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Biochem > Exam 6 > Flashcards

Exam 6 Flashcards

1
Q

What are the three proton pumps in the ETC?

A

Complex 1, Complex 3, Complex 4

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2
Q

What is the name of complex 1?

A

NADH - Q oxidoreductase

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3
Q

What is the name of Complex 3?

A

Q - cytochrome C oxidoreductase

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4
Q

What is the name of Complex 4?

A

Cytochrome C oxidase

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5
Q

Is complex 2 a proton pump?

A

No

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6
Q

What is the name of Complex 2?

A

succinate Q reductase

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7
Q

What does Complex 2 do?

A

It accepts electrons from FADH2, but does not export protons into the cytoplasm because it is not a proton pump.

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8
Q

What are the types of electron carriers?

A

NADH, FADH2, coenzyme Q (ubiquinone), and cytochrome C

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9
Q

What do NADH and FADH2 do in the ETC?

A

They bring electrons to the ETC

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10
Q

Describe coenzyme Q

A

It is a non-protein that brings 2 electrons at a time from complex 1 to complex 3 and brings 2 electrons at a time from complex 2 to complex 3.

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11
Q

Describe cytochrome C

A

It is a protein that brings 1 electron at a time from complex 3 to complex 4.

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11
Q

What does the Q pool do?

A

It stores the Q molecule so that the when the ETC is ready to electron transport it pulls from the Q pool.

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12
Q

Where are the electrons kept before being transported by coenzyme Q?

A

In the Q pool

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13
Q

Describe the process of the Q cycle

A

QH2 binds to complex 3, from complex 3 1 electron is carried by cytochrome C and the other electron binds to a Q to generate a Q.- radical for a short amount of time. the 2 protons leave the pump into the cytoplasm. A new QH2 binds complex 3 1 electron leaves to cytochrome C and the other binds to the Q.- radical to form a new QH2 to reenter the Q pool. 2 protons leave the pump into the cytoplasm.

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14
Q

How many protons leave the ETC due to the Q cycle?

A

4 protons

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15
Q

What is the oxidized form of Coenzyme Q?

A

Q

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16
Q

What is the reduced form of coenzyme Q?

A

QH2

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17
Q

Is QH dangerous?

A

Yes because it is a radical

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18
Q

What electron carrier brings two electrons to complex 1?

A

NADH and turns into NAD+

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19
Q

Iron-sulfur cluster…

A

Has electron flow through it, it goes from Fe3+ to Fe2+

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20
Q

Why do the 4 protons get pumped out into the cytoplasm?

A

because the electron transfer leads to a conformational change

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21
Q

What electron carrier brings electrons to complex 2?

A

FADH2 which turns into FAD

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22
Q

In complex 3 how many protons get pumped out as one electron moves through?

A

2 protons move through into the cytoplasm as an electron moves through.

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23
Q

What does complex 4 do?

A

Transfers electrons from cytochrome C to O2 to make H2O

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24
Q

What causes reactive oxygen species?

A

the partial reduction of O2

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25
Q

O2 plus 1 electron form what?

A

superoxide

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26
Q

O2 plus 2 electrons forms what?

A

peroxide

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27
Q

What enzymes help neutralize ROS?

A

Superoxide dismutase (SOD) and catalase

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28
Q

How does the ETC help make ATP?

A

The proton gradient that is formed from the ETC helps make ATP.

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29
Q

Chemiosmotic theory…

A

The idea that the chemical and charge gradient are neded to harness energy to make ATP

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30
Q

What is another term for ATP synthase?

A

ball and stick model

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31
Q

What does the stick in stick model stand for?

A

F0 which is the transmembrane region

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32
Q

What is the ball in the ball and stick model?

A

F1 which is the catalytic domain

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33
Q

What are the five subunits of the catalytic domain of ATP synthase?

A

alpha 3, beta 3, gamma and epsilon

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34
Q

Of the five subunits of the catalytic domain of ATP synthase which is the most important?

A

beta 3

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35
Q

describe the catalytic domain of ATP synthase

A

F1 is alpha and beta which rotate around the ring (gamma) and stalk (epsilon)

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36
Q

How many beta and alpha make F1?

A

3 alpha and 3 beta

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37
Q

What are the three subunits of beta 3?

A

L = loose - bind ADP and Pi
T = tight - convert ADP and Pi to ATP
O = open - release ATP

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38
Q

What shuttle do muscle cells use?

A

glycerol 3 - phosphate shuttle

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39
Q

What shuttle do liver and cardiac cells use?

A

malate - aspartate shuttle

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40
Q

What does the glycerol 3-phosphate shuttle do?

A

bringelectronf from the cytoplasm into the mitochondria. It does this by NADH from glycolysis give electrons to DHAP to generate glycerol-3-phosphate which gives electrons to glycerol-3-phosphate dehydrogenase to cross the membrane into the miotchondria. The electrons then bind to FAD to make FADH2 for complex 2

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41
Q

What does the malate-aspartate shuttle do?

A

uses NADH from glycolysis and transfers the electrons to oxaloacetate to generate malate.malate enters into the mitochondria through the channel. Malate gives electrons back NAD+ to make NADH and oxaloacetate. Oxaloacetate leave by reacting with glutamate to make alpha ketogluterate and aspartate which leave. In cytoplasm they regenerate ozaloacetate

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42
Q

What does ADP/ATP translocase do?

A

decreases the charge gradient which makes it more favorable because it decreases the membrane potential

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43
Q

What is cellular respiration based on?

A

ATP needs and O2

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44
Q

About how many protons are pumped out to generate 1 ATP?

A

4 protons are pumped out

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45
Q

What are the 4 protons usedfor to generate 1 ATP used for?

A

3 protons tuen ATP synthase and 1 proton is lost to ADP/ATP translocase

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46
Q

How much ATP is produced in muscle cells?

A

30 ATP

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47
Q

How much ATP is produced in liver cells?

A

32 ATP

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48
Q

How do endurance athletes account for the extra need for ATP?

A

They increase their mitochondria to make more ATP and increase the number of blood vessels to muscles to increase the O2 in muscles

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49
Q

What are the three functions of the pentose phosphate pathway (PPP)?

A

To make 5 carbon building blocks of deoxyribose and ribose, generate NADPH for reductive biosynthesis, and generate NADPH for detoxification of ROS

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50
Q

What are the two phases of the pentose phosphate pathway (PPP)?

A

oxidative phase and the non-oxidative phase

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51
Q

What does the oxidative phase of the pentose phosphate pathway do?

A

generate NADPH and generate ribose 5-phosphate

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52
Q

What does the non-oxidative phase of the pentose phosphate pathway do?

A

return carbons back to glycolysis and gluconeogenesis through interconverting carbons 3, 4, 5, 6, and 7

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53
Q

What are the steps for the oxidative phase of the pentose phosphate pathway?

A

G6P to 6-phosphoglucono-sigma-lactone using glucose 6-phosphate dehydrogenase. 6-phosphoglucono-sigma-lactone to 6-phosphogluconate using lactonase. 6-phosphogluconate to ribulose 5-phosphate and CO2 using 6-phosphogluconate dehydrogenase. ribulose 5-phosphate to ribose 5-phosphate using phosphopentose isomerase.

54
Q

What are the enzymes that are used in the non-oxidative phase of the pentose phosphate pathway?

A

transketolase and transaldolase

55
Q

what are the different fates of glucose 6-phosphate?

A

store as glycogen, catabolism via glycolysis, catabolism/biosynthesis via PPP

56
Q

How are the different fates of G6P determined?

A

the fates are dependent on energy charge

57
Q

What is the key regulatory step of the oxidative phase for G6P in the PPP?

A

it is the first step

58
Q

What are the key regulators for the first step of the oxidative phase of G6P for the PPP?

A

NADP+ is an activator
NADPH is a competitive inhibitor

59
Q

How many possible floe modes are there for the PPP?

A

4

60
Q

What is mode 1 of the PPP?

A

it is for when a lot of ribose 5-phosphate is needed but NADPH is not needed

61
Q

what is mode 2 of the PPP?

A

it is for when both ribose 5-phosphate and NADPH are needed

62
Q

What is mode 3 of the PPP?

A

for when a lot of NADPH is needed but not ribose 5-phosphate

63
Q

What is mode 4 of the PPP?

A

when both NADPH and ATP are needed

64
Q

Mode 1 pathway to make ribose 5-phosphate?

A

G6P to F6P + GAP from glycolysis to ribose 5-phosphate using transketolase and transaldolase of the nonoxidative phase

65
Q

Mode 2 pathway?

A

Only use oxidative pathway
G6P + 2NADP+ + H2O to R5P + NADPH + 2H+ + CO2

66
Q

Mode 3 pathway?

A

synthesis of fatty acid in adipose tissue

67
Q

Mode 4 pathway?

A

oxidative phase to make R5P
non-oxidative phase to convert R5P to F6P
enters glycolysis

68
Q

What is required for rapid cell growth?

A

a lot of DNA synthesis and membrane synthesis is needed to rapid cell growth and nucleotide biosynthesis requires R5P and fatty acid biosynthesis requires NADPH so the PPP helps make those for rapid cell growth.

69
Q

Glucose 6-phosphate dehydrogenase is a key regulatory enzyme in what pathway?

A

In the PPP

70
Q

What happens when there are mutations in the glucose 6-phosphate dehydrogenase enzyme?

A

decrease in nucleotide production
decrease in NADPH
causes anemia
increase sensitivity to fava bean
increase resistance to malaria

71
Q

what reduces ROS

A

glutathione

72
Q

What is glycogen?

A

Stores glucose

73
Q

What is the 3 step mechanism for glycogen breakdown?

A
  1. release glucose 1-phosphate from glycogen
  2. remodel glucose 1-phosphate to the isozyme glucose 6-phosphate
  3. modify glycogen due to alpha-1,6 bonds
74
Q

What is the key regulatory enzyme for glycogen breakdown?

A

glycogen phosphorylase

75
Q

What does glycogen phosphorylase do?

A

cleave glycogen by adding Pi to make glucose 1-phosphate

76
Q

What does phosphoglucomutase do?

A

Move Pi group in glucose 1-phosphate to produce glucose 6-phosphate

77
Q

What does glucose 6-phosphatase do?

A

it is only in the liver to further releases glucose
it dephosphorylates glucose 6-phosphate to glucose

78
Q

What are the debranching enzymes required in glycogen breakdown?

A

phosphorylase and transferase and alpha-1,6-glucosidase

79
Q

What does the debranching enzyme phosphorylase do?

A

stops 4 residues from branching (alpha-1,6 linkage)

80
Q

what does the debranching enzyme transferase do?

A

moves block 3 residues from branching to another branch

81
Q

What does the debranching enzyme alpha-1,6-glucosidase do?

A

cleaves alpha-1,6 bonds and hydrolyzes the release of glucose

82
Q

What are the three levels of glycogen phosphorylase regulation?

A

regulated by hormones , allosteric regulation, and glycogen phosphorylase phosphorylation

83
Q

What form does the a and b glycogen phosphorylase exist in?

A

they exist in a dimer. a are with a and b are with b. a is never with b.

84
Q

What is the active form of glycogen phosphorylase?

A

phosphorylase a, the R-state

85
Q

What is the inactive form of glycogen phosphorylase?

A

phosphorylase b, the T state

86
Q

What causes glycogen phosphorylase to shift from form A to form b?

A

dephosphorylation

87
Q

What causes glycogen phosphorylase to shift from b form to a form?

A

phosphorylation

88
Q

Where is glycogen phosphorylase A most prevalent?

A

in the liver

89
Q

Where is glycogen phosphorylase b most prevalent?

A

in the muscles

90
Q

what is the allosteric regulator for glycogen phosphorylase in the liver? Is it an inhibitor or an activator?

A

glucose it is an inhibitor because is causes a shift towards the T state

91
Q

What can switch glycogen phosphorylase b on in the muscles?

A

an energy need because energy charge is a key regulator

92
Q

What are the activators and inhibitors of glycogen phosphorylase b in the muscle?

A

ATP is the inhibitor and AMP is the activator

93
Q

What is the role of glucose 6-phosphate for glycogen phosphorylase b in the muscles?

A

glucose 6-phosphate stabilizes the T state. It is an inhibitor

94
Q

What is phosphorylase kinase regulated by

A

calcium and protein kinase A (PKA)

95
Q

What are the characteristics of phosphorylase kinase when it is inactive?

A

it is dephosphorylated and there is no calcium

96
Q

What are the characteristics of phosphorylase kinase when it is active?

A

calcium binds and it is activated by getting phosphorylated by PKA

97
Q

What hormone regulates phosphorylase kinase in the liver?

A

glucagon

98
Q

What hormone regulates phosphorylase kinase in the muscles?

A

epinephrin

99
Q

What is the mechanism of phosphorylase kinase being regulated by hormones?

A

The hormone binds to GPCR
GPCR activates Galpha s
Galpha s activates adenylyl cyclase
AC converts ATP into cAMP
cAMP binds and activates PKA
PKA phosphorylates phosphorylase kinase and calcium binds to activate it
the active phosphorylase kinase phosphorylates phosphorylase b to phosphorylase a to activate phosphorylase

100
Q

What are the three ways the regulation of phosphorylase kinase by hormones can be inhibited?

A

The G protein hydrolyzes GTP to GDP which is triggered by GAP, phosphodiesterase cleaves cAMP to AMP
protein phosphatase 1 dephosphorylates phosphorylase kinase and phosphorylase

101
Q

How many ATPs are used in order to store glucose and glycogen?

A

1 ATP

102
Q

What is the pathway of glycogen synthesis?

A

glucose 6-phosphate is converted to glucose 1-phosphate using phosphoglucomutase, activate glucose by using UDP-glucose phosphorylase to convert glucose 1-phosphate to glucose, form the first 10-20 glucose molecules in a chain with glycogenin, form an alpha-1,4 glycosidic bond to the nonreducing end of glycogen, with the branching enzyme for alpha-1,6 glycosidic bonds to make branches

103
Q

What is the key regulatory enzyme of glycogen synthesis regulation?

A

glycogen synthase

104
Q

What are the forms of glycogen synthase and when are they active/ inactive?

A

glycogen synthase A is more active and is phosphorylated, glycogen synthase B is less active and is phosphorylated

105
Q

Which form of glycogen synthases is allosterically regulated?

A

glycogen synthase b

106
Q

Why is the regulation of glycogen synthase important?

A

regulation minimizes energy waste because storage of glucose as glycogen uses only 1 ATP

107
Q

What is the reciprocal regulation of glycogen synthases?

A

it is the phosphorylation of glycogen synthases where PKA and glycogen synthases kinase phosphorylate glycogen synthase to inactivate it

108
Q

What does protein phosphatase 1 do?

A

it is a reverse phosphorylation event and inactivates phosphorylates A, phosphorylase kinase, and glycogen synthase

109
Q

When is protein phosphatase 1 active?

A

When at rest and after a meal due to insulin release

110
Q

How is protein phosphatase 1 indirectly activated by PKA?

A

PKA is either activated by glucagon of epi depending on cell type, glycogen Gm is activated and is then controls PP1 activity, phosphorylation of glycogen Gm by PKA releases PP1 and then is less active. PKA is a competitive inhibitor of PP1

111
Q

What is glycogen metabolism regulated by?

A

insulin

112
Q

How does insulin signaling regulate glycogen metabolism?

A

Insulin binds to RTK which allows IRS to bind and phosphorylate the receptor which starts a phosphorylation cascade. Protein kinase phosphorylates glycogen synthase kinase and inactivates it so PP1 can now dephosphorylate glycogen synthase to activate it.

113
Q

What are the four functions of fatty acids?

A

Furl molecules, building blocks for phospholipids and glycolipids, covalently attached to proteins to target them to membranes, act as hormones and intracellular messengers

114
Q

What is the fatty acid degradation pathway?

A

oxidation, hydration, oxidation, cleavage

115
Q

What is the fatty acid synthesis pathway?

A

condensation, reduction, dehydration, reduction

116
Q

How are fatty acids released from triglycerides?

A

triglycerol undergoes a hydrolysis reaction to release one fatty acid using lipase, diglycerol undergoes a hydrolysis reaction to release one fatty acid using lipase, monoacylglycerol in left

117
Q

how many fatty acids can be made from one triglycerol molecule?

A

3 fatty acids

118
Q

How are fatty acids processed into fuel?

A

the lipids get mobilized and triglycerols get broken down with a hydrolysis reaction into one glycerol and 3 fatty acid molecules. The fatty acids travel from the adipocyte tissue to other tissues.
The fatty acids are activated and move to the mitochondria.
beta-oxidation generates acetyl CoA from the fatty acids and enters into the citric acid cycle.

119
Q

How are the lipids mobilized?

A

glucagon and epinephrine activate hormones stimulated by lipase.

120
Q

What is the mechanism of mobilizing lipids?

A

glucagon activates PKA.
PKA phosphorylates perilipin and becomes active.
Perilipin restructures fat droplets so they are more accessible to enzymes to increase reaction rates. This triggers the release of adipose triglyceride lipase which converts triacylglyceride to DAG and fatty acid.
PKA phosphorylates HS lipase and becomes active. HS lipase cleaves DAG into Mag and fatty acid.
MAG lipase then cleaves MAG into fatty acid and glycerol.

121
Q

What happens to glycerol after the triacylglyceride is fully broken down?

A

it enters glycolysis or gluconeogenesis by being converted into DHAP

122
Q

What happens to the fatty acids after triacylglyceride is fully broken down?

A

the fatty acids go through fatty acid oxidation which turns into acetyl CoA and then enters the CAC

123
Q

what is the mechanism for fatty acids being able to enter into the CAC?

A

Acyl CoA synthase is used to attach a CoA to the acyl group. The acyl CoA reacts with carnitine to make acyl carnitine so the CoA is replaced with carnitine. Acyl carnitine translocase shuttles acyl carnitine into the mitochondria. carnitine acyltransferase II is used to regenerate acyl CoA by removing the carnitine. the carnitine leaves the mitochondria through translocase. Acyl Coa then gets converted into acetyl CoA using beta-oxidation to enter the CAC

124
Q

What are the detailed steps of beta-oxidation to convert acyl CoA to acetyl CoA?

A
  1. oxidation of FAD to FADH2 converts acyl CoA to trans-delta2-enoyl CoA.
  2. hydration using H2O converts trans-delta2-enoyl CoA to L-3-hydroxyacyl CoA.
  3. oxidation of NAD+ to NADH and H+ converts l-3-hydroxyacyl CoA to 3-ketoacyl CoA.
    cleavage using thiolysis cleaves 3-ketoacyl CoA to acetyl CoA and another Acyl CoA that can go through beta-oxidation until only acetyl CoA is made.
125
Q

How many FADH2 are generated per acetyl CoA in the CAC?

A

1

126
Q

How many NADH is generated per acetyl CoA in the CAC?

A

3

127
Q

How many ATP are generated per acetyl COA per CAC?

A

1

128
Q

How many FADH2 are generated from 1 beta-oxidation cycle?

A

1

129
Q

How many NADH are generated from 1 beta-oxidation cycle?

A

1

130
Q

How many ATP are generated from 1 beta-oxidation cycle?

A

-2 because 2 ATP are used to attach the CoA don’t to the acyl group of the fatty acid

131
Q

For unsaturated fatty acids with a double bond on an odd carbon, what is the pathway?

A

Do beta-oxidation until the double bond is at carbon 3 making cis-delta3-enoyl CoA. use cis-delta3-enoyl CoA isomerase to move the double bond to carbon 2 to make trans-delta2-enoyl CoA and continue beta-oxidation

132
Q

for unsaturated fatty acids with a double bond on an even carbon that is not carbon 2, what is the pathway?

A

use acyl COA dehydrogenase to make a double bond on carbon 2. Use reductase and NADP+ to reduce the double bonds and shift the double bond to carbon 3. Use cis-delta3-enoyl CoA isomerase to take trans-delta2-enoyl CoA. Subtract one FADH2 from energy counting for the formation of the double bond.

Biochem (2 decks)

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