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biochemistry > LM4 bioenergetics > Flashcards

LM4 bioenergetics Flashcards

1
Q

what are the two laws of thermodynamics

A

energy is not created or destroyed

disorder tends to increase in a reaction

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2
Q

describe what occurs when DG>0

A

the reaction requires free energy and is non-spontaneous

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3
Q

describe what occurs when DG<0

A

it releases free energy and is a spontaneous process

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4
Q

define exergonic

A

releases free energy

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5
Q

define catabolic reactions

A

breaks down complex molecules, releasing stored chemical energy

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6
Q

define endergonic reaction

A

requires free energy

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7
Q

define anabolic reaction

A

store chemical energy in complex molecules made out of many simpler molecules

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8
Q

what is the equilibrium constant

A

it establishes a relationship between concentrations

k = ([C][D]/[A][B])

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9
Q

What is Gibbs free energy equation

A

DG=DH-TDS

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10
Q

what does DS>0 mean

A

more products than reactants - increase in entropy/disorder

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11
Q

what is DG°’

A

standard free energy change as commonly used in biochemistry 1M reactants and products at pH7

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12
Q

how is DG°’ useful

A

useful for comparison of different biochemical reactions and gives an idea which direction a reaction would proceed in, everything else being “equal “

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13
Q

describe the equation for standard free energy change of a reaction

A

DG=DG°’ +RTln([C][D]/[A][B])

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14
Q

what are coupled reactions

A

free energies are additive so thermodynamically unfavourable reactions can be driven by coupling them to favourable processes

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15
Q

what enzyme catalyses the first steps of glycolysis

A

hexokinase

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16
Q

describe the action of hexokinase

A

hexokinase brings substrates together in the correct orientation facilitating the transfer of phosphate from ATP directly to glucose.

in the closed form the active site clamps down around the glucose molecule so specificity of binding improves, water is excluded from the active centre so spontaneous hydrolysis of ATP is prevented

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17
Q

describe passive and active transport in terms of free energy

A

passive transport will release free energy DG<0
active transport will require free energy DG>0

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18
Q

describe a coupled reaction with passive ion transport

A

passive ion transport may be coupled to a thermodynamically favourable chemical reaction for example synthesis of ATP in mitochondria

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19
Q

describe a coupled reaction with active ion transport

A

may be coupled to a thermodynamically favourable chemical reaction for example active transport in ion pumps and ATP drive proton pumps

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20
Q

what kind of cellular compartments do semi-permeable membranes separate

A

nucleus, mitochondria, plasmids]
endoplasmic reticulum, golgi vesicles

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21
Q

why is hydrolysis of ATP useful

A

it can be used to drive biosynthetic reactions and other processes with DG>0

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22
Q

what is the enthalpy change of hydrolysis of ATP

A

-32kJ/mol
AMP to adenosine is -14 kJ/mol

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23
Q

under what conditions does ATP release even more energy

A

physiological conditions

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24
Q

what enzyme interconverts adenine nucleotides at near equilibrium

A

adenylate kinase

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25
Q

what does AMP act as

A

a metabolic signal to increase rate of catabolic reactions

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26
Q

what enzyme converts ATP to any other nucleotide triphosphate

A

nucleoside diphosphate and this enzyme is non-specific

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27
Q

compare ATP and other nucleotideTP

A

They can participate in several cellular phosphorylation reactions and they are energetically equivalent to ATP

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28
Q

what compounds have free energy hydrolysis higher than ATP

A

PEP (phosphoenolpyruvate) DG°’=-62kJ/mol

1,3-bis-phosphoglycerate (BPG)
DG°’=-49kJ/mol

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29
Q

what are the main principles that govern metabolic pathways

A

each reaction is catalysed by a specific enzymes

most metabolic pathways are very similar for all organisms indicating a common evolutionary origin

in eukaryotes, pathways are compartmentalised and take place inside specific structures or organelles

each pathway is regulated at some key steps by activating or inhibiting the enzyme catalysing them

30
Q

what are the two main classes of metabolic pathways

A

catabolic
anabolic

31
Q

what are some examples of catabolic pathways

A

oxidation of carbon compounds

glycolysis
fermentation

32
Q

define metabolism

A

the totality of chemical reactions that occur continuously in the cells of living organisms to sustain life

33
Q

how are metabolic pathways interconnected

A

by common intermediates

34
Q

what is an example of an anabolic reaction

A

forming polypeptides from amino acids

35
Q

what are the 4 roles of ATP in metabolism

A

ATP hydrolysis into ADP occupies an intermediate in phosphate transfer potential

ATP acts as a phosphate donor to produce low energy phosphorylated molecules

ATP can be synthesised by transfer of phosphates to ADP from high energy phosphorylated molecules

Cycle ADP/ATP connects the pathways that generate phosphoanhydride bonds to those that hydrolyse them

36
Q

what is stage 1 of catabolism

A

fats proteins and carbohydrates are broken down into smaller molecules

respiratory substrates are oxidised to a 2 carbon group, acetyl CoA

electrons are transferred to carriers, some CO2 is released and some ATP is produced

37
Q

what is stage 2 of catabolism

A

aerobic

Acetyl CoA is further to CO2 in the citric acid cycle and more electrons are also transferred to carriers

all electrons are used to reduce oxygen into water

energy is used to produce ATP

38
Q

what is the equation for oxidising oxygen to water

A

O2+4H+4e- = 2H2O

39
Q

why is a multistep enzyme pathway better than a single step combustion

A

there is a release of energy in smaller more manageable units

40
Q

what are some general consideration for the oxidation of carbon molecules

A

electrons are removed from the carbon molecule stepwise by electron carries

in aerobic conditions the ultimate electron acceptor is oxygen and it is reduced to oxygen

carbon atoms are oxidised to carbon dioxide

in anaerobic conditions less free energy is released but electron carriers are regenerated

41
Q

how much energy is released from the oxidation of NADH by oxygen

A

DG°’ = -220kJ/mol

42
Q

describe glycolysis

A

oxygen-independent metabolic pathway that takes place in the cytoplasm

43
Q

what are the 2 stages of glycolysis

A

5 reactions each -
investment phase and payback phase

44
Q

what is the investment phase in glycolysis

A

first five reactions, some consume ATP and ends with splitting 6-carbon intermediate into two molecules of glyceraldehyde 3-phosphate

45
Q

describe the pay back phase of glycolysis

A

last five reactions, some produce ATP and one transfer electrons to NAD+ to form NADH and ends in the three carbon molecule pyruvate

46
Q

describe in depth the investment phase of glycolysis

A

there is a transfer of a phosphoryl groups to glucose, which uses an ATP molecule - hexokinase and glucokinase

the isomerisation of glucose 6-phosphate into fructose 6-phosphate - isomerase

then another ATP molecules is used to add another phosphoryl group to form fructose 1,6-bisphosphate -phosphofructokinase

aldolase catalyses formation of triose phosphates which rapidly interconvert

47
Q

give an in depth description of the payback phase

A

glyceraldehyde-3-phosphate is turned into 1,3-bisphosphoglycerate by a dehydrogenase enzyme and an NAD+ is reduced

and during the conversion of 1,3-bisphosphate to pyruvate 4 ATP molecules are produced and one H2O - pyruvate kinase catalyses formation of pyruvate

48
Q

what is the overall reaction of glycolysis

A

glucose +2ADP +2NAD +2Pi

2 pyruvate +2 ATP +2 NADH + 2H+ +2H2O

49
Q

what are the further metabolisms of pyruvate

A

oxidised to acetyl CoA

ethanol and lactate in fermentation

50
Q

what problem of glycolysis does fermentation solve

A

glycolysis produced ATP faster than oxidative phosphorylation but NAD+ would become depleted and fermentation reactions convert NADH back to NAD+ to allow glycolysis to proceed as a source of energy

51
Q

describe the lactic acid fermentation pathway

A

pyruvate+NADH = lactate + NAD+

catalysed by lactate dehydrogenase

52
Q

describe the alcohol fermentation pathway

A

pyruvate –>acetaldehyde (pyruvate decarboxylase)

acetaldehyde–> ethanol (alcohol dehydrogenase)

no net oxidation or reduction

53
Q

describe the link reaction

A

pyruvate is decarboxylated and joins coenzyme A to form Acetyl CoA and carbon dioxide as well as reducing NAD in the process

54
Q

describe the pyruvate dehydrogenase complex

A

large, three enzymes, molecular groups travel across subunits

24*E1 - pyruvate oxidative decarboxylation

24*E2 - transfer of acetyl group to CoA

12*E3 - cofactor regeneration

55
Q

what enzyme catalyses the link reaction

A

pyruvate dehydrogenase

56
Q

where does the citric acid cycle take place

A

mitochondrial matrix in eukaryotes and cytoplasm in bacteria

57
Q

how is the free captured in the citric acid cycle

A

GDP

58
Q

why is the Krebs cycle a cycle

A

because the starting material oxaloacetate is ready to accept another acetate group from acetyl CoA and it operates twice for each glucose molecule

59
Q

what is the respiratory chain

A

it is an electron transport chain located in the inner mitochondrial membrane and because of the extensive folding of the mitochondrial membrane there is more room for the proteins to be involved in the reaction than there would be in a membrane with less surface area.

60
Q

what is a positive of the large surface area of the mitochondrial membrane

A

because of the extensive folding of the mitochondrial membrane there is more room for the proteins to be involved in the reaction than there would be in a membrane with less surface area.

61
Q

describe the structure of cytochrome c

A

it is a small peripheral protein that lies in the intermembrane space and it is loosely attached to the outer surface of the inner mitochondrial membrane also has a haem group

62
Q

describe the structure of ubiquinone

A

(coenzyme Q10 or Q)
small nonpolar lipid molecule that moves freely within the hydrophobic interior of the phospholipid bilayer of the inner of the mitochondrial membrane

63
Q

what is the name of complex 2

A

succinate dehydrogenase

64
Q

what is the name of complex 1

A

NADH-Q reductase

65
Q

describe what occurs between complexes one and two

A

NADH passes electrons to the first protein complex which in turn passes the electrons to Q reducing it to ubiquinol. This electron transfer is accompanied by a large drop in free energy - the free energy is used to translocate 4H+ to the matrix per 2e- transferred to intermembrane space

complex 2 passes electrons to Q and reducing it to ubiquinol from FADH2 which was generated in step 6 of the Krebs cycle - these electrons enter the chain later than NADH and will ultimately produce less ATP and these electrons are not translocated across the membrane

66
Q

describe what occurs at complex 3

A

transfers 2e- from QH2 to two molecules of cytochrome c and Fe(III) and free energy is used to translocate 4H+

two from the matrix and two from QH2 oxidised to Q

67
Q

describe what occurs at complex

A

transfers 4e- from 4 cytochrome c to O2
4H+ are captured from the matrix to form 2H2O and free energy is used to translocate 2H+

68
Q

describe chemiosmosis

A

the protons diffuse back into the mitochondrial matrix through a channel protein, ATP synthase which couples this diffusion to the synthesis of ATP

the inner mitochondrial membrane is impermeable to protons so the only way for them to diffuse out is through the channel

a proton concentration gradient is established across two sides of the inner mitochondrial membrane - proton motive force

69
Q

describe complex 5

A

ATP synthase
composed of a knobF1 and stalk F0 which is the proton channel

F1 has 3α, 3β, γ, δ, ε subunits and each β subunit has an active site for ATP synthesis. At any given time, each β subunit is in one of three states:
* loose – ADP/Pi bound
* Tight – ATP formed
* Open – releases TP and binds ADP/Pi again

70
Q

describe rotational catalysis

A

loose - tight - tight - open , open - loose

71
Q

describe the products of the citric acid cycle

A

10 ATP for each acetyl CoA

72
Q
A

biochemistry (6 decks)

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