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Questions and Answers
What is the function of TFIIH in the context of RNA polymerase II?
What is the function of TFIIH in the context of RNA polymerase II?
What does the CTD of RNA polymerase II consist of?
What does the CTD of RNA polymerase II consist of?
What is the role of upstream elements in relation to RNA polymerase II binding?
What is the role of upstream elements in relation to RNA polymerase II binding?
How many polypeptides are typically included in the initiation complex for RNA polymerase II?
How many polypeptides are typically included in the initiation complex for RNA polymerase II?
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What is required for RNA polymerase II to bind and initiate transcription at minimal promoters?
What is required for RNA polymerase II to bind and initiate transcription at minimal promoters?
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What is the relationship of the largest subunit of RNA polymerase II to bacterial RNA polymerase?
What is the relationship of the largest subunit of RNA polymerase II to bacterial RNA polymerase?
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What is the typical length of upstream elements that interact with transcription factors?
What is the typical length of upstream elements that interact with transcription factors?
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What happens to RNA polymerase II after TFIIH phosphorylates its tail?
What happens to RNA polymerase II after TFIIH phosphorylates its tail?
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What role does the Rho protein play in transcription termination?
What role does the Rho protein play in transcription termination?
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Which of the following statements about Rho-dependent terminators is true?
Which of the following statements about Rho-dependent terminators is true?
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What characteristic of the Rho protein allows it to bind to mRNA?
What characteristic of the Rho protein allows it to bind to mRNA?
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How does the Rho protein reach the RNA polymerase at the terminator?
How does the Rho protein reach the RNA polymerase at the terminator?
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What happens when the mRNA reaches the hairpin structure during termination?
What happens when the mRNA reaches the hairpin structure during termination?
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What is a defining feature of Rho-independent terminators?
What is a defining feature of Rho-independent terminators?
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Which of the following best describes the structure of the Rho protein?
Which of the following best describes the structure of the Rho protein?
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Which sequence length is typically recognized by the Rho protein for binding?
Which sequence length is typically recognized by the Rho protein for binding?
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What role does the MalT protein play in the metabolism of maltose in Escherichia coli?
What role does the MalT protein play in the metabolism of maltose in Escherichia coli?
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What must occur for the MalT protein to bind to DNA?
What must occur for the MalT protein to bind to DNA?
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What is the function of the specific sequence of DNA that MalT binds to?
What is the function of the specific sequence of DNA that MalT binds to?
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What happens to the shape of MalT when it binds to maltose?
What happens to the shape of MalT when it binds to maltose?
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In the context of gene regulation, what is typically the initial event that triggers the process?
In the context of gene regulation, what is typically the initial event that triggers the process?
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Which of the following statements about the MalT protein is false?
Which of the following statements about the MalT protein is false?
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Why is the presence of the MalT protein crucial for the transcription of maltose utilization genes?
Why is the presence of the MalT protein crucial for the transcription of maltose utilization genes?
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How does the presence of maltose affect the MalT protein indirectly?
How does the presence of maltose affect the MalT protein indirectly?
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Study Notes
Transcription of Genes
- Genes are expressed by creating RNA
- Short segments of chromosomes become messages
- Terminology includes cistrons, coding sequences, and open reading frames
- Recognizing the beginning of a gene is crucial
Manufacturing the Message
- RNA polymerase determines where to stop
- Cells control which genes turn on
- Activator proteins are activated
- Repressor proteins cause negative regulation
Transcription in Eukaryotes
- Eukaryotic transcription is more complex than prokaryotic transcription
- rRNA and tRNA transcription differs in eukaryotes
- Protein-encoding gene transcription in eukaryotes
- Upstream elements improve RNA polymerase II binding efficiency
- Enhancers regulate transcription from a distance
Short Segments of the Chromosome Are Turned into Messages
- Only a fraction of genes are active at any given time in a typical bacterial cell (about 25%).
- Housekeeping genes are expressed consistently.
- Expression of other genes is dependent on environmental changes.
Terminology
- Cistron: a genomic segment encoding a single protein or RNA molecule
- Open Reading Frame (ORF): a sequence of bases that could be translated into a protein.
- Structural gene: codes for protein or non-translated RNA
Monocistronic vs. Polycistronic mRNA
- In eukaryotes, each mRNA carries a single gene (monocistronic).
- In prokaryotes, several genes can be present on a single mRNA (polycistronic).
How Is the Beginning of a Gene Recognized?
- Promoters are regulatory DNA sequences before each gene.
- RNA polymerase binds to the promoter.
- The 5' untranslated region (5' UTR) separates the promoter from the protein-coding sequence
- The 3' Untranslated Region (3'-UTR) is not translated.
Manufacturing the Message
- RNA polymerase opens the DNA to form a transcription bubble
- The template strand is used to create RNA
- The RNA strand grows from 5' to 3'
- Sigma subunit detaches from the DNA and core enzyme continues building the mRNA.
Manufacturing the Message (continued)
- Transcription begins at the 5' end, usually with an A and two pyrimidines
- mRNA sequence is usually synthesized at 40 nucleotides per second.
- Different parts of RNA polymerases have different functions.
- Transcription can also be paused which helps determine where it stops transcribing.
Manufacturing the Message (continued)
- Terminator signals cause RNA polymerase to stop.
- These signals are inverted repeats separated by a short sequence of bases from a string of U's.
- This often results in a loop in the mRNA.
Negative Regulation by a Repressor
- Repressor proteins bind to DNA, turning off gene expression/blocking RNA polymerase from binding
- Repressors are proteins that switch genes off
- An activator protein binds to the DNA only when the gene is to be turned on
- In negative regulation, a repressor protein binds to the operator and blocks transcription.
- The Lacl protein is an example of a repressor protein, controlling lactose metabolism
How Does the Cell Know Which Genes to Turn On?
- Housekeeping genes are permanently on because they are critical for the cell
- Activator proteins are needed when special circumstances or conditions occur.
What Activates the Activator?
- Small molecules bind to activator proteins causing the protein to change shape to regulate gene expression
- These proteins usually change conformation in specific ways, and this exposes DNA binding sites.
Many Regulator Proteins
- Regulator proteins bind small molecules and change shape.
- Small molecules may cause regulatory proteins to change shape and binding sites for DNA.
Transcription of rRNA and tRNA in Eukaryotes
- rRNA genes are clustered on chromosomes, and several copies exist.
- The transcribed rRNA undergoes processing.
Transcription of rRNA and tRNA (continued)
- rRNA and rRNA processing happen in the nucleolus.
- Specific transcription factors are required to produce appropriate amounts of rRNA.
Transcription of Protein-Encoding Genes in Eukaryotes
- Eukaryotic cells have multiple RNA polymerases, RNA polymerase II being the main player for transcription of protein encoding genes in eukaryotes.
- A range of transcription factors involved in regulating the transcription of specific protein coding genes.
Upstream Elements
- Upstream elements are DNA sequences near the genes that influence how often those genes transcribe.
- Enhancers are regulatory elements farther away from the transcription starting point.
Enhancers Control Transcription at a Distance
- Enhancers regulate gene expression, especially during development.
- Enhancers can be located far from the gene they control.
- Loops of DNA form to allow enhancers to signal the transcription apparatus.
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Description
This quiz covers the fundamental concepts of gene transcription, including the creation of RNA from DNA, the roles of RNA polymerase, and the regulation of gene expression in eukaryotic cells. It also touches on the differences between prokaryotic and eukaryotic transcription processes. Test your knowledge on key terms and mechanisms involved in transcription.
