cell phys

Synthesis of proteins begins

on cytosolic ribosomes

How does a ribosome dock onto ER membrane

By using a signal sequence, a signal recognition particle, and a signal sequence receptor

SRP and SRP receptor do what to ribosome and protein on ER

Docks ribsosome on ER translocon and cotranslationally inserts the nascent protein to ER membrane

What is the pathway for the secretory protein synthesis

Protein starts in cytosol, translated on N term side, the hydrophobic core of the signal sequence, SRP binds to hydrophobic core, SRP allows docking of peptide/ribosome to ER, polypeptide channeled through hydrophobic translocon of ER into lumen

What are the 6 types of proteins in ER membrane

Type 1, type 1, type 3, tail-anchored, type 4, and GPI anchored

What is type 1 ER membrane protein

have a cleaved N term ER signal sequence and have hydrophobic N term on lumen side. Has stop-transfer anchor which stops the protein moving through translocon and embed into ER membrane

Type 2 ER membrane protein

N terminal faces the cytosol side, do not have cleaved ER signal sequence. Has signal-anchor sequence which take protein from translocon and embed into ER membrane

Type 3 ER membrane protein

N term faces lumenal side, but do not have cleaved ER signal sequence, Has signal-anchor sequence which take protein from translocon and embed into ER membrane

Type 4 ER membrane protein

have two or membrane spanning segments, N term on lumenal side

Tail anchored ER membrane protein

Hydrophobic region at C term side on cytosol, tail is embedded in membrane, does not really cross into lumen

GPI ER membrane proteins

have a signal sequence which tell protein to go to ER, but the protein has to be post-translationally modified to have glycol phosphatidylinostiol anchor added to it

hydropathy graph for type 1 protein

large spike at the beginning and another towards middle

hydropathy graph for type 2+3 protein

large spike past beginning

hydropathy graph for type 4 protein

lots of spikes throughout the graph

tail anchored insertion into ER membrane

No SRP, not translated at ER; need GET proteins to mediate post-translational modification

what is the point of glycosylation

to increas the half life of proteins

where does o-linked glycosylation occur

the golgi

how to get proteins to mitochondria

proteins are synthesized on cytosolic ribosomes, maintained in unfolded shape by chaperones, the N term side of proteins is directed to translocons in the membrane

mitochondrial import steps

cytosolic proteins (partially unfolded) carried by chaperones have a matrix signaling sequence on their N term side which directs them to a import receptor TOM on outer mitochondrial membrane, protein goes through multiple translocons TIMs, protein folded in matrix

what is a nuclear pore

a complex in the nucleus membrane which is composed of phenylalanine and glycine “netting”, cytosolic filaments, and a nuclear basket which all work to catch proteins

What is GEF

guanine nucleotide exchange factor (GDP to GTP)

what is GAP

GTPase activating protein

what is RAN

a protein which interacts with nuclearporins and is also the protein that is going to recognize nuclear localization sequences (GAP GEF)

nuclear import

protein translated and folded in cytosol, gets the nuclear localization sequence, binds to protein importin, importin complex gets modified by RAN GAP. modified complex gets through nuclear pore, protein in nucleus, RAN GEF causes importin to disassociate with protein and importin gets carried out of nucleus by RAN GEF

nuclear export

RAN GAP modifies exportin to go through nuclear pore, in nucleus the exportin binds with finished protein, modified by RAN GEF, protein and exportin leave through pore

membrane spanning portions are usually what type of structure

alpha helices

stages of aerobic oxidation

stage 1: glycolysis and aerobic oxidation, stage 2: citric acid cycle, stage 3: electron transport chain and proton motive force, stage 4: ATP

stage 1: glycolysis steps and where it occurs

cytosolic enzymes convert glucose to two molecules of pyruvate, two ATP, and 2 NADH- occurs in the cytosol

what happens during anaerobic respiration

cells can metabolize pyruvate to lactic acid or ethanol and CO2 to convert NADH back to NAD+ required for glycolysis

what causes anaerobic conditions

intense physical activity and adaptive t cell immune response

what do t-cells need anaerobic respiration

ATP synthesis is a negative feedback system so creating too much during division would not work, using O2 and fermentation helps with rapid cell division

why is pyruvate important

it makes the three carbon structure that can be used as building material

Mitochondria functions examples

biosynthesis: steroid hormones, heme, pyrimidines (AG), AA; Fatty acid oxidation; glucose and energy metabolism

stage 2: pyruvate and acyl oxidation

pyruvate is oxidized to generate one molecule each of CO2, NADH and acetyl CoA; occurs in the mitochondria matrix

why do cells prefer to use carbs over lipids

even though lipids produce more ATP, they also produce heat and are harder to break down because of the FA tails

where is most of the energy from stages 1 and 2 stored

in the NADH/FADH2 molecules as high energy electrons

citric acid intermediates

charged carbons used for building things: citrate, aconitate, succinate, fumarate, malate, oxaloacetate

fatty acid oxidation

fatty acyl CoA converted to acetyl CoA, fatty acid shortened by two carbon atoms (electron transfer reduces FAD to FADH2 and NAD+ to NADH), the cycle is repeated on the shortened acyl CoA until FA with an even number of carbon atoms are completely converted to acetyl CoA

malate-aspartate shuttle goals

to modify NAD+ to NADH, act as transporters for the electron species and maintains the concentrations in the cytosol and matrix

malate-aspartate shuttle brief steps

NADH to NAD+ modifies oxaloacetate to become malate, goes through protein shuttle into the matrix. Malate then modified by NAD+ to NADH to become oxaloacetate, then aspartate, goes through shuttle and then repeats

stage 3: electron transport chain

flow of electrons from NADH/FADH2 go through the chain complexes (pump called cytochromes) and provides energy to drive H+ transport across the inner mitochondria membrane generating a proton motive force

alternative functions of electron transport chain

make reactive oxygen species for defense, release heat, drives ATP/ADP/HPO4 movement

stage 4: proton motive force

drives chemiosmosis, allows for protons to move down their gradient and create energy for ATP to move out of cell, ADP into matrix, O2 etc

what are vesicle protein coats

proteins which determine where the vesicles/proteins are going to go (mediates budding/fusion, etc)

what is COPII

vesicle protein coat- ER to golgi

what is COP I

vesicle coat which goes retrograde

what is clathrin

vesicle protein coat that goes from cell membrane or the trans-golgi to the late endosome

what is protein disulfide isomerase

translates proteins with disulfide bonds in the RER

what is Sar1

a GTPase on a G-protein, mediates the COP II (er to golgi) and initiates coating

what mediates pinching off for membranes in COP

GTPases

what is dynamin

the factor that will help pinch off the vesicle for clathrin coated vesicles in the pit (vital for budding)

what determines where the cargo will go

the specific signal sequences in the cargo proteins

what are Rab proteins

a small single unit soluble G-protein that are specfic for target pathways

what are SNAREs

G-proteins which mediate vesicle fusion (tell the protein where to stop and bind to that location, like velcro)

what are the two types of SNAREs

v-SNARE (vesicle) and t-SNARE (target)

what is an NSF

a G-protein that rips SNAREs off the target protein

what are the two stages/possibilites for the early secretory pathway

COP II coated vesicles transport newly synthesized proteins containing golgi targeting sequences in their cytosolic domains from RER to cis-golgi (anterograde)

COP I coated vesicles transport vesicles carrying ER/ golgi resident proteins in the retrograde direction which recyles

common mutation of cystic fibrosis

Due to lack of correct signal sequence to COP II vesicles in the trachea

late secretory pathway stages or possibilites

trans-golgi network sorts proteins into vesicles for all different locations (could go to plasma membrane, lysosome, or endosome)

how are regulated secretory proteins regulated

they are concentrated and stored until secretion signal

how do constitutively secreted proteins secreted

continuously delivered to plasma membrane

clartin codes for what in the late secretory pathway

endosome paths

AP3 codes for what in the late secretory pathway

lysosome pathway

how does lysosomal delivery work

enzymes bear the M6P (manno6phosphate) residues which are recognized by M6P receptors and delivered by clarthin coated vesicle pathway to lysosomes from the trans-golgi

where does M6P modification occur

modification mediated by specific interactions with enzymes in the cis-golgi, and is further modified once the protein is delivered so that it stays in lysosome

how does receptor mediated endocytosis work

extracell ligands bind to specific cell surface receptors, cytoplasmic domain AP2 targeting sequences are internalized by clathrin coated vesicles

where does the endocytic pathway deliver its ligands

to lysosomes to be degraded

how to send material to lysosome (two ways)

outside: endocytosed membrane proteins targeted for degradation in the lysosome are incorporated into vesicles that bud into interior of endosome

inside: autophagy envelopes a region of cytoplasm or an organelle into a double membrane autophagosome for delivery to a lysosome

multivesicular endosome

(another name for late endosomes)- proteins tagged with a single ubiquitin are destined for degradation

autophagy

self-eating, used for harvesting cytosolic resources, degrade dysfunctional organelles. protect host cell

organizing proteins for autophagy

Atg12, Atg5, etc

types of diffusion

simple or facilitated (no ATP), active- with ATP

describe cotransport

aka secondary active transport- use energy from release of H+/Na+ movement down its gradient to power transport of another molecule or different ion up its concentration gradient

types of transport proteins

channels/gates, uniporter, symporter, antiporter, atp-powered pump

what is Km with transporters

the affinity of a substrate for the enzyme

what is Vmax with transporters

the number of transporters avaliable

how do uniporters transport

convert between two conformational states to facilitate diffusion across

active transport pump classes

P-class (phosphorylated), V-class (vacuole), F-class (factor), and ABC (ATP binding cassette)

what is unique about alpha-keratin

made of two right-handed alpha helices entwined in a left handed superhelix held by van der waals interactions

what is unique about collagen

every third residue is glycine because it can H bond with groups elsewhere, yet is forms a helical shape of three intertwined polypeptides

inhibitors of enzymes

competitive (mimics substrate) and noncompetitve (bind somewhere else on enzyme and change shape)