MMG 409 Exam 1 Flashcards
Explain what a eukaryotic cell is and how eukaryotic cells likely evolved.
Eukaryotic cells have membrane-bound nuclei. Likely evolved from archaea that captured a bacterium, symbiosis.
Know which cellular features are specific to eukaryotes and universal to life on Earth
Eukaryotes: membrane-bound nucleus; membrane-bound organelles, lots of genes and non-coding regions.
All life has ribosomes, require an input of free energy, surrounded by a plasma membrane.
Distinguish between cell types based on their features and properties
Archaea: Extremophiles, no nucleus, single-celled, different cell wall from bacteria.
Bacteria: No nucleus, not usually extremophiles, different cell wall from archaea.
Eukaryotes: Membrane-bound nucleus, multicellular.
Define organelle is and the difference between cytosol and cytoplasm
Organelle: membrane bound, preform specific functions and provide the necessary environment for said function.
Cytosol: fluid in cytoplasm surrounding organelles.
Cytoplasm: Everything between nucleus and membrane.
Describe how protein structure and function are controlled by its environment and intermolecular interactions
Proteins must be folded to be functional. Controlled by environment and intermolecular interactions inducing conformational changes to the protein, directly effecting function.
Explain how enzymes function and how their activity is regulated in cells
Enzymes work by lowering the activation energy needed to preform a reaction. They bind to substrates at active sites and induce conformational changes.
Explain what a model organism is and be able to select appropriate models for specific research problems
Model organisms are eukaryotes best suited for studies. They are accessible in lab, reproduce rapidly, easy to visualize, amenable to genetic manipulation. Examples include Free living eukaryotes: yeast (s. cerevisiae), protist (C. spa.); plants (A. thaliana); Invertebrate animals (Nematode, C. elegans and Fruit fly, D. melanogaster); Vertebrate animals (Frog, x. laevis, and zebrafish, D. melanogaster); and vertebrate mammals (Mouse, m. musculus, and humans)
Explain the difference between cultured primary cells and cell lines and decide which would be most appropriate for a given research problem.
Cultured Primary Cells: Cells isolated from intact tissues, differentiated cells, stem cells, physiologically relevant but hard to access large numbers, limited lifespan.
Cell Lines: Cells replicate indeffidently, Immortalized, sometimes cancer cells. Easy to obtain and easier to manipulate, less physiologically relevant.
Explain the utilities and limitations of antibodies and genetic fusions in cell biological research
Immunoglobulins can bind with high affinity to specific molecules. Antibodies bind with high specificity. Useful in western blotting, fluorescence. Allow researchers to ID the protein/organelle they’re looking at. Limitations are that antibodies recognize epitopes, which can change/they only recognize one.
Compare and contrast the use of cell extracts and microscopy to study protein structure and function
In Vivo: Cells are left in tact. Identifies protein interactions, hard to determine if those interactions are direct/indirect and not always physiologically relevant.
In Vitro: Uses cell extracts from lysing population cells to study structure/function. Components separated by mass/density via centrifugations, molecules isolated by chromatography. Determines relative abundance and localization, ID proteins with post-translational modifications.
Know the difference and utility of light, fluorescence, and electron microscopy.
Light microscopy: Outlines cells, detects nucleus, shows live vs. dead cells
Fluorescence: Spatial org. of cell, organelles, and macromolecules. Need biomarkers and tags and probes. Shows specific molecules. Image live and dead cells.
Electron Microscopy: Spatial org. of cell, organelles, membranes. No biomarkers needed, gold particles show electron dense spots. Expensive, time consuming, only fixed/dead cellsz
Explain how antibodies are used to visualize biomarkers by microscopy
Primary antibodies bind molecules of interest, secondary antibodies bind the constant region of primary antibodies, polyclonal antibodies recognize multiple epitopes on an antigen. Anitgens can be made to emit a fluorescent signal when excited.
Explain how proteins are targeted to cellular compartments by signal sequences.
Sorting signals and receptors direct proteins.
Explain the role of mitochondrial physiology in ATP generation by oxidative phosphorylation.
Oxidative phosphorylation is driven by the ETC, which creates a proton gradient across the IMM, powering ATP synthase.
Differentiate between ATP generation by aerobic respiration and fermentation
Aerobic: Uses oxidative phosphorylation and the ETC to generate ATP, generates more ATP than fermentation which occurs when there is no oxygen (Anaerobic).
Explain how the proton motive force is generated and used to synthesize ATP.
As molecules in the OXPHOS system move through the ETC, carrier molecules are oxidized and release protons, generating the proton motive force. As protons try to cross the membrane (diffuse to an area of low concentration) they power ATP synthase, a trans member protein.
Explain why electron transport and oxidative phosphorylation occur in mitochondrial cristae.
Cristae enhance OXPHOS efficiency to max. ATP synthesis, where proton concentration is highest.
Explain the function and spatial organization of electron transport chain complexes and ATP synthase
Electron Transport Chain Complexes:
Complex 1: NADH hydrogenase, moves electrons from NADH to ubiquinone, largest complex, 1/2 of proton motive force.
Complex 3: Cytochrome C Reductase, accepts protons from Complex 1 and releases them to complex 4.
Complex 4: Cytochrome C Oxidase, pumps protons and reduces oxygen to make h2O.
Complex 2: Succinate dehydrogenase, oxidizes succinate and donates electrons.
ATP Synthase: Mechanical energy caused by concentration gradient causes rotations, which change active sites which synthesizes and releases ATP molecules.
Explain the role of mitochondrial lipids in aerobic respiration and cellular homeostasis.
Mitochondrial lipids help to stabilize the super complex composed of the respiratory chain complexes in the crista membrane.
Distinguish between mitochondrial and nuclear DNA and explain maternal inheritance of mtDNA
Mitochondrial DNA is stored within the mitochondria, inherited maternally, 16 kb, circular, little non-coding DNA. Maternally inherited because there is more cytoplasm in female gamete (egg) that (with lysosomes) degrades male mtDNA.
Explain where mitochondrial matrix, IMM, and OMM proteins originate, and which transporters are required for their localization to the mitochondria.
Most mitochondrial proteins are synthesized in the cytoplasm and encoded for in the nucleus. The mitochondria encodes for components of the ETC, and proteins localized in the IMM.
The transporters needed for nuclear proteins localization are: TOM Complex—OMM, translator, inserts proteins into OMM; SAM Complex—Sorting and assembly in OMM; OXA—cytochrome oxidase activity, hydrophobic, inserts nuclear encoded proteins into IMM; TIM—translator into matrix.
List the products of fermentation and explain why it occurs under anaerobic conditions
Occurs when little to no oxygen available to provide energy to the cell. Produces NAD+, lactate or lactic acid (obligate aerobes) or ethanol ( facilitative aerobes
Describe b-oxidation of fatty acids and metabolic coupling of mitochondria and peroxisomes.
Oxidation of fatty acids into acetyl-coA when sugars are limiting. Exclusive to peroxisomes and mitochondria in humans. Uses 1 ATP to generate 1 NADH, 1 FADH2, and 1 acetyl-coA.
Compare ATP generation by sugar metabolism and fatty acid metabolism.
Sugar metabolism: More ATP produced.
Fatty acid metabolism: Less ATP produces.
Explain how detoxification occurs in peroxisomes and why peroxisome abundance differs by cell type
Detoxification occurs by using oxygen to form hydrogen peroxide. 2 reactions: RH2 + O2 = R + H2O2 and H2O2 + R’H2 = R’ + H2O. Goal is to detox R and ROS.
Explain how cell physiology is influenced by dynamic and stable cytoskeletal filaments
Cytoskeletal filaments help control cell shape, transport, support, and signaling. Keeps polarity in non-motile cells, uses accessory proteins to define spatial distribution.
Differentiate between structure, function, and localization of three cytoskeletal filaments.
Actin: G-actin makes up F-actin, + (barbed) end and - (pointed) end. Help cell shape, mechanical support, motility, transport in cell, located at cytoplasmic cortex. Transmits signals.
Microtubules: Hollow tubes, a- and b- tubular dimers, intracellular transport, organelle positioning, cell motility. Located on centrosome and in cilia and flagella. More rigid than actin.
Intermediate filaments: Rope like, flexible, different proteins make it up, structural stability, resists mechanical stress, anchors organelles. Found throughout cytoplasm and near epithelial, muscle, neurons, and connective tissue cells.
Describe the properties of cytoskeletal proteins and filaments
Actin: 3 isoforms, + (barbed) and - (pointed) ends, branched or straight.
Microtubules: Dynamic, a- and b- (hydrolyzes GTP) tubular dimers, + and - end.
Intermediate filaments: Stable, flexible, different proteins, i.e keratin,
Explain how cytoskeleton accessory proteins regulate filament dynamics.
Actin: Regulated by Formin (causes straight filament branches, accelerated polymerization), ARP 2/3 (binds - end, causes actin to branch, activated by nucleation), cofilin (depolymerization), profilin (binds + end, decreases G-actin affinity), myosin (mediates transport, moves toward + end, carries organelles short distances, needs ATP)
Microtubules: Regulated by y-tubulin (causes nucleaziation), Kinesin, dynein,
Distinguish between actin and microtubule filament nucleation and polymerization dynamics.
Actin: spontaneous nucleation, 3 G-actins need to bind for stability, polymerization at + end.
Microtubule: non-spontaneous nuclearization,
Know what transport vesicles are and how they move cargo around the cell.
Transport vesicles move macromolecules around the cell. Membrane enclosed, carry cargo, uses molecular markers and signals to know where to go. Bud from donor compartments as coated vesicles.
Know how Rab GTPases, SNARE proteins, and phosphoinositides contribute to cargo transport.
Rab GTPases: GTPases that direct vesicles to specific regions of target membranes via lipid anchors. Activated by Rab GEFs.
SNARE proteins: Enable fusion of lipid bilayer to facilitate release into target membrane. Membranes must be close and water displaced from hydrophilic surface. Complimentary v-SNARE and t-SNARE pairing. Bind, form trans-SNARE complex, membranes fuse.
Phosphoinositides: lipids, recruit proteins to specific membrane.
Distinguish between pinocytosis, phagocytosis, and receptor mediated endocytosis
Pinocytosis: Non-selective internalization of cargo, lipids, and fluid from plasma membrane. Continuous uptake via protrusions.
Phagocytosis: Uptake of large particles into phagosomes, cargo-triggered, must activate surface receptors. Membrane protrusions engulf pariticle. Mature into phagolysosomes.
Describe endocytic maturation and how cargo is transported to lysosomes
Early endosomes, can recycle cargo to plasma membrane, mature into late endosomes, stops recycling, fuse with each other to mature into endolysosomes for cargo degradation.
Describe phagosome and endocytic maturation pathways from the plasma membrane to cargo degradation.
Early endosomes, can recycle cargo to plasma membrane, mature into late endosomes, stops recycling, fuse with each other to mature into endolysosomes for cargo degradation, which mature into lysosomes.
Describe clathrin, COPI, COPII, and retromer coated vesicle transport
Clathrin: Non-specific cargo, surface receptors, requires actin polymerization, cargo degraded.
COPI. Heavy and light chain, 2 form triskelion, which assembles into coated vesicles. Introduce curvature in membrane. Linked to cargo to be transported.
COPI: Bud off vesicular tubular structure, transported back to ER to return cargo, including cargo receptors, v-SNARES, leaked ER proteins.
COPII: Deliver folded proteins to Golgi. Form and bud from ER exit sites, cargo contains exit signals.
Explain how and why cargo is transported from the ER to the Golgi apparatus
Cargo is transported from ER to Golgi to allow proteins to mature via glycosylation and to be sorted for their final destination. Delivered via vesicles
Describe how lysosomal hydrolases are synthesized, regulated, and transported around the cell
Delivered from Golgi, include acid hydrolase and v-ATPase, originates in ER, moved via transport vesicles, synthesized in ER, sorted by M6P receptor which divers them away from constitutive secretory pathway.
Explain how and why proteins are glycosylated in the ER and Golgi apparatus.
Glycosylation adds carbohydrate moieties and permits protein folding by chaperones in rough ER.
Know the properties of cargo packaged into secretory vesicles and the difference between constitutive and regulated secretion
Both are forms of vesicle transportation from trans Golgi network, two cargo destinations.
Constitutive: Default pathway, vesicles bud off and move toward plasma membrane.
Regulated pathway: Cargo contains signals for diversion/transport to other organelles. Arrive from ER with N-linked oligosaccharide, patch on protein recognized by GlcNAc phosphotransferase which transfers GlcNAc-phosphate to mannose, GLcNAC removed, exposes M6P which facilitates packaging into transport vesicles.
Describe the basic function of the Nucleus and how to distinguish it by microscopy.
Stores genetic info., main site of DNA, RNA, and ribosome synthesis. Controls movement between cytosol and nucleoplasm, has pore complexes. Can be distinguished with fluorescence or TEM.
Describe the basic function of the Endoplasmic Reticulum and how to distinguish it by microscopy.
Controls the synthesis and transportation of proteins and lipids thought the cell.
Smooth ER: lipid synthesis and metabolism
Rough ER: Specific protein synthesis, has ribosomes, to secrete to other cells. Can be distinguished by fluorescence and TEM.
Describe the basic function of the Golgi apparatus and how to distinguish it by microscopy.
Series of compartments that synthesize carbohydrates attached to proteins. Helps to sort and transport proteins. Microscopy is TEM
Describe the basic function of the Lysosomes and how to distinguish it by microscopy.
Break down and digest macromolecules. Fluorescence and Light microscopy
Describe the basic function of the Mitochondria and how to distinguish it by microscopy.
Cellular respiration, metabolism, and signaling. Light electroscope and fluorescence.
Describe the basic function of the peroxisome and how to distinguish it by microscopy.
Utilizes molecular oxygen, detoxifies, fatty acid metabolism.
Aerobic
Requires oxygen
Anaerobic
Does not require oxygen
Kinesin
Microtubule, moves cargo toward + end.
Dynein
Moves cargo to - end.
PI(3,4)P2
Recruits AP2 to correct membrane.
KDEL
ER retention signal, tells cargo to be packaged into COPI-coated vesicles.
