Epigenetics and Non-coding regulatory RNAs + Cell Membrane Flashcards
What is epigenetics? What processes does it include?
Causing phenotypic changes by modifying how a gene is expressed, rather than modifying the DNA sequence itself. This occurs through histone modification and DNA modification.
What are the four levels of control of gene expression?
Transcriptional level: if/how often genes are transcribed
Processing level: different mRNAs made from a given gene (alternative splicing)
RNA transport: How much mRNA is made into protein and mRNA lifetime
Post-translational level: protein lifetime and activity
What is a pre-initiation complex?
Complex of general transcription factors and RNA polymerase II at the promoter formed in an inefficient way.
What are enhancers and silencer sequences?
Regulatory sites on DNA that are recognized by transrciption factors that allow more efficient rate of transcription.
What are transcription factors?
Structure: Proteins with DNA binding domain and activation domain (binding to other proteins)
Function: Activators or repressors; regulate transcription by binding to silencers (repressors) and enhancers (activators)
How do regulatory sequences and bound transcription factors communicate with promoter from far away?
DNA between regulatory sequence and promoter loops out via mediator protein to bring transcription factors closer to the promoter.
How are histones modified in epigenetic control?
Histone acetyltransferases acetylate histone tails to destabilize tight packaging and leads to euchromatin chromatin state
Histone methyltransferases methylate histone tails which change the chromatin state.
How can DNA be modified in epigenetic control?
DNA methylation occurs on cytosine bases which blocks proteins that attach to DNA to transcribe the gene.
How are histone modifications inherited?
- Daughter double helix receives half of its parent’s histone proteins
- Reader writer complexes mark new nucleosomes to fill in the gaps between inherited modified nucleosomes
- Heterochromatin specific proteins bind to region with modified histones
How many cell types can arise during development via combinations of a few transcription regulators?
2^n where n is the number of transcription regulators
What are regulatory RNA’s?
Non-coding RNA that plays a role in gene expression. Includes microRNAs, small interfering RNAs, CRISPR RNAs and long noncoding RNAs
What are miRNAs?
22 nucleotide microRNA packaged with proteins to form RNA induced silencing complex, patrolling cytosol to bind to mRNA complimentary in sequence.
What does RISC do?
miRNA and protein complex either destroys the complimentary mRNA via nuclease (extensive match) or sequesters the matched section to be degraded by cytoplasmic nucleases (less extensive match)
What is RNA interference?
- Double stranded foreign RNA cut into short fragments via dicer enzyme called small interfering RNAs
- siRNAs are taken up by RISC proteins
- siRNA RISC protein complex discards one strand of siRNA, using the other strand to seek and destroy complimentary molecules.
What are the functions of a cell membrane?
- Receive signals from the environment via receptor proteins
- Import and export of small molecules via channels and transporter proteins
- Allows cell to grow, change shape, heal, and move
How did scientists learn about the bilyaer?
- Isolated lipids from the plasma membranes of purified red blood cells,
- spread them out over a surface of water
- Packed the lipids into a single layer
- Area equals double the area of the original intact cells
What are the frequent and rare movements of the lipid bilayer?
Frequent: continuously exchange places with their neighbours within the same monolayer
Rare: molecules tumbling from one half of the bilayer. to the other. Needs help of proteins.
What does membrane fluidity depend on?
- Length of lipid tails: short = less interactions, long = more interactions
- Number of double bonds in lipids: many = less interactions, few = more interactions
- Presence of cholesterol: @ low temp = increases fluidity by separating hydrocarbon chains, @ high temp = decreases fluidity by packing the open spaces
What is the importance of membrane fluidity?
- Enables proteins to diffuse rapidly
- Ensures membrane molecules are distributed evenly between daughter cells during cell division
- Allows mixing of molecules when membranes fuse with one anotoher
Where are phospholipids manufactured?
By enzymes on the cytosolic surface of the ER, depositing them in the cytosolic half of the bilayer
What is scramblase?
Enzyme that catalyzes phospholipid transfers via random distribution in the ER membrane without the use of ATP hydrolysis
What are flippases?
Proteins that use ATP hydrolysis to transfer specific phospholipids from the outer layer of the bilayer to the inner layer facing the cytosol, resulting in asymmetry in the membrane of the golgi body
What are the functions of membrane proteins?
- Transport particular nutrients, metabolites and ions across the lipid bilayer
- Anchor membrane to macromolecules on either side
- Catalyze specific reactions at the membrane
What are different ways membrane proteins associate with the lipid bilayer?
- Transmembrane: hydrophobic parts in lipid tail region, hydrophilic parts in lipid head region
- Cytosolic: associated with cytosolic half of lipid bilayer by alpha helix on cytosolic monolayer of membrane
- Lipid linked: either on one side or the other attached by lipid groups
- Protein-linked: bound indirectly to one face of the membrane or the other via interactions with other membrane proteins
What is the difference between integral membrane proteins and peripheral membrane proteins?
Integral: removed by disrupting the bilayer with detergents
Peripheral: removed by agents that disrupt protein-protein interactions
what is the structure of a single pass membrane spanning helix?
Hydrophobic side chains interact with the lipids while hydrophilic polypeptide backbone forms hydrogen bonds with one another within the helix
What is the structure of an ion channel?
Multipass transmembrane proteins with one or more membrane spanning regions with hydrophobic R groups facing the lipids and hydrophilic R groups facing the lumen, creating an aqueous pore
What is a beta barrel?
cross linked beta sheets with hydrophilic amino acids facing the inside and hydrophobic amino acids facing the outside creating an aqueous pore.
How do we know a membrane proteins shape?
hard for membrane proteins to pack together in an organized crystal for x ray crystallography as they must be purified in detergent micelles which makes them heterogenous in size
because of this, we use cryo-electron microscopy
What is bacteriorhodopsin?
small membrane protein found in halobacterium halobium that pumps protons outside of the cell
How does bacteriorhodopsin work?
- Light is absorbed by retinal
- Retinal triggers change in shape of alpha helices
- alpha helix pumps proton out of the cell
How do plasma proteins move laterally across the cell membrane?
- tethered at the cell cortex inside the cell
- Tethered to the ECM molecules outside the cell
- tethered to proteins on the surface of another cell
- restricted to certain domains of the membrane by diffusion barriers
What is the cell cortex?
Meshwork of filamentous proteins attached to the underside of the membrane
What is spectrin?
dimeric protein linked with attachment proteins that forms a lattice that supports the membrane of a red blood cell to maintain the cell’s shape.
What is the glycocalyx?
Layer formed by oligosaccharide side chains that are attached to membrane glycolipids and glycoproteins.
How does the glycocalyx aid in immunity?
- Neutrophil has oligosaccharide and infected cell has lectin
- Lectin recognizes carbs on neutrophil in blood
- neutrophil adheres to cell wall and squeezes through cells to find site of infection
What is fluorescence recovery after photobleaching?
FRAP: membrane proteins that are fluorescent are bleached with a laser, and the protein molecules diffuse into the bleached area.
What is single particle tracking microscopy?
Tracks movements of individual membrane proteins by tagging with antibody coated gold nanoparticles.
What are the three outcomes of SPT in 3 levels of protein movement?
Diffuse randomly: large squiggle
Trapped in small area: medium squiggle
Attached to cytoskeleton/immobile: small condensed squiggle
