Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study...
-
Upload
prosper-cross -
Category
Documents
-
view
219 -
download
0
Transcript of Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study...
![Page 1: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/1.jpg)
Last Class: Gene Regulation
1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction
2. Gene regulation on DNAs, gene activators (acting on promoter, enhancer, chromatin etc), repressors
3. regulation of gene activators/repressors4. integrated response.
![Page 2: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/2.jpg)
Posttranscriptional Regulations
![Page 3: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/3.jpg)
Posttranscriptional regulation possibilities
![Page 4: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/4.jpg)
Alternative RNA Splicing
![Page 5: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/5.jpg)
Alternative Splicing of RNA of the Drosophila DSCAM gene (axon
guidance receptors directing growth cone localization)
![Page 6: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/6.jpg)
Negative and Positive Controls of Alternative Splicing (active regulation)
sometimes, the splicing sequence is ambiguous, so constitutive random splicing
![Page 7: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/7.jpg)
Antibodies (membrane-bound, secreted) in B
lymphocytecleavage regulated RNA
processing (CstF)
![Page 8: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/8.jpg)
RNA Editing (inserting Uracil at different sites and change encoding sequence)
![Page 9: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/9.jpg)
Nuclear Export
Rev binds to rev response elelent (RRE), which
binds to nuclear export receptor (exportin 1) to regulate nuclear export even without splicing
a delay of virus infection symptom
![Page 10: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/10.jpg)
Localization in cytoplasmalso determine the fate of RNAs
3’ UTR (untranslated region)
![Page 11: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/11.jpg)
3’ UTR in regulating LocalizationRed: intact 3’ UTR,
Green: 3’ UTR deleted
![Page 12: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/12.jpg)
Translational Regulation
![Page 13: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/13.jpg)
Negative Translational Controlaconitase inhibits ferritin production
![Page 14: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/14.jpg)
Phosphorylation RegulationeIF-2B serving as GEF for eIF-2 and promote translation initiation
phosphorylation locked eIF-2 in inactive form
![Page 15: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/15.jpg)
Internal Ribosome Entry Site (IRES)
![Page 16: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/16.jpg)
Two Mechanisms of mRNA decay
1. regular 3’ tail shortening followed by ‘5 decapping
and degradation2. endonucleolytic cleavage
and fast decapping and degrading
![Page 17: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/17.jpg)
The competition between mRNA translation and decay
initiation machinery and deadenylation proteins are all associated with 5’ and 3’
![Page 18: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/18.jpg)
With Iron, aconitase release enhances the production of ferritin to bind iron while destabilizes transferrin receptor mRNA to reduce the
transportation of more iron intracellularly
![Page 19: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/19.jpg)
Stop Codon CheckingShould after all the exons (nonsense-mediated mRNA decaying)
![Page 20: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/20.jpg)
SiRNA MechanismRNase, ATP hydrolysis
and RNA helicase
![Page 21: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/21.jpg)
Summary• Premature termination
• Alternative RNA Splicing
• 3’ cleavage and Poly A’ addition
• RNA editing
• Necleus transportation
• Localization of RNA at the cytoplasm
• Translational initiation
• Degradation
![Page 22: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/22.jpg)
• Cell Membranes
• Lipid Bilayers
• Cell Membrane
![Page 23: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/23.jpg)
Cell Membrane Views
![Page 24: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/24.jpg)
Phospholipid Molecule
![Page 25: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/25.jpg)
Hydrophilic and Hydrophobic
Molecules interacting
differently with water
![Page 26: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/26.jpg)
Wedge-shaped lipids form micellesCylinder-shaped lipids form bilayers
![Page 27: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/27.jpg)
Spontaneous sealing of phospholipid bilayer
![Page 28: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/28.jpg)
LiposomesProved the self sealing
process
![Page 29: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/29.jpg)
Phospholipid mobilityLateral diffusion:
Diffusion coefficient 10-8 cm2/sec
Migrate in seconds to cover the whole
surface
Flip-Flop: phospholipid translocators
![Page 30: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/30.jpg)
Cis-double bonds affect packing
Saturated: packed and thick
Unsaturated : loose and thin
Phase transition: liquid to solid
![Page 31: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/31.jpg)
Cholesterol and Glycolipids
![Page 32: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/32.jpg)
Function of Cholesterol
1. Provide structural support, prevent small molecule to pass
2. Prevent tight packing and transition
![Page 33: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/33.jpg)
![Page 34: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/34.jpg)
Phospholipid types
![Page 35: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/35.jpg)
Microdomains on plasma membrane
Lipid rafts (~ 50nm)
ChoresterolSphingolipids (long saturated chains)Other proteins
![Page 36: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/36.jpg)
Asymmetrical distribution of
phospholipids and glycolipids
Protein kinase C (PKC) binds to
negatively charged
phosphotidylserine to be functional
![Page 37: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/37.jpg)
Phospholipids in cell signaling
PKCCalcium
GEF, AKT, migrating front
![Page 38: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/38.jpg)
Phospholipase Cleavage sites
![Page 39: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/39.jpg)
Phosphotidylserine exposed on outer surface as apoptosis signal
1. Phospholipid translocator2. Scramblase
![Page 40: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/40.jpg)
Glycolipids
Gm1 Ganglioside with charge can serve as signal for lipid rafts, binds to Cholera toxin
![Page 41: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/41.jpg)
Summary•Lipid molecules: phospholipids, cholesterol, glycolipid, all amphipathic•Lipid bilayer, hydrophobic inside and hydrophilic outside•Subdomains on membrane, asymmetry important for functions•Phospholipids as signals
![Page 42: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/42.jpg)
Membrane Proteins
Glycosylphosphatidylinositol (GPI) anchor protein
Integral membrane proteinPeripheral membrane protein
![Page 43: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/43.jpg)
Fatty acid chain (acyl, N-terminal) or prenyl group modifications (C-terminal)
Or geranylgeranylOr palmitic acid
![Page 44: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/44.jpg)
Hydropathy PlotsIndex of hydrophobicity
![Page 45: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/45.jpg)
Membrane proteins are glycosylated
Sugar are added in the lumen of the ER and
Golgi apparatus, therefore, sugar are
outside of cell surface
Cytosol has reduced environment,
preventing disulfide bonds
![Page 46: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/46.jpg)
A detergent micelle
Detergent to solubilize and purify membrane proteins
![Page 47: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/47.jpg)
Solubilize membrane proteins with detergent
![Page 48: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/48.jpg)
Different DetergentsIonic (strong) or nonionic
(weak)
![Page 49: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/49.jpg)
Mild detergent for the solubilizing,
purification, and reconstitution of
membrane protein functions to study the
functions of membrane proteins in simplified
environment
![Page 50: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/50.jpg)
The study of membrane proteinsMost prominent example
red blood cells
No nucleus or internal organelles
![Page 51: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/51.jpg)
The preparation of red blood cell membranes
![Page 52: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/52.jpg)
15 major membrane proteins in red blood cells
Label them with impermeable dyes can
determine the location on layers
![Page 53: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/53.jpg)
Membrane proteins are diffusible
![Page 54: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/54.jpg)
Techniques to study protein motion on membrane(Fluorescence Recovery After Photobleaching
![Page 55: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/55.jpg)
(Fluorescence Loss In Photobleaching)
![Page 56: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/56.jpg)
Proteins restrictionsTight Junction is one kind of them
Proteins and lipids on the outer layers can’t move to other compartments
![Page 57: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/57.jpg)
Protein distributions in a guinea pig sperm cell
![Page 58: Last Class: Gene Regulation 1. DNA-protein interaction, different motifs, techniques to study DNA-protein interaction 2. Gene regulation on DNAs, gene.](https://reader036.fdocuments.in/reader036/viewer/2022062314/56649ead5503460f94bb4aec/html5/thumbnails/58.jpg)
4 ways of protein restrictions1. self-assembly2. Tethered to macromolecules outside3. Tethered to macromolecules inside
4. Cell-cell adhesion