Essential Cell Bio Exam 2

T-SNAREs

SNAREs on the target membrane

V-SNAREs

SNAREs on the vesicle

cytosol

part of cytoplasm that is partitioned off within intracellular membranes; largest single compartment of cells; where most fundamental cellular reactions take place

signal-recognition particle (SRP)

particle present in the cytosol which bind to the ER signal sequence when it is exposed on the ribosome; protein synthesis slow once an SRP binds to a signal sequence until it can located an SRP receptor

symport

coupled transporter that moves the two solutes that are coupled in the same direction across the membrane

antiport

coupled transporter that moves two coupled solutes opposite directions

unsaturated fats

phospholipids that have long hydrocarbon chains with double bonds; do not have the max amount of hydrogen bonds

saturated fats

phospholipids that have no double bands, they have the max amount of hydrogen bonds

patch-clamp recording

procedure for measuring and detecting the electric current flowing through a single channel molecule

glycosylation

process carried out by glycosylating enzymes present in the ER (not the cytosol); oligosaccharides are added--> they can protect the protein from degradation, hold it in the ER until it's folded, help guide it to the right organelle (serves as a transport signal)

exocytosis

process where newly made proteins, lipids, carbs are delivered from the ER, via the Golgi, to the cell surface by vesicles that fuse with the membrane; molecules are often chemically modified en route

carbohydrate layer

sugar coating on non-cytosolic side of membrane; made of glycoproteins, proteoglycans, glycolipids; this helps protect the cell surface from mechanical, chemical damage; gives cell a slimy surface, helps motile cells squeeze through narrow areas, prevents sticking; also is involved in cell-cell recognition; this recognition layer depends on the cell's specialized function

signal sequence

the amino acid sequence that is the sorting signal; it's usually 15-60 amino acids long (usually on the N terminus)

clathrin coated pit

the initial stage of a clathrin coated vesicle; when it first starts to bud off (it's still connected to the membrane)

membrane potential

electric potential difference between the outside and inside of the cell; generated by transfers of charges across the membrane which leave one side unbalanced

importance of membrane fluidity

enables membrane proteins to diffuse rapidly through the bilayer and interact with each other (i.e. cells signaling), permits lipids/proteins to diffuse from sites where they are inserted into bilayer after synthesis to other regions of cell, allows membranes to fuse with one another and mix molecules, insures membrane molecules are distributed evenly between daughter cells in cell division

flippases

enzymes that transfer newly made phospholipds from cytosolic side of the forming bilayer to the opposite monolayer; this maintains even growth of the membrane

Nernst equation

equation used to calculate the theoretical resting potential of the membrane

Rab proteins

family of proteins on which target membrane recognition depends; are found on the surface of vesicle, are recognized by tethering proteins on the cytosolic surface of the target membrane; they are unique to make the sure the correct membrane is identified

SNAREs

family of transmembrane proteins; once vesicle is tethered to the membrane by the Rab proteins interacting with the tethering protein, those on the vesicles interact with the complementary ones on the membrane

lipid aggregates

fatty acids form micelles, triacylglycerols form spherical fat droplets, phospholipids and glycolpids form lipid bilayers

plasma membrane

fatty film that is so thin and transparent that it cannot be seen under a light microscope; made of two-ply sheets of lipids; is selectively permeable

membrane domains

functionally specialized regions in the membrane; are created when membrane proteins are localized

electrochemical gradient

gradient due to both charge of solute and the concentration gradient of the solute; when net charge, concentration work together the gradient is steep; when they don't, gradient is small, there is not much net movement

action potential

happens in neurons; where a strong local electrical stimulus triggers an explosion of electrical activity in the plasma membrane that is propagated rapidly along the membrane of the axon and sustained by automatic renewal

glycolipids

have hydrophobic region, two long hydrocarbon tails, a polar region, one or more; located mainly in plasma membrane, found only in the noncytosolic half of the bilayer so their sugar groups are exposed to the cell interior; they acquire their sugar group in the golgi in this specific orientation

steroids

have multiple ring structure, made of isoprenes

vesicular transport

highly organized transport done through vesicles; proteins are synthesized in the ER, enter the ER, go the golgi apparatus, sometimes lysosomes

membrane flexibilty

important property for membranes; allows membranes to bend, sets vesicle size limit

what will not diffuse across a membrane

ions and charged molecules no matter size, their charge and electrical attraction to water inhibits them from enter the hydrocarbon phase of the lipid bilayer

endoplasmic reticulum (ER)

irregular maze of interconnected spaces enclosed by a membrane; where proteins destined for export are made; once they enter the ER they will not re-enter the cytosol, they will be ferried by transport vesicles from then on; rough ER has ribosome attached to it; smooth ER does not

phosphatidylcholine

most common phospholipid in cell membrane; has a small choline molecule attached to a phosphate as its hydrophilic head; two hydrocarbon chains are its hydrophobic tails

osmosis

movement of water from a region of high solute concentration (high water concentration) to a region of high solute concentration (low water concentration)

neuron

nerve cell which receives, transmits, and conducts signals; has an axon and nerve terminal

beta barrel

open-ended keg-like structure formed by a beta sheet curving into a cylinder; amino acid side chains on inside of barrel are hydrophilic, those on the outside touching the hydrophobic core of the lipid bilayer are hydrophobic; they form wide channels because beta sheets cannot curve a lot

transporter

opening in membrane that only allows the passage of molecules or ions that fit into a binding site on the protein; it transfers these molecules by changing its conformation; they bind with great specificity

channels

openings in cell membrane that discriminate based on size, charge

coupled transporters

transporters that use the downhill movement of one solute down its gradient to provide energy for the uphill movement of another solid against its gradient

three types of active transport

1. coupled transport--> coupling of an uphill transport with a downhill transport of another 2. ATP-driven pumps--> couple uphilll transport to hydrolysis of ATP 3. Light-driven pumps--> found mainly in bacterial cells they couple uphill transport to light energy (i.e. bacteriorhodopsin)

Ways proteins associate with lipid bilayer

1. they extend through bilayer with part of their mass on each side; have both hydrophobic and hydrophilic regions; hydrophobic regions are on the interior, the hydrophilic regions exposed to the environment on both sides of membrane; 2. located entirely in the cytosol; associate with the inner leaflet of the bilayer by an amphipathic alpha helices exposed on surface; 3. located entirely outside of bilayer, on one side or another; attach to membrane by covalent lipid groups; 4. are bound indirectly to one or the other membrane face; held in place by interactions with other membrane proteins

types of proteins transferred form cytosol to ER

1. water soluble proteins which are completely translocated across the ER membrane, into the lumen; destined for secretion or the lumen of another organelle 2. prospective transmembrane proteins which are only partly translocated across the ER membrane, become embedded in it; destined for the ER membrane, another organelle membrane, or the plasma membrane

cystic fibrosis

a common genetic disease that produces a plasma membrane transport protein that is misfolded; it could function correctly but because it is misfolded it is not allowed to leave the ER

polyribosome

a complex of multiple ribosomes and an mRNA transcript

adaptin

a coat protein that is involved in capturing specific molecules for transport; this protein secures the clathrin coat to the vesicle membrane and selects cargo molecules for transport; do so by capturing cargo receptors for specific cargo

ER retention signal

a C-terminal sequence of 4 amino acids that retains proteins that are destined to function in the ER, in the ER; is recognized by a membrane bound receptor protein in the ER and the Golgi

lipid bilayer

universal basis of membrane structure, its properties are responsible for properties of all cell membranes

spectrin

a long, flexible rod-shaped protein about 100 nm in length; the main component of the cell cortex of red blood cells

stop-transfer sequence

a sequence of hydrophobic amino acids that halts synthesis of a transmembrane protein; its released from the translocation channel and forms an alpha helical segment that anchors the protein to the membrane (N-terminal sequence is cleaved off and we now have a translocated protein in the membrane; N-terminus = the lumen, the C-terminus = the cytosolic side)

retinal

a single nonprotein molecule in bacteriorhodopsin that absorbs light energy; this gives the bacteria its purple color; is covalently attached to one of bacteriorhodopsin's 7 transmembran alpha helices; when it absorbs light, it changes shape; conformation change leads to transfer of H+ to outside of bacterium; H+ is replaced from cytosol; essentially this process drives the H+ pump in bacteriorhodopsin

start-transfer sequemce

an internal signal sequence that is used to start protein transfer; its never removed; occurs in some transmembrane proteins; in this case there are usually two hydrophobic sequences that are released into the bilayer, these proteins become "stiched" into the membrane

disulfide bonds

bonds formed by the oxidation of pairs of cysteine side chains; formation is catalyzed by an enzyme in the ER lumen; these bonds help stabilize the structure of proteins that may encounter changes in pH and degradative enzymes; can't form in the cytosol, it has a reducing environment

ligand-gated channel

channel controlled by the binding of some molecule (ligand) to the channel

voltage-gated channel

channel that depends on membrane potential

stress-gated channel

channel that is controlled by a mechanical force applied to the channel; i.e. in auditory hair cells, sound vibrations pull the channel open by causing movement that disturbs the cell membrane

voltage-gated Na+ channels

channels that open when a stimulus causes a sufficiently large depolarization to pass a certain threshold; Na+ then enters the cell down its electrochemical gradient; the more Na+ enters, the more depolarized the membrane becomes and the more these channels open; this self amplifying process continues down a neuron to create a moving action potential; goes from resting -60 to +40; during this process the channels immediately open, then close, then become inactive before they can open again

ion channels

channels that show ion selectivity (which depends on the diameter and shape of the ion channel and the distribution of the charges amino acid that lines it--> ion channels are narrow so the ions are forced to come in contact with the sides); are not continuously open, are gated; b/c they do not need a conformation change they are much more efficient

detergents

commonly used agents for disrupting the lipid bilayer: they are small amphipathic, lipid-like molecules; have a single hydrophobic tail, so are shaped like cones; in water they aggregate into micelles; hydrophobic ends bind to the hydrophobic regions of the transmembrane proteins and phospholipids, separating the proteins from the bilayer and bringing them into solution

polyisoprenoids

long polymers chains of isoprenes

resting membrane potential

membrane potential in steady state conditions; the flow of positive and negative ions is balanced; not charge accumulates on either side of the membrane

cell cortex

meshwork of fibrous proteins that determines the mechanical properties of the plasma membrane

inositol phospholipids

minor components of the plasma membrane that play a role in relaying signals from the cell surface to intracellular components; act after signal has been transmitted across the membrane so they are found only on the cytosolic side

cholesterol

molecule that modulates membrane fluidity in animals; present in large amounts in the plasma membrane (20% of phospholipids by weight); are short and rigid so they fill spaces between phospholipids caused by kinks in their unsaturated tails; bilayer is therefore stiffened- more rigid, less permeable

phospholipids

molecule with hydrophilic head linked to the rest of the molecule by a phosphate group

hydrophobic molecules

molecules that are insoluble in water because most or all of them in uncharged/nonpolar; they cannot interact with water molecules; water molecules are forced to form cage-like structures around these molecules, this takes a littler energy but energy = minimized because the molecules squeeze together

hydrophilic molecules

molecules that dissolve steadily in water because of charged atoms/polar groups

clathrin

protein that makes up the coat of many vesicles; vesicles coated with this bud from the Golgi on the outward secretory path, from the membrane on the inward endocytic path; they assemble into basket-like networks on the cytosolic surface, thereby shaping the vesicle

ER or other endomembrane system to another importation

proteins are ferried by transport vesicles which pinch off from the membrane and are loaded with proteins in their lumen; they discharge their content by fusing with a second membrane; membrane proteins and lipids are also transported`

Cytosol to ER, mitochondria, chloroplasts importation

proteins are transported across membranes by protein translocators in the membrane; transported protein usually must unfold in order to go through the membrane

Cytosol to nucleus importation

proteins are transported through nuclear pores; the pores function as selective gates that actively transport larger specific molecules but allow free diffusion of smaller ones

chaperon proteins

proteins residing in the ER that hold onto protein until they are properly folded (ER selectivity means that only correctly folded proteins can leave)

peripheral membrane proteins

proteins that can be removed from the membrane by gentler techniques that just disrupt protein-protein interactions, not the lipid bilayer

integral membrane proteins

proteins that can only be removed from the membrane by disrupting the lipid bilayer

membrane proteins

proteins that carry out most membrane functions; they transport nutrients, metabolites, and ions across bilayer; anchor membrane to macromolecules; act as receptors and detect chemical signals, relay them to cell interior; each cell membrane has a unique set of these, reflects specialized functions of cell membranes

porin proteins

proteins that have a beta barrel shape; they form large, water-filled pores in mitochondrial and bacterial membranes; they allow for the passage of smaller nutrients, ions across the membranes without letting large molecules

membrane transport proteins

proteins that span the lipid bilayer, provide private passageways across the membrane for select substances; specifically for those that can't use simple diffusion across a membrane

SRP receptor

receptor embedded in the membrane of the ER, which recognizes the SRP; when an SRP recognizes and binds to it the polypeptide chain is threaded into the lumen

membrane bound ribosomes

ribosomes attached to the cytosolic side of the the rough ER membrane; they are making proteins that are being translocated into the ER

free ribosomes

ribosomes that are unattached to any membranes and make all of the other proteins encoded by the DNA

depolarization

shift in the membrane potential to a less negative value (shift towards zero)

sorting signal

signal that directs the protein to the organelle in which it is required; these are contained in the amino acid sequences

tight junction

site where specialized junctional proteins form a continuous belt around the cell where it contacts neighboring cells creating a seal between adjacent cells; membrane proteins cannot diffuse past these

dynamin

small GTP-binding protein which assembles as a ring around the neck of each clathrin coated pit; it recruit other proteins, the ring constricts, and then the vesicle is pinched off

what will diffuse across a membrane

small non-polar molecules (i.e. O2, CO2), they readily dissolve in lipid bilayers and rapidly diffuse across them; uncharged polar molecules--> will diffuse if they are small enough (i.e. water,ethanol, glycerol a little less, glucose hardly at all)

peroxisomes

small organelles with a single membrane; they contain enzymes used in oxidative reactions that break down lipids and destroy toxic molecules

bacteriorhodopsin

small protein (250 AAs) found in large amounts in plasma membrane of an archean, halo bacteria (which lives in salty areas); is a membrane transport protein that pumps H+ out; gets energy from sunlight through retinal; is a transporter protein

voltage sensors

specialized charged protein domains that are extremely sensitive to changes in the membrane potential; changes at a certain level exert an electrical force that encourages voltage-gated channels to open or close

dolichol

specialized lipid in the ER membrane where the oligosaccharide is originally attached before glycosylation;

Golgi apparatus

stacks of flattened membrane-enclosed sacs (cisternae); this organelle recieves and often chemically modifies molecules made in the ER; then it directs them to the exterior of cell or other locations in the cell; usually located near the nucleus

isoprenes

subunit that forms steroids, polyisoprenoids

voltage-gated K+ channels

these channels help return neurons to their resting potential; they stay open as long the membrane remains depolarized

rough ER

this is created when ribosomes attached to the ER as they need to be attached while they are synthesizing their proteins if the protein needs to be threaded through the membrane

Na+ - K+ pump

this transporter expels Na+ that is constantly entering through other transporters and ion channels; it keeps the Na+ concentration in the cytosol 10-30 times lower, the K+ concentration in the cytosol 10-30 times higher

glucose transporter

transporter that mediates the passive transport of glucose; protein consists of a polypeptide chain that crosses the membrane at least 12 times; transporter can adopt two conformations and switches randomly between them; one exposes binding site to the interior of the cell, the other to the exterior

glucose-Na+ symport

transporter that takes up glucose from the (i.e. gut) lumen by active transport; this is not usually favorable but the steep Na+ gradient "drags" sugar into the cell; they bind cooperatively

COP-coated vesicles

vesicles coated with the COP protein that are involved in transporting molecules between the ER and the golgi and from one part of the golgi to another

coated vesicles

vesicles that bud from membranes that have distinctive protein coats on their cytosolic surface; they shed their coats once they had budded off in order to interact with the surface they are fusing with; coat--> 1. shapes the membrane into a bud, 2. helps capture molecules for onward transport

transport vesicles

vesicles that transport proteins and such between compartments in the endomembrane system

active transport

when a solute moves across a membrane against its concentration gradient; is carried out by special transporters that can harness energy; another process that produces energy has to be coupled with this process

passive transport

when a solute will move across a membrane down its concentration gradient spontaneously (from more to less concentrated); this requires no energy

osmotic pressure

when the driving force for the water movement is equivalent to a difference in water pressure