Transcription Process in Prokaryotes

Nucleic Acids

• Two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next
• DNA provides directions for its own replication
• DNA directs RNA synthesis and, through RNA, controls protein synthesis

RNA

• Folded domains of RNA molecules may have catalytic capacities. These catalytic RNAs are called ribozymes
• Although ribozymes are usually associated with proteins that stabilize the ribozyme structure, the RNA acts as a catalyst
• Some ribozymes can catalyze splicing, a remarkable process in which an internal RNA sequence is cut and removed, and the two resulting chains are ligated

Types of RNA

• The majority of genes in a cell's DNA specify amino acid sequences of proteins
• Some genes code for RNA molecules
• Important RNAs for transcription include:
  • mRNA: Encodes proteins
  • tRNA: Acts as adaptor between mRNA and amino acids
  • rRNA: Forms the ribosome
• Other non-coding RNAs are used in RNA splicing, gene regulation, telomere maintenance, and many other processes

Transcription and Translation

• Genes provide instructions for making specific proteins
• A gene does not build a protein directly; the bridge is RNA
• The flow of genetic information: DNA → RNA → protein
• Getting from DNA to protein requires two major stages: transcription and translation

Transcription and Translation Diagram

Basic Principles of Transcription

• The simplest definition of a gene is a "unit of DNA that contains the information to specify synthesis of a single polypeptide chain or functional RNA" (such as tRNA).
• The vast majority of genes carry information to build protein molecules and it is RNA copies of the protein-coding genes that constitute the mRNA molecules of cells.
• During RNA synthesis, the four-base language of DNA (A, G, C, and T) is copied into the four-base language of RNA (identical except that U replaces T)
• During transcription of DNA, one DNA strand acts as a template, determining the order in which ribonucleoside triphosphate (rNTP) monomers are polymerized to form a complementary RNA chain.
• Bases in template DNA strand base-pair with complementary incoming rNTPs, which are joined in a polymerization reaction catalyzed by RNA polymerase.
• mRNA nucleotide triplets are called codons and RNA molecules are always synthesized in the 5'→3' direction.
• Transcription of a protein-coding eukaryotic gene results in pre-mRNA, and further processing yields the finished mRNA.
• The initial RNA transcript from any gene, including those specifying RNA that is not translated into protein, is more generally called a primary transcript

DNA Polymerase vs RNA Polymerase

• RNA polymerase catalyzes the linkage of ribonucleotides, not deoxyribonucleotides
• RNA polymerases can start an RNA chain without a primer; this difference is thought possible because transcription need not be as accurate as DNA replication
• RNA polymerases are absolutely processive; the same RNA polymerase that begins an RNA molecule must finish it without dissociating from the DNA template

Molecular Components of Transcription

• Steps of Transcription:
  • Initiation of Transcription
  • Elongation of the RNA Strand
  • Termination of Transcription

Initiation of Transcription

• RNA polymerase binds to the promoter sequence in duplex DNA ("closed complex").
• RNA Polymerase melts duplex DNA near transcription start site, forming a transcription bubble ("open complex").
• RNA polymerase catalyzes phosphodiester linkage of two initial rNTPs

Elongation

• Polymerase advances 5' to 3' down template strand, melting duplex DNA and adding rNTPs to growing RNA

Termination

• At transcription stop site, polymerase releases completed RNA and dissociates from DNA.

Initiation of Transcription in Prokaryotes

• In bacteria, a subunit of RNA polymerase, the sigma (σ) factor, is primarily responsible for recognizing the promoter sequence on the DNA.
• Together, sigma factor and core enzyme (RNA polymerase holoenzyme) complex adheres weakly to bacterial DNA, slides rapidly along the long DNA molecule, then dissociates

Abortive Initiation

• RNA polymerase binds to promoter DNA to form an RNA polymerase-promoter closed complex.
• RNA polymerase unwinds one turn of DNA surrounding the transcription start site to yield an RNA polymerase-promoter open complex
• RNA polymerase enters into abortive cycles of synthesis and releases short RNA products (contains less than 10 nucleotides)
• RNA polymerase escapes the promoter and enters into the elongation step of transcription.

Transcription in Eukaryotes

• In contrast to bacteria, which contain a single type of RNA polymerase, eukaryotic nuclei have three: RNA polymerase I, RNA polymerase II, and RNA polymerase III.

• The three polymerases are structurally similar to one another and share some common subunits, but they transcribe different categories of genes.

  • RNA polymerase I, located in the nucleolus, transcribes genes encoding precursor rRNA (pre-rRNA), which is processed into 28S, 5.8S, and 18S rRNAs.
  • RNA polymerase III transcribes genes encoding tRNAs, 5S rRNA, and an array of small, stable RNAs, including one involved in RNA splicing (U6).
  • RNA polymerase II transcribes most genes, including all those that encode proteins. It also produces four of the five small nuclear RNAs that take part in RNA splicing.

• While similar in structure, bacterial and eukaryotic RNA polymerases have these differences:

  • Bacterial RNA polymerase requires only a single transcription initiation factor (σ) to begin transcription, whereas eukaryotic require many such factors, collectively called general transcription factors.
  • Eukaryotic transcription initiation must take place on DNA that is packaged into nucleosomes and higher-order forms of chromatin structure features that are absent from bacterial chromosomes.

Transcription in Eukaryotes (Summary)

• After binding to a promoter, RNA polymerase separates the DNA strands, making the template strand bases available for base pairing with incoming ribonucleoside triphosphates.
• Cellular RNA polymerases melt approximately 14 base pairs of DNA around the transcription start site, which is located on the template strand within the promoter region.
• Transcription initiation is considered complete when the first two ribonucleotides of an RNA chain are linked by a phosphodiester bond.

Elongation of Transcription

• After several ribonucleotides have been polymerized, RNA polymerase dissociates from the promoter DNA and general transcription factors.
• During the stage of strand elongation, RNA polymerase moves along the template DNA one base at a time, opening the double-stranded DNA in front of its direction of movement and hybridizing the strands behind it.
• One ribonucleotide at a time is added to the 3' end of the growing (nascent) RNA chain during strand elongation by the polymerase.

Termination of Transcription

• During transcription termination, the final stage in RNA synthesis, the completed RNA molecule (primary transcript) is released from the RNA polymerase, and the polymerase dissociates from the template DNA.
• Once released, an RNA polymerase is free to transcribe the same gene again or another gene.

Test your knowledge of the transcription process in prokaryotes, focusing on the roles of RNA polymerase and the sigma factor. This quiz covers aspects such as transcription initiation, termination, and the characteristics of RNA synthesis. Perfect for students learning about molecular biology and genetics.