Exam Five Flashcards
1
Q
What is the ultimate electron acceptor in oxidative phosphorylation?
A
O2
2
Q
In oxidative phosphorylation, the proton is moved from the ____________ to the _________________
A
mitochondrial matrix; intermembrane spaces
3
Q
A proton gradient is formed in between the mitochondrial matrix and the intermembrane spaces. Which has a higher proton concentration?
A
intermembrance space
4
Q
What is the proton motive force?
A
the proton gradient that powers the ATP synthase and produces ATP
5
Q
What is the tendency of a substrate to accept electrons?
A
reduction potential
6
Q
How does the reduction potential change as the ETC progresses?
A
becomes more positive/favorable as the chain goes on
7
Q
What does the protonmotive force power?
A
ATP synthase
8
Q
How many multiprotein clusters are there?
A
4
9
Q
Which complexes pump protons into the intermembrane space?
A
I, III, and IV
10
Q
What is the electron donor in complex I?
A
NADH
11
Q
What is the electron acceptor in complex I?
A
Q
12
Q
What are the main electron transport components in complex I?
A
FMN and Iron-Sulfur Clusters
13
Q
What is the enzymatic name for complex I?
A
NADH-CoQ Reductase
14
Q
What is the electron donor in complex II?
A
Succinate
15
Q
What is the electron acceptor in complex II?
A
Q
16
Q
What are the main electron transport components in complex II?
A
FAD
17
Q
What is the enzymatic name for complex II?
A
Succinate CoQ reductase or succinate dehydrogenase
18
Q
What is the electron donor in complex III?
A
QH2
19
Q
What is the electron acceptor in complex III?
A
cytochrome c
20
Q
What are the main electron transport components in complex III?
A
Rieske ISP, cyt c, cyt bL, and cyt bH
21
Q
What is the enzymatic name for complex III?
A
cyt. c oxidoreductase
22
Q
What is the electron donor in complex IV?
A
cyt c
23
Q
What is the electron acceptor in complex IV?
A
O2
24
Q
What are the main electron transport components in complex IV?
A
cyt a, Cu
25
What is the enzymatic name for complex IV?
cyt c oxidase
26
How can you skip complex I in the ETC?
start from succinate DH
27
what are the flavin containing electron carriers?
FMN or FAD
28
What is a nonpolar mobile electron carrier?
ubiquinone
29
How many electrons do FMN and FAD accept at a time?
Up to two
30
How many electrons do FMN and FAD donate at a time?
one
31
What are the proteins called that contain porphyrin?
cytochromes
32
How many electrons do iron-sulfur clusters carry?
one
33
How many sulfur atoms are present in a cluster if there are 2 iron atoms?
2
34
What occurs during complex I?
FMN accepts two electrons from NADH, several iron-sulfur clusters pass one electron at a time toward the Q binding site, and 4 protons are moved to the intermembrane space
35
What occurs during complex II?
FAD accepts two electrons from succinate, electrons are passed one at a time via iron-sulfer centers to ubiquinone
36
What occurs during complex III?
it accepts two electrons from QH2 to reduce cyt c, translocate 4 protons to the intermembrane space
37
What occurs during the Q cycle?
2 electrons from QH2 split and require another molecule of QH2 to complete the cycle
38
What is the main reaction of the Q cycle?
QH2 + 2 cyt c (Fe3+) ---> Q + 2 cytc (Fe2+)
39
What is cytochrome c?
a soluble heme-containing protein in the intermembrane space
40
What is cytochrome c's job?
carry a single electron from the complex III to cytochrome c oxidase (complex IV)
41
Cytochrome c is ________
a. integral membrane protein
b. a part of complex III
c. a part of complex IV
d. peripheral membrane protein
d. peripheral membrane protein
42
is heme hydrophilic or hydrophobic?
hydrophobic
43
What is the hydrophilic part of cytochrome c?
Lys
44
Cytochrome c has a large amount of Lysine residues. Therefore it is a/an (acidic/basic) protein because its pI is (high/low)
basic; high
45
cytochrome c oxidase (complex IV) contains __ heme groups
2
46
What ions are present in cytochrome c oxidase?
copper
47
What does CuA do?
accepts electrons from cytochrome c
48
What does CuB do?
transfers electrons to oxygen
49
Where does O2 get reduced to water?
matrix
50
Which inhibitor of the ETC stops the chain after NADH and before Q?
rotenone
51
Which inhibitor of the ETC stops the chain after Cyt b and before Cyt c1?
antimycin A
52
Which inhibitor of the ETC stops the chain after Cyt (a + a3) and before O2?
cyanide or carbon monoxide
53
electron carriers before the block (inhibited spot) become _________ and those after the block become __________
reduced;oxidized
54
How does the F0 subunit of ATP Synthase rotate?
by H+ flow
55
Which parts of ATP synthase rotate?
F0 and gamma
56
Which parts of ATP synthase do not rotate?
catalytic parts
57
O form of ATP synthase means
open: binding site for ADP and Pi is open
58
L form of ATP synthase means
loose: ADP and Pi bind to site L
59
T form of ATP synthase means
tight: catalytically active
60
From which conformation is ATP released from ATP synthase?
O
61
How many ATP are released per one revolution of ATP synthase?
3
62
How many protons does it take to drive one revolution of the camshaft to produce 3 ATP molecules?
9-12
63
In which direction to ATP synthase operate?
either direction, depending on concentrations
64
electron transport translocated protons and formed a concentration gradient and a charge gradient across the membrane
chemiosmosis
65
energy created by the proton gradient
proton motive force
66
How many protons move to the intermembrane space if you start with 1 NADH molecule?
10
67
How many protons move to the intermembrane space if you start with 1 Succinate molecule?
6
68
What is the P:O ratio?
phosphorylation of ADP per oxygen atom
69
What is the approximate P:O ratio for NADH oxidation?
2.5 ATP/O
70
What is the approximate P:O ratio for QH2 oxidation?
1.5 ATP/O
71
How many protons are needed for one complete rotation of ATP synthase?
number of c subunits in ATP synthase
72
what is a chemical that can diffuse through the nonpolar membrane?
uncoupler
73
Why is an uncoupler important in biochemistry?
it can move H+ across the membrane without ATP synthase
74
Dichyclohexylcarbodiimide (DCCD) reacts with Asp and Glu residues in the c-s.u. of F0 and blocks ATP synthase activity. What happens to the rate of electron transport if DCCD is added to the respiring molecule?
the rate will decrease, although NADH will continue to oxidize at first, but the protons will get backed up and not be converted to ATP, reducing the rate
75
ATP synthesis can be uncoupled from ETC to generate _______
heat
76
Why does uncoupling ATP synthesis generate heat?
the protons pass through and nothing happens, so the energy is transferred to heat
77
What is the only irreversible step in the ETC?
complex IV (cyt c oxidase)
78
What regulates the ETS?
cyt c oxidase
79
What regulates cyt c oxidase?
level of oxidation/reduction of cyt c
80
What regulates the level of redox of cyt c?
NADH and ATP
81
When is the ETS rate the highest?
when [NADH] >>>> [NAD] and [ADP] >>>> [ATP]
82
What facilitates the movement of specific molecules within an organism?
transport proteins
83
one thing moves one direction
uniport
84
2 things move one direction
symport
85
2 things move opposite directions
antiport
86
What kind of transport protein is GLUT 1?
uniport
87
What is the goal of the malate/aspartate shuttle?
move NADH from the cytosol into the mitochondria
88
How does the malate/aspartate shuttle work?
moves the electrons as malate and then uses it to reduce NAD+ to produce NADH in the mitochondria
89
Why is the glycerophosphate shuttle considered as a part of complex II?
it adds to the pool of QH2
90
How does the glycerophosphate shuttle work?
takes an NADH molecule to the mitochondria as FADH2, but makes less ATP
91
How does ATP get moved from the mitochondria to the cytosol?
ADP-ATP translocator
92
What symport helps facilitate the move of ATP from the mitochondria to the cytosol?
Pi-H+ symport
93
light energy is converted to ATP in a plant's __________
chloroplasts
94
What is the main idea of respiration?
NADH ----> H2O
95
What is the main idea of photosynthesis?
H2O ----> NADPH
96
Where does the proton gradient accumulate in photosynthesis?
thylakoid lumen
97
Where does the proton gradient accumulate in respiration?
intermembrane space
98
Photosynthesis happens at the interface of _________
stroma and thylakoid
99
Respiration happens at the interface of _________
matrix and intermembrane
100
what is the membrane electron transport in photosynthesis?
plastoquinone (Q)
101
what is the membrane electron transport in respiration?
CoQ
102
What is the source of electrons in photosynthesis?
water
103
What is the source of electrons in respiration?
NADH
104
What is the final electron acceptor in photosynthesis?
NADP+
105
What is the final electron acceptor in respiration?
O2
106
Why do lipids yield more energy per carbon than carbohydrates?
fatty acids are much more reduced compared to carbohydrates
107
What is the enzyme in the small intestine that releases fatty acids?
lipase
108
What activates lipases?
glucagon and epinephrine
109
What happens to the fatty acids after being cleaved off from TG?
beta oxidation
110
How is the fatty acid "activated" for beta oxidation?
it is attached to CoA
111
What is used to form one thioester bond to activate a fatty acid?
2 ATP equivalent of free energy
112
What is the transporter to take a fatty acid from the cytosol to the mitochondria for beta oxidation?
acyl-carnitine/carnitine transporter
113
How does beta oxidation work?
2 carbons at a time are oxidized/degraded as acetyl-coa
114
Describe the spiral pathway of beta oxidation
each round takes two carbons off the chain from the carboxyl end, which produces 1 acetyl-coa, 1 QH2, and 1 NADH, consisting of 4 enzymatic steps
115
Why is it called beta oxidation?
the attack occurs on the beta carbon (second carbon from the carbonyl carbon)
116
The 4 reactions/2 carbons per round of beta oxidation produces _______
1 QH2, 1 NADH, and 1 acetyl-coA
117
What are the 4 enzymes of beta oxidation?
1. acyl-coa dehydrogenase (AD)
2. enoyl-coa hydratase (EH)
3. 3-L-hydroxyacyl dehydrogenase (HAD)
4. beta-ketoacyl-coa thiolase (KT)
118
What is the energy yield of beta oxidation?
14 ATP
119
Would unsaturated fatty acids yield more or less energy than the saturated fatty acid?
less
120
Odd number carbon double bonds lose how much ATP overall?
1.5
121
Even number carbon double bonds lose how much ATP overall?
2.5
122
What mechanisms are controlled so only one goes on at a time?
beta oxidation and fatty acid synthesis
123
Where does fatty acid biosynthesis occur?
cytosol
124
How does acetyl-coa get to the cytosol from the mitochondria to produce fatty acids?
tricarboxylate transport system
125
How and where is acetyl-coa produced?
in matrix from fatty acid oxidation or pyruvate dehydrogenase
126
What is the 2 carbon donor for fatty acid biosynthesis?
malonyl CoA
127
Why is the conversion of acetyl-coa to malonyl-coa so important?
it is the first committed step and one of the rate controlling steps
128
What affects the conversion of acetyl-coa to malonyl-coa?
citrate stimulates it, long chain fatty acids inhibit it, and insulin activates the enzyme
129
What is the acyl carrier for synthesis?
ACP
130
What is the overall goal of fatty acid synthesis?
attach acetate unit from malonyl-coa to a growing chain and then reduce it
131
What are the four enzyme-catalyzed steps of fatty acid synthesis?
condensation of the chain with activated acetate, reduction of carbonyl to hydroxyl, dehydration of alcohol to trans-alkene, and reduction of alkene to alkane
132
How is the growing fatty acid chain initially attached to the enzyme?
thioester linkage
133
What is required if you a have a fatty acid beyond a saturated 16C?
elongases in ER or mitochondria OR desaturases for unsaturated fatty acids
134
Where is there a futile cycle control in fatty acid biosynthesis?
Acetyl-CoA carboxylase: inhibited by AMP- and cAMP-dependent phosphorylation and activated by insulin-dependent phosphorylation
135
What is the controlling point of F.A. oxidation?
lipase
136
What is the controlling point of F.A. synthesis?
ACCase
137
How does insulin affect lipids?
it activates phosphatases that dephosphorylate enzymes, which activate ACCase and increase fatty acid synthesis
138
How does glucagon affect lipids?
it triggers cAMP production, which activates proteinase kinase A, which phosphorylates enzymes that activate TG lipases and inhibit ACCase, increasing oxidation of F.A., decreasing synthesis of F.A., and decreasing cholesterol synthesis
139
What is another alternative fate for acetyl-coa when large amount from fats inhibits the citric acid cycle?
ketone bodies
140
What is the purpose of ketone bodies?
provide fuel during starvation for the brain, heart, and skeletal muscles
141
What are the three ketone bodies?
acetoacetate, acetone, and D-beta-hydroxybutyrate
142
What organ is the source of ketone bodies?
liver
143
What is the name of the enzyme that is a major controlling point of cholesterol biosynthesis, inhibited by phosphorylation, and is what statin inhibits?
HMG CoA reductase
144
How does statin work?
lowers serum cholesterol by inhibiting HMG CoA reductase
145
Where does digestion and absorption of dietary lipids occur?
small intestine
146
Why do we need to package the dietary lipids before sending them to other tissues?
they are nonpolar and cannot be transported otherwise
147
What transfers lipids from the intestine to the liver?
chylomicrons
148
What transfers lipids from the liver to other tissues?
VLDLs and LDLs
149
What transfers lipids from other tissues to the liver?
HDL
150
Which is denser, fat or protein?
protein
151
Low density = (high/low) fat?
high
152
High density = (high/low) fat?
low
153
What is bad cholesterol?
LDL
154
What is the purpose of LDLs?
deliver cholesterol and cholesterol esters to cells
155
What is missing in people with familial hypercholesterolemia?
LDL receptor
156
What is good cholesterol?
HDL
157
What is the purpose of HDLs?
remove excess cholesterol from cells
158
What is required for HDLs?
membrane transporter/flippase
159
How many genes does the X chromosome carry?
about 1500
160
How many genes does the Y chromosome carry?
about 100
161
What comprises a nucleotide?
a five-carbon sugar, a nitrogen containing ring, and one or more phosphate group
162
What are the purines?
adenine and guanine
163
What are the pyrimidines?
cytosine, thymine, and uracil
164
Do purines or pyrimidines have two rings?
purines
165
Do purines or pyrimidines have one ring?
pyrimidines
166
What is the difference between ribose and deoxyribose?
ribose has one extra OH group compared to deoxyribose
167
Why does DNA twist?
once you make a double stranded structure, it twists to accommodate its size
168
In which direction does DNA run?
antiparallel
169
Is DNA right or left handed?
right
170
How many base pairs are there per turn of DNA?
10
171
Exposed ____ binds to ______ to reduce repulsion in DNA
P; Mg2+
172
Are the base pairs interior or exterior to the helix axis?
interior
173
Edges of base pairs exposed at grooves can be recognized by what?
DNA binding proteins
174
DNA strands make double stranded helix by _______ bonds between the bases
hydrogen
175
The ________ of the bases in DNA are the information.
sequence
176
The _________ of the bases in DNA is the key in transmitting the information.
complementarity
177
When can double-stranded nucleic acids be denatured?
at high temperatures
178
What occurs to DNA at lower temperatures?
complementary polynucleotides anneal
179
What kind of bonds always remain intact throughout DNA denaturation and renaturation and why?
covalent bonds so that the genetic code itself remains intact
180
What occurs if you rapidly cool denatured/separated DNA?
improper base pairing
181
What is the Tm?
melting temperature of DNA
182
The higher the ___ content, the higher the Tm
GC
183
Why does GC content raise the Tm?
stacking energy
184
What does stacking energy mean?
the energy required to untwist the DNA
185
The Tm is also equal to....
the temperature at which 50% of the DNA has been denatured
186
What does the hybridization technique do?
identify where partner is
187
What does southern blot identify?
DNA to DNA hybridization
188
What does northern blot identify?
RNA-DNA hybridization
189
What does western blot identify?
protein to antibody reaction
190
What do restriction enzymes do?
digests the phosphodiester bonds that connect nucleotides
191
How do restriction enzymes know where to cut?
they recognize very specific patterns of 4-6 bases in DNA, normally in palindrome format
192
What is the purpose of dideoxy sequencing?
figure out base order/sequence
193
What is the purpose of polymerase chain reaction (PCR)?
amplify sections of DNA
194
DNA polymerase adds deoxynucleotides at the ___ end of the growing chain of nucleic acid
3'
195
Where does DNA polymerase add the complementary nucleotides?
the 3' - OH of the primer
196
What are the ingredients for a DNA sequencing reaction?
DNA, primer, dNTPs, ddNTPs, DNA polymerase, buffer
197
Why does DNA polymerase stop elongation when ddNTP is added instead of dNTP?
ddNTPs lack a 3'-OH group, so no more NTPs can attach
198
What is PCR?
enzymatic amplification of a segment of DNA
199
What are the ingredients for a PCR reaction?
DNA, primers (a pair), dNTPs, DNA polymerase (normally Taq polymerase), buffer
200
What are the 3 steps of PCR?
1. strand separation
2. primer annealing
3. primer extension
201
At what temperature does strand separation occur?
90-95 degrees C
202
At what temperature does primer annealing occur?
45-55 degrees C
203
At what temperature does primer extension occur?
70 degrees C
204
What are the four things PCR is used for?
1. identify mutations
2. site-directed mutagensis
3. detection of signature sequences
4. forensic use
205
How many strands of DNA are used in sequencing reactions?
one
206
How many strands of DNA are used in PCR reactions?
two
207
Is the inner membrane of the mitochondria directly permeable to small molecules and hydrogen ions?
no
208
The electron transport chain operates (independently/dependently) of other metabolic processes.
dependently
209
Where is H+ ion concentration higher?
intermembrane space
210
Where is the pH higher?
matrix
211
What are the two electron transport inhibitors?
cyanide and rotenone
212
What is the uncoupling agent that increases membrane proton permeability?
FCCP
213
What is the ATP synthase inhibitor that binds to F0 and blocks the proton channel?
oligomycin
214
What is the transport inhibitor that binds to inward-facing site of ATP-ADP translocase?
bongkrekic acid
215
What provides the energy that excites the electrons in the chlorophyll molecules?
light
216
What is the source of the electrons that replace the excited electrons lost from chlorophyll?
water
217
What is the first step of ATP synthase?
protons from the intermembrane space bind to proton binding sites on c subunits
218
What is the second step of ATP synthase?
as the c ring rotates past the a subunit c, subunits release their protons into the matrix
219
What is the third step of ATP synthase?
the gamma subunit rotates past the a subunit, c subunits release their protons into the matrix
220
What is the fourth step of ATP synthase?
the gamma subunit rotates and interacts with the three alpha-beta subunit pairs, causing conformational changes in the beta subunits
221
What is the last step of ATP synthase?
each beta subunit binds ADP and Pi, converts ADP + Pi to ATP, and releases ATP once during one turn of the gamma subunit
222
How is oxaloacetate modified to a form that can be transported out of the matrix?
transamination
223
Which compound transfers reducing equivalents (electrons) into the mitochondrial matrix?
malate
224
What kind of reaction is the first reaction of beta oxidation?
oxidation
225
What kind of reaction is the second reaction of beta oxidation?
hydration
226
What kind of reaction is the third reaction of beta oxidation?
oxidation
227
What kind of reaction is the fourth reaction of beta oxidation?
cleavage
228
What does CAT1 do?
converts carnitine into acyl-carnitine
229
What does CAT2 do?
converts acyl-carnitine into carnitine
230
Which of the three ketone bodies is the only one reduced to alcohol form?
beta-hydroxybutyrate
231
Which of the three ketone bodies is only made up of three carbons?
acetone
232
Increased levels of which cholesterol is associated with atherosclerosis?
LDL
233
Do nucleosides contain a phosphate group?
no
234
What is the product when a base bonds at C1 of ribose or deoxyribose?
nucleoside
235
Are nucleosides found in both RNA and DNA?
yes
236
What is true for both DNA and RNA?
sugars are connected with a 3'-5' phosphodiester link
237
What is true for RNA only?
it commonly exists in a variety of secondary structures
238
Which purine has a ketone?
guanine
239
Which purine doesn't have any oxygens?
adenine
240
Which pyrimidine only has one ketone group?
cytosine
241
Which pyrimidine has two ketone groups, but no methyl group?
uracil
242
Which pyrimidine has two ketone groups AND a methyl group?
thymine
243
