Podcast
Questions and Answers
The core promoter is the binding site for ______ factors.
The core promoter is the binding site for ______ factors.
general transcription
The ______ is a DNA sequence found in the core promoter region that indicates the point at which a genetic sequence can be found, read, and decoded.
The ______ is a DNA sequence found in the core promoter region that indicates the point at which a genetic sequence can be found, read, and decoded.
TATA Box
The ______ is the simplest functional promoter that can direct transcription without a TATA Box.
The ______ is the simplest functional promoter that can direct transcription without a TATA Box.
Inhibitor Element
DPE, or ______ ______, functions cooperatively with the INR for the binding of TFIID in transcription of core promoters in the absence of the TATA Box.
DPE, or ______ ______, functions cooperatively with the INR for the binding of TFIID in transcription of core promoters in the absence of the TATA Box.
Which of the following are considered regulatory promoter elements? (Select all that apply)
Which of the following are considered regulatory promoter elements? (Select all that apply)
Transcription factors are RNA molecules that bind to specific DNA sequences.
Transcription factors are RNA molecules that bind to specific DNA sequences.
The transcription factor has a ______ signal which allows the protein to get into the nucleus and get to the DNA.
The transcription factor has a ______ signal which allows the protein to get into the nucleus and get to the DNA.
Transcription factors have ______ domains, which is where they bind to specific DNA sequences.
Transcription factors have ______ domains, which is where they bind to specific DNA sequences.
Transcription factors can have activating or repressing domains that regulate whether the gene is needed or not.
Transcription factors can have activating or repressing domains that regulate whether the gene is needed or not.
What is the function of the WRKY22 protein?
What is the function of the WRKY22 protein?
Explain the role of the bHLH domain in transcription factors.
Explain the role of the bHLH domain in transcription factors.
Describe the function of the zinc finger domain in the regulation of HIV.
Describe the function of the zinc finger domain in the regulation of HIV.
Explain how the leucine zipper domain facilitates DNA binding.
Explain how the leucine zipper domain facilitates DNA binding.
Describe the function of the Rel homology domain (RHO) in the Rel family of transcription factors.
Describe the function of the Rel homology domain (RHO) in the Rel family of transcription factors.
Describe the mechanism of DNA binding by the helix-turn-helix motif.
Describe the mechanism of DNA binding by the helix-turn-helix motif.
Explain the mechanism of DNA binding by the homeodomain.
Explain the mechanism of DNA binding by the homeodomain.
What is the function of the NAC domain in plants?
What is the function of the NAC domain in plants?
What are the roles of the different eukaryotic RNA polymerases?
What are the roles of the different eukaryotic RNA polymerases?
What are the roles of general transcription factors for RNA polymerase II?
What are the roles of general transcription factors for RNA polymerase II?
Which step of transcription involves unwinding of DNA to expose the template strand?
Which step of transcription involves unwinding of DNA to expose the template strand?
What is the function of the C-terminal domain (CTD) of RNA polymerase II?
What is the function of the C-terminal domain (CTD) of RNA polymerase II?
Mutations that result in the loss of kinase function for TFIIH are lethal because TFIIH loses its ability to phosphorylate, and no RNA can be made or proteins.
Mutations that result in the loss of kinase function for TFIIH are lethal because TFIIH loses its ability to phosphorylate, and no RNA can be made or proteins.
What is the function of FACT in transcription?
What is the function of FACT in transcription?
Explain how the transcription bubble is formed during transcription.
Explain how the transcription bubble is formed during transcription.
During termination of transcription, RNA polymerase II continues to transcribe DNA while the pre-mRNA is cut off and released.
During termination of transcription, RNA polymerase II continues to transcribe DNA while the pre-mRNA is cut off and released.
Explain the function of the 5' exonuclease XRN2 in mRNA processing.
Explain the function of the 5' exonuclease XRN2 in mRNA processing.
RNA polymerase I is responsible for the synthesis of ribosomal RNA (rRNA), which is essential for ribosome assembly and protein synthesis.
RNA polymerase I is responsible for the synthesis of ribosomal RNA (rRNA), which is essential for ribosome assembly and protein synthesis.
RNA polymerase III transcribes mRNA, which contains the genetic code for proteins.
RNA polymerase III transcribes mRNA, which contains the genetic code for proteins.
Which of the following factors is involved in the initiation of transcription by RNA polymerase I?
Which of the following factors is involved in the initiation of transcription by RNA polymerase I?
Explain the mechanism of termination of transcription by RNA polymerase I.
Explain the mechanism of termination of transcription by RNA polymerase I.
RNA polymerase III utilizes the same general transcription factors as RNA polymerase II for initiation.
RNA polymerase III utilizes the same general transcription factors as RNA polymerase II for initiation.
What is the purpose of processing rRNA?
What is the purpose of processing rRNA?
The processing of rRNA, tRNA, and mRNA involves the action of ribozymes.
The processing of rRNA, tRNA, and mRNA involves the action of ribozymes.
What is the purpose of 5' capping of mRNA?
What is the purpose of 5' capping of mRNA?
The addition of a poly A tail to mRNA occurs at the 5' end of the mRNA.
The addition of a poly A tail to mRNA occurs at the 5' end of the mRNA.
What are the functions of NELF and DSIF in mRNA processing?
What are the functions of NELF and DSIF in mRNA processing?
Explain the role of P-TEFb in mRNA processing.
Explain the role of P-TEFb in mRNA processing.
Describe the role of the polyadenylation signal in mRNA processing?
Describe the role of the polyadenylation signal in mRNA processing?
What is the function of the spliceosome?
What is the function of the spliceosome?
Explain the function of the snRNAs in splicing.
Explain the function of the snRNAs in splicing.
Histone acetylation is often associated with increased transcription, while histone deacetylation is often associated with repressed transcription.
Histone acetylation is often associated with increased transcription, while histone deacetylation is often associated with repressed transcription.
Histone methylation can either activate or repress transcription depending on the specific amino acid residue that is methylated.
Histone methylation can either activate or repress transcription depending on the specific amino acid residue that is methylated.
Explain how chromatin remodeling factors regulate gene expression.
Explain how chromatin remodeling factors regulate gene expression.
LncRNAs can act as scaffolds to recruit chromatin remodeling factors, ensuring that the transcription region is accessible.
LncRNAs can act as scaffolds to recruit chromatin remodeling factors, ensuring that the transcription region is accessible.
Explain how tRNAs are activated for use in translation.
Explain how tRNAs are activated for use in translation.
Ribosomes are composed of two subunits, a large subunit that catalyzes peptide bond formation and a small subunit that binds to mRNA.
Ribosomes are composed of two subunits, a large subunit that catalyzes peptide bond formation and a small subunit that binds to mRNA.
Explain the roles of the three sites within the ribosome (A, P, and E sites).
Explain the roles of the three sites within the ribosome (A, P, and E sites).
The process of translation initiation involves the assembly of the ribosome, the binding of the initiator tRNA, and the binding of mRNA to the ribosome.
The process of translation initiation involves the assembly of the ribosome, the binding of the initiator tRNA, and the binding of mRNA to the ribosome.
What is the function of eIF3 in translation initiation?
What is the function of eIF3 in translation initiation?
Explain the role of eIF2 in translation initiation.
Explain the role of eIF2 in translation initiation.
What is the role of the eIF4 complex in translation initiation?
What is the role of the eIF4 complex in translation initiation?
Explain the function of eIF5B in translation initiation.
Explain the function of eIF5B in translation initiation.
During translation elongation, what is the role of eEF1a?
During translation elongation, what is the role of eEF1a?
During translation elongation, GTP is hydrolyzed to GDP, providing the energy for the ribosome to move one codon along the mRNA transcript.
During translation elongation, GTP is hydrolyzed to GDP, providing the energy for the ribosome to move one codon along the mRNA transcript.
What are the three stop codons that signal the termination of translation?
What are the three stop codons that signal the termination of translation?
Explain the role of release factors in translation termination.
Explain the role of release factors in translation termination.
Organelles, such as mitochondria and chloroplasts, have their own translation machinery, which is similar to that of bacteria.
Organelles, such as mitochondria and chloroplasts, have their own translation machinery, which is similar to that of bacteria.
Flashcards
Core Promoter
Core Promoter
A DNA sequence located near the transcription start site. It binds general transcription factors, which are essential for initiating transcription.
TATA Box
TATA Box
A DNA sequence found within the core promoter, rich in adenine (A) and thymine (T) bases. It serves as the binding site for TFIID, a general transcription factor crucial for initiation.
INR (Inhibitor Element)
INR (Inhibitor Element)
A simple DNA sequence that functions as a promoter, capable of initiating transcription even in the absence of a TATA box.
DPE (Downstream Promoter Element)
DPE (Downstream Promoter Element)
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Regulatory Promoter
Regulatory Promoter
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Enhancer
Enhancer
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Transcription Factors
Transcription Factors
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Cis Element
Cis Element
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DNA Binding Domain
DNA Binding Domain
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Activating/Repressing Domains
Activating/Repressing Domains
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RNA Polymerase I
RNA Polymerase I
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RNA Polymerase II
RNA Polymerase II
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RNA Polymerase III
RNA Polymerase III
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TFIID
TFIID
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TFIIB
TFIIB
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TFIIF
TFIIF
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TFIIE and TFIIH
TFIIE and TFIIH
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Mediators
Mediators
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Phosphorylation of RNA Polymerase II CTD
Phosphorylation of RNA Polymerase II CTD
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FACT (Facilitated Chromatin Transcription)
FACT (Facilitated Chromatin Transcription)
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Transcription Bubble
Transcription Bubble
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Polyadenylation Signal
Polyadenylation Signal
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5' Capping
5' Capping
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3' Polyadenylation
3' Polyadenylation
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Splicing
Splicing
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Spliceosome
Spliceosome
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snRNAs (Small Nuclear RNAs)
snRNAs (Small Nuclear RNAs)
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Histone Modifications
Histone Modifications
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Acetylation
Acetylation
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Methylation
Methylation
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Chromatin Remodeling Factors
Chromatin Remodeling Factors
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lncRNAs (Long Noncoding RNAs)
lncRNAs (Long Noncoding RNAs)
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Polyubiquitination
Polyubiquitination
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Proteasome
Proteasome
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UPR (Unfolded Protein Response)
UPR (Unfolded Protein Response)
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Study Notes
Transcription Factors
- Transcription factors are proteins that bind to specific DNA sequences.
- Core promoter is the binding site for general transcription factors.
- TATA box is a DNA sequence in the core promoter region, indicating the start of a gene.
- INR (Inhibitor Element) is a simple functional promoter that controls transcription without a TATA box.
- DPE (Downstream Promoter Elements) cooperatively work with INR to bind TFIID in transcription without a TATA box.
- Core promoters are about 60 nucleotides.
- Regulatory Promoters are where specific transcription factors bind that are necessary to activate specific genes.
- Enhancers are upstream distant enhancers and repressors that are 1000 to 10,000 base pairs from transcription start sites and bend the DNA to contact the start site.
- Transcription factors have a nuclear localization signal for entry into the nucleus.
- DNA binding domains allow transcription factors to bind to specific DNA sequences.
- Activating and repressing domains regulate whether a gene is needed or not.
DNA Binding Domains
- Basic Helix-Loop-Helix (bHLH): Contains two alpha-helices for DNA binding.
- Zinc finger: Contains 3 base pairs for DNA interactions, involves Zn ions. An example includes HIV regulation.
- Leucine Zipper (ZIP): Contains alpha-helices with leucine residues every 7th amino acid; binds to 2 different major grooves of DNA.
- Rel homology domain (RHO): Contains an internal DNA binding region and recognition loop.
- Homeodomain: Contains an alpha helix and amino acid residues to contact DNA.
Helix-Turn-Helix (HTH)
- The last helix in HTH motif is the recognition helix which inserts into the DNA major groove for recognizing specific DNA locations.
- Examples include Lac repressor.
- Used in DNA repair and RNA metabolism.
RNA polymerase functions
- RNA polymerase I makes ribosomal RNA (rRNA).
- RNA polymerase II makes messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (IncRNA).
- RNA polymerase III makes transfer RNA (tRNA).
- RNA polymerases IV and V make plant-specific RNA for DNA methylation.
General transcription factors for RNA polymerase II
- TFIID, TFIIB, TFIIF, TFIIE, TFIIH
- Mediators join in the beginning of initiation
- Phosphorylation of RNA Polymerase II CTD is done by TFIIH, leading to release of RNA polymerase for elongation
RNA Polymerase I
- Initiation: Upstream binding factor (UBF) and factor 1 (SLF1) bind to promoter. Then, polymerase I binds to and moves away after the polymerase is released.
- Elongation is the same as RNA polymerase II.
- Termination: TFII-1
RNA Polymerase III
- Initiation: TFIIB and polymerase III
- Elongation: Same as RNA polymerase II
- Termination: Section of 4–7 Us signals end of gene
RNA Processing
- 5.8s, 18s, and 28s rRNA are made from a single transcript.
- 5s rRNA comes from a different transcript.
- Pseudouradine is formed from the isomerization of ribose.
- rRNA are processed through methylation and snoRNPs.
- tRNA are processed through cleavage and CCA addition.
- mRNA is processed through 5' capping, splicing, and 3' polyadenylation.
- 5' capping prevents degradation.
- Splicing removes introns and joins exons.
- 3' polyadenylation adds a poly-A tail to stabilize mRNA.
RNA Processing (small nuclear ribonucleoproteins; snRNPs)
- Small nuclear RNAs (U1, U2, U4, U5, and U6) are part of the spliceosome.
- These form a complex that recognizes the splice sites, removes introns, and joins exons together.
- Additional snRNAs bind and catalyze splicing.
Epigenetics
- Affects transcription by controlling areas of tightly packed or loosely packed chromatin.
- Acetylation/deacetylation - Histone acetylation (associated with transcription) and deacetylation (associated with repression).
- Methylation- affects transcription depending on the active and non active sites.
- Phosphorylation- may change the function of the tail with adding methyl, acetyl or phosphate groups.
- Chromatin remodeling factors loosen and tighten histones to make areas accessible to allow or prevent transcription.
- Non-coding RNA (ncRNA) affects expression positively or negatively.
Translation
- tRNA activation for translation involves specific enzymes (aminoacyl-tRNA synthetases). Each amino acid requires its own synthetase.
- Eukaryotic ribosomes (80S) are composed of a large subunit (60S) and a small subunit (40S).
- mRNA, ribosome subunits, and initiator tRNA assemble during initiation.
- Elongation factors bring charged tRNAs and position new amino acids for peptide bond formation.
- Termination occurs with release factors at stop codons.
Translation Elongation
- eEF1a brings in next charged tRNA, checks for match, peptide bond formed by ribosome.
- Translocation occurs, tRNA moves to next sites.
Translation Termination
- Release factors bind to stop codons.
- Peptide chain released from tRNA and ribosome subunits disconnect.
Translation in organelles
- Mitochondria and chloroplasts have their own translation machinery.
Protein Degradation
- Proteins tagged with ubiquitin are targeted for degradation by the proteasome.
- Steps involve E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme, and E3 ubiquitin ligase.
- Tagged proteins are recognized by the proteasome and unfolded, leading to degradation.
Proteasome
- Made of two subunits (26s and 20s)
- 26s- the regulatory subunit (19s) lid recognizes Poly Ub.
- 20s- the catalytic subunit.
- Protein unfolding and breakdown occurs in the proteasome.
ER-stress response (UPR)
- ER stress involves accumulation of misfolded proteins.
- UPR response lowers global protein production, upregulates membrane lipid biosynthesis, increases ERAD (ER Associated Degradation) pathway, expands secretory pathway.
- Chronic UPR leads to apoptosis.
Post-Translational Processing
- Protein folding/unfolding is crucial for function.
- Enzymes like protein disulfide isomerase and peptidyl prolyl isomerase help in folding proteins.
- Chaperones and chaperonins assist in proper protein folding and prevent aggregation.
- Glycosylation: Addition of sugars to proteins.
- Lipidation: Addition of lipids to proteins.
Proteolysis
- Cleavage of a polypeptide to activate protein from inactive precursor.
- Steps include signal peptide removal and polypeptide chain cleavage, activating proteins.
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Description
This quiz covers essential concepts related to transcription factors, including their role in gene expression and the different elements of core promoters. Learn about the significance of the TATA box, INR, DPE, and regulation through enhancers. Test your understanding of how these components work together in transcription regulation.