RR9-11 bio 200 (this one is good)

A modification added to the 5' end of pre-mRNA, crucial for stability and ribosome binding.

A process where pre-mRNA is cut at a specific site and a poly(A) tail is added to the 3' end for stability and translation.

The removal of non-coding introns from pre-mRNA and joining of coding exons to create mature mRNA.

The initial RNA molecule transcribed from DNA, which needs modification to become mature mRNA.

The processed form of mRNA, ready for translation into proteins.

The C-terminal domain of RNA polymerase II (Pol II), a flexible tail with multiple repeats of a seven amino acid sequence, playing a crucial role in RNA processing.

The phosphorylated form of the CTD, where specific serine residues are modified by the addition of phosphate groups.

Phosphorylation of serine residues at position 2 in the CTD repeats, specifically attracting splicing, polyadenylation, and export factors to the Pol II.

Phosphorylation of the CTD provides binding sites for specific factors involved in RNA capping, splicing, and polyadenylation, allowing these events to occur only on Pol II transcripts.

The CTD of Pol II undergoes phosphorylation, creating binding sites for specific factors involved in these modifications. Other RNA polymerases lack this phosphorylated CTD.

Nuclear proteins that bind to newly made mRNA and help with processing and transport.

They regulate splicing, move mRNA out of the nucleus, and perform other tasks.

They bind to mRNA through their RNA-binding domains.

They associate with mRNA from the time it is made by RNA polymerase II until it exits the nucleus.

They regulate splicing by influencing the selection of splice sites, ensuring the correct exons are joined.

A large complex of proteins and small nuclear ribonucleoproteins (snRNPs) that removes introns from pre-mRNA during RNA splicing.

A chemical reaction that involves the transfer of an ester group from one molecule to another, crucial for the cutting and rejoining of pre-mRNA during splicing.

A non-coding sequence within a gene that is removed during RNA splicing, leaving the coding exons to be joined.

A coding sequence within a gene that is retained after RNA splicing, forming part of the mature mRNA.

A protective guanine nucleotide structure added to the 5' end of mRNA during transcription, vital for mRNA stability, nuclear export, and translation initiation.

A dimeric enzyme that adds the 5' cap to nascent mRNA. It interacts with the CTD of RNA polymerase II, ensuring that the cap is added only to Pol II transcripts.

The 5' cap protects mRNA from degradation, facilitates its export from the nucleus, and allows it to be recognized by translation factors, ensuring efficient protein synthesis.

The C-terminal domain (CTD) of RNA polymerase II (Pol II) is a flexible tail with multiple repeats of a seven amino acid sequence. It interacts with the capping enzyme, ensuring that the cap is added only to Pol II transcripts.

Capping is coupled with elongation. As the nascent mRNA emerges from the RNA polymerase II, the capping enzyme interacts with the phosphorylated CTD, indicating that elongation is ongoing and signaling the addition of the 5' cap.

One of the five snRNAs in the spliceosome, it binds to the 5' splice site at the intron-exon boundary.

Another snRNA in the spliceosome, it recognizes the branch point sequence within the intron.

A lasso-shaped structure formed during splicing, where the 5' end of the intron is linked to the branch point adenine.

Chromatin is the complex of DNA and proteins (histones) that makes up chromosomes. It's how DNA is packaged inside the nucleus of a cell.

Euchromatin is less condensed and accessible to the transcriptional machinery, meaning genes within it can be actively transcribed. Heterochromatin is densely packed and transcriptionally inactive, meaning genes within it are not being transcribed.

A structure formed by DNA wrapped around histone proteins. It's the basic unit of chromatin.

Histones are proteins that DNA wraps around to form nucleosomes. They help package and condense DNA within the nucleus, which is essential for organizing the genome efficiently.

Metaphase chromosomes are highly condensed chromosomes visible during cell division, they form during mitosis or meiosis.

The process of adding acetyl groups to histone proteins. This modification loosens the DNA's grip on the histones, allowing for easier access by transcription factors. Acetylation is a mark of gene activation.

The process of removing acetyl groups from histone proteins. This modification tightens the DNA's grip on the histones, making it harder for transcription factors to access the genes. Deacetylation is a mark of gene repression.

Histone Deacetylases (HDACs) are enzymes that remove acetyl groups from histone proteins. They are recruited by transcriptional repressors to suppress gene expression.

Histone acetylation is associated with gene expression. When acetyl groups are added to histones, the DNA becomes more accessible to transcription factors, allowing for gene transcription.

Traits passed down without altering the DNA sequence.

Adding methyl groups to DNA, which can silence genes by attracting proteins that compact DNA.

Chemical changes to histones, the proteins DNA wraps around. These changes can affect how tightly DNA is packed and gene expression.

Tightly packed DNA that is transcriptionally inactive. It's like a 'closed' book that can't be read.

During DNA replication, old methylation marks are used to add new marks to the new DNA strands, ensuring the silenced state is maintained.

Regions on yeast chromosome III that contain inactive copies of mating type genes (HML and HMR) which are kept silent by the action of silencers and heterochromatin.

The central mating type locus on yeast chromosome III that controls the active expression of either the "a" or "α" mating type genes. It's the 'switch' that determines a yeast cell's gender.

Transcriptionally silent regions on yeast chromosome III that contain inactive copies of either the "a" or "α" mating type genes.

A process where genetic material is exchanged between two DNA molecules but not equally. One molecule loses material, while the other gains it.

The inactive genes at HML/HMR can be transferred to the MAT locus via non-reciprocal recombination, switching the mating type of the cell.

A process that equalizes the expression of X-linked genes between males and females, despite the different number of X chromosomes they possess (XY in males, XX in females).

An inactive X chromosome in females, condensed and visible as a dark spot in the nucleus.

A long non-coding RNA that coats and silences one X chromosome in females.

A gene located on the X chromosome that prevents XIST from silencing both X chromosomes in early development, ensuring both are initially active.

A gene or regulatory element that affects the same DNA molecule it is located on.

RAP1 is a protein that binds to DNA in the region of the silencer, helping to regulate gene expression. It also binds to telomeres.

SIR1 is a protein that cooperates with RAP1 to bind to the silencer region in DNA, contributing to gene silencing. It plays a key role in the inactive mating type loci.

SIR2, 3, and 4 are proteins that bind to hypoacetylated histone tails, leading to chromatin compaction and transcriptional silencing. They form complexes with telomeric DNA.

SIR proteins bind to hypoacetylated histone tails, promoting chromatin compaction and making DNA less accessible to transcription factors. This results in gene silencing.

Telomeres are the protective caps at the ends of chromosomes. They are involved in silencing by binding to proteins like RAP1 and forming large complexes with SIR proteins.

The idea that gene expression, specifically transcription, occurs in bursts, meaning periods of intense activity followed by periods of inactivity.

The idea that gene expression occurs at a constant rate, with no significant fluctuations in activity.

The effectiveness of a gene's transcription, determined by the strength of the promoter and enhancer regions.

The degree to which an enhancer region can stimulate gene transcription. A stronger enhancer leads to higher expression.

The position of an enhancer relative to the promoter (5' or 3') can influence the level of transcription, suggesting a complex regulatory mechanism.

A large protein complex that acts as a bridge between transcription factors and RNA polymerase II, facilitating the initiation of transcription.

The Mediator complex interacts with activation domains of transcription factors, binds to enhancers and promoters, and recruits RNA polymerase II to initiate transcription.

Long stretches of DNA that loop out from the chromosome and interact with the Mediator complex, bringing distant enhancers and promoters closer together.

A complex of proteins formed at the promoter region of a gene, including RNA polymerase II, transcription factors, and the Mediator complex, which is necessary for the initiation of transcription.

The Mediator complex plays a key role in forming the pre-initiation complex (PIC) by bringing together RNA polymerase II, transcription factors, and other PIC components, ultimately initiating transcription.

A protein that binds to a specific sequence added to the 5' region of a gene, allowing researchers to track the gene's transcription activity.

A method used to observe active transcription in living cells, only capturing RNA molecules that are currently being transcribed, excluding degraded ones.

The reporter protein binds to a specific added sequence on the 5' end of the transcribed RNA, allowing visualization of active transcription. This makes it easier to see which genes are being transcribed.

The added sequence serves as a binding site for the reporter protein, which allows researchers to identify and follow the transcribed RNA.

Degraded RNA molecules no longer carry information about active gene expression, so focusing solely on actively transcribed RNA provides a more accurate picture of ongoing transcription.

Compartments within cells that concentrate proteins involved in transcription, forming through liquid-liquid phase separation.

The process by which proteins and other macromolecules assemble into distinct compartments within cells, driven by factors like concentration and valency.

Factors like concentration of macromolecules, valency (interactions like electrostatic forces), and properties of proteins like being intrinsically disordered, all influence the formation of liquid-liquid condensates.

The ability of molecules to interact and form multiple bonds, as in electrostatic interactions, influences condensate formation.

Proteins that lack a fixed 3D structure and can easily interact with other molecules, facilitating condensate formation.

A model explaining how enhancers and promoters interact on the surface of transcriptional condensates to activate gene expression.

Dense, localized regions within the nucleus where transcription factors, RNA polymerase, and DNA come together to initiate and regulate gene expression.

A DNA sequence that can control the transcription of a gene, typically located far from the start site.

A DNA sequence located near the start of a gene, where RNA polymerase binds to initiate transcription.