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Biochemistry > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Glycogen

A

Storage form of glucose. Highly branched structure.

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2
Q

Glycogenesis

A

The formation of glycogen from sugar. It takes place in the liver and muscle.
Glucose (using hexokinase) Glucose-6-P Glucose-1-P -> UDP-Glucose->GLYCOGEN (in muscle)
Glucose (using glucokinase) Glucose-6-P Glucose-1-P -> UDP-Glucose->GLYCOGEN (in liver)
Glucokinase is an isozyme and has a high Km value.
Consumes the free energy of UTP.

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3
Q

Glycogenolysis

A

The biochemical breakdown of glycogen to glucose.
Glycogen->Glucose-1-P->Glucose-6-P->GLUCOSE (liver)
Glycogen->Glucose-6-P->Glycolysis->ATP (Muscle)
Glycogen degradation

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4
Q

Glycogenin

A

An enzyme converting glucose to glycogen. A glycogen primer that glycogen synthesis needs.

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5
Q

Glucagon

A

Peptide hormone produced by alpha cells of the pancreas. Stimulates glycogen breakdown.

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6
Q

Gluconeogenesis

A

Synthesis of glucose from non-carbohydrate precursors (amino acids, lactate, glycerol); occurs in liver; occurs in fasting state; the reverse of glycolysis.

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7
Q

General overview to gluconeogenesis

A

RBC-lactate-pyruvate-oxaloacetate (glucogenic amino acids)-triose phosphate (DHP & GAP)-glucose.
Glucogenic amino acids are all acids except Leu and Lys. They are ketogenic.

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8
Q

Step 1

Pyruvate is converted in 2 steps.

A

Pyruvate is an a-ketoacid.
Pyruvate carboxylase takes a bicarbonate ion + ATP and releases ADP + Pi.
Oxaloacetate is formed (an acetate group on carbon 4). This conversion requires energy.
Phosphoenolpyruvate carboxykinase takes GTP and releases GDP + CO2.
Phosphoenolpyruvate is a 3 carbon chain with a phosphate group on carbon 2.
This is an irreversible step.

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9
Q

Pyruvate carboxylase uses ________ as a cofactor.

A

Biotin

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10
Q

Biotin is covalently attached to a _______ residue in the enzyme.

A

Lys (Lysine)

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11
Q

True/False
CO2 reacts with ATP such that some of the free energy released in the removal of ATP’s phosphoryl group is conserved in the formation of the “activated” compound carboxyphosphate.

A

True

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12
Q

Like ATP, _________ releases a large amount of free energy when its phosphoryl group is liberated.

A

Carboxyphosphate

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13
Q

In the pyruvate carboxylase mechanism, the enzyme abstracts a ______ from _______, forming a carbanion.

A

Proton; pyruvate

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14
Q

In the pyruvate carboxylase mechanism, the carbanion attacks the ________ group attached to ______, generating oxaloacetate.

A

Carboxyl; biotin

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15
Q

Step 2

Enolase

A

Converts (2) PHOSPHOENOLPYRUVATE (alkene) + H2O to (2) 2-PHOSPHOGLYCERATE
Reversible reaction
Enolase catalyze a dehydration reaction

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16
Q

Step 3

Phosphoglycerate mutase

A

Converts (2) 2-PHOSPHOGLYCERATE to (2) 3-PHOSPHOGLYCERATE
Reversible reaction.
Isomerase reaction

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17
Q

Step 4

Phosphoglycerate kinase

A

Converts (2) 3-PHOSPHOGLYCERATE + ATP to (2) 1,3-BISPHOSPHOGLYCERATE + ADP
Reversible reaction
Transferase reaction
1,3-bisphosphoglycerate is a high energy intermediate

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18
Q

Step 5

Glyceraldehyde-3-phosphate dehydrogenase

A

Converts (2) 1,3-BISPHOSPHOGLYCERATE + NADH plus H+ to GLYCERALDEHYDE-3-PHOSPHATE plus NAD+
Reversible reaction.
NADH plus H+ is oxidized to NAD+; phosphate group does not come from ATP.
Reaction is both a phosphorylation and an oxidation-reduction.
1,3-bisphosphoglycerate is a high energy intermediate.
Covalent catalysis (direct bond between enzyme and substrate)

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19
Q

Step 6

Triose phosphate isomerase

A

Converts glyceraldehyde-3-phosphate to Dihydroxyacetone phosphate
Isomerization reaction (moves a group or a double bond within the same molecule)
Reversible reaction
Can convert back and forth

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20
Q

Step 7

Aldolase

A

Converts GAP and DHP to fructose-1,6-bisphosphate
Reversible reaction
Aldolase is a lyase (cleaves to make the 2 molecules)
GAP and DHP have 3 carbons each. After condensation it makes 1, 6 carbon chain.

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21
Q

Step 8

Fructose-1,6-bisphosphatase

A

Converts Fructose-1,6-bisphospate and H2O to fructose-6-phosphate and Pi.
Irreversible step.
Removes the phosphate group on carbon 1.
#1 regulated step.

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22
Q

Step 9

Phosphoglucose isomerase

A

Converts fructose-6-phosphate to glucose-6-phosphate.

Reversible step

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23
Q

Step 10

Glucose-6-phosphatase

A

Converts glucose-6-phosphate and H2O to glucose and Pi.

Irreversible step

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24
Q

What would happen if glycolysis and gluconeogenesis occurred simultaneously?

A

There would be a net consumption of ATP. Goal of producing ATP would be futile. Instead, glycolysis and gluconeogenesis are regulated based on the cell’s needs.

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25
Q

Fructose-2,6-bisphosphate increases/decreases the activity of __________ and increases/decreases the activity of ____________.

A

Increases; phosphofructokinase; decreases; fructose-1,6-bisphosphatase

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26
Q

Precursor molecules for gluconeogenesis

A

Amino acids, lactate and glycerol. No carbohydrates

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27
Q

What enzyme is used to convert glucose to glucose-6-phosphate in glycogenesis in the liver?

A

Glucokinase; it is an isozyme; only happens in the liver. This enzyme takes longer to get saturated by the substrate (less efficient for binding to substrate).

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28
Q

Phosphoglucomutase

A

Converts glucose-6-phosphate to glucose-1-phosphate.
Reversible step.
Isomerase
Moves phosphate group from carbon 6 to carbon 1.

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29
Q

UDP-glucose pyrophosphorylase

A

Converts glucose-1-phosphate to UDP-glucose and hydrolyzes the 2 phosphate groups (pyrophosphate) as PPi. Inorganic pyrophosphatase converts it to 2 Pi.
UDP-glucose is the activated form of glucose.
The hydrolysis of inorganic pyrophosphate drives the reaction; dG=-19.2 KJ*mol-1 (exergonic).

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30
Q

Glycogen synthase

A

Converts UDP-glucose and glycogen to UDP + Glycogen (n+1 residues) which is an alpha-1,4-glycosidic bond. First molecule on the left, carbon 1 determines alpha or beta.
Glycogen used is an existing strand.

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31
Q

What is transglycosylase?

A

It’s a branching enzyme that cleaves off the seven residue segment and reattaches it to the glucose C6-OH to create an alpha-1,6 branch point.
Seven-residue segment is a 7-glucose strand.

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32
Q

How are linear chains in glycogen broken down?

A

Via phosphorolysis with the enzyme glycogen phosphorylase; makes glucose-1-P

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33
Q

How are branched chains in glycogen broken down?

A

Via hydrolysis with the enzyme glucose-6-phosphatase; yields glucose

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34
Q

Which step does glucose-6-phosphate enter in glycolysis for glycogenolysis in the muscle?

A

At step 2; it will be an inhibitor.
One less ATP is consumed in the muscle compared to glucose from the bloodstream;the net gain of ATP is higher (3 ATP instead of 2)

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35
Q

What type of receptor does glucagon use?

A

G-protein receptor.

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36
Q

What type of bonds are found in the active form of insulin?

A

Disulfide bonds; insulin is a zymogen and must be cleaved to be active.

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37
Q

How does insulin stimulate glycogen synthesis?

A

A ligand binds to the receptor tyrosine kinase, it is transported through the membrane where it goes through autophosphorylation (phosphorylation of the kinase by itself). ATP -> ADP (Kinase 1 goes from an inactive state to active). The active kinase 1 is phosphorylated by ATP kinase 2 goes from inactive to active. It then goes through changes in metabolic activity and gene expression.

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38
Q

How does glucagon stimulate glycogen breakdown?

A

A ligand binds to a G-protein receptor, the G-protein goes from inactive to active and is now a substrate that is bound to an enzyme. The substrate is broken down to a second messenger, cAMP. 3 alpha/beta subunits are target proteins.

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39
Q

Explain regulation of glycogen synthesis

A

Glucagon leads to phosphorylation of glycogen synthase. If glucagon is being released and phosphorylating glycogen synthase, you don’t want to make glycogen.

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40
Q

In the presence of glucagon, is glycogenolysis active or inactive?

A

Active. During fasting or starvation, glucagon is released to make glucose, so there is no need to make glycogen.

41
Q

What are the 3 pathways of glucose-6-P in the muscle?

A

1) NADPH -> reductive biosynthesis (anabolic pathway)
2) Fructose-6-phosphate, Glyceraldehyde-3-phosphate -> glycolysis/gluconeogenesis
3) Ribose-5-phosphate -> nucleic acid synthesis

42
Q

What is the oxidative reactions of the pentose phosphate pathway to produce NADPH?

A

1) Glucose-6-phosphate is reduced by the enzyme glucose-6-phosphate dehydrogenase; this step is an oxidative reduction (removing hydrogen) where NADPH plus H+ are released. 2) 6-phosphoglucose-delta-lactone; this molecule contains a cyclized ester at carbon 1, where the bond will be broken during hydrolysis. 3) 6-phosphogluconate + NADPH + H+ is formed from a cyclical 6 carbon to a linear 6 carbon chain.

43
Q

Explain the third pathway of the pentose phosphate pathway that involves oxidative decarboxylation.

A

6-phosphogluconate is a 6 carbon linear chain with a carbonyl group on the first carbon. The enzyme 6-phosphogluconate dehydrogenase takes NADP+ and oxidizes it to then release NADPH + CO2. Ribulose-5-phosphate is generated with a ketone on carbon 2. This will be reductive biosynthesis, an irreversible reaction.

44
Q

Ribose-5-phosphate is a precursor of what?

A

The ribose unit of nucleotides.

45
Q

Describe the isomerazation of ribulose-5-phosphate to ribose-5-phosphate.

A

The ketose, ribulose-6-phosphate, is converted with enzyme, ribulose-5-phosphate isomerase, to make the aldose, ribose-5-phosphate. The aldehyde group, O=C-H, is located on carbon 1 of the chain. This step is reversible.

46
Q

What is the non-oxidative reaction of the pentose phosphate pathway?

A

It is a set of interconversions that produce 3,4,5,6 and 7 carbon sugars. The non-oxidative reactions are reversible. It either becomes a nucleic acid synthesis or glycolysis/gluconeogenesis.

47
Q

Net reaction for pentose phosphate pathway

A

Ribose derivative is produced
2 NADPH molecules are formed
Pathway is active in rapidly dividing cells

48
Q

What are other names for the citric acid cycle?

A

Kreb’s cycle and Tricarboxylic acid cycle (TCA)

This occurs in the mitochondria matrix

49
Q

What is the oxidized and reduced form of nicotinamide adenine dinucleotide?

A

Oxidized- NAD+

Reduced- NADH

50
Q

What is the oxidized and reduced form of nicotinamide adenine dinucleotide phosphate?

A

Oxidized- NADP+

Reduced- NADPH

51
Q

What is the oxidized and reduced form of flavin adenine dinucleotide?

A

Oxidized- FAD

Reduced- FADH2

52
Q

What is the oxidized and reduced form of flavin mononucleotide?

A

Oxidized- FMN

Reduced- FMNH2

53
Q

What is the oxidized and reduced form of ubiquinone/ubiquinol?

A

Oxidized- Q

Reduced- QH2

54
Q

What is the pyruvate dehydrogenase reaction?

A

Pyruvate + CoA + NAD+ -> Acetyl-CoA + CO2 + NADH + H+

Pyruvate dehydrogenase is a multisubunit enzyme.

55
Q

What are the cofactors of the pyruvate dehydrogenase reaction?

A 
Thiamine pyrophosphate (TPP)
Lipoamide
Flavin adenine dinucleotide (FAD)
all are bound to the three subunits 
(CoA and NAD+ are also cofactors)
56
Q

What is happening in the E1 phase of pyruvate dehydrogenase reaction?

A

Pyruvate goes through decarboxylation, which is removing the carboxylate group on pyruvate.

57
Q

What is happening in the E2 step of pyruvate dehydrogenase reaction?

A

The acetyl group is transferred to thiamine pyrophosphate and then to lipoamide.

58
Q

What is happening in the E3 step of pyruvate dehydrogenase reaction?

A

The acetyl group is transferred from the E2 subunit to CoA to become Acetyl-CoA.
FAD gets reduced to FADH2, and NAD+ is reduced to NADH + H+.
Acetyl-CoA then moves on to the Kreb’s cycle.

59
Q

How is pyruvate dehydrogenase regulated?

A

By product inhibition (NADH and Aceytl-CoA) And phosphorylation or dephosphorylation

60
Q

In the regulation of pyruvate dehydrogenase, what are the allosteric inhibitors (low energy)?

A

CoA, pyruvate, NAD+

These inhibitors will slow down the process of making acetyl-CoA when there are too many in the system.

61
Q

In the regulation of pyruvate dehydrogenase, what are the allosteric activators ( high energy)?

A

ATP, Acetyl-CoA, NADH

These activators will cause pyruvate to produce more acetyl-CoA.

62
Q

In the regulation of pyruvate dehydrogenase, what does calcium do?

A

Calcium, which comes from the muscle, can activate protein phosphatase and pyruvate dehydrogenase. The phosphatase will remove a phosphate group and this is what engages the Krebs cycle. Pyruvate dehydrogenase is then active by being dephosphorylated.

63
Q

What is the TCA cycle overview?

A

Eight reactions; acetyl-CoA + oxaloacetate; two carbon dioxide lost, oxaloacetate regenerated; 3 NADH, 1 QH2, 1 GTP produced; regulation at three steps

64
Q

The citric acid cycle is an energy generating cycle. How many ATPs does 1 glucose make?

A

In glycolysis it yields 7 ATP; in the conversion of pyruvate to acetyl-CoA, it yields 5 ATP; and in the TCA cycle it yields 20 ATP; for a total of 32 ATP.

65
Q

What is an example of product inhibition?

A

Citrate can inhibit its own enzyme, citrate synthase.

66
Q

When NADH or ATP inhibit Isocitrate or alpha ketoglutarate, what can activate the enzyme?

A

ADP and Ca2+ can activate isocitrate dehydrogenase.

Ca2+ can activate a-ketoglutarate dehydrogenase.

67
Q

Which intermediates flow in the citric acid cycle?

A

Anaplerotic reactions:
Amino acids (to fumarate, succinyl-CoA, a-ketoglutarate and oxaloacetate)
Odd chain fatty acids (to succinyl-CoA)
Pyruvate (to oxaloacetate)

68
Q

Which intermediates flow out of the citric acid cycle?

A

Glucose (from oxaloacetate)
Fatty acids and cholesterol (from citrate)
Heme (from succinyl-CoA)

69
Q

Describe an example of an amino acid formation from the citric acid cycle intermediate

A

Alpha ketoglutarate and NH4+ (an amine group) is converted to glutamate + H2O by the enzyme glutamate dehydrogenase. NADH + H+ is oxidized to NAD+. Glutamate will have two carboxylic acid’s at carbon 1 and 5, and NH3+ on carbon 4.

70
Q

How can citrate and pyruvate cross the mitochondrial membrane?

A

Via specific transport proteins. The citrate crosses the inner mitochondrial membrane from the matrix to the cytosol; the pyruvate crosses from the cytosol to the matrix.

71
Q

Give an example of a half reaction of ubiquinone

A

Q + 2H+ + 2e- QH2

72
Q

What is reduction potential?

A

Reduction potential indicates a substance’s tendency to accept electrons. The greater the reduction potential, the greater the tendency of a substance to accept electrons, and be reduced.

73
Q

What is the reducing equivalent in the electron transport chain of NADH?

A

NAD+ + H+ + 2e-

74
Q

What is the reducing equivalent in the electron transport chain of FADH2?

A

FAD + 2H+ + 2e-

75
Q

What is the reducing equivalent in the electron transport chain of QH2?

A

Q + 2H+ + 2e-

76
Q

What is the reducing equivalent in the electron transport chain of Cytochrome (FE2+)?

A

Cytochrome (Fe3+) + e-

It has a prosthetic group (Heme)

77
Q

Where does the electron transport take place?

A

In the mitochondrion.
The outer membrane is porous.
The inner membrane is impermeable, that’s where the electron transport chain runs through.
The inter-membrane space is cytosol.
In the matrix, the citric acid cycle and fatty acid oxidation takes place. Oxidative phosphorylation occurs as electrons flow through the respiratory chain from reduced cofactors to oxygen; the formation of ATP.

78
Q

What transports reducing agents across the inner mitochondrial membrane?

A

The malate-aspartate shuttle.
Aspartate is in the matrix and is transported by the aspartate transporter protein to the cytosol. Aspartate -> Oxaloacetate where NADH + H+ is oxidized by cytosolic malate dehydrogenase to Malate. Malate is transported from the cytosol to the matrix via the malate transporter protein. NAD+ is reduced to NADH + H+ with the enzyme matrix malate dehydrogenase to form Oxaloacetate, which is converted to Aspartate.
NADH is generated through intermediaries that are reduced within the matrix.

79
Q

Which complexes mediate the oxidation-reduction reactions in the electron transport?

A

Complex I, II, III.

The free energy powers ATP synthesis. All 3 complexes are highly exergonic.

80
Q

What is another name for Complex I?

A

NADH dehydrogenase

81
Q

What does Complex I do?

A

It transfers electrons from NADH to Q. The electrons transfer from NADH to FMN, then from FMNH2 to Q (Q is lipid soluble).
The electrons come from the matrix not NADH.

82
Q

What else is happening while the electrons are being transferred from NADH to ubiquinone (Q)?

A

Complex I transfers 4 protons (H+) from the matrix to the intermembrane space.
2e- -> 4 H+

83
Q

What is another name for Complex II?

A

Succinate dehydrogenase
In this step, there is no flow of H+.
Electrons from FADH2 directly enter Complex II.
Complex I & II can produce QH2.

84
Q

How else is Complex III referred to?

A

Cytochrome bc1
Cytochromes are proteins with the heme prosthetic group.
The heme in cytochrome c undergoes reversible one-electron transfer.
In heme b, the central iron atom is either oxidized (Fe3+) or reduced (Fe2+)

85
Q

Where does Complex III transfers the electrons?

A

From ubiquinol to cytochrome c.

2 e- from QH2 reduce two molecules of cytochrome c.

86
Q

How many protons are pumped into the intermembrane space in Complex III?

A 
4 protons (H+)
2 from QH2 in the first round and 2 from QH2 in the second round.
87
Q

What is another name for Complex IV?

A

Cytochrome a + a3
Complex IV oxidizes cytochrome c and reduced O2.
It also generates H2O.

88
Q

How many electrons and protons are donated or translocated in Complex IV?

A

For every 2 e- donated by cytochrome c, 2 H+ are translocated to the intermembrane space.

89
Q

How many protons are generated in Complex I-IV?

A

10 H+ total
Complex I = 4 H+
Complex III = 4 H+
Complex IV = 2 H+

90
Q

What is the chemiosmotic theory?

A

The imbalance of protons represents a source of free energy, also called a protonmotive force, that can drive the activity of an ATP synthase.

91
Q

What is the protein that taps the electrochemical proton gradient to phosphorylate ADP?

A

ATP synthase (Complex V)

92
Q

In Complex V, what is F1 and F0 responsible for?

A

F1 is responsible for synthesis of ATP

F0 is responsible for the transport of H+ to the matrix side.

93
Q

Describe the different parts of the ATP Synthase

A

a is located in the intermembrane space and does not move
b is the peripheral stalk located in the matrix
c is the ring that moves (8 total)
gamma, epsilon and delta are the central stalk and gamma will rotate
alpha and beta are the subunits; there are 3 alpha and 3 beta that alternate their order

94
Q

Explain how ATP synthase works

A

ATP synthase rotates as it translocates protons.
H+ binds to a c subunit.
The c subunit moves away from the a subunit.
As a new c subunit reaches the a subunit, a proton is released.
ONE ROTATION OF THE RING TRANSLOCATES 8 PROTONS.

95
Q

What is the ATP translocase protein?

A

A transport system used to move ATP from the matrix to the cytosol.
It moves ATP from the matrix to the cytosol and ADP from the cytosol to the matrix.
A symport protein permits simultaneous movement of Pi and H+.

96
Q

What are the three conformational changes the beta subunit undergo?

A

The beta-subunit takes ADP + Pi and releases ATP.
Loose: bind ADP and Pi
Tight: form ATP
Open: release ATP

97
Q

What is the conversion between NADH & ATP and QH2 & ATP?

A

1 NADH = 2.5 ATP

1 QH2 = 1.5 ATP

98
Q

What are the four unique enzymes found in gluconeogenesis and not in glycolysis?

A

Pyruvate carboxylase
Phosphoenolpyruvate carboxykinase
Fructose bisphosphatase
Glucose-6-phosphatase

Biochemistry (7 decks)

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