L12: Regulating Gene Expression Flashcards
What is the first step in gene expression after DNA?
DNA is transcribed into messenger RNA (mRNA) through the process of transcription
What does the primary mRNA transcript contain?
The primary mRNA transcript contains both exons (coding regions) and introns (non-coding regions)
What is the role of splicing in gene expression?
Splicing removes introns and joins exons together to form a mature mRNA sequence that can be translated into protein
What modifications occur to mRNA after splicing?
The mRNA undergoes a 5’ cap addition (guanine cap) and a 3’ polyadenylation (Poly-A tail) before being exported to the ribosome for translation
How many genes are estimated to be expressed in humans?
Around 20,000 genes are expressed in the human genome
What is differential splicing?
Differential splicing refers to the process by which different combinations of exons are joined together, creating various mRNA variants and, therefore, different proteins
How do specialised cell types like muscle and nerve cells differ despite having the same genome?
Specialised cells express different subsets of genes, leading to the production of unique proteins that give rise to their specialised functions
What are housekeeping genes?
Housekeeping genes are essential for basic cell functions and are expressed in nearly all cells (e.g., those encoding histones, RNA polymerase, and glycolytic enzymes)
What is the role of specific proteins in specialised cells?
Specific proteins, such as myosin in muscle cells or microtubule-associated proteins in neurons, are responsible for the distinct functions of each cell type
How are gene expression levels regulated in cells?
Gene expression is regulated through mechanisms such as chromatin modifications, transcriptional control, splicing, translation, and protein degradation
What is the difference between constitutive and inducible gene expression?
Constitutive gene expression is always active, while inducible gene expression is activated under specific conditions or stimuli
What is the significance of microRNAs in gene regulation?
MicroRNAs help fine-tune gene expression by binding to mRNA and inhibiting its translation or promoting its degradation
What is transcriptional regulation?
Transcriptional regulation controls whether genes are transcribed into mRNA, influencing protein production
How does the stability of mRNA affect protein production?
The stability of mRNA determines how long it remains in the cell, impacting how much protein is produced from it. Less stable mRNA may degrade before translation, while more stable mRNA may produce more protein
What role does phosphorylation play in protein regulation?
Phosphorylation can activate or deactivate proteins, influencing their activity within the cell
What is an example of rapid protein regulation in response to environmental changes?
Hypoxia-inducible factor (HIF1) is a protein that is usually degraded but stabilises when oxygen levels are low, allowing it to activate responses to low oxygen conditions
What percentage of the human genome is involved in coding for proteins?
About 24% of the human genome is involved in coding for proteins, while the rest consists of non-coding regions, including introns
What is alternative splicing? How does it contribute to protein diversity?
Alternative splicing allows different combinations of exons to be joined together, leading to the production of multiple protein isoforms with distinct functions from a single gene
What is the role of RNA polymerase in gene expression?
RNA polymerase is an enzyme that synthesises RNA from a DNA template during the transcription process
How do transcription factors regulate gene expression?
Transcription factors are proteins that bind to specific DNA sequences near genes, either promoting or inhibiting the transcription of those genes
What is the function of histone proteins in gene regulation?
Histones help package DNA into chromatin and can be modified (e.g., acetylation or methylation) to regulate gene accessibility and expression
What is the significance of epigenetic modifications in gene expression?
Epigenetic modifications, such as DNA methylation and histone modification, can turn genes on or off without altering the DNA sequence itself, influencing gene expression
What is the difference between gene expression in prokaryotes and eukaryotes?
In prokaryotes, gene expression is simpler with transcription and translation occurring simultaneously, while in eukaryotes, transcription happens in the nucleus, and translation occurs in the cytoplasm after mRNA processing
What is RNA interference (RNAi)?
RNA interference is a process where small RNA molecules, such as microRNAs or small interfering RNAs (siRNAs), regulate gene expression by targeting mRNA for degradation or inhibiting translation
What are polycistronic and monocistronic mRNA?
Polycistronic mRNA can encode multiple proteins from a single transcript (common in prokaryotes), while monocistronic mRNA encodes a single protein (typical in eukaryotes)
How is gene expression regulated within a cell?
Gene expression can be active, repressed, or silenced. If a gene is not needed, it may be methylated and never expressed, or it can be dynamically regulated and activated
What percentage of genes do not have introns?
About 3% of genes do not have introns and are single exon genes
What is the general size of exons and introns in most genes?
Exons are usually smaller, around 200 base pairs or less, while introns are much larger, ranging from 10 base pairs to over 100,000 base pairs
How are exons and introns processed during transcription?
Exons are spliced together, and introns are removed in a highly regulated, co-transcriptional process involving RNA polymerase and splicing factors
How can you experimentally determine if splicing has occurred in a gene?
- By using PCR with primers designed for amplification of exon regions, you can identify splicing events by comparing the size of DNA and RNA fragments
- A smaller band in the RNA sample indicates that splicing has occurred and introns have been removed
How has gene sequencing improved the study of splicing?
With advanced techniques like rapid gene sequencing, you can now identify which splice variants are expressed in RNA populations within a cell
What evolutionary advantage does the intron-exon structure of genes provide?
Introns allow for genetic rearrangement and exon shuffling, where exons (which code for important protein sites) can be rearranged and combined with other genes, facilitating the generation of nre protein functions and increasing genetic diversity
Why is exon shuffling considered an important mechanism in evolution?
Exon shuffling enables recombination of exons from different gene, creating new protein combinations and functional domains, leading to novel protein functions and contributing to evolutionary diversity
Can introns be included in protein products?
Yes, there are cases where intronic sequences can be retained in the protein product and can add new functional domains or regulatory elements to the protein, contributing to its functionality
What is the role of splicing factors in gene regulation?
Splicing factors bind to the RNA during transcription and regulate the removal of introns and the joining of exons, a process that is essential for generating mature mRNA
What is a co-transcriptional process in RNA processing?
Co-transcriptional processes occur during transcription, where RNA polymerase synthesises RNA and splicing factors simultaneously process the RNA, including capping and splicing
What is the relationship between RNA polymerase and splicing factors?
RNA polymerase assembles on DNA to transcribe RNA, and splicing factors are associated with the carboxy terminus of RNA polymerase to facilitate RNA splicing during transcription
How does the chromatin structure affect RNA splicing?
Chromatin structure, including epigenetic modifications like methylation, can influence the accessibility of splicing factors to the gene, thus affecting the splicing process
Why do exons vary in size compared to introns?
Exons are usually smaller because they contain the coding sequences that will become part of the protein, while introns are non-coding regions that can be larger and may serve regulatory or structural roles
What role does methylation play in gene expression regulation?
Methylation of DNA, particularly in the promoter region or around genes, typically represses gene expression by making the gene less accessible for transcription
What is the significance of the carboxy terminus of RNA polymerase in transcription?
The carboxy terminus of RNA polymerase is where splicing factors are recruited to regulate the splicing process as RNA is synthesised
What sequence signals the start of an intron on the 5’ end?
An AG followed by a GQ sequence on the 5’ end signals the start of an intron
What sequence signals the end of an intron on the 3’ end?
A sequence on the 3’ end of an intron signals the end of the intron and the beginning of the next exon
What is the “branch point” in RNA splicing?
- The branch point is a sequence in the middle of the intron crucial for the initial splicing process - allows lariat formation, initiating the loop structure that allows intron excision
- Typically an adenine
What is the function of the 5’ donor site and 3’ acceptor site?
The 5’ donor site and 3’ acceptor site are where the intron is cut out, allowing exon ends to join
What are snRNPs in RNA splicing?
snRNPs (small nuclear ribonucleoproteins) are complexes containing small nuclear RNAs essential for recognising exon-intron boundaries and aiding in splicing
Which small nuclear RNAs are involved in RNA splicing?
Small nuclear RNAs like U1, U2, U4, U5, and U6 are involved in the splicing complex
What is the spliceosome?
The spliceosome is a complex of proteins and snRNPs that facilitates the splicing of RNA by recognising and binding to exon-intron boundaries
How do small nuclear RNAs (snRNAs) contribute to splicing specificity?
snRNAs pair with complementary sequences on the RNA, guiding the snRNPs to the correct intron-exon boundaries
What are heterogeneous nuclear ribonucleoproteins (hnRNPs)?
hnRNPs are proteins that bind to exons, prevent unintended splicing by suppressing splicing or modulating exon inclusion to regulate mRNA diversity, stabilising exon-exon boundaries
What role do serine-arginine-rich (SR) proteins play in splicing?
SR proteins promote splicing by binding to specific exon sequences, enhancing spliceosome assembly
What is alternative RNA splicing?
Alternative RNA splicing is a process where different combinations of exons are joined, leading to diverse protein products from a single gene
How does cellular context affect RNA splicing?
Cellular context, including factors like cell type and environment, can influence which exons are included or skipped in splicing
What is the role of U1 and U2 snRNPs in splicing initiation?
U1 binds to the 5’ splice site, while U2 binds to the branch point sequence, marking the start of the splicing process
How do lariat structures form in splicing?
A lariat loop forms when the intron’s branch point connects to the 5’ splice site, enabling the spliceosome to join exon ends
How does the spliceosome facilitate exon joining?
The spliceosome brings the ends of the exons together, allowing them to connect and release the intron lariat
What is the fate of introns after they are spliced out?
Introns are usually degraded after splicing
What is exon skipping?
Exon skipping is when a particular exon is excluded from the final mRNA transcript due to regulatory proteins
What effect does alternative splicing have on protein diversity?
Alternative splicing increases protein diversity by allowing different proteins to be produced from the same gene
How does alternative splicing contribute to cellular specialisation?
Alternative splicing creates cell-specific proteins, enabling specialised functions in different cell types
How does alternative splicing relate to disease?
Misregulation of splicing can lead to disease by creating faulty proteins, such as in certain cancers, spinal muscular atrophy, and cystic fibrosis
What is an example of a protein affected by alternative splicing?
Vascular endothelial growth factor (VEGF) has multiple splice variants that influence cell association and diffusion properties
How does alternative start site selection affect gene expression?
Different start sites can lead to different exon combinations, influencing which protein variants are produced in each cell type
What can happen if a splice site is skipped, mutated, or retained inappropriately?
A mutation, skipping or retaining splice sites incorrectly can lead to exon skipping, intron retention or production of a truncated or non-functional proteins, impacting cell function
What role do splice silencers play in RNA splicing?
Splice silencers are RNA sequences that bind regulatory proteins to inhibit splicing at specific sites, modulating which exons are included
How do splice enhancers influence the splicing process?
Splice enhancers are sequences within RNA that recruit proteins to promote splicing at nearby exon-intron junctions
Why is U6 snRNA considered essential in splicing?
U6 snRNA helps catalyse the splicing reaction by forming the active site within the spliceosome for exon ligation
How does the spliceosome ensure accuracy during splicing?
The spliceosome assembles stepwise, allowing multiple checkpoints for ensuring correct recognition and pairing of exon-intron boundaries
What effect does alternative 3’ or 5’ splice site selection have on the mRNA product? What is the effect on the immune system?
- Alternative 3’ or 5’ splice site selection can alter exon length, leading to proteins with altered or truncated domains
- In immune cells can produce different antibody forms or cytokine variants, crucial for immune response diversity