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Flashcards in RNA synthesis and processesing Deck (66):
1

transcription unit

The segment of DNA which gets transcribed into RNA

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gene

comprised of a transcription unit plus flanking non-transcribed “regulatory” DNA sequences.

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Transcription

Is DNA-directed RNA synthesis. Transcription is unidirectional and completely processive. The first base pair where transcription initiates is designated +1; downstream bases are assigned positive numbers and upstream bases -ve numbers. The amount of RNA transcribed from each gene is very carefully controlled. When these control mechanisms are corrupted serious problems can result. nherited pre-dispositions to colon cancer, retinoblastoma, and skin cancer are due to mutations in the transcriptional regulatory proteins, Inherited mutations in genes for transcriptional regulatory proteins cause developmental defects, Transcription factors are important drug targets

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RNA pol II

an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA also encodes for non-coding RNAs

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primary transcript

The product of transcription, which may be extensively processed into a mature form.

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Adenomatous polyposis coli (APC)

a negative regulator that controls Beta-catenin concentrations and is a tumor suppressor gene.

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retinoblastoma protein (pRB)

is a tumor suppressor protein that is dysfunctional in several major cancers. Rb restricts the cell's ability to replicate DNA by preventing its progression from the G1 (first gap phase) to S (synthesis phase) phase of the cell division cycle.[8] Rb binds and inhibits transcription factors of the E2F family.

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XPB (Xeroderma Pigmentosum B)

is an ATP dependent human DNA helicase that is a part of the TFIIH transcription factor complex. XPB plays a significant role in normal basal transcription, transcription coupled repair (TCR), and nucleotide excision repair (NER).

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XP-D

a protein involved in transcription-coupled nucleotide excision repair. Defects in this gene can result in three different disorders: the cancer-prone syndrome xeroderma pigmentosum complementation group D, photosensitive trichothiodystrophy, and Cockayne syndrome. Just like XPB, XPD is also a part of human transcriptional initiation factor TFIIH and has ATP-dependent helicase activity.

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mRNA profiling

the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function.

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Burkitt’s lymphoma

a cancer of the lymphatic system, particularly B lymphocytes found in the germinal center. All types of Burkitt's lymphoma are characterized by disregulation of the c-myc gene by one of three chromosomal translocations.

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p53

it regulates the cell cycle and, thus, functions as a tumor suppressor, preventing cancer.

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c-myc

a transcription factor that activates expression of many genes through binding on consensus sequences (Enhancer Box sequences (E-boxes)) and recruiting histone acetyltransferases (HATs). It can also act as a transcriptional repressor. It is a multifunctional, nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation

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acute promyelocytic leukaemia

a form of acute myeloid leukemia, a cancer of the blood-forming tissue (bone marrow). The PML-RARα protein functions differently than the protein products of the normal PML and RARA genes. The protein produced from the RARA gene, RARα, is involved in the regulation of gene transcription, which is the first step in protein production. Specifically, this protein helps control the transcription of certain genes important in the maturation (differentiation) of white blood cells beyond the promyelocyte stage. The protein produced from the PML gene acts as a tumor suppressor, which means it prevents cells from growing and dividing too rapidly or in an uncontrolled way. The PML-RARα protein interferes with the normal function of both the PML and the RARα proteins.

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Retinoic acid receptor alpha (RAR-α)

is involved in the regulation of gene transcription

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sex reversal (SRY)

a DNA-binding protein (also known as gene-regulatory protein/transcription factor) encoded by the SRY gene that is responsible for the initiation of male sex determination in humans. Mutations in this region result in sex reversal, where the opposite sex is produced. also known as Testis-determining factor (TDF)

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dwarfism (PIT-1)

PIT1 is a pituitary-specific transcription factor responsible for pituitary development and hormone expression, are necessary for high affinity DNA binding on genes encoding growth hormone

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cyclosporinA

an immunosuppressant drug widely used in organ transplantation to prevent rejection. Blocks calcineurin, prevents calcineurin from dephosphorlyating and activating NFAT (a TF of pro-inflammitory genes)

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Duchenne muscular dystrophy (DMD)

is a recessive X-linked form of muscular dystrophy, affecting around 1 in 3,600 boys, which results in muscle degeneration and eventual death. The disorder is caused by a mutation in the dystrophin gene, the largest gene located on the human X chromosome, which codes for the protein dystrophin, an important structural component within muscle tissue that provides structural stability to the dystroglycan complex (DGC) of the cell membrane.

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5' tri phosphate

The 5′ cap is found on the 5′ end of an mRNA molecule and consists of a guanine nucleotide connected to the mRNA via an unusual 5′ to 5′ triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vivo by a methyl transferase (7-methylguanylate cap), as found in eukaryotes. The process of 5′ capping is vital to creating mature messenger RNA, which is then able to undergo translation. Capping ensures the messenger RNA's stability while it undergoes translation in the process of protein synthesis, and is a highly regulated process that occurs in the cell nucleus. Because this only occurs in the nucleus, mitochondrial and chloroplast mRNA are not capped.

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RNA pol I

the enzyme that only transcribes ribosomal RNA (but not 5S rRNA, which is synthesized by RNA Polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell

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RNA pol III

transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs.

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mitochondrial RNA pol

more closely related to prokaryotic RNA pol

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bacterial RNA pol

In bacteria, the same enzyme catalyzes the synthesis of mRNA and ncRNA.

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mobile clamp

the mobile “clamp” domain forms a conformation that results in a narrow active site cleft, blocked at the upstream end by the “wall” domain. This arrangement of the cleft effectively prevents double-stranded promoter DNA from reaching the active site (marked by the red circle). The DNA strands separate when the transcription bubble is formed, allowing the template strand to reach the active site.

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downstream jaw

Where DNA reunites after being transcribed and exists the RNA polymerase

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secondary channel of rna polymerase

allow the diffusion of small molecules both into and out of the active center of the enzyme. regulatory factors and small molecules can exploit the secondary channel to gain access to the active site and modify the transcription properties of RNA polymerase.

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bridge helix of RNA polymerase

The RNA polymerase 'bridge helix' is a metastable α-helix that spans the leading edge of the enzyme active-site and coordinates the concerted movement of several other domains during catalysis through kinking of two discrete molecular hinges.

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RNA exit chanel of RNA polymerase

where newly transcribed RNA exists the RNA polymerase

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CTD

The RNA pol II large subunit has a unique C-terminal domain, CTD, composed of heptad repeats (YSPTSPS) which are reversibly phosphorylated. The CTD binds to proteins that regulate elongation and processing of the RNA transcript.

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α-amanitin

a cyclic peptide of eight amino acids. It is possibly the most deadly of all the amatoxins. α-Amanitin is an inhibitor of RNA polymerase II. It binds the bridge helix and blocks RNA chain elongation by preventing translocation

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Rifampicin

a broad spectrum antibiotic, binds bacterial RNA polymerase and blocks the RNA exit channel

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Promoters

direct RNA polymerase to the start of genes.! They control the direction and the frequency of transcription.! The TATA box is a conserved element in many promoters!

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TATA-binding protein (TBP)

a general transcription factor (is shared among all three RNA polymerase) that binds specifically to a DNA sequence called the TATA box. Inserts itself into minor groove, causing a major distortion of DNA, is not highly sequence specific

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Transcription factor II D (TFIID)

is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. is itself composed of several subunits called TATA-binding protein

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Transcription factor II H

one of several general transcription factors that make up the RNA polymerase II preinitiation complex.[1] TFIIH consists of ten subunits, 7 of which (XPD, XPB, p62, p52, p44, p34 and TTDA) form the core complex. Mutations in the XPB, XPD! and p44 subunits cause Xeroderma pigmentosum! Cockaynes syndrome! Trichothiodystrophy

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CDK 7

cyclin-dependent kinase shown to be not easily classified. CDK7 is both a CDK-activating kinase (CAK) and a component of the general transcription factor TFIIH.

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pre-initiation complex (PIC)

RNA pol II and general transcription factors (GTFs) assemble into a pre-initiation complex (PIC) on the core promoter. This process is highly regulated to control initiation of transcription!

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Nascent RNA

is immediately formed RNA. In this RNA no posttranscriptional modification has occurred.

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transcription start site

is the location where transcription starts at the 5'-end of a gene sequence

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5' UTR

the region of an mRNA that is directly upstream from the initiation codon.

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3' UTR

the section of messenger RNA (mRNA) that immediately follows the translation termination codon.

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initiation codon

the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and a modified Met (fMet) in prokaryotes. The most common start codon is AUG.

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termination codon

a nucleotide triplet within messenger RNA that signals a termination of translation. UAA, UGA, UAG

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Polyadenylation

the addition of a poly(A) tail to a primary transcript RNA. The poly(A) tail consists of multiple adenosine monophosphates

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mRNA processing

modifies mRNA to enhance nuclear export and translation and to prevent degradation. The 3 major pre-mRNA processing steps are capping, splicing and cleavage/polyadenylation

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5' cap

1) triphosphatase 2) guanylyltransferase 3) Guanine 7 methyl transferase

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triphosphatase

One of the terminal phosphate groups is removed (by RNA terminal phosphatase), leaving two terminal phosphates i.e. 5'ppNp[Np]n

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guanylyltransferase

GMP is added to the terminal phosphates (by a guanylyl transferase), losing two phosphate groups (from the GTP substrate) in the process. This results in the 5′–5′ triphosphate linkage.

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Guanine 7 methyl transferase

The 7-nitrogen of guanine is methylated (by a methyl transferase)

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S-adenosylmethionine

universal methyl donor and becomes S-adenosylhomocysteine

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cap binding complex

enhances splicing, 3' processing and nuclear export. In the cytoplasm it is replaced by EIF4E

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decapping

an important step in regulated mRNA degradation

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Introns

are recognized through short, conserved sequences. Consensus sequences around 5ʹ′ (GU) and 3ʹ′ (AG) splice sites in vertebrate pre-mRNA. Branch point (A) lies close to the 3'. The 5’ splice site is 1st recognized (RNA-RNA base pairing) by base pairing to the U1 snRNA. The branch point is recognized by base pairing to the U2 snRNA. Splicing of pre-mRNA is probably an RNA catalyzed reaction

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U1 snRNA

the small nuclear RNA (snRNA) component of U1 snRNP (small nuclear ribonucleoprotein), an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.

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U2AF

contains a sequence-specific RNA-binding region that recognizes 3' splice site

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spliceosome

a large ribonucleoprotein complex composed of the pre-mRNA, over 100 proteins,
 and 5 small nuclear RNAs (snRNAs). Pre-mRNA Splicing Occurs by Two Transesterification Reactions. the number of phosphodiester bonds are conserved at all times, therefore does not require use of ATP. First, the 2'OH of a specific branchpoint nucleotide within the intron that is defined during spliceosome assembly performs a nucleophilic attack on the first nucleotide of the intron at the 5' splice site forming the lariat intermediate. Second, the 3'OH of the released 5' exon then performs a nucleophilic attack at the last nucleotide of the intron at the 3' splice site thus joining the exons and releasing the intron lariat.

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Alternative Splicing

a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. Consequently the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions. occurs though Exon retained or removed! “Exon skipping”, Mutually exclusive exons, Exon truncation/extension at 5’ end, Exon truncation/extension at 3’ end, Intron retained or removed

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composition of splicosomes

Each spliceosome is composed of five small nuclear RNAs (snRNA), and a range of associated protein factors. When these small RNA are combined with the protein factors, they make an RNA-protein complex called snRNP. The snRNAs that make up the major spliceosome are named U1, U2, U4, U5, and U6, and participate in several RNA-RNA and RNA-protein interactions. The RNA component of the small nuclear ribonucleic protein or snRNP (pronounced "snurp") is rich in uridine (the nucleoside analog of the uracil nucleotide).

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Alternative Splicing in HIV

Makes both Unspliced genomic RNA and over 30 Singly and Doubly Spliced Transcripts from a single primary transcript transcript!

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Abnormal splicing

rare form of inherited mutation, changes in open reading frame can mess up alternative splicing. One example found in CD44. are a good target for gene therapy

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cd44

important in cell migration (metastesis), Abnormal splicing of CD44 contributes to tumor metastasis and splice variants can be used as diagnostic and prognostic markers!

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spinal muscular atrophy

is an autosomal recessive disease caused by a genetic defect in the SMN1 gene, which encodes SMN1, a protein widely expressed in all eukaryotic cells. SMN1 is apparently selectively necessary for survival of motor neurons. Rescue of SMN1 mutations that spinal muscular atrophy the most common fatal genetic disease of children under 2 years. could force SMN2 to not splice a certan intron and therefore produce larger amounts of the full gene SMN1

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3’ polyA tail

is added by two enzymatic steps: 1. cleavage of the 3'-most part of a newly produced RNA The cleavage is catalysed by the enzyme CPSF and occurs 10–30 nucleotides downstream of its binding site. This site is often the sequence AAUAAA on the RNA 2. polyadenylation- When the RNA is cleaved, polyadenylation starts, catalysed by polyadenylate polymerase. Polyadenylate polymerase builds the poly(A) tail by adding adenosine monophosphate units from adenosine triphosphate to the RNA, without a template, cleaving off pyrophosphate.

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Poly(A)-binding protein (PAB)

The poly(A) tail is located on the 3' end of mRNA and stabilizes the mRNA

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alternative polyadenylation

Membrane and secreted forms of IgM are generated by alternative polyA site choice which changes the message at the 3' end. alternative polyadlyation can have effects on 3' reading frame or on 3'UTR (effects on translation). Cancer cells tend to shorten 3'UTR by alternative cleavage and polyadenylation, maybe to avoid regulation. 3’ end formation by cleavage-polyadenylation is coupled to termination of transcription by RNA pol II