PHRD5025 Biochem Lecture 9 (Bain) - Chemical Logic & Thermodynamics

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PHRD5025 Biochem Lecture 9 (Bain) - Chemical Logic & Thermodynamics
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2013-10-27 23:57:12
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Chemical Logic Thermodynamics
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Chemical Logic & Thermodynamics
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  1. Km
    [S] when enzyme is half its maximal velocity (half of enzyme working, half not)
  2. Why is Hb not an enzyme?
    enzymes involve making/breaking covalent bonds, Hb does not
  3. process in which organisms take chemical energy present in fuel sources & convert in to synthesize complex, highly ordered macromolecules capable of doing biochemical work
    energy transduction

    (ex: gas in car converted into mechanical energy)
  4. catabolism
    • oxidation of carbs, proteins, fat, which produce CO2, H2O, and release of energy
  5. products of catabolism
    CO2, H2O, energy release
  6. anabolism
    • simple precursor molecules are built up into complex molecules - lipids, proteins, nucleic acids
    • biosynthesis
    • requires energy
  7. removal of electrons
    oxidation
  8. 1st thermodynamic law
    energy may be changed/transported, but cannot be created/destroyed
  9. 2nd thermodynamic law
    in any natural process, the entropy (disorder) of the universe increases
  10. "heat death" of the universe
    there is always a loss of useful energy (G) and an increase in unusable energy (heat) and entropy (S), while total energy stays the same
  11. pathways used to form acetyl-CoA for CAC (4)
    • 1) glycolysis
    • 2) -oxidation 
    • 3) urea cycle
    • 4) amino acid degradation
  12. what makes ATP so stable?
    even during removal of a phosphate, charge repulsion is reduced, leading to both molecules moving from a higher to a lower energy state (large -G)
  13. important high energy thioester
    acetyl-CoA
  14. 2 central features of metabolism
    • 1) phosphoryl group transfers
    • 2) electron transfer
  15. how chemotrophs obtain energy
    from the oxidation of molecules such as glucose or FAs
  16. final acceptor of electrons
    O2
  17. how are electrons transferred?
    via pyridine nucleotides
  18. molecule that is reducing-agent/reductant
    electron-donating molecule
  19. molecule that is the oxidizing agent/oxidant
    electron-accepting molecule
  20. what NAD+ & NADP+ are derived from
    niacin
  21. ____ (NAD+/NADH) is the electron acceptor.
    NAD+
  22. ____ (NADP/NADPH) is the electron acceptor.
    NADP
  23. what NAD stands for
    nicotinamide adenine dinucleotide
  24. reaction by which ethanol is broken down
    redox
  25. molecules such as NAD+, NADP+, and FAD are ______ during catabolism.
    reduced (gain electrons)
  26. the 3 stages of energy extraction
    • 1) acetyl-CoA production (glycolysis)
    • 2) acetyl-CoA oxidation (TCA)
    • 3) electron transfer & oxphos
  27. 3 levels of metabolic regulation
    • 1) [regulatory enzymes]
    • 2) catalytic activities of various enzymes (allosteric regulation, covalent modification)
    • 3) relative levels of ATP, ADP, AMP
  28. starting components of energy extraction (3)
    • 1) carbohydrates
    • 2) proteins
    • 3) fats
  29. carbohydrates are predominantly...
    cyclized polyhydroxyl aldehydes or ketones
  30. empiric formula of many (but not all) carbohydrates
    (CH2O)n
  31. 2 common hexoses
    • 1) glucose (aldohexose)
    • 2) fructose (ketohexose)
  32. pentose components of nucleic acids (2)
    • 1) D-ribose (aldopentose)
    • 2) 2-deoxy-D-ribose (aldopentose)
  33. monosaccharides are ____ (chiral/achiral).
    chiral
  34. -D-glucopyranose OR -D-glucose
  35. -D-glucopyranose OR -D-glucose
  36. what kind of significant bond do disaccharides contain?
    glycosidic bond
  37. components of lactose
    galactose & glucose
  38. components of sucrose
    glucose & fructose
  39. components of trehalose
    2 glucose
  40. describe the structure of starch
    unbranched, (1->4)-linked D-glucose
  41. describe the structure of glycogen
    polymer of (1->4)-linked subunits of glucose, with (1->6)-linked branches
  42. effects of glycogen branches (2)
    • 1) increase solubility of glycogen
    • 2) involved in regulation of glycogen breakdown
  43. stored fuel in animal cells
    glycogen
  44. where glycogen is found (2)
    • liver
    • skeletal muscle
  45. if K'eq >1, G'o is ___ and the reaction proceeds ___.
    negative (-); forward
  46. if K'eq =1, G'o is ___ and the reaction proceeds ____.
    0; is at equilibrium
  47. if K'eq <1, G'o is ____ and the reaction proceeds ____.
    positive (+); in reverse
  48. (formula): G'o =
    G'o = -RT ln K'eq
  49. (formula): Keq=Ka=
  50. units of Ka
    1/Molar
  51.  =
     OR 
  52. Gibbs free energy thermodynamics has a direct relationship to the speed of the
    reaction. True or False?
    FALSE
  53. What value can we find when =0.5?
    Kd
  54.  is equivalent to Vo.  True or false?
    TRUE
  55. Kd
    • ligand concentration ([L]) at which P is half saturated
    • 1/Ka
  56. Which has the stronger affinity: Anti-­HIV Immunoglobulin (Kd = 4x10-­10M) or
    Calmodulin (Kd = 3x10-­6M)?
    Anti-HIV Ig 

    (larger negative exponent, higher affinity)

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