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BIOL 102 - December Exam Summary

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Department
Biology
Course Code
BIOL 102
Professor
Daniel Lefebvre

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Biology – December Exam Summary Notes Chapter 4 – Cell Theory Microscopes  Magnification: image size/actual size.  Resolution (clarity): able to distinguish between adjacent objects.  Contrast: distinguishing different structures (enhanced with dyes). Light microscope Electron microscope Uses Light Electron beam Resolution 0.2μm 2nm Observes -Mitochondria -Lipids -Most bacteria -Ribosomes -Nucleus -Viruses -Most plant/animal cells -Smallest bacteria (also same as light microscope) -Standard light -Transmission electron microscope: thin  Unstained sample: simple, inexpensive slices stained w/ heavy metals some electrons scattered, others pass but little contrast.  Stained sample: better contrast. through forming an image. -Phase contrast: controls path of light to amplify differences in light transmitted/reflected by -Scanning electron micrograph: sample sample. Used for living, unstained cells. coated w/ heavy metal & beam scans -Differential interference contrast: similar to surface to make 3D image. above but used for viewing whole cells or larger structures (e.g. nuclei). -Fluorescence microscope: label particular type cell/organelle (e.g. proteins). -Confocal microscope: uses lasers to give 3D image. Prokaryotic Cells Eukaryotic cells Small Much larger Simple structure Shape, size & organization vary No membrane-enclosed nucleus DNA housed inside nucleus Can have a small amount of internal organization. More complex compartmentalization. Primitive cytoskeleton.  Organelles in membrane bound compartments. Allows rxns to occur that might be incompatible & interfere with rxns in other regions. Bacteria: abundant, mostly not harmful Archaea: less common, extreme environments Organelle Structure Function Cell wall (plants) Provides support & protection. Nuclear Double membrane enclosing nucleus. Helps protect and organize the envelope Formed from endomembrane system. chromosomes. Nuclear pore Passageway into/out of nucleus. Nucleus Inner nuclear matrix proteins form -Contains genetic material (DNA). meshwork organizing each chromosome -Site for ribosome assembly (nucleolus) into its own territory. Endoplasmic Membrane continuous with outer -Protein secretion & sorting (Rough ER) reticulum membrane of nuclear envelope. -Lipid synthesis (smooth ER) Membrane of network forming fluid- -Metabolic filled tubules (cisternae). Golgi apparatus Stack of flattened, membrane-bound Modification/processing, sorting and compartments, not continuous with the secretion of proteins. Glycosylation. ER. Mitochondrion Have outer and inner membranes Site of ATP synthesis – Intermembrane space – Mitochondrial matrix Lysosomes/ -Breakdown of macromolecules, vacuoles -Autophagy (recycling thru endocytosis) -Storage, accumulation of water Peroxisomes Small & found in all eukaryotic cells. Catalyze reactions, breaking down peroxides and other toxic molecules. Ribsomes Synthesize polypeptides – involved in protein synthesis. Plasma Phospholipid bilayer. Acts as a barrier. Controls movement of membrane Semi-fluid mosaic. substances in and out of cell (semi permeable). -Cell signaling and cell adhesion. Cytoplasm Contains everything inside plasma Contains enzymes for metabolism. membrane (including organelles). Cytosol Milieu surrounding organelles inside Site of many metabolic activities of plasma membrane. . eukaryotes. Outside plasma membrane:  Pili: attach bacteria to surfaces and to each other.  Flagella: enable movement (locomotion) & swimming.  Cell wall: provides support and protects cell from damage and bursting.  Glycocalyx: outer gelatinous covering that traps water & provides protection. Metabolism Cytosol is central coordinating region for many metabolic activities. Catabolism: breakdown of molecule into smaller components. Anabolism: synthesis of cellular molecules and macromolecules. Cytoskeleton Mutations of CS proteins often lead to disease. Three types of protein filaments: Cytoskeletal Filaments Microtubules Intermediate filaments Actin Filaments Structure Hollow tube Twisted filament Spiral filament. Location Attached to Around nucleus. Near cell membrane. centrosome. Protein Tubulin Keratin, desmin, lamin… 2 intertwined actin strands. Function -Cell shape -Cell shape -Cell shape -Organelle organization -Mechanical strength -Muscle contraction -Chromosome sorting -Anchorage of cell & -Cell movement -Cell motility (flagella) nuclear membraines - Animal cell division Myosin is a motor protein that uses ATP to walk along actin filaments. What is needed for movement: actin, myosin, ATP! Motor proteins Use ATP to promote movement. -Head, hinge and tail. Three kinds of movement: – Moves cargo along cytoskeleton. – Motor protein remains in place and moves filament. – Motor protein attempts to walk (both the motor protein and filament restricted in their movement), exerting a force causing filament to bend. Chapter 5 – Systems Biology Living organisms studied in terms of their underlying network structure to understand how cell organization arises by complex interactions between various components and parts. Genomes, Proteomes and Cell Structure & Organization  Genome: complete collection of organism’s DNA. Proteome: entire collection of proteins that cell makes, responsible for structure and function. All cells have IDENTICAL DNA but DIFFERENT proteomes. o Gene regulation makes proteome dynamic  Amounts of proteins vary in different cells = specialized.  Cells can respond to changes in environment. o Protein-protein interactions  Guided by sorting signals – direct proteins to correct location.  Very specific allow organizational structures to be built. o Continual synthesis/breakdown of molecules  Enzymes break down proteins into their amino acids. Molecular Machines (e.g. flagella, ribosome)  Moving parts & does useful work  Provide structure & organization to cells  Allow cells to perform complex processes  E.g. ATP synthase o Forms due to molecular recognition  Subunits recognize each other and bind in a specific way Attaining Structure in Cells Cell uses the following to survive by responding to changes in its environment OR diving into 2 cells:  Molecular machines  Genome (provides info. to make mRNA and proteins)  Pre-existing organization  Proteome Lipid synthesis in ER 2 fatty acids + 2 activated molecules (CoA) + glycerole-phosphate  Lateral diffusion o ER  nuclear membrane  Transported via vesicles o Bud of ER, fuse with Golgi  Lipid exchange proteins The Cell is a System with Four Major Components 1. The nucleus  Protects DNA from damage, replicating & packaging DNA for cell division  Using DNA to make RNA and processing RNA  Gene regulation  Organization/protection of chromosomes 2. The cytosol  Coordinates response to environment o Changing expression of genes in the nucleus  Coordinates metabolism  Synthesis of proteome (major site of translation)  Organization/movement via cytoskeleton and motor proteins 3. Semi-autonomous organelles (contain own genetic material)  Mitochondria (ATP synthesis) & chloroplasts (photosynthesis) 4. Endomembrane system  Network of membranes enclosing the nuclear envelope, ER, Golgi, lysosomes, peroxisome, vacuoles & including plasma membrane.  Does not inlclude materials within nucleus.  Very dynamic – structure changes over time  Transport via vesicles amongst various compartments o ER  Golgi  plasma membrane Sorting Proteins Sorting signals: short stretches of amino acid sequences - direct proteins to correct cellular location. Most eukaryotic proteins begin synthesis on ribosomes in the cytosol.  No sorting signal if they are to stay in cytosol (e.g. plant NADHK)  Cotranslational: to ER, Golgi, lysosome/vacuole or plasma membrane. o ER retention signal recognized by SRP so translation is paused. o Other proteins transported by vesicles  Coat proteins = specificity & help vesicle bud off.  V-Snares, recognized by t-snares in target membrane.  Post-translational: nucleus, mitochondria, chloroplast, peroxisomes. SRP – signal recognition particle 1. SRP binds to ER signal sequence, pausing translation. 2. SRP binds to receptor in ER membrane. 3. SRP released and translation resumes. Growing polypeptide threaded into channel protein directely into ER lumen. 4. Protein completely formed and released into ER lumen. Molecular Recycling Large molecules have finite life times (EXCEPT DNA)  Half life: time for 50% of molecules to be broken down) o Prokaryotic mRNA 5 min. o Eukaryotic mRNA 30min – several days  Lysomes: autophagy  Cytosolic enzymes: degrate RNA, polysaccharides & lipids  Proteases: recognize proteins and take them to proteasome o Ubiquitin directs unwanted proteins to proteasomes o Degraded by proteases into peptides and amino acids o Targets misfolded proteins. o Critical for environmental response. Extracellular matrix Provides strength, support, organization and cell signaling. No sorting Post- Cotranslational signal translational Synthesis halts until ribosome is bound to ER After protein is made. Sorted to •Golgi Stay in cytosol •Lysome/vacuole •Plasma membrane Sorted to • Nucleus Polypeptide • Mitochondria containes ER • Chloroplasts retention signal • Peroxisome Proteome Gene Protein- Continual regulation protein synthesis/b interactions reakdown Amountsof Cells respond to Guided by proteins environmental sorting Very Enzymes vary changes signals specific Proteins --> aminoacids Chapter 6 – Membrane Structure and Transport 6.1 Membrane Structure and Composition Phospholipid bilayer Lipids Proteins Carbohydrates Amphipathic Integral Cholesterol found only in animal cells. Form basic matrix Peripheral Hydrophobic, non-polar fatty acyl tails (faces interior) Hydrophilic, polar head (exterior) -Move laterally relative to each other. -Rotate freely along axis. -Only flip with aid of flippase.  Two leaflets of phospholipid bilayer are highly asymmetrical. More fluid Less fluid Shorter acyl tail (less likely to interact) Longer tail Double bond (creates kink) No double bonds (saturated) Cholesterol: makes membrane more Cholesterol: makes membrane less fluid fluid at low temps. at high temps. Glycosylation  Involves covalently attaching carbohydrates to: o Lipid: glycolipid. o Protein: glycoprotein.  Recognition signals for other cellular proteins  Cell surface regulation (migration of individual cells)  Protective: cell coat (glycocalyx  carbohydrate rich zone shielding cell) Microscopy TEM (transmission electron microscopy) FFEM (freeze fracture electron microscopy)  Thin sectioned sample  Specialized TEM  Stained with heavy metal dyes  Analyze interior of bilaryer  Dye binds well to polar head groups  Sample frozen then fractured, leaflets but not nonpolar tails separate  Good 3-D detail. The Phospholipid Bilayer as a Barrier Hydrophobic interior prevents hydrophilic molecules from passing freely. Diffusion Movement of solute from region of higher concentration to lower concentration -Passive: w/o transport protein -Fast (gases and uncharged polar molecules) Slow (ions, larger polar molecules – sugars & amino acids, macromolecules) Cells maintain gradients 1. Transmembrane gradient: conc. of solute is higher on one side of membrane. 2. Ion electrochemical gradient: both an electrical AND chemical gradient.
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