Term
| What is the span (in nm) of the lipid bilayer? |
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Definition
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Term
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Definition
a)Secretory proteins contain a signal sequence at their N-terminus that directs the emerging polypeptide and ribosome to the ER membrane
b)Polypeptide moves in cisternal space of ER through a translocon and its synthesized cotranslationally. |
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Term
| Explain the idea of sorting signals |
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Definition
| Secreted proteins, lysosomal enzymes, and membranes proteins are routed to their appropriate cellular destinations by virtue of specific "addresses" or SORTING SIGNALS that are encoded in the amino acid sequence of the proteins or in the attached oligosaccharides; recognized by specific receptors that reside in the membranes or surface coats of budding vesicles, ensuring that the proteins is transported to the appropriate destination. |
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Term
| The ways the lipid of composition of membranes are modified |
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Definition
a) the head groups of phospholipids of the bilayer are modified enzymatically
b) the membrane of a forming vesicle contains a different phospholipid composition from the membrane it buds from.
c)Phospholipids can be removed from one membrane and inserted into another membrane by phospholipid-transfer proteins. |
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Term
| What is the strength of a -C-C- bond (covalent bond)? |
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Definition
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Term
| What is the strength of a hydrogen bond? |
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Definition
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Term
| What is the strength of a van der waals force? |
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Definition
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Term
| AMINO ACIDS: What is the character of a polar charged side chain? |
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Definition
| Hydrophilic side chains act as acids or bases which tend to be fully charged (+ or -) under physiologic conditions. Side chains form ionic bonds are often involved in chemical reactions. |
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Term
| AMINO ACIDS: What is the character of a polar uncharged side chain? |
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Definition
| Hydrophilic side chains tend to have partial + or - charge allowing them to participate in chemical reactions, form H-bonds, and associate with water. |
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Term
| AMINO ACIDS: What is the character of a nonpolar side chain? |
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Definition
| Hydrophobic side chains consist almost entirely of C and H atoms. Theses amino acids tend to form the inner core of soluble proteins, buried away from the aqueous medium. They play an important role in membranes by associating with the lipid bilayer. |
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Term
| What is the unique side chain property that Glycine (Gly or G) possesses? |
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Definition
| Side chain consists only of hydrogen atom and can fit into either a hydrophilic or hydrophobic environment. Glycine often resides at sites where two polypeptides come into close contact. |
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Term
| What is the unique property of the side chain Cysteine (Cys or C)? |
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Definition
| Though side chain has polar, uncharged character, it has the unique property of forming a covalent bond with another cysteine to form a disulfide link. |
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Term
| What is the unique side chain property of Proline (Pro or P)? |
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Definition
| Though side chain has hydrophobic character, it has the unique property of creating kinks in polypeptide chains and disrupting ordered secondary structure. |
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Term
| How does the strength of ionic bonds chains in the presence and absence of water? |
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Definition
| When negatively charged phosphate atoms in a DNA molecules are closely associated with positively charged groups on the surface of a protein, ionic bonds between them help hold the complex together. The strength of ionic bonds in a cell is generally weak (about 3kcal/mol) due to the presence of water, but deep within the core of a protein, where water is often excluded, such bonds are much stronger. |
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Term
| What are glycosidic bonds? |
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Definition
| Glycosidic bonds link monosaccharides to form oligo- and polysaccharides. |
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Term
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Definition
| An artificial lipid bilayer that self-assembles into a spherical vesicle or vesicles when in an aqueous environment. |
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Term
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Definition
| The reactions by which sugar groups (carbohydrates) are added to proteins and lipids. |
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Term
| What is freeze-fracture replication? |
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Definition
| Frozen, fracture occurs between bilayer leaflets, metals are then deposited on the exposed surfaces to create a shadowed replica that is analyzed by electron microscopy. |
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Term
| What is used to remove proteins from a membrane? |
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Definition
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Term
| What is a transmembrane domain? |
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Definition
| Transmembrane domains consist of a string of 20 nonpolar aa's that span the core of the lipid bilayer as an alpha-helix. |
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Term
| How is hydrophobicity measured? |
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Definition
| Hydrophobicity is measured by the free energy required to transfer each segment of the polypeptide from a nonpolar solvent to an aqueous medium. |
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Term
| What are factors that affect membrane fluidity? |
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Definition
The degree of unsaturation of fatty acids in the bilayer, temperature, cholesterol concentration, the length of the fatty acid chain affect membrane fluidity.
More unsaturation = takes lower temperatures to cause bilayer to gel
Warmer rather than colder = more fluid, phospholipid movement
Shorter chain = lower melting temperature
More cholesterol = increases membrane durability, disrupts the close-packing of fatty acid chains, but decreases membrane permeability. |
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Term
| What are lipid rafts? What is their importance? |
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Definition
Lipid rafts are very concentrated domains of sphingolipids and cholesterol. Important for:
a) membrane trafficking
b) cellular adhesion
c) targets for antibodies, bacteria, and various toxins to enter cells |
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Term
| What percentage of the cell is internalize per minute? |
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Definition
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Term
| How longs does it takes for the whole plasma membrane to replaced? |
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Definition
| The whole plasma membrane is replaced, via endocytosis, in an hour. |
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Term
| What are the steps in the secretory pathway? |
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Definition
| RER -> Golgi -> Secretory vesicles/granules -> Plasma membrane |
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Term
| What are the constituents of the cell theory? |
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Definition
1) All organisms are composed of one or more cells
2) The cell is the structural unit of life
3) Cells can arise only by division from a pre-existing cell |
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Term
| What is the basis of biological evolution? |
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Definition
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Term
| What is the size of a bacteria cell? |
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Definition
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Term
| What is the size of a eukaryotic cell? |
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Definition
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Term
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Definition
| Noncellular pathogens that can only reproduce when present within a living cell; obligatory intracellular parasites; outside of the cell, the virus exists only as a macromolecular package, or virion. Virions consist of viral nucleic acid enclosed in a wrapper containing viral proteins. |
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Term
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Definition
| Glucose to Fru 1, bis 6- bisP to pyruvate, |
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Term
| What are the first ATP invested in glycolysis used for? |
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Definition
| Kinase activity by Hexose kinase and Phosphofructokinase |
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Term
| What is the net yield per glucose from glycolysis? |
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Definition
| 2 ATP, 2 NADH, and 2 pyruvate |
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Term
| What factors inhibit glycolysis and gluconogenesis? |
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Definition
| High levels of ATP feedback glycolysis, likewise high levels of AMP inhibit gluconeogenesis. |
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Term
| What is the limiting factor in glycolysis? |
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Definition
NAD+ concentration; In the absence of O2, NAD+ is consumed and not replaced
When all NAD+ is reduced to NADH, glycolysis halts for lack of an e- acceptor (NAD+ is in short supply in cells), and ATP production ceases |
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Term
| In the absence of oxygen, pyruvate is reduced to lactate for what purpose? |
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Definition
| Because NAD+ is in short supply and can be regenerated by pyruvate reduction. |
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Term
| What percentage of energy is lost in the fermentation product of pyruvate in glycolysis? |
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Definition
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Term
| What is the fermentation product in yeasts? |
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Definition
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Term
| What is the purpose of the TCA Cycle? |
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Definition
| To generate high energy electron carriers for further oxidative phosphorylation via complete oxidation of pyruvate to generate high energy electron carriers and CO2 as a by-product |
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Term
| Is pyruvate transported to the mitochondria without oxygen? |
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Definition
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Term
| Where does fermentation occur? |
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Definition
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Term
| Where is the first fully oxidized carbon found? |
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Definition
| When pyruvate enters the mitochondria and is oxidized by pyruvate dehydrogenase to acetyl-coA |
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Term
| Overview of the TCA Cycle? |
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Definition
First step is condensation of acetyl group (2C) to oxaloacetate (4C) to form citric acid (6C)
Four reactions occur in the TCA cycle in which a pair of electrons are transferred from substrate to a co-enzyme: 3 reduce NAD+ to NADH, 1 reduces FAD to FADH2
Two carbons are removed during the TCA cycle in the form of CO2. |
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Term
| How many pairs of electrons are produced in TCA? |
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Definition
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Term
| What does the TCA cycle produce? |
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Definition
| The "Citric acid cycle" oxidizes acetyl groups to CO2 producing 3 NADH, 1 FADH2, 1 GTP, and 2 CO2 |
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Term
| Why do fats store more energy than sugars? |
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Definition
| The relative oxidation state of an organic molecule can be roughly determined by counting the number of hydrogen versus oxygen and nitrogen atoms per carbon atom; oxidation state is a measure of an organic molecule's free energy content. The degree of reduction of a compound is also a measure of its ability to perform chemical work within the cell. Since fats have more H atoms than sugars, via long hydrocarbon tails, they can be reduced to a greater degree and generate many more electron carriers and acetyl co-A for TCA |
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Term
| Where do all catabolic pathways converge? |
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Definition
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Term
| What is the purpose of oxidative phosphorylation? |
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Definition
| To harvest the energy in NADH and FADH2 to synthesize ATP |
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Term
| Where is oxidative phosphorylation localized to? |
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Definition
| The inner membrane of the mitochondria |
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Term
| What is the purpose of oxidative phosphorylation? |
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Definition
| To harvest the energy in NADH and FADH2 to synthesize ATP |
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Term
| What is the Electron Transport Chain? |
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Definition
The electron transport chain is a large collection of proteins in the inner membrane organized into massive multi-protein complexes
This electron “bucket brigade” incrementally harvests energy of e- transfer to generate ATP |
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Term
| Overview of the TCA Cycle |
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Definition
| 3 large drops in ∆G; coupled to H+ pumping |
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Term
| What mechanism powers ATP production in the ETC? |
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Definition
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Term
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Definition
| The F0F1 ATP synthase is a proton-powered turbine in the inner mitochondrial membrane |
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Term
| How does ATP Synthase work? |
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Definition
| Proteins flowing through transmembrane channel (formed by subunit a and c ring) power rotation of rotor and stalk...Rotation of y-subunit in stalk drives conformational change in alpha and beta catalytic heads driving ATP synthesis. |
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Term
| Since F0F1 ATP synthase is a 3-state turbine what are the 3 states? |
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Definition
| 1. Open, 2. Loose, 3. Tight, then open again with release of the ATP |
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Term
| How many protons are need to generate one ATP? |
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Definition
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Term
| Where do the light reactions occur? |
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Definition
| light reactions, e- transfer occur in the thylakoid membrane |
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Term
| Where do the dark reactions occur? |
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Definition
| The dark reactions, carbon fixation occurs in the stroma producing sugar |
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Term
| Where are MTs nucleated from? |
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Definition
| pericentriollar material (PCM) sites |
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Term
| What is the relationship between MTs and ER and Golgi? |
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Definition
| MTs provide a scaffold for organizing the ER and Golgi |
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Term
| Growth and shortening of MTs are regulated by hydrolysis of what molecule? |
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Definition
| Regulated by GTP hydrolysis; MTs are “dynamically unstable”: growth and shrinkage |
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Term
| What roles do different myosins play in cells? |
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Definition
Type I Myosin: Vesicle transport
Cytoplasmic streaming: vesicles, ER, and other organelles move along actin bundles in the subcortical cytoplasm (light activated)
“Conventional” Type II: movement,
Contraction, cell division |
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Term
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Definition
| Disruption of type II myosin disrupts cell division but not motility |
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Term
| Type I unconventional myosin |
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Definition
Type I and other unconventional myosins (green) are found in the leading edge;
Disruption of unconventional myosins stops motility |
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Term
| What is the function of an integrin? |
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Definition
Integrins also act as a “bridge” between internal keratin intermediate filaments and external ECM filaments
- |
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Term
| What do hemidesmosomes do? |
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Definition
| Hemidesmosomes link the cytoskeleton to the extracellular matrix via integrin transmembrane adhesion proteins |
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Term
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Definition
| Cadherins are transmembrane proteins. Their extracellular domains bind each other with high affinity (homophilic adhesion). Their intracellular domains bind linker proteins (e.g. a and b catenins) that bind the cytoskeleton. Thus, cadherin proteins “bridge” the cytoskeletons of cells providing a strong linkage either during development/movement (transient) or mature tissues (permanent). |
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Term
| What is the function of a desmosome? |
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Definition
| Desmosomes link keratin intermediate filaments in adjacent cells via Cadherin-family adhesion proteins |
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