Vest 1 Flashcards
Flashcards for Vest Lecture 1
The process of removing intron sequences from pre-mRNA and joining exon sequences is called __________.
Splicing
The __________ structure is added to the 5’ end of a pre-mRNA during transcription to protect it from degradation.
7-methyl G cap
The __________ at the 3’ end of a mRNA molecule facilitates translation.
poly(A) tail
__________ are a class of non-coding sequences that are removed from pre-mRNA during splicing.
Introns
The __________ is a large ribonucleoprotein complex that catalyzes the splicing of pre-mRNA.
Spliceosome
__________ are a family of small nuclear ribonucleoprotein particles that are essential components of the spliceosome.
snRNPs
The __________ is a sequence element, typically AAUAAA, found near the 3’ end of pre-mRNA that signals where the poly(A) tail should be added.
Polyadenylation signal (PAS)
__________ is a type of alternative RNA processing that allows a single gene to code for multiple protein isoforms by including or excluding different exons in the mature mRNA.
Alternative splicing
__________ RNA splicing occurs without the need for any protein enzymes.
Self-splicing
List three functions of the 5’ cap:
- Protects pre-mRNA and mRNA from degradation by 5’ exonucleases
- Enhances splicing of the 5’ most exon
- Necessary for targeting mRNAs for export to the cytoplasm through the nuclear pores
__________ RNA methylation is a common internal modification to RNA that can influence stability, splicing, and translation of RNA.
N6-methyladenosine (m6A)
__________ are a newly discovered class of non-coding RNAs that form covalently closed loop structures and have been implicated in a variety of cellular processes.
Circular RNAs (circRNAs)
Three primary functions of circRNAs are:
- miRNA sponges – regulate translation and expression
- Protein sponges – regulate transcription and alternative splicing
- Encode novel proteins using alternative translation initiation mechanisms – IRES and m6A residues
The __________ of the RNA polymerase II plays a crucial role in coordinating the different steps of pre-mRNA processing, including capping, splicing, and polyadenylation.
carboxy-terminal domain (CTD)
The phosphorylation state of __________ on the CTD of RNA polymerase II is associated with the recruitment of capping enzymes.
Serine 5
The presence of both __________ and __________ on the CTD of RNA polymerase II is associated with the recruitment of splicing proteins.
Phospho-Ser 5, Ser 2
__________ of the CTD of RNA polymerase II leads to the recruitment of cleavage and polyadenylation factors.
Phosphorylation of Serine 2
__________ is the process of adding a poly(A) tail to the 3’ end of an RNA molecule.
Polyadenylation
The 5’ splice site is typically characterized by the consensus sequence __________.
GU A/G AGU
The 3’ splice site is typically characterized by the consensus sequence __________.
CAGG
The __________ is an adenine nucleotide located 18-40 nucleotides upstream of the 3’ splice site that plays a crucial role in the splicing reaction.
Branch point
The __________ is a pyrimidine-rich sequence located upstream of the 3’ splice site.
Polypyrimidine tract
The __________ binds to the 5’ splice site of pre-mRNA.
U1 snRNP
The __________ binds to the branch point of the pre-mRNA.
U2 snRNP
The __________ plays a crucial role in holding the 5’ and 3’ exons in close proximity during splicing.
U5 snRNP
__________ and __________ interact near the branch point during the splicing reaction.
U4-U6 snRNPs
The __________ binds to the polypyrimidine tract and helps recruit the U2 snRNP to the branch point.
U2AF (U2 associated factor)
In addition to the five main snRNPs, there are over __________ other proteins that can contribute to the spliceosome.
24
The 5’ end of the intron base pairs with the __________ during splicing.
U6 snRNP
The __________ binds to the AG dinucleotide at the 3’ splice site.
U2AF-35
__________ refers to the skipping of an exon during the splicing process, leading to its exclusion from the mature mRNA.
Exon skipping
__________ splicing refers to the process where exons are included in the mature mRNA in the order in which they appear in the gene.
Default sequential
Alternative splicing can occur if something disrupts __________.
default sequential splicing
The protein __________ can act as a major deciding factor that influences alternative splicing.
RBM25
__________ elements within RNA are recognized by activator proteins, which commonly belong to the SR (serine-arginine rich) family of proteins.
Enhancer
__________ elements within RNA are bound by repressor proteins, often part of the hnRNP (heterogenous nuclear ribonucleoprotein) protein family.
Silencer
__________ enhance the binding of the spliceosome to regulated splice sites.
Activators
__________ inhibit the binding or function of spliceosomal components.
Repressors
__________ are sequences within exons that promote splicing.
ESEs (exonic splicing enhancers)
__________ are sequences within introns that inhibit splicing.
ISSs (intronic splicing silencers)
__________ are sequences within introns that enhance splicing.
ISEs (intronic splicing enhancers)
The __________ binds to the AAUAAA sequence of the PAS.
Cleavage and Polyadenylation Specificity Factor (CPSF)
The __________ binds to the GU-rich or U-rich downstream element of the pre-mRNA.
Cleavage Stimulatory Factor (CSTF)
__________ adds adenine residues to the 3’ end of the pre-mRNA.
Poly-A polymerase (PAP)
The __________ binds to the poly(A) tail.
Nuclear Poly-A binding protein (PABPN1)
The __________ is responsible for cleaving the pre-mRNA downstream of the PAS.
Endonuclease activity of CPSF2
__________ and __________ are exonucleases that degrade the 5’ end of the cleaved RNA.
XRN2, RAT1
__________ polyadenylation involves the regular dissociation of PAP, allowing only a few adenine residues to be added at a time.
Distributive
__________ polyadenylation occurs when PABPN1 binds to short poly(A) sequences, stabilizing the binding of PAP and leading to the addition of adenine residues without PAP dissociation.
Processive
Approximately __________ of mammalian mRNAs contain more than one PAS.
75%
What are the four splicing sequences?
The four splicing sequences are: 5’ splice site, 3’ splice site, polypyrimidine tract, and branch point.
