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MICRO 442 > BIOCHEM lecture 1-10 > Flashcards

BIOCHEM lecture 1-10 Flashcards

1
Q

strength between non-covalent interactions

A

permanent dipoles> dipole-induced dipole> London dispersion forces

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2
Q

The water
molecule is non-
linear and

A

carries a
permanent
dipole moment.

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3
Q

The “van der Waals envelope” is the

A

effective “surface of the molecule”.

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4
Q

Two atoms from different molecules rarely come closer together than the sum of

A

their van der Waals
radii

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5
Q

exception to van der waals radii being the closest two atoms can get

A

Hydrogen

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6
Q

unit conversion for vdW radius

A

10 Å = 1 nm = 10 -9 m

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7
Q

when water is ice it

A

interacts tetrahedrally with four other molecules

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8
Q

D-H =

A

weakly acidic “donor” group, such as O-H, N-H

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9
Q

A =

A

weakly basic “acceptor” atom such as O, N

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10
Q

D-H…A

A

hydrogen bond

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11
Q

The permanent dipoles of water molecules interact very favorably with charged ions in
solution,

A

forming a “hydration shell”.

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12
Q

no difference in enthalpy (entropy drive) in a

A

transfer of hydrocarbaons from water to nonpolar solvents

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13
Q

amphiphillic/amphipathic

A

have both polar and non-polar segments

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14
Q

clustering lipids

A

increase the entropy of a system (less rotational restriction)

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15
Q

H-bonding within water facilitates its

A

ionization

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16
Q

H+ should be written as

A

H3O+ technically

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17
Q

1 liter of water there is

A

55.5 moles

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18
Q

Kw[10E-14]=

A

[H+ 10E-07][[OH- 10E-07]

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19
Q

HH equation

A

pH = pKa +log ([base]/[acid])

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20
Q

protons can be used to:

A
  • Induce a large conformational change of a protein.
  • Store energy – as a proton concentration difference
    across a membrane
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21
Q

The pH of fluids surrounding
cells, and of the cytosol inside
the cell, is around 7.

A

However, in the organelles
called endosomes, the pH is
lower. -> used by influenza virus to infect a host cell bc pH differences inducesconformational change in surface protein

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22
Q

protons cannot cross a

A

lipid membrane

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23
Q

periplasm

A

the space between two membrane of bacterial cells

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24
Q

low proton concentration in

A

cytoplasm

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25
Q

high proton concentration in

A

periplasm

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26
Q

serine=ser=s

A

polar

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27
Q

hydrophobicity of side chains

A

phe>ile>ala

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28
Q

proline

A

makes ring with N in backbone

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29
Q

isoleucine

A

1 of 2 CHIRAL side chaines

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30
Q

uncharged + polar

A

serine

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31
Q

uncharged + polar

A

cycsteine

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32
Q

uncharged + polar

A

threonine

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33
Q

uncharged + polar

A

glutamine

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34
Q

uncharged + polar

A

asparagine

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35
Q

aliphatic + nonpolar

A

glycine

36
Q

aliphatic + nonpolar

A

alanine

37
Q

aliphatic + nonpolar

A

proline

38
Q

aliphatic + nonpolar

A

valine

39
Q

aliphatic + nonpolar

A

leucine

40
Q

aliphatic + nonpolar

A

isoleucine

41
Q

aliphatic + nonpolar

A

methionine

42
Q

Threonine

A

1 of 2 CHIRAL side chains

43
Q

His

A

pK of ~ 6 means that at neutral pH the imidazole ring is both in its protonated and unprotonated state; at a pH below the pK a larger fraction is protonated than unprotonated; at pH
values above the pK a larger fraction of the side chain is unprotonated than protonated.

44
Q

negatively charged

A

aspartate (COO-)

45
Q

negatively charged

A

glutamate (COO-)

46
Q

aspartate and glutamate

A
  • These side chains are very hydrophilic.
  • The side chain carboxylates are often found in active sites
  • The carboxylates can coordinate metals – in particular Mg2+ and Ca 2+.
47
Q

aromatic

A

phenylalanine

48
Q

aromatic

A

tyrosine

49
Q

aromatic

A

trytophan

50
Q

alanine

A

a

51
Q

arginine

A

R
pKa 12.5

52
Q

asparagine

A

N

53
Q

aspartic acid

A

D
pKa 3.9

54
Q

cycsteine

A

C
pKa 8.3

55
Q

glutamine

A

A

56
Q

glutamic acid

A

E
pKa 4.2

57
Q

glycine

A

G

58
Q

Histidine

A

H
pKa 6

59
Q

isoleucine

A

I

60
Q

leucine

A

L

61
Q

lysine

A

K
pKa 10

62
Q

methionine

A

M

63
Q

phenylalanine

A

F

64
Q

proline

A

P

65
Q

serine

A

S

66
Q

threonine

A

T

67
Q

tryptophan

A

W

68
Q

tyrosine

A

Y
pKa 10.1

69
Q

Valine

A

V

70
Q

amino group

A

-below pka nh3+
-above pka nh2

71
Q

hydroxyl group

A

-below pka oh
-above pka o-

72
Q

SH-group

A

-below pka sh
-above pka s-

73
Q

imidazole

A

-below pka one positive charge
-above pka uncharged

74
Q

the pka of the SAME functional group can be different in

A

different molecules

75
Q

oxidation of cysteine to cystine

A

forms disulfide bonds

76
Q

non-standard enzymes come from

A

post-translational modifications

77
Q

protein kinases

A

attach phosphates

78
Q

O-glycosylation

A

The oligosaccharide is attached to side chain O of a Ser or Thr

79
Q

N-glycosylation

A

The oligosaccharide is attached to side chain N of an Asn

80
Q

core protein

A

pentasaccharide “core in protein glycosylation

81
Q

antenna protein

A

Such complex
antennas are very
specific markers
of proteins on a
cell surface.

82
Q

protein glycosylation

A

addition of suagrs onto aa side chains

83
Q

pka of N-terminal NH3+

A

8

84
Q

pka of C-terminal COO-

A

4

85
Q

if one peptide unit is fixed phi and psi define

A

orientation of second peptide unit

86
Q

course of a polypeptide chain is defined by a

A

pair of dihedral angles (phi and psi) per aa residue

MICRO 442 (25 decks)

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