BIO - TERMS - PROTEIN Flashcards
19S regulatory caps
Multisubunit component of the proteasome that functions to capture ubiquitinated proteins for degradation in the catalytic core.
20S catalytic core
Multisubunit component of proteasome responsible for protein degradation.
abatacept
An Fc fusion protein containing the CTLA-4 extracellular domain used in treating rheumatoid arthritis that blocks co-stimulation of T cells by binding B7 molecules.
adipose differentiation related protein
A protein that functions in the maintenance and storage of neutral lipid droplets in many types of cells.
Adrenodoxin
A mitochondrial iron-sulfur protein that participates in hydroxylation reactions of steroids.
Agrin
Signal protein released by an axonal growth cone during formation of the synapse between it and a muscle cell.
alefacept
Recombinant CD58–IgG1 fusion protein that blocks CD2 binding by CD58 used in treatment for psoriasis.
Allosteric effector
A ligand that affects the equilibrium between the alternative conformations of an allosteric protein.
Allosteric transition
A reversible interaction of a small molecule with a protein molecule that causes a change in the shape of the protein and a consequent alteration of the interaction of that protein with a third molecule.
allostery (adjective allosteric)
Change in a protein’s conformation brought about by the binding of a regulatory ligand (at a site other than the protein’s catalytic site), or by covalent modification. The change in conformation alters the activity of the protein and can form the basis of directed movement
amphitropic proteins
Proteins that associate reversibly with the membrane and thus can be found in the cytosol, in the membrane, or in both places.
Amyloid
Abnormally folded, insoluble proteins with β-pleated sheet structure.
amyloidoses
A variety of progressive conditions characterized by abnormal deposits of misfolded proteins in one or more organs or tissues.
angiotensin I
A liver protein produced from angiotensinogen through the actions of the kidney enzyme renin.
anti-apoptotic Bcl2 family proteins
Proteins (e.g., Bcl2, BclXL) on the cytosolic surface of the outer mitochondrial membrane that bind and inhibit pro-apoptotic Bcl2 family proteins and thereby help prevent inappropriate activation of the intrinsic pathway of apoptosis.
Antifreeze proteins
Proteins of animals, plants, fungi, and bacteria bind to ice crystals and inhibit their growth.They protect against freezing damages.
antiporter
Carrier protein that transports two different ions or small molecules across a membrane in opposite directions, either simultaneously or in sequence.
antiviral protein (AVP)
A protein made in response to interferon that blocks viral multiplication.
Apaf1
Adaptor protein of the intrinsic apoptotic pathway; on binding cytochrome c, oligomerizes to form an apoptosome.
ARF proteins
Monomeric GTPase in the Ras superfamily responsible for regulating both COPI coat assembly and clathrin coat assembly.
ARP (actin-related protein) complex (Arp 2/3 complex)
Complex of proteins that nucleates actin filament growth from the minus end.
ASC (PYCARD)
An adaptor protein containing pyrin and CARD domains involved in activating caspase 1 in the inflammasome.
ATP-binding cassette (ABC)
A large family of proteins containing a particular domain for nucleotide-binding that includes many transporters, such as TAP1 and TAP2, but also various NOD members.
Autocrine growth stimulation
Stimulation of cell growth by proteins produced and sensed by the same cell. (Chapter 6)
Avidin
A biotin-binding protein in egg white.
axoneme
Bundle of microtubules and associated proteins that forms the core of a cilium or a flagellum in eukaryotic cells and is responsible for their movements.
Backbone
The continuous chain of atoms running the length of a protein or other polymer.
Bak
A main effector Bcl2 family protein of the intrinsic pathway of apoptosis in mammalian cells that is bound to the mitochondrial outer membrane even in the absence of an apoptotic signal; activation is usually by activated pro-apoptotic BH3-only proteins.
Bax
A main effector Bcl2 family protein of the intrinsic pathway of apoptosis in mammalian cells; located mainly in the cytosol and translocates to the mitochondria only after activation, usually by activated pro-apoptotic BH3-only proteins.
Bcl-2 family
Family of intracellular proteins that includes members that promote apoptosis (Bax, Bak, and Bok) and members that inhibit apoptosis (Bcl-2, Bcl-W, and Bcl-XL).
Bcl2
Anti-apoptotic Bcl2 family protein of the outer mitochondrial membrane that binds and inhibits pro-apoptotic Bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis.
Bcl2 family
Family of intracellular proteins that either promote or inhibit apoptosis by regulating the release of cytochrome c and other mitochondrial proteins from the intermembrane space into the cytosol.
BclXL
Anti-apoptotic Bcl2 family protein of the outer mitochondrial membrane that binds and inhibits pro-apoptotic Bcl2 family proteins and prevents inappropriate activation of the intrinsic pathway of apoptosis.
BH3-only proteins
The largest subclass of Bcl2 family proteins. Produced or activated in response to an apoptotic stimulus and promote apoptosis mainly by inhibiting antiapoptotic Bcl2 family proteins.
binding site
The crevice or pocket on a protein in which a ligand binds.
BiP
Endoplasmic reticulum (ER)-resident chaperone protein member of the family of hsp70-type chaperone proteins.
BLNK
B-cell linker protein. See SLP-65.
C2
Complement protein of the classical and lectin pathways that is cleaved by the C1 complex to yield C2b and C2a. C2a is an active protease that forms part of the classical C3 convertase C4bC2a.
C4
Complement protein of the classical and lectin pathways. C4 is cleaved by C1s to C4b, which forms part of the classical C3 convertase.
C4b-binding protein (C4BP)
A complement-regulatory protein that inactivates the classical pathway C3 convertase formed on host cells by displacing C2a from the C4bC2a complex. C4BP binds C4b attached to host cells, but cannot bind C4b attached to pathogens.
C6, C7, C8, C9
Complement proteins that act with C5b to form the membrane-attack complex, producing a pore that leads to lysis of the target cell.
Ca2+ pump (calcium pump, Ca2+ ATPase)
Transport protein in the membrane of sarcoplasmic reticulum of muscle cells (and elsewhere). Pumps Ca2+ out of the cytoplasm into the sarcoplasmic reticulum using the energy of ATP hydrolysis.
Ca2+/calmodulin-dependent kinase (CaM-kinase)
Serine/ threonine protein kinase that is activated by Ca2+/calmodulin. Indirectly mediates the effects of an increase in cytosolic Ca2+ by phosphorylating specific target proteins.
calcium-calmodulin-dependent protein kinase (CaMK)
A protein kinase activated by elevations of internal Ca²⁺ concentration.
CaM-kinase II
Multifunctional Ca2+/calmodulin-dependent protein kinase that phosphorylates itself and various target proteins when activated. Found in most animal cells but is especially abundant at synapses in the brain, and is involved in some forms of synaptic plasticity in vertebrates.
capsomere
A protein subunit of a viral capsid.
casein
Milk protein.
CD59, protectin
Cell-surface protein that protects host cells from complement damage by blocking binding of C9 to the C5b678 complex, thus preventing MAC formation.
Cdc25
Protein phosphatase that dephosphorylates Cdks and increases their activity.
Cdk inhibitor protein (CKI)
Protein that binds to and inhibits cyclin–Cdk complexes, primarily involved in the control of G1 and S phases.
Cdk-activating kinase (CAK)
Protein kinase that phosphorylates Cdks in cyclin–Cdk complexes, activating the Cdk.
cell-cycle control system
Network of regulatory proteins that governs progression of a eukaryotic cell through the cell cycle.
Ceruloplasmin
A copper-containing plasma protein.
channel (membrane channel)
Transmembrane protein complex that allows inorganic ions or other small molecules to diffuse passively across the lipid bilayer
channel rhodopsin
Photosensitive protein forming a cation channel across the membrane that opens in response to light. charge separation In photosynthesis, the light-induced transfer of a high-energy electron from chlorophyll to an acceptor molecule resulting in the formation of a positive charge on the chlorophyll and a negative charge on a mobile electron carrier.
chaperonin
One of two major classes of chaperones found in virtually all organisms; a complex of proteins that functions in protein folding, either GroES/GroEL in bacteria or Hsp60 in eukaryotes.
Chediak–Higashi syndrome
A defect in phagocytic cell function caused by a defect in a protein involved in intracellular vesicle fusion. Lysosomes fail to fuse properly with phagosomes, and killing of ingested bacteria is impaired.
Cholesterol ester transfer protein
A protein that transfers cholesterol esters from high-density lipoprotein (HDL) to other lipoproteins.
Chromophore
Chemical compound that can absorb light at a certain wavelength and therefore appears colored in bright light. cofactor of a protein that is responsible for the absorption of light.
circular dichroism spectroscopy
A method used to characterize the degree of folding in a protein, based on differences in the absorption of right-handed versus left-handed circularly polarized light.
cisternal maturation model
One hypothesis for how the Golgi apparatus achieves and maintains its polarized structure and how molecules move from one cisterna to another. This model views the cisternae as dynamic structures that mature from early to late by acquiring and then losing specific Golgiresident proteins as they move through the Golgi stack with cargo.
classical cadherins
Family of cadherin proteins, including E-cadherin, N-cadherin, and P-cadherin, that are closely related in sequence throughout their extracellular and intracellular domains.
Cluster-of-differentiation markers
Distinct surface proteins that are recognized by specifi c monoclonal antibodies; these antibodies bind to various cluster-of-diff erentiation markers and are used to distinguish diff erent cell types (e.g., CD4 on helper T cells). Also called CD markers. (Chapter 4)
co-translational
Occurring as translation proceeds. Examples include the import of a protein into the endoplasmic reticulum before the polypeptide chain is completely synthesized, and the folding of a nascent protein into its secondary and tertiary structure as it emerges from a ribosome.
co-transport
A transport mechanism in cells in which two compounds or substances are simultaneously transported across a membrane by the same carrier protein. Co-transport may or may not require ATP.
coated vesicle
Small membrane-enclosed organelle with a cage of proteins (the coat) on its cytosolic surface. Formed by the pinching off of a coated region of membrane (coated pit). Some coats are made of clathrin, others are made from other proteins.
cochlear amplifier
Outer hair cells, including the motor proteins in the outer hair cell membrane, that amplify displacements of the basilar membrane in the cochlea.
cohesin, cohesin complex
Complex of proteins that holds sister chromatids together along their length before their separation.
collagen fibers
Strong, flexible protein located within many connective tissues.
colloid
(kol′oyd) Opaque mixture composed of water and solute (usually protein); substance within thyroid follicles.
complement activation
The activation of the normally inactive proteins of the complement system that occurs on infection. See classical pathway, alternative pathway, lectin pathway.
complement regulatory proteins
Proteins that control complement activity and prevent complement from being activated on the surfaces of host cells.
condensin, condensin complex
Complex of proteins involved in chromosome condensation prior to mitosis. Target for M-Cdk.
conjugated protein
A protein containing one or more prosthetic groups.
connexon
Water-filled pore in the plasma membrane formed by a ring of six connexin protein subunits. Half of a gap junction: connexons from two adjoining cells join to form a continuous channel through which ions and small molecules can pass.
Constitutive proteins
Proteins that are synthesized at all times.
constitutive secretory pathway
Pathway present in all cells by which molecules such as plasma membrane proteins are continually delivered to the plasma membrane from the Golgi apparatus in vesicles that fuse with the plasma membrane. The default route to the plasma membrane if no other sorting signals are present.
corepressor
A molecule that binds to a repressor protein, enabling the repressor to bind to an operator.
CTR1
Copper transport protein 1; a membrane bound copper-binding protein that imports copper into cells.
cyclin–Cdk complex
Protein complex formed periodically during the eukaryotic cell cycle as the level of a particular cyclin increases. A cyclin-dependent kinase (Cdk) then becomes partially activated.
cyclophilins
A family of prolylisomerases that affect protein folding, that also bind cyclosporin A to produce a complex that associates with calcineurin, preventing its activation by calmodulin.
De novo sequencing
Determination of a new protein sequence not previously described in data bases.
death effector domain (DED)
Protein-interaction domain originally discovered in proteins involved in programmed cell death or apoptosis. As part of the intracellular domains of some adaptor proteins, death domains are involved in transmitting pro-inflammatory and/or pro-apoptotic signals.
Denatured
The physical changes that occur in a protein when secondary and tertiary structures are disrupted.
denatured protein
A protein that has lost enough of its native conformation by exposure to a destabilizing agent such as heat or detergent that its function is lost.
dephosphorylation
The removal of a phosphate group from a molecule, usually a protein.
divalent metal transporter 1 (DMT1)
A protein on the small-intestinal absorptive surface that is responsible for the absorption of iron and copper in their inorganic forms.
Duchenne muscular dystrophy
A severe inherited muscle disease caused by defects of the structural protein dystrophin.
dynamic instability
Sudden conversion from growth to shrinkage, and vice versa, in a protein filament such as a microtubule or actin filament.
E3 ubiquitin ligase
Proteins or protein complexes that specifically link ubiquitin polypeptides to lysine residues of target proteins.
Ectomycorrhizins
Symbiosis related proteins unique to ectomycorrhizae.
effector Bcl2 family proteins
Pro-apoptotic proteins of the intrinsic pathway of apoptosis that in response to an apoptotic stimulus become activated and aggregate to form oligomers in the mitochondrial outer membrane, inducing the release of cytochrome c and other intermembrane proteins. Bax and Bak are the main effector Bcl2 family proteins in mammalian cells.
Electrospray ionization (ESI)
Ion source technique in mass spectrometers for ionization of biomacromolecules (e.g., petides and proteins) present in a liquid phase.
endosome maturation
Process by which early endosomes mature to late endosomes and endolysosomes; in the conversion process, the endosome membrane protein composition changes, the endosome moves from the cell periphery to close to the nucleus, and the endosome ceases to recycle material to the plasma membrane and irreversibly commits its remaining contents to degradation.
Epidermolysis bullosa
A group of inherited skin-blistering diseases caused by abnormalities of proteins in the dermal-epidermal junction.
ER resident protein
Protein that remains in the endoplasmic reticulum (ER) or its membranes and carries out its function there, as opposed to proteins that are present in the ER only in transit.
ESCRT protein complexes
Four protein complexes (ESCRT-0, ESCRT-1, ESCRT-2, and ESCRT-3) that act sequentially to shepherd mono-ubiquitylated membrane proteins on endosomal membranes into intralumenal vesicles. ESCRT-3 complex catalyzes the pinching-off reaction.
Extracellular signal-regulated kinases (ERKs)
Serine/ threonine kinases of the mitogen-activated protein (MAP) kinase family.
ferroportin
A membrane protein that transports iron from inside a cell to the outside.
Fibrillin
Protein in microfibrils that is defective in Marfan syndrome.
flagellin
A protein that is the major constituent of the flagellum, the tail-like structure used in bacterial locomotion. TLR-5 recognizes intact flagellin protein that has dissociated from the flagellum.
flippases
Membrane proteins in the ABC transporter family that catalyze the movement of phospholipids from the extracellular leaflet to the cytosolic leaflet of a membrane bilayer.
floppases
Membrane proteins in the ABC transporter family that catalyze movement of phospholipids from the cytosolic leaflet to the extracellular leaflet of a membrane bilayer.
fluorescence recovery after photobleaching (FRAP)
Technique for monitoring the kinetic parameters of a protein by analyzing how fluorescent protein molecules move into an area of the cell bleached by a beam of laser light.
Fluorescent proteins
Have intrinsic fluorescence properties by containing covalently bonded chromophores build-up by a tripeptide (Ser–Tyr–Gly); the first one (green fluorescent protein GFP) has been isolated from the jellyfish Aequorea victoria and exhibits bright green fluorescence when exposed to blue to ultraviolet light; nowadays a great variety of engineered GFP derivatives and fluorescent proteins of different families exist.
formin
Dimeric protein that nucleates the growth of straight, unbranched actin filaments that can be cross-linked by other proteins to form parallel bundles.
fractionation
The process of separating the proteins or other components of a complex molecular mixture into fractions based on differences in properties such as solubility, net charge, molecular weight, or function.
FRAP (fluorescence recovery after photobleaching)
A technique used to quantify the diffusion of membrane components (lipids or proteins) in the plane of the bilayer.
gated transport
Movement of proteins between the cytosol and the nucleus through nuclear pore complexes in the nuclear envelope that function as selective gates.
geminin
Protein that prevents the formation of new prereplicative complexes during S phase and mitosis, thus ensuring that the chromosomes are replicated only once in each cell cycle.
gluten-sensitive enteropathy
Sometimes referred to as celiac disease. Inflammation of the small intestine due to an autoimmune inflammatory disease precipitated by the ingestion of the wheat protein, gluten.
Gq
Class of G protein that couples GPCRs to phospholipase C-β to activate the inositol phospholipid signaling pathway.
GTP (guanosine 5′-triphosphate)
Nucleoside triphosphate produced by the phosphorylation of GDP (guanosine diphosphate). Like ATP, it releases a large amount of free energy on hydrolysis of its terminal phosphate group. Has a special role in microtubule assembly, protein synthesis, and cell signaling.
Heat shock proteins
Chaperones that are induced by heat exposure.
Heinz bodies
Abnormal protein aggregates in erythrocytes.
Helper virus
A virus that provides viral proteins needed for the reproduction of a coinfecting defective virus or subviral agents. (Chapter 12) .
heme carrier protein (hcp1)
A protein in the small intestine mucosal cells that transports a heme molecule from the gut lumen into an enterocyte.
heme protein
A protein containing a heme as a prosthetic group.
Hemopexin
A heme-binding protein in serum.
hephaestin
A copper-containing protein that transports iron from the mucosal cells of the small intestine to the
High-density lipoprotein
A protein-rich lipoprotein that transports cholesterol to the liver.
Hill coefficient
A measure of cooperative interaction between protein subunits.
HLA-DO
An invariant MHC class II molecule that binds HLA-DM, inhibiting the release of CLIP from MHC class II molecules in intracellular vesicles. A homologous protein in mice is called H-2O or H2-DO.
homeodomain
The protein domain encoded by the homeobox; a regulatory unit that determines the segmentation of a body plan.
homologous proteins
Proteins having similar sequences and functions in different species; for example, the hemoglobins.
IFIT (IFN-induced protein with tetratricoid repeats)
A small family of host proteins induced by interferons that regulate protein translation during infection in part by interactions with eIF3.
IFITM (interferon-induced transmembrane protein)
A small family of host transmembrane proteins induced by interferons that function in the cell’s vesicular compartment to restrain various steps in viral replication.
IKK
The IkB kinase, IKK, is a multisubunit protein complex composed of IKKα, IKKβ, and IKKγ (or NEMO).
Inducible proteins
Proteins whose synthesis is regulated.
inhibitors of apoptosis (IAPs)
Intracellular protein inhibitors of apoptosis.
inner nuclear membrane
One of two concentric membranes comprising the nuclear envelope; continuous with the outer nuclear membrane; contains specific proteins as anchoring sites for chromatin and the nuclear lamina.
integral proteins
Proteins firmly bound to a membrane by hydrophobic interactions; as distinct from peripheral proteins.
Intermediate filament
A type of cytoskeletal fiber formed from proteins in a coiled coil conformation.
intrinsically disordered proteins
Proteins, or segments of proteins, that lack a definable three-dimensional structure in solution.
