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Biochem Exam 1 > Lecture 5 > Flashcards

Lecture 5 Flashcards

1
Q

amelogenin

A

protein that causes hydroxyapatite to crystalize into highly elongated fibers (rods) that become woven into enamel

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2
Q

L configuration

A

configuration that proteins are naturally synthesized in

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3
Q

glycine (gly, g)

A

very flexible, no steric hindrance
achiral, most flexible amino acid

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4
Q

alanine (ala, a)

A

more hydrophobic than glycine, still relatively flexible. almost every protein contains this

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5
Q

alanine and glycine

A

neutral, small R group (low accessible surface area), non-polar, flexible

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6
Q

collagens

A

have lots of glycine in them due to flexibility
have triple helical structure that is very stable
glycine occurs approx. 1 in every 3 amino acids, necessary for the formation of the triple helix because flexibility is required

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7
Q

aliphatic amino acids

A

valine (val, v), leucine (leu, L), isoleucine (ile, I), methionine (met, M)

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8
Q

valine (val, v), leucine (leu, L), isoleucine (ile, I), methionine (met, M)

A

neutral, high surface area, non-polar, hydrophobic, Van der Waal’s interactions in folded interior, structural units with a variety of shapes

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9
Q

isoleucine (ile, I)

A

side chain is chiral

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10
Q

aromatic amino acids

A

phenylalanine (phe, f), tyrosine (tyr, y) tryptophan (trp, w)

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11
Q

phenylalanine (phe, f), tyrosine (tyr, y), tryptophan (trp, w)

A

neutral, very high accessible surface area

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12
Q

phenylalanine (phe, f)

A

very non-polar, hydrophobic, aromatic

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13
Q

tryptophan (trp, W)

A

rare aromatic amino acid, fluorescent properties

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14
Q

tryptophan (trp, w), tyrosine (tyr, y)

A

responsible for 280 nm absorbance

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15
Q

tyrosinate

A

tyrosine that is above pH 10
by removing the OH group, you create slightly larger ring and shift absorbance to bigger wavelength

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16
Q

amino acids with aliphatic hydroxyl group

A

serine (ser, S), threonine (thr, T)

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17
Q

serinine (ser, S), threonine (thr, T)

A

neutral, polar H-bonding donors or acceptors, sites of post-transcriptional modification, phosphorylation, O-glycosylation

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18
Q

threonine (thr, T)

A

amphipathic amino acid, side chain chiral

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19
Q

zwitterionic form

A

when the net charge of an ion is zero

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20
Q

cysteine (cys, c)

A

sulfhydryl (thiol) most reactive group in proteins, oxidation in the presence of oxygen, very nucleophilic, reactions with electrophiles, must be alkylated (stabilized) for protein analysis, reactions with metal ions, participates in disulfide bonding with other identical residues, antioxidant, precursor to glutathione

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21
Q

insulin

A

regulatory enzyme that helps cystine form correct disulfide bonds

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22
Q

basic amino acids

A

lysine (lys, K), arginine (arg, R), histidine (his, H)

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23
Q

arginine (arg, R), lysine (lys, K)

A

positively charged at pH 7
most basic protein groups (also N-term)

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24
Q

histidine (his, H)

A

can participate in acid/base reactions at pH 7, often found in enzyme active sites for this reason

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25
Q

amino acids with side chain

A

aspartate (asp, D), glutamate (glu, E), asparagine (asn, N), glutamine (gln, Q)

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26
Q

aspartate (asp, D), glutamate (glu, E)

A

pI= 3-4, very polar, usually uncharged in proteins, esterification reactions possible

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27
Q

asparagine (asn, N), glutamine (glu, Q)

A

neutral, polar H-bonding, deamidation reactions (protein aging)

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28
Q

asparagine (asn, N)

A

residues can deaminate during protein aging
if deamination is occuring, this amino acid is converted to aspartic acid changing the acid/base properties of a protein
site of glycosylation

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29
Q

sequon

A

present in all eukaryotic proteins, if there is an amino acid sequence NXT or NXS, necessary sequences for glycosylation

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30
Q

proline (pro, P)

A

cyclic imino acid, no rotation about N-Calpha bond, no backbone N-H-H bonding, no resonance stabilization of amide bond, peptide bond more likely to be in cis-conformation than are other amino acids

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31
Q

4-hydroxyproline (4Hyp)

A
  • a non-proteinogenic amino acid, produced by hydroxylation of the amino acid proline by the enzyme prolyl hydroxylase following protein synthesis (as a post-translational modification)
  • comprises roughly 13.5% of mammalian collagen
  • plays key roles for collagen stability, permits the sharp twisting of the collagen helix
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32
Q

proteins

A

polymers of L-amino acids linked by peptide (amide) bonds

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33
Q

amide bond

A
  • have a substantial degree of planar character
  • have resonance structures, lots of double bond character (cannot rotate due to double bond)
  • chemically unreactive unless there is a digestive enzyme present
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34
Q

trans peptide bonds

A

more favorable because of much less steric hinderence, tolerates bigger side chains

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35
Q

cis peptide bonds

A

tolerates smaller side chains

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36
Q

peptide bond equilibrium

A

lies towards hydrolysis (- delta G)
slow reaction that requires digestive enzyme such as trypsin to overcome energy activation barrier

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37
Q

secondary structure

A

repeating periodic structures (alpha helix, beta sheets), turns and loops (beta turns, omega loops), random chain structure (tightly packed, globular shape)

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38
Q

alpha helix

A
  • right handed helix, side chains are pointing out radially from the helix, slightly upward point
  • very stable because every hydrogen bond is formed, all these hydrogen bonds stabilize the helix
  • orderly secondary structure
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39
Q

amount of residues separating H-bonding atoms in alpha helices

A

3.6

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40
Q

tissues where alpha helices are found

A

fibrin (blood clots), keratin (hair), cytoskeleton, porcupine quills, tropomyosin (muscle)

41
Q

antiparallel beta sheets

A

more stable, found on surface of cells, hydrogen bonds that are formed are relatively straight making it more stable and shorter bond length

42
Q

parallel beta sheets

A

present inside of cells, hydrogen bonds are bent and slightly longer making it less stable

43
Q

protein folding motif

A

twisted beta sheet

44
Q

beta barrell

A

when a beta sheet is folded into a tube
often found as a membrane pore, allowing some molecules to go in or out of the cell
antiparallel strand weaving back and forth, connected by loop that involve bends that have amino acid side chains that allow twist in backbone

45
Q

reverse turn

A

structure of a beta sheet, all four sides pointed in same direction out of screen–> tend to favor small amino acid side chains or those that are fine being located on all the same side of the turn

46
Q

loops

A

are able to connect different strands or allow for protein-protein interactions

47
Q

beta turn (hairpin turn)

A

stabilized by H bonding

48
Q

tertiary structure

A

overall three dimensional fold of a polypeptide chain

49
Q

quaternary structure

A

spatial arrangement of multi subunit proteins (made of more than one polypeptide chain)

50
Q

protein that causes hydroxyapatite to crystalize into highly elongated fibers (rods) that become woven into enamel

A

amelogenin

51
Q

configuration that proteins are naturally synthesized in

A

L configuration

52
Q

very flexible, no steric hindrance
achiral, most flexible amino acid

A

glycine (gly, g)

53
Q

more hydrophobic than glycine, still relatively flexible. almost every protein contains this

A

alanine (ala, a)

54
Q

neutral, small R group (low accessible surface area), non-polar, flexible

A

alanine and glycine

55
Q

have lots of glycine in them due to flexibility
have triple helical structure that is very stable
glycine occurs approx. 1 in every 3 amino acids, necessary for the formation of the triple helix because flexibility is required

A

collagens

56
Q

valine (val, v), leucine (leu, L), isoleucine (ile, I), methionine (met, M)

A

aliphatic amino acids

57
Q

neutral, high surface area, non-polar, hydrophobic, Van der Waal’s interactions in folded interior, structural units with a variety of shapes

A

valine (val, v), leucine (leu, L), isoleucine (ile, I), methionine (met, M)

58
Q

side chain is chiral

A

isoleucine (ile, I)

59
Q

phenylalanine (phe, f), tyrosine (tyr, y) tryptophan (trp, w)

A

aromatic amino acids

60
Q

neutral, very high accessible surface area

A

phenylalanine (phe, f), tyrosine (tyr, y), tryptophan (trp, w)

61
Q

very non-polar, hydrophobic, aromatic

A

phenylalanine (phe, f)

62
Q

rare aromatic amino acid, fluorescent properties

A

tryptophan (trp, W)

63
Q

responsible for 280 nm absorbance

A

tryptophan (trp, w), tyrosine (tyr, y)

64
Q

tyrosine that is above pH 10
by removing the OH group, you create slightly larger ring and shift absorbance to bigger wavelength

A

tyrosinate

65
Q

serine (ser, S), threonine (thr, T)

A

amino acids with aliphatic hydroxyl group

66
Q

neutral, polar H-bonding donors or acceptors, sites of post-transcriptional modification, phosphorylation, O-glycosylation

A

serinine (ser, S), threonine (thr, T)

67
Q

amphipathic amino acid, side chain chiral

A

threonine (thr, T)

68
Q

when the net charge of an ion is zero

A

zwitterionic form

69
Q

sulfhydryl (thiol) most reactive group in proteins, oxidation in the presence of oxygen, very nucleophilic, reactions with electrophiles, must be alkylated (stabilized) for protein analysis, reactions with metal ions, participates in disulfide bonding with other identical residues, antioxidant, precursor to glutathione

A

cysteine (cys, c)

70
Q

regulatory enzyme that helps cystine form correct disulfide bonds

A

insulin

71
Q

lysine (lys, K), arginine (arg, R), histidine (his, H)

A

basic amino acids

72
Q

positively charged at pH 7
most basic protein groups (also N-term)

A

arginine (arg, R), lysine (lys, K)

73
Q

can participate in acid/base reactions at pH 7, often found in enzyme active sites for this reason

A

histidine (his, H)

74
Q

aspartate (asp, D), glutamate (glu, E), asparagine (asn, N), glutamine (gln, Q)

A

amino acids with side chain

75
Q

pI= 3-4, very polar, usually uncharged in proteins, esterification reactions possible

A

aspartate (asp, D), glutamate (glu, E)

76
Q

neutral, polar H-bonding, deamidation reactions (protein aging)

A

asparagine (asn, N), glutamine (glu, Q)

77
Q

residues can deaminate during protein aging
if deamination is occuring, this amino acid is converted to aspartic acid changing the acid/base properties of a protein
site of glycosylation

A

asparagine (asn, N)

78
Q

present in all eukaryotic proteins, if there is an amino acid sequence NXT or NXS, necessary sequences for glycosylation

A

sequon

79
Q

cyclic imino acid, no rotation about N-Calpha bond, no backbone N-H-H bonding, no resonance stabilization of amide bond, peptide bond more likely to be in cis-conformation than are other amino acids

A

proline (pro, P)

80
Q
  • a non-proteinogenic amino acid, produced by hydroxylation of the amino acid proline by the enzyme prolyl hydroxylase following protein synthesis (as a post-translational modification)
  • comprises roughly 13.5% of mammalian collagen
  • plays key roles for collagen stability, permits the sharp twisting of the collagen helix
A

4-hydroxyproline (4Hyp)

81
Q

polymers of L-amino acids linked by peptide (amide) bonds

A

proteins

82
Q
  • have a substantial degree of planar character
  • have resonance structures, lots of double bond character (cannot rotate due to double bond)
  • chemically unreactive unless there is a digestive enzyme present
A

amide bond

83
Q

more favorable because of much less steric hinderence, tolerates bigger side chains

A

trans peptide bonds

84
Q

tolerates smaller side chains

A

cis peptide bonds

85
Q

lies towards hydrolysis (- delta G)
slow reaction that requires digestive enzyme such as trypsin to overcome energy activation barrier

A

peptide bond equilibrium

86
Q

repeating periodic structures (alpha helix, beta sheets), turns and loops (beta turns, omega loops), random chain structure (tightly packed, globular shape)

A

secondary structure

87
Q
  • right handed helix, side chains are pointing out radially from the helix, slightly upward point
  • very stable because every hydrogen bond is formed, all these hydrogen bonds stabilize the helix
  • orderly secondary structure
A

alpha helix

88
Q

3.6

A

amount of residues separating H-bonding atoms in alpha helices

89
Q

fibrin (blood clots), keratin (hair), cytoskeleton, porcupine quills, tropomyosin (muscle)

A

tissues where alpha helices are found

90
Q

more stable, found on surface of cells, hydrogen bonds that are formed are relatively straight making it more stable and shorter bond length

A

antiparallel beta sheets

91
Q

present inside of cells, hydrogen bonds are bent and slightly longer making it less stable

A

parallel beta sheets

92
Q

twisted beta sheet

A

protein folding motif

93
Q

when a beta sheet is folded into a tube
often found as a membrane pore, allowing some molecules to go in or out of the cell
antiparallel strand weaving back and forth, connected by loop that involve bends that have amino acid side chains that allow twist in backbone

A

beta barrell

94
Q

structure of a beta sheet, all four sides pointed in same direction out of screen–> tend to favor small amino acid side chains or those that are fine being located on all the same side of the turn

A

reverse turn

95
Q

are able to connect different strands or allow for protein-protein interactions

A

loops

96
Q

stabilized by H bonding

A

beta turn (hairpin turn)

97
Q

overall three dimensional fold of a polypeptide chain

A

tertiary structure

98
Q

spatial arrangement of multi subunit proteins (made of more than one polypeptide chain)

A

quaternary structure

Biochem Exam 1 (7 decks)

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