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Biochemistry 2 > Citric acid cycle and electron transport chain > Flashcards

Citric acid cycle and electron transport chain Flashcards

1
Q

Pathways that metabolize carbohydrates

A 
Glycolysis
Glucoenogenesis
Glycogenesis
Glycogenolysis
PPP
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2
Q

Pathways for protein metabolism

A 
Transamination
Urea cycle
AA catabolism
AA synthesis
Synthesis of AA derivatives
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3
Q

Pathways for synthesis of fat metabolism

A

Beta-oxidation
FA synthesis
TG synthesis
Cholesterol synthesis

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4
Q

Nucleic acids require precursors from what food groups

A

From carbohydrates and proteins

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5
Q

How can we get acetyl-CoA

A

Beta-oxidation
Some AA (leucine, threonine,etc.)
Pyruvate

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6
Q

Conversion of pyruvate to acetyl-CoA ( what enzymes , what products)

A

Pyruvate dehydrogenase complex(PDC) (3 enzymes) uses CoA-SH and NAD+ to convert pyruvate to acetyl-CoA

Products: CO2, NADH

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7
Q

What type of reaction is the conversion of pyruvate to Acetyl-CoA

A

Oxidative decarboxylation

Irreversible

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8
Q

Each cluster of PDC has how many copies of 3 enzyme clusters?

A

60 copies

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9
Q

What are three enzymes within PDC

A

Pyruvate dehydrogenase (E1)

Dihydrolipoyl transacetylase (E2)

Dihydrolipoyl dehydrogenase (E3)

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10
Q

Explain the mechanism of pyruvate conversion to acetyl-CoA

A

Pyruvate is taken by TPP arm, which is on enzyme 1 and the carboxylic group is removed in the form of CO2. The leftover is hydroxyethyl

Hydroxyethyl is then transferred to another prosthetic group: lipoate on enzyme 2, which becomes acyl lipoyllysine. This interacts with CoA-SH and converts to acetyl-CoA

Lipoyllysine is left in reduced form, that cannot accept incoming hydroxyethyl, so it is oxidized by third prosthetic group FAD , FAD->FADH2 and gives H2 to NAD+

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11
Q

TPP arm stands for

A

Thiamine PyroPhosphate

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12
Q

How many intermediates in TCA cycle

A

9

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13
Q

How many steps and enzymes are there in TCA cycle

A

8

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14
Q

What are enzymes of TCA cycle

A

So———-citrate Synthetase

At———-Aconitase

Another———-Aconitase

Dance———-isocitrate Dehydrogenase

Devon———-alpha-ketoglutarate Dehydrogenase

Sipped———-Succinyl-CoA Synthetase

Down———-Succinate Dehydrogenase

Five———-Fumarase

Drinks———-malate Dehydrogenase

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15
Q

What are 3 steps that are irreversible

A

Acetyl-CoA->citrate

Isocitrate ->alpha-ketogluterate

alpha-ketogluterate->succinyl-CoA

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16
Q

Why it is important that TCA cycle has only 3 irreversible reactions

A

So it has entering and exiting points for other cycles- amphybolic

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17
Q

How many carbons do acetyl-CoA donate

A

Acetyl-CoA donates 2 carbons to 4 carbon compound (oxaloacetate)

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18
Q

Two carbons of Acetyl-CoA do not contribute _____

A

Its carbons to CO2 in the first pass

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19
Q

Overall equation for TCA cycle

A

2 CO2+3NADH+1FADH2+1 ATP

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20
Q

What enzymes produce electron carriers in TCA cycle

A

NADH: isocitrate, alpha-ketogluterate
and malate dehydrogenases

FADH2:succinate dehydrogenase

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21
Q

At what steps we get CO2 in TCA cycle

A

Isocitrate ->alpha-ketogluterate

alpha-ketogluterate->succinyl-CoA

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22
Q

Why the step of conversion of succinyl-CoA to succinate to succinyl-CoA dehydrogenase is important

A

It uses ATP usually, but as it is a reverse reaction it produces one ATP

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23
Q

What are anaplerotic reaction

A

Replenishing reactions that feed TCA cycle

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24
Q

Citrate can be taken out of TCA for

A

FAs

Sterols

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25
Q

alpha-ketogluterate can be taken out of TCA for

A

Transamination->glutamate

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26
Q

Succinyl-CoA can be used out of TCA cycle for

A

Porphyrins

Heme

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27
Q

Oxaloacetate can be used outside of TCA

A

Glucoenogenic pathway

Used in AAs synthesize

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28
Q

Anaplerotic reactions for replenishing oxaloacetate with enzyme and in what tissues

A

Pyruvate->oxaloacetate (pyruvate carboxylase)->liver and kidney

Phosphoenolpyruvate->oxaloacetate with PEP carboxykinase in heart and and with PEP carboxylase

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29
Q

Malate can be regenerated from

A

Pyruvate with malic enzyme

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30
Q

Classical regulations of TCA cycle

A

By regulation of irreversible reactions. Activated by substrates, inhibited by products

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31
Q

an additional Pyruvate conversion regulation

A

by phosphorylation on enzyme 1-> inactivation

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32
Q

Succinyl-CoA regulates which two enzymes and for what

A

It inhibits citrate synthase and KDH ( alpha-ketogluterate complex) to regulate alpha-ketogluterate for AA metabolism

33
Q

What ion activates TCA cycle

34
Q

Do FAs contribute to gluconeogenesis

A

Odd number FA lead to succinate-> imbalance

Succinate enter TCA cycle->oxaloacetate->gluconeogenesis

Also acetyl-CoA can be converted to ketone bodies

Acetone can be converted to methylglyoxal or 1,2-Propanediol

35
Q

Energy from ___ is used to synthesize ATP

A

Reduced fuels

36
Q

What are reduced fuels

A

CHO
Lipids
AA

37
Q

What happens in oxidative phosphorylation

A

Energy from NADH and FADH2 is used for ATP synthesis

38
Q

3 types of electron carriers

A

Coenzyme Q
Cytochrome C
Iron-sulfur complex

39
Q

What is the most important feature of coenzyme Q

A

It is a mobile electron carrier

40
Q

Other names for coenzyme Q

A

(ubiquinone-oxidized or ubiquinol-reduced)

41
Q

What does Coenzyme Q do

A

Transfers electrons from complex 1/2 to Complex 3

42
Q

What happens first at electron transport chain

A

NADH along with another H+ donates 2 protons to iron-sulfur complex ultimately converting ubiquinine to ubiquinol

43
Q

Sources of NADH

A

Beta-oxidation -1 NADH per cycle

Glycolysis- 2NADH

Pyruvate to Acetyl-CoA 1 NADH

AA oxidation to pyruvate, etc.

44
Q

Another name of complex II in electron transport chain (ETC)

A

succinate dehydrogenase

45
Q

What does succinate dehydrogenase do

A

Takes protons from FADH2 to put it ubiquinone

46
Q

Acetyl-CoA dehydrogenase is present in

A

First enzyme for beta-oxidation

Electron transport chain (takes electrons form FADH2 and ultimately donates it to ubiquinone)

47
Q

Complex I is ____ of the four complexes

A

The largest : 43 subunits encoded by nuclear and mitochondrial genes

48
Q

How many hydrogens does complex I throw in intermembrane space

49
Q

How many hydrogens is actually used by complex I

A

NADH+Q+5H+=NAD+QH2+4H

So it is actually working with 6 hydrogens

50
Q

What is a cofactor for complex II

51
Q

Is there a movement of hydrogens in complex II

52
Q

What happens at complex III of electron transport chain

A

Ubiquinol transfers its 2 electrons to cytochrome C and oxidized coenzyme Q is thrown into the membrane. 2 hydrogens from 2 electrons are thrown out

By cytochrome C cannot accept two electrons at a time. So for now oxidized coenzyme Q get one electron and becomes an intermediate called ubisemiquinone.

At stage 2, ubisemiquinone accepts one more electron from upcoming ubiquinone and one more cycle from cytochrome C and takes 2 hydrogens form the matrix and becomes a fully reduced ubiquinol

53
Q

So what is a net equation at complex III

A

2 cytochrome C get reduced
4 H+ get thrown out
One QH2 comes in and one Q is thrown out in the membrane

54
Q

What happens at complex IV

A

Cytochrome donates its electrons and gets oxidized and oxygen ( as a terminal acceptor) receives electrons

55
Q

Per one molecule of water how many cytochromes you need, hydrogens and oxygen you need

A

2
2 hydrogens
1/2 oxygen

56
Q

how many electrons are pumped at complex IV

57
Q

How many electrons do NADH and FADH2 pumps

A

NADH- 10H+

FADH2-6 H+

58
Q

What is the equation for 1 NADH and 1 FADH2 in the electron transport chain

A

1NADH+11H(matrix)+1/2O2—>NAD+10H+(inter)+H2O

FADH2+6H(m)+1/2O2—->FAD+6H(inter)+H2O

59
Q

What is respirosome

A

This word shows that electron transport chain functions as one unit

60
Q

ATP synthase needs___ for synthesize of ATP

A

Electrochemical gradient

61
Q

What systems contribute to electrochemical gradient of H+

A

Active transport Complex I and IV

Release of protons into intermembrane space ->oxidation of QH2 (complex III)

Chemical removal of protons from the matrix -> reduction of Q (complex I,II,III) and oxygen (complex IV)

62
Q

Two subunits of ATP synthase

A

F0-> in the membrane-> transports protons dwon the gradient; transfers energy to F1
F1-> in the matrix-> enzymatic capacity in both directions

63
Q

How many dimensions are there in ATP synthase

A

3 parts that are the same form alpha and beta

64
Q

How three alpha and beta parts are connected

A

with gamma-shaft

65
Q

How many hydrogens do you need for synthesis of ATP

A

To turn the ATP synthase itself , you need three hydrogens from intermembrane space to matrix
+
1 hydrogen in the matrix for the transfer of P to ADP

66
Q

How many ATP NADH and FADH2 yield

A

NADH: 10/4=2.5
FADH2: 6/4=1.5 ATP

67
Q

How many subunits ATP synthase do ATP

A

ALL of them, when the shaft turns in their direction, ATP is thrown out

68
Q

How do we get NADH from the cytoplasm to matrix if the inner membrane is impermeable to NADH?

A

Malate-Aspartate shuttle

Oxaloacetate is converted to malate with NADH and malate dehydrogenase

Now there is malate-alpgaketogluterate trasnporter and malate is in matrix.

Malate-> oxaloacetate-> yield NADH

To balance it out, oxaloacetate is converted to aspartate with aspartate aminotrasnferase and converting glutamate to alpha-ketogluterate

Aspartate is thrown out through glutamate-aspartate shuttle

69
Q

Malate-aspartate shuttle is used by

A

Most cells( brain and muscles as well)

70
Q

What shuttle is used for NADH transport in skeletal muscle and brain

A

G3P shuttle

71
Q

Explain G3P shuttle

A

NADH is used for conversion of dihydroxyacetone phosphate to G3P with cytosolic glycerol 3-phosphate dehydrogenase

G3P comes to intermembrane space, where there is mitochondrial glycerol 3-phosphate dehydrogenase bound to the inner membrane.

This enzyme converts G3P back to dihydroxyacetone and puts two hydrogens on FAD->coenzyme Q->complex 3

72
Q

What shuttle yields more energy? and what is strange about it

A

Malate-aspartate shuttle gives more ATP because it uses NADH, but G3P shuttle uses FADH2, which is strange because G3P shuttle is in muscles that need more energy, but his shuttle is more quick, because it goes directly to respirosome

73
Q

So how many ATP from complete oxidation of glucose

A

30 or 32

Depends on which shuttle to take NADH from cytoplasm from glycolysis to the matrix ( 2NADH->3 ATP or 5 ATP)

74
Q

one palmitoyl-CoA yield how many ATPs

75
Q

Regulation of oxidative phosphorylation

A
  • Any substrate acts positively on the reaction, when any product inhibits
  • Acceptor control of respiration (ADP). It depends on how much ADP is available , not oxygen. As soon as it gets available, respiration starts
76
Q

Acceptor control is measured with

A

Mass action ratio ATP/ADP*P

77
Q

ATP is synthesized when

A

It is utilized, it is synthesized as fast as it is utilized

78
Q

Mitochondrial respiration in brown adipose tissue

A

There is uncoupling protein (UCP1). It provides an additional route for the flow of protons to the matrix.

These hydrogens lead to heat synthesize

79
Q

UCP1 another name is

A

Thermogenin

Biochemistry 2 (17 decks)

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