Gene Expression Flashcards
1
Q
A multi step process that ultimately results in the production of a functional gene product (either ribonucleotide acid or a protein)
A
Gene expression
2
Q
What are the two classification of genes?
A
- housekeeping
- regulated
3
Q
Housekeeping genes
A
- involved in basic cellular functions that are requires regardless of the cell type or environmental cues
- constitutively expressed and not regulated
4
Q
Regulated genes
A
- 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
5
Q
What is the main site of gene control in prokaryotes?
A
Transcription
6
Q
Gene regulation in eukaryotes
A
- transcriptional
- Post-transcription
- Translation
- Post translation
7
Q
What is rresponsible for sophisticated gene regulation control in eukaryotes?
A
Nucleus separation
8
Q
Regulatory molecules
A
- Depressors
2. Activators
9
Q
Regulatory molecules that suppress the transcription of a gene?
A
Repressors
10
Q
Regulatory molecules that increase the transcription of a gene
A
Activators
11
Q
Types of operons
A
- Repressible
2. Inducible
12
Q
Repressible operon
A
Transcription is usually on but can be inhibited
13
Q
Inducible operon
A
Transcription is usually off by can be stimulated
14
Q
What is the preferred carbon source for E. coli?
A
Glucose
15
Q
Can E coli use other sugars?
A
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
16
Q
When does E coli produce the enzymes to use other sugars?
A
- glucose is absent
- another sugar is present (lactose)
17
Q
Is the lac operon off or on when only glucose is present?
A
Off
18
Q
What is the repressor protein encoded by?
A
Lacl gene
19
Q
Repressor protein for the lac operon when glucose only is present
A
- encoded by lacl gene
- always present and bound to the operator
- blocks RNA polymerase
20
Q
Adenyly cyclase when the lac operon is off
A
- Glucose present
- glucose inhibits adenyly cyclase, no cAMP, cannot form CAP/cAMP complex, cannot initiate transcription
21
Q
Lac operon when lactose is present
A
Its on
22
Q
When the lac operon is on and glucose is absent
A
Adenyly cyclase makes cAMP, CAP/cAMP complex forms, binds to CAP binding site, RNA polymerase can efficiently initiate transcription
23
Q
When glucose is absent and the lac operon is on, what can efficiently initiate transcription?
A
RNA polymerase
24
Q
If the lac operon is on and lactose is present
A
A small amount of allolactose is produced that binds to the repressor, and prevents it from binding to the operator
25
When lactose is present, what is produced?
Allolactose
26
Lac operon when both glucose and lactose are present
Off
27
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
28
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
29
Why do eukaryotes have 5 different levels of transcription?
We are more complex and need more cell types
30
What is regulation of transcription controlled by in eukaryotes?
Regulatory sequences of DNA
31
What are the regulatory sequences of DNA in eukaryotic transcription control
- usually embedded in the noncoding regions of the genome
- cis-acting
- interacts with trans acting regulators
32
Where are the regulatory sequences of DNA imbedded in?
Noncoding regions of the genome
33
What are these regulatroy sequences of DNA that are embedded in the noncoding region of the genome called?
Cis-acting
34
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
35
What are the cis-acting DNA regulatory sequences capable of interacting with?
Trans-acting regulators
36
Trans-acting regulator
- transcription factors
- they are proteins
- transcription not possible without this
37
How is binding of the trans-acting regulators (TF) to DNA achieved?
- Zinc finger
- leucine zipper
- helix-turn-helix in the protein
38
DNA sequences that increase the rate of initiation of transcription
Enhancers
39
Where are enhancers typically located>?
On the same chromosome
40
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
41
How do the enhancers act?
In a tissue specific manner if the DNA binding proteins (transcription factors) are only present in certain tissues
42
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
43
Transcription factors
- =trans-acting molecules
- DNA binding domain
- activation domain
44
Activation domain
- transcription factors
- bind to other transcription factors, interact with RNA polymerase II to stabilize formation of the invitation complex, recruit chromatin modifying proteins
45
What is PEPCK gene expression induced by?
Cortisol
46
Steroid hormone that diffuses into hepatocyte
Cortisol
47
What binds to intracellular receptors in PEPCK gene?
Cortisol
48
What does the cortisol-receptor complex enter?
Nucleus
49
Once in the nucleus, what does the cortisol-receptor complex bind to?
Glucocorticoid response element (GRE)
50
What happens after cortisol-receptor complex binds to the glucocorticoid response element (GRE)
PEPCK transcription is induced
51
What can be made by the same pre-mRNA by the use of alternative splice sites
Tissue specific ISO forms or proteins
52
What percentage of genes in humans undergo alternative splicing
60% of the ~25,000
53
Topomyosin
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
54
Additional posttranscriptional modification in which a base in the mRNA is altered
mRNA editing
55
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
- mRNA editing
- results in a shorter protein apo-B48
56
Apo B-100
In the liver, fulllength, is made and incorporated into VLDL
57
Mechanism of reducing gene expression
RNA interface (RNAi)
58
What are the mechanisms of reducing gene expression (RNAi)
- repressing translation
| - increasing the degradation of specific mRNAs
59
RNAi is a fundamental role in what
Cell proliferation, differentiation, and apoptosis
60
What is RNAi widely used for?
A tool in research
61
Therapeutic potential of RNAi
Huge therapeutic potential: currently more than 20 are in clinical trials for various diseases
62
1st clinical trial of RNAi-based therapy
Involved patients with the neovascular form of ARMD, a leading form of adult blindness
63
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)
64
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
65
What is RNAi mediated by?
Very short RNA (~20-22bp) called microRNA (miRNA)
66
What does miRNA act as?
Guide strand to target specific mRNAS that contain the complementary sequence
67
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
68
Double stranded short interfering RNAs (siRNAs)
Introduced into a cell from exogenous sources can also trigger RNAi
69
Phosphorylation of eIF2
Inhibits its function by inhibited GDP-GTP exchange and so inhibits translation at the initiation step
70
What is phosphorylation catalyzed by?
Kinases that are activated in response to environmental conditions
- AA starvation
- heme deficiency in erythroblasts
- presence of double stranded RNA 9signaling viral infection)
- accumulation of misfolded proteins in the rough ER
71
Post translational control: modifications of the polypeptide chain
1. Trimming
2. Covalent attachment
3. Protein folding
4. protein degradation
72
Trimming
Initially synthesized as large precursors many proteins undergo cleavage to become functionally active (protein digestion enzymes)
73
Covalent attachment
Phosphorylation, glycosylation, hydroxylation, others
74
Protein folding
Directed by chaperones
75
Protein degradation
By ubiquination
76
Loosely packed accessibly for transcription
Euchromatin
77
Tightly packed, inaccessible
Heterchromatin
78
Regions in DNA rich in CG that are prone to modifications
CpG islands
79
Epigentics regulation: modifications of DNA
- histones
| - DNA
80
Methylation of DAN and histones
Causes nucleosomes to pack tightly together. Transcription factors cannot bind the DNA, and genes are not expressed
81
Histone acetylation
Results in loose packing of nucleosomes. Transcription factors can bind the DNA and genes are expressed
82
Mobile segments of DNA that move in a random manner from one site to another on the same or a different chromosome
Transposons (Tns)
83
What is the movement of the transposons mediated by?
Transposase, an enzyme encoded by the Tn itself
84
Direct movement of transposons
Transposon cuts out and then inserts the Tn at a new site
85
Replication movement of transposons
Tn is copied and the copy inserted elsewhere while the original remains in place
86
What has transposition contributed to?
The structural variation in the genome but it also associated with diseases
87
What diseases is transpostion associated with?
- rare cases of hemophilia A
- Duchenne muscular dystrophy
- antibiotic resistance in bacteria is party due to this phenomena
