Genetics: Alternative Splicing and Mutations

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Questions and Answers

What role do master transcription factors play in early development?

They suppress ncRNA activity.

They bind to super-enhancers to define cellular identity. (correct)

They induce mutations in the genome.

They enable DNA replication.

How does alternative splicing contribute to protein diversity?

By eliminating unnecessary exons entirely.

By synthesizing identical protein variants.

By creating isoforms specific to different tissues. (correct)

By increasing peptide bond formation.

Which of the following processes can lead to nonsense mediated decay?

Increased RNA turnover.

Enhanced miRNA activity.

Formation of stem loop structures in mRNA.

Presence of poison exons. (correct)

What is the significance of RNA editing in post-transcriptional regulation?

It alters the secondary structure of mRNA. Signup and view all the answers

What effect do ncRNAs such as miRNA have on target mRNAs?

They repress expression, leading to decreased protein production. Signup and view all the answers

What is the function of X-inactivation specific transcript (XIST) during embryogenesis?

To recruit repressive proteins and facilitate X chromosome inactivation Signup and view all the answers

In the context of dosage compensation in females, what occurs when one of the X chromosomes is inactivated?

Cells randomly choose which X chromosome to inactivate, maintaining balanced gene products. Signup and view all the answers

Which statement accurately reflects the role of promoter regions in transcription regulation?

Availability of the promoter influences the efficiency of RNA polymerase II elongation. Signup and view all the answers

Which mechanism is primarily involved in enhancing transcription through the interaction between enhancers and promoters?

DNA looping facilitated by the structure of topologically associated domains (TADs) Signup and view all the answers

What is the significance of the pseudoautosomal region (PAR) on the inactivated X chromosome?

It allows for some gene access even on the inactivated X chromosome. Signup and view all the answers

Which chromatin state allows for transcription activity?

Euchromatin Signup and view all the answers

What is the primary role of DNA methylation in gene expression?

Repressing transcription Signup and view all the answers

What is a function of ncRNAs in gene regulation?

Bind to chromatin remodeling complexes Signup and view all the answers

What happens during gametogenesis related to DNA methylation?

A wave of demethylation occurs Signup and view all the answers

Which loci is responsible for X-inactivation in female mammals?

X-inactivation center (XIC) Signup and view all the answers

How does histone tail modification affect gene expression?

It can lead to various chromatin states influencing transcription levels Signup and view all the answers

What characterizes interphase chromosomes regarding TADs?

They are organized into domains that can be active or repressed based on cell type Signup and view all the answers

What typically occurs to the CpG islands in gene regulation?

They are usually not methylated Signup and view all the answers

What results from intron retention during mRNA processing?

Presence of introns in mature mRNA. Signup and view all the answers

Which statement best describes alternative polyadenylation?

It can generate sequence diversity at the 3' end of mRNA. Signup and view all the answers

What characterizes a missense mutation in genetics?

It modifies one coding codon. Signup and view all the answers

What is the primary difference between a normal allele and a mutated allele?

Mutated alleles cause disease or specific conditions. Signup and view all the answers

How does a neutral mutation (conservative substitution) generally affect protein function?

It usually has no measurable impact on protein function. Signup and view all the answers

What role do mutations play in evolution?

They are a source of genetic variation. Signup and view all the answers

What is a key feature of ribosome size in translation compared to transcription?

Ribosomes are larger than those involved in transcription. Signup and view all the answers

What is a consequence of splicing errors in mRNA processing?

Alteration in the peptide sequence leading to diseases. Signup and view all the answers

What is necessary for the new restriction site when isolating a gene of interest?

It must exist on the vector before gene insertion. Signup and view all the answers

What indicates a forward orientation of the gene of interest during gel electrophoresis?

Matching the theoretical bp readings of the white colony cells. Signup and view all the answers

Which outcome signifies that the plasmid was successfully ligated but did not contain the correct insertion?

Colored colonies that are blue. Signup and view all the answers

What occurs to bacteria that do not absorb a plasmid in the presence of antibiotic?

They die due to lack of antibiotic resistance. Signup and view all the answers

Which of the following is true regarding white colonies on an antibiotic plate?

They indicate proper hybridization of the gene of interest. Signup and view all the answers

What role does Xgal play on the bacterial growth plate?

It provides an analog for the lacZ gene to produce blue colonies. Signup and view all the answers

What happens if ligation fails during plasmid insertion?

Only the gene of interest is absorbed by the bacteria. Signup and view all the answers

How many SmaI restriction sites are present in the provided vector initially?

3 Signup and view all the answers

Study Notes

Alternative Splicing

Can lead to different protein isoforms
Can be tissue specific
Some examples include neuronal ion channels and receptors
Can involve enhancers and suppressors creating different gene expression
Can result in poison exons (premature stop codons) leading to nonsense mediated decay

Mutations

Allele refers to sequence variation, which can be neutral to the organism
Mutated allele is a sequence variation that causes disease or a specific condition
Wild type allele is a normal allelic variation in a population
Mutant alleles are specific to population studies because they produce alternate phenotypes
Mutations are part of evolution
Mutations are a source of disease and can help scientists understand disease pathology
Mutagenesis is the utilization of mutation to understand gene expression and regulation

Missense Mutation

A mutation that modifies a single coding codon
Can impact protein folding, specifically alpha helices, beta sheets, and the formation of disulfide bridges
Can impact genes essential for development, often in the form of compound heterozygotes, with two different hypomorphic variants
A minimum threshold of protein activity is suspected to be required for normal development

Neutral Mutation

A mutation with no measurable impact on protein function or the phenotype of the individual
Often called conservative substitution
Mutant amino acid may have similar properties to the original
Silent mutation is an alteration in the DNA sequence where the mRNA produces a synonymous codon, resulting in no change in the protein sequence or structure.
Can however alter the efficiency of production. Most have to do with promoter availability

Chromatin Conformation

Transcription requires access to the promoter, which involves chromatin being in a relaxed state.
Chromosome territories and mini territories are associated with active or repressed DNA sequences
Interphase chromosomes are organized into TADs (Topologically Associating Domains) which are active or repressed depending on the cell type.
Euchromatin and heterochromatin exist and are controlled by the level of H1 association.
Histone tail modifications can produce a variety of chromatin states associated with different levels of transcription, alongside other chromatin binding proteins.
ncRNAs can bind DNA and proteins that bind DNA/RNA, found in scaffolding complexes that impact chromatin structure. They can recruit chromatin remodeling complexes

Epigenetic Profile and Imprinting

DNA methylation
- C bases of CpG dinucleotides can be methylated to produce 5-methylcytosine (5-meC)
- Methylated DNA attracts proteins that bind to it, which can recruit more proteins to bind, often resulting in transcription repression as transcription factors can’t bind to methylated DNA
- CpG islands are usually not methylated
- Heritability of DNA methylation: 5-meC is copied to the complementary strand through an enzyme, allowing heritability of methylation. Gametes go through a wave of demethylation during gametogenesis and will then be methylated at specific loci following a pattern based on the parent of origin, called differentially methylated region (DMR)

X-inactivation

Females have two X chromosomes, while males have one.
The Y chromosome primarily carries genes related to male development and fertility.
X chromosomes contain essential genes.
Female X chromosomes can not exist as two together, so X-inactivation must occur.
The X-inactivation center (XIC) is a locus on the X chromosome where the X-inactivation specific transcript (XIST), a large non-coding RNA is synthesized during embryogenesis.
The XIST binds to and inactivates the X chromosome, recruiting other repressive proteins.
Dosage compensation: With two X chromosomes, females would translate double the amount of required products, so one X is inactivated.
Most genes on the inactivated X chromosome will be constitutive heterochromatin.
Each cell of the blastula randomly chooses the maternal or paternal X chromosome to inactivate, for females. This means cells within a single individual can differ from each other.
About 15% of the genes on the inactivated X chromosome can be accessed on the Pseudoautosomal region (PAR) which is located at the top and bottom of the X chromosome.

Transcription Regulation and Initiation

Promoter regions must be devoid of nucleosomes for transcription factors, with downstream regions having loosely packed nucleosomes.
Transcription factors may recruit additional proteins important for co-activation/repression, impacting the accessibility of promoters and regulatory sequences.
Promoters can be bound by the pre-initiation complex (PIC) even if downstream regions are not being expressed.
The efficiency of RNA polymerase II's ability to begin elongation likely regulates gene expression, rather than the assembly of the PIC.
Alternative promoters can exist, leading to protein variation, as seen in alternative splicing.
Enhancers require DNA looping, which is facilitated by the structure of the TAD. Changes in the TAD can alter the ability of enhancers to reach promoters.
Antisense and bi-directional transcription of ncRNAs interfere with sense transcription, DNA methylation, histone code modifications, inducing heterochromatic states, and silencing transposons.

Waddington's Epigenetic Landscape

Master transcription factors bind to super-enhancers in early development to shape and define cellular identity.
Later in life, cellular identity is controlled with fine-tuned expression and limited regulatory sequences bound by regulatory proteins.

Post-Transcriptional Regulation

Alternative splicing can lead to different protein isoforms.
This can be important for different tissues that require different proteins through expression change.
This is especially important for neurons in creating ion channel and receptor variants.
Alternative splicing can involve splicing enhancers and suppressors, leading to changes in gene expression.
Alternative splicing can also lead to poison exons with premature stop codons, causing nonsense mediated decay.
RNA turnover (abundance and availability) and RNA editing.

Regulation of Translation

Leader peptides can regulate translation.
Structure of mRNA: mRNA can have stem loop structures that impact the ribosomes ability to move forward. These structures can also create sites that are more open to RNA binding regulatory proteins.
ncRNAs (miRNA, siRNA, piRNA) can repress the expression of target mRNAs.

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Description

Explore the intricacies of alternative splicing, mutations, and missense mutations in this comprehensive quiz. Learn how these genetic phenomena can lead to varied protein isoforms and contribute to disease pathology. Test your knowledge on key concepts like wild type alleles and mutagenesis.