BIOB10 - Cell Biology - Midterm

Stored information in double helix

Nucleotide: sugar phosphate + base (a,c,t,g)

Sugar phosphate backbone, bases connect but aren’t stuck together

Complimentary strand, templated polymerization, hydrolysis aids, monophosphate attaches.

Using another strand to make another strand. Using a template to make a complimentary strand.

GTP → High E bonds break → GDP + energy

Addition of water

Nucleoside with extra one or more phosphate group attached (monoguanosine).

The sugar and the backbone with phosphate group mentioned

Cell needs to make sense of information. Take one strand and use it as a template to form RNA strand.

DNA → RNA

Read one at a time, RNA called transcript. Complimentary base pairings (T = U)

“What amino acid do I add?”

RNA → Protein

Read three nucleotids (1 codon) at a time. 1 codon = 1 amino acid. Ribosome does readings.

Cell is closed in. Selective barrier → how things move in and out, semi-permeable

Amphiphilic → hydrophobic tails face inward, hydrophilic head towards water

House genetic information in nucleus. Bigger genome, difference in cell structure.

Like protein or nucleic acid.

Fold into energetically favourable confirmation, what makes the most sense.

Proteins that facilitate certain reactions. Like DNA polymerase (hydrolysis happens and it takes nucleotide away)

Enzyme that cuts nucleic acid

Exo: cutting from end

Endo: snipping from middle

Multiple amino acids connected by peptide bonds.

Backbone (peptide bonds connecting), Side chain.

N-terminus front end (amino group), C-terminus back end (carboxyl group)

Dropping protein into an aqueous watery environment causes proteins to move to protect parts from water.

Non-polar parts are hydrophobic.

Treat proteins with a solvent to mess up their bonds (unfold)

Remove solvent and protein folds again

Proteins that help proteins fold properly. Folding helpers.

They do not determine shape, just help form it. Side chain interactions determine shape, exposed hydrophobic parts are meant to fold inward.

Exposed hydrophobic regions can result in this. Desperately going around and binding to stuff and making a mess.

Coiled-coil (hydrophobic face eachother), Protein complex (protein subunits join together, clump), Dimer (2, head to head arrangement. chains bind together)

Fibrous (long, coiled-coil, helix) OR globular (clump, DNA polymerase)

Can be disordered in regions (nuclear pores, gates)

Tight or weak

Specificity

Referring to something that is doing bonding. Like enzymes, often first step of what an enzyme does. Fits with binding site.

Surface contours of the molecule fit very closely to the protein. Sending communication from one molecule to another (like to change formation)

Surface-string, helix-helix, surface-surface (most common)

Pores where things can go in and out. Referring to nuclear pore complex.

Proteins need to get to a destination; transmembrane proteins.

The protein uses transmembrane protein to snake through.

(main mean of protein transportation) Take a vesicle that transport from one place to another.

Sorting signal. Sequences on the N-terminus or in the middle of the polypeptide chain.

No signal sequence, is just in the cytoplasm

Cells move proteins into the ER before completion of polypeptide synthesis.

ER sequence shows up and protein synthesis continues on ER as chain gets snaked into ER

Finishes making protein and THEN goes to where it needs to be.

Guided to the ER by two main parts.

Signal-recognition particle (SRP) and SRP receptor.

Signal specifically on N-terminus.

SRP binds to ER signal sequence, SRP bends and block elongation factor site (pauses translation). SRP receptor binds SRP and it moves whole junction of ribosome and SRP down to ER. SRP receptor bonding. Protein elongates through protein translocator while ribosome is released.

Where stuff is going to get closer and closer to exterior of the cell

Physically on the ER, doing translation on the ER.

Transcript with 5’ and 3’ end (read from 5’)

Ribosome keeps reading and moving down. Second and third ribosomes don’t wait till first one is done, they’ll go when there’s enough room.

Once done, ribosome disassembles into individual subunits.

ER signal sequence, SRP bounding to ER membrane. Continues elongating as protein snakes through. As soon as there is space, the next one attaches and binds to membrane next to first ribosome.

Core of translocator. Has a plug, when it recognizes the sequence, the plug moves aside and allows protein to enter.

Signal peptide is hydrophobic and cannot snake through

Work with translocator to help with the process of protein translocation.

BiP

Binding protein in the ER. ATP → ADP through hydrolysis. Happens in order for this to pull the protein through.

Translocator + accessory proteins.

(part of SRP cycle) Start-transfer sequence, signal sequence doesn’t need to stay and can be cut off.

Stop transfer.

It is recognized by ribosome, it opens up the translocator and enters.

Get out and the little protein is embedded in the membrane

Goes into membrane, doesn’t get cleave off, serves as an anchor. With or without stop transfer sequence. It is stuck in membrane.

Rest of protein snakes in, no stop transfer, just goes straight through and it’s done. Double pass if there is a stop transfer.

If they wanna be right inside the ER. One signal sequence, cleaved off by signal peptidase. Snakes right through.

Stays in the ER for whatever reason. BiP is one. Have and ER retention signal.

ER must make sure protein folds correctly.

Done with Oligosaccharides and ER chaperones.

Added to proteins. Adds three sugars to proteins (protein glycosylation), catalyzes (transferase).

Proteins help proteins fold properly.

Lectins (calnexin and calreticulum)

Bind to oligosaccharides on incompletely folded proteins and retain them in ER.

Adding 3 glucose to unfold protein. Glucosidase trim these off one at a time.

The cutting process. Protein folding process doesn’t work out, it goes around the second time.

Removes mannose on the core oligosaccharide tree. Not gonna get glucose added back. Mannose is removed. Protein without mannose gets destroyed.

enzyme. Stick onto the protein and protein translocator complex. Stamps it to be destroyed.

Like BiP, helps pull protein out. Does this by hydrolyzing ATP. In retrotranslocation.

Enzyme, still has the ubiquitin chain. It saves the chain. In retrotranslocation.

Wants more chaperones to be made, needs to go all the way back to the DNA to get that coding sequence.

Misfolding with a lot of heat → stimulates transcription of genes encoding cytosolic chaperones that help refold proteins

Making more proteins involved in retrotranslocation, protein degredation in the cytosol, and ER chaperones

Doors/gates that allow protein to pass.

Mitochondria → TOM, TIM(22/23), SAM, OXA complexes

Transfer proteins across the outer mitochondrial membrane. Initial recognition.

Transfer proteins across inner mitochondrial membrane. Continue journey down, helps bring the protein down.

Once protein enters TOM, this helps them fold properly in beta porin

Some proteins can be made in mitochondria and it does that.

Helps protein snake through, get’s cleaved in matrix. This will help it and stick it in inner membrane.

(importing to mitochondrial matrix) Interacting with protein, gonna keep it unfolded. Helps that interaction. Comes off once recognized by translocator. Binds on and off to fish through.

Chaperone protein. Interacts with protein and once it comes through, this helps it fold through ATP hydrolysis.

Post-translationally, translocation, ATP hydrolysis, uses TOC/TIC, added thylakoid.

Where the reaction rate will max out

Enzyme that cut cell walls of bacteria, cell bursts. Needs to be in transition state, bound to enzyme.

Small molecules bind to these. Separate from active sites. Recognizes a regulatory molecule.

Part of enzyme that recognizes substrate, and then stuff changes when it binds with stuff.

Inactive → active (both easily bind)

Active → inactive (molecules don’t want the same thing)

Binding of one inhibitor at a time, opens it up one subunit at a time. First inhibitor binds with difficulty (changes confirmation of second inhibitor in the process) and second inhibitor binds with ease.

Pinching in of plasma membrane. Removes plasma membrane components and delivers them to internal compartments called endosomes.

Leads inward from plasma membrane

Secretory pathway delivers new proteins to plasma membrane or extracellular space.

Leads outward from ER towards Golgi and cell surface (or side route to lysosomes)

Cage of protein covering cytosolic surface, discard cote before fusing. Coat has 2 layers.

Golgi to plasma membrane, 3 heavy and 3 light chains form outerlayer (triskelyons, make buds), clathrin protein component, adaptor proteins (bind to coat and trap proteins), PIPs

Bind to AP2s and change adaptor proteins conformation. Can become phosphorylated at different regions and then bind to APs and change them. Then it is possible to bind to receptors.

They control when protein is active or inactive (no coat when inactive)

Coated transport vesicle, Golgi → ER

Arf involved

Coated transport vesicle, ER → Golgi

Sar1 involved

Have crescent shaped domains (BAR domains). Bind to and impose shape, help form circular bud.

During uncoating of membrane, PIP that is packed into vesicles leave, this weakens adaptor protein’s bind. Adaptor proteins uncoat, as soon as they pinch off coat is useless. Uses uncoating ATPases

GDP → GTP

Molecular switch, GTPases, activate protein, turn on

GTP → GDP

Molecular switch, GTPases, inactivate protein, turn off.

Inactive bound to GDP, needs to work with molecular switch. GEF takes inactive protein and activates it.

Active, bound to GTP. Works with GAPs to inactivate.

GTPases, plays a role in vesicle arriving at correct target membrane.

__-GDP is inactive

__-GEF binds and activates protein (GDP → GTP)

Tail unfolds into membrane when activated (anchor)

Rab-GTP works with them, they’re tethers, catch vesicles and bring em in. Tethering proteins. Long-threadlike.

Responsible for vesicles completing membrane fusion (lipid bilayers merging to dump contents)

V: found on vesicle with 1 protein

T: found on target membrane with 3 proteins

v- and t-SNARES wrap around to form a stable 4 helix bundle; locks the 2 membranes together for membrane fusion.

Two vesicles have their trans-SNARE complexes separated by NSF. Two vesicle’s clusters bind together and then have membrane fusion

COPII vesicles going from ER to Golgi, fusing into a large tubular cluster

Things need to go back to ER as cluster or individual (ER resident protein or COPI)

ER resident proteins have retrieval signals if they’re sent out. BiP has KDEL sequence on C-terminal signal. Retention mechanism (ER resident protein bind to each other and form complexes too big to enter).

CGN → cis cisterna → medial cisterna → trans cisterna → TGN → lysosomes

Leaving TGN. Destined for lysosomes (digestive enzymes), exocytosis (sent to cell membrane, straight to cell surface)

Membrane enclosed organelles filled with enzymes that digest macromolecules. There is proteases and nucleases within them.

Enzymes in lysosomes need an acidic environment to function. Controls them from going and destroying everything. They’re physically contained and the pH isn’t suitable for them.