2.15 Eukaryotic Transcription Control Flashcards
View that genes cause trait
Genetic determinism
Reads DNA and tells you about your risk factors for certain diseases
DNA Test
Requirement for DNA Test
Saliva sample
RNAs synthesized by a cell or organism
Transcriptome
Set of protein sequences that can be derived by translation of all protein coding genes of a completely sequenced genome
Proteome
True or False
mRNA levels are not well-correlated with protein levels
True
Differentiation is anchored on ___
Gene expression
Study of changes in gene expression that are stable over rounds of cell division, and sometimes between generations but do not involve changes in the underlying DNA sequence of the organism
Epigenetics
Affects the phenotype of the organism
Epigenetics
Helps explain how environmental factors can impact gene expression, perhaps even after exposure to the original factor is over
Epigenetics
From double helix to chromosome
Gene has to be accessible for it to be transcribed
DNA Packaging
Difference between euchromatin (on) and heterochromatin (off)
Chromatin remodeling
Number of copies of a certain gene
Gene dosage
Important in expression
Gene dosing
In human cells, there are __ rDNA clusters located in ___. Each cluster contains ___ copies
5;
Chromosome 13, 14, 15, 21, 22;
-70
Leads to over expression of gene product
Gene amplification
Selective increase in number of a certain gene without affecting the quantity of the other genes
Gene amplification
Seen in multiple drug resistant genes, which code for pumps that eject molecules as drugs from the cell, and cancer cells
Gene amplification
Important for breast cancer
HER-2/neu (erbB-2, EGFR-2)
Monoclonal antibody that binds to Her-2 receptor
Herceptin
Prevents dimerization from happening
Herceptin
Transcription happens in ___ while translation happens in ___
Nucleus
Cytosol
RNA contains ___ in the C-2. This makes RNA more prone to hydrolysis
Hydroxyl group
3 regions of gene
Promoter
Coding Region
Termination sequence
Signals how much RNA/protein to produce and when and in which tissues
Promoter
Consensus promoter sequences in eukaryotes
TATA
CAAT
Composed of exons
Encodes the information for what protein to produce
Coding region
Signals the end of the gene
Termination sequence
Bind at promoter for the transcription initiation complex
SRB and RNA polymerase
Produced in the transcription
pre-mRNA
Done to protect and stabilize the primary transcripts as they exit into the cytosol
Posttranscriptional modifications
Posttranslational modifications
Capping 5’ end
Attaching poly-A tail
Splicing introns
Binds the cap
Initiation factor
Searches for the start codon on the mRNA
eIFs
40s
RNA polymerase type I Location
Nucleus
RNA polymerase type I Cellular Transcripts
5.8s, 18s, 28s
RNA polymerase type I Effects of alpha-amanitin
Insensitive
RNA polymerase type II Location
Nucleoplasm
RNA polymerase type II Cellular Transcripts
mRNA precursors, snRNA, miRNA
RNA polymerase type I Effects of alpha-amanitin
Strongly inhibited
RNA polymerase type III Location
Nucleoplasm
RNA polymerase type III Cellular Transcripts
tRNA
5s
rRNA
RNA polymerase type III Effects of alpha-amanitin
Inhibited by high concentrations
Lies in DNA
Landing strip for RNA and general transcription factors
Promoters
Binding site of promoters are always in the ___ of the sequence
Beginning
Lies in DNA
Landing strip for specific transcription factors
Enhancers
Can be upstream, downstream or in the midst of a transcribed gene
Enhancers
Lies in DNA
Binds with transcription regulation factors
Silencers
Silencer-TRF complex prevents ___ from binding to promoter, hindering gene expression
RNA polymerase
Proteins
Bind to regulatory sites on DNA can be regarded as passwords that cooperatively open multiple locks, giving RNA polymerase access to specific gene
Transcription factors
Which genes will be transcribed
Localization of transcription factors
Stimulate transcription at start sites thousands of bases away
Enhancers
Enhancers increase effectiveness of ___
Promoters
Eukaryotic promoters
Multiple transcription factors
Composed of the basal/general transcription factors and RNA polymerase
Basal Transcription Apparatus
Transcription factor subunits are recruited in the following order to form the complex:
TFIIA, TFIIB, TFIIF, TFIIE
ATP-dependent helicase initially separates DNA duplex for the polymerase
TFIIF
Illustrates the modular nature of transcription factors
Pax6 (Paired box 6) TF
Illustrates many keys and multiple concept
Pax6 (Paired box 6) TF
Enhancer of the rat somatostatin gene
Pax6 (Paired box 6) TF
with Pdx1 TF
2 major promoters initiating transcription
Exon 0
Exon 1
Alternatively spliced exon
Exon 5a
Active in the pancreas
Enhancer A
Lens and cornea
Enhancer B
Neural tube
Enhancer C
Retina
Enhancer D
Within the DNA molecule
Can be located in a promoter or enhancer
Positions may vary but do not need to be next to the exons
Cis-acting elements
Diffusable elements
Not the sequences themselves but the products of the sequences
Trans-acting elements
Control gene expression by binding to cis-acting factors
Trans-acting elements
Importance of 5’ cap
Stabilize mRNAs by protecting their ends from phosphatases and nucleases
Enhance translational of mRNAs by eukaryotic proteins
Protection and recognition
Importance of poly-A tail
Translation
Export to cytoplasm
mRNA is hydrolyzed downstream of the polyadenylation signal sequence to form pre-mRNA
Cleaving
Polyadenylation signal sequence
AAUAAA
Removes introns from RNA
Spliceosome
mRNA has to be transported from the nucleus to the cytosol through ____
Nuclear pore complex
3 general mechanisms for localization of mRNAs
mRNAs directed transport via cytoskeleton
Random diffusion and trapping
Generalized degradation + local protection
Function
mRNAs for actin
Cell movement and contraction
Function
mRNAs for tubulin
Mitotic spindles, cilia, flagella
Function
mRNAs for hypoxanthine phosphoribosyltransferase
Purine synthesis
Function
mRNAs for metalloproteinases
Implantation in uterus
Polarity of the bicoid signal is due to attachment of ___ to the cytoskeleton of the anterior region of egg
3’ UTR
mRNA regulatory element that controls gene expression of bicoid protein
Bicoid 3’ UTR regulatory element
Untranslated region
Indicates that there are still remaining mRNA
3’UTR
3’ UTR is the target binding site of the ___
miRNAs
Regulates endogenous gene expression
RNAi
dsRNA cleaved by ___ into 21-25 nucleotide siRNA
Dicer
Mediates unwinding of siRNA
Slicer
siRNA forms complex with ___
RISC
Activates RISC
siRNA duplex
Cleaving mRNA
Gene silencing
(High/low) miRNA stops protein production
High
High lin-4RNA -> __ LIN-14
Low
High let-7 RNA -> __ LIN-41 protein
Low
Small RNAs that regulate gene expression
Repress translation by binding to or cleaving mRNA
miRNA
Does not need to be perfect binding, it can deal with multiple targets
Imperfect binding
Imperfect binding creates __
P-bodies
Complex that blocks translation
P-bodies
miRNA regulates degradation usually at the ___
3’UTRs
The 19-25nt miRNA;miRNA duplex is produced by ___
Dicer
True or false
Hormones can affect miRNA
True
