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Biochem Exam 1 > Lecture 5 > Flashcards

Lecture 5 Flashcards

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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
amino acids with side chain
aspartate (asp, D), glutamate (glu, E), asparagine (asn, N), glutamine (gln, Q)
26
aspartate (asp, D), glutamate (glu, E)
pI= 3-4, very polar, usually uncharged in proteins, esterification reactions possible
27
asparagine (asn, N), glutamine (glu, Q)
neutral, polar H-bonding, deamidation reactions (protein aging)
28
asparagine (asn, N)
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
29
sequon
present in all eukaryotic proteins, if there is an amino acid sequence NXT or NXS, necessary sequences for glycosylation
30
proline (pro, P)
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
31
4-hydroxyproline (4Hyp)
- 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
32
proteins
polymers of L-amino acids linked by peptide (amide) bonds
33
amide bond
- 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
34
trans peptide bonds
more favorable because of much less steric hinderence, tolerates bigger side chains
35
cis peptide bonds
tolerates smaller side chains
36
peptide bond equilibrium
lies towards hydrolysis (- delta G) slow reaction that requires digestive enzyme such as trypsin to overcome energy activation barrier
37
secondary structure
repeating periodic structures (alpha helix, beta sheets), turns and loops (beta turns, omega loops), random chain structure (tightly packed, globular shape)
38
alpha helix
- 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
39
amount of residues separating H-bonding atoms in alpha helices
3.6
40
tissues where alpha helices are found
fibrin (blood clots), keratin (hair), cytoskeleton, porcupine quills, tropomyosin (muscle)
41
antiparallel beta sheets
more stable, found on surface of cells, hydrogen bonds that are formed are relatively straight making it more stable and shorter bond length
42
parallel beta sheets
present inside of cells, hydrogen bonds are bent and slightly longer making it less stable
43
protein folding motif
twisted beta sheet
44
beta barrell
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
reverse turn
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
loops
are able to connect different strands or allow for protein-protein interactions
47
beta turn (hairpin turn)
stabilized by H bonding
48
tertiary structure
overall three dimensional fold of a polypeptide chain
49
quaternary structure
spatial arrangement of multi subunit proteins (made of more than one polypeptide chain)
50
protein that causes hydroxyapatite to crystalize into highly elongated fibers (rods) that become woven into enamel
amelogenin
51
configuration that proteins are naturally synthesized in
L configuration
52
very flexible, no steric hindrance achiral, most flexible amino acid
glycine (gly, g)
53
more hydrophobic than glycine, still relatively flexible. almost every protein contains this
alanine (ala, a)
54
neutral, small R group (low accessible surface area), non-polar, flexible
alanine and glycine
55
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
collagens
56
valine (val, v), leucine (leu, L), isoleucine (ile, I), methionine (met, M)
aliphatic amino acids
57
neutral, high surface area, non-polar, hydrophobic, Van der Waal's interactions in folded interior, structural units with a variety of shapes
valine (val, v), leucine (leu, L), isoleucine (ile, I), methionine (met, M)
58
side chain is chiral
isoleucine (ile, I)
59
phenylalanine (phe, f), tyrosine (tyr, y) tryptophan (trp, w)
aromatic amino acids
60
neutral, very high accessible surface area
phenylalanine (phe, f), tyrosine (tyr, y), tryptophan (trp, w)
61
very non-polar, hydrophobic, aromatic
phenylalanine (phe, f)
62
rare aromatic amino acid, fluorescent properties
tryptophan (trp, W)
63
responsible for 280 nm absorbance
tryptophan (trp, w), tyrosine (tyr, y)
64
tyrosine that is above pH 10 by removing the OH group, you create slightly larger ring and shift absorbance to bigger wavelength
tyrosinate
65
serine (ser, S), threonine (thr, T)
amino acids with aliphatic hydroxyl group
66
neutral, polar H-bonding donors or acceptors, sites of post-transcriptional modification, phosphorylation, O-glycosylation
serinine (ser, S), threonine (thr, T)
67
amphipathic amino acid, side chain chiral
threonine (thr, T)
68
when the net charge of an ion is zero
zwitterionic form
69
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
cysteine (cys, c)
70
regulatory enzyme that helps cystine form correct disulfide bonds
insulin
71
lysine (lys, K), arginine (arg, R), histidine (his, H)
basic amino acids
72
positively charged at pH 7 most basic protein groups (also N-term)
arginine (arg, R), lysine (lys, K)
73
can participate in acid/base reactions at pH 7, often found in enzyme active sites for this reason
histidine (his, H)
74
aspartate (asp, D), glutamate (glu, E), asparagine (asn, N), glutamine (gln, Q)
amino acids with side chain
75
pI= 3-4, very polar, usually uncharged in proteins, esterification reactions possible
aspartate (asp, D), glutamate (glu, E)
76
neutral, polar H-bonding, deamidation reactions (protein aging)
asparagine (asn, N), glutamine (glu, Q)
77
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
asparagine (asn, N)
78
present in all eukaryotic proteins, if there is an amino acid sequence NXT or NXS, necessary sequences for glycosylation
sequon
79
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
proline (pro, P)
80
- 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
4-hydroxyproline (4Hyp)
81
polymers of L-amino acids linked by peptide (amide) bonds
proteins
82
- 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
amide bond
83
more favorable because of much less steric hinderence, tolerates bigger side chains
trans peptide bonds
84
tolerates smaller side chains
cis peptide bonds
85
lies towards hydrolysis (- delta G) slow reaction that requires digestive enzyme such as trypsin to overcome energy activation barrier
peptide bond equilibrium
86
repeating periodic structures (alpha helix, beta sheets), turns and loops (beta turns, omega loops), random chain structure (tightly packed, globular shape)
secondary structure
87
- 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
alpha helix
88
3.6
amount of residues separating H-bonding atoms in alpha helices
89
fibrin (blood clots), keratin (hair), cytoskeleton, porcupine quills, tropomyosin (muscle)
tissues where alpha helices are found
90
more stable, found on surface of cells, hydrogen bonds that are formed are relatively straight making it more stable and shorter bond length
antiparallel beta sheets
91
present inside of cells, hydrogen bonds are bent and slightly longer making it less stable
parallel beta sheets
92
twisted beta sheet
protein folding motif
93
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
beta barrell
94
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
reverse turn
95
are able to connect different strands or allow for protein-protein interactions
loops
96
stabilized by H bonding
beta turn (hairpin turn)
97
overall three dimensional fold of a polypeptide chain
tertiary structure
98
spatial arrangement of multi subunit proteins (made of more than one polypeptide chain)
quaternary structure

Biochem Exam 1 (7 decks)

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