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Biochem 1 (WPH) > Proteins 1 - amino acids 09/04 Traish > Flashcards

Proteins 1 - amino acids 09/04 Traish Flashcards

1
Q

G

A

glycine
gly
hydrogen R group

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2
Q

A

A

alanine
ala
beta carbon

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3
Q

V

A

valine
val
dimethyl branch at the beta carbon

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4
Q

L

A

leucine
leu
dimethyl branch at the gamma carbon

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5
Q

first five letters of the greek alphabet

A

alpha beta gamma delta epsilon

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6
Q

I

A

isoleucine
ile
methyl ethyl branch at beta carbon

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7
Q

P

A

proline
pro
five member ring including primary amino group

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8
Q

F

A

phenylalanine
phe
benzene ring at beta carbon

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9
Q

Y

A

tyrosine
tyr
phenol group at beta carbon
pKa 10.1

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10
Q

W

A 
tryptophan
trp
beta indole group
(5 member ring off beta C w/ delta N
and benzene)
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11
Q

amino acid with indole group

A

W

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12
Q

what is an indole group

A

five member ring with secondary amino group and benzene

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13
Q

S

A

serine
ser
beta hydroxl group

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14
Q

T

A

Threonine
thre
ethyl + beta hydroxyl group

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15
Q

C

A

Cysteine
cys
beta thiol group
pKa 8.3

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16
Q

pKa of the functional group of cysteine

A

8.3

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17
Q

pKa of the functional group of tyrosine

A

10.1

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18
Q

M

A

methionine
met
gamma methyl thiol group

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19
Q

D

A

aspartic acid
asp
beta carboxyl group
pKa 3.9

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20
Q

pKa of the functional group of aspartic acid

A

3.9

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21
Q

E

A

glutamic acid
glu
gamma carboxyl group
pKa 4.2

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22
Q

N

A

asparagine
asn
beta amide group

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23
Q

pKa of the functional group of asparagine

A

functional group does not ionize. trick question!

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24
Q

pKa of the functional group of glutamine

A

functional group does not ionize. trick question!

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25
Q

Q

A

glutamine
gln
gama amide group

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26
Q

R

A

arginine
arg
delta guanidinium group
pKa 12.5

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27
Q

what is a guanidinium group?

A

three amino groups bonded to a central carbon. one is double bonded

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28
Q

H

A

histidine
his
beta 5 membered ring with 2 Nitrogen (imidozole group)
pKa 6.0

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29
Q

pKa of the functional group of histidine

A

6.0

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30
Q

K

A

lysine
lys
epsilon amino group
pKa 10.0

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31
Q

pKa of the functional group of arginine

A

12.5

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32
Q

pKa of the functional group of lysine

A

10.0

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33
Q

7 amino acids with functional group pKa’s are:

A

D,E,R,H,K,Y,C

34
Q

pKa of the functional group of glutamic acid

A

4.2

35
Q

do human amino acids exist in the D or L configuration?

A

L

36
Q

do serine and threonine ionize?

A

no, just H-bond

37
Q

what aa residue can form strong, heat stable covalent bonds with another of itself?

A

cysteine, di-sulfide bonds

38
Q

which aa’s absorb UV light?

A

F, Y, W, the aromatics

39
Q

~what wavelength of light do F, W, and Y abosorb?

A

~280 nm

40
Q

which aa essentially lacks a side chain?

A

glycine

41
Q

which aa residue is the smallest and least sterically hindering?

A

glycine G gly

42
Q

which aa is useful in terminating secondary structures?

A

P pro proline

43
Q

is glycine hydrophobic?

A

no, it can fit into hydrophobic or hydrophilic environments due to minimal side chain

44
Q

are Y and W predominantly polar or non-polar?

A

non-polar

45
Q

can Y and W hydrogen bond?

A

yes

46
Q

these two aa’s are negatively charged at pH 7.37

A

D and E

47
Q

these aa’s are positively charged at pH 7.37

A

R and K

48
Q

what is net charge of H at pH 7.37

A

0 (pKa side chain is 6)

49
Q

this aa functions as an efficient acid-base catalyst at physiological pH

A

H (pKa 6)

50
Q

this aa is found in sharp turns of the pp backbone

A

G (small R group confers high flexibility)

51
Q

this aa confers a high degree of local flexibility on the polypeptide

A

G

52
Q

this aa occurs abundantly in certain fibrous proteins (such as collagen) due to its flexibility and small size

A

G

53
Q

this aa is the most rigid of the 20

A

P

54
Q

can all aa’s act as buffers?

A

yes, all have weakly acidic C terminus and weekly basic N terminus

55
Q

henderson hasselbalch equation

A

pH = pKa + log(conj base/acid)

56
Q

an ampholyte is

A

a molecule that possesses both acidic and basic groups

57
Q

a zwitterion is

A

an ampholyte with equal numbers of + and - charges

58
Q

what is an isoelectric point?

A

the pH at which the net charge for all forms of an ampholyte is 0

59
Q

in isoelectric focusing, which end is + and which is - ?

A

cathode is - (attracts +)

anode is + (attracts -)

60
Q

galvanic cell which ends are + and - ?

A

cathode is +

anode is -

61
Q

electrolytic cell which ends are + and - ?

A

cathode is -

anode is +

62
Q

in isoelectric focusing on a gel with a supplied current, a net + charged aa will migrate to the ___; a net - aa will migrate to the ____

A

net + will migrate to the cathode

net - will migrate to the anode

63
Q

how do you calculate pI for an aa with acidic side chain?

A

(pKa1 + pKa2) / 2

64
Q

how do you calculate pI for an aa with neutral side chain?

A

(pKa1 + pKa2) / 2

65
Q

how do you calculate pI for an aa with basic side chain?

A

(pKa2 + pKa3) / 2

66
Q

which aa’s have pI’s found between pKa’s 1 and 2 and not 3?

A

D, E, Y, C

67
Q

which aa’s have pI’s found between pKa’s 2 and 3?

A

R, H, K

68
Q

on a titration graph with pH y-axis & moles OH- x-axis, what do ~horizontal and ~vertical regions signify?

A 
horizontal = pKa
vertical = pI
69
Q

a polyampholyte is..

A

a molecule with multiple acidic and basic groups

70
Q

which is an indicator of acidic vs basic aa, pKa or pI?

A

pI – examples where pKa does not indicate:
H is basic – acidic pKa but basic pI
C and Y are acidic – basic pKa but acidic pI

71
Q

what is the ~pKa of a guanidinium group?

A

~12

72
Q

what is the ~pKa of an imidozole group?

A

~6.5

73
Q

what is the ~pKa of a thiol group?

A

~8.5

74
Q

what is the ~pKa of a phenol group?

A

~10

75
Q

what is the is the ~pKa of an inisitol group?

A

trick question – inisitol group does not ionize

76
Q

what is the is the ~pKa of an amide group?

A

trick question – amide group does not ionize

77
Q

what is the is the ~pKa of an aa N terminus?

A

~2

78
Q

what is the is the ~pKa of an aa C terminus?

A

~9.5

79
Q

this modified amino acid is an important component of mature collagen fibers, and the absence of this modification results in protein deformation and loss of fiber strength

A

hydroxyproline – permits sharp twisting of the collagen helix. absence of hydroxylation results in protein deformation and loss of collagen fiber strength

80
Q

what is hydroxyproline

A

proline with a gamma hydroxyl group. modified post-translationally by prolyl hydroxylase in the ER lumen. permits sharp twisting of the collagen helix.

Biochem 1 (WPH) (15 decks)

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