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2013-05-05 01:30:32
biochemistry chemistry organic molecues

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  1. Aldose
    Monosaccharide that has an aldehyde group.
  2. Ketose
    Monosaccharide that has a ketone group.
  3. Monosaccharide
    Simple sugar (carbohydrate) such as glucose and fructose
  4. Polysaccharide
    • Polymer that contins many monosaccharides
    • eg. cellulose in plants, glycogen in animals
  5. Glucose
    Simple carbohydrate,  main energy source in plants and animals. 

  6. Sucrose
    The molecule is a disaccharide composed of the monosaccharides glucose and fructose.

  7. Fatty Acid
    Monocarboxylic acid (R-COOH) that contains an even number of C atoms.  Under normal physiological conditions exists in ionized state (R-COO-).  Component of lipids, insoluble in H2O.

    • Saturated: no C=C
    • Unsaturated: one or more C=C
  8. Ester
    Carbonyl adjacent to an ether linkage.
  9. Nucleophile

    Negatively charged anions or neutral species containing non-bonding electron pairs.  Donates an electron pair to an electrophile to form a chemical bond. Because nucleophiles donate electrons, they are Lewis bases.

    "Attacking species"
  10. Electrophile

    Deficient in electron density, easily attacked by nucleophile.
  11. Oxidation-reduction (redox) reaction
    Transfer of electrons from donor, reducing agent, to acceptor, oxidizing agent.

    • Oxidized: molecule gains O or loses H
    • Reduced: molecule loses O or gains H

    *The more reduced (many H atoms) the more energy contained.
  12. Metabolism
    Enzyme-catalyzed reactions in organisms.

    • Anabolic: complex molecules synthesized
    • Catabolic: complex molecules degraded
  13. Free energy
    The energy available to do chemical work.
  14. Spontaneous reaction
    Physical or chemical change occuring with the release of energy.
  15. ATP
    A nucleotide composed of an adenine (purine), ribose and triphosphate unit.

    Phosphate anion is resonance stabilized and is more stable than ATP, therefore easily removed and exothermic.

    Metabolic processes that use ATP as an energy source convert it back into its precursors. ATP is continuously recycled in organisms.

    Often called the "molecular unit of currency"
  16. -ose
    Sugar; carbohydrate

    The suffix -ose is used in biochemistry to form the names of sugars. This Latin suffix means "full of", "abounding in", "given to", or "like".
  17. Carbohydrate
    Organic compound, consists only of C, H and O, usually with a H:O atom ratio of 2:1 (as in water)

    Synonym of saccharide.

    Divided into four chemical groupings: monosaccharides, disaccharides, oligosaccharides, and polysaccharides.

    The most abundant biomolecule.

    Used for energy storage and structural components.
  18. Ribose
    Ribose is an organic compound with the formula C5H10O5; a monosaccharide (simple sugar) with linear form H−(C=O)−(CHOH)4−H, which has all the hydroxyl groups on the same side in the Fischer projection.
  19. Dehydration synthesis
    • Also called condensation reaction
    • Two molecules or moieties combine to form a larger molecule with the loss of H2O.
  20. Hydrolysis
    The cleavage of chemical bonds by the addition of water. Generally a step in the degradation of a substance.
  21. Phosphate
    The phosphate ion is a polyatomic ion with the empirical formula PO3−4 and a molar mass of 94.97 g/mol. It consists of one central phosphorus atom surrounded by four oxygen atoms in a tetrahedral arrangement. The phosphate ion carries a negative three formal charge.
  22. Moiety
    a part of a molecule that includes parts of functional groups as substructures.

    eg. carboxylate (RCOO-) and alkyl (-R') moieties.
  23. Fischer projection
    • 2-D representation of a 3-D organic molecule by projection.
    • B
    • bonds are depicted as horizontal or vertical lines. Carbon chain is vertical, carbon atoms represented by the center of crossing lines.

    C1 carbon is at the top. In an aldose, the carbon of the aldehyde group is C1; in a ketose the carbon of the ketone group has the lowest possible number (usually C2).
  24. van't Hoff's rule
    When there are n chiral C atoms there are 2n stereoisomers.

    eg. n=4 there are 2or 16 stereoisomers
  25. Stereoisomer
    Same molecular formula and sequence of bonded atoms (constitution), but that differ only in the three-dimensional orientations of their atoms in space.

    • Can be either:
    • enantiomer: mirror images
    • diastereomer: not mirror images
  26. Chiral
    Not identical to its mirror image, it cannot be superposed onto it.

    A chiral molecule and its mirror image are enantiomers.
  27. Enantiomers
    A kind of steroisomer.

    A chiral molecule and its mirror image.

    • Can be either:
    • chiral - cannot be superimposed
    • achiral - can be superimposed
  28. Sterochemical formula
  29. Achiral
    Identical to it's mirror image, can be superimposed onto it.

    An achiral molecule and it's mirror image are enantiomers.
  30. Epimer
    Diastereomer that differ at only one asymmetric C.
  31. Asymmetric Carbon
    C attached to four different types of atoms or four different groups of atoms.

    van't Hoff's rule: When there are n chiral C atoms there are 2n stereoisomers.

    eg. n=4 there are 24 or 16 stereoisomers.

    If n is the number of asymmetric carbon atoms then the maximum number of isomers = 2n
  32. Hemiacetals
    Ring conformation of monosaccharide containing 4 or more C and an aldehyde group.

    Aldehyde group reacts with -OH group reversibly and anomeric C directly attached.

    Anomeric C bonded directly to H.

    The carbonyl (C=O) C becomes new chiral center, the anomeric C atom.
  33. Hemiketals
    Ring conformation of monosaccharide containing 4 or more C and a ketone group.

    Ketone group reacts with -OH group reversibly and anomeric C directly attached.

    Anomeric C not bonded directly to H.

    The carbonyl (C=O) C becomes new chiral center, the anomeric C atom.
  34. Ketone
    Ketones feature a carbonyl group (C=O) bonded to two other C atoms.

  35. Carbonyl group
    Moeity: (C=O)
  36. Aldehyde group
    R-CHO, consists of a carbonyl center (C=O) bonded to H and C (R group).

  37. Haworth projection
    Common way of representing cyclic structure of monosaccharides with 3-D perspective.

    Carbon 1 is the Anomeric Carbon.

    Groups below plane of ring equivalent to right-hand side of Fischer projection.
  38. Anomeric C
    • The C of the carbonyl group when a monosaccharide is in ring conformation.
    • C bonded to two O, single bond (O-C-O)
    • Two possible diastereomers may form, anomers.

    • Bonded directly to H? Y=acetal N=ketal
    • Bonded to -OH moeity? Y=hemi N=not hemi
  39. Anomer
    The two possible diasteromers tat may form from cyclization.
  40. Entropy (spontaneous reaction)
    The concept of entropy is central to the second law of thermodynamics. The second law determines which physical processes can occur. For example, it predicts that the flow of heat from a region of high temperature to a region of low temperature is a spontaneous process – it can proceed along without needing any extra external energy. When this process occurs, the hot region becomes cooler and the cold region becomes warmer. Heat is distributed more evenly throughout the system and the system's ability to do work has decreased because the temperature difference between the hot region and the cold region has decreased. Referring back to our definition of entropy, we can see that the entropy of this system has increased. Thus, the second law of thermodynamics can be stated to say that the entropy of an isolated system always increases, and such processes which increase entropy can occur spontaneously. Since entropy increases as uniformity increases, the second law says qualitatively that uniformity increases.
  41. Enthalpy (ΔH)
    The change ΔH is positive in endothermic reactions, and negative in heat-releasingexothermic processes. ΔH of a system is equal to the sum of non-mechanical work done on it and the heat supplied to it.
  42. Furanose
    5 membered hemiacetal ring; structural similarity to furan
  43. Pyranose
    6 membered hemiacetal ring; structural similarity to pyran

    Glucose 99% in aqueous solution
  44. Phosphodiester bond
    A phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates(pentoses) over two ester bonds.
  45. Metabolic pathway
    Sequence of linked chemical reactions by which energy is extracted from food.

    Catalyzed by enzymes.
  46. Glycolysis
    The metabolic pathway that convertsglucose C6H12O6, into pyruvate, CH3COCOO− + H+.
  47. TCA cycle
    aka Krebs cycle

    Series of chemical reactions used by all aerobic organisms to generate energy through the oxidization ofacetate derived from carbohydrates, fats and proteins into carbon dioxide. In addition, the cycle provides precursors including certain amino acids as well as the reducing agent NADH that is used in numerous biochemical reactions.
  48. Carbon polymers
    • Lipids
    • Proteins
    • Carbohydrates

    e- rich, oxidized by O2 to produce CO2, H2O and ATP
  49. Free radical
    Chemical species with one or more unpaired e-.

    Unpaired electrons cause radicals to be highly chemically reactive.
  50. Reduced C
    e- rich C.  Less electronegative H allows e- to crowd more around C.

    At the beginning of metabolic cycle is rich in energy.  The digestive process oxidizes the C to transfer e- and make energy available to cell.
  51. Assign oxidation state to C
    • Bond
    • C and more electronegative atom +1  H
    • C and less electronegative atom    -1  O,N,S
    • C and same electronegative atom   0  C
    • C and O double bond (2x(+1))     +2  O
  52. Mutarotation
    Cyclic sugars show mutarotation as α and β anomeric forms interconvert.

    The open chain formed during mutarotation can participate in redox reactions.
  53. Aldonic acid
    Oxidation of an aldehyde group
  54. Uronic acid
    Oxidation of a CH2OH group but not an aldehyde.
  55. Aldaric acid
    Oxidation of both an aldehyde group and CH2OH group.
  56. CH2OH
    Hydroxymethyl group.

    The 6th C on glucose.
  57. Reduction of aldehyde and ketone groups
    Produces sugar alcohols - alditols
  58. Acetal linkage
    Glycosidic bond

    The structure of glycogen consists of long polymer chains of glucose units connected by an alpha acetal linkage. ..... All of the monomer units are alpha-D-glucose, and all the alpha acetal links connect C # 1 of one glucose to C # 4 of the next glucose.In cellulose which has beta glucose units joined 1-4 the bond is a beta acetal linkage.
  59. Glycosidic bond
    A molecule containing monosaccharides linked by glycosidic likage is a polysaccharide.  Covalently bonded carbohydrates (sugar). Formed between the hemiacetal group of a saccharide and the hydroxyl group of another organic compound. Water produced, condensation reaction.
  60. Lactose
    • Disaccharide found in milk.
    • Galactose bonded thru the -OH on C1 in a β-glycosidic likage to the -OH of C4 in a glucose molecule.
  61. Maltose
    Disaccharide formed from two units of glucose joined with an α(1→4) bond, formed from a condensation reaction.
  62. Sucrose
    • Disaccharide composed of themonosaccharides glucose and fructose with the molecular formula C12H22O11.
    • α-glucose and β-fructose are linked via an ether bond between C1 on the glucosyl subunit and C2 on the fructosyl unit. The bond is called a glycosidic linkage.
  63. Condensation reaction
    • Dehydration synthesis
    • Two molecules or moieties (functional groups) combine to form a larger molecule with the loss of an H2O molecule.
  64. L- and D- molecules
    • Fischer projection, next to last C of D sugars are depicted with hydrogen on the left and hydroxyl on the right. L sugars will be shown with the hydrogen on the right and the hydroxyl on the left.
    • Left= up
    • Right= down
  65. Hexokinase
    Class of kinase that catalyse the phosphorylation of hexoses.

    ATP is a cosubstrate, complexes with Mg2+
  66. Kinase
    Enzyme that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific substrates, a process referred to as phosphorylation.
  67. Phosphorylation
    The addition of a phosphate (PO43-) group to a protein or other organic molecule.
  68. Isomerase
    Enzyme that catalyzes the structural rearrangement of isomers. Isomerases catalyze reactions of the form A → B where B is an isomer of A.
  69. Substrate-level phosphorylation
    Reaction that forms (ATP) or (GTP) by direct transfer and donation of (PO3) group (ADP) or (GDP) from a phosphorylated reactive intermediate. Does not have to come directly from the substrate.
  70. Condensation recation
    Add H2O between two molecules that bond.