Podcast
Questions and Answers
What does the primary transcript (mRNA precursor) contain?
What does the primary transcript (mRNA precursor) contain?
- Exons
- Ribosomes
- Nucleotides
- Introns (correct)
Which machinery is responsible for removing introns from the primary transcript?
Which machinery is responsible for removing introns from the primary transcript?
- Endoplasmic reticulum
- Golgi apparatus
- Ribosome
- Splicesome (correct)
U6 is classified as what type of molecule?
U6 is classified as what type of molecule?
- Protein Enzyme
- Liposome
- Ribozyme (correct)
- Carbohydrate
What is defined as multiple ribosomes bound to a single mRNA?
What is defined as multiple ribosomes bound to a single mRNA?
What provide mechanical support and chromatin anchoring within the nuclear envelope?
What provide mechanical support and chromatin anchoring within the nuclear envelope?
What is the process by which RNA products are transported out of the nucleus?
What is the process by which RNA products are transported out of the nucleus?
What structure is the site of transcription in eukaryotic cells?
What structure is the site of transcription in eukaryotic cells?
What is the role of the 5' and 3' untranslated regions (UTRs) of mRNA?
What is the role of the 5' and 3' untranslated regions (UTRs) of mRNA?
What occurs when eIF2 is phosphorylated?
What occurs when eIF2 is phosphorylated?
What stress conditions can inhibit translation through phosphorylation of initiation factors?
What stress conditions can inhibit translation through phosphorylation of initiation factors?
Which of the following processes is specifically affected by the global regulation of translation?
Which of the following processes is specifically affected by the global regulation of translation?
Which of the following can lead to inhibition of translation?
Which of the following can lead to inhibition of translation?
What primarily determines the transcriptional state of myofibers and skin fibroblasts?
What primarily determines the transcriptional state of myofibers and skin fibroblasts?
Which type of transcription factor is responsible for stimulating transcription?
Which type of transcription factor is responsible for stimulating transcription?
What percentage of the genome is estimated to encode transcription factors?
What percentage of the genome is estimated to encode transcription factors?
Which domain of a transcription factor promotes binding with another protein of similar structure?
Which domain of a transcription factor promotes binding with another protein of similar structure?
Which type of motif binds to DNA through ionic bonds and hydrogen bonds?
Which type of motif binds to DNA through ionic bonds and hydrogen bonds?
Which type of transcription factor can interact directly with specific DNA sequences?
Which type of transcription factor can interact directly with specific DNA sequences?
What role do nucleoporins play in the nuclear pore complex?
What role do nucleoporins play in the nuclear pore complex?
What are the signaling sequences involved in the transport of proteins across the nuclear envelope?
What are the signaling sequences involved in the transport of proteins across the nuclear envelope?
Which statement best describes the nature of transcription factors?
Which statement best describes the nature of transcription factors?
What type of DNA-binding domain is known for its zinc ions and recognition helix?
What type of DNA-binding domain is known for its zinc ions and recognition helix?
Which proteins are responsible for ferrying proteins across the nuclear envelope for import?
Which proteins are responsible for ferrying proteins across the nuclear envelope for import?
Which of the following best describes how transcription factors interact with DNA?
Which of the following best describes how transcription factors interact with DNA?
What characterizes the structure of the nuclear pore complex?
What characterizes the structure of the nuclear pore complex?
What is the function of repressors in gene regulation?
What is the function of repressors in gene regulation?
Which of the following statements about mRNA export across the nuclear envelope is true?
Which of the following statements about mRNA export across the nuclear envelope is true?
What is the primary function of importin α/β in the transport process?
What is the primary function of importin α/β in the transport process?
What is the distinction between mRNA export and protein transport across the nuclear envelope?
What is the distinction between mRNA export and protein transport across the nuclear envelope?
Which components are necessary for binding nuclear export signals?
Which components are necessary for binding nuclear export signals?
Which statement about the genetic information in cells is accurate?
Which statement about the genetic information in cells is accurate?
What is the role of histone acetyltransferases (HATs) in transcription?
What is the role of histone acetyltransferases (HATs) in transcription?
How does the addition of an acetyl group affect the binding of histones to DNA?
How does the addition of an acetyl group affect the binding of histones to DNA?
What is the impact of chromatin remodeling complexes on transcription?
What is the impact of chromatin remodeling complexes on transcription?
Which of the following coactivators is mentioned as having the ability to acetylate and initiate transcription?
Which of the following coactivators is mentioned as having the ability to acetylate and initiate transcription?
What type of modification do histone acetyltransferases perform on histones?
What type of modification do histone acetyltransferases perform on histones?
Which transcription factor is highlighted in the example provided?
Which transcription factor is highlighted in the example provided?
What is the primary effect of reducing the binding of histones to DNA?
What is the primary effect of reducing the binding of histones to DNA?
Which complex is known to enhance the accessibility of chromatin for transcription?
Which complex is known to enhance the accessibility of chromatin for transcription?
What characterizes the function of coactivators in transcription?
What characterizes the function of coactivators in transcription?
What effect does acetylation typically have on histones?
What effect does acetylation typically have on histones?
What role do acetyl groups play when transferred to histone lysine residues?
What role do acetyl groups play when transferred to histone lysine residues?
Which of the following best describes the function of chromatin remodeling complexes?
Which of the following best describes the function of chromatin remodeling complexes?
Which coactivator is known for both acetylating histones and initiating transcription?
Which coactivator is known for both acetylating histones and initiating transcription?
What effect does the acetylation of histones have on chromatin structure?
What effect does the acetylation of histones have on chromatin structure?
Which interaction is primarily facilitated by the action of histone acetyltransferases (HATs)?
Which interaction is primarily facilitated by the action of histone acetyltransferases (HATs)?
What role does the nuclear envelope play in the transport of molecules?
What role does the nuclear envelope play in the transport of molecules?
Which of the following is a function of the nucleolus?
Which of the following is a function of the nucleolus?
What characterizes the structure of chromatin?
What characterizes the structure of chromatin?
How does the outer membrane of the nuclear envelope relate to the endoplasmic reticulum?
How does the outer membrane of the nuclear envelope relate to the endoplasmic reticulum?
What happens to RNA products after transcription in the nucleus?
What happens to RNA products after transcription in the nucleus?
Which statement about the mechanical support provided by the nuclear envelope's inner membrane is accurate?
Which statement about the mechanical support provided by the nuclear envelope's inner membrane is accurate?
What is the purpose of the poly(A) tail in eukaryotic mRNA?
What is the purpose of the poly(A) tail in eukaryotic mRNA?
What is primarily responsible for regulating the transcriptional state of different cell types?
What is primarily responsible for regulating the transcriptional state of different cell types?
Which type of transcription factor binds specifically to regulatory sites of particular genes?
Which type of transcription factor binds specifically to regulatory sites of particular genes?
Which domain of a transcription factor is responsible for its interaction with other proteins?
Which domain of a transcription factor is responsible for its interaction with other proteins?
What type of binding do transcription factors use to attach to DNA?
What type of binding do transcription factors use to attach to DNA?
Which transcription factor structure is characterized by the presence of zinc ions?
Which transcription factor structure is characterized by the presence of zinc ions?
How do activators function in relation to transcription?
How do activators function in relation to transcription?
Which of the following best describes the regulation of gene expression by transcription factors?
Which of the following best describes the regulation of gene expression by transcription factors?
What is the role of repressors in transcriptional regulation?
What is the role of repressors in transcriptional regulation?
What is the primary role of nuclear pore complexes (NPCs) in cellular function?
What is the primary role of nuclear pore complexes (NPCs) in cellular function?
Which feature of nucleoporins is crucial for their function in the nuclear pore complex?
Which feature of nucleoporins is crucial for their function in the nuclear pore complex?
What specific signal indicates that a protein should be transported into the nucleus?
What specific signal indicates that a protein should be transported into the nucleus?
What distinguishes the export of mRNA from the export of proteins across the nuclear envelope?
What distinguishes the export of mRNA from the export of proteins across the nuclear envelope?
Which of the following pairs of receptors is involved in the transport of proteins across the nuclear envelope?
Which of the following pairs of receptors is involved in the transport of proteins across the nuclear envelope?
What is the diameter of the central channel within the nuclear pore complex?
What is the diameter of the central channel within the nuclear pore complex?
How do importins interact with proteins meant for nuclear transport?
How do importins interact with proteins meant for nuclear transport?
What is the structural symmetry characteristic of nuclear pore complexes?
What is the structural symmetry characteristic of nuclear pore complexes?
Which of the following accurately describes the relationship between the nuclear genetic content and cellular function?
Which of the following accurately describes the relationship between the nuclear genetic content and cellular function?
What is a common characteristic of Helix-Loop-Helix (HLH) transcription factors?
What is a common characteristic of Helix-Loop-Helix (HLH) transcription factors?
Which amino acids are primarily responsible for the DNA binding capabilities of Helix-Loop-Helix transcription factors?
Which amino acids are primarily responsible for the DNA binding capabilities of Helix-Loop-Helix transcription factors?
What is the role of enhancers in relation to transcription factors?
What is the role of enhancers in relation to transcription factors?
Which statement accurately describes the function of co-activators in transcription control?
Which statement accurately describes the function of co-activators in transcription control?
What distinguishes proximal promoter elements from distal promoter elements?
What distinguishes proximal promoter elements from distal promoter elements?
What is a characteristic function of transcription factors (TFs)?
What is a characteristic function of transcription factors (TFs)?
What defines the Leucine Zipper motif in transcription factors?
What defines the Leucine Zipper motif in transcription factors?
Which of the following correctly identifies the role of response elements?
Which of the following correctly identifies the role of response elements?
How do distal promoter elements affect gene expression?
How do distal promoter elements affect gene expression?
What is a key feature distinguishing basic Helix-Loop-Helix (bHLH) from Leucine Zipper transcription factors?
What is a key feature distinguishing basic Helix-Loop-Helix (bHLH) from Leucine Zipper transcription factors?
What is the function of the nucleolus?
What is the function of the nucleolus?
Which protein complex is crucial for nuclear import of proteins?
Which protein complex is crucial for nuclear import of proteins?
Which adaptation of chromatin affects accessibility for transcription?
Which adaptation of chromatin affects accessibility for transcription?
What role do nucleoporins play in nuclear trafficking?
What role do nucleoporins play in nuclear trafficking?
Which factor is most likely to inhibit gene expression by modifying chromatin structure?
Which factor is most likely to inhibit gene expression by modifying chromatin structure?
In the context of gene expression, what does a polysome refer to?
In the context of gene expression, what does a polysome refer to?
What is the significance of the 5’-Cap in mRNA?
What is the significance of the 5’-Cap in mRNA?
What role do sequence-specific transcription factors play in gene regulation?
What role do sequence-specific transcription factors play in gene regulation?
Which domain is directly responsible for interaction with other proteins in transcription factors?
Which domain is directly responsible for interaction with other proteins in transcription factors?
What type of interaction is primarily involved in the binding of DNA-binding motifs to DNA?
What type of interaction is primarily involved in the binding of DNA-binding motifs to DNA?
Which structural feature of zinc fingers allows them to interact with DNA?
Which structural feature of zinc fingers allows them to interact with DNA?
What is a characteristic of the transcription factors’ regulatory capabilities?
What is a characteristic of the transcription factors’ regulatory capabilities?
Why is the transcriptional state of cells not considered fixed?
Why is the transcriptional state of cells not considered fixed?
What structural characteristic allows transcription factors to form dimers?
What structural characteristic allows transcription factors to form dimers?
Which transcription factor type is known for stimulating transcription?
Which transcription factor type is known for stimulating transcription?
What role do general transcription factors play in the transcription process?
What role do general transcription factors play in the transcription process?
How do transcription factors vary across different cell types?
How do transcription factors vary across different cell types?
What mechanism do coactivators use to alter nucleosome structure for transcriptional activation?
What mechanism do coactivators use to alter nucleosome structure for transcriptional activation?
Which action is NOT performed by histone acetyltransferases (HATs)?
Which action is NOT performed by histone acetyltransferases (HATs)?
Which of the following alterations may result from chromatin remodeling complexes?
Which of the following alterations may result from chromatin remodeling complexes?
What is a characteristic effect of coactivators during transcriptional regulation?
What is a characteristic effect of coactivators during transcriptional regulation?
Which of the following statements about the role of coactivators is correct?
Which of the following statements about the role of coactivators is correct?
What mechanism do Nxf1 and Nxt1 utilize for mRNA export?
What mechanism do Nxf1 and Nxt1 utilize for mRNA export?
What structural feature distinguishes Helix-Loop-Helix (HLH) transcription factors?
What structural feature distinguishes Helix-Loop-Helix (HLH) transcription factors?
What is the primary function of the FG domain in nucleoporins?
What is the primary function of the FG domain in nucleoporins?
Which proteins are necessary for transporting proteins with a Nuclear Localization Signal (NLS)?
Which proteins are necessary for transporting proteins with a Nuclear Localization Signal (NLS)?
Which amino acids are specifically mentioned as basic residues that play a role in DNA binding?
Which amino acids are specifically mentioned as basic residues that play a role in DNA binding?
What is a primary function of transcription factors (TFs) when bound to response elements?
What is a primary function of transcription factors (TFs) when bound to response elements?
What characteristic is unique to the structure of the nuclear pore complex (NPC)?
What characteristic is unique to the structure of the nuclear pore complex (NPC)?
What distinguishes a Nuclear Export Signal (NES) from a Nuclear Localization Signal (NLS)?
What distinguishes a Nuclear Export Signal (NES) from a Nuclear Localization Signal (NLS)?
Which component is commonly found in proximal promoters that serves as a consensus sequence for general transcription factors?
Which component is commonly found in proximal promoters that serves as a consensus sequence for general transcription factors?
What defines enhancer sites in gene regulation?
What defines enhancer sites in gene regulation?
Why are only mature mRNAs exported from the nucleus?
Why are only mature mRNAs exported from the nucleus?
What role do transport receptors like importins and exportins play in nuclear trafficking?
What role do transport receptors like importins and exportins play in nuclear trafficking?
What function do co-activators serve in transcription?
What function do co-activators serve in transcription?
How do nucleoporins contribute to the functionality of the nuclear pore complex?
How do nucleoporins contribute to the functionality of the nuclear pore complex?
What characteristic is shared by both basic Helix-Loop-Helix (bHLH) and basic Leucine Zipper (bZIP) transcription factors?
What characteristic is shared by both basic Helix-Loop-Helix (bHLH) and basic Leucine Zipper (bZIP) transcription factors?
What type of dimer is formed by Helix-Loop-Helix (HLH) transcription factors?
What type of dimer is formed by Helix-Loop-Helix (HLH) transcription factors?
What indication do proteins have for their transport to the nucleus?
What indication do proteins have for their transport to the nucleus?
How do distal promoter elements typically differ from proximal promoters?
How do distal promoter elements typically differ from proximal promoters?
Which statement accurately describes how transcription factors interact with DNA?
Which statement accurately describes how transcription factors interact with DNA?
Flashcards
mRNA precursor
mRNA precursor
The initial RNA molecule transcribed from a gene before any modifications.
Splicesome
Splicesome
The molecular machinery that removes introns from pre-mRNA.
Ribozyme
Ribozyme
An RNA molecule with enzymatic activity, such as in splicing.
Polysome
Polysome
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Nuclear Envelope
Nuclear Envelope
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Nuclear Trafficking
Nuclear Trafficking
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Chromatin
Chromatin
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Nuclear Pore Complex (NPC)
Nuclear Pore Complex (NPC)
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Nuclear Localization Signal (NLS)
Nuclear Localization Signal (NLS)
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Nuclear Export Signal (NES)
Nuclear Export Signal (NES)
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Importins
Importins
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Exportins
Exportins
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mRNA Export
mRNA Export
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ribonucleoproteins (RNPs)
ribonucleoproteins (RNPs)
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FG domain
FG domain
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Gene Regulation
Gene Regulation
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Transcriptional State
Transcriptional State
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Transcription Factors (TFs)
Transcription Factors (TFs)
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General Transcription Factors
General Transcription Factors
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Sequence-Specific Transcription Factors
Sequence-Specific Transcription Factors
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Activators
Activators
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Repressors
Repressors
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DNA-binding Motifs
DNA-binding Motifs
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Zinc Fingers
Zinc Fingers
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Helix-Loop-Helix (HLH)
Helix-Loop-Helix (HLH)
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Global Translational Regulation
Global Translational Regulation
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eIF2 Phosphorylation
eIF2 Phosphorylation
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What happens when eIF2 is phosphorylated?
What happens when eIF2 is phosphorylated?
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Stress and Translation
Stress and Translation
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Transcription Factor
Transcription Factor
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Co-activator
Co-activator
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Chromatin Remodelling Complex
Chromatin Remodelling Complex
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HAT (Histone Acetyltransferase)
HAT (Histone Acetyltransferase)
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What is the effect of adding acetyl groups to histone proteins?
What is the effect of adding acetyl groups to histone proteins?
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What is the role of SWI/SNF in transcription?
What is the role of SWI/SNF in transcription?
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CBP (CREB-binding Protein)
CBP (CREB-binding Protein)
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TFIID
TFIID
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How do CBP and TFIID affect transcription?
How do CBP and TFIID affect transcription?
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What is the relationship between co-activators and transcription?
What is the relationship between co-activators and transcription?
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Nucleoporins
Nucleoporins
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mRNA Transport
mRNA Transport
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What is a Zinc Finger?
What is a Zinc Finger?
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Helix-Loop-Helix (HLH) Motif
Helix-Loop-Helix (HLH) Motif
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Leucine Zipper Motif
Leucine Zipper Motif
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SWI/SNF
SWI/SNF
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Histone Acetyltransferase (HAT)
Histone Acetyltransferase (HAT)
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Chromatin Remodeling
Chromatin Remodeling
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How does acetylation affect transcription?
How does acetylation affect transcription?
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Basic Amino Acids in HLH
Basic Amino Acids in HLH
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HLH Dimers
HLH Dimers
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Leucine Zipper
Leucine Zipper
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Basic Leucine Zipper (bZIP)
Basic Leucine Zipper (bZIP)
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Response Elements
Response Elements
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Proximal Promoter
Proximal Promoter
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Distal Promoter
Distal Promoter
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Enhancers
Enhancers
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Co-activators-Direct Interactions
Co-activators-Direct Interactions
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Co-activators-Chromatin Remodeling
Co-activators-Chromatin Remodeling
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Mediator Complex
Mediator Complex
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Study Notes
HSS2305: Molecular Mechanisms of Disease
- The course covers molecular mechanisms of disease.
- Lecture 11 focused on the control of gene expression.
Lecture Outline
- Announcements
- Sample questions
- Control of gene expression
- Midterm and assignment reminders
- Important topics covered in this semester included rare disease assignments, topics emailed out, deadlines, reminders about plagiarism, reference managers, and APA formatting.
Lecture 10 Review Questions
-
Question 1: The primary transcript (mRNA precursor) contains:
- Poly(A) tail
- Introns
- 5'-Cap
- Amino acids
-
Question 2: What is the machinery that removes introns?
- Spliceosome
- Proteasome
- Autophagosome
- Ribosome
-
Question 3: U6 is an example of what?
- Carbohydrate
- Protein enzyme
- Ribozyme
- Inorganic catalyst
-
Question 4: A polysome is:
- A single ribosome bound to a single mRNA
- A transcriptional machine
- Multiple ribosomes bound to a single mRNA
- A single ribosome bound to multiple mRNAs
Nucleus
- Site of transcription
- Tightly packed DNA and protein complex (chromatin)
- Nuclear envelope
- Nuclear pores
- Nucleolus
- Proteins for transcription transported into nucleus
- RNA products transported out of nucleus
Nuclear Envelope
- Double membrane
- Outer membrane continuous with rough endoplasmic reticulum (RER)
- Inner membrane with lamina for support and chromatin anchoring
- ~60 transmembrane proteins
-
1000 nuclear pore complexes
Nuclear Pore Complex (NPC)
- Composed of nucleoporins (~30 different)
- Gateway for RNAs and proteins
- Octagonal symmetry
- Central channel ~20-40nm in diameter
- Nucleoporins line the channel with FG domains (phenylalanine-glycine repeats)
- Hydrophobic mesh blocks free diffusion of large macromolecules
Nuclear Trafficking: Transport of Proteins Across Nuclear Envelope
- Proteins with specific amino acid sequences (NLS) are transported.
- Nuclear export signal (NES)
- Transport receptors (importins and exportins)
- Heterodimeric receptor (importin α/β) binds NLS
- Exportins and RanGTP
- Proteins transported across the nuclear envelope via nuclear pores
Nuclear Trafficking: Transport of mRNA Across Nuclear Envelope
- mRNAs transported as ribonucleoproteins (RNPs)
- Associated proteins interact with FG domains of nucleoporins
- Only mature mRNAs (fully processed) are exported
- Nxf1 and Nxt1-dependent
- Not exportin or RanGTP dependent
Genetic Blueprint and Transcriptional State
- Every cell in an organism has the same DNA, but not every cell looks or acts the same.
- Gene expression and the transcriptional state determine cell types (e.g. myofibers vs. skin fibroblasts)
- Cell type-specific gene expression is tightly controlled and varies between cell types and conditions.
Overview of Gene Regulation
- There are 4 levels of gene regulation:
- Transcriptional
- Processing
- Translational
- Post-translational
- These processes can be regulated independently or in conjunction to achieve a wide range of cellular outcomes.
2 - mRNA Processing Control
- RNA transcripts undergo processing.
- Only processed mRNA can exit the nucleus.
- Splicing via action of snRNPs in the nucleus.
- Different splice sites can be repressed or activated.
- SR proteins activate splice sites (e.g., exon/intron splicing enhancers). hnRNPs repress.
3 - Translational control
- Initiation and progression of translation.
- Global regulation affects all mRNAs (phosphorylation of initiation factors like eIF2 inhibits translation).
- Specific regulation affects the translation of specific mRNAs (e.g. Ferritin) with stem loops in the mRNA's 5' and 3' UTR and other regulatory factors like microRNAs (miRNAs)
- mRNA localization to specific cellular sites.
- mRNA stability within the cytoplasm.
4 - Post-Translational Control
- Protein degradation (proteasomes)
- Proteasomes degrade proteins within the nucleus and cytosol.
- Ubiquitin ligases (e1, e2, e3) attach ubiquitin to proteins to be degraded.
- Polyubiquinated proteins bind to the proteasome.
- Proteasome unfolds target proteins and degrades them to smaller peptides and amino acids.
RNA interference (RNAi)
- Some types of RNA inhibit gene expression via destruction of specific mRNA molecules (small interfering RNAs (siRNAs) in plants and microRNAs (miRNAs) in mammals)
MicroRNAs (miRNAs)
- Important regulators in biological processes.
- Abnormalities in miRNA can play a major role in the development of diseases.
- miRNAs bind to sites in the 3' UTR of mRNAs and have multiple target mRNAs
siRNAs
- Unknown if naturally occurring in mammals but found in plants.
- Clinical applications using designed siRNAs to silence disease-related genes.
- Strategies being developed for diseases like HIV, Hepatitis, and Cancer.
siRNAs - Clinical Applications
- Techniques are promising, but delivery complications and immune responses can be obstacles.
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Description
This quiz focuses on Lecture 11 of the HSS2305 course, which discusses the control of gene expression. Key concepts such as mRNA processing, spliceosomes, and polysomes are covered. Test your understanding of molecular mechanisms involved in gene expression.
