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Biochemistry > BB450 exam 1 > Flashcards

BB450 exam 1 Flashcards

(90 cards)

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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
5 groups of amino acids
``` aliphatics hydrophobics polar positive R group ( R amine) negative R group (R carboxyl) ```
26
Aliphatics
``` glycine alanine proline valine leucine ```
27
hydrophobics
isoleucine methionine tryptophan phenylalanine
28
polar
``` serine threonine tyrosine asparagine glutamine cysteine ```
29
positive R-group
lysine arginine histidine
30
negative R- group
aspartate | glutamate
31
glycine
smallest R group - H | most flexible
32
proline
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)
33
methionine
C-S-C (not very reactive) | first aa in virtually every protein
34
cysteine
sulfhydryl S-H (very reactive) | reacts with other cysteines --> disulfide bond
35
peptide bond
between carboxyl on left, amino on right
36
phi
rotational angle between alpha amino and alpha carbon
37
psi
rotational angle around alpha carboxyl and alpha carbon
38
secondary structure
regular repeating structures arising from interactions between amino acids less than 10 apart
39
proteins with only primary and secondary structure
fibrous proteins | ex: collagen
40
separating large from small molecules
dialysis | gel filtration/gel exclusion
41
separate charged molecules
ion exchange chromatography | cation exchange or anion exchange
42
separate proteins that bind to a specific molecule
affinity chromatography
43
separate molecules on basis of polarity
HPLC (high performance liquid chromatography)
44
separate negatively charged molecules by size
agarose gel electrophoresis | SDS - PAGE (polyacrylamide gel electrophoresis)
45
separate by pI
isoelectric focusing
46
2D gel electrophoresis
``` isoelectric focusing (by pI) then SDS - PAGE (by size) ```
47
MALDI - TOF
determine molecular weight of large molecules | by time it takes volatized crystal to hit electrode
48
cleaving agents
cyanogen bromide trypsin chymotrypsin carboxypeptidase
49
cyanogen bromide
cleaves carboxyl side of methionine
50
trypsin
cleaves carboxyl side of lysine and arginine
51
chymotrypsin
cleaves carboxyl side tyrosine, tryptophan, phenylalanine, leucine, methionine
52
carboxypeptidase
cleaves amino side of carboxy-terminal aa
53
DDT
reduces SS to SH
54
heme
protoporphyrin IX complexed with iron
55
iron held in place by
4 N from protoporphyrin IX and a histadine
56
form of iron involved in carrying oxygen
Fe2+ ferrous
57
T state
releases O2 | low O2 affinity
58
R state
bind O2 | high O2 affinity
59
bind of O2 help flip from ___ to ___
T to R
60
release of O2 help flip from __ to __
R to T
61
binding of 2,3-BPG converts hemoglobin from ___ to ___
R to T (releases O2)
62
fetal hemoglobin exists more in
R state (doesn't release O2 as readily)
63
____ favors release of oxygen
CO2, 2,3- BPG, protons
64
rapidly metabolizing tissues generate...
protons, lower pH
65
negative delta G
reaction goes forward
66
positive delta G
reaction goes backwards
67
delta G = 0
at equilibrium
68
plot of velocity vs. substrate concentration
hyperbolic plot
69
Vmax
when enzyme is saturated with substrate | depends on amount of enzyme
70
Kcat
``` # molecules of product made/molecule of enzyme/1 sec turnover number constant for enzyme ```
71
Km
substrate concentration that give Vmax/2 affinity of enzyme for substrate constant for enzyme
72
higher Km...
lower affinity | need more substrate to reach Vmax/2
73
lower Km...
higher affinity | need less substrate to reach Vmax/2
74
equilibrium
forward reaction = reverse reaction
75
lineweaver- Burk plots
double reciprocal plot | 1/V vs. 1/[S]
76
y intercept of lineweaver - burk
I/vmax
77
x intercept of lineweaver - burk
-1/Km
78
slope of lineweaver - burk
Km//vmax
79
competitive inhibition.. Vmax
does not vary
80
competitive inhibition... Km
does vary (need more substrate to get to same velocity)
81
non-competitive inhibition ... Vmax
lowered
82
non- competitive inhibition... Km
unchanged (increased substrate cannot eliminate effect of inhibitor)
83
Forces that stabilize tertiary structure
``` H bonds Disulfide (cysteine) Ionic Hydrophobic interactions Metallic ```
84
Polar and charged on ___
Outside | Interacting with water to dissolve
85
Non polar and uncharged on___
Inside | To avoid water
86
Pourin
In cell membranes Allow water to pass through Polar, charged on inside
87
Beta-mercaptoethanol
Disulfide to sulfhydryl | SS- SH SH
88
Urea
Destroys H bonds | Affects 2, 3, and 4 structure
89
DTT
Reduces disulfide to sulfhydryl bonds
90
Guanidium chloride
Denatures H bonds

Biochemistry (11 decks)

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