Epigenetics and Non-coding regulatory RNAs + Cell Membrane

Question 1

What is epigenetics? What processes does it include?

Answer 1

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.

Question 2

What are the four levels of control of gene expression?

Answer 2

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

Question 3

What is a pre-initiation complex?

Answer 3

Complex of general transcription factors and RNA polymerase II at the promoter formed in an inefficient way.

Question 4

What are enhancers and silencer sequences?

Answer 4

Regulatory sites on DNA that are recognized by transrciption factors that allow more efficient rate of transcription.

Question 5

What are transcription factors?

Answer 5

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)

Question 6

How do regulatory sequences and bound transcription factors communicate with promoter from far away?

Answer 6

DNA between regulatory sequence and promoter loops out via mediator protein to bring transcription factors closer to the promoter.

Question 7

How are histones modified in epigenetic control?

Answer 7

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.

Question 8

How can DNA be modified in epigenetic control?

Answer 8

DNA methylation occurs on cytosine bases which blocks proteins that attach to DNA to transcribe the gene.

Question 9

How are histone modifications inherited?

Answer 9

1. Daughter double helix receives half of its parent’s histone proteins
2. Reader writer complexes mark new nucleosomes to fill in the gaps between inherited modified nucleosomes
3. Heterochromatin specific proteins bind to region with modified histones

Question 10

How many cell types can arise during development via combinations of a few transcription regulators?

Answer 10

2^n where n is the number of transcription regulators

Question 11

What are regulatory RNA’s?

Answer 11

Non-coding RNA that plays a role in gene expression. Includes microRNAs, small interfering RNAs, CRISPR RNAs and long noncoding RNAs

Question 12

What are miRNAs?

Answer 12

22 nucleotide microRNA packaged with proteins to form RNA induced silencing complex, patrolling cytosol to bind to mRNA complimentary in sequence.

Question 13

What does RISC do?

Answer 13

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)

Question 14

What is RNA interference?

Answer 14

1. Double stranded foreign RNA cut into short fragments via dicer enzyme called small interfering RNAs
2. siRNAs are taken up by RISC proteins
3. siRNA RISC protein complex discards one strand of siRNA, using the other strand to seek and destroy complimentary molecules.

Question 15

What are the functions of a cell membrane?

Answer 15

1. Receive signals from the environment via receptor proteins
2. Import and export of small molecules via channels and transporter proteins
3. Allows cell to grow, change shape, heal, and move

Question 16

How did scientists learn about the bilyaer?

Answer 16

1. Isolated lipids from the plasma membranes of purified red blood cells,
2. spread them out over a surface of water
3. Packed the lipids into a single layer
4. Area equals double the area of the original intact cells

Question 17

What are the frequent and rare movements of the lipid bilayer?

Answer 17

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.

Question 18

What does membrane fluidity depend on?

Answer 18

1. Length of lipid tails: short = less interactions, long = more interactions
2. Number of double bonds in lipids: many = less interactions, few = more interactions
3. Presence of cholesterol: @ low temp = increases fluidity by separating hydrocarbon chains, @ high temp = decreases fluidity by packing the open spaces

Question 19

What is the importance of membrane fluidity?

Answer 19

1. Enables proteins to diffuse rapidly
2. Ensures membrane molecules are distributed evenly between daughter cells during cell division
3. Allows mixing of molecules when membranes fuse with one anotoher

Question 20

Where are phospholipids manufactured?

Answer 20

By enzymes on the cytosolic surface of the ER, depositing them in the cytosolic half of the bilayer

Question 21

What is scramblase?

Answer 21

Enzyme that catalyzes phospholipid transfers via random distribution in the ER membrane without the use of ATP hydrolysis

Question 22

What are flippases?

Answer 22

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

Question 23

What are the functions of membrane proteins?

Answer 23

1. Transport particular nutrients, metabolites and ions across the lipid bilayer
2. Anchor membrane to macromolecules on either side
3. Catalyze specific reactions at the membrane

Question 24

What are different ways membrane proteins associate with the lipid bilayer?

Answer 24

1. Transmembrane: hydrophobic parts in lipid tail region, hydrophilic parts in lipid head region
2. Cytosolic: associated with cytosolic half of lipid bilayer by alpha helix on cytosolic monolayer of membrane
3. Lipid linked: either on one side or the other attached by lipid groups
4. Protein-linked: bound indirectly to one face of the membrane or the other via interactions with other membrane proteins

Question 25

What is the difference between integral membrane proteins and peripheral membrane proteins?

Answer 25

Integral: removed by disrupting the bilayer with detergents

Peripheral: removed by agents that disrupt protein-protein interactions

Question 26

what is the structure of a single pass membrane spanning helix?

Answer 26

Hydrophobic side chains interact with the lipids while hydrophilic polypeptide backbone forms hydrogen bonds with one another within the helix

Question 27

What is the structure of an ion channel?

Answer 27

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

Question 28

What is a beta barrel?

Answer 28

cross linked beta sheets with hydrophilic amino acids facing the inside and hydrophobic amino acids facing the outside creating an aqueous pore.

Question 29

How do we know a membrane proteins shape?

Answer 29

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

Question 30

What is bacteriorhodopsin?

Answer 30

small membrane protein found in halobacterium halobium that pumps protons outside of the cell

Question 31

How does bacteriorhodopsin work?

Answer 31

1. Light is absorbed by retinal
2. Retinal triggers change in shape of alpha helices
3. alpha helix pumps proton out of the cell

Question 32

How do plasma proteins move laterally across the cell membrane?

Answer 32

1. tethered at the cell cortex inside the cell
2. Tethered to the ECM molecules outside the cell
3. tethered to proteins on the surface of another cell
4. restricted to certain domains of the membrane by diffusion barriers

Question 33

What is the cell cortex?

Answer 33

Meshwork of filamentous proteins attached to the underside of the membrane

Question 34

What is spectrin?

Answer 34

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.

Question 35

What is the glycocalyx?

Answer 35

Layer formed by oligosaccharide side chains that are attached to membrane glycolipids and glycoproteins.

Question 36

How does the glycocalyx aid in immunity?

Answer 36

1. Neutrophil has oligosaccharide and infected cell has lectin
2. Lectin recognizes carbs on neutrophil in blood
3. neutrophil adheres to cell wall and squeezes through cells to find site of infection

Question 37

What is fluorescence recovery after photobleaching?

Answer 37

FRAP: membrane proteins that are fluorescent are bleached with a laser, and the protein molecules diffuse into the bleached area.

Question 38

What is single particle tracking microscopy?

Answer 38

Tracks movements of individual membrane proteins by tagging with antibody coated gold nanoparticles.

Question 39

What are the three outcomes of SPT in 3 levels of protein movement?

Answer 39

Diffuse randomly: large squiggle

Trapped in small area: medium squiggle

Attached to cytoskeleton/immobile: small condensed squiggle