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BIOL330 Cell Biology
Study aids for BIOL330 at Queen's University
116
Biology
Undergraduate 4
12/17/2009

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Term
What is unique about the endoplasmic reticulum with respect to the importation of proteins?
Definition
The endoplasmic reticulum imports proteins as they are being synthezized -- contranslational import.
Term
What are the three main ways that proteins can travel from one cellular compartment to another?
Definition
1. Gated transport through nuclear pore complex.
2. Transmembrane transport through membrane-bound protein translocators.
3. Vesicle transport.
Term
What are the two types of sorting sequences in proteins and how do they work?
Definition
1. Signal sequence -- stretch of amino acids cleaved by signal peptidase after transduction.
2. Signal patch -- 3D folding of the protein.
Term
How are membrane bound organelles replicated in cellular division?
Definition
The membrane bound organelles must be grown and divided in order for cell division to occur -- the cell cannot produce a new membrane bound organelle without existing epigenetic information.
Term
Describe the structure of the nuclear membrane(s).
Definition
The nucleus is wrapped in two membranes. The inner membrane contains specific proteins that act as binding sites for chromatin, as well as the nuclear lamina. The outer membrane is studded with ribosomes that are involved in protein synthesis.
Term
What is a nuclear pore complex?
Definition
A nuclear pore complex is a protein channel composed of nucleoporin that allows the importation of water-soluble molecules.
Term
How is a protein localized in the nucleus?
Definition
Specific signalling sequences known as nucleus localization signals (NLS) form loops and patches on the surface of the protein. When the NPC detects the NLS, it expands using a diaphragm-like structure to accomodate the size of the molecule.
Term
What does the ability of the NPC to expand mean for protein importation?
Definition
Proteins are able to be imported fully formed, unlike in other membrane-bound organelles where they are imported in an unfolded state.
Term
What are nuclear import receptors?
Definition
Nuclear import receptors are proteins that bind to the nuclear localization signal, guiding the protein to the NPC (and importing it by walking down F-G repeats on the NPC).
Term
Where is the energy required for importing proteins into the nucleus against the concentration gradient derived from?
Definition
This energy comes from the hydrolysis of GTP via Ran GTPase.
Term
What are shuttling proteins?
Definition
Shuttling proteins have a nuclear export receptor and a nuclear localization signal, either of which can be activated or deactivated by phosphorylation so it can shunted between the nucleus and the cytosol.
Term
What is characteristic of the signal sequence of mitochondrial precursor proteins?
Definition
They induce the protein to form an alpha helix at one of their ends.
Term
What complexes are used to import proteins into the mitochondria?
Definition
The TOM complex (outer membrane) and the TIM23 and 22 complexes (inner membrane) are used. TOM transports the signal into the intermembrane space, and the TIM23 complex then translocates this into the inner mitochondria. The TIM22 complex is responsible for embedding proteins in the inner membrane.
Term
How are mitochondrial precursor proteins kept from folding up after they are synthesized but before they reach the mitochondria?
Definition
Chaperone proteins known as hsp70s prevent the MPPs from folding after synthesis.
Term
Where does the energy for mitochondrial import come from? How does this contrast with nuclear import?
Definition
Mitochondrial import requires ATP hydrolysis and establishment of an electrochemical gradient. Nuclear import requires GTP hydrolysis via Ran GTPase.
Term
How are proteins that are first translocated into the matrix eventually embedded in the inner membrane?
Definition
These proteins have a hydrophobic sequence directly after their n-terminal signalling sequence, so when the n-terminus is cleaved by signal peptidase, this hydrophobic region is exposed and the OXA complex transports it to the inner mitochondrial membrane.
Term
How are proteins destined for the inner membrane that do NOT translocate into the matrix make it to to embedation?
Definition
In this case, TIM23 complex recognizes the hydrophobic region after the signal and binds to it, causing it to act as a stop-transfer sequence. The signal peptide is then cleaved and the TOM complex imports the rest of the protein into the intermembrane space.
Term
How do the chloroplast and mitochondria differ with respect to energy requirements for transporting proteins across the membrane?
Definition
Mitochondria harness the energy from the H+ chemical gradient and ATP hydrolysis, chloroplasts just use nucleoside hydrolysis.
Term
How are proteins destined for the thylakoid membrane embedded in it?
Definition
First they pass through the inner and outer chloroplast membranes, then through the thylakoid membrane into the stroma. Following this, signal peptidase cleaves the N-terminal signalling sequence, exposing a hydrophobic region known as the thylakoid signalling sequence, causing it to be transported to the thylakoid membrane.
Term
What is the function of the endoplasmic reticulum?
Definition
The ER plays a large role in lipid and protein biosynthesis. It is the synthesis organelle for the transmembrane proteins of the entire cell.
Term
What are the two types of proteins taken up by the endoplasmic reticulum and what are their eventual destinations?
Definition
1. Water-soluble proteins, destined for the lumens of organelles.
2. Transmembrane proteins, which become embedded in the membranes of organelles.
Term
What are the two types of proteins taken up by the endoplasmic reticulum and what are their eventual destinations?
Definition
1. Water-soluble proteins, destined for the lumens of organelles.
2. Transmembrane proteins, which become embedded in the membranes of organelles.
Term
In what tissues are endoplasmic reticulum the largest?
Definition
The ER is most active in tissues involved in lipid synthesis or toxin degradation, such as liver hepatocytes.
Term
What is another function of the endoplasmic reticulum?
Definition
It acts as a store of Ca2+ ions. Ca2+ binding proteins located in the endoplasmic reticulum aid in reuptake (important in muscle contraction and relaxation).
Term
What are signal recognition particles?
Definition
Signal recognition particles (SRPs) are able to detect signalling sequences directing proteins to the endoplasmic reticulum. They bind to the protein as soon as the signal sequence is synthesized, then the ribosome synthesizing the protein binds to the endoplasmic reticulum and synthesis continues.

The SRP-ribosome complex then binds to an SRP-receptor on the membrane of the rough ER, which then binds to a protein translocator, causing the SRP and SRP-receptor to be released and allowing the growing membrane to be transported across the membrane.
Term
How is the protein channel on the endoplasmic reticulum opened?
Definition
The signalling sequence of the protein itself is thought to serve as an opening signal.
Term
What is the second function of the ER signalling sequence?
Definition
It directs the protein to the endoplasmic reticulum and opens the protein translocator start gate.
Term
What are the three ways single-pass transmembrane proteins become embedded in the membrane of the endoplasmic reticulum?
Definition
1. The presence of a hydrophobic stop-transfer sequence region downstream of the signalling sequence will get 'stuck' in the membrane, thus causing a transmembrane protein when signal peptidase cleaves the signal molecule.
2/3. An alpha-helical region can orient itself either positive or negative in the membrane, thus causing signal peptidase to cleave the starting signal and resulting in a transmembrane protein.
Term
What are the three types of vesicles?
Definition
1. Clathrin-coated vesicles
2. COP II-coated vesicles
3. COP I-coated vesicles.
Term
Describe the process of clathrin-coated vesicle formation.
Definition
The major component of clathrin coated vesicles is clathrin itself. Clathrin subunits assemble into a basketlike framework that forms a pit on the membrane surface. Adaptin binds the clathrin coat to the plasma membrane, trapping various transmembrane proteins, including cargo receptors.

As the clathrin coated vesicle forms, a protein known as dynamin uses GTP hydrolysis to mediate the rate at which it pinches off the membrane. Once it is separate, the clathrin coat quickly degrades.
Term
Where do COPII and COPI vesicles bud from?
Definition
COPII vesicles bud from the endoplasmic reticulum while COPI vesicles bud from the golgi apparatus.
Term
What enzymes ensure coats assemble only when they are needed?
Definition
The enzymes controlling for this are coat-recruitment are known as coat-recruitment GTPases, including ARF proteins and Sar1-protein.
Term
How are SNAREs able to ensure membrane specificity with respect to vesicular transport?
Definition
There are two components to SNAREs -- T-Snares (target SNAREs) and V-SNAREs (vesicular SNAREs). When complementary V-SNAREs and T-SNAREs meet, they form a stable trans-SNARE, which locks the membranes together.
Term
What is the function of RAB proteins?
Definition
RAB proteins on a vesicle bind to RAB effectors on the target membrane, guiding the V and T-SNAREs together.
Term
How do glycosylated proteins exit the endoplasmic reticulum?
Definition
Proteins exit the endoplasmic reticulum from ER Exit Sites via COPII coated vesicles.
Term
What happens to unproperly folded proteins in the endoplasmic reticulum?
Definition
These proteins are unable to leave the ER, as Binding protein (BiP) and calnexin attach to it, blocking its exit signals or anchor it to the ER. They are eventually transported into the cytosol where they are broken down by proteases.
Term
What is homotypic fusion?
Definition
Homotypic fusion occurs after vesicles are secreted from the endoplasmic reticulum. This is the process where multiple vesicles fuse together to form a large aggregate due to T and V-SNARE interactions. This forms what's known as the vesicular tubular clusters.
Term
What is retrograde transmission?
Definition
The vesicular tubular cluster forms COPI-coated vesicles as soon as it forms, sending proteins with ER resident signals back to the endoplasmic reticulum.
Term
ER resident proteins may also be formed into ___________ that prevent them from escaping the endoplasmic reticulum.
Definition
Multi-subunit aggregates.
Term
What is the general path that proteins take through the Golgi apparatus?
Definition
1. Cis face
2. Cis-Golgi network
3. Trans-Golgi network
4. Trans-face
Term
What are the two types of glycosylated proteins that arise in the Golgi apparatus? How are they formed?
Definition
1. Complex oligosaccharides. If it is subject to additional trimming in the golgi apparatus, it will likely become a complex oligosaccharide.
2. High-mannose oligosaccharides. Not subject to much trimming, remains in high mannose forms.
Term
The heaviest glycosylation of all produces ________ which are secreted to form the ____________.
Definition
Glycoproteins; extracellular matrix.
Term
What happens in the medial-Golgi compartment? What happens in the trans-Golgi compartment?
Definition
1. Removal of mannose
2. Addition of N-acetylglucosamine.
Term
What are the two models potentially explaining the way proteins move through the Golgi apparatus?
Definition
1. Vesicular transportation model -- The golgi apparatus is static, and molecules in transit bud from one compartment to the next. These vesicles are tethered by binding proteins that restrict their movement.
2. Cisternal maturation model -- the vesicular tubular clusters fuse with each other to become the cis-Golgi network, then mature into the trans-Golgi network.
Term
What is the pathway that endocytosed materials take to the lysosome?
Definition
Endocytosed vesicles are taken in by early endosomes. Some of these are taken to the plasma membrane while others are delivered to the late endosomes which then mature into lysosomes.
Term
What is autophagy?
Definition
Autophagy involves degradation of intracellular parts. First the organelle is surrounded by an autophage, and then the autophage fuses with the lysosome.
Term
How are phagocytosed materials degraded?
Definition
A phagosome engulfs a pathogen and then is converted to a lysosome.
Term
How are lysosomal hydrolases delivered to lysosomes?
Definition
They carry a unique marker known as mannose-6-phosphate groups, which are added on the cis-Golgi network. These are recognized by M6P receptor proteins in the trans-Golgi network, and then packaged into clathrin-coated vesicles which are transported to late endosomes. This M6P group is returned to the trans-Golgi network.
Term
What is the difference between endocytosis and phagocytosis?
Definition
Endocytosis is the process where a membrane invaginates and surrounds a material in order to ingest it. Phagocytosis occurs when a special brand of cell known as a phagosome engulfs dead tissue to clear erroneous material.
Term
What is receptor-mediated endocytosis?
Definition
Receptor-mediated endocytosis in the process that allows the importation of selected extracellular material. Macromolecules bind to receptors on the membrane, which then pinch off into clathrin-coated vesicles.
Term
What are three paths that transmembrane proteins could take from the late endosome?
Definition
1. Progression to lysosome.
2. Transport to plasma membrane.
3. Transport to other organelle membrane.
Term
What is the difference between the constitutive and the regulative secretory pathways?
Definition
The constitutive pathway is common to all cells, the regulative secretory pathway is specialized to some gland and excretory cells, and allows for products to be stored for later secretion.
Term
What are the three destinations for proteins in a cell capable of regulated secretion?
Definition
1. Lysosomes
2. Immediate secretion (default pathway)
3. Packaging into secretory vesicles for later secretion.
Term
What is the function of intermediate filaments? Microfilaments? Microtubules?
Definition
Intermediate filaments provide structural strength. Actin microfilaments determine the structure of the cell's skeleton and are essential for whole cell locomotion. Microtubules determine the position of membrane bound organelles.
Term
What function does twisting into a helix serve microtubules and microfilaments?
Definition
It makes it harder for them to spontaneously break down due to thermal stress.
Term
What is nucleation?
Definition
The process of forming a large subunit capable of rapid elongation (ie. it's strong enough to not spontaneously disassociate).
Term
How are microfilaments arranged in filapodia?
Definition
They are in parallel and tightly bound, growing in one direction.
Term
What is the cellular benefit of treadmilling and dynamic instability?
Definition
Although treadmilling (cytoskeletal elements are being added at one end and taken away from the other simultaneously) has an energy cost, it is beneficial because it is much easier to quickly modify a filament in flux than one at rest.
Term
Why do we say that intermediate filaments are "like a rope"?
Definition
Because of the large number of strong alpha coils, the lateral association of polypeptides, and the hydrophobic interactions of coil-coil proteins, intermediate filaments are easy to bend but impossible to break.
Term
What is the main difference between elongation of microtubules and microfilaments?
Definition
Elongation of microtubules uses GTP hydrolysis for energy, whereas microfilaments use ATP hydrolysis.
Term
What is the Critical Concentration?
Definition
This is the concentration of filamentous subunits where addition is equal to removal.
Term
What happens when the concentration is above the critical concentration at the positive end but below it at the negative end?
Definition
Treadmilling occurs.
Term
What is the "cap" of a polymer typically composed of?
Definition
A series of monomers with nucleoside triphosphates.
Term
What is gamma-tubulin used for?
Definition
Gamma-tubulin binds the negative end of microtubulus in the microtubule organizing center, forming gamma-tubulin ring structures that serve as effective nucleation sites.
Term
Where does actin filament polymerization mostly occur?
Definition
The plasma membrane of the cell.
Term
What is the actin related protein complex?
Definition
The ARP complex is a dimer of two "actin-related proteins" that serves as a nucleator for actin filament polymerization.
Term
Given the high concentration of free actin, why does it not constantly polymerize?
Definition
A protein known as thymosin binds to actin to prevent polymerization.
Term
What is profilin?
Definition
Profilin is a protein that regulates thymosin activity by antagonistically binding to thymosin, causing it to be free for actin polymerization.
Term
What is stathmin?
Definition
Stathmin is a protein that binds to tubulin dimers and prevents them from being added to the protofilament.
Term
What are tubulin-binding motifs?
Definition
These are a portion of microtubule accessory proteins that greatly accelerate nucleation by stabilizing tubulin oligomers prior to polymerization.
Term
What is XMAP225?
Definition
XMAP225 is a MAP that stabilizes microtubules by binding inhibiting the switch from a growing to a shrinking state. These are phosphorylated in mitosis, greatly increasing dynamic instability.
Term
What are the main MAPs in actin filaments?
Definition
1. Troponomyosin which prevents actin filaments from interacting with other proteins, thus stabilizing it.
2. Cofilin -- actin depolymerization factor -- causes the actin filament to twist tighter so the subunits are more easily severed.
Term
How are actin filaments uncapped to promote rapid polymerization at the cell periphery?
Definition
An inositol phospholipid, known as PIP2.
Term
How are long-lived actin filaments regulated?
Definition
1. CapZ at positive end.
2. Tropomodulin at negative end.
Term
What are catastrophins?
Definition
Catastrophins are MAPs that rip tubulin subunits apart.
Term
What are the two ways that actin filaments can be cross-linked?
Definition
1. Bundling proteins arrange them in a parallel array.
2. Gel-forming proteins -- attaches actin at angles to each other, creating a weblike structure.
Term
What are some examples of actin bundling proteins?
Definition
1. Fimbrin -- responsible for filapodia.
2. Alpha-actinin -- responsible for contractile stress-fibres in the cell.
Term
What is an example of a gel-forming actin protein?
Definition
Spectrin, found in red blood cells.
Term
How are microtubules severed?
Definition
Microtubules are severed by katanin, a two-subunit complex that hydrolyses ATP to cut the bonds between tubulins.
Term
How are microfilaments severed?
Definition
When Ca2+ concentration increases, the protein known as gelsolin is activated. Gelsolin works by inserting itself into the space between active subunits and then acting as a capping protein. It can be deactivated by PIP2.
Term
What are focal contacts?
Definition
Focal contacts are attachments between actin filaments and the extracellular matrix that allows a cell to pull on the substrate to which it is bound, using stress fibres attached to integrins (clusters of transmembrane adhesion proteins).
Term
What are cadherins?
Definition
Clusters of transmembrane proteins that allow attachment to other tissues.
Term
What is the function of kinesin?
Definition
It shuttles membrane bound organelles around the cytoplasm.
Term
What do dynenins require to bind to the microtubule effectively?
Definition
Dynactin
Term
What are the three generalized types of cellular junctions?
Definition
1. Anchoring junctions
2. Occluding junctions (as in epithelium)
3. Communication junctions
Term
What are the major proteins in tight junctions?
Definition
Claudin and occludin. These bind to similar proteins on other cells
Term
What is the difference between an adherens junction and a focal adhesion?
Definition
An adherens junction uses cadherins to join actin filaments to other cells. A focal adhesion uses integrins to link actin filaments to the extracellular matrix.
Term
What is the difference between a desmosome and hemidesmosome?
Definition
Desmosomes uses microfilaments to hold cells together. Hemidesmosomes uses microtubules.
Term
What is the chemical composition of the extracellular matrix?
Definition
The extracellular matrix is an aggregate of proteins such as glycosaminoglycans (GAGs), glycoproteins, collagen, and elastin.
Term
What cells primarily secrete the extracellular matrix?
Definition
Fibroblasts.
Term
What is the function of the GAGs in the extracellular matrix?
Definition
When they aggregate, they attract ions which increases their affinity for water, thus causing a cushioning matrix to form (hyaluronan is an example of this, formed from repeatig subunits of N-aminoglucosamine and glucoronic acid)
Term
What are proteoglycans?
Definition
Proteoglycans are complexes of GAGs linked to extracellular proteins. One of the largest is aggrecan: formed with a core protein surrounded by GAGs. Aggrecan + hyaluronan = aggrecan aggregate.
Term
How is collagen synthesized?
Definition
Ribosomes bound to the rough ER secrete large pro-A chains into the endoplasmic reticulum. These are then glycosylated and trimerized to form procollagen, which is then broken down by proteolytic enzymes to form collagen.
Term
What is the most important class of enzymes that degrades the extracellular matrix?
Definition
Matrix metalloproteinases (MMPs).
Term
What is the chemical difference between a glycoprotein and a proteoglycan?
Definition
Glycoproteins are proteins glycosylated with sugar groups. Proteoglycans are proteins glycosylated with glycosaminoglycan groups.
Term
What is the primary structural difference between a phosphoglyceride and a sphingolipid?
Definition
Phosphoglycerides have a glycerol backbone and two fatty acids. Sphingolipids have a spingosine backbone and one fatty acid.
Term
What is the function of cholesterol in the plasma membrane?
Definition
Cholesterol embeds itself in the plasma membrane, pushing the phospholipid heads closer together but increasing fluidity in the hydrophobic tails.
Term
What are four factors that affect membrane fluidity?
Definition
(1) length of fatty chain acids
(2) chemical structure of the polar head
(3) saturation
(4) physical conditions of the membrane
Term
What is a hydropathy plot used for?
Definition
These are used to determine what proportions of proteins a cell makes will be transmembrane proteins.
Term
Why is the glycosylated side of a transmembrane protein usually the extracellular side?
Definition
Glycosylation provides some measure of protection against breakdown in the ECM.
Term
What are some ways that cells are able to control the location of transmembrane proteins?
Definition
(1) Tight junctions
(2) Cytoskeletal interactions (anchored to actin filaments)
(3) Extracellular domains
(4) Self-assembly makes aggregates too large to move
Term
What are the three types of ATPases?
Definition
1) P-Type ATPase (controlled by phosphorylation)
(2) V-Type ATPase (used to generate ATP, turbine-like)
(3) ABC Transporters -- Two ATP binding cassettes dimerize when ATP binds and dissociate when it is hydrolysed, involved in multidrug resistance in cancer.
Term
On what do nuclear hormone receptors exert their effects?
Definition
Gene transcription.
Term
What are the three basic types of ligand receptors?
Definition
(1) Ionotropic receptors
(2) G-Protein Linked Receptors
(3) Enzyme-linked receptors
Term
What is:

(1) Relay protein
(2) Messenger protein
(3) Adaptor protein
(4) Amplifier protein
(5) Transducer protein
Definition
(1) Protein that passes message from one stage of signal transduction to the next.
(2) Carries signal from one part of cell to another
(3) Link one signalling protein to another without actually conveying a signal
(4) Greatly increase signalling strength
(5) Convert a signal into another modality
Term
How do -RTKs work?
Definition
When the ligand binds, two inactive domains dimerize and autophosphorylate, causing increased kinase activity. This attracts adaptor proteins to the -RTK, which then get phosphorylated and attract Raf GEF (guanine exchange factor), thus inducing Ras to change its GDP for GTP, causing a phosphorylation in the MAP-KKK cascade.
Term
What effect does MAPK have?
Definition
MAPK phosphorylates protein kinases and gene regulatory proteins.
Term
How does G-Protein signal transduction work?
Definition
(1) Ligand binds to receptor
(2) Receptor recruits trimeric G-protein
(3) Nucleoside exchange, alpha subunit separates from beta-gamma subunit.
(4) Activation of target protein.
(5) Adenylate cyclase-> ATP to cAMP
(6) cAMP activates PKA (cAMP-dependent protein kinase)
(7)
Term
What proteins support mitochondrial networking and fusion?
Definition
Fuzzy onion protein and dynamin.
Term
How does brown fat generate heat?
Definition
A protein known as thermogenin (UCP1) shortcuts the proton gradient, increasing VO2 max and heat production.
Term
What are caspsases?
Definition
Caspsases are DNA 'killers' in apoptosis that cut DNA between histones.
Term
What is the caspase cascade?
Definition
When the mitochondria is sufficiently depolarized, cytochrome C escapes and binds to Apaf-1. This aggregate binds to an initiator procaspase, activating it. This then activates other procaspsases until executioner caspsases are activated.
Term
What is Bcl2? Bid and BAD?
Definition
Bcl2 prevents cell death by restricting mitochondrial pore. Bad and Bid bind to Bcl2 to prevent it from preventing cell death.
Term
What are two extracellular ways that apoptosis can be initiated?
Definition
(1) Tumor necrosis factor alpha (from macrophages
(2) FAS ligand (from killer T-cells), binds to procaspsases, activating them.
Term
Procaspsases already have weak proteolytic activity. How are they kept from activating themselves?
Definition
xIAP (x-linked inhibitor of apoptosis) binds to give it even weaker activity in order to keep apoptosis in check.
Term
What protein blocks xIAP?
Definition
Hid.
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