Bio-225 First Midterm

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Bio-225 First Midterm
2010-10-03 18:24:36
cells proteins

Cells, Proteins
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  1. Themes of Life
    • -Death
    • -Growth
    • -Ability to heal small injuries
    • -Reproduction
    • -Homeostasis
    • -Open Thermodynamic System (Recycling)
    • -Reaction to environment
    • -Order
  2. Cell Theory
    • -Shedien & Schwann in 1838 stated cells make up all life, come from pre-existing cells, and are basic units of life
    • -Hooke observed cells in cork
    • -Leeuwenhoek observed sperm cells
  3. Common Features of Cells
    • -semi permeable membrane
    • -DNA as info carrier for reproduction and protein synthesis
    • -ribosomes
    • -compartmentalized
    • -similar mechanisms for energy metabolism (Krebs Cycle)
    • -same issues (acquiring energy, making new materials for growth, sorting and organizing things, reproduction, awareness of surroundings)
  4. Prokaryotic Cells
    • -flagellum, pilus, nucleoid, plasma membrane, cell wall, capsule, ribosomes
    • -much smaller
    • -simple shapes (spherical, rod-shaped, spiral)
    • -can form multicellular structures (chains, clusters, etc.)
    • -single compartment with cytoplasm and DNA
    • -can't change shape due to cell wall
    • -some have surface appendages (flagella and pili)
    • -some have infoldings of plasma membrane
  5. Eukaryotic Cells
    • -"true nucleus"
    • -form multicellular organisms
    • -plasma, nucleus, nucleolus (ribosomal RNA synthesis), actin micro filaments (dense mesh at the edge and stress fibers used for structural support across cell), centrosome attachment center for microtubules (reproduction and transporting materials throughout cell), intermediate filaments (structural support), mitochondria (energy), golgi apparatus (mailing center), rough and smooth ER (proteins manufactured in ribosomes and enter smooth, then go to golgi apparatus and sent through transport vesicles to membrane), lisosomes (digestion), endosomes, peroxisomes
    • -plant cells have chloroplasts, cell walls, and a vacuole
  6. Basic Chemistry
    • -building blocks are sugars (polysaccharides store energy), fatty acids (cell membrane and energy storage), nucleotides (DNA and RNA), amino acids (proteins; required for everything)
    • -condensation reactions to make polymers (release water molecule)
    • -DNA --> messenger RNA --> protein
    • -DNA can replicate and divide --> transcription with mRNA --> translation for protein
    • -prions are proteins that make themselves
    • -DNA is in nucleus only due to safety (no mutations can occur)
  7. Amino Acids
    • -monomers in a cell to form polymers
    • -proteins are made of amino acids (monomers)
    • -amino group (partially negative charge, accepts protons in water), carboxyl group (acid, donates proton to water and oxygen becomes more negative), side chain
    • -amino acids ionize in water
    • -nonpolar side chains, polar side chains, electrically charged side chains (can have two carboxyl groups)
  8. Bonds
    • -atoms have electron clouds (shells/orbitals)
    • -nucleus at center
    • -most stable state is when outer-most energy level is complete with 8 electrons
    • -metals are more likely to donate electrons
    • -covalent bond = when two atoms share electrons to form a molecule
    • -non-polar = equal sharing of electrons
    • -polar = non-equal sharing due to number of electrons in outer shell (elements are partially or negatively charged)
    • -hydrophilic = polar molecules that interact with water and form H bonds
    • -hydrophobic = non polar molecules don't mix with water
    • -transferring electrons = ionic bond
  9. Ionization
    • -acetic acid and water --> negatively charged acetate ion and positively charged H3O ion
    • -acid donates H+ in water and becomes negative (attracted to negative oxygen pull)
    • -bases accept H+ in water and becomes positive
    • -dissolving water in water creates hydronium and hydroxides
    • -most amino acids are found in ionized form after reacting with water
  10. Proteins
    • -made of amino acids linked together by peptide bonds
    • -peptide (oligopeptide) = less than 50 amino acids (covalent bonds)
    • protein = 50 or more amino acids
    • polypeptide = peptide (if <50) or protein (if>50)
    • -amino acids join together to form a chain
    • -titin = largest protein; muscle elasticity (34,350 amino acids)
    • -proteins fold in 3-D structures (enabled by side chains) --> identified by function
    • -every protein has one "native confirmation" which usually occurs under normal conditions and is most stable
    • -protein confirmation is determined by amino acid sequence and supported by interaction between amino acid side chains
    • -proteins fold into their native confirmation following an unknown set of rules
  11. Protein Structure Primary
    unfolded, planning stage of amino acid sequence
  12. Protein Structure Secondary
    • -regular local structures formed by short amino acid sequences (non-polar)
    • -Alpha-helix
    • -Beta plated-sheet
    • -hydrophobic interactions
  13. Protein Structure Tertiary
    • -complete three-dimensional form (confirmation) of protein
    • -determines overall fold of protein
    • -binding focus for other molecules
    • -brings together distance amino acids (30-200 amino acids long, can form independently, well-defined, free associated with particular functions)
    • -interactions determine tertiary structure of proteins
    • -hydrogen bond between side chain and carboxyl group; hydrogen bond between two side chains
    • -van der waals interaction (hydrophobic region) --> polar on surface of polypeptide, non-polar side chains in core region, packed very tight
    • -disulfide bonds are formed between two systems in the ER which reinforce the most favored conformation; important for secreted proteins (interchain is strongest) and enforces fold of protein
    • -ionic bond can be acidic, basic, polar, or neutral
  14. Protein Structure Quaternary
    • -assembly of two or more individual molecules
    • -dimer = macromolecular complex formed by two (non-covalent) macromolecules
    • -closed structure = limited capacity to associate (2 to hundreds)
    • -open structures = can polymerize more or less indefinitely
    • -all proteins formed in rough ER
  15. Necessity of Membranes
    • -to protect inside of cell (barrier) and regulate internal environment
    • -regulates what permeates through (semipermeable)
    • -separates contents of cells and organelles --> creates compartments to separate reactions
    • -membrane grows with cell and can deform without tearing
    • -can heal holes
    • -sensor = get information about environment
  16. Membrane Structure
    • -lipid bilayer with incorporated proteins (lipids provide structure but proteins have specialized functions)
    • -hydrophilic head (polar, mixes with water) and hydrophobic tails (nonpolar)
    • -planar with edges exposed is not energetically favorable --> sealed compartments minimizes surface area exposed to water
    • -membrane fluidity is determined by lipid composition
    • -short chain fatty acids (less interaction between tails) allows for more fluidity (more space in bilayer so more movement)
    • -unsaturated fatty acids (double bonds); unsaturated (oils) can't pack as tightly
    • -high cholesterol (stiff, small molecule) --> rigidity (increases when temperature decreases)
  17. Membrane Proteins
    • -transmembrane = nonpolar (polar sequestered inside within lipid bilayer)
    • -membrane-associated
    • -lipied-linked (hook hangs it at membrane)
    • -protein attached = interaction with protein that's already bonded (H and ionic bonds, hydrophobic interaction --> bonds)
    • -membrane fluidity enables membrane proteins to move
  18. Solute Concentration
    • -ions are very small charged particles that can't dissolve in lipids; osmosis never requires energy
    • -isotonic is when the amount of ions in the cell and solution are the same
    • -hypertonic is when the amount of solute is greater outside the cell (opposite for water content)
    • -hypotonic is when the amount of solute is smaller outside the cell (opposite for water content)
  19. Passive Transport
    • -simple diffusion where certain proteins travel through ion channels (pore charged membrane, alpha helix)
    • -generally only inorganic ions
    • -discriminate on basis of size and electric charge (ion selective)
    • -transport is extremely fast
    • -some channels are always open, and some are grated
    • -source of electrical signaling
    • -electrical gradient
  20. Carrier Proteins
    • -bind solute on one side of membrane, release to other side
    • -happens via change in information of carrier protein upon binding solute
    • -required for transport of almost all small organic molecules across cell membranes
    • -act like turnstile
    • -transport is very selective
  21. Active Transport
    • -moves solutes against gradients (creating gradient --> distinct concentrations)
    • -maintain correct intracellular ionic composition
    • -import solutes whose concentration is lower outside cell
    • -pump out the solutes whose concentration is higher outside
    • -coupled transporters link uphill transport of one solute to downhill transport of another
    • -ATP-driven pumps couple uphill transport to hydrolysis of ATP
    • -Light-driven pumps mostly in bacteria and couple uphill transport to energy from light
  22. Entry Points
    • -proteins made in cytosol can either stay or travel to nucleus, transported through pores --> to chloroplasts, mitochondrion, or peroxisomes
    • -proteins made on ER, transported by vesicles (cells decide which proteins will be synthesized on ER by signal sequence); mRNA encoding a protein targeted to ER remains membrane-bound; polyribosome bound to ER membrane by multiple nascent polypeptide chains
    • -Signal Recognition Protein --> SRP, then SRPR (receptor) binds to SRP, ER transports location channel and ribosome binds, synthesis continues, signal peptidose
    • -anterograde secretion pathway (ER --> GA --> PM)
  23. Exocytosis
    • -releases something to the environment
    • -cell picks up something from the environment
  24. Cytoskeleton
    • -microtubules (25um thick --> thickest); tubulin makes it up
    • -actin micro filaments (7um --> thinnest); made up of actin
    • -intermediate filaments (10-15um); different protein composition depending on cell type
  25. Cytoskeleton Functions
    • -maintains cell's shape
    • -anchors organelles in place
    • -makes cell movement possible (cell migration is either crawling or with flagellum)
    • -moves parts of the cell (intracellular transport, cell division, sperm tails, cilia in fallopian tubes and respiratory tract)
  26. Microtubules
    • -long hollow tubes made of tubulin dimers (alpha and beta tubulin)
    • -nucleate at MOTC (main one = centrosome)
    • -matrix proteins --> centrioles
    • -gamma tubulin (negative/bottom end) --> polymerization
    • -beta tubulin at plus end (more likely to grow) --> depolymerization
    • -dynamic instability
  27. Microtubules Functions
    • -cell shape and motility, holding everything in place
    • -intracellular transport - motor proteins (kinesins at + directed end, ER would collapse if blocked; dyneins at - directed end, bring to center)
    • -hold golgi apparatus and ER in place near centromere due to proteins that will bring it back if they escape
    • -cell division in spindle
    • -form cilia and flagella
  28. Intermediate Filaments
    • -stable, not very dynamic
    • -strong and resistant to degradation
    • -provide mechanical support
    • -vary greatly depending on tissue (keratins = epithelial, hair, nails; neurofilaments = strengthen axons of neurons; vilmentins = support for various cells)
    • -intermediate filaments in nucleus (nuclear lamins stabilize inner membrane)
  29. Actin Microfilaments
    • -very variable (strands, networks, bundles, gels)
    • -most abundant protein
    • -very dynamic (reorganization is important for function)
    • -associate with myosin (contractile forces for cell migration and muscles)
    • -can form dense networks with help from accessory proteins and initiate growth of new filaments
    • -actin + myosin = contractility muscle
  30. Cell Motility
    • -immune response (neutrophil chase and leukocytes migrating to wound site)
    • -wound healing
    • -embryonic development
    • -misregulation --> problems (can't get food, escape from predators, congenital birthday effects, cancer metastasis, chronic inflammatory diseases)
    • -migration cycle = 1.protrusion--> confined to leading edge, polymerization of actin pushes the PM forward, need to deliver new membrane components 2. attachment (form new adhesions 3. contraction (actin + myosin) 4. release of attachments at cell rear (focal adhesion dynamics)