Transcription Process in Prokaryotes

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Questions and Answers

What marks the start of transcription for a gene?

The terminator sequence

The enhancer region

The promoter sequence (correct)

The RNA transcript

Which term describes the direction in which RNA polymerase transcribes the template DNA strand?

Transverse

Lateral

Downstream (correct)

Upstream

What is the role of the sigma (σ) factor in prokaryotic transcription?

It binds to the terminator sequence.

It halts transcription.

It recognizes the promoter sequence. (correct)

It initiates RNA synthesis.

How does RNA polymerase begin the transcription process?

By opening the double helix at the promoter Signup and view all the answers

Which statement about the terminator sequence is correct?

It signifies the end of transcription. Signup and view all the answers

What does a negative sign indicate in the nucleotide positions relative to the transcription start site?

Upstream position Signup and view all the answers

What happens when RNA polymerase encounters the terminator during transcription?

It releases the RNA and DNA template. Signup and view all the answers

What characterizes the binding of RNA polymerase to bacterial DNA?

It initially adheres weakly and then slides along the DNA. Signup and view all the answers

What does the σ factor do during the initiation of transcription?

Binds to the promoter DNA and stabilizes the transcription bubble Signup and view all the answers

During abortive initiation, what characterizes the RNA products released by RNA polymerase?

They contain less than 10 nucleotides Signup and view all the answers

What happens to the RNA polymerase after abortive initiation?

It escapes the promoter and begins elongation Signup and view all the answers

How does RNA polymerase begin RNA synthesis during transcription?

By pulling upstream DNA into its active site Signup and view all the answers

What structural feature marks the region of unwound DNA during transcription?

Transcription bubble Signup and view all the answers

What happens at the terminator during the transcription process?

RNA polymerase halts and releases the RNA molecule Signup and view all the answers

What is the role of the core enzyme following transcription?

It reassociates with free σ factor to form a new holoenzyme Signup and view all the answers

Which mechanism allows RNA polymerase to extend the RNA chain?

By moving forward one base pair for each nucleotide added Signup and view all the answers

What is the primary function of RNA polymerase I in eukaryotic cells?

To transcribe genes encoding precursor rRNA Signup and view all the answers

Which RNA polymerase is responsible for the transcription of tRNAs and 5S rRNA?

RNA polymerase III Signup and view all the answers

What distinguishes eukaryotic RNA polymerases from bacterial RNA polymerase in terms of initiation factors?

Eukaryotic RNA polymerases require more than one initiation factor Signup and view all the answers

Where does RNA polymerase II primarily operate within eukaryotic cells?

In the nucleus Signup and view all the answers

What is the role of general transcription factors in eukaryotic transcription?

They assist in the initiation and release of RNA polymerase at the promoter Signup and view all the answers

What identifies the TATA box in a promoter region?

A sequence primarily composed of T and A nucleotides Signup and view all the answers

What role does TFIID play at the promoter region?

It causes a distortion in the DNA of the TATA box. Signup and view all the answers

Which transcription factor is considered the most complicated among the general transcription factors?

TFIIH Signup and view all the answers

What is the function of the TATA-binding protein (TBP)?

To recognize and bind to the TATA box Signup and view all the answers

What is the primary function of TFIIH during transcription initiation?

To unwind the DNA and expose the template strand. Signup and view all the answers

Which of the following statements correctly describes eukaryotic transcription initiation?

It must occur on DNA packaged into chromatin Signup and view all the answers

How does RNA polymerase II transition into the elongation phase of transcription?

Through phosphorylation of its C-terminal domain. Signup and view all the answers

What happens to RNA polymerase II after it binds to the promoter?

It separates the DNA strands to access the template. Signup and view all the answers

What is required for RNA polymerase II to effectively assemble the initiation complex?

A complete set of transcription factors. Signup and view all the answers

What significance does the melting of approximately 14 base pairs of DNA near the transcription start site have?

It allows for base pairing with ribonucleoside triphosphates. Signup and view all the answers

What occurs after the phosphorylating of the CTD of RNA polymerase II?

The RNA splicing machinery loads onto the polymerase. Signup and view all the answers

What roles do RNA molecules play in the process of protein synthesis?

RNA provides directions for protein synthesis. Signup and view all the answers

Which statement accurately describes transcription?

It synthesizes RNA using information from DNA. Signup and view all the answers

What is one function of ribozymes in RNA?

They act as catalysts for biochemical reactions. Signup and view all the answers

Which of the following correctly describes the flow of genetic information?

DNA -> mRNA -> Protein Signup and view all the answers

Where does the synthesis of mRNA take place?

In the nucleus Signup and view all the answers

What characterizes TERRA in relation to RNA?

It is a long non-coding RNA generated from telomeres. Signup and view all the answers

What is the primary role of mRNA during translation?

It acts as a template for protein synthesis. Signup and view all the answers

Which process occurs after mRNA moves into the cytoplasm?

Protein synthesis at ribosomes Signup and view all the answers

What is the primary role of RNA polymerase during transcription?

To synthesize RNA by linking ribonucleotides Signup and view all the answers

What does the term 'pre-mRNA' refer to?

The primary transcript of a protein-coding gene Signup and view all the answers

In which direction is RNA synthesized during transcription?

5’3’ direction Signup and view all the answers

Which of the following is true regarding the initiation of transcription?

It is where the cell decides which RNAs or proteins to produce Signup and view all the answers

What is the role of the template DNA strand during transcription?

It determines the order of nucleotides in the RNA strand Signup and view all the answers

How does RNA polymerase differ from DNA polymerase?

RNA polymerase synthesizes RNA instead of DNA Signup and view all the answers

What are codons in the context of mRNA?

Sequences of nucleotides that specify amino acids Signup and view all the answers

What is the significance of RNA polymerases being processive?

They finish synthesizing the same RNA molecule without detaching Signup and view all the answers

Study Notes

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.

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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.