RNA synthesis and processesing Flashcards
transcription unit
The segment of DNA which gets transcribed into RNA
gene
comprised of a transcription unit plus flanking non-transcribed “regulatory” DNA sequences.
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
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
primary transcript
The product of transcription, which may be extensively processed into a mature form.
Adenomatous polyposis coli (APC)
a negative regulator that controls Beta-catenin concentrations and is a tumor suppressor gene.
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.
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).
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.
mRNA profiling
the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function.
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.
p53
it regulates the cell cycle and, thus, functions as a tumor suppressor, preventing cancer.
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
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.
Retinoic acid receptor alpha (RAR-α)
is involved in the regulation of gene transcription
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)
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
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)
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.
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.
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
RNA pol III
transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs.
mitochondrial RNA pol
more closely related to prokaryotic RNA pol
bacterial RNA pol
In bacteria, the same enzyme catalyzes the synthesis of mRNA and ncRNA.
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.
downstream jaw
Where DNA reunites after being transcribed and exists the RNA polymerase