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CHM 432 > Exam Five > Flashcards

Exam Five Flashcards

1
Q

What is the ultimate electron acceptor in oxidative phosphorylation?

A

O2

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2
Q

In oxidative phosphorylation, the proton is moved from the ____________ to the _________________

A

mitochondrial matrix; intermembrane spaces

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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

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4
Q

What is the proton motive force?

A

the proton gradient that powers the ATP synthase and produces ATP

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5
Q

What is the tendency of a substrate to accept electrons?

A

reduction potential

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6
Q

How does the reduction potential change as the ETC progresses?

A

becomes more positive/favorable as the chain goes on

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7
Q

What does the protonmotive force power?

A

ATP synthase

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8
Q

How many multiprotein clusters are there?

A

4

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9
Q

Which complexes pump protons into the intermembrane space?

A

I, III, and IV

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10
Q

What is the electron donor in complex I?

A

NADH

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11
Q

What is the electron acceptor in complex I?

A

Q

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12
Q

What are the main electron transport components in complex I?

A

FMN and Iron-Sulfur Clusters

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13
Q

What is the enzymatic name for complex I?

A

NADH-CoQ Reductase

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14
Q

What is the electron donor in complex II?

A

Succinate

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15
Q

What is the electron acceptor in complex II?

A

Q

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16
Q

What are the main electron transport components in complex II?

A

FAD

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17
Q

What is the enzymatic name for complex II?

A

Succinate CoQ reductase or succinate dehydrogenase

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18
Q

What is the electron donor in complex III?

A

QH2

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19
Q

What is the electron acceptor in complex III?

A

cytochrome c

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20
Q

What are the main electron transport components in complex III?

A

Rieske ISP, cyt c, cyt bL, and cyt bH

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21
Q

What is the enzymatic name for complex III?

A

cyt. c oxidoreductase

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22
Q

What is the electron donor in complex IV?

A

cyt c

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23
Q

What is the electron acceptor in complex IV?

A

O2

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24
Q

What are the main electron transport components in complex IV?

A

cyt a, Cu

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25
Q

What is the enzymatic name for complex IV?

A

cyt c oxidase

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26
Q

How can you skip complex I in the ETC?

A

start from succinate DH

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27
Q

what are the flavin containing electron carriers?

A

FMN or FAD

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28
Q

What is a nonpolar mobile electron carrier?

A

ubiquinone

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29
Q

How many electrons do FMN and FAD accept at a time?

A

Up to two

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30
Q

How many electrons do FMN and FAD donate at a time?

A

one

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31
Q

What are the proteins called that contain porphyrin?

A

cytochromes

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32
Q

How many electrons do iron-sulfur clusters carry?

A

one

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33
Q

How many sulfur atoms are present in a cluster if there are 2 iron atoms?

A

2

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34
Q

What occurs during complex I?

A

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

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35
Q

What occurs during complex II?

A

FAD accepts two electrons from succinate, electrons are passed one at a time via iron-sulfer centers to ubiquinone

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36
Q

What occurs during complex III?

A

it accepts two electrons from QH2 to reduce cyt c, translocate 4 protons to the intermembrane space

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37
Q

What occurs during the Q cycle?

A

2 electrons from QH2 split and require another molecule of QH2 to complete the cycle

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38
Q

What is the main reaction of the Q cycle?

A

QH2 + 2 cyt c (Fe3+) —> Q + 2 cytc (Fe2+)

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39
Q

What is cytochrome c?

A

a soluble heme-containing protein in the intermembrane space

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40
Q

What is cytochrome c’s job?

A

carry a single electron from the complex III to cytochrome c oxidase (complex IV)

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41
Q

Cytochrome c is ________
a. integral membrane protein
b. a part of complex III
c. a part of complex IV
d. peripheral membrane protein

A

d. peripheral membrane protein

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42
Q

is heme hydrophilic or hydrophobic?

A

hydrophobic

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43
Q

What is the hydrophilic part of cytochrome c?

A

Lys

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44
Q

Cytochrome c has a large amount of Lysine residues. Therefore it is a/an (acidic/basic) protein because its pI is (high/low)

A

basic; high

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45
Q

cytochrome c oxidase (complex IV) contains __ heme groups

A

2

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46
Q

What ions are present in cytochrome c oxidase?

A

copper

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47
Q

What does CuA do?

A

accepts electrons from cytochrome c

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48
Q

What does CuB do?

A

transfers electrons to oxygen

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49
Q

Where does O2 get reduced to water?

A

matrix

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50
Q

Which inhibitor of the ETC stops the chain after NADH and before Q?

A

rotenone

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51
Q

Which inhibitor of the ETC stops the chain after Cyt b and before Cyt c1?

A

antimycin A

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52
Q

Which inhibitor of the ETC stops the chain after Cyt (a + a3) and before O2?

A

cyanide or carbon monoxide

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53
Q

electron carriers before the block (inhibited spot) become _________ and those after the block become __________

A

reduced;oxidized

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54
Q

How does the F0 subunit of ATP Synthase rotate?

A

by H+ flow

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55
Q

Which parts of ATP synthase rotate?

A

F0 and gamma

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56
Q

Which parts of ATP synthase do not rotate?

A

catalytic parts

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57
Q

O form of ATP synthase means

A

open: binding site for ADP and Pi is open

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58
Q

L form of ATP synthase means

A

loose: ADP and Pi bind to site L

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59
Q

T form of ATP synthase means

A

tight: catalytically active

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60
Q

From which conformation is ATP released from ATP synthase?

A

O

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61
Q

How many ATP are released per one revolution of ATP synthase?

A

3

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62
Q

How many protons does it take to drive one revolution of the camshaft to produce 3 ATP molecules?

A

9-12

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63
Q

In which direction to ATP synthase operate?

A

either direction, depending on concentrations

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64
Q

electron transport translocated protons and formed a concentration gradient and a charge gradient across the membrane

A

chemiosmosis

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65
Q

energy created by the proton gradient

A

proton motive force

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66
Q

How many protons move to the intermembrane space if you start with 1 NADH molecule?

A

10

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67
Q

How many protons move to the intermembrane space if you start with 1 Succinate molecule?

A

6

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68
Q

What is the P:O ratio?

A

phosphorylation of ADP per oxygen atom

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69
Q

What is the approximate P:O ratio for NADH oxidation?

A

2.5 ATP/O

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70
Q

What is the approximate P:O ratio for QH2 oxidation?

A

1.5 ATP/O

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71
Q

How many protons are needed for one complete rotation of ATP synthase?

A

number of c subunits in ATP synthase

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72
Q

what is a chemical that can diffuse through the nonpolar membrane?

A

uncoupler

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73
Q

Why is an uncoupler important in biochemistry?

A

it can move H+ across the membrane without ATP synthase

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74
Q

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?

A

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

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75
Q

ATP synthesis can be uncoupled from ETC to generate _______

A

heat

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76
Q

Why does uncoupling ATP synthesis generate heat?

A

the protons pass through and nothing happens, so the energy is transferred to heat

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77
Q

What is the only irreversible step in the ETC?

A

complex IV (cyt c oxidase)

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78
Q

What regulates the ETS?

A

cyt c oxidase

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79
Q

What regulates cyt c oxidase?

A

level of oxidation/reduction of cyt c

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80
Q

What regulates the level of redox of cyt c?

A

NADH and ATP

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81
Q

When is the ETS rate the highest?

A

when [NADH]&raquo_space;» [NAD] and [ADP]&raquo_space;» [ATP]

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82
Q

What facilitates the movement of specific molecules within an organism?

A

transport proteins

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83
Q

one thing moves one direction

A

uniport

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84
Q

2 things move one direction

A

symport

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85
Q

2 things move opposite directions

A

antiport

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86
Q

What kind of transport protein is GLUT 1?

A

uniport

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87
Q

What is the goal of the malate/aspartate shuttle?

A

move NADH from the cytosol into the mitochondria

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88
Q

How does the malate/aspartate shuttle work?

A

moves the electrons as malate and then uses it to reduce NAD+ to produce NADH in the mitochondria

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89
Q

Why is the glycerophosphate shuttle considered as a part of complex II?

A

it adds to the pool of QH2

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90
Q

How does the glycerophosphate shuttle work?

A

takes an NADH molecule to the mitochondria as FADH2, but makes less ATP

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91
Q

How does ATP get moved from the mitochondria to the cytosol?

A

ADP-ATP translocator

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92
Q

What symport helps facilitate the move of ATP from the mitochondria to the cytosol?

A

Pi-H+ symport

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93
Q

light energy is converted to ATP in a plant’s __________

A

chloroplasts

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94
Q

What is the main idea of respiration?

A

NADH —-> H2O

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95
Q

What is the main idea of photosynthesis?

A

H2O —-> NADPH

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96
Q

Where does the proton gradient accumulate in photosynthesis?

A

thylakoid lumen

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97
Q

Where does the proton gradient accumulate in respiration?

A

intermembrane space

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98
Q

Photosynthesis happens at the interface of _________

A

stroma and thylakoid

99
Q

Respiration happens at the interface of _________

A

matrix and intermembrane

100
Q

what is the membrane electron transport in photosynthesis?

A

plastoquinone (Q)

101
Q

what is the membrane electron transport in respiration?

A

CoQ

102
Q

What is the source of electrons in photosynthesis?

A

water

103
Q

What is the source of electrons in respiration?

A

NADH

104
Q

What is the final electron acceptor in photosynthesis?

A

NADP+

105
Q

What is the final electron acceptor in respiration?

A

O2

106
Q

Why do lipids yield more energy per carbon than carbohydrates?

A

fatty acids are much more reduced compared to carbohydrates

107
Q

What is the enzyme in the small intestine that releases fatty acids?

A

lipase

108
Q

What activates lipases?

A

glucagon and epinephrine

109
Q

What happens to the fatty acids after being cleaved off from TG?

A

beta oxidation

110
Q

How is the fatty acid “activated” for beta oxidation?

A

it is attached to CoA

111
Q

What is used to form one thioester bond to activate a fatty acid?

A

2 ATP equivalent of free energy

112
Q

What is the transporter to take a fatty acid from the cytosol to the mitochondria for beta oxidation?

A

acyl-carnitine/carnitine transporter

113
Q

How does beta oxidation work?

A

2 carbons at a time are oxidized/degraded as acetyl-coa

114
Q

Describe the spiral pathway of beta oxidation

A

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
Q

Why is it called beta oxidation?

A

the attack occurs on the beta carbon (second carbon from the carbonyl carbon)

116
Q

The 4 reactions/2 carbons per round of beta oxidation produces _______

A

1 QH2, 1 NADH, and 1 acetyl-coA

117
Q

What are the 4 enzymes of beta oxidation?

A
  1. acyl-coa dehydrogenase (AD)
  2. enoyl-coa hydratase (EH)
  3. 3-L-hydroxyacyl dehydrogenase (HAD)
  4. beta-ketoacyl-coa thiolase (KT)
118
Q

What is the energy yield of beta oxidation?

A

14 ATP

119
Q

Would unsaturated fatty acids yield more or less energy than the saturated fatty acid?

A

less

120
Q

Odd number carbon double bonds lose how much ATP overall?

A

1.5

121
Q

Even number carbon double bonds lose how much ATP overall?

A

2.5

122
Q

What mechanisms are controlled so only one goes on at a time?

A

beta oxidation and fatty acid synthesis

123
Q

Where does fatty acid biosynthesis occur?

A

cytosol

124
Q

How does acetyl-coa get to the cytosol from the mitochondria to produce fatty acids?

A

tricarboxylate transport system

125
Q

How and where is acetyl-coa produced?

A

in matrix from fatty acid oxidation or pyruvate dehydrogenase

126
Q

What is the 2 carbon donor for fatty acid biosynthesis?

A

malonyl CoA

127
Q

Why is the conversion of acetyl-coa to malonyl-coa so important?

A

it is the first committed step and one of the rate controlling steps

128
Q

What affects the conversion of acetyl-coa to malonyl-coa?

A

citrate stimulates it, long chain fatty acids inhibit it, and insulin activates the enzyme

129
Q

What is the acyl carrier for synthesis?

A

ACP

130
Q

What is the overall goal of fatty acid synthesis?

A

attach acetate unit from malonyl-coa to a growing chain and then reduce it

131
Q

What are the four enzyme-catalyzed steps of fatty acid synthesis?

A

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
Q

How is the growing fatty acid chain initially attached to the enzyme?

A

thioester linkage

133
Q

What is required if you a have a fatty acid beyond a saturated 16C?

A

elongases in ER or mitochondria OR desaturases for unsaturated fatty acids

134
Q

Where is there a futile cycle control in fatty acid biosynthesis?

A

Acetyl-CoA carboxylase: inhibited by AMP- and cAMP-dependent phosphorylation and activated by insulin-dependent phosphorylation

135
Q

What is the controlling point of F.A. oxidation?

A

lipase

136
Q

What is the controlling point of F.A. synthesis?

A

ACCase

137
Q

How does insulin affect lipids?

A

it activates phosphatases that dephosphorylate enzymes, which activate ACCase and increase fatty acid synthesis

138
Q

How does glucagon affect lipids?

A

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
Q

What is another alternative fate for acetyl-coa when large amount from fats inhibits the citric acid cycle?

A

ketone bodies

140
Q

What is the purpose of ketone bodies?

A

provide fuel during starvation for the brain, heart, and skeletal muscles

141
Q

What are the three ketone bodies?

A

acetoacetate, acetone, and D-beta-hydroxybutyrate

142
Q

What organ is the source of ketone bodies?

A

liver

143
Q

What is the name of the enzyme that is a major controlling point of cholesterol biosynthesis, inhibited by phosphorylation, and is what statin inhibits?

A

HMG CoA reductase

144
Q

How does statin work?

A

lowers serum cholesterol by inhibiting HMG CoA reductase

145
Q

Where does digestion and absorption of dietary lipids occur?

A

small intestine

146
Q

Why do we need to package the dietary lipids before sending them to other tissues?

A

they are nonpolar and cannot be transported otherwise

147
Q

What transfers lipids from the intestine to the liver?

A

chylomicrons

148
Q

What transfers lipids from the liver to other tissues?

A

VLDLs and LDLs

149
Q

What transfers lipids from other tissues to the liver?

A

HDL

150
Q

Which is denser, fat or protein?

A

protein

151
Q

Low density = (high/low) fat?

A

high

152
Q

High density = (high/low) fat?

A

low

153
Q

What is bad cholesterol?

A

LDL

154
Q

What is the purpose of LDLs?

A

deliver cholesterol and cholesterol esters to cells

155
Q

What is missing in people with familial hypercholesterolemia?

A

LDL receptor

156
Q

What is good cholesterol?

A

HDL

157
Q

What is the purpose of HDLs?

A

remove excess cholesterol from cells

158
Q

What is required for HDLs?

A

membrane transporter/flippase

159
Q

How many genes does the X chromosome carry?

A

about 1500

160
Q

How many genes does the Y chromosome carry?

A

about 100

161
Q

What comprises a nucleotide?

A

a five-carbon sugar, a nitrogen containing ring, and one or more phosphate group

162
Q

What are the purines?

A

adenine and guanine

163
Q

What are the pyrimidines?

A

cytosine, thymine, and uracil

164
Q

Do purines or pyrimidines have two rings?

A

purines

165
Q

Do purines or pyrimidines have one ring?

A

pyrimidines

166
Q

What is the difference between ribose and deoxyribose?

A

ribose has one extra OH group compared to deoxyribose

167
Q

Why does DNA twist?

A

once you make a double stranded structure, it twists to accommodate its size

168
Q

In which direction does DNA run?

A

antiparallel

169
Q

Is DNA right or left handed?

A

right

170
Q

How many base pairs are there per turn of DNA?

A

10

171
Q

Exposed ____ binds to ______ to reduce repulsion in DNA

A

P; Mg2+

172
Q

Are the base pairs interior or exterior to the helix axis?

A

interior

173
Q

Edges of base pairs exposed at grooves can be recognized by what?

A

DNA binding proteins

174
Q

DNA strands make double stranded helix by _______ bonds between the bases

A

hydrogen

175
Q

The ________ of the bases in DNA are the information.

A

sequence

176
Q

The _________ of the bases in DNA is the key in transmitting the information.

A

complementarity

177
Q

When can double-stranded nucleic acids be denatured?

A

at high temperatures

178
Q

What occurs to DNA at lower temperatures?

A

complementary polynucleotides anneal

179
Q

What kind of bonds always remain intact throughout DNA denaturation and renaturation and why?

A

covalent bonds so that the genetic code itself remains intact

180
Q

What occurs if you rapidly cool denatured/separated DNA?

A

improper base pairing

181
Q

What is the Tm?

A

melting temperature of DNA

182
Q

The higher the ___ content, the higher the Tm

A

GC

183
Q

Why does GC content raise the Tm?

A

stacking energy

184
Q

What does stacking energy mean?

A

the energy required to untwist the DNA

185
Q

The Tm is also equal to….

A

the temperature at which 50% of the DNA has been denatured

186
Q

What does the hybridization technique do?

A

identify where partner is

187
Q

What does southern blot identify?

A

DNA to DNA hybridization

188
Q

What does northern blot identify?

A

RNA-DNA hybridization

189
Q

What does western blot identify?

A

protein to antibody reaction

190
Q

What do restriction enzymes do?

A

digests the phosphodiester bonds that connect nucleotides

191
Q

How do restriction enzymes know where to cut?

A

they recognize very specific patterns of 4-6 bases in DNA, normally in palindrome format

192
Q

What is the purpose of dideoxy sequencing?

A

figure out base order/sequence

193
Q

What is the purpose of polymerase chain reaction (PCR)?

A

amplify sections of DNA

194
Q

DNA polymerase adds deoxynucleotides at the ___ end of the growing chain of nucleic acid

A

3’

195
Q

Where does DNA polymerase add the complementary nucleotides?

A

the 3’ - OH of the primer

196
Q

What are the ingredients for a DNA sequencing reaction?

A

DNA, primer, dNTPs, ddNTPs, DNA polymerase, buffer

197
Q

Why does DNA polymerase stop elongation when ddNTP is added instead of dNTP?

A

ddNTPs lack a 3’-OH group, so no more NTPs can attach

198
Q

What is PCR?

A

enzymatic amplification of a segment of DNA

199
Q

What are the ingredients for a PCR reaction?

A

DNA, primers (a pair), dNTPs, DNA polymerase (normally Taq polymerase), buffer

200
Q

What are the 3 steps of PCR?

A
  1. strand separation
  2. primer annealing
  3. primer extension
201
Q

At what temperature does strand separation occur?

A

90-95 degrees C

202
Q

At what temperature does primer annealing occur?

A

45-55 degrees C

203
Q

At what temperature does primer extension occur?

A

70 degrees C

204
Q

What are the four things PCR is used for?

A
  1. identify mutations
  2. site-directed mutagensis
  3. detection of signature sequences
  4. forensic use
205
Q

How many strands of DNA are used in sequencing reactions?

A

one

206
Q

How many strands of DNA are used in PCR reactions?

A

two

207
Q

Is the inner membrane of the mitochondria directly permeable to small molecules and hydrogen ions?

A

no

208
Q

The electron transport chain operates (independently/dependently) of other metabolic processes.

A

dependently

209
Q

Where is H+ ion concentration higher?

A

intermembrane space

210
Q

Where is the pH higher?

A

matrix

211
Q

What are the two electron transport inhibitors?

A

cyanide and rotenone

212
Q

What is the uncoupling agent that increases membrane proton permeability?

A

FCCP

213
Q

What is the ATP synthase inhibitor that binds to F0 and blocks the proton channel?

A

oligomycin

214
Q

What is the transport inhibitor that binds to inward-facing site of ATP-ADP translocase?

A

bongkrekic acid

215
Q

What provides the energy that excites the electrons in the chlorophyll molecules?

A

light

216
Q

What is the source of the electrons that replace the excited electrons lost from chlorophyll?

A

water

217
Q

What is the first step of ATP synthase?

A

protons from the intermembrane space bind to proton binding sites on c subunits

218
Q

What is the second step of ATP synthase?

A

as the c ring rotates past the a subunit c, subunits release their protons into the matrix

219
Q

What is the third step of ATP synthase?

A

the gamma subunit rotates past the a subunit, c subunits release their protons into the matrix

220
Q

What is the fourth step of ATP synthase?

A

the gamma subunit rotates and interacts with the three alpha-beta subunit pairs, causing conformational changes in the beta subunits

221
Q

What is the last step of ATP synthase?

A

each beta subunit binds ADP and Pi, converts ADP + Pi to ATP, and releases ATP once during one turn of the gamma subunit

222
Q

How is oxaloacetate modified to a form that can be transported out of the matrix?

A

transamination

223
Q

Which compound transfers reducing equivalents (electrons) into the mitochondrial matrix?

A

malate

224
Q

What kind of reaction is the first reaction of beta oxidation?

A

oxidation

225
Q

What kind of reaction is the second reaction of beta oxidation?

A

hydration

226
Q

What kind of reaction is the third reaction of beta oxidation?

A

oxidation

227
Q

What kind of reaction is the fourth reaction of beta oxidation?

A

cleavage

228
Q

What does CAT1 do?

A

converts carnitine into acyl-carnitine

229
Q

What does CAT2 do?

A

converts acyl-carnitine into carnitine

230
Q

Which of the three ketone bodies is the only one reduced to alcohol form?

A

beta-hydroxybutyrate

231
Q

Which of the three ketone bodies is only made up of three carbons?

A

acetone

232
Q

Increased levels of which cholesterol is associated with atherosclerosis?

A

LDL

233
Q

Do nucleosides contain a phosphate group?

A

no

234
Q

What is the product when a base bonds at C1 of ribose or deoxyribose?

A

nucleoside

235
Q

Are nucleosides found in both RNA and DNA?

A

yes

236
Q

What is true for both DNA and RNA?

A

sugars are connected with a 3’-5’ phosphodiester link

237
Q

What is true for RNA only?

A

it commonly exists in a variety of secondary structures

238
Q

Which purine has a ketone?

A

guanine

239
Q

Which purine doesn’t have any oxygens?

A

adenine

240
Q

Which pyrimidine only has one ketone group?

A

cytosine

241
Q

Which pyrimidine has two ketone groups, but no methyl group?

A

uracil

242
Q

Which pyrimidine has two ketone groups AND a methyl group?

A

thymine

243
Q
A

CHM 432 (4 decks)

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