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Biochemistry and molecular science > Module 7 > Flashcards

Module 7 Flashcards

Metabolic pathways

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Biology 101 flashcards
1
Q

difference between anabolic and catabolic processes

A

Anabolism converts simple sugars, amino acid, fatty acids, nitrogenous base to complex structures like polysaccharides,proteins, lipid and nucleic acid using ATP, NADH, NADPH and FADH2

Catabolism uses carbohydrates, fats, protein and convert to energy depleted end products like CO2, H2O, NH3 while producing energy like ATP etc

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2
Q

structures of the key energy transfer molecules of ATP

A

Phosphate group, main base is adenosine (2 cyclic nitrogenous base)

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3
Q

energy transfer molecules of CoA

A

acetly group, pantothenic acid(2 double O, 1 OH), beta-mercaptoethylamine(sulphide end) transfer molecule, Vitamine B5, adenosine base, phosphate connected to sugar

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4
Q

energy transfer molecules of FADH2/FAD

A

a pair of sugar with one adenosine and transfer molecule nicotinamide(cyclic with O double bond with NH2)

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5
Q

energy transfer molecules of NADH/NAD+

A

FMN, 3 cyclic at the end, nitrogen gains H

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6
Q

What is reaction 1 of glycolysis

A

Phosphorylation of Glucose
Glucose to glucose 6 phosphate, irreversible(ΔG is small), Mg 2+ needed

enzyme used : hexokinase in most tissue and glucokinase in liver

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7
Q

Reaction 2 of glycolysis

A

Isomerisation of Glucose-6Phosphate to Fructose-6-Phosphate(ring of 6 to 5), reversible, higher ΔG, Mg 2+ needed

Enzyme used: PHOSPHOHEXOSE ISOMERASE

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8
Q

Reaction 3 of glycolysis

A

Conversion of Fructose-6Phosphate to Fructose-1,6-bisphosphate, irreversible, ΔG small, first commited step(rate-limiting step) Mg 2+ needed
Enzyme used : PFK-1

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9
Q

Reaction 4 of glycolysis

A

Cleavage of F-1,6-bP
reversible( called aldol condensation), get 2 product, DHAP(dihydroxyacetone phosphat) and GA-3-P( glyceraldehyde 3-phosphate)

Enzyme used: aldolase

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10
Q

Reaction 5 of glycolysis

A

Isomerisation of DHAP to Glyceraldehyde-3-Phosphate
adding H to the =O, reversible. A special glutamate amino acid in the active site (Glu165) performs the transfer

Enzyme used: Triose Phosphate Isomerase

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11
Q

How many steps are there in the Payoff Phase

A

5

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12
Q

Reaction 6 of glycolysis

A

Oxidation of Glyceraldehyde-3-Phosphate to 1,3-Bisphosphoglycerate,
, generate NADH. Adding a phosphate, Rapid turnover of NAD+ is only achieved under anaerobic conditions

Enzyme used: Glyceraldehyde 3-Phosphate Dehydrogenase (3gpd)

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13
Q

Reaction 7 of glycolysis

A

Conversion of 1,3-Bisphosphoglycerate to 3-phosphoglycerate
Formation of ATP, transferring phospate. First ATP generated. irreversible. Mg2+ needed

Enzyme used: Phosphoglycerate Kinase

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14
Q

Reaction 8 of glycolysis

A

Mutase Reaction Converting 3-phosphoglycerate to 2-phosphoglycerate.
Moving the C3 phosphate to C2. Mg2+ needed

Enzyme used: Phosphoglycerate Mutase

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15
Q

Reaction 9 of glycolysis

A

Dehydration of 2phosphoglycerate to Phosphoenolpyruvate
remove the hydroxyl and hydrogen group to form PEP. For H2O.

Enzyme used: Enolase

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16
Q

Reaction 10 of glycolysis

A

Production of ATP from the Conversion of PEP to Pyruvate
Attaching the phosphate to ADP, irreversible

The enzyme used: Pyruvate Kinase

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17
Q

What does chemotherapeutic agent inhibit

A

hexokinase (eg. 2-deoxyglucose)

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18
Q

What is Warburg Hypothesis

A

most cancer cells produce energy by anaerobic glycolysis rather than by oxidation of pyruvate in the mitochondria

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19
Q

What are the enzyme used for glycolysis in chronological order

A

(1) HexoK
(2) PHI
(3) PFK1
(4) Aldolase
(5) TPI
(6) GAPDH
(7) PGK
(8) PGM
(9) Enolase
(10) PK

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20
Q

What are the 3 irreversible step of gluconeogenesis(GNG)

A

(1) Conversion of Pyruvate to PEP occurs via Oxaloacetate using mitochondrialPyruvate Carboxylase& cytosolicPEP carboxykinase
(2) Conversion of F-1,6-bisP to F-6P is catalyzed by Fructose 1,6bisphosphatase
(3) Conversion of G-6-P to Glucose occurs in the ER lumenusing Glucose-6-Phosphatase

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21
Q

step 1A of reversible step gluconeogenesis(GNG)

A

Pyruvate Carboxylase
Uses ATP to attach carboxylic acid to pyruvate using biotin as a cofactor. Change from pyruvate to oxaloacetate. Mitochondrial enzyme

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22
Q

Structure of pyruvate

A

CH3-C=-O,C=-O,O

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23
Q

Structure of glycerate

A

C3H5O4. carboxylic end, C2,3 with hydroxyl

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24
Q

step 1B reversible step of gluconeogenesis(GNG)

A

Adding phosphate to 2C oxaloacetate using GTP, lose the CO2. From oxaloacetate to phosphoenolpyruvate(PEP)

Enzyme used Phosphoenol pyruvate Carboxykinase(PEPCK)

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25
Q

step 2 reversible step of gluconeogenesis(GNG)

A

Fructose-1,6-bisphosphate is converted to Fructose-6-phosphate by Fructose-1,6-Bisphosphatase. Occurs in the cytosol

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26
Q

step 3 reversible step of gluconeogenesis(GNG)

A

Conversion of Glucose-6-Phosphate to Glucose by Glucose-6 Phosphatase
occurs in the lumen of the Endoplasmic Reticulum in hepatocytes of the Liver and in the cortex of the Kidney.

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27
Q

structure of substrates and products for the Cori cycle

A

Lactate>blood lactate>Lactate>glucose>blood glucose>glycogen>lactate

ATP produced when glycogen converts to lactate, used when converting Lactate to glucose

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28
Q

why is lactate dehydrogenase important during anaerobic glycolysis

A

Generating NAD+ in step 6

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29
Q

Describe the metabolic fate of lactate produced in the muscle and how this is linked to metabolism in the liver.

A

Lactate will be convert to blood lactate and transferred to Liver to using ATP to synthesis glucose during recovery

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30
Q

What can pyruvate turn into?

A

alanine, ethanol, lactate, oxaloacetate and acetyl CoA(last 2 are form inside the mitochondrial matrix)

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31
Q

chemical equation of fermentation

A

Pyruvate >(pyruvate decarboxylase) acetaldehyde > (alcohol dehydrogenase) ethanol

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32
Q

Anaerobic Glycolysis chemical equation

A

Pyruvate . L-Lactate using lactate dehydrogenase
LDH plays an important role in regenerating NAD+
High amounts of Lactic acid can produce acidosis.

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33
Q

Structure of L-Lactate

A

CH3—H, OH, C=-OO

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34
Q

What is the structure of glycogen

A

Glycogen is a polysaccharide comprised of α-D-glucose units linked via α1→4 glycosidic bonds withα1→6 branch points

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35
Q

What is the structure of starch

A

1,4 glycosidic bond, all R group are on the same side

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36
Q

What is the structure of cellulose

A

1,4 glycosidic bond, all R group are on the alternating side

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37
Q

What is glycogen

A

storage form of carbohydrate in the body

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38
Q

Why is glycogen important

A

critical during fasting, since liver glycogen provides a source of blood glucose

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39
Q

What is Muscle glycogen for

A

cannot give rise to blood glucose, but is used to power muscle contraction for extended periods of time

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40
Q

What is glycogenolysis for

A

breakdown of glycogen & involves the enzymes (1) Glycogen Phosphorylase, (2) Debranching enzyme and (3) Phosphoglucomutase

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41
Q

What is glycogenesis

A

synthesis of glycogen & involves the enzymes (1) UDP-glucose pyrophosphorylase, (2) Glycogen Synthase, (3) amylo (1 → 4) to (1 → 6) transglycosylase(glycogen-branching enzyme)

42
Q

Which side the glycogenolysis cleave

A

The nonreducing end(left side)

43
Q

What is the debranching enzyme for

A

oligo ( α 1 > 6) to ( α 1 > 4) glucan-transferase] transfers from the branch to the nearby nonreducing end , hydrolyzes the α1>6 linkage to release free glucose

44
Q

What is the use of phosphoglucamutase

A

transfers a phosphoryl group on Glucose-1-Phosphate from C-1 to C-6 to form Glucose-6-Phosphate, which is freely reversible.

45
Q

What is the final product of glycogenolysis

A

glucose 6-phosphate, to convert to glucose or 2 pyruvate for 2 ATP

46
Q

UDP-Glucose Pyrophosphorylase

A

synthesizes UDP-glucose from UTP and Glucose-1-Phosphate and also produces pyrophosphate (PPi)

47
Q

Glycogen Synthase

A

Elongation of glycogen

48
Q

Glycogen Branching Enzyme

A

[Amylo (1>4) to (1>6) Transglycosylase]
catalyzes the transfer of a block of 6 or7 glucose residues from the nonreducing end of a glycogen branch having at least 11 residues to the C6 hydroxyl group of a glucose residue

49
Q

Glycogenin

A

intitiate of a new glycogen chain. Glycogenin is both the primer on which new chains are synthesized and the enzyme that catalyzes their assembly.

50
Q

PDH Complex

A

considered the 1stcontrol point of the Krebs cycle
E1 (pyruvate dehudrogenase), E2 (dihydrolipoyl transacetylase), E3 (Dihydrolipoyl dehydrogenase)
Low G, irreversible, converts from pyruvate to acetyl-CoA. producing NADH

51
Q

Why are B group vitamins important?

A

Most are vital for energy storage, conversion

52
Q

Steps of the citric cycle

A

1) condensation
2a) dehydration
2b) hydration
3) oxidative decarboxylation
4) oxidative decarboxylation
5) substrate-level phosphorylation
6) dehydrogenation
7) hydration
8) dehydration

53
Q

What is the the reaction 1 of kreb cycle

A

formation of citrate from oxaloacetate and acetyl-CoA catalyzed by Citrate Synthase. highly exergonic because it involves the hydrolysis of a thio-ester(i.e.S-CoA) irreversible( low ΔG

54
Q

What is the the reaction 2 of kreb cycle

A

Citrate is converted to isocitrate in two-steps (via a cis-aconitate intermediate) catalyzed by Aconitase

55
Q

What is the the reaction 3 of kreb cycle

A

Isocitrate is then converted to α-ketoglutarate by Isocitrate dehydrogenase producing CO2 and also redox energy in the form of NADH that is equivalent to 2.5 ATP. 2nd control point

56
Q

What is the the reaction 4 of kreb cycle

A

α-ketoglutarate is converted to succinyl-CoA by the
α -ketoglutarate
dehydrogenase complex and represents the 3rd & last control point in the cycle.

57
Q

What does The sequence structure and functional similarities between PDH and α-KDH complexes suggest

A

divergent evolution

58
Q

What is the the reaction 5 of kreb cycle

A

Succinyl-CoA is then converted to succinate by succinyl Co-A synthetase, which involves energy release in the form of hydrolysis of a thioester bond that is used to drive the synthesis of GTP. high GTP inhibits oxidative metabolism

59
Q

What is the the reaction 6 of kreb cycle

A

succinate is converted to fumarate by Succinate Dehydrogenase which utilizes FAD as a cofactor and thus produces a FADH2

60
Q

how many ATP does FAH2 equal to

A

1.5

61
Q

What is the the reaction 7 of kreb cycle

A

Fumarateisconvertedto L-malate via a carbanion intermediate by the enzyme Fumarase (also known as Fumarate Hydratase)

62
Q

Fumarase

A

The enzyme is highly stereospecific and thus cannot bind or react with cis isomer of fumarate (i.e. maleate) orthe D-malate isomer

63
Q

What is the the reaction 7 of kreb cycle

A

conversion of malate to oxaloacetate by Malate Dehydrogenase produces another NADH

64
Q

how many ATP does NADH equal to

A

2.5

65
Q

Total number of ATP form in Aerobic Glycolysis, PDH Complex & Krebs Cycle

A

30-32

66
Q

What is the sequence of product produced in the kreb cycle

A

acetyl-CoA > citrate > isocitrate > α-ketoglutarate > succinyl-CoA > succinate > fumarate > malate > oxaloacetate

67
Q

What does Oxidative phosphorylation mean

A

process of transforming redox energy formed under aerobic conditions during Glycolysis and the Citric Acid Cycle (i.e. NADH and FADH2) into chemical energy in the form of ATP

68
Q

How many major steps of Oxidative Phosphorylation

A

4

69
Q

What is the step 1 of Oxidative Phosphorylation

A

Transfer of electrons from NADH to Complex I and/or from FADH2 to Complex II

70
Q

What is the step 2 of Oxidative Phosphorylation

A

Flow of electrons through large multi-component inner mitochondrial membrane complexes and mobile electron transporters of the Electron Transport Chain

71
Q

What is the step 3 of Oxidative Phosphorylation

A

Pumping of protons (H+) from the matrix to the intermembrane space (IMS) using the proton pumps of Complex I, III and IV as electrons flow through these complexes

72
Q

What is the step 4 of Oxidative Phosphorylation

A

Flow of protons (H+) from the IMS through the F0 component of ATP Synthase (F0F1 ATPase) back into the matrix resulting in the rotation of the F0 component & γ subunit of F1 and the synthesis of ATP from ADP and Pi by the F1 component.

73
Q

Describe how the Electron Transport Chain is linked to the Krebs Cycle.

A

It uses NADH made in kreb to drive ATP synthesis as it pumps H+ into the intermembrance space

74
Q

Where does the electron transport chain occur

A

pumping of protons from the matrix into the intermembrane space (IMS)creates a proton gradient that is used to drive ATP synthesis

75
Q

Function of complex I

A

Uses H from NADH, pump 4H+ to the intermembrance space. attaching 2H to coenzyme Q

76
Q

What is coenzyme Q

A

lipophillic inner mitochondrial membrane dwelling mobile electron carrier that transfers electrons from Complex I and Complex II to Complex III.

77
Q

What is the oxidised form of Q

A

ubiquinone

78
Q

What is the reduced form of Q known as

A

the reduced form (QH2) is referred to as ubiquinol

79
Q

What is enzyme II called

A

succinate dehydrogenase, not a H+ pump

80
Q

What does complex III compromised of

A

Cytochrome c and cytochrome b

81
Q

What is the cytochrome c protein for

A

soluble protein that resides in the inter membrane space that accepts electrons from Complex III and donates them to Complex IV

82
Q

What does cytochrome c contain

A

prosthetic group Heme C with a central Fe3+ atom that becomes reduced to Fe2+ after accepting an e- from Complex III, and returns to Fe3+ when the e- is donated to Complex IV

83
Q

What does complex IV do

A

Pumps 2H+ use ½ O2 per 2e i.e. per NADH or FADH2 and converts to H2O

84
Q

How is ATP synthase synthesise ATP

A

Mitochondrial ATP Synthase uses the H+ gradient formed via the pumping of protons by Complexes I, III & IV to drive the unfavourable synthesis of ATP from ADP + Pi

85
Q

What does ATP synthase compromised of

A

FO (stalk) & a F1 (head) component

86
Q

What does the inner mitochondrial membrane compromised of

A

α, β, γ, δ, ε subunits

87
Q

What mechanic is used to drive the ATP synthesis

A

rotational catalysis mechanism

88
Q

What are the components of F1 in ATP synthase

A

3 nonequivalent adenine nucleotide-binding sites, one for each α/βpair.

89
Q

What is β-ATP conformation in ATP synthase for

A

binds ATP tightly, a second is in the β-ADP conformation, which binds ADP + Pi. third is in the β-empty conformation

90
Q

What causes the rotation of the γ subunit

A

proton motive force as H+ is pumped through the Fo component

91
Q

What is phosphate transocase for

A

to pump phosphate hydrogen into the mitochondria. a symporter

92
Q

How many Protons is required for ATP for yeast

A

10 protons are required to turn the ATPsynthase through one complete cycle to synthesize 3 ATP and 3 H to pump 3 Pi in.

93
Q

How many Protons is required for ATP for mammals

A

8 protons are required to turn the ATP synthase through one complete cycle. 3 H to pump 3 Pi in.

94
Q

How many protons are pumped into IMS per NADH

A

10, 2.5 ATP

95
Q

How many protons are needed to make 1 ATP

A

approx 4

96
Q

How many protons are pumped into IMS per FADH2

A

6, 1.5 ATP

97
Q

How many H+ are pump in complex I

A

4

98
Q

How many H+ are pump in complex III

A

4

99
Q

How many H+ are pump in complex IV

A

2

100
Q

What is adenine nucleotide translocase for

A

transport ATP out and ADP in, antiporter

101
Q

Where does FADH2 oxidised

A

complex II

Biochemistry and molecular science (12 decks)

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