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Cell and Molecular Biology
w/William Bates @ UBC-O
86
Biology
Undergraduate 2
12/13/2007

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Term
SRP
Definition
Signal recognition particle; G-protein involved in the signal hypothesis for protein synthesis
Term
Proteosome
Definition
Organelle where proteases digest polyubiquitinized peptides for "quality control" in protein synthesis.
Term
BiP
Definition
Molecular chaperone which folds proteins.
Term
Sar
Definition
G-protein which regulates COPII vesicle formation.
Term
Synaptobreven
Definition
A v-SNARE (originating on the vesicle) which binds with a t-SNARE (originating on the target) in an α-helix for endocytosis.
Term
Alzheimers
Definition
When brain MAP (microtrubule associated proteins) 'tau' has increased phosphorylation the microtubule array becomes malformed and synaptic transmission is interrupted.
Term
Translocon
Definition
The receptor for the protein synthesis stop sequence, which is embedded in ER transmembrane pore/protein.
Term
G-protein
Definition
Catalyzes GTP for conformational change.
Term
Mannose-6-Phosphate Receptor
Definition
Binds to lysosomal hydrolytic enzymes in trans-Golgi lumen to select for a forming lysosome.
Term
Dolichol
Definition
Carrier for sugars in glycosylation; has 20 isoprene units
Term
Arf
Definition
G-protein which regulates te formation of COPI vesicles.
Term
Clathrin
Definition
Has a triskelion structure with hooks, supported by AP2 complex, to form a coat for bi-directional vesicles.
Term
Autoradiography
Definition
Radioactively labelled amino acids become incorporated into proteins, which then emit emulsions in photographic emulsion.
Term
Cytoskeletal Elements (3 Types)
Definition
1) Tubulin aka Microtubules 2) Actin Superfamily 3) Intermediate Filaments
Term
Glycosyl Transferase
Definition
Transfers sugars for glycosylation to dolichol.
Term
Lipofuscin Pigment Granules
Definition
Residual body (lysosome after phaging) or 'left-overs' in a cell, which may correlate to a cell's age because of accumulation over time.
Term
NLS
Definition
Nuclear Localization Sequence; a short positively-charged amino acid sequence which alpha-importin binds to so the NLS protein can be moved into the nucleoplasm.
Term
Rab
Definition
G-protein which regulates SNARE interaction; it tethers the vesicle to the target.
Term
Syntaxin
Definition
t-SNARE (located on target) which entwine in an α-helix with v-SNARES to join vesicle and target membrane.
Term
SNAP-25
Definition
t-SNARE (located on target) which entwine in an α-helix with v-SNARES to join vesicle and target membrane.
Term
Protofilaments
Definition
Subunits of microtubules; α-tubulin and β-tubulin dimers, which treadmill from negative (-) to positive (+) ends making microtubules dynamic.
Term
Dynamin
Definition
G-protein which is recruited to form a pinching ring of constriction around budding vesicle, when hydrolyzed back to subunits the vesicle will bud.
Term
Kinase
Definition
Enzyme which catalyzes phosphorylation.
Term
Phosphotase
Definition
Enzyme which catalyzes dephosphorylation.
Term
Myosin
Definition
Molecular motor associated with actin; important for muscle contraction; has a head domain - S1- which is the motor.
Term
Lamina
Definition
Intermediate filament; Cytoskeletal protein for nuclear membrane; it's phosphorylative state corresponds with the cell cycle; functional as a staggered tetramer.
Term
Kinesin
Definition
Molecular motar associated with microtubules; (+) end direction; Head domain is moter; Tail domain holds the cargo; Stock domain is a flexible hinge; most likely 'hand-over-hand' movement.
Term
Nucleolus
Definition
Region of nucleus which has ramped up amplification of genes that code for ribosomal RNA.
Term
MAPs
Definition
Microtubule associated proteins; due to their state of phosphorylation they will generate 3D arrays of microtubules.
Term
Cytoplasmic Dynein
Definition
Molecular motor associated with microtubules; (-) end direction; has high molecular weight with two heavy chains and many light and medium chains; involved in chromosomal and vesicular movement, Golgi body positioning, and cilia and flagella motion.
Term
Robert Hook
Definition
Invented the microscope; first looked at cork and observed what he termed the "cell".
Term
Leeuwenhoek
Definition
Looked at a drop of pond water and saw organisms termed "animalcules"; also discovered bacteria by scraping his teeth.
Term
Schleiden & Schwann
Definition
Proposed the first bit of cell theory: that all organisms are made of one or more cells and that the cell is the structural unit of life.
Term
Virchow
Definition
Added the third tenant countering sontaneous generation: that all cells come from pre-existing cells.
Term
Hans Driesch
Definition
Isolated the four cells of sea urchin embryos and observed that each became four whole larvae.
Term
Three Domain Scheme
Definition
Division into Bacteria, Archaea, and Eukarya based on genetic sequences of ribsomes.
Term
Provirus
Definition
Viral DNA inserted into host DNA which can be activated by UV.
Term
Co-option (or Recruitment)
Definition
When inserted pro-viral DNA has a different function in the host than a virus on its own.
Term
Viroids
Definition
Nucleic acid particles without a protein coat; 1/10 size of typical viral genome; hijacks host RNA polymerase to reprodue itself; eg) cadang attacked cconut tree monoculture.
Term
Prion
Definition
Protein only; responsible for Creutzfeld-Jakob / mad-cow disease; a mutant protein with abnormal folding which triggers normal proteins to change as well; mutant protein is insoluble aggregate which causes holes in brain tissue.
Term
Transmission Electron Microscopes
Definition
Form images using electrons that are transmitted through the specimen.
Term
Scanning Electron Microscope
Definition
Form images using electrons that have bounced off the surface of the specimen.
Term
Davson-Danielli Plasma Membrane Model
Definition
Two-layered; universal bilayer.
Term
Singer and Nicolson Plasma Membrane Model
Definition
"Fluid-mosaic"; realization of utilization of membrane proteins.
Term
Current Plasma Membrane Model
Definition
Associated with membrane proteins are sugar chains beyond the lipid bilayer.
Term
Integral Proteins
Definition
Span e and p face of membrane; alpha-helical structure; domain architecture (external, membrane, and cytoplasmic).
Term
Peripheral Proteins
Definition
Have covalent interaction with integral proteins or phosphate heads of phospholipids.
Term
Third class of Membrane Proteins?
Definition
Lipid-anchored.
Term
PAGE
Definition
Polyacrylamide Gel Electrophoresis; analysis is based on the relative mobility in an electrical field which determines relative molecular weight of proteins.
Term
FRAP
Definition
Fluorescence recovery after photobleaching: studies the movements of membrane proteins.
Term
Freeze-Fracturing
Definition
Fractures along the membranes can tell us directly which side membrane proteins are associated with.
Term
Glycophorin A (B, C, D)
Definition
Integral membrane which spans the erythrocyte membrane once; 60% of weight made up by 16 oligosaccharide chains; has negative charge due to sialic acid whic keeps red blood cells from clumping; first membrane protein to be comletely sequenced; also fuctions as receptor for malarial protozoa.
Term
Hydropathy Plot
Definition
Looks at the free energy of each amino acid in a protein; when plotted a ΔG+ spike corresponds to a membrane-spanning domain because it is un-charged, stable, and requires energy to break it down.
Term
Band 3 Membrane Protein
Definition
In erythrocytes; a channel for anion movement: HCO3- and Cl- for gas exchange.
Term
3 Types of Passive Transport
Definition
1) Diffusion 2)Ion Channels 3) Facilitated Diffusion
Term
Aquaporin
Definition
Channel for which water enters cells via osmosis.
Term
Ion Channels (2 Types)
Definition

1) Voltage-gated: differences in ion charges across membrane.

2) Ligand-gated: binding of a ligand. 

Term
GLUT
Definition
Glucose Transporter proteins: Facilitated diffusion; Proteins' presence in membrane is regulated by insulin.
Term
Patch-clamp
Definition
A microelectrode in a micropipette applies a voltage to the enclosed patch of membrane and the responding flow of ions is measured.
Term
S4 Domain of K+ Channel
Definition
One of six membrane spanning domains; functions as a voltage sensor to affect the closure of the channel: resting - pore closed ball in place, polarized - globular ball region pops out.
Term
Site-directed Mutagenesis
Definition
Change single amino acids in a polypeptide and look at the effect on its function.
Term
Active Transport
Definition
Transport that requires energy from ATP; Receptor has ATPase activity which causes phosphorylation and conformational change to affect the binding domain and move ions against their concentration gradient.
Term
Secondary Active Transport of Co-transport
Definition

Active transport plus utilization of concentration gradients; spatial differences in cell of different types of pumps. Eg) Na+/glucose - apical, GLUT2 - basal, Na+/K+ - lateral. 

 

Term
Neuron Directionality
Definition
Dendrite → Axon → Effector
Term
Action Potential
Definition
  1. Resting
  2. Na+ channels open so Na+ flows into cell, K+ channels are closed
  3. Na+ channes close, K channels open so K+ flows out of cell
  4. K+ channels close slowly
  5. Cell returns to resting state
Term
Saltatory Conduction
Definition
Neurons are sheathed with gaps called Nodes of Ranvier; an action potential can only be generated at a node and then can trigger an action potential at the next node, so the impulse jumps from node to node very fast.
Term
Synaptic Transmission
Definition
  1. Action potential reaches terminal knob (cytoplasmic extensions)
  2. Ca2+ gates open and Ca2+ goes into presynaptic cell
  3. Ca acts as a fusigen for vesicles containing the neurotransmitter to be released into the cleft
  4. Binding and transport of neurotransmitter into postsynaptic cell
  5. Depolarization or hyperpolarization generated
  6. Enzymes break down the neurotransmitter
Term
4 Main Types of Extracellular Materials
Definition
  1. Collagens
  2. Proteoglycans
  3. Fibroectin
  4. Leminin
Term
Collagen
Definition
Most abundant protein in human body; family of fibrous glycoproteins; acts like steel frame for structure; made by fibroblasts; made of α-helical trimer.
Term
Proteoglycans (with GAGs)
Definition
Protein-polysaccharide complexes; core protein with GAGs (glycosaminoglycans), which are repeat disaccharides with a negative charge; the negative charge binds to lots of water making it a shock-absorbant gel found in cartilage.
Term
Fibronection
Definition
Dimer with multiple binding domains - for other extracellular matrix molecules - for cell surface receptors; important in embryonic cell migrations.
Term
Laminin
Definition
Glycoprotein made of three different types of polypeptides for specific conformation; important in axon guidance, germ cells, and cancer.
Term
RGD
Definition
Amino acid sequence arg-gly-asp on extracellular matrix molecules which binds to integrins.
Term
Aggrastat
Definition
Antithrombic agent: nonpeptide drug with RGD-like domain that binds to platelet integrins.
Term
ReoPro
Definition
Antithrombic agent: specific antibody against αIIbβ3.
Term
Integrins
Definition
Integral membrane proteins with two membrane-spanning proteins held non-covalently together; each has an extracellular domain for ligand binding and cytoplasmic domain for link to cytoskeleton.
Term
Hemidesmosomes
Definition
Basal eithelial surface and basement membrane complex.
Term
Focal Adhesions
Definition
Sites that bind cells to their substrates.
Term
Selectins (3 types)
Definition

Cells return to where they were made because of a specific glycoprotein; long extracellular domain.

  1. E-selectin: endothelial cells
  2. P-selectin: endothelial platelets
  3. L-selectin: leukocytes 
Term
Immunoglobin Superfamily (IgSF)
Definition

Cell-adhesion molecules; basis of immunology.

  • VCAM: vascular cell adhesion
  • NCAM: neural cell adhesion - CNS
  •  L1: adhesions between cells, nerve outgrowth, synapse development
Term
Cadherins
Definition

Glycoprotein family; join cells of similar type so tissue specific.

  • E - epithelial
  • N - neural
  • P - placental 
Term
Adherans junctions
Definition
Cadherins and Ca2+ hold cells together; important for signal transduction.
Term
Desmosomes
Definition
Made of desmogleins and desmocollins which join together like velcro; related to caherins; for epithelium.
Term
Tight Junctions (Zonulae Occludens)
Definition
Integral protein in the apical membrane region; responsible for the blood-brain barrier.
Term
Gap Junctions
Definition
Allow cell-to-cell communication by flow of specific solutes; made of connexon and connexin, which can close with increase of intracellular Ca2+ and phosphorylation of connexin.
Term
Plasmodesmata
Definition

Cylindrical channels in plants; can dialate to allow movement of RNA and protein so signal transduction can take place; made of 3 molecules:

  • hemicellulose - branched polysaccharides
  • pectin - (-) charged polysaccharides (like GAGs)
  • structural proteins 
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