Podcast
Questions and Answers
Which factor is commonly aimed at controlling during transcriptional regulation?
Which factor is commonly aimed at controlling during transcriptional regulation?
- Transcription elongation
- Gene expression at the ribosome
- Post-transcriptional modification
- Initiation of transcription (correct)
The α helix in transcription factors is too wide to fit into the major groove of the DNA double helix.
The α helix in transcription factors is too wide to fit into the major groove of the DNA double helix.
False (B)
What is the role of a recognition helix in transcription factors?
What is the role of a recognition helix in transcription factors?
To make contact with and recognize a base sequence along the major groove of DNA.
The formation of __________ may inhibit gene expression in localized regions of a chromosome.
The formation of __________ may inhibit gene expression in localized regions of a chromosome.
Match the following motifs with their functions:
Match the following motifs with their functions:
What is the main reason for modulating the functions of regulatory transcription factors (RTFs)?
What is the main reason for modulating the functions of regulatory transcription factors (RTFs)?
Covalent modifications can alter the functions of regulatory transcription factors.
Covalent modifications can alter the functions of regulatory transcription factors.
What are the three common ways by which the functions of RTFs are controlled?
What are the three common ways by which the functions of RTFs are controlled?
RTFs must be able to bind to DNA and influence __________.
RTFs must be able to bind to DNA and influence __________.
Match the following aspects of regulatory transcription factors with their definitions:
Match the following aspects of regulatory transcription factors with their definitions:
Flashcards
Helix-turn-helix motif
Helix-turn-helix motif
A protein structural motif where two alpha helices are linked by a short turn. The recognition helix interacts with specific DNA sequences in the major groove.
Alpha helix in transcription factors
Alpha helix in transcription factors
The protein secondary structure that is commonly found in transcription factors. It provides the perfect width to interact with the major groove of the DNA double helix.
DNA binding specificity
DNA binding specificity
The ability of a protein to recognize and bind to a specific DNA sequence. This is crucial for gene regulation.
Helix-loop-helix motif
Helix-loop-helix motif
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Transcriptional regulation
Transcriptional regulation
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What are Regulatory Transcription Factors (RTFs)?
What are Regulatory Transcription Factors (RTFs)?
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How are RTF functions modulated?
How are RTF functions modulated?
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What do small effector molecules do?
What do small effector molecules do?
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How do protein-protein interactions affect RTFs?
How do protein-protein interactions affect RTFs?
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What are covalent modifications and how do they affect RTFs?
What are covalent modifications and how do they affect RTFs?
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Study Notes
Gene Regulation in Eukaryotes
- Gene expression involves accessing information within genes to produce RNA and polypeptides, affecting cellular properties
- Gene regulation controls the level of gene expression to maintain optimal levels for cellular function
- Eukaryotic gene expression is regulated at various stages of polypeptide synthesis, including transcription (discussed here and in chapter 16), translation (chapters 13 & 17), and post translation (chapters 14 & 23)
- Regulatory transcription factors can activate or inhibit transcription
- Nucleosome arrangements and composition influence transcription
- DNA methylation typically inhibits transcription
- Alternative splicing and RNA editing alter RNA sequences
Regulatory Transcription Factors and Enhancers
- Transcription factors influence RNA polymerase's ability to transcribe DNA into RNA. They regulate the binding of the preinitiation complex, influencing the switch between initiation and elongation
- General transcription factors (GTFs) are essential for all transcription, regulating RNA polymerase binding and elongation
- Regulatory transcription factors (RTFs) are diverse and regulate transcription rates
- RTFs have domains with specific functions, such as DNA binding or interaction with effector molecules
- Structural motifs, such as helix-turn-helix, helix-loop-helix, zinc fingers, and leucine zippers, are commonly found in RTFs and allow them to bind to DNA
- These domains recognize specific DNA sequences due to complementary biochemical properties and ionic interactions
- Enhancers are DNA regions containing regulatory elements that increase or decrease transcription rates when bound to RTFs; these are frequently located some distance from the promoter
- Activators bind to enhancers to promote transcription rates, while repressors prevent transcription
- Enhancers function bidirectionally
- Enhancer location relative to the gene's promoter can vary significantly
- Gene regulation involves combinatorial control, where the combined effect of multiple factors determines gene expression
Chromatin Remodeling, Histone Variants, and Histone Modifications
- Chromatin remodeling refers to dynamic changes in chromatin structure, affecting DNA accessibility to regulatory elements
- Chromatin remodeling complexes, such as SWI/SNF, ISWI, INO80, and Mi-2, use ATP to reposition and restructure nucleosomes
- Histone variants have altered amino acid sequences that influence chromatin structure and gene regulation
- Histone modifications (acetylation, methylation, and phosphorylation) affect transcription by influencing nucleosome interactions and interactions with other proteins
DNA Methylation
- DNA methylation involves attaching a methyl group to a cytosine base
- Full methylation affects transcription by blocking the binding of proteins; hemimethylation occurs when methylation of only one strand has occurred
- Methylation commonly occurs at CpG islands near gene promoters
- Methylated CpG islands are often correlated with inactive genes
- Maintenance methylation ensures the inheritance of DNA methylation patterns during cell division
- De novo methylation is the addition of methyl groups to unmethylated DNA
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