biochem 2

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biochem 2
2013-05-12 19:09:59
biochem bio

biochem 2
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  1. What are six functions of proteins and give example
    • transport: hemoglobin binds to oxygen + transport
    • movement: myosin caises contraction o muscle fibres w/ actin
    • hormones: insulin binds to receptors in plasma memb. o target cells causing them to remove glucose fr blood
    • defence: immunoglobin act as antibodies to inactivate/destroy foreign antigens
  2. Explain significance of polar and non-polar amino acids (3)
    • controlling position of proteins in membranes
    • creating hydrophilic channels through membranes
    • specificity o active sites in enzyme
    • polar have hydrophilic r group, non polar opp
  3. Explain non polar / polar AA for position o proteins in membranes
    • polar aa found on parts protein molecule tt protrude fr membrance b/c water exists there, in ECF and cytoplasm
    • non polar Aa found in parts o membrane proteins embedded in plasma membrane = keeps proteins embedded /stabilizes structure
    • polar aa create channels in transport proteins where hydrophilic substance can diffuse through P.M.
  4. specificity o active sites in enzymes (polar/non polar aa)
    • If the amino acids in the active site of an enzyme are non-polar -> active site specific to non-polar substrates
    • if the active site = polar amino acids then the active site is specific to a polar substance
    • AA w/ postively charged r groups -> attract negatively charged substrate ions; vice versa
  5. hydrophilic channels through membranes
    • polar aa on surface o proteins make them water soluble
    • non polar aa in centre = stabilize
    • non polar aa cause proteins to remain embedded in membranes
    • polar aa create channels which hydrophilic substances can dissolve
  6. enzyme
    • biological catalysts for chemical reactions
    • Are globular proteins (tertiary or quaternary structure)
    • Have active site where the specific substrates bind
    • Influence stability of bonds in the reactants, can form bonds (anabolic)or break bonds (catabolic)
    • affected by temperature, pH,
      lowers activation energy o chemical reaction
  7. active site
    • Region on the surface of an enzyme to which substrates bind
    • catalyzes a chemical reaction involving the substrates.
  8. similarities lock and key model and induced fit model for enzyme activity
    • both involve quaternary/tertiary protein w/ an active site
    • lowering o activation energy in chemical reaction
    • product detaches fr active site after reaction
  9. differences lock and key model and induced fit model for enzyme activity
    • LK: assumes active site and sub match exactly
    • IF: not exactly
    • LK: substrate fits exactly into active site
    • IF: induced after binding
    • LK: active site fits only one substrate
    • IF: several similar but different substrates can bind
  10. lock and key model
    • assumes active site and sub match exactly, not other molec fit or attracted
    • enzyme lock, sub key
    • enzyme sub collide; sub binds
    • active site catalyzes chemical reaction
    • sub turns into product and detaches
  11. induced fit model
    • until substrate binds, active site doesnt fit sub exactly
    • sub approaches active site w/ KMT
    • shape of active site changes as sub approaches and binds
    • then fits exactly
    • sub induces change in enzyme which weakens sub bonds -> product
    • detaches fr enzyme b/c doesnt fit active site anymore
    • several diff but similar sub can bind to one enzyme
  12. denaturation
    • structural change in protein that results in loss (usually permanent) of biological properties
    • caused by heat and pH
  13. what four factors affect enzyme activity?
    • enzyme concentration
    • substrate concentration
    • temperature
    • pH
  14. enzyme concentration
    • if plenty substrate available, increasing enzyme concentration increase reaction rate
    • direct positive correlation
  15. substrate concentration
    • if concentration enzyme fixed and conc. substrate increase, rate o reation will increase then level
    • enzyme becomes saturated as active sites filled
  16. temperature effect on enzyme activity
    • higher temperatures increas rate o collision b/twn sub and enzyme
    • reaction rate increase
    • however few can tolerate temp above 50 - 60 degress cel
    • enzymes have optimal temp
    • above, heat denatures enzyme
  17. pH on enzymes
    • all have optimum pH generally b/twn 6 and 8
    • extremes o pH reduce enzyme activity
    • both acids and bases denature enzymes
  18. explain use o lactase in production o lactose free milk
    • example o industrial process depending on biotech
    • methods are huge and increasing economic importance
    • lactose naturally in milk, -> changed into glucose + galactose by lactase
    • people intolerant can't produce those enzymes;= diarrhea, cramps, bloating
    • can consume lactose free milk produced using lactase obtained fr yeast, naturally grows in milk
    • lactase extracted fr yeast, purified sold as immobilized enzyme
    • milk passed through column lactase, breaks down lactose = lactose free milk w/o lactase
    • lactase can be added as well
  19. what do metabolic pathways consist of?
    Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.
  20. how do enzymes lower the activation energy of the chemical reactions that they catalyse?
    • Most reactions are exothermic
    • energy released by the new bonds formed is less than the activation energy.
    • Reactants of a chemical reaction need to gain energy (activation energy) before they can undergo the reaction.
    • needed to break bonds within the reactants.
    • substrate changed into transition state, diff fr trasition state during reaction when enzyme not involved
    • transition state w/ binding to active site has less energy and is how enzymes reduce activation energy
    • later stage in the reaction energy will be released as new bonds form.
  21. competitive w/ ref to ex
    • competitive: inhibiting molecule structurally similar to substrate binds to active site, competes w/ substrate binding
    • ex
    • inhib folic acid synthesis in bacteria by prontosil
    • can be overcome by increasing substrate concentration, increases chance that sub binds to enzyme
  22. non competitive inhibition and ex
    • non competitive: binds to enzyme, not active site, causes conformational change
    • change in active site -> reduces effectiveness or makes it unable to bind at all
    • does not compete directly for active site
    • sub cant prevent binding o inhibitor despite concentration so maximum enzyme activity rate lower than no inhibitor
    • ag+, cn- inhibit enzymes cytochrome oxidase (cellular resp) binds to -SH group, breaks disulfide linkages that hold tert. structure o enzyme
  23. allosteric regulation
    • allosteric enzymes have two non-overlapping binding sites; one active, one allosteric site
    • regulatory molc behave like REVERSIBLE non competitive inhibitors
    • change enzymes shape and function by binding weakly to allosteric site; specific receptor site on enzyme molc remote fr active site
    • structure enzyme altered so substrate less likely to bind to active site
  24. explain role control o metabolic pathways by end product inhibition and role o allosteric sites
    • metabolic pathways, product o last reaction inhibits enzyme that catalyses first reaction = end product inhibition, allosteric inhibitor
    • end product if amount large enough will bind to allost site shutting down pathway preventing creation o more end product
    • reversible,when end product lessens,detached enzyme returnes to original shape so active site can bind substrate again
    • regulates metabolism according to req o organism
    • negative feedback or feedback inhibition, stops or slows chemical reactions inside cell
    • e.g. surplus ATP = allosteric reg o one or more pathways involved in cellular resp by binding to phosphofructokinase
    • e.g. threonine binds to theronine dehydratase, end product isoleucine inhibits threonine dehydratase
  25. Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate, draw
    • DNA composed o subunits called nucleotides
    • deoxyribonucleic acid
    • circle phosphate group
    • pentagon sugar (deoxyribose)
    • rectangle nitrogenous base
  26. Name four bases o DNA
    • GACT
    • guanine
    • adenine
    • cytosine
    • thymine
  27. Outline how DNA nucleotides are linked together by covalent bonds into a single strand
    A covalent bond forms between the sugar of one nucleotide with a phosphate group and the phosphate group of another nucleotide.
  28. draw 3 rungs of DNA ladder with letters labelled, relative sizes and positions of deoxyribose should be accurate, hydrogen bonds
  29. explain how DNA double helix is formed w/ complementary base pairing and hydrogen bonds
    • DNA is made up of two nucleotide strands.
    • connected together by covalent bonds within each strand.
    • sugar of one nucleotide forms a covalent bond with the phosphate group of another.
    • two strands themselves connected by hydrogen bonds.
    • hydrogen bonds found between the nitrogen bases of the two strands of nucleotides.
    • Adenine forms hydrogen bonds with thymine
    • Guanine forms hydrogen bonds with cytosine.
    • called complementary base pairing.
    • A nucleotide will only pair with another if it is “upside down”, therefore 1 strand runs opposite though parallel
    • Bonds between the strands creates a double helix shape that resembles a twisted ladder