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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
what does AMP act as
a metabolic signal to increase rate of catabolic reactions
26
what enzyme converts ATP to any other nucleotide triphosphate
nucleoside diphosphate and this enzyme is non-specific
27
compare ATP and other nucleotideTP
They can participate in several cellular phosphorylation reactions and they are energetically equivalent to ATP
28
what compounds have free energy hydrolysis higher than ATP
PEP (phosphoenolpyruvate) DG°'=-62kJ/mol 1,3-bis-phosphoglycerate (BPG) DG°'=-49kJ/mol
29
what are the main principles that govern metabolic pathways
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
what are the two main classes of metabolic pathways
catabolic anabolic
31
what are some examples of catabolic pathways
oxidation of carbon compounds glycolysis fermentation
32
define metabolism
the totality of chemical reactions that occur continuously in the cells of living organisms to sustain life
33
how are metabolic pathways interconnected
by common intermediates
34
what is an example of an anabolic reaction
forming polypeptides from amino acids
35
what are the 4 roles of ATP in metabolism
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
what is stage 1 of catabolism
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
what is stage 2 of catabolism
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
what is the equation for oxidising oxygen to water
O2+4H+4e- = 2H2O
39
why is a multistep enzyme pathway better than a single step combustion
there is a release of energy in smaller more manageable units
40
what are some general consideration for the oxidation of carbon molecules
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
how much energy is released from the oxidation of NADH by oxygen
DG°' = -220kJ/mol
42
describe glycolysis
oxygen-independent metabolic pathway that takes place in the cytoplasm
43
what are the 2 stages of glycolysis
5 reactions each - investment phase and payback phase
44
what is the investment phase in glycolysis
first five reactions, some consume ATP and ends with splitting 6-carbon intermediate into two molecules of glyceraldehyde 3-phosphate
45
describe the pay back phase of glycolysis
last five reactions, some produce ATP and one transfer electrons to NAD+ to form NADH and ends in the three carbon molecule pyruvate
46
describe in depth the investment phase of glycolysis
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
give an in depth description of the payback phase
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
what is the overall reaction of glycolysis
glucose +2ADP +2NAD +2Pi 2 pyruvate +2 ATP +2 NADH + 2H+ +2H2O
49
what are the further metabolisms of pyruvate
oxidised to acetyl CoA ethanol and lactate in fermentation
50
what problem of glycolysis does fermentation solve
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
describe the lactic acid fermentation pathway
pyruvate+NADH = lactate + NAD+ catalysed by lactate dehydrogenase
52
describe the alcohol fermentation pathway
pyruvate -->acetaldehyde (pyruvate decarboxylase) acetaldehyde--> ethanol (alcohol dehydrogenase) no net oxidation or reduction
53
describe the link reaction
pyruvate is decarboxylated and joins coenzyme A to form Acetyl CoA and carbon dioxide as well as reducing NAD in the process
54
describe the pyruvate dehydrogenase complex
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
what enzyme catalyses the link reaction
pyruvate dehydrogenase
56
where does the citric acid cycle take place
mitochondrial matrix in eukaryotes and cytoplasm in bacteria
57
how is the free captured in the citric acid cycle
GDP
58
why is the Krebs cycle a cycle
because the starting material oxaloacetate is ready to accept another acetate group from acetyl CoA and it operates twice for each glucose molecule
59
what is the respiratory chain
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
what is a positive of the large surface area of the mitochondrial membrane
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
describe the structure of cytochrome c
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
describe the structure of ubiquinone
(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
what is the name of complex 2
succinate dehydrogenase
64
what is the name of complex 1
NADH-Q reductase
65
describe what occurs between complexes one and two
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
describe what occurs at complex 3
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
describe what occurs at complex
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
describe chemiosmosis
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
describe complex 5
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
describe rotational catalysis
loose - tight - tight - open , open - loose
71
describe the products of the citric acid cycle
10 ATP for each acetyl CoA
72

biochemistry (6 decks)

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