Term
Genetic information and processing
process, sort, and target cell to correct compartment
energy and metabolic activities
movement
recognizing and interacting with environment |
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Definition
nucleus
endomembrane system
mitochondria, chloroplast, peroxisomes
cytoskeleton
plasma membrane/cell surface |
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Term
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Definition
Network of communicating membranes w/ related functions in the cell; communicate via vesicular transport function in protein processing & lipid synthesis |
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Term
| where does protein synthesis take place and where does it begin? |
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Definition
| it takes place on free and membrane bound ribosomes; begins on free cytosolic ribosomes; they must fold before they are functional |
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Term
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Definition
| made of flat sacs; has ribosomes; functions in protein synthesis and processing |
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Term
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Definition
| the lumen of the ER; accounts for 10% of total cell volume |
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Term
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Definition
| where vesicles exit to the Golgi |
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Term
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Definition
| tube shaped; associated with lipid synthesis |
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Term
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Definition
| transports contents from Golgi to outside of cell by fusing to the plasma membrane. |
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Term
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Definition
| rough ER to Golgi to secretory vesicles to cell exterior |
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Term
| protein sorting in membrane bound ribosomes vs cytosolic ribosomes |
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Definition
free ribosomes: transport to nucleus, chloroplast, mitochondria, or peroxisomes (ENERGY)(post-translational)
membrane bound: plasma membrane, secretory vesicles, endosomes, ER, golgi, cell exterior(co translational) |
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Term
| how do ribosomes know to bind to the ER membrane |
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Definition
| they are targeted by the amino acid sequence of the polypeptide chain being synthesized (SIGNAL SEQUENCE); they're usually cleaved from the polypeptide chain during its transfer to the ER |
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Term
| which terminus of the polypeptide is made first? |
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Definition
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Term
| co-translational targeting |
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Definition
free ribosome starts making protein from mRNA info
SRP binds to signal sequence
signal sequence is taken to SRP receptor after translation slows
Ribosome binds to translocon
Now SRP is released and translation begins again and signal sequence goes into ER
Peptidase cleaves signal sequence
Signal sequence folds and becomes functional |
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Term
| post translational targeting |
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Definition
ribosome makes protein and when it is complete, it's released from the ribosome
chaperone keeps protein from folding
signal sequence attaches directly to sec 62/63 (receptor proteins)
Bip pulls signal sequence inside
now protein can fold |
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Term
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Definition
| signal recognition particle; recognizes signal sequences; consists of 6 polypeptides and RNA; binds the ribosome along with the signal sequence |
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Term
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Definition
| membrane channel; signal sequence goes through this to get through ER lumen; SEC 61 |
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Term
| what causes the SRP to dissociate from the SRP receptor? |
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Definition
| GTP binds to both SRP and the receptor and hydrolyzes to GDP causing dissociation |
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Term
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Definition
| about 20 HYDROPHOBIC AA's; usually at N terminus |
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Term
| what are cytosolic chaperones? |
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Definition
| used to maintain the polypeptide chain in an unfolded conformation; BIP is an chaperone w/in ER |
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Term
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Definition
| stops polypeptide TRANSFER; doesn't stop translation; cleaves signal sequence so the amino terminus is exposed to the lumen; when the stop transfer sequence reaches the translocon, translocation is blocked so the C terminus of the growing polypeptide remains in cytosol |
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Term
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Definition
| signal sequence isn't cleaved; can occur in direction of either N terminus or C terminus; targets polypeptide to ER |
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Term
| What are other things that happen in the ER? (5) |
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Definition
protein folding: chaperones catalyze protein folding; HSP= heat shock protein; makes chaperones to help folding
assembly of multisubunit proteins
disulfide bond formation:; disulfide isomerase: helps protein to go through different isomers using disulfide bonds
glycolipid anchor: carb+lipid; this is how some proteins attach to membrane
initial stages of glycosylation: covalently attaching carbs to protein; attaches to side chain of AA |
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Term
| 2 ways membrane lipids are synthesized |
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Definition
on pre-existing membranes
using water soluble cytosolic precursors
phospholipids are NOT readily water soluble |
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Term
| membrane lipid synthesis through water soluble precursors |
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Definition
| water soluble precursors transferred to membrane bound enzyme and then phosphatidic acid is inserted in membrane; enzymes on cytosolic side add polar group to convert phosphatidic acid to other P-lipids |
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Term
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Definition
| catalyze the translocation of phospolipids across ER membrane to create bilayer (lumenal side) |
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Term
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Definition
transmembrane proteins possess di-acidic or di-hydrophobic AA sequences in their cytosolic domain; Also act as receptors for lumenal and GPI-anchored proteins
Lumenal proteins have signal patches |
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Term
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Definition
targeting sequence on proteins C terminus that directs their retrieval back to the ER
addition of KDEL blocks protein secretion |
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Term
| what happens to ER proteins containing KDEL or KKXX signals? |
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Definition
| they are retrieved from the Golgi and returned to the ER by binding to specific recycling receptors and being transported back |
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Term
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Definition
receives and processes proteins from the ER and sorts them so they can be transported
it is also where polysaccharides of the cell wall are made |
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Term
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Definition
made of flattened membrane enclosed sacs (cisternae)
cis side is where molecules come in from ER; closer to the nucleus
Lumen of golgi is topologically equivalent to the cell surface
trans side is where molecules exit to their final destination |
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Term
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Definition
| addition of a carb to a protein; covalently attached to AA side chain |
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Term
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Definition
| begins in the ER; carbs are attached to N terminus of protein; further processed in the cis Golgi; addition and modification of preformed structures |
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Term
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Definition
| carb attached to oxygen of serine or threonine; occurs in the Golgi; sequential addition of sugar residue |
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Term
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Definition
sphingomyelin and glycolipids are made on the lumenal side of golgi from ceramide
glycolipids cant translocate across the golgi so they are only on lumenal side
ceramide is made in the ER |
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Term
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Definition
Cellulose is the main component of cell wall; linear; synthesized on cell surface by enzymes in the membrane
hemicellulose and pectins are complex branched molecules; synthesized in the golgi and transported to the surface in vesicles |
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Term
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Definition
| epithelial cells that assist in transport of proteins to the plasma membrane; they have different surfaces to make sure the proteins get from one surface to another; they have signals to direct membrane protein from one surface to another |
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Term
| domains of plasma membrane |
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Definition
apical- face the lumen; specialized for efficient absorption of nutrients
basolateral- covers the rest of the cell; rests on the ECM |
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Term
| what determines glycosylation pattern of protein? |
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Definition
structure of proteins; accessibility of region
amount of processing enzymes present within golgi of different types of cells |
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Term
| N-linked glycosylation for lysosomal targeting |
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Definition
| instead of initial removal of mannose residues, proteins are modified by mannose phosphorylation; the enzyme involved in this contain a signal patch |
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Term
| targeting in vesicular transport |
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Definition
establishes and maintains the functional organization in the cell
its selectivity is determined by combination of vesicle coat proteins, GTP binding proteins & other associated proteins |
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Term
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Definition
| transport vesicles that carry secretory proteins from the ER to subsequent compartments and are coated with cytosolic coat proteins |
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Term
| formation of transport vesicle |
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Definition
regulated by GTP binding protein (Arf 1); they recruit and regulate adaptor proteins that interact directly with a vesicle coat protein
involves sorting of cargo and budding of vesicle
coat proteins (clathrin) and adaptor proteins (GGA, AP1) involved |
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Term
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Definition
composed of coat protein (clathrin), adaptor protein (GGA, AP1), GTP binding protein (ARF1)
assemblies into a basket like lattice that distorts the membrane and initiates a bud |
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Term
| how do adaptor proteins mediate clathrin binding? |
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Definition
| adaptor protein attaches clathrin to membrane; transmembrane protein attaches to adaptor protein; adaptor interacts w/ transmembrane receptor to help select vesicle contents; receptor is attached to lysosomal protein and this will be inside vesicle |
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Term
| transport of lysosomal protein by clathrin coated vesicle |
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Definition
Lysosomal pro bound on lumenal face to R; R = transmembrane pro Adaptors (GGA & AP1) binds cytosolic portion of R; Designates clathrin the lysosomal target |
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Term
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Definition
ARF 1 initiates vesicle budding ARF is activated by ARF-GEF: ARF(GDP) → ARF(GTP) ARF(GTP) recruits adaptor protein: GGA GGA recruits receptor which carries the lysosomal protein (a lysosomal hydrolase) GGA also recruits AP1 which is binding site for clathrin |
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Term
| movement of transport vesicle |
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Definition
recycle ARF, coat proteins and adaptors; travel along cytoskeleton
GTP hydrolysis on ARF weakens coat Hsp 70s remove some of coat proteins Remaining coat pro bind tubulin & molecular motors |
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Term
| Vesicle fusion w/ target organelle |
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Definition
transmembrane proteins called SNAREs bring vesicle and target membrane close together to destabilize and fuse
vSNARE=vesicle tSNARE=target membrane
specific GTP-binding proteins (Rab family) form complexes on vesicle & target membrane that help in the process |
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Term
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Definition
| exocysts are protein complexes on the plasma membrane made of 8 different proteins formed during exocytosis from proteins are transport vesicles. |
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Term
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Definition
| membrane enclosed organelle; enzymes digest all biological polymers; they are acid hydrolases that are active at pH 5; has to actively pump H+ to maintain conc. |
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Term
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Definition
| digests material taken up by endocytosis; endosomes mature into lysosomes after pH becomes acidic enough |
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Term
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Definition
phagocytosis-macrophages take up and degrade large particles that need to be eliminated from the body
autophagy-the turnover of the cell's own components; small area of cytoplasmic organelle is enclosed by a cytosolic membrane and this fuses with a lysosome |
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Term
| what are organelles involved in metabolism and how are they related? |
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Definition
| mitochondria, chlorplast, peroxisome; assembly of most proteins occur on free ribosome and imported; they replicate by division; mitochondria and chloroplast have their own genome |
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Term
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Definition
| .5 micrometers; at least 50 enzymes; proteins are made from membrane bound and free ribosomes |
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Term
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Definition
carry out oxidative reactions for h202; they have an enzyme catalase that decomposes h202 to h20; breaks down purines, AAs, uric acid, long chain FAs
involved in the biosynthesis of lipids and lysine
glycoxylate cycle in plants: uses carbons from fats to make carbs which are building blocks for other things
photorespiration in plants: uses o2 instead of co2 to recover carbons |
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Term
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Definition
cristae: increases SA
inner membrane: high proton content; about 70%; impermeable to most ions; transporter for metabolites such as pyruvate and FAs
outer membrane: has porins so small molecules can flow through (<1kd)
intermembrane space: composition resembles cytosol |
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Term
| oxidative metabolism in mitochondria |
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Definition
| oxidative breakdown of glucose and fatty acids is the principal source of metabolic energy; glycolysis occur in the cytosol where glucose is converted to pyruvate; pyruvate is then transported into the mitochondria where it is oxidized to co2 |
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Term
| where is the proton gradient in mitochondria? |
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Definition
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Term
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Definition
| circular dna; multiple copies per organelle; vary in size in species, vary in number of genes; encode all rRNA and tRNA; "Universal code" requires 30 tRNA; human mitochondria has 22 tRNA |
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Term
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Definition
| deals with protein synthesis; codons of mrna correspond to AA; tRNA reads code w/ anticodon w/ H-bonding; at the third spot on the nucleotide, the binding is more flexible and the U can bind to other base pairs |
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Term
| protein import in mitochondria |
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Definition
| genes that encode proteins for replication of mitochondrial DNA are contained in nucleus; proteins targeted to the matrix have to cross both the inner and outer membranes; there must be sequences on proteins and receptors; the protein needs to partially or completely unfolded; may require special folding later on which SAM will do |
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Term
| mechanism of oxidative phosphorylation |
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Definition
| electrons from NADH and FADH2 are transferred to O2; used to drive synthesis of ATP from ADP; transfer of electrons from NADH to O2 is a high energy yielding rxn |
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Term
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Definition
| electrons pass through a series of carriers, carriers are organized into 4 complexes and 2 mobile carriers; 5th complex couples energy yielding rxns of electron transport to ATP synthesis |
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Term
| complexes from ETC (electrons from NADH |
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Definition
complex I: 4 protons pumped/ 2e's coenzyme q: small lipid soluble molecule complex III: 4 protons transferred/ 2e's from cytochrome b to c cytochrome c: peripheral membrane bound protein; outer face of inner mito. membrane complex IV: transfer e's to O2, 2 protons pumped/2e's, protons combine with O2 to form H2O |
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Term
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Definition
| goes to complex 2, bypasses complex 1, electrons passed to coenzyme q, no H+ pumped; then continue like NADH |
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Term
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Definition
coupling electron transport to ATP; as e's pass through complex 1,3,and 4, H+ are pumped across membrane, this establishes a electrochemical gradient
pH of the matrix is 8 and pos b/c protons are pumped out of matrix to intermembrane space (ph 7 & neg)
complex V responsible for using electrochemical potential to make ATP |
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Term
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Definition
F0= channel for H+ to flow through membrane F1= catalyzes synthesis of ATP
ATP is more negative than ADP |
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Term
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Definition
3 membranes: inner, outer, thylakoid
thylakoid: forms a network of flattened discs called thylakoids which are arranged in stacks called grana
stroma: space b/w inner membrane and thylakoid |
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Term
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Definition
| dark rxns: uses ATP and NADPH from light rxns for carbon fixation; synthesis of amino acid, fatty acids and membrane lipids; reduce nitrite to ammonia |
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Term
| chloroplast membrane permeability |
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Definition
outer: freely permeable to small molecules inner: impermeable to ions, transporter required thylakoid: impermeable to H+, permeable to small ions |
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Term
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Definition
| Energy collected from light used to create proton gradient as e- pass thru e- transport chain; uses PSI and PSII, makes NADH and ATP |
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Term
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Definition
noncyclic: ATP and NADH
cyclic: ATP only |
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Term
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Definition
Light excites e- that leave PS II e- from H2O replace e- in PSII e- from PSII thru series of carriers e- from PSII ultimately replace e- in PSI Light excites e- that leave PSI e- from PSI |
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Term
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Definition
| only ATP synthesized, cytochrome bF pumps H+, electrons return back to PSI instead of NADP+ |
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Term
| chemiosmotic coupling in mitochondria and chloroplast |
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Definition
| thylakoid permeability: neutralizes voltage component; greater H+ difference in stroma than lumen |
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Term
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Definition
| network of protein filaments, function is structural framework, cell movement, integrity/stability of cell interconnections |
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Term
| cytoskeleton protein filaments |
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Definition
actin/microfilaments: made of actin intermediate: made of various things microtubules: made of tubulin |
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Term
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Definition
major cytoskeleton protein of most cells individual monomers: G actin organized into bundles and networks regulated by actin binding protein barbed end=+ pointed end= - F actin is filament form |
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Term
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Definition
G actin binds to barbed end and dissociates from pointed end ATP hydrolyze to ADP at barbed end |
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Term
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Definition
| at a specific actin conc: net loss at minus = net gain at plus |
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Term
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Definition
| binds ADP actin so increases dissociation rate; depolymerizes actin |
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Term
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Definition
| opposite of cofilin; stimulates exchange of ATP for ADP to form F actin |
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Term
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Definition
cross linked into parallel arrays; closely spaced: connected by small rigid actin binding protein; supports projection of plasma membrane loosely spaced: connected by spacers, capable of contraction |
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Term
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Definition
| loosely cross linked 3d array, form semisolid gels, held together by actin binding protein filamin, forms a V dimer |
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Term
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Definition
| actin filament+ABP; forms 3d network, determines cell shape, anchors transmembrane protein |
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Term
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Definition
actin binding protein; forms actin spectrin network; Ankyrin links spectrin to a transmembrane protein = Band 3 Protein 4.1 binds spectrin-actin jxns links to Glycophorin |
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Term
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Definition
| mediate attachment to substratum via ECM; theyre discrete regions of membrane; the inside is attached to bundles of actin filaments; outside attached to ECM |
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Term
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Definition
| transmembrane proteins that connect inside and outside |
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Term
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Definition
Actin filaments connect to catenins on cytoplasmic side Catenins link actin to cadherins Cadherins – transmembrane protein, link to cadherins from adj cell |
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Term
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Definition
Microvilli – inc surf area & absorption Sterocilia – specialized form microvilli of auditory hairs Pseudopodia – phagocytosis, amoeboid movement |
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Term
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Definition
Actin filament attach to plasma membrane by lateral arms of myosin I & calmodulin Movement of plasma membrane along actin bundle of microvillus Base attached to cell cortex Filaments align w/ plus ends embedded in cap of protein at tip of microvillus |
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Term
| how does the cytoskeleton participate in cell movement |
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Definition
| interacts with molecular motor (protein that converts chemical energy in form of atp to mechanical energy) |
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Term
| examples of molecular motor |
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Definition
myosin: interacts with actin dynein and kinesin: interacts with microtubules
kinesin= + end of microtubule dinesin= - end of microtubule |
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Term
| binding between myosin and actin |
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Definition
| they are parallel; Attachment of filaments to opposite ends allow contraction as they slide past each other |
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Term
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Definition
| ADP is released and myosin head returns to its initial conformation; triggered by the myosin head being in the cocked position |
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Term
| how is movement regulated in the cytoskeleton |
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Definition
| troponins protein blocks interaction of actin with myosin when Ca+2 concentration is low |
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Term
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Definition
Not directly involved in cell movements Provide mechanical strength & anchoring of cellular components Generally more stable Do not exhibit as dynamic behavior Not polar (equivalent ends) classified into 6 different groups based on AA some create elaborate network extending from nucleus to plasma membrane often bound to microtubules and microfilaments: integrates elements of the cytoskeleton (see Fig 12.40) other proteins can mediate binding to structures in the cell |
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Term
| intermediate filament composition |
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Definition
central domain: alpha helical rod, filament assembly head and tail:determin function |
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Term
| intermediate filament assembly |
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Definition
| 2 polypeptides form dimers which form antiparallel tetramers which form protofilaments |
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Term
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Definition
| family of proteins that bind intermediate filaments and link them to other cellular structures |
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Term
| desmosomes and hemidesmosomes |
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Definition
Keratin filaments of epithelial cells anchored to plasma membrane at two specialized areas des: cell-cell contact; Cytoplasmic side=dense plaque of protein Desmoplakin; related to cadherins
hemi: cell-substratum contact; Cytoplasmic side=dense plaque of proteins Plectin; ECM=integrins |
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Term
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Definition
rigid and hollow; determine cell shape and polarity; Intracellular transport & positioning of organelles Separation of chromosomes during mitosis Cell movement |
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Term
| composition of microtubules |
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Definition
Composed of α, β subunits – dimers; 13 protofilaments around hollow core dimers parallel & head to tail filament is polar (+/- ends)
γ tubulin=found in centrosome; nucleation of microtubules during mitosis δ tubulin found in triplets of microtubules in centrioles |
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Term
| cell polarity in microtubules |
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Definition
MAP’s: microtubule associated proteins modify microtubule stability mediate association w/ other elements of cytoskeleton & parts of the cell different MAP’s associate w/ microtubules e.g. axons & dendrites of neurons |
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Term
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Definition
Axons + ends away from cell body contain tau protein (a type of MAP)
Dendrites some + ends to cell body some + to cell periphery contain MAP-2 |
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Term
| positioning of organelles with microtubules |
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Definition
| kinesin carry cargo toward cell periphery, dyneins carry cargo towards center of cell; Drugs that depolymerize microtubules cause ER to retract & Golgi to disperse into small vesicles |
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Term
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Definition
help with cell movement; microtubles; “9+2” pattern (2 microtubules in the center; 9 doublets around outer edge); flagella is longer than cilia Dynein moves toward minus end causing bending |
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Term
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Definition
in animal cells most microtubules extend outward from the centrosome; Site of initiation for assembly; centrosomes Duplicate then form poles during mitosis; centrosome is where the minus ends of the microtubules are anchored |
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Term
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Definition
kinetochore: attach to chromosomes at their centromeres chromosomal: connects to ends of chromosomes coming from centromere polar: stabilized by overlapping with each other in center of cell astral: extend outward toward pluss ends |
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Term
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Definition
Anaphase A: movement of chromosomes Anaphase B: separation of spindle poles |
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Term
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Definition
| movement of chromosomes toward spindle poles along kinetochore microtubles that shorten as chromosomes move; chromosomes move toward minus end with help of kinetochore associated motor proteins; dynein helps with this as well; this is coupled to disassembly and shortening of both kinetochore and chromosomal microtubules |
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Term
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Definition
Separation of spindle poles; requires coordinated push/pull Polar microtubules: plus end-directed kinesin push poles apart; elongation, slide past each other Astral microtubules: minus end-directed motor (dynein) anchored to cortex pulls poles apart; depolymerization/shortening of astral microtubules; leading to separation of spindle poles |
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Term
| structure of phospholipid bilayer |
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Definition
made of phospholipids and proteins; exterior: made of mostly carbs; sphingomyelin and phosphatidyl choline cytosolic face: net negative charge bc of phosphatidylserine and phosphatidyl inositol |
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Term
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Definition
fluidity determined by temp and liquid composition; FA saturation (bonds) and cholesterol determine composition; lipid determines structure; protein determines function |
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Term
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Definition
| protein that catalyzes translocation of lipids across membrane |
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Term
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Definition
| usually alpha helices that are inserted into the membrane of the ER during synthesis of the polypeptide chain; theyre then transported to the golgi then the plasma membrane; ex: glycophorin and band 3; they can be beta barrels too |
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Term
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Definition
| class of proteins that form channels in the outer membrane of some bacteria; cross membrane as beta barrels |
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Term
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Definition
| lipid with carb attached; GPI anchors are added to the C terminus of some proteins; the transmembrane region is cleaved so the protein remains attached to the membrane only by the glycolipid; the positively charged regions of the polypeptide may interact with negatively charged head of lipid on cytosolic side of membrane |
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Term
| factors that affect mobility of membrane proteins |
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Definition
their association with the cytoskeleton; other membrane proteins; proteins on surface of adjacent cells; ECM
tight junctions form between adjacent cells so protein cant go from one domain of a protein to another
lipid composition can affect free diffusion of membrane proteins; GPI anchored proteins cluster in lipid rafts |
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Term
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Definition
| formed by oligosaccharides of glycolipids and transmembrane glycoproteins; covers the surface of the cell; protection; identification |
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Term
| adhesion of leukocytes to endothelial cells |
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Definition
| mediated by transmembrane proteins called selectins that recognizes specific carbs on cell surface; L-selectin recognizes the glycocalyx on endothelial cells |
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Term
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Definition
ATP binding cassettes; have highly conserved ATP binding domains; use energy from ATP hydrolysis to transport molecules
MDR: first eukaryotic ABC transporter discovered by this gene; makes cancer cells resistant to a variety of drugs in chemotherapy
CFTR: responsible for cystic fibrosis; affects ion balance |
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Term
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Definition
| the Na+ gradient from the Na+/K+ pump provides a source of energy to power active transport in mammals; coupled transport |
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Term
| antiport, symport, uniport |
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Definition
uniport: transport 1 molecule; ex: facilitated diffusion of glucose symport: transport 2 molecules in same direction ex: glucose transported in with Na+ antiport: transport 2 molecules in opposite direction; ex: Na+/K+ pump
symport and antiport= apical domain uniport= basal lateral domain |
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Term
| bacteria and fungi cell wall |
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Definition
bacteria: made of peptidoglycan; polysaccharides cross linked by short peptides
fungi: made of chitin carb |
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Term
| plant cell wall and animal ecm |
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Definition
plant: made of cellulose; pectins; lignins
animal: made of polysaccharides and proteins |
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Term
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Definition
thin sheet: basal lamina; where epithelial cells attach thick matrix: loose matrix in connective tissue sturdy matrix: bone, tendon, cartilage |
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Term
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Definition
| made of fibrous proteins like elastin and collagen, polysaccharide gel aka ground substance, and adhesion proteins like laminin and fibronectin |
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Term
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Definition
| major cell surface receptor responsible for attachment of cells to ECM; focal adhesions and hemidesmosomes are 2 types of integrins |
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Term
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Definition
| the cytoplasmic domain of beta subunit of integrins anchor the actin cytoskeleton; attach cells to ECM |
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Term
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Definition
| anchor epithelial cells to basal lamina |
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Term
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Definition
| general more stable than non junctional; involves cytoskeleton of adjacent cells; based on cadherins |
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Term
| non junctional cell adhesion |
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Definition
| involves various cell receptors; may involve cytoskeleton but its a less complex junction |
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Term
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Definition
selectins, integrins, Ig superfamily, and cadherins; theyre divalent cation dependent;
selectins recognize cell surface carbs; cadherins are responsible for maintenance of stable junctions between cells in tissues |
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Term
| stable cell-cell junctions |
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Definition
adherens junction, tight junctions, desmosomes, gap junctions
adherens junction: cadherins linked to actin bundles with beta catenin
desmosomes: desmosomal cadherins link to intermediate filaments with desmoplakin |
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Term
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Definition
| made of Protein network of occludins, claudins & junctional adhesion molecules (JAMs); they form a seal to prevent passage b/w cells; separate apical and basolateral domain; provide minimal adhesive strength; part of junctional complex with adherins and desmosomes |
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Term
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Definition
| Form open channels; free passage small molec & ions; Composed of connexins; Membranes separated by gap |
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