Flashcards in Gene Expression Deck (87):
A multi step process that ultimately results in the production of a functional gene product (either ribonucleotide acid or a protein)
What are the two classification of genes?
-involved in basic cellular functions that are requires regardless of the cell type or environmental cues
-constitutively expressed and not regulated
-required only in certain cells types and/or only under certain conditions
-subject to various control mechanisms that determine if and when these genes will be expressed
What is the main site of gene control in prokaryotes?
Gene regulation in eukaryotes
4. Post translation
What is rresponsible for sophisticated gene regulation control in eukaryotes?
Regulatory molecules that suppress the transcription of a gene?
Regulatory molecules that increase the transcription of a gene
Types of operons
Transcription is usually on but can be inhibited
Transcription is usually off by can be stimulated
What is the preferred carbon source for E. coli?
Can E coli use other sugars?
Yes, however, this requires more enzymes (and energy) so E. coli only produces the enzymes to use other sugars if glucose is absent and another sugar is present
When does E coli produce the enzymes to use other sugars?
-glucose is absent
-another sugar is present (lactose)
Is the lac operon off or on when only glucose is present?
What is the repressor protein encoded by?
Repressor protein for the lac operon when glucose only is present
-encoded by lacl gene
-always present and bound to the operator
-blocks RNA polymerase
Adenyly cyclase when the lac operon is off
-glucose inhibits adenyly cyclase, no cAMP, cannot form CAP/cAMP complex, cannot initiate transcription
Lac operon when lactose is present
When the lac operon is on and glucose is absent
Adenyly cyclase makes cAMP, CAP/cAMP complex forms, binds to CAP binding site, RNA polymerase can efficiently initiate transcription
When glucose is absent and the lac operon is on, what can efficiently initiate transcription?
If the lac operon is on and lactose is present
A small amount of allolactose is produced that binds to the repressor, and prevents it from binding to the operator
When lactose is present, what is produced?
Lac operon when both glucose and lactose are present
when lactose is present and the lac operon is off
A small amount of allolactose is produced that binds to the repressor and prevents it from binding to the operator
Transcription when lac operon is off in the presence of lactose and glucose
Although the repressor is inactive, the transcription can not be initiated because the CAP site is empty
Why do eukaryotes have 5 different levels of transcription?
We are more complex and need more cell types
What is regulation of transcription controlled by in eukaryotes?
Regulatory sequences of DNA
What are the regulatory sequences of DNA in eukaryotic transcription control
-usually embedded in the noncoding regions of the genome
-interacts with trans acting regulators
Where are the regulatory sequences of DNA imbedded in?
Noncoding regions of the genome
What are these regulatroy sequences of DNA that are embedded in the noncoding region of the genome called?
Why are the regulatory sequences of DNA that are embedded in the noncoding regions of the genome called cis-acting
They influence expression of genes only on the same chromosome
What are the cis-acting DNA regulatory sequences capable of interacting with?
-they are proteins
-transcription not possible without this
How is binding of the trans-acting regulators (TF) to DNA achieved?
-helix-turn-helix in the protein
DNA sequences that increase the rate of initiation of transcription
Where are enhancers typically located>?
On the same chromosome
Where on the chromosome is the enhancer in comparison to the gene?
-Can be close to the gene they are controlling or thousands of base pairs away
-can be located upstream, downstream, or even within intron regions or other chromosomes
How do the enhancers act?
In a tissue specific manner if the DNA binding proteins (transcription factors) are only present in certain tissues
How can the enhancers be brought closer to where they need to be?
Can be brought close to the basal promoter by bending o the DNA molecule
- =trans-acting molecules
-DNA binding domain
-bind to other transcription factors, interact with RNA polymerase II to stabilize formation of the invitation complex, recruit chromatin modifying proteins
What is PEPCK gene expression induced by?
Steroid hormone that diffuses into hepatocyte
What binds to intracellular receptors in PEPCK gene?
What does the cortisol-receptor complex enter?
Once in the nucleus, what does the cortisol-receptor complex bind to?
Glucocorticoid response element (GRE)
What happens after cortisol-receptor complex binds to the glucocorticoid response element (GRE)
PEPCK transcription is induced
What can be made by the same pre-mRNA by the use of alternative splice sites
Tissue specific ISO forms or proteins
What percentage of genes in humans undergo alternative splicing
60% of the ~25,000
Actin filament-binding proteins, interaction with the cytoskeleton in most cells, and the contractile apparatus of muscle cells, undergoes tissue specific alternative splicing to produce multiple isoforms of the protein
Additional posttranscriptional modification in which a base in the mRNA is altered
the C residue in the CAA codon for glutamine in the intestine only
Is deaminated to U, changing the sense codon to a nonsense or stop codon
-results in a shorter protein apo-B48
In the liver, fulllength, is made and incorporated into VLDL
Mechanism of reducing gene expression
RNA interface (RNAi)
What are the mechanisms of reducing gene expression (RNAi)
-increasing the degradation of specific mRNAs
RNAi is a fundamental role in what
Cell proliferation, differentiation, and apoptosis
What is RNAi widely used for?
A tool in research
Therapeutic potential of RNAi
Huge therapeutic potential: currently more than 20 are in clinical trials for various diseases
1st clinical trial of RNAi-based therapy
Involved patients with the neovascular form of ARMD, a leading form of adult blindness
What is neovascular AMD triggered by?
Overproduction of vascular endothelial growth factor (VEGF), leading to the sprouting of excess blood vessels behind the retina. The vessels leak, clouding and often entirely destroying vision (wet)
SiRNA for VEGF
An siRNA designed to target the mRNA of VEGF and promote its degradation went to clinical trials
-FIRST APPROVED FOR CLINICAL TRIALS
What is RNAi mediated by?
Very short RNA (~20-22bp) called microRNA (miRNA)
What does miRNA act as?
Guide strand to target specific mRNAS that contain the complementary sequence
RISC-RNA-induced silencing complex
Together with this protein complex, expression of the gene is reduced by the cleaving of RNA (degradation) and/or physically blocking translation
Double stranded short interfering RNAs (siRNAs)
Introduced into a cell from exogenous sources can also trigger RNAi
Phosphorylation of eIF2
Inhibits its function by inhibited GDP-GTP exchange and so inhibits translation at the initiation step
What is phosphorylation catalyzed by?
Kinases that are activated in response to environmental conditions
-heme deficiency in erythroblasts
-presence of double stranded RNA 9signaling viral infection)
-accumulation of misfolded proteins in the rough ER
Post translational control: modifications of the polypeptide chain
2. Covalent attachment
3. Protein folding
4. protein degradation
Initially synthesized as large precursors many proteins undergo cleavage to become functionally active (protein digestion enzymes)
Phosphorylation, glycosylation, hydroxylation, others
Directed by chaperones
Loosely packed accessibly for transcription
Tightly packed, inaccessible
Regions in DNA rich in CG that are prone to modifications
Epigentics regulation: modifications of DNA
Methylation of DAN and histones
Causes nucleosomes to pack tightly together. Transcription factors cannot bind the DNA, and genes are not expressed
Results in loose packing of nucleosomes. Transcription factors can bind the DNA and genes are expressed
Mobile segments of DNA that move in a random manner from one site to another on the same or a different chromosome
What is the movement of the transposons mediated by?
Transposase, an enzyme encoded by the Tn itself
Direct movement of transposons
Transposon cuts out and then inserts the Tn at a new site
Replication movement of transposons
Tn is copied and the copy inserted elsewhere while the original remains in place
What has transposition contributed to?
The structural variation in the genome but it also associated with diseases