How Do Enzymes Determine When To Initiate Translation And When To Stop?

The process of protein synthesis, or translation, involves the decoding of an mRNA message into a polypeptide (protein) product. Amino acids are covalently strung together by peptide bonds in lengths ranging from approximately 50. The start codon always has the code AUG in mRNA and codes for the amino acid methionine, which is the signal where enzymes start transcription. There are several stop codons (UAA, UAG, and UGA) that do not code for an amino acid but only act as a signal for the enzyme to stop transcription.

In E. coli, a representative prokaryote, the process of translation occurs in three stages: initiation, elongation, and termination. The start codon always has the code AUG in mRNA and codes for the amino acid methionine, which is the signal where enzymes start transcription. There are several stop codons (UAA, UAG, and UGA) that do not code for an amino acid but only act as a signal for the enzyme to stop transcription.

Transcription and translation are the two processes that convert a sequence of nucleotides from DNA into a sequence of amino acids to build the desired protein. These two processes are essential for life and can be found in various organisms.

The process of translation can be seen as the decoding of instructions for making proteins, involving mRNA in transcription as well as tRNA. There are three different stop codons: UAG, UAA, and UGA, which signal the end of the polypeptide chain during translation. The ribosome provides a set of handy slots where tRNAs can find their matching codons on the mRNA template and deliver their amino acids.

How does a cell know where to begin the process of transcription?

To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter. Basically, the promoter tells the polymerase where to “sit down” on the DNA and begin transcribing.

How do cells know when to stop translation?

Stop Codons Mark the End of Translation. The end of the protein-coding message is signaled by the presence of one of three codons (UAA, UAG, or UGA) called stop codons (see Figure 6-50 ). These are not recognized by a tRNA and do not specify an amino acid, but instead signal to the ribosome to stop translation. Proteins known as release factors bind to any ribosome with a stop codon positioned in the A site, and this binding forces the peptidyl transferase in the ribosome to catalyze the addition of a water molecule instead of an amino acid to the peptidyl-tRNA ( Figure 6-73 ). This reaction frees the carboxyl end of the growing polypeptide chain from its attachment to a tRNA molecule, and since only this attachment normally holds the growing polypeptide to the ribosome, the completed protein chain is immediately released into the cytoplasm. The ribosome then releases the mRNA and separates into the large and small subunits, which can assemble on another mRNA molecule to begin a new round of protein synthesis.

Figure 6-73. The final phase of protein synthesis. The binding of a release factor to an A-site bearing a stop codon terminates translation. The completed polypeptide is released and, after the action of a ribosome recycling factor (not shown), the ribosome dissociates (more…)

Release factors provide a dramatic example of molecular mimicry, whereby one type of macromolecule resembles the shape of a chemically unrelated molecule. In this case, the three-dimensional structure of release factors (made entirely of protein) bears an uncanny resemblance to the shape and charge distribution of a tRNA molecule ( Figure 6-74 ). This shape and charge mimicry allows the release factor to enter the A-site on the ribosome and cause translation termination.

How does the translation process know where to start and stop?

The genetic code There are ‍ different codons for amino acids. Three “stop” codons mark the polypeptide as finished. One codon, AUG, is a “start” signal to kick off translation (it also specifies the amino acid methionine)

How does the enzyme know where to start and stop transcription?

This, of course, brings us to an obvious question- how do RNA polymerases “know” where to start copying on the DNA. Unlike the situation in replication, where every nucleotide of the parental DNA must eventually be copied, transcription, as we have already noted, only copies selected genes into RNA at any given time. What indicates to an RNA polymerase where to start copying DNA to make a transcript? Signals in DNA indicate to RNA polymerase where it should start (and end) transcription. These signals are special sequences in DNA that are recognized by the RNA polymerase or by proteins that help RNA polymerase determine where it should bind the DNA to start transcription. A DNA sequence at which the RNA polymerase binds to start transcription is called a promoter.

A promoter is generally situated upstream of the gene that it controls. What this means is that on the DNA strand that the gene is on, the promoter sequence is “before” the gene. Remember that, by convention, DNA sequences are read from 5′ to 3′. So the promoter lies 5′ to the start point of transcription.

Also notice that the promoter is said to “control” the gene it is associated with. This is because expression of the gene is dependent on the binding of RNA polymerase to the promoter sequence to begin transcription. If the RNA polymerase and its helper proteins do not bind the promoter, the gene cannot be transcribed and it will therefore, not be expressed.

What determines the start of translation?

In initiation, the ribosome assembles around the mRNA to be read and the first tRNA (carrying the amino acid methionine, which matches the start codon, AUG). This setup, called the initiation complex, is needed in order for translation to get started.

How does mRNA know where to begin and end transcription?

“How does the protein that transcribes DNA into mRNA know where to start and end?” Great question! The short answer is that there are special sequences on our DNA that indicate where to start and stop for a specific gene.

Great question! The short answer is that there are special sequences on our DNA that indicate where to start and stop for a specific gene.

Before we dive into the nitty gritty details, let’s back up a bit. Each person has a lot of DNA. It’s basically the entire cookbook to make a person!

Research on the human genome has found that we have around 20, 000 genes encoded in our DNA! That includes genes for eye color, making muscles, building nerve cells, and so much more.

How do you know where to stop translating?

“Identify objects around you in English.” The first way to stop translating in your head is to identify the objects around you in your target language. So, if you’re studying English, that means you look at the objects around the room, look at the things in your life. Don’t think of them in your native language first.

How do enzymes know where to go?

Enzymes are proteins that stabilize the transition state of a chemical reaction, accelerating reaction rates and ensuring the survival of the organism. They are essential for metabolic processes and are classified into six main categories: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. These enzymes catalyze specific reactions within their categories, with some being inactive until bound to a cofactor. The cofactor and apoenzyme complex is called a holoenzyme.

Enzymes are proteins composed of amino acids linked together in polypeptide chains. The primary structure of a polypeptide chain determines the three-dimensional structure of the enzyme, including the shape of the active site. The secondary structure describes localized polypeptide chain structures, such as α-helices or β-sheets.

The tertiary structure is the complete three-dimensional fold of a polypeptide chain into a protein subunit, while the quaternary structure describes the three-dimensional arrangement of subunits. The active site is a groove or crevice on an enzyme where a substrate binds to facilitate the catalyzed chemical reaction. Enzymes are typically specific because the conformation of amino acids in the active site stabilizes the specific binding of the substrate. The active site typically occupies a small part of the enzyme and is usually filled with free water when not binding a substrate.

How does transcription know where to stop?

RNA polymerase identifies where to stop transcribing by recognizing specific sequences in the DNA template called termination signals or terminators. These sequences indicate the end of the gene or transcription unit.

RNA polymerase identifies where to stop transcribing by recognizing specific sequences in the DNA template called termination signals or terminators. These sequences indicate the end of the gene or transcription unit. Once RNA polymerase encounters a termination signal, it halts transcription and releases the newly synthesized RNA molecule.

In prokaryotes, termination of transcription occurs through two mechanisms: rho-dependent and rho-independent. Rho-dependent termination relies on a protein called Rho factor. When RNA polymerase transcribes certain genes, it encounters a specific DNA sequence called the rho utilization (rut) site. Rho-independent termination, also known as intrinsic termination, relies on the formation of a stable RNA hairpin structure followed by a run of uracil (U) nucleotides in the mRNA transcript.

In eukaryotes, transcription termination involves two elements: a downstream terminator sequence and a poly(A) signal. Transcription termination in eukaryotes involves the recognition of a polyadenylation signal sequence (AAUAAA) in the pre-mRNA transcript. This sequence signals the addition of a polyadenylate (poly(A)) tail to the mRNA transcript. The cleavage and polyadenylation complex, which includes specific proteins, recognizes the poly(A) signal and cleaves the pre-mRNA transcript downstream of the signal. Sequences, located downstream of the poly(A) signal, contribute to the termination of transcription by promoting the release of RNA polymerase from the DNA template.

How does transcription know where to start?

The process of transcription begins when an enzyme called RNA polymerase (RNA pol) attaches to the template DNA strand and begins to catalyze production of complementary RNA. Polymerases are large enzymes composed of approximately a dozen subunits, and when active on DNA, they are also typically complexed with other factors. In many cases, these factors signal which gene is to be transcribed.

Three different types of RNA polymerase exist in eukaryotic cells, whereas bacteria have only one. In eukaryotes, RNA pol I transcribes the genes that encode most of the ribosomal RNAs (rRNAs), and RNA pol III transcribes the genes for one small rRNA, plus the transfer RNAs that play a key role in the translation process, as well as other small regulatory RNA molecules. Thus, it is RNA pol II that transcribes the messenger RNAs, which serve as the templates for production of protein molecules.

The first step in transcription is initiation, when the RNA pol binds to the DNA upstream (5′) of the gene at a specialized sequence called a promoter (Figure 2a). In bacteria, promoters are usually composed of three sequence elements, whereas in eukaryotes, there are as many as seven elements.

How does RNA know where to go?

The molecular language of RNA transport. For a handful of mRNAs – or RNA sequences coding for specific proteins – researchers have an idea about how they’re transported. They often contain a particular string of nucleotides, the chemical building blocks that make up RNA, that tell cells about their desired destination. These sequences of nucleotides, or what scientists refer to as RNA ” ZIP codes,” are recognized by proteins that act like mail carriers and deliver the RNAs to where they are supposed to go.

My team and I set out to discover new ZIP codes that send RNAs to neurites, the precursors to the axons and dendrites on neurons that transmit and receive electrical signals. We reasoned that these ZIP codes must lie somewhere within the thousands of nucleotides that make up the RNAs in neurites. But how could we find our ZIP code needle in the RNA haystack?

We started by breaking eight mouse neurite-localized RNAs into about 10, 000 smaller chunks, each about 250 nucleotides long. We then appended each of these chunks to an unrelated firefly RNA that mouse cells are unlikely to recognize, and watched for chunks that caused the firefly RNA to be transported to neurites. To extend the mail analogy, we took 10, 000 blank envelopes (firefly RNAs) and wrote a different ZIP code (pieces of neurite-localized RNA) on each one. By observing which envelopes were delivered to neurites, we were able to discover many new neurite ZIP codes.