Which of the following events occur during the initiation stage of transcription?

What is Transcription?

Transcription generally refers to the written form of something. In biology, transcription is the process whereby DNA is used as a template to form a complementary RNA strand – RNA is the “written” form of DNA. This is the first stage of protein production or the flow of information within a cell. DNA stores genetic information, which is then transferred to RNA in transcription, before directing the synthesis of proteins in translation. Three types of RNA can be formed: messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).

Transcription occurs in four stages: pre-initiation, initiation, elongation, and termination. These differ in prokaryotes and eukaryotes in that DNA is stored in the nucleus in eukaryotes, and whereas DNA is stored in the cytoplasm in prokaryotes. In eukaryotes, DNA is stored in tightly packed chromatin, which must be uncoiled before transcription can occur. The production of mRNA from RNA in eukaryotes is particularly more complicated than it is in prokaryotes, involving several additional processing steps.

Pre-initiation, or template binding, is initiated by the RNA polymerase σ subunit binding to a promoter region located in the 5’ end of a DNA strand. Following this, the DNA strand is denatured, uncoupling the two complementary strands and allowing the template strand to be accessed by the enzyme. The opposing strand is known as the partner strand. Promoter sequences on the DNA strand are vital for the successful initiation of transcription. Promoter sequences are specific sequences of the ribonucleotide bases making up the DNA strand (adenine, thymine, guanine,and cytosine), and the identity of several of these motifs have been discovered, including TATAAT and TTGACA in prokaryotes and TATAAAA and GGCCAATCT in eukaryotes. These sequences are known as cis-acting elements. In eukaryotes, an additional transcription factor is necessary to facilitate the binding of RNA polymerase to the promoter region.

RNA polymerase catalyzes initiation, causing the introduction of the first complementary 5’-ribonucleoside triphosphate. Remember that each DNA nucleotide base has a complement: adenine and thymine, and guanine and cytosine. However, the ribonucleotide base complements differ slightly as RNA does not contain thymine, but rather a uracil, and so adenine’s complement is uracil. After the introduction of the first complementary 5’-ribonucleotide, subsequent complementary ribonucleotides are inserted in a 5’ to 3’ direction. These ribonucleotides are joined by phosphodiester bonds, and at this stage, the DNA and RNA molecules are still connected(see Figure 1).

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Figure 1: Initiation of transcription. RNAP® refers to RNA polymerase.

Chain elongation occurs when the σ subunit dissociates from the DNA strand, allowing the growing RNA strand to separate from the DNA template strand. This is facilitated by the core enzyme (see Figure 2).

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Figure 2: Elongation in transcription

Termination occurs when the core enzyme encounters a termination sequence, which is a specific sequence of nucleotides which acts as a signal to stop transcription. At this point, the RNA transcript forms a hairpin secondary structure by folding back on itself with the aid of hydrogen bonds. Termination in prokaryotes can be assisted by an additional termination factor known as rho(ρ). Termination is complete when the RNA molecule is released from the template DNA strand. In eukaryotes, termination requires an additional step known as polyadenylation in eukaryotes, whereby a tail of multiple adenosine monophosphates is added to the RNA strand.

Figure 3: The main events in each stage of transcription

What is Reverse Transcription?

Reverse transcription is the process of transcribing a DNA molecule from an RNA molecule. This method of replication is utilized by retroviruses, such as HIV, and produces altered DNA, which can be incorporated directly into a host cell, allowing rapid reproduction. This is made possible by the reverse transcriptase enzyme. This can be seen in Figure 4.

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Figure 4: The process of reverse transcription.

What is Translation?

Translation refers to the conversion of something from one language or form to another. In biology, translation is the process whereby messenger ribonucleic acid, or mRNA, synthesizes proteins – mRNA is converted to proteins. This is accomplished by the production of a chain of amino acids (a polypeptide chain) determined by the chemical information stored by a specific strand of mRNA. These polypeptides fold to form proteins. Each strand of mRNA is coded by a different gene and codes a different protein. This is important for gene expression.

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Figure 5: The triplet code is translated into amino acids, some of the amino acids code for the start and end of translation

Translation has three main stages: initiation, elongation, and termination. These differ slightly in prokaryotic and eukaryotic organisms: in prokaryotes, translation occurs in the cytoplasm, while in eukaryotes, translation takes place in the endoplasmic reticulum. Essential to the process of translation is the ribosome; ribosomal structure also differs in prokaryotes and eukaryotes, mostly concerning the rate of the migration of their subunits when centrifuged, and the number of proteins their subunits contain.

Initiation begins with the small ribosomal subunit binding to the 5’ end of the mRNA, the messenger RNA created in transcription from DNA. This occurs in two stages: the small ribosomal subunit first binds to several proteinaceous initiation factors, before the combined structure binds to mRNA. This binding site is several ribonucleotides before the start codon of the mRNA. Following this, a charged molecule of tRNA binds to the small ribosomal subunit. The large ribosomal subunit then goes on to bind to the complex formed by the small ribosomal subunit, the mRNA, and the tRNA. This process hydrolyzes the GTP (guanosine-5′-triphosphate) needed to power the bonds. After the large ribosomal subunit joins the complex, the initiation factors are released.

The charging of the molecule of tRNA utilized in the process of translation refers to the linking of the tRNA molecule with an amino acid. This occurs as a result of aminoacyl-tRNAsynthetases, which reacts with the amino acid and ATP (adenosine triphosphate) to form a reactive form of the amino acid, known as an aminoacyladenylic acid. This binds with the ATP to form a complex which can react with a tRNA molecule, forming a covalent bond between the two. The tRNA can now transfer the amino acid to the mRNA molecule.

Elongation begins when both the small and large ribosomal subunits have been bound to the mRNA. A peptidyl site and an aminoacyl site are formed on the mRNA molecule for further binding with tRNA. The tRNA first binds to the P site (peptidyl site), and elongation begins with the binding of the second tRNA molecule to the A site (aminoacyl site). Both these tRNA molecules are transporting amino acids. An enzyme known as peptidyl transferase is released and forms a peptide bond between the amino acids transported by the two tRNA molecules. The covalent bond between the tRNA molecule at the P site and its amino acid is broken, releasing this tRNA to the E site (exit site) before it is released from the mRNA molecule entirely. The tRNA located at the A site then moves to the P site, utilizing the energy produced from the GTP. This leaves the A site free for further binding while the P site contains a tRNA molecule attached to an amino acid, that is attached to another amino acid. This forms the basis of the polypeptide chain. Another tRNA molecule then binds to the A site, and peptidyl transferase catalyzes the creation of a peptide bond between this new amino acid and the amino acid attached to the tRNA located at the P site. The covalent bond between the amino acid and tRNA at the P site is broken and the tRNA is released. This process repeats over and over again, adding to add amino acids to the polypeptide chain.

Termination occurs when the ribosome complex encounters a stop codon(see figure 5). At this stage, the polypeptide chain is attached to a tRNA at the P site, while the A site is unattached. GTP-dependent release factors break the bond between the final tRNA and the terminal amino acid. The tRNA is released from the ribosome complex, which then splits again into the small and large ribosomal subunits, which are released from the mRNA strand. This polypeptide chain then folds in on itself to form a protein. This process is depicted in Figure 6 and Figure 7.

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Figure 6: The overview of the process of translation

Figure 7: The main events in each stage of translation.

How is Translation Different from Transcription?

Both transcription and translation are equally important in the process of genetic information flow within a cell, from genes in DNA to proteins. Neither process can occur without the other. However, there are several important differences in these processes.

To begin with, initial transcription components include DNA, RNA polymerase core enzyme, and the σ subunit. Translation components include mRNA, small and large ribosomal subunits, initiation factors, elongation factors and tRNA. In transcription, a DNA double helix is denatured to allow the enzyme to access the template strand. In translation, no such denaturing is necessary, as the template is a single mRNA strand. The product of transcription is RNA, which can be encountered in the form mRNA, tRNA or rRNA while the product of translation is a polypeptide amino acid chain, which forms a protein.

Transcription occurs in the nucleus in eukaryotic organisms, while translation occurs in the cytoplasm and endoplasmic reticulum. Both processes occur in the cytoplasm in prokaryotes. The factor controlling these processes is RNA polymerase in transcription and ribosomes in translation. In transcription, this polymerase moves over the template strand of DNA, while in translation, the ribosome-tRNA complex moves over the mRNA strand.

These differences are summarized in Table 1 below.

Table 1: The differences between transcription and translation

Wrapping Up Translation vs. Transcription

For as powerful as it is, DNA is as good as its products. It is for this very reason that the processes of transcription and translation are so important. For a smooth operation of cell processes both the DNA sequences and the products thereof must work according to plan. This is where transcription and translation come into play and fulfill a vital purpose in the DNA function.

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