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Biochemistry > BB450 exam 1 > Flashcards

BB450 exam 1 Flashcards

1
Q

DNA bases and how they bind

A

adenine - thymine (2 H bonds)

guanine - cytosine (3 H bonds)

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2
Q

acid

A

anything that can give a proton

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3
Q

salt

A

something that has lost a proton

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4
Q

Ka =

A

[H+][A-]/[HA]

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5
Q

pKa

A

-logKa

constant for an acid, strength

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6
Q

lower pKa

A

stronger acid

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7
Q

higher pKa

A

weaker acid

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8
Q

extend of dissociation of weak acid related to…

A

pH of solution

by Henderson - Hasselbalch equation

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9
Q

Henderson - Hasselbalch equation

A

pH = pKa = log [A-]/[HA]

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10
Q

ratio of salt to acid increases…

A

pH increases

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11
Q

ratio of salt to acid decreases

A

pH decreases

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12
Q

equal amounts of salt and acid…

A

log of 0 = 1

pKa = pH where salt = acid

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13
Q

Le Chatelier’s principle

A

system responds to disruption by trying to reestablish equilibrium

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14
Q

if add HCl…

A

A- will bind to them

decrease A- and increase HA, driven to left

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15
Q

if add NaOH…

A

OH- will bind to H+ to form water
protons needed from HA, driven to right
HA decreases, A- increases

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16
Q

buffer will be at maximum capacity when…

A 
[HA] = [A-]
acid = salt
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17
Q

buffering range

A

+ or - 1 pH unit from pKa

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18
Q

buffer maximally effective when..

A

pH = pKa

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19
Q

if add HCl in buffer region…

A

each HCl molecule –> one mol/molecule salt to convert to 1 mol/molecule of weak acid

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20
Q

if add NaOH in buffer region…

A

each NaOH molecule –> one mol/molecule acid to convert to one mol/molecule of salt

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21
Q

estimating charge…

A

pH is 1 or more units above pKa - proton OFF

pH is 1 or more units below pKa - proton ON

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22
Q

pI

A

pH at which charge is 0

average of 2 pKa values where charge of aa is 0

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23
Q

pKa describes pH at which…

A

1/2 of each protons are off and 1/2 are on

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24
Q

almost all amino acids exist is ___ form

A

L (rarely D)

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25
Q

5 groups of amino acids

A 
aliphatics 
hydrophobics 
polar
positive R group ( R amine)
negative R group (R carboxyl)
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26
Q

Aliphatics

A 
glycine 
alanine 
proline
valine
leucine
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27
Q

hydrophobics

A

isoleucine
methionine
tryptophan
phenylalanine

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28
Q

polar

A 
serine
threonine 
tyrosine 
asparagine 
glutamine
cysteine
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29
Q

positive R-group

A

lysine
arginine
histidine

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30
Q

negative R- group

A

aspartate

glutamate

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31
Q

glycine

A

smallest R group - H

most flexible

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32
Q

proline

A

R group connects with amine –> ring
can’t rotate, very inflexible
–> bends in protein structure
only favors trans peptide bond 100:1 (not 10,000:1)

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33
Q

methionine

A

C-S-C (not very reactive)

first aa in virtually every protein

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34
Q

cysteine

A

sulfhydryl S-H (very reactive)

reacts with other cysteines –> disulfide bond

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35
Q

peptide bond

A

between carboxyl on left, amino on right

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36
Q

phi

A

rotational angle between alpha amino and alpha carbon

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37
Q

psi

A

rotational angle around alpha carboxyl and alpha carbon

38
Q

secondary structure

A

regular repeating structures arising from interactions between amino acids less than 10 apart

39
Q

proteins with only primary and secondary structure

A

fibrous proteins

ex: collagen

40
Q

separating large from small molecules

A

dialysis

gel filtration/gel exclusion

41
Q

separate charged molecules

A

ion exchange chromatography

cation exchange or anion exchange

42
Q

separate proteins that bind to a specific molecule

A

affinity chromatography

43
Q

separate molecules on basis of polarity

A

HPLC (high performance liquid chromatography)

44
Q

separate negatively charged molecules by size

A

agarose gel electrophoresis

SDS - PAGE (polyacrylamide gel electrophoresis)

45
Q

separate by pI

A

isoelectric focusing

46
Q

2D gel electrophoresis

A 
isoelectric focusing (by pI)
then SDS - PAGE (by size)
47
Q

MALDI - TOF

A

determine molecular weight of large molecules

by time it takes volatized crystal to hit electrode

48
Q

cleaving agents

A

cyanogen bromide
trypsin
chymotrypsin
carboxypeptidase

49
Q

cyanogen bromide

A

cleaves carboxyl side of methionine

50
Q

trypsin

A

cleaves carboxyl side of lysine and arginine

51
Q

chymotrypsin

A

cleaves carboxyl side tyrosine, tryptophan, phenylalanine, leucine, methionine

52
Q

carboxypeptidase

A

cleaves amino side of carboxy-terminal aa

53
Q

DDT

A

reduces SS to SH

54
Q

heme

A

protoporphyrin IX complexed with iron

55
Q

iron held in place by

A

4 N from protoporphyrin IX and a histadine

56
Q

form of iron involved in carrying oxygen

A

Fe2+ ferrous

57
Q

T state

A

releases O2

low O2 affinity

58
Q

R state

A

bind O2

high O2 affinity

59
Q

bind of O2 help flip from ___ to ___

A

T to R

60
Q

release of O2 help flip from __ to __

A

R to T

61
Q

binding of 2,3-BPG converts hemoglobin from ___ to ___

A

R to T (releases O2)

62
Q

fetal hemoglobin exists more in

A

R state (doesn’t release O2 as readily)

63
Q

____ favors release of oxygen

A

CO2, 2,3- BPG, protons

64
Q

rapidly metabolizing tissues generate…

A

protons, lower pH

65
Q

negative delta G

A

reaction goes forward

66
Q

positive delta G

A

reaction goes backwards

67
Q

delta G = 0

A

at equilibrium

68
Q

plot of velocity vs. substrate concentration

A

hyperbolic plot

69
Q

Vmax

A

when enzyme is saturated with substrate

depends on amount of enzyme

70
Q

Kcat

A 
# molecules of product made/molecule of enzyme/1 sec 
turnover number
constant for enzyme
71
Q

Km

A

substrate concentration that give Vmax/2
affinity of enzyme for substrate
constant for enzyme

72
Q

higher Km…

A

lower affinity

need more substrate to reach Vmax/2

73
Q

lower Km…

A

higher affinity

need less substrate to reach Vmax/2

74
Q

equilibrium

A

forward reaction = reverse reaction

75
Q

lineweaver- Burk plots

A

double reciprocal plot

1/V vs. 1/[S]

76
Q

y intercept of lineweaver - burk

A

I/vmax

77
Q

x intercept of lineweaver - burk

A

-1/Km

78
Q

slope of lineweaver - burk

A

Km//vmax

79
Q

competitive inhibition.. Vmax

A

does not vary

80
Q

competitive inhibition… Km

A

does vary (need more substrate to get to same velocity)

81
Q

non-competitive inhibition … Vmax

A

lowered

82
Q

non- competitive inhibition… Km

A

unchanged (increased substrate cannot eliminate effect of inhibitor)

83
Q

Forces that stabilize tertiary structure

A 
H bonds
Disulfide (cysteine) 
Ionic 
Hydrophobic interactions 
Metallic
84
Q

Polar and charged on ___

A

Outside

Interacting with water to dissolve

85
Q

Non polar and uncharged on___

A

Inside

To avoid water

86
Q

Pourin

A

In cell membranes
Allow water to pass through
Polar, charged on inside

87
Q

Beta-mercaptoethanol

A

Disulfide to sulfhydryl

SS- SH SH

88
Q

Urea

A

Destroys H bonds

Affects 2, 3, and 4 structure

89
Q

DTT

A

Reduces disulfide to sulfhydryl bonds

90
Q

Guanidium chloride

A

Denatures H bonds

Biochemistry (11 decks)

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