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Differential splicing allows the same DNA to produce different proteins in various cell types.
True
Constitutive genes are expressed only when needed by the cell.
False
Inducible gene expression is always active and does not respond to external signals.
False
Calcitonin functions as both a hormone and a neurotransmitter.
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Post-transcriptional regulation involves the modification of mRNA after it has been transcribed.
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The poly(A) tail addition occurs at the 5’ end of the transcript.
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The addition of adenine residues to the cleaved 3’ end of mRNA by Poly(A) Polymerase ranges from 40 to 250 residues.
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MRNA must be fully processed before it can be translated.
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Exons encode the non-coding regions of a gene.
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The stability of an mRNA molecule is determined by its 3’ UTR sequence.
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The 5’ CAP of mRNA helps to protect against degradation.
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Transfer RNAs (tRNAs) are essential for protein synthesis as they act as adaptors between mRNA and amino acids.
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Exonucleases degrade mRNA starting from the 5’ end.
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Basal promoters are bound by RNA polymerase I and transcription factors.
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The TATA box is more common and stronger than the CCAT box in basal promoter elements.
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RNA polymerase II transcribes both DNA strands during the transcription process.
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The transcription bubble remains unwound during the elongation phase of transcription.
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The 3' UTR is part of the coding region in mRNA.
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5' capping of mRNA involves the addition of a 7-methylguanosine residue.
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The primary transcript synthesized by RNA pol II is known as heterogenous nuclear RNA (hnRNA).
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Polyadenylation signals RNA polymerase II to continue transcribing past the 3' UTR.
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Exonucleases help in the stabilization of the RNA molecule after synthesis.
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Inducible gene expression is controlled by transcription factor proteins.
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RNA polymerase II reads the DNA template strand in the 5' to 3' direction.
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Steroid hormones bind to enzymes to form a homodimer that recognizes specific inducible transcription factors.
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Inducible transcription factors are always expressed in the cell.
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Beta cells of the pancreas regulate insulin transcription based on fasting and fed states.
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Transcription factors can directly interact with RNA polymerase II to promote transcription.
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The rate of transcription is not affected by the number of binding sites for a transcription factor in a promoter.
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MRNA is responsible for forming the basic structure of ribosomes.
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Inducible transcription factors allow a rapid response to stimuli in cells and tissues.
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TRNAs act as adaptors between mRNA and amino acids.
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Small nuclear RNAs (snRNAs) are primarily involved in protein synthesis.
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Non-coding RNAs (ncRNAs) play a role in regulating gene expression.
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The majority of the human genome is composed of sequences that code for proteins.
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MicroRNA (miRNA) is made up of 50-100 nucleotides.
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MiRNA promotes gene expression by blocking RNA degradation.
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Regulatory non-coding DNA was previously referred to as 'junk' DNA.
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Complementarity is the basis of miRNA's mechanism of action.
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The main sugar found in RNA is deoxyribose.
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All types of RNA contribute to protein synthesis.
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Promoters are located downstream of the transcription start site (TSS).
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RNA polymerase II is responsible for the transcription of protein-coding genes.
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Uracil is the nitrogenous base found in DNA, replacing adenine.
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The basal promoter element is one of the types of promoter regions that direct transcription.
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Transfer RNAs (tRNAs) are involved in the regulation of gene expression.
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Distinct 'start' and 'stop' signals in DNA are crucial for the process of transcription.
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Messenger RNA (mRNA) serves as the 'blueprint' of the cell for protein synthesis.
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Transcription factors play a crucial role in both constitutive and inducible gene expression.
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The addition of a poly(A) tail to mRNA occurs at the 5' end of the transcript.
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Post-transcriptional regulation includes processes like splicing and capping of mRNA.
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RNA polymerase II transcribes both strands of DNA during the transcription process.
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The stability of an mRNA molecule is primarily determined by its 5' UTR sequence.
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Alternative splicing allows the same gene to produce different protein variants.
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Exons are the coding regions of a gene that are expressed in the final mRNA product.
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Steroid hormones bind to transcription factors to form a homodimer that allows for the switching on of specific genes.
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Inducible transcription factors are present in the cell at all times, regardless of environmental conditions.
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The amount and activity of transcription factors can influence the rate of transcription of specific genes.
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The rate of transcription remains constant regardless of the number of binding sites for transcription factors in a promoter.
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Beta cells in the pancreas regulate insulin transcription differently during fasting and fed states.
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MRNAs are responsible for forming ribosomes and are primarily structural.
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Inducible transcription factors allow only the necessary genes to be activated, providing a rapid response mechanism.
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Transcription factors do not have the ability to bring in chromatin modifiers to assist with gene transcription.
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The 3’ poly(A) tail addition occurs at the 5’ end of an mRNA transcript.
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MRNAs contain both introns and exons, but only exons encode the protein-coding region.
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The stability of mRNA is completely independent of its 3’ UTR sequence.
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The poly(A) tail gradually shortens over the lifetime of the mRNA molecule.
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Ribosomal RNAs (rRNAs) play no role in protein synthesis.
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Endonucleases degrade RNA starting from the 3’ end of the molecule.
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The addition of adenine residues to mRNA by Poly(A) Polymerase can vary from 20 to 150 residues.
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Transfer RNAs (tRNAs) are not involved in protein synthesis.
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Introns are retained in mature RNA after transcription.
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SnRNPs are composed solely of proteins.
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The spliceosome is a complex that facilitates the splicing of pre-mRNA.
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The process of splicing occurs after the addition of the 5' cap but before the transport of RNA into the cytoplasm.
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A specific adenine nucleotide plays a crucial role in the splicing process.
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Exons are non-coding portions of a gene that are removed during RNA processing.
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Introns can vary greatly in size, from as few as 50 nucleotides to more than 10,000 nucleotides.
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The 5’ end of the intron becomes attached to a specific nucleotide during the splicing process.
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The process of polyadenylation adds 40-250 guanine residues to the 3’ end of mRNA.
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The addition of the poly(A) tail significantly enhances the stability of mRNA by preventing degradation.
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Exons are responsible for coding regions that do not contribute to the final protein product.
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Destabilizing sequences within the 3’ UTR of mRNA can target it for degradation.
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A 5’ cap on mRNA molecules is crucial for ribosomal assembly and initiation of translation.
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Transfer RNAs (tRNAs) are primarily responsible for coding the protein-coding regions of mRNA.
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MRNA stability is primarily determined by its 5’ UTR sequence.
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Poly(A) binding protein (PABP) binds to the poly(A) tail and stabilizes mRNA when it has more than 30 residues.
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Inducible genes are continuously expressed regardless of environmental conditions.
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Basal promoters bind RNA polymerase II before any transcription factors.
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Constitutive transcription factors are always active and regulate genes essential for life.
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Cell type differentiation occurs despite all cells having the same DNA content.
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Transcription factors can bind to both enhancer elements and basal promoters to regulate gene transcription.
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The CCAT box is more commonly found than the TATA box within basal promoter elements.
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Extracellular cues do not influence the expression of inducible genes.
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Post-transcriptional regulation only affects the coding regions of mRNA.
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During transcription, RNA polymerase II synthesizes RNA in a 3' to 5' direction.
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The addition of a 7-methyl-guanidine residue is a part of the 3' capping process.
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The terminator region is where RNA polymerase II disengages from the mRNA being transcribed.
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Heterogenous nuclear RNA (hnRNA) encompasses all RNA molecules in the nucleus, including mRNA and rRNA.
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The transcription bubble created during elongation remains stationary along the DNA template.
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Polyadenylation signals that RNA polymerase II should stop transcription at the 5' UTR.
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The primary transcript synthesized by RNA polymerase II is an mRNA molecule ready for translation.
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Transcription factors interact with RNA polymerase II to inhibit transcription.
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Beta cells of the pancreas can regulate insulin transcription in response to fasting and fed states.
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Steroid hormones bind to steroid receptor proteins to form heterodimers for gene regulation.
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Inducible transcription factors are always present in active form in cells.
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The presence of multiple binding sites for transcription factors in a promoter increases the likelihood of transcription occurring.
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Inducible gene expression allows for a static and unresponsive gene regulation mechanism.
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MRNAs primarily encode for proteins and are categorized as non-coding RNAs.
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RNA polymerase II is responsible for transcribing all genes, including ribosomal RNA.
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The splicing of pre-mRNA involves the removal of exons and retention of introns.
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SnRNPs are formed from small nuclear RNAs and a variety of proteins.
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The spliceosome consists of multiple snRNPs and is responsible for recognizing and interacting with specific sequences at exon-intron boundaries.
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Intron sizes can vary from 100 to 10,000 nucleotides in length.
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The loop of RNA formed during splicing involves the attachment of the 3' end of the intron to a specific nucleotide.
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Non-coding RNAs (ncRNAs) are involved solely in regulating gene expression and do not have other cellular functions.
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The splicing process occurs before the mRNA is transported into the cytoplasm.
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The free 3' end of one exon does not interact with the 5' end of another exon during splicing.
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Study Notes
Promoter Elements
- The basal promoter of a gene consists of two types:
- TATA box: Located 20-30 base pairs upstream of the transcription start site, binds basal transcription factors (TFs) and RNA polymerase II (RNAPII)
- CCAT box: Located 50-130 base pairs away from the transcription start site, less common and weaker than the TATA box
- Promoter elements are essential for the transcription of all genes
- They recruit RNAPII for the initiation of transcription
Transcription
- RNA Pol II transcribes just one strand of DNA (the template strand)
- RNAPII reads the template strand 3’ to 5’ and creates an RNA copy 5’ to 3’
- Transcription proceeds in 3 stages:
- Initiation: RNAPII binds to the promoter and unwinds a 17-18 bp segment, forming the ‘Open Complex’
- Elongation: RNAPII moves along the template strand, synthesizing RNA until it reaches the terminator region
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Termination: Transcription continues beyond the protein-coding region, resulting in a 3’UTR (UnTranslated Region)
- The Polyadenylation signal sequence (AAUAAA) within the transcribed sequence signals RNA Pol II to disengage
- The nascent mRNA molecule is released for processing and degradation if necessary
mRNA Processing
- The RNA molecule transcribed by RNAPII is called the primary (1°) transcript
- Primary transcripts are also known as heterogenous nuclear RNA (hnRNA)
- hnRNA undergoes extensive modification
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5’ Capping: Addition of a 7-methylguanosine residue to the 5’ end of mRNA
- The 5' cap protects mRNA from degradation, promotes export, and aids recognition by the translation machinery
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3’ poly(A) tail: Addition of a string of adenine residues (~40-250) to the cleaved 3’ end of mRNA
- The poly(A) tail confers stability to mRNA molecules
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5’ Capping: Addition of a 7-methylguanosine residue to the 5’ end of mRNA
Post-Transcriptional Regulation
- After transcription, a pre-mRNA molecule contains introns and exons
- Introns are non-coding, while exons encode the protein-coding region
- Pre-mRNA must undergo processing before translation
- Key areas of post-transcriptional regulation:
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mRNA stability: The longevity of mRNA can be determined by specific sequences present in the 3’UTR
- Sequences within the 3’UTR can target mRNAs for degradation
- The 5’ cap protects mRNA from degradation
- The poly(A) tail confers stability to mRNA molecules
- Differential mRNA splicing: Specific combinations of exons are joined together, resulting in production of different protein isoforms from the same gene
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mRNA stability: The longevity of mRNA can be determined by specific sequences present in the 3’UTR
Different Types of RNA
- mRNA: Messenger RNAs that code for proteins
- rRNA: Ribosomal RNAs, involved in protein synthesis and form the structure of the ribosome
- tRNA: Transfer RNAs, responsible for transferring amino acids to the ribosome during protein synthesis
- snRNA: Small nuclear RNAs, involved in a variety of nuclear processes, including pre-mRNA splicing
- ncRNA: Non-coding RNAs, regulate gene expression and participate in diverse cellular processes
Regulatory Non-coding DNA
- Formerly referred to as “junk DNA”
- The ENCODE (Encyclopaedia of DNA Elements) project revealed that a significant portion of the genome is actively transcribed and plays regulatory roles
miRNA
- Small non-coding RNA strands (20-25 nucleotides)
- Regulate gene expression by binding to complementary mRNA sequences
- Can either block translation or promote mRNA degradation
- Primarily act as negative regulators of gene expression
Inducible Transcriptional Regulation
- Cells have the ability to switch genes on or off in response to environmental cues, through the action of inducible transcription factors
- The activity of transcription factors is critical in controlling gene expression
- Transcription factors bind to specific DNA sequence elements and control the rate of transcription, helping to create a dynamic response to stimuli
Constitutive Gene Expression
- Some genes are constantly expressed, often encoding essential proteins involved in metabolism, repair, and essential cellular functions
- These genes are called constitutive genes due to their continuous expression
Inducible Gene Expression
- Inducible genes are only expressed when required, enabling responsiveness to environmental changes
- Induction of gene expression can be triggered by extracellular cues like hormones, cytokines, and cell-cell interactions
- Signals are transduced into the cell to initiate transcription of new genes, resulting in the synthesis of required proteins
RNA structure and function
- RNA is a nucleic acid similar to DNA, but with key differences
- RNA contains ribose sugar instead of deoxyribose
- RNA contains uracil (U) instead of thymine (T)
- RNA is single-stranded unlike DNA which is double-stranded.
- RNA plays a crucial role in gene expression by copying genetic information from DNA and contributing to ribosome formation.
Types of RNA
- mRNA (messenger RNA): carries genetic information from DNA to ribosomes for protein synthesis
- rRNA (ribosomal RNA): forms the structural and catalytic core of ribosomes, essential for protein synthesis
- tRNA (transfer RNA): acts as an adapter molecule during protein synthesis, carrying specific amino acids to the ribosomes based on the mRNA sequence
- snRNA (small nuclear RNA): involved in various nuclear processes, particularly pre-mRNA splicing
- ncRNA (non-coding RNA): a diverse group of RNA molecules that do not code for proteins, involved in various cellular processes: gene regulation, X-inactivation.
Transcription
- Transcription is the process of copying genetic information from DNA to RNA
- Transcription initiates at the Transcription Start Site (TSS)
- Promoters are DNA regions upstream of the TSS that regulate transcription initiation
- Two types of promoters: basal promoter elements and enhancer elements.
- Transcription ends at a termination sequence in the DNA.
Post-Transcriptional Processing
- Newly transcribed RNA molecules undergo post-transcriptional processing to become mature mRNAs.
- This process includes:
- 5' capping: a modified guanine nucleotide is added to the 5' end of the mRNA, protecting it from degradation and aiding in ribosome binding.
- 3' Polyadenylation: a string of adenine nucleotides (poly-A tail) is added to the 3' end of the mRNA, increasing its stability and facilitating export from the nucleus.
- Splicing: non-coding introns are removed from the pre-mRNA, and coding exons are stitched together to form mature mRNA.
mRNA Stability
- The stability of mRNA molecules varies and is influenced by sequences within the mRNA, particularly in the 3' UTR.
- Destabilizing sequences in the 3' UTR can target mRNA for degradation by endonucleases.
- The 5' cap protects against degradation from exonucleases.
- The poly-A tail confers stability and is bound by poly-A binding protein (PABP), which protects the mRNA from degradation.
Splicing
- Splicing is the removal of non-coding introns from pre-mRNA
- Splicing is carried out by the spliceosome, a complex molecular machine composed of snRNAs and proteins.
- snRNPs (small nuclear ribonucleoproteins) are formed by the association of snRNAs with proteins.
- snRNPs recognize specific sequences at the ends of introns, cut the RNA at these sites and join the adjacent exons.
Inducible Gene Expression
- Inducible gene expression is controlled by transcription factors, which are proteins that regulate the rate of transcription of a gene.
- Inducible transcription factors are only active in response to specific stimuli.
- Transcription factors bind to specific DNA sequences, called response elements, and interact with RNA polymerase II to promote transcription.
- Some transcription factors can also recruit chromatin modifiers to aid in unwinding DNA or co-activators to enhance transcription.
Factors Affecting Transcription
- The number of binding sites for a specific transcription factor in a promoter determines the rate of transcription.
- Inducible transcription factors allow rapid and dynamic response to stimuli.
Basal Promoter Elements
- Essential for transcription of all genes.
- Recruits RNA Pol II for transcription.
- Binds basal transcription factors first, followed by RNA Pol II binding.
- Two main types:
- TATA box: Most common, located 20-30 base pairs upstream of the transcriptional start site. Can bind basal transcription factors and RNA Pol II independently, making it a strong element.
- CCAT box: Less common and weaker, located 50-130 base pairs upstream of the start site.
Transcription
- Catalyzed by RNA Polymerase II, transcribing one DNA strand from 3' to 5', creating an RNA copy from 5' to 3'.
- Incorporates ribonucleotide triphosphates (NTPs - A, G, C, & U) to build the mRNA copy.
- Three stages:
- Initiation: RNA Pol II binds to DNA, unwinding a 17-18 bp segment of the promoter, forming the 'Open Complex'.
- Elongation: RNA Pol II moves along the DNA template, synthesizing RNA until reaching the terminator region. A region of DNA under RNA Pol II remains unwound, creating the 'Transcription Bubble' that moves along the DNA.
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Termination: Transcription continues past the protein-coding region into the 3'UTR (UnTranslated Region) forming a new mRNA molecule. Most eukaryotic mRNA precursors contain the motif 'AAUAAA' which:
- Signals RNA Pol II to disengage.
- Recruits an endonuclease to cleave the mRNA.
- Poly(A) polymerase adds 40-250 adenine residues to the cleaved 3' end, forming the Poly(A) tail.
Post-Transcriptional mRNA Processing
- Primary transcript: RNA molecule synthesized by RNA Pol II.
- Heterogenous nuclear RNA (hnRNA): Collection of precursor molecules.
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Extensive modifications:
- 5' capping: A 7-methyl-guanosine residue is added to the 5' end of the mRNA, creating an unusual 5' to 5' triphosphate linkage. This is catalyzed by guanylyltransferase (capping enzyme), followed by methylation by an ethyltransferase enzyme. The first and second nucleotides are also methylated.
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Functions of 5' cap:
- Protects mRNA from degradation by exonucleases.
- Promotes nuclear export.
- Aids recognition by translational machinery.
- 3' poly(A) tail addition: After recognizing the polyadenylation signal sequence (AAUAAA), an endonuclease is recruited and cleaves the mRNA. Poly(A) polymerase then adds 40-250 adenine residues to the cleaved 3' end.
Post-Transcriptional Regulation: mRNA Processing
- Gene transcribes to produce mRNA containing introns and exons.
- Exons: Encode the protein coding region.
- Introns: Non-coding sequences removed during processing.
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Processing involves:
- mRNA stability: 3' UTR determines mRNA stability, with destabilizing sequences in the 3' UTR being targeted for endonuclease degradation. The 5' cap protects against degradation, and exonucleases degrade from the poly(A) tail.
- Differential mRNA splicing: Removal of introns while RNA is being synthesized, after capping but before transport to the cytoplasm.
Splicing of mRNA Precursors
- Introns are removed and adjacent exons are joined together.
- Introns range in size from 50 to ≥ 10,000 nucleotides.
- Spliceosome: Molecular machine carrying out splicing.
- Spliceosome components: Consists of RNA and protein.
- Small nuclear RNAs (snRNA): Combine with proteins to form small nuclear ribonucleoproteins (snRNPs), which facilitate splicing by recognizing and interacting with specific sequences at each end of the intron, cutting and rejoining the exons.
- Differential splicing/exon shuffling: Allows different combinations of exons to be joined, leading to the production of different proteins from the same gene, contributing to protein diversity.
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Examples:
- Calcitonin processing: Produces calcitonin (thyroid) and cGRP (nerve).
- Tropomyosin alternative splicing: Leads to the production of different isoforms of tropomyosin, contributing to muscle tissue diversity.
Importance of Gene Regulation
- All cells have the same DNA content but differentiate into distinct cell types.
- Precise regulation of gene expression is crucial to generate cell specificity by switching genes on and off.
Tissue Specificity
- Stem cells differentiate into various cell types, each displaying specific gene expression patterns, regulated by specific transcription factors.
Constitutive and Inducible Gene Expression
- Constitutive gene expression: Genes continuously expressed, such as those coding for metabolic or repair enzymes.
- Inducible gene expression: Genes expressed only when needed, allowing cells to respond to external signals.
Types of Genes
- Constitutive genes: Essential, continuously expressed.
- Inducible genes: Expressed only when needed, important for development and environmental response.
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Inducible gene expression is triggered by external cues:
- Hormones: Estrogen, testosterone.
- Cytokines: Interferons, growth factors.
- Cell-cell interactions: Cell-matrix interactions.
Inducible Transcription Factors
- Necessary for controlling inducible gene expression.
- Only present or activated when necessary.
- Allow cells and tissues to respond to environmental cues.
- Example: Insulin transcription in pancreatic beta cells.
Transcription Factor Activity
- Determines the rate of transcription.
- Binds to specific DNA sequences called response elements.
- Interacts with RNA Pol II to facilitate transcription.
- Can recruit chromatin modifiers to aid in DNA unwinding.
- Can also recruit coactivators.
- Example: SP1 binding sites influence the rate of transcription by their number in a promoter.
Importance of Inducible Transcription Factors
- Allow for quick and dynamic responses to stimuli.
- Ensure only necessary genes are activated, contributing to efficient and relevant responses to changing conditions.
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Description
Explore the key elements of gene transcription, including the roles of the TATA and CCAT boxes as basal promoter components. This quiz covers the stages of transcription initiated by RNA polymerase II, detailing the process from initiation to termination. Test your knowledge of these essential molecular biology concepts.
