Exam terms Flashcards
To pass Biol 330
translocase
a general term for a protein that assists in moving another molecule, usually across a membrane.
vesicle
A bubble-like membranous structure that stores and transports cellular products, and digests metabolic wastes within the cell; an intracellular membranous sac that is separated from the cytosol by at least one lipid bilayer.
Most vesicles are coated with proteins such as clathrin and COP
signal sequence
A (usually N-terminal) sequence of a protein that directs its processing or localization within the cell.
(=targeting sequences) on the protein direct them to correct place
signal peptidase
enzymes that convert secretory and some membrane proteins to their mature forms by cleaving their signal peptides from their N-terminals.
The signal sequences are often (not always) cleaved by signal peptidases
post-translational import
Proteins are fully translated then sent to the correct location
co-translational import
Proteins are simultaneously translated and imported.
nuclear pore
Nuclear pores are large protein complexes that cross the nuclear envelope
nuclear export signal
a short amino acid sequence of 4 hydrophobic residues in a protein that targets it for export from the cell nucleus to the cytoplasm through the nuclear pore complex using nuclear transport.
nuclear import signal
Proteins that need to be transported through nuclear pores have nuclear localization signals (NLS)
TIM
The TIM/TOM complex is a process in cellular biochemistry which describes the translocation of proteins produced from nuclear DNA through the mitochondrial membrane for use in oxidative phosphorylation.
Following transport through the cytosol from the nucleus, the signal sequence is recognized by a receptor protein in the transporter outer membrane (TOM) complex. The signal sequence and adjacent portions of the polypeptide chain are inserted in the TOM complex, then begin interaction with a transporter inner membrane (TIM) complex, which are hypothesized to be transiently linked at sites of close contact between the two membranes. The signal sequence is then translocated into the matrix in a process that requires an electrochemical hydrogen ion gradient across the inner membrane. Mitochondrial Hsp70 binds to regions of the polypeptide chain and maintains it in an unfolded state as it moves into the matrix
TOM
Transport across Outer Membrane) complexes include receptors and translocation channels
Outer and inner mitochondrial membranes join at contact sites, where TOM complex interacts with TIM complex
signal recognition particle
an abundant, cytosolic, universally conserved ribonucleoprotein that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes
BiP
Binding immunoglobulin protein:
Hsp70 member
a molecular chaperone located in the lumen of the endoplasmic reticulum (ER) that binds newly synthesized proteins as they are translocated into the ER, and maintains them in a state competent for subsequent folding and oligomerization.
BiP lives in the ER lumen and helps pull proteins through the channel, and prevents premature folding
stop-transfer signal
Hydrophobic amino acid sequence that halts translocation of a polypeptide chain through the endoplasmic reticulum membrane, thus anchoring the protein chain in the membrane
typically a stretch of amino acids that give rise to a hydrophobic a-helix
These sequences can cause the protein to be oriented N-terminal in or out
ER
endoplasmic reticulum , network of membranous tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane. It usually has ribosomes attached and is involved in protein and lipid synthesis.
The ER is the site of co-translational import, the gateway for entry proteins destined for many other compartments, and secretion
golgi
Part of the cellular endomembrane system, the Golgi apparatus packages proteins inside the cell before they are sent to their destination; it is particularly important in the processing of proteins for secretion
clathrin
Clathrin is a protein that plays a major role in the formation of coated vesicles
COP-I
COPI is a protein complex that coats vesicles transporting proteins from the cis end of the Golgi complex back to the rough endoplasmic reticulum (ER), where they were originally synthesized and between golgi compartments. This type of transport is termed as retrograde transport
As soon as the network is formed, COP-I vesicles form to return ER proteins to the ER
COP-II
a type of vesicle coat protein that transports proteins from the rough endoplasmic reticulum to the Golgi apparatus. This process is termed anterograde transport,
One type of protein (COP II) binds to the ER membrane and extracts a layer of membrane to form a vesicle
glycosylation
The process of adding sugar units such as in the addition of glycan chains to proteins. An occurrence where a carbohydrate is added to a protein molecule, which can occur in the golgi apparatus.
KDEL
KDEL: receptor protein, characteristic signal sequences
microtubule
a component of the cytoskeleton, found throughout the cytoplasm. They are tubular polymers of tubulin.
SNAREs
SNARE (an acronym derived from “SNAP (Soluble NSF Attachment Protein) REceptor”) proteins.
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).
SNAREs can be divided into two categories: vesicle or v-SNAREs, which are incorporated into the membranes of transport vesicles during budding, and target or t-SNAREs, which are located in the membranes of target compartments.
help vesicles dock and fuse to membranes
dynamin
Dynamin is a GTPase responsible for endocytosis in the eukaryotic cell. Dynamins are principally involved in the scission of newly formed vesicles from the membrane of one cellular compartment and their targeting to, and fusion with, another compartment,
Mannose-6-phosphate
Mannose-6-phosphate is a molecule bound by lectin in the immune system. M6P is converted to fructose 6-phosphate by mannose phosphate isomerase. M6P is a key targeting signal for acid hydrolase precursor proteins that are destined for transport to lysosomes
M6P receptor
proteins that bind newly synthesized lysosomal hydrolases in the trans-Golgi network (TGN) and deliver them to pre-lysosomal compartments.
A M-6-P receptor in the Golgi binds the protein and undergoes a conformational change, leading to formation of a clathrin-coated pit
endocytosis
the taking in of matter by a living cell by invagination of its membrane to form a vacuole.
pinocytosis
the ingestion of liquid into a cell by the budding of small vesicles from the cell membrane.
phagocytosis
the ingestion of bacteria or other material by phagocytes and ameboid protozoans
endosome
membrane-bounded compartment inside eukaryotic cells.
a vesicle formed by the invagination and pinching off of the cell membrane during endocytosis
autophagy
he basic catabolic mechanism that involves cell degradation of unnecessary or dysfunctional cellular components through the actions of lysosomes.
Actin
Actin is a globular multi-functional protein that forms microfilaments. It is found in all eukaryotic cells
Most organisms have multiple isoforms of actin
- most cells have b, g - muscles have a
Microfilaments
Microfilaments or actin filaments are the thinnest filaments of the cytoskeleton, a structure found in the cytoplasm of eukaryotic cells.
Thin filament
a myofilament of the one of the two types making up myofibrils that is about 5 nanometers (50 angstroms) in width and is composed chiefly of the protein actin
tubulin
a protein that is the main constituent of the microtubules of living cells.
Tubulin monomers join end to end to form protofilaments
microtubule
a microscopic tubular structure present in numbers in the cytoplasm of cells, sometimes aggregating to form more complex structures.
Protofilaments join side by side to form microtubules
intermediate filament
Any of a class of usually insoluble cellular protein fibers (as a neurofilament or an epithelial-cell cytoplasmic filament of keratin) composed of various fibrous polypeptides that serve especially to provide structural stability and strength to the cytoskeleton and are intermediate in diameter between microfilaments and microtubules
Each subunit is a tetramer
microtubule-associated protein
any of the high molecular weight proteins that bind to microtubules, enhancing polymerization.
flagella
slender threadlike structure, esp. a microscopic whiplike appendage that enables many protozoa, bacteria, spermatozoa, etc., to swim
cilia
a short, microscopic, hairlike vibrating structure. Cilia occur in large numbers on the surface of certain cells, either causing currents in the surrounding fluid, or, in some protozoans and other small organisms, providing propulsion.
pseudopodia
a temporary protrusion of the surface of an ameboid cell for movement and feeding.
lamellapodia
a flattened extension of a cell, by which it moves over or adheres to a surface
fillipodia
a long, slender, tapering pseudopodium, as found in some protozoans and in embryonic cells.
MTOC
The abbreviation for microtubule organizing center, a region inside the cell where microtubules are organized into tubular structures.
accessory proteins
MTs anchored by g-tubulin and accessory proteins that form ring structures
motor proteins
Motor proteins are a class of molecular motors that are able to move along the surface of a suitable substrate. They are powered by the hydrolysis of ATP and convert chemical energy into mechanical work
myosin
a fibrous protein that forms (together with actin) the contractile filaments of muscle cells and is also involved in motion in other types of cells.
Myosin moves along actin (toward + end)
Length of the neck influences “step size” (=unitary displacement)
Longer neck allows longer steps in each catalytic cycle
dynein
Dynein is a motor protein in cells which converts the chemical energy contained in ATP into the mechanical energy of movement.
Movement along microtubules uses kinesin (mostly toward +) and dynein (mostly -ve)
kinesin
A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule filaments, and are powered by the hydrolysis of ATP
Movement along microtubules uses kinesin (mostly toward +) and dynein (mostly -ve)
capping
If the plus end of the polymer has a series of monomers with NTPs, this is referred to as a “cap”
A capped polymer is more likely to grow
A capped microtubule is stable
GTP hydrolysis accelerates disassembly
Both microfilaments and microtubules have proteins that can bind the ends to alter the ability to assemble or disassemble
Actin: tropomodulin, CapZ
Microtubules: g-tubulin
cross-linkers
A cross-link is a bond that links one polymer chain to another. They can be covalent bonds or ionic bonds.
Assembly of MT and MF into 3 dimensional networks requires proteins that interconnect strands
MAPs
microtubule associated proteins
bind to the sides of microtubules to stabilize or destabilize (example: tau protein)
focal contacts
The points of contact between a moving amoeboid cell and the surface over which it moves
focal contacts which connect the cell to a surface
Cadherins
Cadherins are a class of type-1 transmembrane proteins. They play important roles in cell adhesion, forming adherens junctions to bind cells within tissues together. They are dependent on calcium ions to function
cadherins, which connect cells to other cells
Cell to cell connections are mediated by cadherins.
These receptors extend out from the cell, binding to other cadherens
cytoskeleton
a network of microtubules (MT), microfilaments (MF), intermediate filaments (IF), and their accessory proteins used in conjunction with motor proteins.
Its capacity to undergo assembly and disassembly is central to its many structural and functional roles.
Roles of the cytoskeleton
Cell structure Cell shape (microvilli) Internal organization (membrane networks) Physical robustness (erythrocyte deformability)
Cell function Cell movement (lamellapodia, flagella, cilia) Organismal movement (muscles) Intracellular traffic (vesicle and organelle traffic) Signal transduction
Nucleation
2 monomers can join together to begin the formation of a polymer (nucleation)
This first step is the slowest step in polymer formation
What are the molecular motors?
Enzymes that use the hydrolysis of ATP to provide the energy to move along cytoskeletal “tracks”
Each specific type of motor protein moves:
- on a specific type of track
- in a characteristic direction (toward + or - end)
Duty cycle:
Proportion of time in a contractile cycle where myosin is attached to actin microfilament
Integrins
Integrins are transmembrane receptors that mediate the attachment between a cell and its surroundings, such as other cells or the extracellular matrix. In signal transduction, integrins pass information about the chemical composition and mechanical status of the ECM into the cell
tight junction
a specialized connection of two adjacent animal cell membranes such that the space usually lying between them is absent.
Each cell possesses integral membrane proteins that bind to similar proteins in the adjacent, forming a continuous “weld”
desmosome
a structure by which two adjacent cells are attached, formed from protein plaques in the cell membranes linked by filaments.
adhesion belt
Beltlike adherens junction that encircles the apical end of an epithelial cell and attaches it to the adjoining cell.
hemidesmosome
Hemidesmosomes are very small stud- or rivet-like structures on the inner basal surface of keratinocytes in the epidermis of skin. They are similar in form to desmosomes
gap junction
A gap junction or nexus is a specialized intercellular connection between a multitude of animal cell-types. It directly connects the cytoplasm of two cells, which allows various molecules and ions to pass freely between cells.
Gap junctions allow cells to exchange electrical and/or chemical signals
Composed of proteins that form channels that allow small molecules to pass.
Subunits of these channels are connexins that are assembled together to make connexons. The connexons from 2 cells join together to make a gap junction.
connexin/connexan
Connexins, or gap junction proteins, are a family of structurally related transmembrane proteins that assemble to form vertebrate gap junctions. Each gap junction is composed of two hemichannels, or connexons, which are themselves each constructed out of six connexin molecules.
Basal lamina
The basal lamina is a layer of extracellular matrix secreted by the epithelial cells, on which the epithelium sits.
connective tissue
tissue that connects, supports, binds, or separates other tissues or organs, typically having relatively few cells embedded in an amorphous matrix, often with collagen or other fibers, and including cartilaginous, fatty, and elastic tissues.
fibroblast
a cell in connective tissue that produces collagen and other fibers.
proteoglycan
compound consisting of a protein bonded to glycosaminoglycan groups, present esp. in connective tissue.
Proteoglycans (made of both proteins and GAGs) also differ in physical properties
Synthesized in Golgi prior to secretion
In addition to structural roles, proteoglycans can also bind hormones (e.g., inflammatory chemokines, FGF, TGFb) to alter cell signaling pathways
Examples include:
-decoran, aggrecan (the main component of cartilage)
GAG (glycosaminoglycan)
ong unbranched polysaccharides consisting of a repeating disaccharide unit. Glycosaminoglycans are highly polar and attract water. They are therefore useful to the body as a lubricant or as a shock absorber.
Composed of repeating sugar + amino sugar units (e.g. N-acetylglucosamine, N-acetylgalactosamine)
They occur in long strings, often attached to proteins
Examples include:
-hyaluronan, chondroitin sulfate, heparan sulfate, keratan sulfate
GAGs attract a great deal of water. Hydroxyl groups form hydrogen bonds, and the many negative charges attract clouds of cations (Na+) that induce an osmotic movement of water. These hydrated gels resist compression (useful for joints).
hyaluronin
Hyaluronan is an anionic, nonsulfated glycosaminoglycan distributed widely throughout connective, epithelial, and neural tissues.
Attracts water and fills spaces between cells with non-compressible gel (found around joints)
Some cells secrete it to isolate themselves from other cells (e.g. myoblasts). These cells can secrete hyaluronidase to break it down, allowing contact
aggrecan
the main component of cartilage
One of the largest macromolecules, consisting of a core protein with GAGs attached to form a feather-like appearance.
An aggrecan core protein is very large but also binds many (different) GAGs
Each aggrecan can be attached to a hyaluronan backbone to form an aggrecan aggregate
collagen
the main structural protein found in animal connective tissue, yielding gelatin when boiled.
Prior to secretion they self- assemble into trimers
Upon secretion the trimers are processed by proteolytic enzymes then assemble into fibrils
Collagen proteins (trimers) are then cross-linked to form collagen fibers (stiff, not very elastic)
fibronectin
Fibronectin is a high-molecular weight glycoprotein of the extracellular matrix that binds to membrane-spanning receptor proteins called integrins. Similar to integrins, fibronectin binds extracellular matrix components such as collagen, fibrin, and heparan sulfate proteoglycans.
Different exons are able to bind different proteins/GAGs (e.g. integrins, collagen, etc)
Fibronectin dimerizes using 2 similar (not identical) monomers
Occluding junctions
seal cells together into sheets (forming an impermeable barrier) Tight junctions of intestinal epithelium
Anchoring junctions
attach cells (and their cytoskeleton) to other cells or extracellular matrix (providing mechanical support)
Integral membrane proteins connect a cell’s cytoskeleton to another cell or extracellular matrix
Communicating junctions
allow exchange of chemical/electrical information between cells
enzyme-linked receptor
An enzyme-linked receptor, also known as a catalytic receptor, is a transmembrane receptor, where the binding of an extracellular ligand causes enzymatic activity on the intracellular side.
may possess intrinsic enzyme activity or, once ligands bind, activate enzyme activity
5 main classes distinguished by:
type of effector (e.g. kinase vs. phosphatase)
target (serine/threonine, tyrosine, histidine)
type of linkage between receptor and enzyme
- Receptor tyrosine kinase (-RTK)
- Tyrosine kinase linked receptor
- Receptor serine/threonine kinase
- Receptor guanylyl cyclase
- Histidine-kinase associated receptors
G-protein linked receptor
A receptor linked to activation of a G-Protein (see G-protein = G proteins, also known as guanosine nucleotide-binding proteins, are a family of proteins involved in transmitting signals from a variety of different stimuli outside a cell into the inside of the cell. G proteins function as molecular switches.)
are trimeric GTP-binding protein (G-protein) that regulate the activity of other proteins
nuclear hormone receptors
In the field of molecular biology, nuclear receptors are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules
steroid hormone receptor and thyroid hormone receptor
NHRs are transcription factors that respond to specific ligands
Ligands alter the ability to bind to specific DNA regulatory elements
G-protein, adaptor protein
Trimeric protein (a, b, g) attached to the cell membrane by lipid anchors
Once the ligand binds, the activated receptor recruits a G-protein
Nucleotide exchange occurs (GTP replaces GDP) and the trimer dissociates into 2 parts:
- a subunit - bg subunit
Both parts can regulate downstream pathways
Upon dissociation, a Gs protein stimulates an effector enzyme, such as adenylate cyclase
Adenylate cyclase converts ATP to cAMP
Elevated cAMP stimulates cAMP-dependent protein kinase (PKA) by inducing the release of inhibitory subunits
scaffolding protein
A type of large relay protein to which several other relay proteins are simultaneously attached to increase the efficiency of signal transduction.
SH2 domain
The SH2 domain is a structurally conserved protein domain contained within the Src oncoprotein and in many other intracellular signal-transducing proteins. SH2 domains allow proteins containing those domains to dock to phosphorylated tyrosine residues on other proteins.
MAPK
Mitogen-activated protein kinases also known as MAP kinases are serine/threonine-specific protein kinases belonging to the CMGC kinase group.
Ras
Once an adaptor protein (e.g., Grb2) binds to the RTK, it attracts another protein - Ras GEF (guanine nucleotide exchange factor)
Ras GEF induces Ras to exchange its GDP for GTP (activating Ras).
Active Ras then activates MAPKKK, which phosphorylates and activates MAPKK, which phosphorylates and activates MAPK, which phosphorylates many proteins, including transcription factors.
protein kinase
A protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to them. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins.
protein phosphatase
A phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group.
phospholipase
an enzyme that hydrolyzes lecithin or a similar phospholipid.
PLC generates DAG and phosphoinositides, such as IP3 (inositol 1, 4, 5- triphosphate)
phosphodiesterase
an enzyme that breaks a phosphodiester bond in an oligonucleotide
cAMP
abbreviation for cyclic adenosine monophosphate, a second messenger essential in many biological processes of various organisms.
crosstalk
unwanted transfer of signals between communication channels.
Secretory signals
Autocrine-signals affect same cell or cell type
Paracrine-signals affect neighbouring cell
Endocrine-signals affect distant cells
