Chapter 2

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  1. asymmetric aton
    an atom (ex. carbon) bonded to four dissimilar atoms or groups in a nonplanar configuration
  2. asymmetric carbon atom
    has a tetrahedral orientation of bonds; can be arranged in two different ways
  3. chirality
    a property of molecules that are mirror images of each other
  4. stereoisomers (optical isomers)
    molecules that exhibit chirality, or ones that can be mirror images of each other
  5. electronegativity
    the extent of an atom's ability to attract an electron
  6. non-polar bonds
    bonds between atoms with identical or similar electronegativities
  7. resonance hybrid
    the "resonance hybrid" of a molecule is the actual structure of a molecule in the normal quantum state which has the lowest possible value of total energy
  8. most common double bonds in biological molecules:
    • C=O
    • C=N
    • C=C
    • P=O
  9. the energy required to break a non-covalent interaction:
    • 1-5 kcal/mol
    • (at 25 degrees C, thermal energy = .6 kcal/mol; the energy required to break a C - C bond is about 140x larger than that)
  10. increasing the concentration of _____ in a solution of biological molecules can:
    salts, such as NaCl; weaken/disrupt ionic interactions holding the biomolecules together
  11. important feature of H-bonds is:
  12. non-linear H-bonds are ______ than linear ones:
    WEAKER: in the strongest hydrogen bonds the donor atom, hydrogen atom and acceptor atom all lie in a straight line
  13. the ________ group in alcohols and the _____ group in amines can form several hydrogen bonds with water, enabling these molecules to:
    Hydroxyl group in alcohols (-OH) and amino group ( -NH2) dissolve in water to high concentrations
  14. hydrophobic effect
    • because water molecules cannot form H-bonds with non polar molecules or non polar portions of molecules, they tend to form cages of relatively rigid pentagons and hexagons around such molecules: this state is energetically UNfavorable because it decreases the randomness (entropy) of the population of water molecules
    • -to increase entropy (disorder), the nonpolar molecules aggregate with hydrophobic surfaces facing e/a other so less is facing the water -- this means fewer water molecules are needed to form the surrounding cages and more can be free and disorganized
  15. hexane
    it's a nonpolar solvent; good for dissolving non-polar molecules
  16. molecular complementarity
    a lock-and-key kind of fit between their shape, charges or other physical properties that allow them to form multiple non-covalent interactions at close range
  17. Kd
    binding dissociation constant; quantitative measure of affinity
  18. proteins
    linear polymers made up of 10-several thousand AMINO acids linked by PEPTIDE bonds
  19. nucleic acids
    linear polymers made up hundreds to millions of nucelotides linked by PHOSPHODIESTER bonds
  20. polysaccharides
    linear OR branched poluers of monosaccharides (sugars, like glucose) linked by GLYCOSIDIC bonds
  21. dehydration reaction
    what takes place in order for a covalent bond to form between two monomers; involves the loss of a H from one monomer and the loss of an OH (hydroxyl) from the other monomer resulting in the net loss of one water
  22. there are 20 different amino acids
    • 1) these are the building block of proteins
    • 2) when incorporated into protein polymer they are called residues
    • 3) all have a characteristic structure consisting of central α carbon bonded to four different chemical groups
  23. structure of amino acid
    • -central α carbon bonded to four different chemical groups
    • 1) an amino (NH2) group
    • 2) a carboxylic acid or carbonyl group (COOH)
    • 3) hydrogen (H) atom
    • 4) side chain/R group (variable)
  24. all amino acid α carbons are asymmetric:
    • -EXCEPT for glycines
    • -these molecules exist in two mirror images of each other called the D (dextro) and L (levo) isomers
    • -ONLY the levo (L) forms of amino acids are found in proteins
  25. hydrophobic amino acids (8)
    • those that contain uncharged side chains
    • -5 hydrophobic amino acids' side chains consist ENTIRELY of hydrocarbons (except for methionine which has a sulfur); are all noncyclic
    • -the other 3 hydrophobic amino acids have cyclic side chains/are bulky and aromatic
  26. hydrophilic amino acids (9)
    -can be broken up into basic, acidic, and just polar amino acids that confusingly have uncharged R groups
  27. basic amino acids (3)
    • lysine & arginine have positively charged side chains; histidine has a side chain that has a ring with two nitrogens (called imidazole)
    • -this ring can shift from being positively charge (basic) to uncharged depending on the acidity of the surrounding environment
    • -all 3 are hydrophilic
  28. acidic amino acids (2)
    aspartate and glutamate have negatively charged side chains due to the carboxyl groups within them (their uncharged forms are called aspartic acid and glutamic acid); are all hydrophilic
  29. polar amino acids w/ uncharged R groups (4)
    • -asparagine and glutamine: have polar side chains containing amide groups w/ H-bonding capabilities
    • -seine and threonine: have polar hydroxyl groups; can H-bond with other polar molecules
  30. Special Amino Acids (C.G.P.)
    • 1) cysteine: side chain contains a reactive sulfhydryl group (-SH); can oxidize to form disulfide bond w/ another cystine
    • 2) glycine: smallest amino acid; R group = single hydrogen atom
    • 3) proline: has a ring shaped side chain; is very rigid and creates a kink in a protein chain limiting folding capabilities (also has an H2N group in stead of a 3 one)
  31. rarest amino acids (3):
    cysteine, tryptophan and methionine; constitute 5% of amino acids in a protein
  32. most abundant amino acids (4):
    leucine, seine, lysine and glutamic acid; total 32% of residues in a typical protein
  33. acetylation
    the addition of an acetyl group to the amino group of the N-terminal residue = most common form of amino acid chemical (looks like CH3 and O (double bonded) to a C); non acetylated proteins are degraded
  34. nucleic acids
    • -two types: DNA/RNA
    • -monomers of nucleic acids are nucleotides
    • -nucleotide structure: phosphate group linked via phosphoester bond to pentose (or ribose for RNA, 5-carbon sugar), linked to a base (nitrogen/carbon containing ring)
  35. difference between pentose and ribose
    de-oxy-ribose (DNA) at its 2' carbon has only an H, whereas ribose has an OH at its 2' carbon
  36. purines
    adenine and guanine; have a pair of fused rings
  37. pyrimidines
    cytosine, thymine and uracil; contain only one ring
  38. stopped on pg 44 come back to it I'm so bored
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Chapter 2
2011-10-08 19:40:19

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