numbersrRNA(ribosomal RNA) and polypeptides depending on the organism: The general functions of the protein synthesis machinery are comparable from bacteria to human cells. We focus on these similarities. The translation requires at leastasmRNAModel,amino acids,ribosomes,ARNt, a source of energy, and several additional accessory enzymes and small molecules.

    Reminder: amino acids

    Remember that the basic structure of amino acidsconsisting ofa backbone consisting of an amino group, a central carbon (calledA-carbon) and a carboxyl group. attached toA-Carbon is a variable group that helps determine some chemical properties and the reactivity of the amino acid.

    S2023_Bis2A_Singer_Translation (3)

    A generic amino acid.
    assignment:marc t. Facciotti (own work)

    The 20 most common amino acids.
    assignment:marc t. Facciotti (own work)

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    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

    asmRNA is translated

    , 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.



    is called


    S2023_Bis2A_Singer_Translation (5)

    The protein synthesis machinery includes the large and small subunits of the ribosome,mRNA, zARNt.


    ARNtare structural RNA molecules that

    were transcribed

    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 be in

    to the amino acid leucine.

    S2023_Bis2A_Singer_Translation (6)

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    The folded secondary structure of aARNt.The anticodon loop and amino acid receptor bar are indicated..


    The process ofARNtsynthesis by RNA polymerase III produces only the RNA portion of the adapter molecule. The corresponding amino acid shouldto be addedlater theARNt is processedand exported to the cytoplasm. Through the process ofARNt"shop", allARNtMoleculeAre you connectednamed to its correct amino acid by a group of enzymesAminoacyl-tRNASynthasene. at least one kind ofAminoacyl-tRNASynthetase exists for each of the 20 amino acids;oexact number ofAminoacyl-tRNASynthases vary by species. These enzymes first bind and hydrolyze ATP.catalyzea high energy bond between an amino acid and adenosine monophosphate (AMP);Ellaemit a pyrophosphate molecule in this reaction. The activated amino acidthen it will be broadcastFor himARNt, zAMP starts.

    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

    Usually the proteinThe synthesis begins with the formation of an initiation complex. The small ribosomal subunit binds to themRNANOribosomal binding site. Shortly after methionineARNtit will bind to the AUG initiation codon (via a complementary bond to its anticodon). this complexthen it will connectthrough the large ribosomal subunit. This initiation complex then recruits the secondARNtmiThis is where the translation begins.

    S2023_Bis2A_Singer_Translation (7)

    Translation begins when aARNtAnticodon recognizes a codon in themRNA. The large ribosomal subunit binds to the small subunita second tRNA is recruited. WhilemRNAmoves relative to the ribosomethe polypeptide chain is formed. Enter a release factor inoAPropertyendsTranslation and components dissociate.

    bacterialcontra eukaryoteIntroduction

    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.

    it's finished

    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.

    Many eukaryotic mRNAs are translated

    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 discussionS2023_Bis2A_Singer_Translation (8)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

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    ensures specific binding to the corresponding charged tRNA anticodon

    . 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

    to be charged

    with another free amino acid.

    The stretch continues with the load.ARNtget intooAand then moves with each individual codon "passing" from the ribosome to the P site, followed by the E site.Ribosomal steps are induced.by conformational changes that advance the ribosome three bases in the 3' direction. The energy for each step of the ribosome.will be donatedby an elongation factor that hydrolyzes GTP. Peptide bonds are formed between the amino group of the linked amino acidoA-PropertyARNtand the carboxyl group of the amino acid attached to the P siteARNt. The formation of each peptide bond.is catalyzedVonpeptidyltransferase, an RNA-based enzyme thatis integratedin the 50S ribosomal subunit.The energy for the formation of each peptide bond is derivedof GTP hydrolysis, theis catalyzedby a separate expansion factor. The amino acid attached to the P siteARNt is also ingrowing polypeptide chain. When the ribosome crosses themRNA, the former body PARNtenters the E site, is cleaved from the amino acid, andwill be expelled. The ribosome moves along themRNA, one codon each,Catalysteach process that takes place in the three places. A fee at every stepARNtenters the complex, the polypeptide becomes a longer amino acid and aARNtPart. Surprisingly, this process occurs rapidly in the cell, whichE. coliIt takes only 0.05 seconds for the translation machinery to add each amino acid, which means that a polypeptide could be made up of 200 amino acids.to be translatedin just 10 seconds.

    Possible NB discussionS2023_Bis2A_Singer_Translation (9)point 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

    consisting of

    20 common amino acids; Therefore, we can say that the protein alphabet

    consisting of

    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

    is called

    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)

    be coded


    more than

    ein Kodon.

    Three of the 64 codons


    Protein synthesis and release of the polypeptide from the translation machinery. these triplets

    his name is

    stop codons. Another codon, AUG, also has a special function.

    In addition to

    specifying the amino acid methionine, also serves asstart codonfor

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    The reading frame for the translation is defined

    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.

    This figure shows the genetic code for the translation of each nucleotide triplet or codon.mRNAon an amino acid or a termination signal on a nascent protein. (Credit: NIH Work Modification)
    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, ifThey receivedAA codeYou would definitely know which amino acid it codes for, a codon only codes for a specific amino acid. For example, GUU always codes for valine and AUG always codes for methionine. This is important,they are asking youtranslateasmRNAinto a protein using a codon diagram like the one shown above.

    end of translation

    Translation termination occurs when a stop codon (UAA, UAG, or UGA)it's found. when the ribosome stopsA codeNOARNtbelongs inoAProperty. Instead, a protein known asrelease factorconnects to the complex. This interaction destabilizes the translation machinery, causing release of the polypeptide and dissociation of the ribosomal subunits.mRNA. After many ribosomes have completed translation, themRNA is dismantledSoNucleotides can be reusedin another transcription reaction.

    Coupling between transcription and translation

    As mentioned above, bacteria and archaea do not need to transport their RNA transcripts across a bound membrane.Kernand the cytoplasm. Therefore, RNA polymerase transcribes RNA directly in the cytoplasm. This is where ribosomes can bind to RNA and start the translation process, sometimes while transcription is still taking place. The combination of these two processes, and evenmRNADegradation,is relevantnot only because transcription and translation occur in the same compartment, but also because both processes proceed in the same direction: RNA transcript synthesis occurs in the 5' to 3' direction and translation reads the transcript in the 5' to 3' direction. 5' to 3''. Address. This "coupling" of transcription and translation occurs in both bacteria and archaea, and is indeed sometimes essential for proper gene expression.

    S2023_Bis2A_Singer_Translation (11)

    Several polymerases can transcribe a single bacterial genenumerousRibosomes simultaneously translate themRNAtranscribed into polypeptides. In this way, a specific protein can quickly reach a high concentration in the bacterial cell.

    protein separation


    the context of

    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

    are determined

    to the plasma membrane, which others require in eukaryotic cells

    to be judged

    to various organelles, some proteins, such as hormones or nutrient-binding proteins,

    are determined

    are secreted by cells while others need it

    to be judged

    Parts of the cytosol to perform structural functions. How did this happen?

    As we discovered various mechanisms, the details of this process

    cannot be easily summarized

    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.

    is determined

    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.

    consisting of

    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

    They start

    in the endoplasmic reticulum and later in the Golgi apparatus where the proteins are "ennobled".

    are modified

    and packaged in vesicles destined for different parts of the cell.

    Your teacher can discuss some specific mechanisms in the classroom.

    . 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-translationalprotein modification

    Aftertranslationindividual amino acids canbe chemically modified. These modifications add chemical variations and new properties.they are rootedin the chemistry of added functional groups. Common modifications include phosphate groups,Methyl,Acetate, zBetweengroups. Some typically membrane-targeted proteins will belipidated-a lipid is added. other proteinsbe glycosylated- Sugar cravingsto be added. Another common post-translational modification isnecklineor join parts of the protein itself. Signal peptides canbe divided, the parts canbe cutfrom the middle of the protein, ornew covalent bonds can be formedbetween cysteine ​​or other amino acid side chains. The enzymes arecatalyzealmost all modifications and all modifications change the functional behavior of the protein.

    summary section

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    mRNAIt is used to synthesize proteins through the translation process. The genetic code is the correspondence between the three nucleotidesmRNAcodon and an amino acid. The genetic code is "translated" by theARNtMolecules that connect a specific codon to a specific amino acid. The genetic code isdegeneratebecause there are 64 triplet codons in itmRNAspecify only 20 amino acids and three stop codons. This means thatmore thana codon corresponds to an amino acid. Almost every species on the planet uses the same genetic code.

    The players in the translation include themRNAmodel, ribosomes,ARNtand various enzymatic factors. The small ribosomal subunit binds to themRNAModel. The translation starts at the beginning of August atmRNA. Bond formation occurs between consecutive amino acids indicated by themRNAmodel according to the genetic code. The ribosome accepts charge.ARNt, and as you progress through themRNA, catalyzes the binding between the new amino acid and the end of the growing polypeptide.SetmRNAis translatedin three nucleotide "steps" of the ribosome. If a stop codonit's found, a release factor, binds and dissociates the components and releases the new protein.


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