Biochemistry Flashcards
1
Q
steps of the gabriel synthesis
A
deprotonation to anion
addition of R-Br
amide hydrolysis to a di-carboxyl
2
Q
L
A
Leucine
3
Q
cysteine
A
Cys
C
4
Q
secondary structure
A
alpha helicies and beta sheets
5
Q
immune system proteins
A
antigens and antibodies
6
Q
are the R groups parallel or perpendicular in beta sheets
A
perpendicular
7
Q
mannose
A
C6H12O6
8
Q
negatively charged amino acids
A
aspartic acid
glutamic acid
9
Q
sugars with the formula C3H6O3
A
glyceraldehyde
dihydroxyacetone
10
Q
isomerases
A
rearrangements
11
Q
charge below the isoelectric point
A
positive
12
Q
Glycine
A
Gly
G
13
Q
what is the preferred model of enzyme specificity
A
induced fit
14
Q
what proton is donated first from an amino acid
A
COOH
15
Q
R
A
arginine
16
Q
characteristics of amino acids
A
alpha carbon stereocenter
absolute configuration
R group chemistry
17
Q
C
A
cysteine
18
Q
minerals
A
inorganic molecules essential for bone formation
19
Q
isoelectric point of basic amino acid
A
amine and R group
20
Q
galactose
A
C6H12O6
21
Q
glutamic acid
A
Glu
E
22
Q
can enzymes become saturated
A
yes
23
Q
x intercept of lineweaver burke plots
A
-1/Km
24
Q
T
A
threonine
25
ligases
large molecule synthesis
26
cell adhesion molecules are an example of
binding protein
27
isoprene
C5H8 with one C=C double bond on the end and one attached to C3
28
peptide bond formation
dehydration synthesis and acyl substitution
29
what enantiomer is found in the human body
D
30
what direction do amino acids flow
N --> C
31
what filaments are present in actin
thin and microfilaments
32
non-reducing sugar example
sucrose
33
charge above the isoelectric point
negative
34
sucrose
glucose+fructose
35
pka of acidic R groups
3. 7 Asp
| 4. 5 Glu
36
lock and key model
active site of an empty enzyme is an exact fit for the substrate
37
terpenes
mostly conjugated unsaturated polymer of isoprene
38
polysaccharides
Cn(H2O)x
39
tertiary structure
geometric 3D folding on alpha helicies and beta sheets to form a globular/ structural protein
40
V
valine
41
isoelectric point of neutral amino acid
amine and carboxyl pKa
42
how is competitive inhibition overcome
increasing substrate concentration
43
pka of basic R groups
10.7 Lys
| 12 Arg
44
where does proline occur in an alpha helix
often the first residue, not found within the helix
45
what type of isomers are glucose and galactose
epimers
46
alpha linkages
linked through oxygen on the opposite plane from CH2OH
47
lipids
hydrophobic biomolecules
48
asparagine
Asn
| N
49
monosaccharides
(CH2O)n
50
molten globule
partially folded
51
what is fibroin and what secondary structure does it have
silk
| beta sheets
52
are coenzymes permanently attached to an enzyme
no
53
conjugated protein
associated with cofactors by covalent or intermolecular forces
54
what linkages attach a triacylglycerol
ester linkages
55
what are kinesins and dyneins used for
vesicles, cell division, cilia and flagella
56
mixed inhibition
inhibitor has unequal affinity for ES and E, favoring one over the other
57
lactose
glucose and galactose
58
what is keratin and what secondary structure does it have
found in hair and nails
| alpha helix
59
transferases
functional group transfer
60
nonpolar amino acids
```
proline
glycine
alanine
valine
leucine
isoleucine
methionine
```
61
intramolecular nucleophilic substitution
ring closing reaction
62
how does competitive inhibition change Km
increases
63
H
histidine
64
isoelectric point separation
uses a gel with a stable pH gradient and protein moves through an increasing pH and will stop moving when pH is equal to pI
65
does the non-competitive inhibitor show preference for ES or E?
neither
66
beta glucose
OH up
67
how does mixed inhibition change Km
decreases when ES increases over E
increases when E increases over ES
68
isoelectric point
pH when a molecule has no net charge
[pka(1)+pka(2)]/2
69
are vitamins organic
yes
70
hydrolases
hydrolysis
71
how does competitive inhibition change Vmax
unchanged
72
M-M saturation curve
graph of reaction velocity versus substrate concentration
73
characteristics of an active site
contains amino acids that will associate with the substrate
74
triacylglycerol
glycerol backbone attached to r chain
75
are the positive amino acids acidic or basic?
basic
76
what filaments are present in tubulin
microtubules
77
solvation layers
layer of water surrounds a dissolved protein interaction with one another and the protein surface
78
oxidoreductases
redox reactions
79
example of positive cooperativity
hemoglobin
80
feedback inhibition
negative feedback
inhibition that applies to a multi-step synthetic pathway where a product later in the chain acts as an inhibitor for an enzyme in an earlier step
81
two protein separation techniques
isoelectric point
| electrophoresis
82
are the R groups directed into or out of the helix
out of
83
how does mixed inhibition change Vmax
decreases
84
how many residues occur between alpha helicies
four
85
S
serine
86
strecker synthesis
aldehyde with NH3 and HCN add cyano and NH2 to the C
| Add hydrogen ions and water for the amino acid
87
what type of isomers are D and L
enantiomers
88
positively charged amino acids
arginine
histidine
lysine
89
glycogen
alpha linkages, branched
| animals
90
autocrine
self-target
91
substrate
molecule acted upon by an enzyme
92
quaternary structure
association of multiple folded proteins into a multi-subunit complex
93
salt bridges
acidic and basic R groups go through neutralization reactions resulting in salt formation
94
when is Km equal to [S]
half of Vmax
95
oligopeptide
small chain of amino acids
96
non-competitive inhibition
inhibitor binds away from the active site and changes the enzyme shape
97
triacylglycerol is the same as
triglycerides
98
transcription factors are an example of
binding protein
99
sulfur linkage
S-S between cysteines
100
I
isoleucine
101
are the negative amino acids acidic or basic?
acidic
102
forms of tertiary structure (6)
```
hydrogen bonding
disulfide bonds
hydrophobic/hydrophilic interactions
ionic interactions
van der waals interactions
proline turns
```
103
lineweaver burke plots
double inverse plot of reaction rate (1/v) versus substrate concentration (1/[S])
104
Vmax
rate of reaction at saturation levels of substrate, theoretical maximum velocity
105
serine
Ser
| S
106
cofactors
metal ions or small molecules that assist in catalysis
107
are prosthetic groups permanently attached to an enzyme
yes
108
what type of isomers are alpha and beta glucose
anomers
109
tryptophan
Trp
| W
110
fatty acid
carboxyl attached to an R chain
111
proline
Pro
| P
112
how are vitamins acquired
diet
113
fat soluble vitamins
A D E K
114
does a lower or higher pka lose a proton?
lower
115
positive feedback
product of reaction acts as an agonist to activate a receptor
116
arginine
Arg
| R
117
histidine
His
| H
118
what is the electrophile in an intramolecular nucleophilic substitution
Carbon with carbonyl
119
active site
section of the enzyme where the substrate is converted to product
120
methionine
met
| M
121
glycolipids
sugars attached to lipids
122
reversible enzyme inhibition
inhibitor is not permanently bound and the enzyme is not completely disabled
123
ribose
C5H10O5
124
sphingolipid
fatty acid derivatives of shingosine
125
lysine
Lys
| K
126
how does non-competitive inhibition change Vmax
decreases
127
positive cooperativity
ligand affinity increases with the binding of each subsequent ligand
128
tryosine
Tyr
| Y
129
what filaments are present in elastin
connective tissue
130
protein folding
hydrophobic r groups fold into the core and hydrophilic are common on the surface
131
structural proteins
actin, tubulin, keratine, elastin
132
cellulose
beta linkages
| plants
133
calmodulin is an example of
binding protein
134
what is the pka of a strong acid
lower
135
hemoglobin is an example of
binding protein
136
Km
michaelis constant
| relative measure of an enzyme's affinity for substrate
137
y intercept of lineweaver burke plots
1/Vmax
138
competitive inhibition
inhibitor binds at active site, inhibitor resembles substrate
139
initial velocity is equal to
[VmaxS]/[Km+S]
140
agonist
activates a receptor to a response
141
simple protein
contains only amino acids and no non-protein cofactors
142
uncompetitive inhibition
inhibitor binds only to the enzyme-substrate complex
143
lysases
cleavage
144
L configuration
OH on the left
145
enzyme-substrate complex
formed when the substrate is bound in the activated site and the substrate is catalyzed to product
146
G
glycine
147
molten
fully unfolded, denatured
148
deoxyribose
C5H10O4
149
alpha glucose
OH down
150
induced fit
active site changes as the substrate binds, increases affinity for the substrate and for the transition state (lowers Ea)
151
examples of lipids
fats, oils, waxes, steroids, glycerides
152
alpha helicies
hydrogen bonding between the carbonyl O and amide H
153
what are the exceptions of the L/S configuration of amino acids
glycine (not chiral)
cysteine
154
disulfide bonds
two oxidized cysteine residues (R-S-S-R)
between alpha helicies in keratin makes hair curly or straight
155
pka of NH3+
9
156
how does non-competitive inhibition change Km
unchanged
157
are minerals organic
no
158
is an enzyme or a general catalyst faster
enzyme
159
apoenzyme
simple enzyme
160
what charge will a protein have in a pH below the pI
positive charge
161
aspartic acid
Asp
| D
162
are saturated or unsaturated molecules healthier
unsaturated
163
ketose
from a ketone
164
K
lysine
165
glutamine
Gln
| Q
166
A
alanine
167
M
methionine
168
where are waxes found
coatings on leaves and stems
169
michaelis menten kinetics
M-M
170
hydrophobic core
hydrophobic R groups fold into the interior of a globular protein to escape water
171
troponin is an example of
binding protein
172
saponification
hydrolysis of an ester using KOH into a glycerol and an acid
173
what is the difference between kinesins and dyneins
direction
| kinesins move from - to +, from the center to the periphery in a cell, from nerve to dendrite
174
how does uncompetitive inhibition change Km
decreases
175
pka of histidine
6
176
fructose
C6H12O6
177
glyceraldehyde
C3H6O3
178
Proteins
amino acid polymers
179
aldose
from an aldehyde
180
irreversible inhibition
inhibitor binds covalently to the enzyme and active site disabling the enzyme for a prolonged period of time, or permanently
181
leucine
Leu
| L
182
is cellulose digestible by humans
no
183
D
aspartic acid
184
P
proline
185
how does uncompetitive inhibition change Vmax
increases
186
what does the strecker synthesis create
alpha-aminonitriles
187
glucose
C6H12O6
188
paracrine
immediate vicinity
189
zwitterion
+ and - functional groups cancel one another out
| @ pH of 7.4 the COOH is COO- and NH2 is NH3+
190
polypeptide
longer chain of amino acids
191
what type of isomers are epimers
diastereomers
192
Valine
Val
| V
193
deoxy
-OH is replaced by H
194
E
glutamic acid
195
beta linkages
linked through oxygen on the same plane as CH2OH
196
linkages used to attach glycolipids
glycosidic bond
R-O-CH2 of glycerol backbone
197
what linkages attach lactose
beta
198
what is the configuration of almost all amino acids
L and S
199
exceptions to zwitterion at pH of 7.4
charged R groups
200
allosteric enzymes
activity is influenced by the reversible, non-covalent binding of another molecule
201
maltose
glucose+glucose
202
reducing sugar
can reduce a free aldehyde or ketone group
| all monosaccharides
203
what is the strongest type of protein folding interactions?
disulfide bonds
204
what is the nucleophile in an intramolecular nucleophilic substitution
OH on the chiral C
205
phenylalanine
Phe
| F
206
isoleucine
Ile
| I
207
are enzymes universal
no, specific
208
hydrophilic surface
surface R groups are polar or charged
209
polar amino acids
```
serine
threonine
cysteine
asparagine
gluamine
```
210
electrophoresis
separate based on size with the smallest traveling the farthest
211
what does mercaptoethanol do
reduce disulfide bonds
212
F
Phenylalanine
213
what is Km inversely proportional to?
E-S binding affinity
214
zymogen
inactive enzyme precursor that when activated, converts to the active form
215
beta sheets
hydrogen bonding beween the carbonyl O and amide H
216
how to irreversibly denature a protein
heat
217
where do resonance bonds form in a protein
carbonyl and nitrogen
218
why are zymogens important
important for enzymes needed quickly but that would be detrimental if active at all times
219
Y
tyrosine
220
N
asparagine
221
aromatic amino acids
phenylalanine
tryptophan
tyrosine
222
motor proteins
myosin, kinesins/dyneins
223
where does proline occur in a beta sheet
at the end to enable the 180° shift to the next row
224
electrostatic interactions
interactions between charged R groups
225
dihydroxyacetone
C3H6O3
226
starch
alpha linkages, branched
| plants
227
vitamins
relatively small, organic molecules that are essential nutrients for metabolism
228
globule
fully folded
229
steroids
4 membered ring structures
230
phospholipids
polar head group (phosphate) attached to a triacylglycerol
231
protein denaturing agents
acid
heat
urea
mercaptoethanol
232
isoelectric point of acidic amino acid
R and carboxyl pKa
233
alanine
ala
| A
234
furanose
5 carbons
235
D configuration
OH on the right
236
holoenzyme
enzyme and cofactors
237
waxes
ester of a long-chain (12-32 C) alcohol and a fatty acid
fatty acid-ester-alcohol
238
where are sphingolipids found
cell membrane of brain and nervous tissue
239
are enzymes organic or inorganic
organic
240
mercaptoethanol structure
HS-C-C-OH
241
sugars with the formula C6H12O6
glucose
fructose
galactose
mannose
242
what do alpha-aminonitriles do
intermediates in amino acid synthesis
243
residues
amino acids
244
prostaglandins
lipid mediators that have autocrine and paracrine functions in the body
245
example of a steroid
cholesterol
246
pyranose
6 carbon
247
what filaments are present in keratin
intermediate filaments
248
primary structure
amino acid sequence
249
pka of COOH
2
250
Threonine
Thr
| T
251
Q
glutamine
252
what charge will a protein have in a pH above the pI
negative charge
253
what is myosin used for
cellular transport
254
histones are an example of
binding protein
255
W
tryptophan
