question

?-glucosidase

answer

A lysosomal enzyme. A polysaccharidase and oligosaccharidase that acts on glycogen.

question

?-mannosidase

answer

A lysosomal enzyme. A polysaccharidase and oligosaccharidase that acts on mannosyloligosaccharides.

question

?-N-acetylglucosaminidase

answer

A lysosomal enzyme. A GAG-hydrolyzing enzyme that acts onf heparan sulfate.

question

?-galactosidase

answer

A lysosomal enzyme. A GAG-hydrolyzing enzyme that acts on keratin sulfate.

question

?-hexosaminidase

answer

A lysosomal enzyme. A sphingolipid hydrolyzing enzyme that acts on G_M2 ganglioside.

question

?GTP

answer

A non-hydrolyzable analog of GTP. Causes dynamin ring polymerization to continue without twisting and pinching off. Results in an extended bud "stalk" and no scission event.

question

A-mannosidase I

answer

Localized in the cis cisternae. Removes three mannose sugars from the core oligosaccharide.

question

A. thaliana

answer

A model organism. Used in plant sciences.

question

ABC nuclear lamins

answer

Proteins that make up the nuclear lamina. Related to cytosolic intermediate filaments. Three proteins: lamin A, B, and C.

question

Absorption spectrum

answer

A plot of the intensity of light absorbed relative to its wavelength. Measures the wavelengths of light absorbed by pigments.

question

Accessory proteins

answer

Proteins of the TOM complex. Serve as a scaffold to mediate protein transfer from the receptor to the channel.

question

Achondrogenesis type 1A

answer

A severe disease that results from mutation in GMAP-210. Chondrocytes are most affected; matrix material does not move through the Golgi due to a lack of solid interaction with the cytoskeleton. The ER is swollen, resulting from stalled transport to the Golgi.

question

Acid deoxyribonuclease

answer

A lysosomal enzyme. A nuclease that acts on DNA.

question

Acid hydrolase

answer

Enzymes that have an optimal activity at an acidic pH. All lysosomal enzymes are acid hydrolases, suited to the low pH of the lysosomal compartment, 4.6. Found in the MVB, and are activated when it fuses with the lysosome.

question

Acid lipase

answer

A lysosomal enzyme. A lipid hydrolyzing enzyme that acts on triaclyglycerols.

question

Acid phosphatase

answer

A lysosomal enzyme. A phosphatase that acts on phosphomonoesters.

question

Acid phosphodiesterase

answer

A lysosomal enzyme. A phosphatase that acts on phosphodiesters.

question

Acid ribonuclease

answer

A lysosomal enzyme. A nuclease that acts on RNA.

question

Action spectrum

answer

A plot of the relative rate of photosynthesis produced by light of various wavelengths. Identifies wavelengths effective in bringing about physiologic response.

question

Activating transcription factor 6 (ATF6)

answer

A pathway in UPR. BiP is released from ATF6, revealing a Golgi localization signal, so that it moves from the ER to the Golgi complex via transport vesicles. In the Golgi complex, the cytosolic-facing transcription factor domain is cleaved off by a Golgi-associated protein domain. This transcription factor has an NLS and targets the nucleus, and up-regulates a number of genes including ER molecular chaperones (assist in protein folding0, ER export components (assist in moving folded proteins from the ER), and ERAD components (assist in degrading misfolded proteins). ER stress is alleviated, and if not, cell death occurs.

question

Aerobes

answer

Organisms that are dependent on oxygen for their metabolisms. Gave rise to oxygen-dependent prokaryotes and eukaryotes.

question

Aerobic respiration

answer

Occurs in mitochondria
O₂ + energy rich carbohydrates > CO₂ + ATP

question

Albert Claude and Christian De Duve

answer

In the 1950s and 60s, used techniques to homogenize cells and isolate organelles.

question

Alzheimer's disease

answer

Misfolded proteins accumulate in the ER and form toxic aggregates. PERK pathway is activated in neurons, leading to cell death.

question

Amphipathic

answer

Not hydrophobic, but has a positive charge.

question

Anaerobes

answer

Organisms that capture and use energy by oxygen-independent metabolisms such as glycolysis and fermentation.

question

Angstrom (A)

answer

One tenth of a nanometer. A unit of measurement commonly used to describe structures in cells. Commonly used by molecular biologists for atomic dimensions. Approximately the diameter of a hydrogen atom.

question

Antenna

answer

Pigment molecules that harvest photons of varying wavelengths and transfer the energy rapidly to the reaction-center chlorophyll.

question

Anterograde

answer

"Forward"
Transport from ER to Golgi, and from Golgi to plasma membrane.

question

AP2

answer

A soluble cytosolic adaptor protein, recruited to coated pits on the plasma memrbane by PIP2. Analogous to GGA adaptors at the TGN. A linker protein with multiple binding domains: PIP2, cytosolic domains of transmembrane proteins, and clathrin. Recruit clathrin triskelions, which form an outer scaffold lattice on the growing vesicle during receptor-mediated endocytosis. Released into the cytosol after vesicle formation.

question

APEM9

answer

Tethers PEX6 and PEX1 to the peroxisome membrane during peroxisome targeting.

question

ARC1

answer

A protein required for plant pollination, involved in recognition of self-incompatible pollen. Shuttles between the cytosol and nucleus. Possesses a classic NLS, and a positive NES. Mutation of residues 261 - 266 result in it being mislocalized entirely to the cytosol. Fusion of these residues leads to cytosolic passenger proteins being mislocalized to the nucleus.

question

Arf1

answer

Analogous to Sar1. A G-protein that recruits GGA proteins. Arf1-GTP binds to the TGN, resulting in initial curvature of the membrane in formation of a clathrin coated-vesicle. After the vesicle pinches off, it is converted to Arf1-GDP, and is released into the cytosol.

question

Artifact

answer

A coagulation or precipitation of materials that had no structure in a living cell, found in a speciment due to effects of the fixative. Cyrofixation is less likely to lead to artifacts.

question

Arylsulfatase A

answer

A lysosomal enzyme. A sphingolipid hydrolyzing enzyme that acts on galactosylsulfatide.

question

ATP synthase

answer

A mushroom-shaped protein complex that synthesizes ATP. Consists of a spherical F₁ head and a basal F₀ section embedded in the inner membrane.

question

ATPase proton pump

answer

A membrane-bound pump that maintains the low pH of 4.6 within the lumen of the lysosome. Pumps H⁺ into the lumen of the lysosome, using ATP.

question

Autolysosome

answer

A lysosome fused to an autophagosome. The inner membrane of the original phagophore, as well as the organelle, are degraded. The residual body is either released into the cytoplasm or retained indefinitely as a lipofuscin pigment granule.

question

Autophagosome

answer

The mature phagophore. Fuses with a lysosome, creating an autolysosome.

question

Autophagy

answer

Damaged or old organelles are destroyed. An organelle is surrounded by a phagophore, which matures into an autophagosome, which fuses with a lysosome, forming an autolysosome. After degradation, the residual body is released into the cytoplasm or stored as a lipofuscin pigment granule. Includes mitophagy.

question

Autoradiography

answer

Provides a means to visualize biochemical processes. Can determine the location of radioactively labelled materials within a cell. Tissue sections with radioactive isotopes are covered with a thin layer of photographic emulsion, which is exposed to the radiation.

question

Autotroph

answer

Organisms that create organic compounds from carbon dioxide. Include chemoautotrophs and photoautotrophs.

question

Avram Hershko, Aaron Ciechanover, Irwin Rose, and Alexander Vashasky

answer

Israeli and American scientists who studied selective protein degradation.

question

Bag of marbles

answer

A gene that is responsible for generating the male germ line.

question

Barbara Pearse

answer

From the Medical Research Council in Cambridge, England. In 1975, made the first studies of the biochemical nature of vesicle coats. Developed a procedure in which membrane vesicles from pig brains were centrifuged through a succession of sucrose density gradients, to produce a purified fraction of coated vesicles, from which an SDS-PAGE procedure could purify the coat proteins.

question

Barentz

answer

A gene that if mutated, the protein gets stuck. Named after a man who tried and failed to fidn the Northeast passage, because his ship got stuck in the ice.

question

Binding immunoglobulin protein (BiP)

answer

A chaperone protein in the ER. Binds to membrane sensor proteins that initiate UPR response, and is stored in this form. PERK and ATF6 sensors are inactive when bound to BiP. Needed in the folding of accumulated misfolded proteins.

question

Biosynthetic pathway

answer

A pathway in the endomembrane system. Lipids, and complex polysaccharides are synthesized in the ER, modified as they move through the Golgi complex, and transported from the Golgi complex to the plasma membrane, lysosome, or large vacuole.

question

Bipartite NLS

answer

KR-------KKKK
An NLS composed of two short stretches of basic amino acids, and a 7 - 10 amino acid long spacer sequence.

question

Bright-field microscope

answer

A cone of light illuminates the specimen, and is seen as a bright background against which the image of the specimen is contrasted. Ideally suited for specimens with high contrast, such as stained sections of tissues. Includes a light source, condenser lens, stage, objective lens, and ocular lens.

question

Britton Chance and coworkers

answer

From the University of Pennsylvania. Determined the specific sequence of electron carriers in the electron transport chain using a variety of inhibitors that blocked electron transport at specific sites.

question

Bulk-phase endocytosis

answer

Pinocytosis
"Cellular drinking"
A type of endocytosis. Non-specific uptake of extracellular fluids and plasma memrbane protein turnover.

question

C.B. van Niel

answer

A graduate student at Stanford University who in 1931 proposed the equation for photosynthesis, based on work with sulfur bacteria. Oxygen is created from breakdown of two water molecules, not from breaking carbon dioxide.
CO₂ + H₂O > (CH₂O) + O₂

question

C. elegans

answer

A model organism. A worm. 1031 cells.

question

C₃ plants

answer

Plants that utilize the three-carbon molecule PGA as the first intermediate in carbon fixation.

question

C₄ pathway

answer

A second mechanism of fixation of CO₂. PEP carboxylase converts CO₂ into PEP, which transports to bundle sheath cells, concentrating CO₂ around Rubisco. PEP carboxylase is not inhibited by O₂.

question

C₄ plants

answer

Plants that utilize the C₄ pathway. Primarily tropical grasses.

question

Calnexin

answer

A chaperone protein in the ER. A membrane-bound reticuloplasmin that mediates the final folding steps of a glycoprotein. Nascent glycoproteins (with a single remaining terminal glycose residue) bind to it. The protein is sequestered away from other proteins, allowing it to fold properly.

question

Calreticulin

answer

A chaperone protein in the ER.

question

Calvin cycl

answer

Calvin-Benson cycle
The pathway for conversion of CO2 into carbohydrates. Occurs in cyanobacteria and all photosynthetic cells. Occurs in the stroma of the chloroplast. Consitsts of carboxylation of RuBP to form PGA, reduction of PGA to the level of a sugar by forming GAP using NADPH and ATP, and regeneration of RuBP using ATP.

question

CAM plants

answer

Adapted to hot, dry habitats. Use PEP carboxylase to fix CO₂. Light-dependent reactions occur at a different time than light-independent reactions. Stomata are kept closed in the day, and opened at night.

question

Camillo Golgi

answer

An Italian biologist who invented staining procedures. Discovered the Golgi complex in 1898. Observed it as a darkly staining reticular network near the cell nucleus. Won the Nobel Prize in 1906.

question

Cardiolipin

answer

A lipid unique to the mitochondrial outer membrane. Phospholipase D converts it into phosphatidic acid when forming lipid microdomains during mitochondrial fusion.

question

Cargo proteins

answer

Destined for the recipient compartment. Possess cytosolic-facing ER export signal sequences, recognized by Sec24 in COPII-coated vesicles.

question

Cargo receptor proteins

answer

Have luminal facing-domains that bind to soluble luminal cargo proteins destined to exit the ER.

question

Carl Woese and colleagues

answer

From the University of Illinois. In the mid-1970s, began studies that compared nucleotide sequences of different organisms of the RNA molecule in the small subunit of the ribosome. Provided strong evidence that chloroplasts evolved from cyanobacteria. In 1977, Carl Woese and George Fox published a paper on the study of molecular evolution. Concluded that Archaebacteria have their own distinct evolutionary line.

question

Cathepsin

answer

A lysosomal enzyme. A protease that acts on proteins.

question

Cell biology

answer

The multidisciplinary study of the composition, structure, and function of various subcellular organelles and other cellular compartments in evolutionarily diverse organisms.

question

Cell-free system

answer

Isolated parts of cells. Lack any whole cells. Capable of cell functions. Allow study of cell functions that would be impossible to study within an intact cell.

question

Central scaffold

answer

Part of the NPC. Anchors the complex to the nuclear envelope. Forms the core of the NPC. Forms an aqueous channel, 20 - 30 nm wide.

question

Centromere

answer

The site of constriction on a chromosome. In humans it contains a randomly repeated 171 bp sequence extending for at least 500 kb. Associates with specific proteins, including those which form the kinetochore, where microtubules attach during cell division. Centromere DNA is not well conserved, even between closely related species.

question

Ceramidase

answer

A lysosomal enzyme. A sphingolipid hydrolyzing enzyme that acts on ceramide.

question

Channel

answer

A protein of the TOM complex. Barrel-shaped, mediates protein translocation across the outer membrane.

question

Chemical fixation

answer

The most common way to fix a specimen for TEM. The specimen is placed in glutaraldehyde. The aldehyde groups rapidly react with amino groups in proteins and other cellular macromolules, to form an insoluble "cross-linked" immobile network. This can lead to artifacts. Kills cells slowly, after 30 seconds to 10 minutes. Does not bind to and immobilize all celular molecules. Lipids can continue to move and alter shape, dimensions, and distribution of cellular structures.

question

Chemiosmotic mechanism

answer

A proton gradient is formed in the intermemrbane space, and an enzyme synthesizes ATP using the energy of their flow as they move back across the membrane.

question

Chemoautotroph

answer

A type of autotroph. Use the chemical energy stored in inorganic molecules such as ammonia, hydrogen sulfide, or nitrates to convert CO₂ into organic compounds. All chemoautotrophs are prokaryotes.

question

Chlorophyll

answer

The most important light-absorbing photosynthetic pigment. Consists of a porphyrin ring that absorbs light and a hydrophobic phytol chain that anchors it to the photosynthetic membrane.

question

Chloroplast

answer

A cytoplasmic organelle. Energy production and carbohydrate synthesis via photosynthesis. Also involved in fatty acid and amino acid biosynthesis, and nitrogen and sulfur assimilation. Evolved from a symbiotic cyanobacterium living within a host cell. Often highly mobile in cells; move along the cytoskeleton. Often connected by stromules. Semi-autonomous; organelle replication is controlled by both the cell and the organelle itself. Arise from only pre-existing chloroplasts. Most of its oenes are transferred to the nucleus. Has a double membrane and complex organization. Sub-compartments include: chloroplast envelope (outer membrane, intermembrane space, and inner membrane), stroma, thylakoid membrane, and thylakoid lumen.

question

Chloroplast envelope

answer

The outer and inner membrane of the chloroplast, and the intermembrane space. The membranes differ in protein and lipid composition and function. Movement of proteins across the envelope is not mediated by electrochemical potential. Targeting signals and insertion mechanisms for chloroplast envelope protein targeting are not well known.

question

Chloroplast intermembrane space

answer

A sub-compartment of the chloroplast.

question

Chloroplast targeting

answer

Similar to mitochondrial targeting. The majority of chloroplast proteins, 95%, are nuclear encoded, synthesized on free ribosomes in the cytosol, and targeted post-translationally to the chloroplast. An efficient but complex process. All chloroplast proteins have targeting sequence that mediates targeting to the chloroplast surface, and to specific sub-compartments. Varies depending on the final location in the chloroplast. There are multiple sub-compartment targeting pathways using different impoart machineries, depending on the targeting signal. There are six possible sub-compartments in the chloroplast: outer membrane, intermembrane space, inner membrane, stroma, thyalkoid membrane, and thylakoid lumen.

question

Chondrocytes

answer

Secrete matrix material to facilitate bone formation. Affected by achondrogenesis type 1A.

question

Chromatin

answer

A complex nucleoprotein material, found in the nucleus. The chromosomes of eukaryotes are packaged into chromatin.

question

Chromatin remodeling complex

answer

Use energy from ATP hydrolysis to alter nucleosome structure and/or location on the DNA. Can slide the histone octamer down the DNA, change conformation of the nucleosome, facilitate replacement of a core histone, or displace the histone octamer completely.

question

Chromosome

answer

Individual DNA molecules. During interphase, they are organized into discrete subdomains within the nucleus. Location of a gene is often related to its activity; more actively transcribed genes are found at the periphery.

question

Cis cisternae

answer

The compartment in the Golgi complex between the CGN and the medial cisternae. A large, flattened cisternae. Osmium tetroxide and mannosidase I is localized here. Mannose is phosphorylated. A phosphotransferase recognizes a signal patch in the protein. N-acetylglusomine-1-phosphate is transferred to a specific mannose residue from a nucleotide sugar donor. Two mannose sugars in the core olgiosaccharide are phosphorylated.

question

Cis Golgi network (CGN)

answer

The cis-most face of the Golgi complex. An interconnected network of tubules. Functions in sorting proteins to be shipped to the ER, or proceeding into the next face of the Golgi complex. Adjacent to the ERES. The recipient compartment of COPII vesicles from the ERES. The site of COPI vesicle assembly for retrograde transport to the ER or anterograde transport as the CGN matures into the rest of the Golgi complex.

question

Cisternae

answer

Flattened stacks of membrane of the Golgi complex.

question

Cisternal progression

answer

Cisternal maturation model
A model for movement through the Golgi complex. The most favoured model. There is evidence for this model: COPI-coated vesicles. Golgi compartments are dynamic structures, each sub-compartment continually moves from the cis to the trans side of the Golgi complex. The composition of each sub-compartment changes while moving from cis to trans through the stack. The composition of each cisternae persists because COPI-coated transport vesicles continually bud from the irregular domain of cisternae and move resident Golgi proteins back to the proper sub-compartment. Incoming COPII-coated transport vesicles from the ER fuse together to form a new CGN, which then progresses through the Golgi stack in the anterograde motion. The TGN eventually disperses into various vesicles.

question

Class I CF

answer

A class of cystic fibrosis. Defective production of the chloride channel. No chloride channel is produced.

question

Class II CF

answer

A class of cystic fibrosis. The chloride channel has defective processing and is degraded.

question

Class III CF

answer

A class of cystic fibrosis. Defective regulation of the chloride channel. Accessory proteins involved in the chloride channel are defective.

question

Class IV CF

answer

A class of cystic fibrosis. Defective conductance of the chloride channel. The chloride channel is present, but does not properly allow passage of chloride.

question

Class V CF

answer

A class of cystic fibrosis. Reduced amount of chloride channel. The chloride channel is produce, but in too small amounts.

question

Classic NLS

answer

KKQRKK
The most common NLS. A short stretch of positively charged amino acid residues. Found in the large T antigen protein of simian virus 40.

question

Clathrin

answer

One molecule of clathrin consists of three "light' chain polypeptides and three "heavy" chain polypeptides. Forms a three-legged triskelion structure. The triskelion self-assembles to form the outer scaffolding of the coat of the growing vesicle. Binds to GGA on the inner surface. Lattice assembly promotes further bending of the membrane.

question

Clathrin-coated vesicles

answer

A type of coated vesicle. Moves materials from the TGN to endosomes (including M6P-tagged cargo), lysosomes, and plant vacuoles. Moves materials from the plasma membane to the cytoplasmic compartments in the endocytic pathway. Protein coats include an outer honey-comb like lattice composed of clathrin and an inner shell composed of protein adaptors. Arf1 recruits GGA to bind to M6P receptors bound to soluble cargo. Clathrin binds to GGA and self-assmbles into a lattice. Lysosomal cargo proteins are concentrated in the growing vesicle. Individual clathrin triskelions initially assmble to form hexagons that lie flat on the membrane surface, then begin to form pentagons that drive the force for membrane curvature into a sphere. Pinching off is mediated by dynamin. The coat disassembles after pinching off.

question

Co-tranlsational import

answer

Polypeptides are inserted into the RER luminal space during translation.

question

Coactivators

answer

Large complexes consisting of numerous subunits, that bind to enhancers and stimulate initiation of transcription at the core promoter. Includes those which interact with components of basal transcription machinery, and those which act on chromain. Some coativators have HAT activity.

question

Coat proteins (COP)

answer

Assemble on the cytosolic surface of membrane. Mediate membrane curvature, and the formation of the budding vesicle. Recognize and concentrate specific proteins and lipids that will be incorporated in the nascent vesicle: cargo proteins, cargo receptor proteins, and molecualr machinery. Appears as a fuzzy surface on the cytosolic surface on the membranes. Three classes: COPII, COPI, and clathrin.

question

Coated pits

answer

Specialized domains of the plasma membrane where recptors collect for RME. Receptor/ligand complexes are concentrated at 10 - 20 times their normal level on the plasma membrane. The surface of the plasma membrane is indented, and covered with clathrin on its cytoplasmic side. The inner leaflet of the plasma membrane is enriched with unique membrane phospholipids, including PIP₂.

question

Coated vesicle

answer

Vesicls with a darkly-staining protein coat on their cytosolic side. COP proteins facilitate curving of the membrane to form the budding vesicle, and select components to be carried within the vesicle. Include COPII, COPI, and clathrin-coated vesicles.

question

Collegenase

answer

A lysosomal enzyme. A protease that acts on collagen.

question

Confocal laser scanning microsope (CLSM)

answer

Similar set-up to standard bright-field microscope, but with some additional features. One or more lasers allow only certain wavelengths of light to strike the living specimen. The specimen does not need to be fixed, allowing for dynamic biological/cellular processes to be viewed live. Lasers can penetrate into thick living specimens. Laser light can be focused on a z-section. Only light signals from the point in focus can pass through the aperture; all out-of-focus fluorescence is excluded, resulting in a less blurry image.

question

Constitutive heterochromatin

answer

A class of heterochromatin. Remains in compacted state in the cell at all times. Represents DNA that is permanently silenced. In mammalian cells, it is found in regions that flank telomeres and centromeres of each chromosome, and in some other sites, such as the distal arm of the Y chromosome. Primarily repeated sequences, with few genes.

question

Constitutive secretion

answer

A type of secretory activity. ER-derived materials are transported in secretory vesicles and discharged into the extracellular space continuously. Most cells have constitutive secretion, contributing to the formation of the extracellular matrix, and the plasma membrane.

question

Contrast

answer

The difference in appearance between adjacent parts of an object, or between an object and its background. Specimens may be dyed to give them contrast.

question

COPI-coated vesicles

answer

A type of coated vesicle. Discovered before COPII-coated vesicles. Move materials in retrograde motion. Return soluble ER resident protins, bound to KDEL receptors, from the Golgi back to the ER.

question

COPII-coated vesicles

answer

A type of coated vesicle. Discovered after COPI-coated vesicles. Move materials in anterograde motion. Proteins in the coat include enzymes in later stages of their biosynthetic pathway, molecular machinery, and membrane proteins that bind to soluble cargo within the vesicle. Bind to microtubules and move via kinesin motor proteins.
1. Soluble COPII component Sar1-GDP is recruited from the cytosolic surface of the EREs. Sar1-GDP binds to a GEF, generating Sar1-GTP.
2. Sar1-GTP integrates into the ER outer leaflet at the ERES. Results in membrane curvatures of the ERES membrane.
3. Sar1-GTP recruits other soluble COPII components from the cytosol to the surface of the ERES membrane: Sec23 and Sec24.
4. Additional soluble COPII components are recruited from the cytosol to the surface of the nascent vesicle: Sec13 and Sec31.
5. After COPII coat assembly, the vesicle bud pinches off the ERES, and the vesicle begins to trafic to the propper recipient membrane.
6. Prior to vesicle fusion, the COPII coat disassembles; proteins are released. Sar1-GTP is converted to Sar1-GDP and released.

question

Copper atoms

answer

Three coper atoms
A type of electron carrier in the electron transport chain. Located within a single protein complex of the inner mitochondrial membrane. Accepts and donates a single electron by alternating between Cu²⁺ and Cu⁺.

question

Core glycosylation

answer

The first step of N-linked glycosylation. A complex 13-step process. Various ER membrane-bound glycosyltransferases synthesize the core oligosaccharide. The core olgiosaccharide is anchored to the ER membrane by dolichol phosphate. Each enzyme adds a specific sugar to a specific position at a time. Synthesis occurs first on the cytosolic side, then is flipped by a flippase halfway through adding mannoses, and continues on the luminal side. The final step involves a glycosyltransferase linking the core to a specific N residue on a soluble or integral membrane protein, as it is inserted into the luminal space through the translocon. Can only transfer oligosaccharides to luminal-facing N residues within the sequence NxS/T.

question

Core modification

answer

The second step of N-linked glycosylation. For some glycoproteins, this stage continues into the Golgi complex. The core oligosaccharide is gradually trimmed and modified. The first two terminal glucoses are removed by glucosidase I. The nascent glycoprotein is properly folded during this stage, mediated by reticuloplasmins. The glycoprotein is subjected to ER quality control, ensuring that the protein possesses the correct sugar attachments and is properly folded.

question

Core oligosaccharide

answer

A highly branched olgiosaccharide chain consisting of 14 sugar residues, including a terminal chain of 3 glucoses.
1. Two residues of NAG in a chain.
2. Nine residues of mannose in a trident formation.
3. Three terminal residues of glucose in a chain.

question

Cristae

answer

Invaginations of the inner mitochondrial membrane, forming membranous sheets. Contain large amounts of membrane surface, housing machinery needed for aerobic respiration and ATP formation.

question

Crystalline core

answer

The location of urate oxidase in the peroxisome. Catalyzes the conversion of uric acid into allatonin in most mammals. In many primates, including humans, the enzyme is lost.

question

Cyclic photophosphorylation

answer

Formation of ATP in the absence of CO₂ or NADP⁺. Carried out by PSI in the chloroplast.

question

Cyrofixation

answer

A method to fix a specimen for TEM. The specimen is flash frozen in liquid nitrogen at high pressure. Immobilizes all cellular molecules including lipids and water simultaneously within miliseconds. Results in fewer fixation artifacts. Requires very expensive equipment.

question

Cystic fibrosis (CF)

answer

A disease in which most patients have a mutant chloride channel protein, CFTR, degraded by ERAD, and therefore it is not targeted to the plasma membrane. Misfolded proteins accumulate in the ER and form toxic aggregates. Different mutations cause different problems with the encoded protein, inclduign processing of translated protein. Results in blocked airways. There are five classes: I - V.

question

Cytochrome

answer

A type of electron carrier in the electron transport chain. Proteins containing a heme prosthetic group. The iron atom undergoes reversible transition between Fe³⁺ and Fe²⁺, accepting and donating a single electron. Includes cytochrome a, b, and c, present in the electron transport chain.

question

Cytochrome oxidase

answer

Complex IV
A huge assembly of polypeptides. Reduces O₂. The first component of the electron transport chain to act as a redox-driven proton pump. For every molecule of O₂ reduced, eight protons are pumped into the intermembrane space. The human body produces 300 mL of water this way each day.

question

Cytoplasmic filaments

answer

Part of the NPC. Long protein filaments that extend into the cytosol on the cytosolic side. Involved in nuclear receptor-cargo protein recognition and import.

question

Cytoplasmic ring

answer

Part of the NPC. Located on the cytoplasmic side of the NPC. Linked to the central scaffold and the cytoplasmic filaments. Holds the membrane in place on the NPC.

question

Cytoskeleton

answer

Serves as a highway for almost all types of intracellular transport. Mediate movement of all vesicles through the cytosol. Movement on the cytoskeleton is actually quite slow.

question

Cytosol

answer

The soluble phase of the cytoplasm.

question

Cytosolic space

answer

The space outside of the ER.

question

D. melanogaster

answer

A model organism. A fruit fly. Easy to manipulate genetically. Breeds quickly.

question

Daniel Arnon

answer

From the University of California, Berkeley. In the 1950s, discovered that isolated chloroplasts were capable of synthesizing ATP in the absence CO₂ or NADP⁺.

question

Deconvolution

answer

Computer software removes the background and out-of-focus parts of digital microscopic image.

question

Deletion

answer

A type of chromosome aberration. A portion of a chromosome is missing. There is irregular pairing during meiosis. Often there are severe malformations in the organism.

question

Deletion mapping

answer

A strategy used to learn which sites a transcription factor interacts with. DNA molecules are prepared that conatin deletions of various parts of the gene's promoter. The cell's ability to initiate transcription are measured. Transcription may decrease, increase, or stay the same.

question

Differentiation

answer

Formation of specialized cells in multicellular organisms. Pathway of differentiation depends on signals from the surrounding environment.

question

Digital camera

answer

Captures the image. More sensitive to low light intensities, allowing for living cells to be viewed without photo damage. Records the image as a digital file. Different light intensities are converted into 2D array of numbers. It is easy to manipulate digital images using computer programs.

question

DJ-1

answer

One of the genes which can cause Parkinson's disease if mutated.

question

DNA footprinting

answer

A strategy used to learn which sites a transcription factor interacts with. Chromatin is isolated and treated with DNase I. Regions not protected by transcription factors are digested, and the fragments are identified.

question

DNA microarray

answer

DNA chip
A technique that allows simultaneous profiling of activity of all genes in an organism or cell type.

question

Dolichol phosphate

answer

A membrane-bound lipid carrier on which oligosaccharides are synthesized before they are added to nascent polypeptides in the RER during core glycosylation. Sugars are added to it one at a time, in a specific order.

question

Dopaminergic neuron

answer

Die from apoptosis due to accumulation of damaged mitochondria in Parkinson's disease patients. The production of dopamine requires a lot of energy, so these cells are sensitive to the loss of reliable energy sources.

question

Douglas Prasher, Martin Chalfie, and colleagues

answer

In the early 1990s, cloned the gene encoding GFP, and showed that it could be expressed in other organisms.

question

Duplication

answer

A type of chromosome aberration. A portion of a chromosome is repeated. Can have deleterious effects.

question

Dynamin

answer

A large, soluble G protein that mediates pinching off of clathrin-coated vesicles. Recruited from the cytosol to form a stalk between the growing clathrin-coated bud and the TGN membrane. Polymerizes to form a ring around the stalk. GTP hydrolysis causes it to twist and pinch off the vesicle.

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Dynamin related protein (Drp1)

answer

Analogous to dynamin. A G-protein. Recruited by Fis1, MiD, and Mff during mitochondrial fission. Forms a ring around the outer mitochondrial membrane. Bound to GTP during ring formation. Hydrolysis causes the ring to constrict and scission to occur.

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Early endosome

answer

A class of endosome. Located near the periphery region of the cell. Fuses with endocytic vesicles. Responsible for sorting and recycling extracellular materials via endocytosis. Acidic interior, pH 6.0, causes dissociation of transmembrane receptors from soluble ligands. The receptors and ligands are concentrated into different portions of the early endosome, which separate: recycling and sorting compartments.

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eIF2?

answer

Cytosolic protein required for initiation of protein synthesis; participates in ribosome-mRNA binding. Inhibited by PERK dimers in the PERK pathway, ceasing protein synthesis in the cell.

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Efraim Racker

answer

From Cornell University. Isolated the inner membrane spheres discovered by Humberto Fernandez-Moran. Discovered that they behaved as an enzyme that hydrolyzed ATP.

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Electromagnetic lens

answer

A component of a TEM. Includes a condenser, objective, and projector lens. Alter beams of electrons by adjusting voltage to allow for control of focus and magnification.

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Electron gun

answer

A component of a TEM. Applied voltage generates a fine electon beam from the top to the bottom of the chamber. Higher voltage leads to higher resolution.

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Electron microscope (EM)

answer

Uses electrons rather than photons, which have a wavelength of 0.0045 nm. This lower wavelength produces higher resolution.

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Electron-transfer potential

answer

How reducing agents are ranked, according to their affinity to electrons.

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Electron transport chain

answer

Respiratory chain
High-energy electrons are transferred through a series of specific electron carriers on the inner mitochondrial membrane arranged in increasingly positive redox potential. Electrons lose energy as they transfer and are finally accepted by O₂, which is reduced to water. Five types of membrane-bound electron carriers: flavoproteins, cytochromes, copper atoms, ubiquinone, and iron-sulfur proteins.

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Elizabeth Blackburn and Carol Greider

answer

From the University of California. Discovered telomerase in 1984.

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Emile Zukerkandl and Linus Pauling

answer

In 1965, suggested that clades be compared based on proteins and nucleic acids rather than physiological characteristics, to determine the relationship of species.

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Endocytic pathway

answer

A pathway in the endomembrane system. Operates in the opposite direction as the secretory pathway. Materials move into the cell from the plasma membrane and extracellular space. Materials are incorporated into the cell via endocytosis, then transported to endosomes and/or lysosomes. Materials are either recycled back to the plasma membrane or transported to the lysosome for degradation. Includes endocytosis and phagocytosis.

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Endocytic vesicle

answer

A vesicle that buds off the plasma membrane in receptor-mediated endocytosis. Contains receptor/ligand complexes. Targets to and fuses with the early endosome, mediated by the cytoskeleton, Rabs, and SNARE complexes. Interior pH is around 7.0.

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Endocytosis

answer

A process for internalization of materials. The process by which the cell internalizes cell-surface receptors and bound extracellular ligands. Selective internalization of the plasma membrane. Includes bulk-phase and receptor-mediated endocytosis.

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Endomembrane system

answer

Conserved in eukaryotes. Dynamic, coordinated network of organelles and related compartments, functioning as a coordinated unit. Organelles are structurally and functionally distinct, each with particular proteins, performing unique activities. Provides compartmentalization and functional diversity. Materials are exchanged between organelles via small, membrane-bound transport vesicles. Includes the endoplasmic reticulum, Golgi complex, endosomes, lysosomes, vacuoles, secretory granules, and the plasma membrane. Excludes peroxisomes, mitochondria, and chloroplasts. Has the biosynthetic, secretory, and endocytic pathways.

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Endoplasmic reticulum (ER)

answer

A network of membrane-enclosed tubules and cisternae that penetrate most of the cytoplasm. Probably evolved from an invagination of the plasma membrane. Encloses the luminal space. A dynamic structure undergoing continual turnover and reorganization. The starting point for the secretory and biosynthetic pathways. The site of protein synthesis, protein folding, and processing. Divided into RER and SER, which are continuous and are found in different ratios in different cells. Has twenty subdomains, each with a unique complement of proteins and distinct functions; includes the outer nuclear membrane, MAM, PAM, and ERES. The ideal processing site of nascent proteins. The first compartment in the endomemrbane system.
Processing of nascent proteins in the ER lumen:
1. N-terminal signal sequence is cleaved off
2. Initial stages of glycosylation.
3. Protein folding and assembly. Nascent proteins are folded into proper 3D conformation by molecular chaperones.
4. Quality control. Misfolded or improperly assembled proteins are recognized and degraded.

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Endosome

answer

A dynamic network of tubules and vesicles. Distribution centres on the endocytic pathway. Fluid in endosomes is acidified by the boundary membrane. Includes early and late endosomes.

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Endosymbiont theory

answer

The more dominant theory for the origin of mitochondria. The idea that mitochondria and chloroplasts evolved from smaller prokaryotic cells that took up residence within the cytoplasm of the host cell in a symbiotic relationship.

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Enhancer

answer

A DNA element that is more distant than a promoter. Contains multiple binding sites for sequence-specific transcriptional activators. Have the ability to be upstream or downstream of the start site, or be inverted, without affecting ability of transcription factors to stimulate transcription. Deletion of an enhancer can decrease trasncription by 100 times or more. The DNA loops around to bring the enhancer near the core promoter region.

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Epigenetic

answer

Inheritance that is not encoded by DNA. Can usually be reversed.

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ER-associated degradation pathway (ERAD)

answer

Misfolded proteins in the ER lumen are destroyed. The misfolded protein is translocated out of the ER into the cytosol via retro-translocation. In the cytosol, oligosaccharide chains are removed and the misfolded protein is poly-ubiquinated and destroyed.

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ER exit sites (ERES)

answer

A subdomain of the ER. Regions where transport vesicles bud off from the ER en route to the Golgi complex. Usually next to the cis face of a Golgi complex. Enriched with molecular machinery responsible for formation of membrane-bound transport vesicles destined for the Golgi complex. Resident ER proteins are usually preventing from entering the vesicles. Vesicles which form are (20 - 50 nm in diameter), and have a fuzzy appearance in EM microscopy, due to a layer of COP on the cytosolic surface of the nascent vesicle membrane.

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ER luminal protein

answer

Regions of an ER membrane protein that face the lumen. Located in the lumans of all other endomembrane compartments in which it resides, and on the outside of the cell at the plasma membrane.

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ER-membrane bound ribosome

answer

A main site for protein synthesis in the cell. Fate of the nascent protein is a soluble or membrane protein of the endomembrane system. May remain in the RER, localize to another subdomain, or target other endomembrane compartments via transport vesicles.

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ER semi-autonomous model

answer

A model for peroxisome biogenesis. A mixture of the ER vesiculation model and the growth and division model. Peroxisomes reproduce by fission, and proteins are imported post-translationally. A pre-peroxisome structure forms from the ER, which then matures into the peroxisome. Group I PMPs are post-translationally inserted either directly into the peroxisome subdomain, or first into the general ER and then routed to the peroxisome. All matrix proteins and group II PMPs are sorted post-translationally from the cytosol daugher peroxisomes and pre-existing peroxisomes, and perhaps pre-peroxisomes and the ERPIC. The true model.

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ER vesiculation model

answer

A model for peroxisome biogenesis. Co-translational import of peroxisome proteins, then vesiculation to form a nascent, functional peroxisome. Not the true model.

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Euchromatin

answer

Chromatin that is dispersed, and is in an active state during interphase.

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Eukaryotic

answer

A class of cells. Includes protists, fungi, plants, and animals. Cells are divided into nucleus and cytoplasm, separated by a nuclear envelope with complex pore structures. Complex chromosomes are capable of copmacting into mitotic structures. Complex membranous cytoplasmic organelles. Endomembrane system with bound ribosomes. Specialized cytoplasmic organelles for aerobic respiration and photosynthesis. Complex cytoskeletal system, and associated motor proteins. Complex flagella and cilia. Ability to ingest particulate material by enclosure within plasma membrane vesicles. Cell division with microtubule-containing mitotic spindle that separates chromosomes. Two copies of gene per cell, one from each parent. Presence of three different RNA synthesizing enzymes. Sexual reproduction requiring meiosis and fertilization. Typically larger.

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Excited state

answer

The higher energy state of a molecule. The electron is in an outer orbital.

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Exocytosis

answer

Fusion of a secretory vesicle or granule with the plasma membrane, and discharge of its contents. Occurs continuously in most cells, delivering proteins to the plasma membrane and extracellular space.

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Exportin

answer

A transport receptor. Moves macromolecules out of the nucleus. Recognizes molecules with an NES. Moves importin ? to the cytoplasm after nuclear import. The protein has an NLS, localizing it in the nucleus.

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Extracellular ligand

answer

Soluble endocytic cargo proteins taken into the cell by receptor-mediated endocytosis. Found in the MVB, and are degraded by lysosommal acid hydrolases when it fuses with the lysosome.

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Facultative heterochromatin

answer

A class of heterochromatin. Specifically inactivated during certain stages in an organism's life or in certain types of differentiated cells.

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Fabry's disease

answer

A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in ?-galactosidase A, causing accumlation of trihexosylceramide. Causes skin rashes, kidney failure, and pain in lower extremities.

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Farber's lipogranulomatosis

answer

A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in ceramidase, causing accumulation of ceramide. Causes painful and progressively deformed joints, skin nodules, and death within a few years.

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FG proteins

answer

Part of the NPC. Filament-like proteins with unusual amino acid composition, containing large numbers of phenylalanine-glycine (FG) repeats. Posssess unique, highly disordered secondary structure, making them extended and flexible. Extended into the central channel, forming a hydrophobic "mesh", limiting diffusion of macromolecules large than 40 kDa in diameter.

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Fission 1 (Fis1)

answer

A protein that binds to the outer mitochondrial memrbane. Recruited to lipid-microdomains that form at the future site of mitochondrial fission. Recruits Drp1 in conjunction with MiD and Mff.

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Fixative

answer

A chemical solution which kills cells in the preparation of sections. A good fixative rapidly penetrates the cell membrane, and immobilizes all the macromolecular materials so that the structure of the cell is maintained as close as possible to the living state. Includes formaldehyde, alcohol, and acetic acid.

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Flavoproteins

answer

A type of electron carrier in the electron transport chain. A polypeptide bound tightly to one of two related groups derived from riboflavin, either FAD or FMN. Can accept and donate two protons and two electrons. Includes NADH dehydrogenase (in the electron transport chain), and succinate dehydrogenase (in the TCA cycle).

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Flippase

answer

Flips the core oligosaccharide from the cytosolic to the luminal side during core glycosylation halfway through adding mannoses.

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Fluorescence

answer

Certain atoms can absorb a photon of a certain wavelength. The atom's electron becomes excited, and moves to a higher energy state. Excited electrons are highly unstable, lose energy, and return to ground state, by emitting a photon with lower energy. The emitting electron has lower energy because some of its energy is initially lost as heat.

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Fluorescent protins

answer

Used for subcellular localization of proteins. ALlow for live-cell microscopic imaging technologies. Includes GFP and its derivatives.

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Fluorophore

answer

Molecules that can re-emit light following excitation, producing fluorescence.

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Francois Jacob and Jacques Monod

answer

From the Pasteur Institute in Paris. Described the mechanism of an operon in 1961.

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Frederick Steward and colleagues

answer

From Cornell University. Demonstrated that a root cell can be induced to grow into a fully developed plant.

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Free ribosomes

answer

A main site for protein synthesis in the cell. In the cytosol. Fate of the nascent protein is to remain in the cytosol, or it is targeted to proper intracellular destinations: mitochondria, chloroplast, nucleus. The translation of all mRNAs begins on free ribosomes.

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Fucosidase

answer

A lysosomal enzyme. A polysaccharide and olgiosaccharide that acts on fucosyloligosaccharides.

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G_M1 gangliosidosis

answer

A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in G_M1 ?-galactosidase, causing accumulation of ganglioside G_M1. Causes mental retardation, liver enlargement, skeletal involvement, and death by age 2.

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Gaucher's disease

answer

A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in glucocerebrosidase, causing accumulation of glucocerebroside. Causes liver and spleen enlargement, erosion of logn bones, and mental retardation in the infantile form only.

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Gene regulator protein

answer

A protein that recognizes a specifc sequence of base pairs within the DNA, and binds to the sequence with high affinity. Plays a prominent role in determining whether or not a segment of the genome is transcribed. Includes repressors.

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Genome-wide location analysis

answer

A strategy used to learn which sites a transcription factor interacts with. Cells are cultured, and treated with an agent that kills cells, such as formaldehyde. Transcription factors are cross-linked to DNA sites where they bind in a living cell. Chromatin is isolated, sheared into small fragments, and incubated with antibody that binds to the transcription factor. Chromatin fragments bound to the antibody precipitate, and segments of the DNA can be purified. The purified DNA can be used in a microarray, or sequenced.

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George Palade, Philip Siekevitz, and colleagues

answer

From Rockefeller University. In the 1960s, studied properties of rough microsomal fractions, with membrane vesicles derived from the RER. Isolated ribosomes were capable of synthesizing proteins in vitro under correct conditions.

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Glucocereobrosidase

answer

A lysosomal enzyme. A sphingolipid hydrolyzing enzyme that acts on glucosylceramide.

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Glucose

answer

Three are found in a chain in the core oligosaccharide.

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Glucosidase

answer

Removes NAG groups in the medial cisternae.

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Glucosidase I

answer

An ER luminal soluble enzyme. Removes the first two terminal glucoses during core modification.

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Glucosidase II

answer

Removes the last glucose unit from the core oligosaccharide, releasing it from calnexin; the final step of protein folding and modification; the protein then functions in the ER, or is transported to other components in the endomembrane system.

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Glycoprotein

answer

Proteins with one or more olgiosaccharides attached to specific amino acids within the nascent polypeptide. Most proteins synthesized in the ER are glycoproteins.

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Glycosylation

answer

Addition of oligosaccharide chains to proteins, forming glycoproteins. Occurs in the ER. Includes N-linked glycosylation. Most glycoproteins, synthesized and N-linked glycosylation in the RER, moving through the Golgi complex undergo additional glycosylation reactions. Glycosylation depends on the final destination of the protein. Each step occurs in a different compartment of the Golgi complex.
1. Mannose trident is trimmed to a five-mannose fork
2. Two NAG residues are added. Targets the glycoprotein to the lysosome.
3. Two galactoses are added.
4. Two sialic acids are added.
5. Two fructoses are added.

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Glycosyltransferase

answer

Membrane-bound enzymes that add sugars to oligosaccharide chains. Transfer specific monosaccharides. Synthesize the core olgiosaccharide during core glycosylation.

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Glyoxysome

answer

Peroxisomes present in plant seedlings. Convert fatty acids into carbohdyrates.

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Golgi cisternae

answer

Have a central domain and an irregular domain where coated vesicles bud. A series of three or more large, flattened cisternae. Make up the majority of the Golgi complex. Divided into three main sections: cis, medial, and trans. Golgi metabolism occurs: synthesis of complex polysaccharides used in modification of proteins and lipids. Have unique glycosyltransferase enzymes to sequentially modify the glycoprotein's core oligosaccharide in specific ways.

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Golgi complex

answer

Flattened, disk-like membranous cisternae with dilated rims. Associates with vesicles and tubules. Cisternae are 0.5 - 1.0 ?m thick, less than eight in number, and arranged in stacks. There may be a few, or several thousand Golgi stacks in one cell. Mammal cells typically have one large Golgi complex near the centre of the cell. Plant and yeast cells often have numerous Golgi complexes throughout the cell. Vesicles bud from peripheral tubular domain of each cisterna. The Golgi complex is supported by a peripheral membrane scaffold composed of proteins, which may consits of motor proteins that move vesicles and tubules. Proteins are modified in different ways sequentially as they move through the cisternae. Divided into compartments arranged along its cis (closest to the ER) and trans (closest to the plasma membrane): CGN, cis cisternae, medial cisternae, trans cisternae, and TGN. Each cisternae has specific polarity and orientation, and is biochemically unique. Modification of proteins and lipids: glycosylation and proteolytic modification. Trnasport and sorting of proteins. Numerous models for traffickign through the Golgi complex have been proposed, including the vesicular transport model and cisternal progression model.

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Golgi-localizing gamma-adaptin ear domain homology ARF-binding proteins (GGA)

answer

Analogous to Sec22. A family of adaptor proteins that escort lysosomal enzymes from the TGN. Have several domains, each capable of grasping a different protein invovled in vesicle formation. Binds to clathrin molecules, and to a sorting signal in M6P receptors on the cytosolic surface, serving as a linker. Recruitment of GGA from the cytosol is mediated by Arf1.

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Golgi matrix

answer

Mediates organization of the Golgi complex stacks. Consists of various Golgi peripheral and integral membrane proteins, inlcuding GRASPs. Cytosolic domains interact to form a scaffold that links the CGN, cisternae, and TGN together. Links the Golgi complex to the cytoskeleton. Positioning and movement of the Golgi complex is controlled by its interaction with the cytoskeleton.

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Golgi microtubule associated protein (GMAP-210)

answer

Facilitates ER to cis-Golgi communication via a direct interaction with microtubules between two organelles. Mutation leads to achondrogenesis.

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Golgi reassembly and stacking proteins (GRASPs)

answer

Serve as tethering proteins, linking different Golgi sub-compartments together. Depletion of GRASP55/65 results in disassembly of the Golgi complex.

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Golgins

answer

Long filamentous proteins that tether various parts of the Golgi to the cytoskeleton, and other subcellular structures. Dimerize and are regulated by G proteins that anchor them to the Golgi membrane. Each component of the Golgi has a unique complement of golgins.

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Grana thylakoid

answer

Thylakoid membranes arranged in flattened membranous disks.

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GRASP 55

answer

A GRASP. Found near the trans face of the Golgi complex.

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GRASP 65

answer

A GRASP. Found near the cis face of the Golgi complex.

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Green fluorescent protein (GFP)

answer

A fluorescent protein discovered in jellyfish, which emits green light. DNA encoding GFP is fused to DNA encoding a protein, and the chimeric protein will fluoresce green, allowing for easy observation. In most cases the presence of GFP has little or no effect on the movement or function of the protein. Genetically modified colour variants are available: BFP, YFP, tangerine, cherry, and others.

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Ground state

answer

The lower energy state of a molecule. The electron is in an inner orbital.

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Growth and division model

answer

A model for peroxisome biogenesis. Peroxisome reproduce by fission, and proteins are imported post-translationally, and lipids are imported by membrane lipid transfer. Not the true model.

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GT monitoring enzyme

answer

An ER luminal soluble glucotransferase. Recognizes misfolded proteins as they are released from calnexin. Recognizes the hydrophobic residues that are usually masked by attached sugars in a correctly folded protein. Adds a single glucose residue to the terminal end of the trimmed core oligosaccharide, leading it to bind to calnexin a second time, repeating the folding process. Continues until the protein is properly folded.

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GTP-binding protein (G protein)

answer

Play key roles in regulation of many cellular processes. Has weak intrinsit GTPase activity. GTP binding and hydrolysis cause conformational changes. Act as "molecular switches". Present in two alternate forms: one bound to GTP (active), and one bound to GDP (inactive). Includes SRP and SRP receptor.

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GTPase activating protein (GAP)

answer

Catalyzes hydrolysis of G proteins, removign P_i, converting active GTP-bound G protein into inactive GDP-bound G protein. Incldues Ran-GAP1.

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Guanine exchange factor (GEF)

answer

Replaces GDP with GTP in an inactive GDP-bound G protein, to produce active GTP-bound G proteins. Includes RCC1.

question

Gunter Blobel, David Sabatini, and Bernhard Dobberstein

answer

From Rockefeller University. Proposed and demonstrated that a signal sequence directs emerging polypeptides to the ER membrane, and that a polypeptide moves to the luminal space through a protein-linked aqueous channel.

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H.G. Hers

answer

From the University of Louvain in Belgium. Suggested that the absence of ?-glycosidase enzyme causes undigested glycogen to accumulate in lysosomes of Pompe disease patients.

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H. sapiens

answer

A model organism. Learning about the "normal" roles of genes by studying diseases.

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H1

answer

A histone with 215 residues. 23.0 kDa. 1% argninine, 29% lysine.

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H2A

answer

A histone with 129 residues. 13.0 kDa. 9% arginine, 11% lysine.

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H2B

answer

A histone with 125 residues. 13.8 kDa. 6% arginine, 16% lysine.

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H3

answer

A histone with 135 residues. 15.3 kDa. 13% arginine, 10% lysine.

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H4

answer

A histone with 102 residues. 11.3 kDa. 14% arginine, 11% lysine.

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Hans Krebs

answer

A British biochemist who worked out the TCA cycle pathway in the 1930s. His paper was originally rejected from Nature.

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Heat shock protein 60 kDa (Hsp60)

answer

A soluble co-chaperone in the stroma of the chloroplast. Ensures the cleaved, mature protein is properly folded.

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Heat shock protein 70 kDa (Hsp70)

answer

A cytosolic chaperone. Controls the overall conformation of the matrix-destined protein. Maintains the nascent protein in a partially unfolded, import-competent state as proteins are inserted into TOM or TOC.

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Heat shock protein 93 kDa (Hsp93)

answer

Analogous to mtHsp70. Serves as the motor ratchet as proteins move through TIC. Drives translocation across the chloroplast envelope. Undergoes an ATP-dependent conformation change that pulls the protein into the stroma and prevents back-sliding.

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Helix-loop-helix motif (HLH)

answer

A common structural motif in transcription factors. There are two ?-helices separated by an intervening loop, often preceded by a stretch of highly basic amino acids, which contact the DNA, and determine the sequence specificity of the transcription factor. Transcription factors are always dimers.

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Heparan N-sulfatase

answer

A lysosomal enzyme. A GAG-hydrolyzing enzyme that acts on heparan sulfate.

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Heterochromatin

answer

Chromatin that remains compacted during interface. Little transcriptional activity. Includes constitutive and facultative heterochromatin. Pushed to near the nuclear envelope, but not around nuclear pores.

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Heterotroph

answer

Organisms that depend on an external source of organic compounds.

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Histone

answer

A group of small proteins that possess high arginine and lysine content. Highly conserved through evolution. There are five: H1, H2A, H2B, H3, and H4.

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Histone acetyltransferase (HAT)

answer

Enzymes that add acetyl groups to lysine residues on core histones.

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Histone code

answer

A hypothesis which postulates that the state and activity of a region of chromatin depends on specific modifications, or combinations of modifications to histone tails.

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Histone deacetylase (HDAC)

answer

Enzymes which remove acetyl groups from histones. Associated with transcriptional repression. Subunits of larger complexes called corepressors.

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Homogenize

answer

To break up a cell. The cytoplasmic membranes become fragmented and fractured, forming vesicles less than 100 nm in diameter, each from different organelles.

question

Hugo Kortschak

answer

In 1965, reported that when sugarcane (a C₄ plant) was supplemented with radioactively labelled CO₂, the radioactive label appeared in compounds containing four-carbon skeletons, rather than three-carbon PGA molecuels in other types of plants.

question

Humberto Fernandez-Moran

answer

From the Massachusetts General Hospital. In the early 1960s, isolated mitochondria and developed negative staining techniques. Discovered a layer of spheres attached to the inner side of the inner membrane, projecting from the membrane on stalks.

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Hutchinson-Gilford progeria syndrome

answer

A disease caused by a point mutation in lamin A (LMNA), resulting in destabilization of the nuclear lamina. Usually a de novo mutation; a recessive condition. Causes aberrant changes in nuclear envelope morphology and function. Nuclear enveloep has irregular shape, and has blebbing. Phenotype resembles premature "aging" in children: hair loss, wrinkles, artery damage, and death by adolescence. Mice with the same mutation display similar phenotype: they are small, have altered bone structure, and do not live long. These mice facilitate studies in the precise molecular mechanism of the disease development and progression.

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Ian Wilmot

answer

A member of a group in Scotland who were able to clone a sheep by transplanting nuclei derived from a cultured mammary gland cell, into an unfertilized egg with its chromosomes removed.

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Iduronate sulfatase

answer

A lysosomal enzyme. A GAG-hydrolyzing enzyme that acts on dermatan sulfate.

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Importin

answer

A transport receptor. Moves macromolecuels into the nucuels. A heterodimer consisting of importin ? and ?. Importin ? recognizes the NLS sequence on the cargo protein. Importin ? binds to cytoplasmic filaments.

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Imprinted

answer

Mammlian genes which have different methylation patterns, depending on if the chromosome was donated by the mother or father. There are at least 80 imprinted genes in mice.

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Inducer

answer

The metabolic substance which induces transcription in an induble operon.

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Inducible operon

answer

The presence of a key metbaolic substance induces transcription of the operon. Includes the lac operon.

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Inner chloroplast membrane

answer

A sub-compartment of the chloroplast. Highly permeable. Contains transporters.

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Inner mitochondrial membrane

answer

A sub-compartment of the mitochondria. Adjacent to the outer mitochondrial membrane, and has cristae that extend into the organelle's interior. Impermeable, maintaining the low pH of the intermembrane space. The site of ATP synthesis.

question

Insulator

answer

Specialized boundary sequences that prevent enhancers from binding to inappropriate promoters.

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Integral membrane protein (IMP)

answer

Proteins embedded in membrane. Most are synthesized on membrane-bound ribosomes in the RER. The N-terminal signal is recognized by the SRP, leading to co-translational inertion into ER. Mechanistic differences in the polypeptide result in the mature protein being inserted laterally into the ER membrane during translation. Different regions of the protein face the cytosol and/or the ER lumen.

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Interchromosomal channels

answer

Nucleoplasm subdomains that serve as barriers between other subdomains, to prevent unwanted DNA-DNA and/or DNA-protein interactions.

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Intraluminal vesicles

answer

Vesicles found in the MVB. Degraded when it fuses with the lysosome.

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Inversion

answer

A type of chromosomal aberration. A chromosome breaks in two places, and the segment between the breaks becomes resealed into the chromsome in reverse orientation. More than 1% of humans carry inversions that can be detected in a karyotype. The chromosome cannot pair properly during meiosis; a loop forms.

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Iron-sulfur protein

answer

A type of electron carrier in the electron transport chain. Iron-containing proteins. Iron atoms are linked to inorganic sulfide ions in the iron-sulfur centre. There are two or four atoms of iron and sulfur, linked to the protein at cysteine residues. Accepts and donates a single electron.

question

James Jamieson and George Palade

answer

From Rockefeller University. Used autoradiography to study the synthesis proteins in pancreatic cells.

question

James Rothman and colleagues

answer

From Stanford University. In 1983, demonstrated that transport vesicles are capable of budding from one Golgi cisternae and fusing with another in vitro.

question

Jerome Lejeune

answer

A French geneticist. In 1963, discovered the chromosomal basis of Down syndrome and Cri-du-chat syndrome.

question

John Gurdon

answer

From Oxford University. Demonstrated that a nucleus could be removed from the intestinal cell of a Xenopus tadpole, and transplanted into an egg with its nucleus destroyed, and the egg will develop into a normal frog.

question

John Walker and colleagues

answer

From the Medical Research Council in England. Published a detailed atomic model of the F₁ of the ATP synthase in 1994. Findings support the hypothesis of Paul Boyer.

question

Karyotype

answer

Individual chromosomes are cut out of a photograph, matched into homologous pairs, and ordered according to decreasing size. Routinely prepared from cultures of blood cells, and used to screen individuals for chromosome abnormalities.

question

Krabbe's disease

answer

A lysosomal storage disorder resultin in accumulation of sphingolipids. Deficiency in galactocerebrosidase, causing accumulation of galactocerebroside. Causes loss of myelin, mental retardation, and death by age 2.

question

Late endosome

answer

A class of endosome. Located near the nucleus. Acidic interior, pH 5.5. Develop from the sorting compartment of the early endosome. Contains endocytic cargo from receptor-mediated endocytosis, and biosynthetic cargo from the TGN. The acidity causes dissociation of ligands from receptors. MPRs are then sent back to the TGN. Endocytic proteins and biosynthetic proteins are concentrated into a portion that detaches and becomes the MVB.

question

Lead

answer

TEM samples are post-stained with lead. It binds to most celular macromolecules, yielding greater electron density, and increased contrast in the image.

question

Leonard Hayflick and Paul Moorhead

answer

From the Wistar Institute in Philadelphia. In 1961 discovered that normal cells stop dividing after 50 - 80 replications, and enter replicative senescence. There is a decrease in length of telomeres.

question

Leucine zipper motif

answer

A common structural motif in transcription factors. Leucines occur every seventh amino acid in an ?-helix, so that they are all facing the same direction. Two leucine zippers can attach together to form a coiled coil. Transcription factors are always dimers.

question

Light-dependent reactions

answer

The first stage of photosynthesis. Energy from sunlight is absorbed and stored as ATP and NADPH.

question

Light-harvesting complex II (LCHII)

answer

A separate pigment-protein complex that contains most of the antenna pigments from PSII. May associate with PSI. Proteins bind to chlorophylls and carotenoids.

question

Light-independent reactions

answer

Dark reactions
The second stage of photosynthesis. Energy stored in ATP and NADPH are used to produce carbohydrates from carbon dioxide.

question

Limit of resolution

answer

Calculated by substitutitng the minimum possible wavelength of illumination, and the greatest possible numerical aperture into the equation d = 0.61?/n sin ?. The limit of resolution of a conventional microscope is 0.2 ?m. For the human eye, 0.1 mm. For a CLSM, 20 nm. For an electron microscope, 0.02 nm.

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Lipid-transfer protein

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Binds to phospholipids, and carries them through the cytosol from one membrane compartment to another, facilitating movement of specific lipids from the ER to other organelles. Occurs where the ER is in close proximity to these organelles.

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Lipfuscin pigment granule

answer

Residual bodies of lysosomes from autophagy. Accumulate in the cell, and expelled when the cell divides. A factor in aging. Neurons don't divide, so they build up and can impinge on neuron function.

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Luminal space

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Cisternal space
The aqueous space within the ER. Different from the cytosolic space.

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Lynn Margulis

answer

From Boston University. Proposed the endosymbiont theory.

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Lysosomal storage disorders

answer

Diseases characterized by deficiency of a singl lysosomal enzyme, and corresponding accumulation of un-degraded substrate. There are over 40 lysosomal storage disorders in humans, occurring in approximately 1 in every 8,000 infants.

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Lysosome

answer

A "digestive" organelle. Degrades all types of macromolecules including lipids, carbohydrates, nucleic acids, and proteins. Plays a key role in autophagy, degrading whole organelles. Contains about 60 different soluble acid hydrolase enzymes, active only at the low pH of 4.6. The low pH in the lumen is produced by ATP proton pumps. Resident proteins, including enzymes, are delivreed through the biosynthetic pathway, and are protected from degradation by carbohydrate groups. Products of degradation are transported to the cytosol and reused by various biosynthetic pathways. Lysosomes are highly dynamic, and can be a wide range of sizes and shapes, depending on the cell. When it fuses with an MVB, lysosomal proteins are activated due to the acidic environment, and intraluminal vesicles are degraded. Can grow, shrink, and divide.

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M. musculus

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A model organism. A mouse. 98% of the genome is similar to humans.

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M6P receptor (MPR)

answer

An integral transmembrane protein. The luminal-facing domain binds to M6P groups on soluble lysosomal proteins in the TGN lumen. Mediates the subsequent concentration of lysosomal proteins into clathrin-coated vesicles. The cytosolic-facing domain binds to GGA adaptor coat proteins with multiple binding domains.

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Magnification

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Microscopy generates a magnified, high quality view of a specimen.

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Mannose

answer

Nine residues are found in a trident formation in the core oligosaccharide. The mannose trident acts as a timer. A slow-acting enzyme degrades it slowly. When it is fully degraded, instead of trying to refold it, the protein is degraded in the ERAD pathway.

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Mannose-6-phosphate (M6P)

answer

A lysosomal targeting signal found on proteins with a signal patch. Phosphorylation of two mannose residues in the protein's core oligosaccharide in the cis Golgi cisternae. Soluble M6P-bearing proteins are recognized by MPR. Cargo proteins with M6P groups are packaged into lysosomal-destined transport vesicles. Cargo protein without an an M6P are packaged into other TGN transport vesicles or granules, destined for the plasma membrane.

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Mannosidase II

answer

Localized in the medial cisternae.

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Marvin Minsky

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From the Massachusetts Institute of Technology. In the late 1950s, invented the confocal microscope.

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Mary Lyon

answer

A British geneticist. In 1961, proposed that inactivation of the X chromosome in female mammals occurs early in embryonic development, that the inactivation is a random process, but all descendants of early cells have the same chromosome inactivated, and that the X chromosome is reactivated in female germ cells prior to meiosis.

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Masasuke Yoshida and colleagues

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From the Tokyo Institute of Technology and Keio University in Japan. In 1997, demonstrated the rotation of the ? subunit of ATP synthase in relation to the ?? subunits. Prepared genetically engineered versions of the F₁ heads, which were fixed to a cover slide. A fluorescently labelled actin filament was bound to the ? subunit and could be seen to be rotating.

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Massively parallel sequencing

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RNA-Seq
A technique that allows simultaneous profiling of activity of all genes in an organism or cell type.

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Matrix

answer

A sub-compartment of the mitochondria. The aqueous environment contained within the inner mitochondrial membrane. Gel-like consistency. High concentration of water-soluble proteins. Initiates cell suicide. The site of TCA cycle and ATP formation from oxidation phosphorylation. Contains the mitochondrial genome and ribosomes used for translation of the mitochondrial genome-encoded proteins. The best understood mitochondrial targeting sub-compartment. Most matrix proteins have a presequence.

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Medial cisternae

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The compartment in the Golgi complex between the cis and trans cisternae. A large, flattened cisternae. Mannosidase II is localized here. NAG group is removed by glycosidase. The lysosomal enzyme now contains a mannose-6-phosphate group.

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Melvin Calvin, Andrew Benson, and James Bassham

answer

From the University of California, Berkeley. After WWII, began a study on the enzymatic reactions by which carbon dioxide is assimilated into organic molecules. Used carbon isotopes and two-dimensional paper chromatography.

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Membrane

answer

All membranes arise from pre-existing membranes; never form de novo. Most membrane proteins and lipids are synthesized in the ER, except for glycolipids synthesized in the Golgi, and unique chloroplasts and mitochondrial proteins and lipids. Nascent ER membrane proteins and lipids can traffic to other membranes in the endomembrane system by diffusion in the bilayer or via transport vesicles. Each organelle possesses a unique complement of membrane proteins and lipids. PRoteins adn lipids are distributed and/or oriented in the bilayer asymmetrically; this asymmetry is established in the ER and maintained throughout the endomembrane system.

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Membrane asymmetry

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Maintained by lipid composition, and the modification and orientation of IMPs. The luminal domain of IMPs remains in the lumen of the endomembrane compartments, and is glycosylated; it forms the extracellular domain on the extracellular face of the plasma membrane. The cytoplasmic domain of IMPs is always facing the cytoplasm.

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Membrane phospholipids

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Distributed unequally between the cytosolic and luminal leaflets of the bilayer.

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Mfn 1/2

answer

GTPase mitofusins
G-proteins. Integral outer mitochondrial membrane proteins. Both possess a cytosolic-facing GTPase domain and a long, coil protein-protein interaction. Mfn1/2 binding prevents self-binding during mitochondrial fusion. Binding forms the organelle tethering complex.

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Michael Brown and Joseph Goldstein

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From the University of Texas Medical School in Dallas. In 1973, begun research in familial hyperchloesterolemia (FH) by examining skin fibroplasts. Found that LDL caused decreased activity in a crucial enzyme, but this requires a specific receptor which is defective in FH patients.

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Micrometer (?m)

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1 x 10^-6 m
A unit of measurement commly used to describe structures in cells.

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Microsome

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A heterogeneous collection of similar sized vesicles, derived from the endomembrane system during subcellular fractionation. Can be fractioned into smooth and rough membrane sections using gradient techniques.

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Misfolded proteins

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Proteins might not fold properly due to mutation. Normal proteins might not fold due to random chance. Usually have exposed hydropobic domains, which make them toxic to the cell. UGGT adds glucose to them in the ER, redirecting them to calnexin.

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Mitochondria

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Organelles of eukaryotes that use oxygen for energy extraction. There are two theories for its origin: the less dominant theory that it evolved from the ER, and the more dominant theory, the endosymbiont theorry. Generate metabolic energy in the form of ATP. Energy is derived from carbohydrate and lipid catabolism via oxidative phosphorylation and the TCA cycle. Carry their own DNA. Semi-autonomous; organelle replication is controlled by both the cell and the organelle. Arise from only pre-existing mitochondria. Traditionally considered to be individual, small, and bean-shaped, however recent imaging shows that they may form a mitochondrial network. Have a double membrane, with the outer and inner membranes not continuous, with different lipid composition, serving different functions.

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Mitochondria and associated membrane (MAM)

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A subdomain of the ER. Regions of the ER that make direct contact with mitochondria. Involved in membrane lipid exchange.

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Mitochondrial dynamics protein (MiD)

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Recruits Drp1 in conjunction with Fis1 and Mff durign mitochondrial fission.

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Mitochondrial fission

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Splitting apart of a mitochondrion. Occurs at the end of G1, and during cell death. Duplication of mitochondria in preparation for cellular division. Rate controls the number, size, and interconnections of the mitochondrial network. Occurs in response to environmental stimuli, developmental status, and/or energy requirements of the cell. Controlled by distinct protein machineries.
1. Assembly of the Drp1 ring. Fis1, MiD, and Mff recruit Drp1.
2. Mitochondrial scission. Drp1 is hydrolyzed, causing the ring to constrict and scission to occur.

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Mitochondrial fission factor (Mff)

answer

Recruits Drp1 in conjunction with Fis1 and MiD during mitochondrial fission.

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Mitochondrial fusion

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Joining together of two mitochondria. Rate controls the number, size, and interconnections of the mitochondrial network. Controlled by distinct protein machineries. Occurs in response to stress (increased need for coordinated functioning). Requires the coordinated fusion of both mitochondrial membranes. The outer membrane fuses first, then the inner membrane. A multi-step process involving mitochondrial membrane protein, GTP, and remodelling of mitochondrial membrane lipids.
1. Outer tethering. Mfn1 and Mfn2 on adjacent mitochondria link in a GTP-dependent manner to form an organelle tethering complex.
2. Outer membrane fusion. The outer membrane forms lipid microdomains at the sites of organelle tethering complexes.
3. Inner membrane fusion. Mediated by OPA1.

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Mitochondrial genome

answer

Codes for 20% - 30% of the factors involved in biogenesis and function of the mitochondria. Circular DNA found in the matrix. Varies in size, copy number, and gene number. In humans it encodes 13 proteins, 2 rRNAs, and 22 tRNAs.

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Mitochondrial heat shock protein 70 kDa (mtHsp70)

answer

A matrix-localized mitochondrial chaperone. Acts as a molecular motor or ratchet. Undergoes an ATP-dependent conformational change that "pulls" the protein into the matrix, preventing it from back-sliding into the cytosol. Involved in the proper folding of the cleaved, mature protein in the matrix.

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Mitochondrial intermembrane space

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A sub-compartment of the mitochondria. The aqueous environment contained between the inner and outer mitochondrial membranes.

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Mitochondrial network

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A form that mitochondria may take. A highly branched, interconnected series of tubules. The traditional bean shape of the mitochondria may be an artifact due to sectioning through a single tubule of the network. Allows for cell-wide co-ordination of organelle functioning and biogenesis. A highly dynamic structure; tubules are mobile and can fuse and/or split apart in response to environmental stimuli, developmental status, and/or energy requirements of the cell. Defects correlate with the progression of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's.

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Mitochondrial processing peptide (MPP)

answer

Cleaves the presequence when the matrix protein is imported through TIM23.

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Mitochondrial targeting

answer

The majority of the mitochondrial proteins, about 1000, are nuclear encoded, synthesized on free ribosomes in the cytosol, and targeted post-translationally to the mitochondria. An efficient but complex process. All mitochondrial proteins possess unique targeting sequences that mediate targeting to the mitochondrion surface, and to a specific mitochondrial sub-compartment. Different pathways rely on different targeting signals and import machinery. Mitochondrial sub-compartments are: outer membrane, intermembrane space, inner membrane, and matrix. Targeting of the matrix:
1. Newly synthesized proteins are recognized by Hsp70. Nascent proteins are enriched in the vicinity of the mitochondrial surface due to diffusion and mRNA localization.
2. At the surface of the mitochondrion, the protein presequence is recognized and imported by TOM.
3. The presequnce binds to mtHsp70 in the matrix, preventing it from back-sliding into the cytosol. The presequence is then cleaved by MPP.

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Mitophagy

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The autophagy of a mitochondrion. Initiated by the poly-ubiquination of outer mitochondrial memrbane proteins, caused by Parkin.

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Model organism

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A "representative" organism focused on by cell and molecular scientists. Comprehensive bodies of work studying these organisms will provide a framework to understand basic processes shared by most organisms.

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Molecular machinery

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Receptors required to traffic and dock vesicles with the proper acceptor membrane. Include Rabs and SNAREs.

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Mono-Ub

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A single ubiquitin. Serves as a signal for membrane protein import into endosomal vesicles.

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Motor porteins

answer

Mediate movement of all vesicles through the cytosol.

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mRNA

answer

Diffuse through the nucleus, concentrated at the gene locus during transcription, and in mobile mRNPs.

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Multivesicular body (MVB)

answer

A fragment of the late endosome containing soluble extracellular ligands from the early endosome, and soluble acidic hydrolase enzymes from the TGN. Has intraluminal vesicles formed by invagination of the MVB membrane. Responsible for getting lipids into the lysosomes. Intraluminal vesicles contain materials derived from the plasma membrane, destined for destruction. Fuses with the lysosome, releasing luminal contents.

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Muscle cells

answer

Have heightened protein synthesis, so they may fuse together to form multinucleate cells.

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N-acetylglucosamine (NAG)

answer

Two are found in a chain in the core oligosaccharide.

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N-linked glycosylation

answer

The most common type of glycosylation. Addition of oligosaccharides to the terminal amino group of an asparagine (N). Consists of two stages: core glycosylation and core modification. Begins in the ER. Completed in the Golgi complex.

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Nanometer (nm)

answer

1 x 10^-9 m
A unit of measurement commonly used to describe structures in cells.

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Negative staining

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A heavy-metal deposit is collected everywhere on a specimen grid, except where particles are present. Specimens stand out by their relative brightness on a viewing screen.

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Neimann-Pick disease

answer

A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in sphingomyelinase, causing accumulation of sphingomyelin. Causes liver and spleen enlargement and mental retardation.

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Nitrogen fixation

answer

Conversion of nitrogen gas (N₂) into reduced forms of nitrogen including ammonia (NH₃). Many cyanobacteria are capable of nitrogen fixation.

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Noncyclic photophosphorylation

answer

Formation of ATP during the process of oxygenic photosynthesis. Electrons move in a linear path from H₂O to NADP⁺.

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Nuclear basket

answer

Part of the NPC. A basket-like structure on the nuclear side of the NPC. Involved in nuclear receptor-cargo protein import and export.

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Nuclear envelope

answer

The boundary between nucleus and cytoplasm. Two phospholipid membranes in parallel, separated by a 10 - 50 nm thick space, which is continuous with the ER. The outer membrane binds ribosomes. The inner membrane contains unique protein composition, including IMPs which connect to the nuclear lamina. Both membranes join at the nuclear pores. Establishes composition of the nucleus, regulating gene expression.

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Nuclear export

answer

Mostly proteins and RNA molecules, may be ribonucleoproteins. Must contain and NES, to whcih exportins bind. Ran-GTP is required to assemble the export complex, which is transported into the cytoplasm. Ran-GTP hydrolysis into Ran-GDP releases the cargo.

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Nuclear export signal (NES)

answer

A sequence of amino acids that is recognized by exportin, and mediates targeting of protein from the nucleus to the cytosol. There are several NES sequences, and all are necessary and sufficient for nuclear export. The most common NES is a leucine-based motif: LxxLxxL.

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Nuclear import

answer

Protein import into the nucleus. Few diseases are associated with faulty nuclear import, because it is critical for cell function. Proteins must contain an NLS.
1. Nascent NLS-containing cargo is recognized and bound to importin ? subunit, bound to importin ?.
2. The complex moves through the cytosol towards the nucleus, via the cytoskeleton. Importin ? binds to a cytoplasmic filament at the NPC.
3. The complex is translocated through the NPC aqueous central channel. The cargo-receptor complex interacts with FG domains, causing them to "dissolve", and allow translocation through the channel.
4. The complex associates with the nuclear basket, and importin ? binds to Ran-GTP, causing release from the NPC, and dissasembly of the complex, releasing importin ? and the cargo protein. The NLS sequence is not cleaved from the cargo protein.
5. Ran-GTP bound to importin ? moves into the cytosol, due to the Ran-GTP gradient. Importin ? binds to exportin, which binds to Ran-GTP, which moves into the cytosol due to the same gradient. In the cytosol, Ran-GTP is hydrolyzed into Ran-GDP by Ran-GAP1, releasing importin ? and ?. Ran-GDP moves into the nucleus due to the gradient. Exportin moves back in to the nucleus by nuclear import.

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Nuclear lamina

answer

A thin filamentous meshwork of integral membrane proteins that is on the inner surface of the nuclear envelope of animal cells. Composed of ABC nuclear lamins. Approximately 10 nm in diameter. Provides mechanical support for the nuclear envelope. Acts as a scaffold for chromatin and nuclear matrix attachment.

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Nuclear localization signal (NLS)

answer

A stretch of amino acids near the C-terminus that enables a protein to pass through nuclear pores, entering the nucleus. Recognized by importin ? in nuclear import. Necessary and sufficient; if the sequence is mutated, the protein fails to target the nucleus. There are sevreal NLSs, including the classic and bitartite NLS. Viruses may hijack an NLS to enter the nucleus.

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Nuclear matrix

answer

An insoluble fibrous protein network "mesh" distributed throughout the nucleoplasm. Analogous to the cytoskeletal network in the cytosol. Functions in strucutre; maintains overall shape of the nucleus. Serves as a scaffold, responsibel for organizing nuclear subdomains and anchoring protein factors. Very little is known about its composition and assembly/disassmbly. So far it has never been purified, so its existence is debated.

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Nuclear pore

answer

The doorway into the nucleus. Inner and outer membranes are fused. Approximately 120 nm in diameter. The NPC fills the nuclear pore. The nucleus depends on import of proteins for structure, DNA replication and repair, transcription, RNA processing and export, and ribosomes synthesis and export. There are no diseases associated with mutations in the nuclear pore, because it is essential for cell life.

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Nuclear pore complex (NPC)

answer

A doughnut-shaped structure that straddles the nuclear envelope, projecting into the cytoplasm and nucleoplasm, forming the nuclear pore. A huge, supramolecular complex 15 - 30 times the mass of a ribosome. Has octagonal symmetry due to eightfold repetition of structures. Consists of 100s of polypeptides, about 30 different NUPs, which are conserved in all eukaryotes. Forms an opening 20 - 40 nm in diameter. Small molecuels may move freely through the NPC in either direction at a rate of 100 mol/min: nucleotides, solutes, histones. Molecules greater than 40 kDa are unable to pass through freely. RNA and most proteins must be selectively imported/exported by an active process, at a rate of 6 mol/min. Import into the nucleus requires energy, specific protein receptors, and an NLS. Consists of the central scaffold, FG proteins, cytoplasmic ring, nuclear ring, cytoplasmic filaments, and nuclear basket.

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Nuclear ring

answer

Part of the NPC. Located on the nuclear side of the NPC. Linked to the central scaffold and nuclear basket. Holds the membrane in place on the NPC.

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Nuclear speckles

answer

Nucleoplasm subdomains where mRNA splicing factors are concentrated. Where pre-mRNA processing occurs. Appear as "speckles" in fluorescence microscopy. Often located in interchromosomal channels, next to transcription factories. Numerous, and highly dynamic. Can move quickly and grow or shrink depending on the needs of the cell.

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Nucleoid

answer

A poorly demarcated region of a prokaryotic cell, lacking a boundary membrane, where the genetic material is found.

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Nucleolus

answer

The most obvious nucleoplasm subdomain. Irregular shape, dense and granular in apperance in electron microscopy. Not bound by membrane. Size and number, 1 - 5, depends on metabolic activity of the cell. Functions in ribosome biogenesis; rDNA genes are transcribed and rRNA is processed, and initial stages of ribosomal assembly occur.

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Nucleoplasm

answer

The highly organized fluid-filled interior of the nucleus. Consists of over 30 specialized subdomains.

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Nucleoplasmin

answer

A nuclear protein. It was detected by coating it with gold particles, and observing it with TEM. Synthesized in the cytoplasm, associates with CF, and translocates into the nucleus.

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Nucleoporin (NUP)

answer

Proteins which make up the NPC. There are about 40 different NUPs.

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Nucleoside diphosphatase

answer

Localized in the trans cisternae.

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Nucleosome

answer

A repeating subunit of DNA and histones. Consists of a nucleosome core particle, 146 bp of DNA wrapped almost twice around a disk-shaped complex of eight histones (two each of H2A, H2B, H3, and H4), with an H1 on the outside.

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Nucleus

answer

A membrane-bound structure in a eukaryotic cell that houses the genetic material. Functions in DNA replication, ribosome assembly, chromatin packing, and RNA transcription and splicing. Coordinates cellular activities; controls metabolism, protein synthesis, and cell division. Has an irregular shape. Typically there is one per cell, and it is the largest organelle, 5% - 10% of the cell volume, 10 ?m in diameter.

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Numerical aperture (NA)

answer

Affects the resolving power of a microscope. The light-gathering quality of the objective lens and the mounting medium.

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O-linked glycosylation

answer

Completed entirely in the Golgi.

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Objective lens

answer

Collects the light rays focused on the specimen in a light microscope. Two sets of light rays enter the objective lens: those which have been altered by the specimen, forming the image, and those which have not, forming the background light. The objective lens focuses these rays to form a real, enlarged image of the specimen.

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Oligosaccharide

answer

A short chain of sugar monomers linked together to form an oligomer. Found on glycoproteins. The order of monomers is important, varies from one glycoprotein to the next, and impacts the function of the glycoprotein. Assist in binding with other macromolecules, protein folding, and important in intracellular trafficking; targets proteins to specific subcellular destinations.

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Operator

answer

A component of an operon. Adjacent to or overlapping with the promoter. The binding site for a regulatory gene. Often a repressor.

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Operon

answer

A functional complex including structural genes, a promoter region, an operator region, and a regulatory gene. All genes in an operon are coordinately controlled by a mechanism described by Jacob and Monod.

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Optic atrophy 1 (OPA1)

answer

An integral inner mitochondrial membrane-bound G-protein. Possesses an intermembrane space-facing GTPase domain. OPA1 is on adjacent inner membranes interact in a GTP-dependent manner to promote inner membrane fusion during mitochondrial fusion. Binding is regulated by other mitochondrial inner membrane proteins, including prohibitin.

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Organelle

answer

Internal structures of cells.

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Organelle biogenesis

answer

Protein targeting, membrane assembly, motility, replication, degradation, and inheritance during cell division.

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Organelle tethering complex

answer

Bound Mfn1 and Mfn2. Formation is regulated by various mitochondrial outer membrane proteins, such as Bax during mitochondrial fusion.

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Osamu Shimomura

answer

In the 1960s, discovered that Aequorea victoria jellyfish have luminescence due to GFP, which he was able to purify and analyze.

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Osmium tetroxide

answer

TEM samples are stained with osmium tetroxide. Selectively reacts with lipids in all cellular membranes, making them electron dense, and visible by TEM. Localized in the cis cisternae.

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Outer chloroplast membrane

answer

A sub-compartment of the chloroplast. Contains porins, but is not as permeable to ions and small molecules as the outer mitochondrial membrane.

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Outer mitochondrial membrane

answer

A sub-compartment of the mitochondria. Permeable to ions and small molecules. Contains porins.

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Outer nuclear membrane

answer

A subdomain of the ER, continuous with the RER. Contains NUPs and attached ribosomes.

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Overall magnification

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Objective lens x ocular lens

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Oxidation-reduction potential

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Redox potential
Affinity of a substance for electrons, relative to the potential for a standard couple. Detected by instruments that detect voltage. The standard couple is arbitrarily chosen as hydrogen (H⁺ - H₂).

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Oxidative phosphorylation

answer

Formation of ATP driven by energy released from electrons removed during subtrate oxidation. Accounts for 2 x 10²⁶ molecuels of ATP produced in our bodies each day.

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P-bodies

answer

Small, transient cytoplasmic granules where deadenylation, decapping, and 5' > 3' degradation of mRNAs occurs. Destroy unwanted mRNAs, and act as sites where mRNAs can be stored where they are not translated.

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P680

answer

Pigment wavelength 680 nm
The reaction-center chlorophyll of PSII. A dimer. Transfers electrons to a primary electron acceptor, and becomes positively charged.

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P700

answer

Pigment wavelength 700 nm
The reaction-center chlorophyll of PSI. A dimer. Transfers electrons to a primary electron acceptor, and becomes positively charged.

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Paraquat

answer

A pesticide banned in Europe. Can affect proteins that cause Parkinson's disease.

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Parkin

answer

One of the genes which can cause Parkinson's disease if mutated. Recruited to the outer mitochondrial membrane of damaged mitochondria by PINK1. Has many protein-protein interactions, stimulating the poly-ubiquination of outer mitochondrial membrane proteins, serving as a signal for mitophagy of the mitochondria.

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Parkinson's disease

answer

90% of cases have no known cause. The other 10% have genetic causes, with 6 identified genes, 3 of which regulate mitochondrial function: Parkin, DJ-1, and PINK1. Damaged mitochondria are not degraded by the PINK1/Parkin pathway and accumulate in the cell, impairing cell function and eventually leading to apoptosis. Only dopaminergic neurons die.

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Paul Boyer

answer

From the UCLA. In 1979, published the binding change mechanism hypothesis: the energy released by the movement of protons is not used to drive ADP phosphorylation directly, but principally to change the binding affinity of the active site for the ATP product. Each active site processes successively through three distinct conformations that have different affinities for substrates and products. ATP is synthesized by rotational catalysis in which one part of the ATP synthase rotates relative to another part.

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Peripheral membrane protein

answer

Located on either the cytosolic or luminal side of the ER membrane.

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Peroxisome

answer

Microbody
A membrane-bound organelle, 0.1 - 1.0 ?m in diameter. It is debated whether it is part of the endomembrane system. Multifunctional, containing over 50 enzymes involved in activities including oxidation of fatty acids and amino acids, and neutralization of free radicles. Produces large amounts of toxic hydrogen peroxide, which it converts into water and oxygen. Three models for its biogenesis: ER vesiculation, growth and division, and ER semi-autonomous. Has a crystalline core.

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Peter Mitchell

answer

From the University of Edinburgh. In 1961, proposed the chemiosmotic mechanism of electron transport and the formation of ATP.

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PEX1

answer

An ATPase tethered to the peroxisome membrane by APEM9. Removes PEX5 from the peroxisome membrane during peroxisome targeting.

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PEX2

answer

A component of the RING complex.

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PEX3

answer

Ubiquinates PEX5 during peroxisome targeting in an ATP-dependent process.

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PEX5

answer

Cytosolic protein that recognizes cargo proteins for peroxisome targeting by PTS1 and PTS2. Associated with teh membrane via interactions with PEX13 and PEX14. Ubiquinated by PEX3 and the RING complex: an ATP-dependent process, recycling receptors back to the cytosol. When ubiquinated, it is removed from the membrane by PEX6 and PEX1.

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PEX6

answer

An ATPase tethered to the peroxisome by APEM9. Removes PEX5 from the peroxisome membrane during peroxisome targeting.

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PEX7

answer

Cytosolic protein that recognizes cargo proteins for peroxisome targeting by PTS1 and PTS2. Cannot dock to the membrane on its own; depends on physical interaction with PEX for docking. Its route through the import cycle is unknown.

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PEX10

answer

A comopnent of the RING complex.

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PEX12

answer

A component of the RING complex.

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PEX13

answer

Interacts with PEX5 and PEX14, to associate PEX5 with the peroxisome membrane during peroxisome targeting.

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PEX14

answer

Interacts with PEX5 and PEX13, to associate PEX5 with the peroxisome membrane during peroxisome targeting.

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pH gradient (?pH)

answer

The concentration difference betwen hydrogen ions on one side of the membrane versus the other side.

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Phagocytosis

answer

"Cellular eating"
A process of internalization of materials. The uptake of large particulate matter into the cell. Occurs only in specialized cells, including amoebas and macrophages (white blood cells).

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Phagophore

answer

A double-membrane structure that wraps around old or damaged organelles during autophagy. Matures into an autophagosome. Origin is unknown; could be from the ER or from mitochondrial membranes.

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Phase-contrast microscope

answer

Makes highly transparent objects more visible. Converts differences in refractive index into differences in light intensity. Separates direct light and diffracted light, then causes them to interfere with each other. Ideally suited for observing intracellular components of living cells at high resolution.

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Phosphatidic acid

answer

A cone-shaped lipid that causes the outer membrane to curve inwards. Phospholipase D converts cardiolipin, forming lipid microdomains during mitochondrial fusion. Promotes Mfn1/2-mediated membrane fusion during mitochondrial fusion.

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Phosphatidylinositol (PIP₂)

answer

PI(4,5)P₂
A unique membrane lipid that serves as the signal for recruitign AP2 to coated pits. The inner leaflet of coated pits is enriched with PIP₂.

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Phospholipase

answer

A lysosomal enzyme. A lipid hydrolyzing enzyme that acts on phospholipids.

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Phospholipase D (PLD)

answer

Converts cardiolipin into phosphatidic acid, forming lipid microdomains during mitochondrial fusion.

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Phosphotransferase

answer

Recognizes a signal patch in proteins in the cis cisternae.

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Photoautotroph

answer

A type of autotroph. Use the energy of the sun to convert CO₂ into organic compounds, using photosynthesis. Includes plants, eukaryotic algae, flagellated protists, and several groups of prokaryotes.

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Photolysis

answer

The splitting of water during photosynthesis. Requires simultaneous loss of four electrons from two molecules of water.

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Photon

answer

A quanta of light. May be thought of as "particles" of light.

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Photorespiration

answer

Production of phosphoglycolate, a two-carbon molecule, when Rubisco reacts with O₂. It is converted into glycolate, and destroyed by peroxisomes, releasing CO₂. It is a waste of the plant's energy.

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Photosynthesis (Ps)

answer

The process in which energy from the sun is transformed into chemical energy stored in carbohydrates and other organic molecules. Low energy electrons are removed and converted into high energy electrons, using energy absorbed from light. Occurs in the chloroplast.
CO₂ + H₂O + sunlight energy > O₂ + energy rich carbohydrates

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Photosynthetic unit

answer

Several hundred chlorophyll molecules acting together. Antenna pigments capture photons and transfer energy to the reaction-center chlorophyll at the centre.

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Photosystem

answer

Large pigment-protein complexes where light absorbing reactions occur. Two types are required to catalyze two light-absorbing reactions in oxygenic photosynthesis, acting in series. Similar in protein composition and architecture. Includes PSII and PSI.

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Photosystem I (PSI)

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A photosystem. Raises electrons from a midway point to an energy level above that of NADP⁺. Its reaction-center chlorophyll is P700.

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Photosystem II (PSII)

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A photosystem. Boosts electrons from an energy level below that of water to a midway point. Its reaction-center chlorophyll is P680. Its antenna proteins are in LHCII. More than 20 different polypeptides, most embedded in the thylakoid membrane.

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Pierre Joliot and Bessek Kok

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In 1970 proposed the S-state hypothesis: PSII accumulates four oxidizing equivalents needed to oxidize water.

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Piggyback

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A protein enters the nucleus without having an NLS by binding to an NLS-containing protein.

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Pigment

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Compounds which appear coloured because they absorb light of particlar wavelengths. Includes chlorophyll.

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Plasma membrane (PM)

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Recycled every 20 - 90 minutes. Receptors are degraded by receptor-bound endocytosis and delivery to the lysosome.

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Plasma membrane and associated membrane (PAM)

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A subdomain of the ER. Regions of the ER that make direct contact with the plasma membrane. Involved in membrane lipid exchange.

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Plastid genome

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Found in the stroma of chloroplasts. Circular DNA. Size and copy/gene number varies with species. Encodes ribosomal proteins, some photosynthesis proteins, including a few located in the thylakoid: tRNA and rRNA and some RNA polymerase subunits. All other plastid proteins, about 3000, are encoded by the nuclear genome.

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Poly-Ub

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More than one ubiquitin. Serves as a signal for ER protein degradation and most other cellular proteins destined for normal turnover via degradation by a proteasome.

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Porin

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Barrel-shaped integral membrane proteins with a large internal channel, found in the outer membranes of the mitochondria and the chloroplast.

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Positive-outside rule

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Positively charged amino acid residues located upstream of the TMD result in the nascent protein being re-oriented by the translocon so that the positively-charged residues face towards the cytosol. The TMD is reoriented so that the N-terminal end is facing the cytosol, before being released laterally into the membrane lipid bilayer.

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Posttranslational control

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A level at which expression is controlled in eukaryotes. Regulates activity and stability of proteins.

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Presenilins-associated rhomboid-like protein (PARL)

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An integral mitochondrial inner membrane protease. Partially degrades PINK1.

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Presequence

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A 15 - 50 amino acid long targeting signal found in most mitochondrial matrix proteins. Located on the N-terminus. Consists of an amphipathic ? helix enriched on one side with positively-charged amino acids. Responsible for targeting the nascent protein to the cytosolic surface of the mitochondrion, and its subsequent translocation across the outer and inner mitochondrial membranes. Cleaved following protein import into the matrix.

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Primary electron acceptor

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Accepts electrons from P680 and P700 when they are boosted to outer orbitals.

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Processing control

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A level at which expression is controlled in eukaryotes. Determines the path by which the primary mRNA transcript is processed into a messenger RNA that can be translated into a polypeptide.

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Prohibitin

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Ensures that OPA1-mediated fusion occurs only between different inner membranes during mitochondrial fusion. Prevents self-fusion of cristae of the same mitochondrion.

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Prokaryotic

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A class of cells. Structurally simpler. Includes bacteria. Live in most habitats on Earth. Have a nucleoid, free ribosomes, and no endomembrane system or mitochondria. Typically small.

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Promoter

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A component of an operon. Where RNA polymerase binds to the DNA promoter to being transcription.
OR
A region upstream of a gene that regulates initiation of transcription. Consists of a core promoter, where the pre-initiation site assembles, and the proximal promote region, consisting of the CAAT and GC boxes.

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Proteasome

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Hollow, cylindrical machines which degrade cellular proteins. A barrel-shaped multi-subunit complex consisting of four rings of polypeptide subunits, stacked on each other with a cap attached at either end. Located in the cytosol and nucleus. Digest proteins that have been selected and marked for destruction, due to abnormal folding or incorrect association with other proteins. One of the only protein structures which cna be seen with an EM. The Ub-protein binds to the lid of the proteasome, its Ub chain is removed and recycled, and the protein is threaded through the proteasome where it is degraded via proteolysis. Amino acids are reused for new protein synthesis. Has caps, ? subunits, and ? subunits.

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Proplastid

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A nonpigmented chloroplast precursor organelle. May develop into a chloroplast.

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Protein kinase RNA-like ER kinase (PERK)

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A pathway in UPR. BiP is released from PERK to aid in folding of misfolded proteins. PERK sensors dimerize to activate. Cytosolic-facing kinase domains of activated PERK dimers phosphorylate and inhibit protein translation factor eIF2? ceasing protein synthesis in the cell. Allows molecular chaperones to focus on pre-existing misfolded proteins in the ER. ER stress is alleviated, and if not, cell death occurs.

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Proton-motive force (?p)

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The electro-chemical gradient of the membrane. Includes the electrical potential and the pH gradient. Proportions of these two depend on the permeability of the membrane. Measured in millivolts.

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PTEN-induced putative kinase 1 (PINK1)

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PTEN = phosphate and tensin homology
One of the genes which can cause Parkinson's disease if mutated. Normally imported into the mitochondrial intermembrane space. MPP cleaves the targeting sequence while it is halfway through TIM23, then the rest of the protein is deposited in the intermembrane space, associating with the inner membrane. Partially degraded by PARL. Final degradation occurs via an unknown protease. When mitochondria are damaged, the intermembrane space is depolarized and PINK1 cannot pass through TOM, so it accumulates on the outer membrane, recruiting Parkin.

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PTS1/2

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Specific targeting signal recognized by PEX5 and PEX7. Bound cargo is released into the matrix of the peroxisome during peroxisome targeting, and receptors are recycled back to the cytosol via a mechanism using ATP-dependent ubiquination of PEX5 and PEX3 and the RING complex.

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Quality control

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A system that screens newly synthesized glycoproteins, determining whether or not they are fit to move on to the next compartment in the biosynthetic pathway.

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Rab

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A class of small G proteins. Associate with membranes by a lipid anchor. There are over 60 Rab genes in humans, associating with different membrane components. Give surface identity to organelles, and play a role in recruiting proteins involved in other aspects of membrane trafficking.

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Ran

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Ras-related nuclear protein
Ras = Rat sarcoma protein
A small G protein that serves as a molecular switch in the nuclear transport process. Has poor native GTPase activity. There is a large concentration of Ran-GTP in the nucleus, and a low concentration in the cytoplasm; this gradient is maintained by accessory proteins. THis gradient drives nuclear import and export.

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Ran-GAP1

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The GAP that acts on Ran-GTP, hydrolyzing it into Ran-GDP. Found in the cytosol; maintains low Ran-GTP levels.

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Randy Schekman and colleagues

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From the University of California, Berkeley. Studied the genetic basis of secretion using mutants of yeast.

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RCC1

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The GEF that acts on Ran-GDP, converting it into Ran-GTP. Found in the nucleus; maintains high Ran-GTP levels.

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Reaction-center chlorophyll

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A chlorophyll at the centre of the photosynthetic unit. Transfers electrson to an electron acceptor.

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Receptor

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A protein of the TOM complex. Binds to positively-charged presequences.

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Receptor-mediated endocytosis (RME)

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A form of endocytosis. Uptake of specific extracellular macromolecules, following their binding to receptors on the external surface of the plasma membrane. Responsible for concentrating and internalizing specific extracellular materials bound to specific receptors on the outer surface of the plasma membrane, including hormones and growth factors, and proteins destined for degredation. Plasma membrane transmembrane recetpros become activated by binding to specific soluble extracellular ligands. The receptor-ligand complexes accumulate in coated pits. PIP₂ recruits AP2, which recruits clathrin triskelions that form a lattice, forming the vesicle. Dynamin mediates pinching off, producing an endocytic vesicle.

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Recyclinc compartment

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A portion of the early endosome that contains receptors and PIP₂. Detaches from the early endosome, and trafficks back to the plasma membrane, recycling the receptors and lipids.

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Regulated secretion

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A type of secretory activity. Occurs only in specialized cells. ER-derived materials are stored as membrane-bound packages, secretory granules, and discharged by fusing with the plasma membrane in response to appropriate stimuli, such as a hormone or neurotransmitter. Example: regulated release of neurotransmitter by nerve cells into the synaptic cleft.

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Regulatory gene

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Encodes the repressor protein.

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Repressor

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A tyep of gene regulatory protein. Encoded by the regulatory gene.

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Resolution

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The minimum distance that can separate two points, and they still remain identifiable as separate points. To increase resolution, use a shorter wavelength of light, or increase the numerical aperture of the microscope. Resolution of a light microscope is limited by diffraction.
Resolution (in nm) = 0.61?/NA

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Response element

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Sites flanking a gene where transcription factors bind.

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Reticulon

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Unique ER integral membrane proteins that have hairpin structures, and regulate ER membrane curvature. Mediate the shape of tubules and cisternae.

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Reticuloplasmin

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A chaperone that operates within the ER. Bind to nascent proteins, and mediate their proper folding and oligomeric assembly, preventing protein aggregation. Molecular chaperones. Includes BiP, calreticulin, and calnexin.

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Retro-translocation

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Lumen-to-cytosol transfer of misfolded proteins in the ERAD pathway. It is not well understood. Occurs through the translocon.

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Retrograde

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"Reverse"
Transport from the plasma membrane to the Golgi, and from the Golgi to the ER.

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Riboswitch

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mRNAs that bind a small metabolite to a 5' UTR. Undergo a change in conformation, allowing for altered expression of the gene involved in the production of the metabolite. Most riboswitches suppress gene expression by blocking termination of transcrition or initiation of translation.

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RING complex

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Ubiquinates PEX5 during peroxisome targeting in an ATP-dependent process. Consists of PEX2, PEX10, and PEX12.

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RNA editing

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A form of posttranscriptional gene expression control. Specific nucleotides in an RNA are converted to other nucleotides, after transcription. Can create new splice sites, stop codons, or amino acid substitutions.

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Robert Emerson and William Arnold

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From the California Institute of Technology. In 1932, carried out an experiment suggesting that not all the chlorophyll molecules in a chloroplast were directly involved in conversion of light energy into chemical energy. Found that one chlorophyll molecule out of every 2500 produced O₂ when exposed to very short flashes of light. Emerson found that eight photons are required to produce one O₂ molecule.

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Robert Hill and Fay Bendall

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From the University of Cambridge. First proposed the Z scheme for oxygenic photosynthesis.

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Robert Laskey and coworkers

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From the Medical Research Council of England. In 1983, found that nucleoplasmin, and abundant nuclear protein in amphibian oocytes, has an NLS.

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Robert Tsein

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From the University of California, San Diego. Generated variants of GFP in other colours: blue (BFP), yellow (YFP), and cyan (CFP). Used mutagenesis of the GFP gene. Won the Nobel Prize in Chemistry in 2008 for discovering GFP, along with Osamu Shimomura and Martin Chalfie.

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Roger Kornberg

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In 1974, proposed that DNA and histones are organized into nucleosomes.

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Rolf Luft

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From the University of Stockholm in Sweden. In 1962, reported on a patient who's mitochondria lacked normal respiratory control.

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Rough endoplasmic reticulum (RER)

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A portion of the ER. Continuosu with the outer memrbane of the nuclear envelope. Has ribosomes bound to its surface. Composed of cisternae. Fragements into rough-surface vesicles durign cell homogenization. Ribosomes produce secreted, integral membrane, and soluble proteins that reside in the endomembrane system.

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S. cerevisiae

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A model organism. A yeast. 4929 genes.

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S. cerevisiae

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A model organism. A yeast. 4929 genes.

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Samuel Ruben and Martin Kamen

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From the University of California, Berkeley. In 1941, confirmed van Niel's hypothesis on the role of water in photosynthesis. Carried out expriments on suspensions of green algae using isotope-labelled oxygen.

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Sandhoff's disease

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A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in hexosaminidases A and B, causing accumultion of ganglioside G_M2 and globoside. Similar to Tay-Sachs disease, but progresses more rapidly.

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Sar1-GDP

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A G protein. Recruited from the cytosolic surface of the ERES during COPII-coated vesicle formation.

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Sec13

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Act as the outer scaffolding of the coat.

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Sec23

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Form a dimer that promotes further bending of the ERES membrane.

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Sec24

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Form a dimer that promotes further bending of the ERES membrane. Binds to the cytosolic-facing domains of selected integral membrane proteins (cargo, cargo receptors, and molecular machinery), which are then concentrated within the growing coated bud. Sec24 also binds to cytosolic domains of selected integral membrane proteins, which are then concentrated in the growing coated "bud".

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Sec31

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Act as the outer scaffolding of the coat.

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Secreted

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Discharged from the cell. Includes constitutive and regulated secretion.

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Secretory granules

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Large, densely packaged membrane-bound packages in which materials are stored before regulated secretion. Form the TGN. Eventually fuse with the plasma membrane and release their cargo into the extracellular space.

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Secretory pathway

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A pathway in the endomembrane system. Includes constitutive secretion and regulated secretion. Most proteins are specifically transoprted between compartments of the endomembrane system via unique targeting signals and receptors.

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Secretory vesicles

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Form from the TGN. Transport cargo to the plasma membrane and extracellular space.

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Sections

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A type of specimen observed with a light microscope. Very thin slices of plant or animal tissues. Thicker peices would be too opaque to see in a light microscope. To prepare a section, cells are first killed by immersing the tissue in a fixative.

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Shinya Yamanaka and Kazutoshi Takhashi

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In 2006, found that introduction of a combination of four transcription factor genes was sufficient to reprogram differentiated mouse fibroblast cells into undifferentiated embryonic stem cells.

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Sialidase

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A lysosomal enzyme. A polysaccharidase and oligosaccharidase that acts on sialyloligosaccharides.

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Sidney Goldfischer and colleagues

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From the Albert Einstein College of Medicine. In 1973, reported that liver and renal cells from Zellweger syndrom patients contained "ghost" peroxisomes, lacking enzymes normally found in peroxisomes.

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Signal patch

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Leads to processing of the core olgiosaccharide into M6P, sending the protein to the lysosome.

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Signal peptidase

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An ER integral membrane protein. A protease located next to the translocon. Its catalytic domain faces the ER lumen. Removes the signal sequence of the nascent polypeptide as it enters the luminal space.

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Signal receptor

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An enzyme that removes the signal sequence from most nascent polypeptides in the RER lumen. An integral membrane protein.

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Signal recognition particle (SRP)

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In mammalian cells, six distinct polypeptides and a small RNA molecule. A G-protein. Binds to the signal sequence of nascent polypeptides, and the ribosome from which it is emerging. Arrests translation of the polypeptide. It then binds the ribosome to the SRP receptor and the tranlocon, and detaches from the complex, allowing translation to continue, so that the polypeptide is inserted into the ER. Once the ribosome is bound to the SRP receptor, SRP has GTP hydrolysis and is released.

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Signal sequence

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A sequence at the N-terminus of a polypeptide, which is first to emerge from the ribosome. Directs the polypeptide to the ER membrane.

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Small compounds

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Chemical or organic. Includes fluorescein. Assist in staining subcellular structures or macromolecules. Direct and indirect immunofluorescence.

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Smooth endoplasmic reticulum (SER)

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A portion of the ER. Lacks ribosomes bound to its cytosolic surface. Membranes are curved and tubular, forming an interconnecting system of pipelines traversing the cytoplasm. Fragment into smooth-surface vesicles during cell hmogenization. Function in synthesis of steroid hormones, detoxification, and sequestering of calcium ions.

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SNAREs

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Over 35 membrane proteins, localized to specific subcellular compartments. Contain a 60 - 70 amino acid motif capable of forming a complex with another SNARE motif. Facilitate the fusion of membranes of a transport vesicle and target compartment. Include v-SNAREs and t-SNAREs.

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Sorting compartment

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A portion of the early endosome. Contains soluble endocytic cargo from the extracellular space, and plasma membrane receptors destined for degradation in the lysosome. ATPase pump becomes activated, lowering the pH, and the compartment progressively matures into the late endosome.

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SRP receptor

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Binds to the SRP and ribosome with nascent polypeptide. A G-protein. A heterodimeric ER integral membrane protein complex. The ribosome then binds to the translocon, and SRP receptor is hydrolyzed and released.

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SRY

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Sex-determining region Y
A gene on the Y chromosome encoding testis-determining factor, a transcription factor.

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Staufen

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A gene found in fruit flies. Takes RNA to the posterior pole of the oocyte. Mutation causes male sterility. Named after a member of ancient European royalty who was infertile and produced an illegitimate heir.

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Stroma

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A sub-compartment of the chloroplast. The aqueous space between chloroplast envelope and thylakoid membrane. Contains the enzymes responsible for carbohydrate synthesis. Contains the plastid genome and prokaryotic-like ribosomes used for translation of plastid genome-encoded proteins. Protein targeting to the stroma is the best understood. Most stomal-destined proteins have a transit peptide, recognized by TOC. The protein moves through TOC and then TIC.

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Stroma thylakoid

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Thylakoid membranes between grana thylakoids.

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Stromule

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Long, stroma-filled tubes that often connect chloroplasts. Highly dynamic and can rapidly extend and contract. Allows for metabolite transfer and communication between chloroplasts and/or other organelles such as mitochondria or peroxisomes.

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Strucutral genes

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A component of an operon. Encodes the enzyme itself. Usually they are adjacent to one another. RAN polymerase moves from one structural gene to the next, producing a polycistronic mRNA, containing information for more than one polypeptide. All the polypeptides are translated together.

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Subcellular fractionation

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Separating vesicles of a homogenized cell based on the different properties from different organelles.

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Subdomains

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Specialized regions of the nucleoplasm, with specific functions. Not bound by membranes. Includes interchromosomal channels and transcription factories.

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Sulfate lipidosis

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A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in arylsulfatase A, causing accumulation of sulfatide. Causes mental retardation and death by age 10.

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Swyer syndrome

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Genetically XY individuals develop as female. They are infertile. There is a mutation in the NLS of the SRY gene, and testis-determining factor cannot enter the nucleus, and has no effect on any cells.

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T. Engelmann

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A German biologist. Identified chloroplast as the site of photosynthesis in 1881. Illuminated cells of green algae, Spirogyra, and found that actively moving bacteria collect near the site of the chloroplast to collect oxygen.

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t-SNAREs

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SNAREs located in membranes of target compartments.

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Tay-Sachs disease

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A lysosomal storage disorder resulting in accumulation of sphingolipids. Deficiency in hexosaminidase A, causing accumulation of ganglioside G_M2. Causes mental retardation, blindness, and death by age 3.

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Telomerase

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An enzyme that can add new repeat units to the 3' end of the overhang strand of a telomere. A reverse transcriptase, synthesizing DNA using an RNA template embedded in the enzyme.

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Telomere

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An unusual stretch of repeated sequences that act with specialized proteins to form a cap at the ends of each chromosome. Telomeres of vertebrates have the sequence TTAGGG repeated 500 - 5000 times.

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Thomas Roth and Keith Porter

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From Harvard University. In 1964, reported on the mechanism by which yolk proteins enter oocytes of mosquitoes. Proposed that the proteins were taken up by endocytosis.

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Thylakoid lumen

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A sub-compartment of the chloroplast. The aqueous interior of the thylakoid membrane. High concentration of H⁺, forming a gradient with the stroma. Functionally analogous to the mitochondrial intermembrane space.

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Thylakoid membrane

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A sub-compartment of the chloroplast. A third internal membrane. Includes grana and stroma thylakoids. The site of ATP synthase. Some thylakoid proteins are encoded by the chloroplast genome, and synthesized on stromal ribosomes bound to the membrane in a process similar to co-translational translocation. Most thylakoid proteins are nuclear and targeted to the thylakoid:
1. Imported into the stroma. Cleavage of the transit peptide exposes the thylakoid transfer domain.
2. Thylakoid transfer domain mediates protein import into the lumen or insertion into the membrane via unique thylakoid translocation complexes.
3. Flattened membranous sacs of teh internal chloroplast membrane. Arranged in grana. The membrane contains the protein complexes comprising the energy-transducing machinery.

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Thylakoid transfer domain

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Found on thylakoid proteins. Exposed after the transit peptide is cleaved off in the stroma. Mediates protein import into the lumen or insertion into the membrane via unique thylakoid translocation complexes.

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Toc34

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A receptor in the TOC complex. Binds to the transit peptide in a GTP-dependent manner.

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Toku Kanaseki and Ken Kadota

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From the University of Osaka. In 1969, took electron microscope images of crude vesicle fractions isolated from guinea pig brains, to show that coated vesicles were covered by a polygonal basketwork.

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Tomography

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Computer generated, 3D images made using EM.

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Tonoplast

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The membrane surrounding the vacuole. Contains active transport systems that pump ions into the vacuolar compartment.

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Trans cisternae

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The compartment of the Golgi complex between the medial cisternae and the TGN. A large, flattened cisternae. Nucleoside diphosphatase is localized here.

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Trans Golgi network (TGN)

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The trans-most face of the Golgi complex. A sorting station where proteins are segregated into different types of vesicles, heading for the plasma memrbane or other intracellular destinations. Interconnected network of tubules and vesicles. The site of clathrin vesicle assembly for transport to the endosome/lysosome. The site of secretory vesicle or granule assembly for transport to the plasma membrane. The site of COPI vesicle assembly for transport to the trans cisternae.

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Transcription factor

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A large group of proteins that orchestrate transcriptional control. Includes general transcription factors, binding to core promoter sites, and sequence-specific transcription factors that bind to a variety of regulatory sites of specific genes. Have two domains: a DNA-binding domain and an activation domain. Many have a surface that promotes binding with another protein to form dimers.

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Transcription factory

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A nucleoplasm subdomain where active genes from different subdomains extend into interchromosomal channels. Transcription factors are concentrated in these areas. Improves gene efficiency.

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Transcriptional control

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A level at which expression is controlled in eukaryotes. Determines whether a particular gene can be transcribed, and how often. Controlled by transcription factors.

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Transit peptide

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An N-terminal targeting signal that targets proteins to the stroma. Recognized by TOC. It is cleaved by a stromal processing protein.

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Translational control

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A level at which expression is controlled in eukaryotes. Determines whether a particular mRNA is translated, and how often.

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Translocase of the inner chloroplast membrane (TIC)

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A multi-protein complex. Analogous to TIM. The protein moves through it after it passes through TOC. As the protein exits TIC, Hsp93 acts as a ratchet. Can insert proteins laterally into the inner chloroplast membrane.

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Translocase of the inner mitochondrial membrane 22 (TIM22)

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Responsible for the insertion and assembly of inner mitochondrial membrane proteins. Proteins are passed from TOM to TIM22, then transferred laterally into the lipid bilayer of the inner mitochondrial membrane.

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Translocase of the inner mitochondrial membrane 23 (TIM23)

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A multi-protein complex that forms a channel, allowing for matrix protein translocation across the inner mitochondrial membrane. Physically connected to TOM with interacting proteins, allowing for translocation across the outer and inner mitochondrial membranes to occur sequentially.

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Translocase of the outer chloroplast membrane (TOC)

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A multi-protein complex. Analogous to TOM. Has a Toc34 receptor that bints to the transit peptide in GTP-dependent manner. Partially unfolded proteins move through the complex channel, and is passed to the TIC complex. Can insert proteins laterally into the outer chloroplast membrane.

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Translocase of the outer mitochondrial membrane (TOC)

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A multie-protein complex consisting of a number of integral outer mitochondrial membrane proteins. Physically connected to TIM23 with interacting proteins, allowing for translocation across outer and inner mitochondrial membranes to occur sequentially. Proteins include the receptor, the channel, and acecssory proteins.

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Translocation

answer

A type of chromosome aberration. A whole chromosome or peice of a chromosme becomes attached to another chromosome. Increases likelihood that the cell will become malignant.

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Translocon

answer

Sec 61
A protein-lined channel embedded in the RER membrane. Contains an ?-helix "plug" that seals the channel when no ribosome is bound. The ribosome with nascent polypeptide binds to it after it binds to the SRP receptor. This leads to continuation of the protein translation, and conformational change in the translocon, opening the pore ring and displacing the "plug" so that the N-terminus is inserted into the luminal space. When the ribosome is completed translating the polypeptide, it is released into the cytoplasm, and the translocon pore ring returns to its closed state with the "plug" in place. Can open to the side, allowing nascent integral membrane proteins to dissolve into the lipid bilayer of the ER. Has a positive charge on its aqueous channel near the luminal side.

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Transmembrane domain (TMD)

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The region of an IMP which is embedded in the membrane. Typically an ?-helix, hydrophobic segment 16 - 25 amino acids long. As the IMP is inserted into the membrane, the TMD interacts with the hydrophobic pore ring of the translocon, halting translocation of the nascent protein, signalling the translocon to open laterally, releasing the TMD into the membrane lipid bilayer. A single polypeptide can have several TMDs, causing looping in the cytosol and/or luminal space. It is possible to analyze the chemistry and physics of amino acid sequences to determine the location of TMDs and the looping patterns of IMPs.

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Transmembrane ring

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A ring within the lumen of the nuclear envelope. Pinches the membrane inwards around the NPC. Not considered a component of the NPC, since it is not physically attached to it.

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Transmission electron microscope (TEM)

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Used to generate highly magnified views of internal cellular structures. An image is formed from electrons that are transmitted through a specimen. Consists of a hollow cylindrical chamber containing a vacuum, an electron gun, electromagnetic lenses, and a viewing screen. When electrons strike the specimen, some are scattered and others are not. Scattering is due to selectively electron dense properties of the specimen. Electrons that pass easily through the specimen are detected by the camera and appear as white or grey areas. Areas through which electrons do not pass easily appear as black areas. Specimen preparation is very important for TEM imaging. After the sample is fixed, it is stained with osmium tetroxide, dehydrated in ethanol, and embedded in plastic epoxy resin, which inflitrates into the sample, and provides mechanical support during sectioning. The sample is cut into sections less than 100 nm in width with an ultramicrotome, a small glass or diamond knife. Thin sections are collected and placed on a grid, and post-stained with heavy metals.

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Transport receptor

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Karyopherin
"Nucleus"
Mobile proteins responsible for moving proteins or RNA across the nuclear envelope. Includes importin and exportin.

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Transport vesicles

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Shuttle materials between organelles. Bud from donor membrane compartments, move through the cytoplasm in a directed manner, pulled by motor proteins operating on the cytoskeleton, and fuse with the membrane of acceptor compartments.

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Tricarboxylic acid (TCA) cycle

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Citric acid cycle
Krebs cycle
CoA is fed into this cyclic pathway, where it is oxidized and energy is conserved. All enzymes reside in the soluble phase of the matrix, except succinate dehydrogenase, which is bound to the inner membrane. Metabolism of carbohydrates and fatty acids.
Acetyl CoA +2 H₂O + FAD + 3 NAD⁺ + GDP + P_i > 2 CO₂ + FADH₂ + 3 NADH + 3 H⁺ + GTP + HS-CoA

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Turnover

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Regulated destruction of a cell's organelles, and their replacement.

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Ubiquinone (UQ)

answer

Coenzyme Q
A type of electron carrier in the electron transport chain. A lipid-soluble molecule with a long hydrophobic chain of five carbon isoprenoid units. Stays in the lipid bilayer and can diffuse laterally. Accepts and donates two electrons and two protons.
Ubisemiquinone = partially reduced UQ
Ubiquinol = fully reduced UQ

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Ubiquitin (Ub)

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A small, highly conserved protein with a number of functions. 76 amino acids long. Involved in diverse cellular functions. It may be enzymatically attached to lysine residues on proteins. Can selectively incorporate proteins into endocytic vesicles, or act as a sorting signal. Polyubiquitin chains target proteins for destruction by proteasomes.

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UDP-glucose glycoprotein (UGGT)

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A glucosyltransferase. Adds glucoses to misfolded proteins in the ER, sending them to calnexin for refolding.

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Unfolded protein response (UPR)

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Occurs when unfolded proteins are generated faster than they can be exported to the cytoplasm for destruction. Hundreds of genes are expressed, to alleviate the condition: chaperone proteins, transport proteins, and proteins invovled in selective destruction. Phosphorylation becomes required for protein synthesis, reducing flow of newly synthesized proteins in the ER. Under certain conditions, misfolded proteins accumulate to levels too high for the ERAD pathway to handle; this could be triggered by a mutation or by heat stress. The stress signals UPR pathways to initiate, mediated by various ER integral membrane sensor proteins. Luminal-facing stress sensing domains bind to molecular chaperones in the ER, including BiP. Three pathways, but only two are discussed: PERK and ATF6.

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Untranslated region (UTR)

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Noncoding regions in the mRNA, found at the 5' and 3' ends. The 5' UTR extends from the 5' cap to the AUG initiation codon. The 3' UTR extends from teh termination codon to the end of the RNA transcript. Contains nucleotide sequences that control translation.

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Uric acid

answer

It is converted into allatonin in the crystalline core of the peroxisome of most mammals, but not including humans. Secreted in the urine. Build-up of uric acid can lead to gout.

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v-SNAREs

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SNAREs located in membranes of transport vesicles.

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Vacuole

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Found only in plant or fungi cells. May occupy as much as 90% of volume of a plant cell. Function in storage of ions, sugars, amino acids, proteins, polysaccharides, and toxins. Water enters the vacuole by osmosis, producign hydrostatic pressure that provides mechanical support to the plant cell. Contain some lysosomal enzymes, and function in some intracellular digestion.

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Vesicle transport

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Trafficking through the endomembrane system via transport vesicles.
1. Cargo-containing vesicle buds off the donor membrane compartment. Vesicle coat proteins select which donor membrane and luminal cargo proteins can enter the nascent vesicle, and regulate vesicle formation and budding.
2. Nascent vesicle is transported through the cytosol to the recipient membrane compartment. Vesicle receptor proteins regulate intracellular trafficking. Involves molecular motors and the cytoskeleton. Motor proteins direct vesicle movement within the cell by linking to the vesicle surface and to the cytoskeleton element.
3. Vesicles fuse with the proper recipient membrane compartment. Receptor proteins regulate vesicle-recipient membrane fusion. Vesicle donor membrane and luminal cargo proteins are incorporated into the recipient compartment.
4. Entire process of budding and fusion is repeated, and can occur in the reverse direction. Other receptor proteins regulate the recycling of proteins that escaped into the recipient compartment, bringing them back to the donor membrane compartment.

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Vesicular transport model

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A model for movement through the Golgi complex. The least favoured model. Cargo is carred in an anterograde motion via transport vesicles. The composition of each sub-compartment changes with the incoming new membrane and cargo. The Golgi complex persists overall because COPI-coated transport vesicles continually move Golgi proteins back to the proper sub-compartment.

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Wavelength (?)

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Affects the resolving power of a microscope. A factor of the illumination light.

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Whole mount

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A type of specimen observed with a light microscope. An intact object. May be a living or dead microorganism, or a small part of a larger organism.

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Wolfgang Baumeister

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From the Max-Planck Institute in Germany. Developed cyro-ET, allowing nanosized intracellular structures to be studied in unfixed, fully hydrated, flash-frozen cells.

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Z-section

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"Optical slice"
A single layer within a specimen being viewed with a CLSM. Can be viewed individually, serially, or stacked together to form a 3D image.

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Zinc-finger motif

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A common structural motif in transcription factors. A zinc ion is coordinated between two cystines on one side of the "finger" and two histidines on the other side. Typically the fingers act independently of each other, and are inserted into the major grove of the DNA molecule. The largest class of mammalian transcription factors have zinc fingers.

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