Exam 1 Study Guide
Exam 1 Study Guide BME 302
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This 7 page Study Guide was uploaded by Hailey Rooney on Wednesday February 25, 2015. The Study Guide belongs to BME 302 at University of Miami taught by Dr. Agarwal in Spring2015. Since its upload, it has received 139 views. For similar materials see Cellular Engineering in Biomedical Sciences at University of Miami.
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Date Created: 02/25/15
Cellular Engineering Exam 1 Study Guide Basic Cell Info 0 Personalized medicine acquire cells from patients differentiate them into different cell types engineer tissues specific to patient test therapies on a patient by patient basis 0 Plasma membrane 0 Phospholipid bilayer impermeable to watersoluble molecules 0 Transmembrane protein channels and transporters actively move nutrients across 0 Ion channels facilitate rapid ion transport 0 Small molecules and ions passively diffuse across the membrane 0 Cytosol liquid inside cells consisting of mostly water pH 774 0 Ion concentrations via ion channels maintain osmolarity so the cell doesn t burst 0 Cytoplasm cytosol organelles 0 Nucleus 0 Contains chromatin DNA and scaffolding proteins and a nucleolus ribosome production factory 0 Nuclear envelope composed of two lipid bilayer membranes forms an impermeable barrier to the cytoplasm I Molecules transported in and out through nuclear pores small molecules freely diffuse through large molecules selectively transported 0 Nuclear lamina network of intermediate filaments lamins inside the envelope that provides mechanical support and organizes chromatin in the nucleus 0 Chromosome DNA and proteins that package and condense it I DNA tightly coiled around histones 0 Histones 0 Core histone segments of DNA tightly coil around 8 core histone proteins to form a nucleosome beads on a string 0 Linker nucleosomes can coil around themselves to form condensed fibers due to linker histone proteins 0 Nucleosomes coil around themselves to form condensed fibers by using linker histones 0 Heterochromatin tightly packed silent DNA sequence 0 Eucrhomatin loosely packed and easily accessed expressed DNA 0 Transcription DNA I RNA 0 1 RNA polymerase binds to DNA 0 2 Polymerase breaks the H bonds between base pairs to open up the DNA 0 3 Polymerase makes a strand of RNA complimentary to the DNA 0 4 H bonds break RNA strand released 0 5 H bonds reform between the original DNA strands 0 6 RNA polymerase releases from the DNA 0 mRNA processing after mRNA is transcribed 0 altered nucleotide added to 5 cap beginning sequence adenines added to end of sequence to create a 3 polyA tail noncoding introns spliced out only coding exons are left mRNA export exported to nucleus after processing nuclear pores recognize the 5 cap and transport the mRNA from the nucleus to the cytoplasm DNA structure 0 Two complimentary strands of nucleotides form a double helix 39 Nucleotide sugarphosphate backbone and a base pair adenine thymine guanine cytosine RNA structure 0 Singlestranded uses uracil in place of thymine different sugar backbone less stable Gene segment of DNA that codes for a specific protein 0 Promoter region DNA sequences that bind transcription factors 0 Transcription factors recruit RNA polymerase to initiate gene transcription downstream of the promoter region tell the cell to express a gene 0 Enhancersuppressor sequences turn on and off gene expression by binding additional transcription factors or repressors RNA polymerase enzyme that synthesizes the formation of RNA from a DNA template RNA types 0 Messenger transported to ribosomes and translates a gene into a protein 0 Transfer recognizes codons on mRNA and carries amino acids into the ribosome I Single strand of RNA folded in a clover leaf type of 3D structure 39 Contains anticodon sequence to bind to mRNA amino acid specific to a codon 0 Ribosomal structural component of ribosomes Histone modification histones bind to DNA electrostatically histone DNA 0 By adding HATs histones lose their positive charge and DNA binding is reduced and DNA is decondensed and can then be transcribed 0 Adding HDACs removes acetyl groups to restore positive charge and helps condense the DNA DNA methylation methyl groups added to cytosine nucleotides which recruits HDACs condenses the DNA and silences expression Know stages of blastocyst development was in homework Epigenetics mechanisms to regulate gene expression beyond the DNA sequence 0 Histone acetylation and DNA methylation are two mechanisms Translation RNA I protein 1 Initiator tRNA binds to start codon on mRNA 2 Ribosome subunits assemble and bind at 5 cap of mRNA 3 In the ribosome tRNA with an amino acid binds to codons on the mRNA 4 Each tRNA attaches to its amino acid to the polypeptide chain 5 Ribosome moves forward on the mRNA and releases the empty tRNA 6 Stop codon is reached release factors halt translation ribosome releases the protein 0 Protein linear chain of covalently bonded amino acids 0 20 amino acids each consisting of a carbon atom carboxyl group amine group H atom and side chain R 0 Ribosome consists of protein and rRNA 0 Bind to mRNA and translate it into amino acids to form a protein 0 Assembled in the nucleus at nucleoli consist of two subunits that only join when they bond to mRNA 0 Some free in the cytoplasm some attached to the rough ER 0 Codon three mRNA nucleotides that code for a specific amino acid 0 Redundant same amino acid can have multiple codons 0 Not ambiguous each codon only codes for one amino acid 0 Start codon AUG binds to initiator tRNA then ribosomes bind to mRNA to begin translation 0 Stop codons UAA UAG UGA don t recognize a tRNA bind to release factors which signal ribosomes to stop translation 0 Endoplasmic reticulum network of membranebound vesicles 0 Rough coated by ribosomes I Two ribosome subunits assemble on mRNA in the cytoplasm if the newly translated protein has an ER docking sequence the ribosome docks to the ER membrane and translates the protein into the lumen 0 Lumen contains proteins that catalyze folding and assembly of newly synthesized proteins misfolded proteins exported to cytosol properly folded proteins packaged into vesicles that bud off the ER to the Golgi 0 Smooth site of lipid synthesis 0 Golgi apparatus stacks of membranebound structures cisternae the cell s post office 0 Receives proteins from the ER and adds carbohydrate side chains 0 Proteins leave the Golgi in vesicles and travel to their final destination 0 Lysosomes break down proteins nucleic acids carbs etc trash incinerator 0 Acidic pH of 50 for optimal hydrolytic enzyme activity 0 Mitochondria regulate metabolism power plant 0 Have their own DNA an outer membrane an inner membrane and intermembrane space similar to cytosol and a matrix 0 Inner membrane proteins that perform oxidative phosphorylation to generate ATP within the matrix is mitochondrial DNA and ribosomes for making mitochondrial RNA and proteins Cytoskeleton 0 Cytoskeleton consists of three types of fibers 0 Actin microfilaments most abundant intracellular protein I Gactin free monomer globular protein hydrolyzes ATP to ADP I Factin linear polymer microfilament consisting of Gactin monomers I Two actin filaments wrap around each other to form a more stable helix 0 Microtubules I Stiff hollow cytoskeletal fibers that radiate from the center of the cell I In all eukaryotic cells I Tubulin subunits consist of a tubulin and btubulin which assemble into linear protofilaments l3 protofilaments assemble into hollow cylindrical tubes microtubules I Dynamic instability constantly growing and shrinking 0 Intermediate filaments ropelike cytoskeletal fibers that form meshed networks I Not in all eukaryotic cells not essential for basic cell functioning I Consist of individual monomer proteins that are elongated and coil around each other into helical dimers I Dimers assemble into ropelike filaments I Prominent in cells under mechanical stress epithelial cells rich in keratin intermediate filaments often outlive the cell itself like in hair and nails Actin treadmilling when subunits are constantly turning over and growing and shrinking occur at similar rates in the actin filament Actin bundling proteins proteins bind to actin to organize filaments into complex networks for cell support and organization Actin force generation actin filaments interact with myosin motor protein myosin heads hydrolyze ATP to slide past actin and generate force All elements are polymers consisting of individual monomers that are noncovalently bonded to allow for rapid assembly and disassembly Sarcomere consists of actin and myosin filaments that slide past each other to shorten the cell and generate muscle contraction link together into long fibers called myofibrils Focal adhesion how cells attach to the extracellular matrix 0 Consist of integrins transmembrane proteins and linker proteins that couple integrins to actin filaments 0 Connect actin cytoskeleton to extracellular matrix Extracellular matrix network of proteins that cells are embedded in Actin polymerization drives cell migration Adherens junctions connect cells into a continuous cytoskeletal network 0 Link together actin filaments of neighboring cells 0 Consist of cadherins transmembrane proteins and linker proteins Tight junctions specialized cellcell junctions usually in epithelial cells that form a selectively permeable barrier 0 Form sealing strands and consist of occludins and claudins transmembrane proteins that bind to others on a neighboring cell 0 Allow tissues to select what molecules in the outside environment can have access to organs Gap junctions cellcell junctions that form pores between cells to allow small molecules to pass through 0 Consist of connexins six connexins assemble into a hexamer pore which couples to connexins on a neighboring cell 0 Allows cells to rapidly communicate with one another Primary functions of actin filaments Mechanically support the cell With myosin filaments generate contractile forces form sarcomeres in muscles Adhere cells to the extracellular matrix via focal adhesions Adhere cells to each other via adherens junctions and tight junctions 0 Drive cell migration OOOO Microtubule organizing center MOTC aka the centrosome 0 Where microtubules emanate from near the center of the cell 0 Lambdatubulin nucleates microtubule growth and caps the minus end of them Intracellular transport microtubules serve as tracks for molecules that transport vesicles and organelles around the cell 0 Molecular motors carry cargo and hydrolyze ATP to walk on microtubules Mitotic spindle formed by microtubules during cell division 0 Centrosomes segregate to opposite ends of the cell microtubules radiate from them and attach to chromosomes motor proteins generate forces to align and separate chromosomes Cilia hairlike appendages that beat with a whiplike motion 0 Consist of microtubules and dynein walks on microtubules Microtubule primary functions 0 Mechanical support 0 Tracks for intracellular transport by molecular motors dynein and kinesin 0 Form mitotic spindle during cell division 0 Form cilia Nuclear lamins intermediate filaments that form a fibrous network underneath the membrane of the nucleus to give it support Desmosomes cellcell junction complexes that couple intermediate filaments from neighboring cells Intermediate filament primary functions 0 Mechanical strength to cells that need it 0 Couple cells together into tissues via desmosomes Tensegrity structures stabilize their shape by tensional integrity rather than continuous compression wires are in tension poles are in compression 0 Muscles generate tension bones bear compression 0 Actin filaments generate tension microtubules bear compression Cell Culture In vivo on a whole living organism 0 Advantages completely native organism monitor effects on organ systems 0 Disadvantages lots of variability difficult to isolate individual factors can only use animal models low throughput expensive 0 Ex vivo on tissues extracted from organisms 0 In vitro on a dish 0 Advantages less variability control over experimental conditions and individual factors can use human cells high throughput cheap 0 Disadvantages nonnative environment no response of other organ systems 0 Enzymatic digestion organtissues extracted from organism incubated with protease enzymes to digest tissue into single cell suspensions O Collagenase cleaves collagen fibers releasing cells from matrix 0 Trypsin cleaves any protein 0 Explant culture organtissue extracted from organism placed into culture dish with media cells migrate out of the explant onto the dish only works if cells are dividing 0 Primary cells taken directly from an organism and their progeny 0 Limited lifespan won t proliferate indefinitely or at all 0 Only way to acquire nondividing cells cardiac myocytes neurons 0 Cell lines cells that can proliferate indefinitely 0 Cells can be immortalized by transfecting them with genes that force them to proliferate indefinitely genes related to cell cycle and aging O Often taken from tumors 0 First cell line taken from Henrietta Lacks HeLa cells 0 Adherent cells attach and grown on surfaces asks Petri dishes multiwell plates 0 Suspended cells don t grow on surfaces often cultured in spin asks 0 Culture media provides nutrients and regulates pH and osmotic pressure 0 Typically contains salts cell function and osmolarity amino acids glucose energy antibiotics buffer maintain pH pH indicator serum growth and adhesion factors 0 Contamination 0 You I Practice sterile technique work in biological safety cabinet coat and gloves spray hands and surfaces with ethanol use sterile tools don t breathetalksneeze over cultures 0 Bacteria most common culture is cloudy and yellow bacterial are smaller than the cells 0 Yeast cloudy look like chain links under microscope O Mycoplasma simple small bacteria difficult to detect can affect behavior wo causing cell death 0 Mold cloudy thin furry filaments O Viruses extremely small and cannot be visualized very rare 0 Cryopreservation cells that divide can be preserved by slowly freezing them and can be thawed and cultured at any time 0 Passaging add trypsin to ask With cells trypsin releases cells from the ask forming a cell suspension suspension can be split into multiple asks 0 Adherent cells that divide can be passaged to grow larger quantities of cells
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