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Bioenergetics Flashcards

1
Q

What are the standard conditions for ΔG

A

pH 7
One atmosphere
298K

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2
Q

ΔG is a state function. What does this mean?

A

ΔG will be the same regardless of the path taken

This also means reactions can be coupled

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3
Q

Why is the hydrolysis of ATP so exothermic

A

Phosphate and ADP have more resonance stabilisation than ATP

Electrostatic repulsion. At pH7, ATP has ~4 negative charges in close proximity, weakening the bridging P-O-P bonds in ATP

Stabilisation due to hydration. More water can bind to ADP and Pi than ATP

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4
Q

What is phosphorylation potential

A

The free energy of ATP hydrolysis

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5
Q

What is the ATP turnover in humans during exercise

A

0.5kg/min

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6
Q

What is ATP often buffered by in mammals

A

Phosphocreatine

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7
Q

Give 3 examples of ATP hydrolysis

A
  1. Phosphorylate glucose to provide enough energy to prime the molecule to be broken down to pyruvate
  2. Peptides are unstable thermodynamically so ATP can be used to build long chains
  3. To join 2 nucleic acids at the start of DNA synthesis
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8
Q

What are the 4 main carrier molecules and what does each carry

What do they all have in common structurally

A

ATP - phosphoryl-
NADH and NADPH: e-
FADH2 and FMNH2: e-
Coenzyme A: acyl

An adenine base is present

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9
Q

What do biotin and uridine diphosphate glucose carry respectively

A

B: CO2
UDG: glucose

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10
Q

What is the main redox system for energy producing pathways

What is it for biosynthesis

A

NAD+/NADH

NADP+/NADPH

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11
Q

What does the phosphate group act as in NADP+

A

A tag allowing recognition of this redox system by biosynthetic enzymes

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12
Q

What does Coenzyme A provide

A

The activated form of acetate

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13
Q

Why is blood important for fuel economy

A

It is a fuel pipe as far as metabolism is concerned, carrying glucose, fructose, lipoproteins, fatty acids, ketone bodies, and amino acids

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14
Q

Why is the small intestine important for fuel economy

A

Absorbs glucose, fructose and amino acids and transfers them to blood
Fats are packed and transferred to lymph and then blood

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15
Q

Why is the liver important for fuel economy

A

Central role in glucose control
‘Fat factory’ in terms of synthesis and export of triglycerides to adipose tissue
Also partially oxidises fats to produce ketone bodies and is central to amino acid metabolism

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16
Q

Why is the heart the ‘dustbin’ of the body

A

It will metabolise a wide variety of substrates left over from other metabolic processes

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17
Q

Why is adipose tissue important for fuel economy

A

Fat storage and energy store

Secretes hormones etc

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18
Q

Why is the brain important for fuel economy

A

Largely uses glucose to maintain neuronal cell function but can use ketone bodies during fasting

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19
Q

What are the beginning and end products of gluconeogenesis

A

Pyruvate to glucose-6-phosphate

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20
Q

What are the beginning and end products of glycolysis

A

Glucose 6 phosphate to pyruvate

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21
Q

What are the beginning and end products of glycogen synthesis

A

Glucose 1 phosphate to glycogen

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22
Q

What are the beginning and end products of fat synthesis

A

Acetyl CoA to fatty acid

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23
Q

What are the beginning and end products of glycogen breakdown

A

Glycogen to glucose 1 phosphate

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24
Q

What are the beginning and end products of fat breakdown

A

Glycogen to glucose-1-phosphate

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25
Q

Why is control necessary in metabolic processes (3)

A
  1. To avoid uncontrolled substrate (futile) cycles
  2. To link energy production to energy usage
  3. To respond to physiological changes
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26
Q

How are enzyme activities controlled

A

Change in the amount of enzyme

Metabolic control of enzyme

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27
Q

How can you change the amount of enzyme

A

Altering rate of synthesis or rate of destruction

Slow long term response

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28
Q

Describe metabolic control of an enzyme

A

Rapid response for quick control of a pathway eg when products of a pathway inhibit steps at the start preventing accumulation of intermediates

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29
Q

What are the mechanisms for controlling enzyme reaction rates

A

Allosteric regulation: binding of an allosteric effector which changes the affinity of the enzyme for its substrates

Covalent modification: usually phosphorylation causing a conformational change

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30
Q

Catabolic vs anabolic

A

Catabolic is degradation

Anabolic is biosynthesis

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31
Q

What are the 3 pathways required to completely oxidise glucose and produce ATP

Sum these processes up in an equation

A

Glycolysis
Krebs Cycle
Oxidative phosphorylation

Glucose + 6O2 —-> 6CO2 + 6H2O + ATP

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32
Q

How is glucose usually transported into cells

A

Via GLUTs

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33
Q

Name 3 insulin independent transporters

A

GluT1,2, and 3

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34
Q

How is entry of glucose into fat controlled by

How does insulin control this

A

GluT4

Prior to exposure to insulin GluT4 proteins are trapped intracellular vesicles
Insulin recruits there by making vesicles fuse with membrane, giving functional glucose transporters

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35
Q

What are the 2 fates of NADH produced in glycolysis

A

It can be transported into the mitochondria for oxidation or can be used to reduce pyruvate to lactate, thus regenerating NAD+

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36
Q

What is another function of glycolysis other than making pyruvate for Krebs cycle

Where is this important

A

Energy production on the absence of O2

Tissue lacking mitochondria (eg RBC and retina)
Tissues where a burst in activity is required eg fast-twitch/ white muscle

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37
Q

How is the oxygen debt repaid

A

Increasing krebs cycle rate to oxidise lactate produced

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38
Q

What are the 2 halves of the citric acid cycle

A

Pruning and energy generation

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39
Q

2 ways to regenerate NAD+

A

NADH oxidation in mitochondria

NADH can also be oxidised by lactate dehydrogenase during the conversion of pyruvate to lactate (anaerobic)

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40
Q

Are white muscles fast twitch or slow twitch

A

Fast twitch

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41
Q

Where does fast twitch muscle derive most of its energy

A

Anaerobic glycolysis

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42
Q

What is the normal blood level of lactate

What happens if it exceeds 5mM
How does this occur

A

1mM

Blood pH drops to pH ~7

Tissue hypoxia

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43
Q

What are the 3 stages of the control of glycolysis

A

Transport of glucose into the cell
Phosphorylation of glucose
PFK-1

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44
Q

What happens when glucose is transported into the cell during glycolysis control

A

GLUT4 transports it into muscle cells and adipocytes

GLUT2 are found in the liver and are non insulin dependent

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45
Q

How is glucose phosphorylated in the liver and in muscle

Why is there a difference and why is it important

A

Liver- glucokinase
Muscle - hexokinase

Glucokinase has a Km(glucose)= 10mM
Hexokinase has a Kn(glucose)= 0.1mM
The liver can deal with high [glucose] while muscle operates at Vmax/2 even under low glucose conditions

This prevents the liver up taking the low [glucose] it releases during fasting

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46
Q

Are both hexokinase and glucokinase inhibited by glucose-6-phosphate

Why

A

Hexokinase is but glucokinase is NOT

Muscles can conserve glucose and shut off glycolysis when glucose-6-phosphate builds up but the liver can keep producing it for glycogen or lipid synthesise

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47
Q

How is PFK-1 inhibited

How is it reactivated

A

ATP is both a substrate and allosteric inhibitor of PFK-1

AMP overcomes this inhibition

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48
Q

2ADP↔️?

What does this

What is the value of its equilibrium constant and what does this mean?

A

ATP+AMP

Adenylate kinase (catalyst)

~1
[AMP]~[ADP]^2/[ATP]

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49
Q

What will a 10% decrease in [ATP] result in for [AMP]

What does this mean about AMP

A

~400% increase because [AMP] are only 2% of [ATP]

It is a very sensitive indicator of energy status in the cell

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50
Q

How does an increase in AMP affect glycolysis

A

Increases glycolysis via control of PFK-1

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51
Q

How is PFK-1 controlled in the liver

A

By fructose-2,6-bisphosphate (as F-2,6-B increases glycolysis increases and gluconeogenesis decreases) which is a potent activator of PFK-1

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52
Q

How is fructose-2,6-bisphosphate formed

A

Phosphorylation of fructose-6-phosphate by PFK-2

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53
Q

What is the key ‘futile cycle’ associated with glycolysis

A

Fructose-6-phosphate to fructose-1,6-bisphosphate by the action of PFK-1 and fructose-1,6-bisphosphatase

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54
Q

What is the importance of substrate cycles

A

They serve the regulatory purpose of signal amplification: at the cost of ATP, the system is made more sensitive to small changes

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55
Q

How is pyruvate kinase activated

A

By fructose-1,6-bisphosphate

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56
Q

Give the 3 key fates of pyruvate

A

Ethanol
Lactate
Becomes Acetyl-CoA for Krebs Cycle

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57
Q

Why is glycogen a good storage molecule

A

Reduced osmotic potential of glucose which would otherwise damage cells in the body and avoids glycosylation of proteins as occurs in diabetes

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58
Q

Give the stages of glycogen synthesis

A

Glucose—> glucose-6-phosphate —-> glucose-1-phosphate —-> (glucose)n+1

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59
Q

Give the stages for the degradation of glycogen

A

Glycogen-> glucose-1-phosphate-> glucose-6-phosphate (which then becomes glucose in the liver, or to pyruvate after glycolysis)

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60
Q

Why is UTP used in the synthesis of glycogen

Give equations

A

Glucose-1-P is not a powerful enough glucose donor to form a gluc-gluc bind so it requires energy from UTP

G1P+UTP—> UDPG+PPi
PPi+water—-> 2Pi

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61
Q

What happens to glycogen during exercise

A

Adrenaline stimulates glycogen metabolism, bonding to a receptor which activates adenylate cyclase to make cAMP, activating protein kinase A.
This activates phosphorylase kinase and inhibits glycogen synthase.
Phosphorylase kinase activates glycogen phosphorylase b to make glycogen phosphorylase a

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62
Q

How Is cAMP broken down

What stimulates and inhibits this

A

By cAMP phosphodiesterase to AMP

Activated by insulin
Inhibited by caffeine

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63
Q

Why does the AMP formed when cAMP is broken down not affect metabolism

A

They are in tiny amounts

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64
Q

How else can phosphorylase b be stimulated

A

5’AMP allosterically stimulates it
ATP opposes this
In muscle Ca2+ activates it

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65
Q

What happens to glycogen in the well fed state

A

We need to turn off the signal to break down glycogen
We do this by hydrolysing cAMP to 5’AMP and protein phosphatases remove phosphates from proteins
Insulin also opposes the action of adrenaline and glucagon by inhibiting Glycogen Synthase Kinase 3 and turns on glycogen synthase

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66
Q

How do glucose pens work

A

Glucose oxidase is entrapped at a Clark oxygen electrode using a dialysis membrane
The decrease in [O2] was proportional to [glucose]

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67
Q

What are the 2 fates of lactate

A

Either oxidised in Krebs cycle or converted back to glucose

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68
Q

Which 3 reactions in glycolysis are NOT readily reversible

A

Phosphorylation of glucose using ATP
Phosphorylation of fructose-6-phosphate using ATP
Conversion of phosphoenolpyruvate to pyruvate

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69
Q

What is required to form oxaloacetate from pyruvate

A

ATP and bicarbonate

Enzyme= pyruvate carboxylase

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70
Q

How does oxaloacetate become PEP

A 
GTP +
PEP carboxylase (enzyme)
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71
Q

What is the reverse action for the action of a kinase

A

Hydrolysis of the phosphate

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72
Q

In the liver how is the balance between glycolysis and gluconeogenesis controlled

A

Through [fructose-2.6-bisphosphate] produced by PFK-2 and recycled to F-6-P by F-2,6-B-ase

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73
Q

When does glucagon act in the liver?

What does glucagon do?

A

When [glucose] is low

Activates protein kinase A which phosphorylates the bifunctional enzyme so that simultaneously PFK-2 decreases and F-2,6-Base increases
The resulting fall in F-2,6-B (an activator of PFK-1) favours gluconeogenesis over glycolysis

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74
Q

What does fructose-2,6-bisphosphate activate and inhibits

A

Activates: PFK-1
Inhibits: Fructose-1,6-bisphosphate

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75
Q

Do muscles have the same Janus enzymes as the liver for glycolysis

What happens in cardiac muscles under exercise

A

No muscles have isoenzymes of PFK-2/ F-2,6-Base

Adrenaline causes phosphorylation of PFK-2 on a different site, INCREASING its rate therefore F-2,6-B increases and glycolysis increases

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76
Q

What happens the PFK-2 in skeletal muscle in exercise

A

PFK-2 is not phosphorylated but the enzyme responds to an increase in [F-6-P]
Therefore F-2,6-B increases, reinforcing the effect of AMP and increasing glycolysis

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77
Q

When is large amounts of lactate produced

What happens to it after and why

A

In muscle during explosive exercise

It is exported into the blood to prevent acidosis. It is converted back to glucose as it still contains a lot of potential energy. After exercise this glucose is transported back to muscle and stored as glycogen

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78
Q

During T2 diabetes what does adipose and skeletal muscle tissues produce in excess

A

Lactate
Alanine
Glycerol

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79
Q

Under normal circumstances how is gluconeogenesis controlled

What happens in T2 diabetes

A

Via expression of PEPCK which is negatively regulated by insulin

This is lost so PEPCK expression rises and glucose production rises adding to hyperglycaemia

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80
Q

What is metformin

A

T2 diabetes treatment

It suppresses gluconeogenesis

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81
Q

Give the other two names of the citric acid cycle

A

Krebs cycle

Tricarboxylic acid cycle

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82
Q

What conditions does the Krebs cycle occur under

A

Oxidative, taking place in the mitochondria

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83
Q

How NADH and FADH2 is generated in each cycle of the Krebs cycle

What happens to these

What else is produced

A

3NADH
1 FADH2

To generate ATP in oxidative phosphorylation

GTP (which is readily converted unto ATP) and CO2

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84
Q

What must happen to pyruvate to start the Krebs cycle

A

Conversion to Acetyl - CoA which is catalysed by pyruvate dehydrogenase

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85
Q

Talk briefly about the structure of pyruvate dehydrogenase and the advantage of it

A

A complex of 3 enzymes

Co-localising these reduces side reactions and increases overall rate

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86
Q

What metabolic processes are in the mitochondria

A

Citrix acid cycle
β oxidation
Respiratory chain

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87
Q

Which metabolic processes are in the cytosol mostly

A

Enzymes of glycolysis
The pentode phosphate pathway
Fatty acid synthesis

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88
Q

What is the problem with the citric acid cycle

A

If we use the cycle to generate new compounds we lose carbon so an anaplerotic (filling up) pathway is needed

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89
Q

Give an equation for an anaplerotic pathway

A

Pyruvate+CO2+ATP+H2O—-> oxaloacetate + ADP + Pi+ 2H+

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90
Q

How much ATP is generates from oxidative glycolysis

What if it is under anaerobic conditions

A

5ATP

2ATP

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91
Q

How many ATP are produced from the citric acid cycle

A

25

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92
Q

How much ATP is produced from aerobic respiration and the citric acid cycle

A

30 ATP

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93
Q

What are the two regulatory enzymes for PDH

A

PDH kinase deactivates

PDH phosphatase activates

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94
Q

What is PDH kinase inhibited by and why

A

Pyruvate

Ensures PDH is ‘on’ when there’s lots of pyruvate

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95
Q

How is PDH phosphatase activated

A

Ca2+
and
insulin in adipocytes

Stimulates PDH during exercise and feeding

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96
Q

How is citrate synthase regulated

A

Allosterically inhibited by ATP which is important during starvation so oxaloacetate is diverted to gluconeogenesis and acetyl-CoA is used to generate ketone bodies instead of generating more citrate

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97
Q

When is isocitrate dehydrogenase activated and inhibited

A

Inhibited: High NADH/NAD+ ratio and by ATP

StimulateD by ADP

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98
Q

When is α-ketoglutarate dehydrogenase activated and inhibited

A

Stimulated by Ca2+

Inhibited by its products (succinyl CoA and NADH)

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99
Q

3 ways to measure the rate of the citric acid cycle

A

Monitoring O2 consumption with an O2 electrode
Both carbon-14 and -13 experiments can be used to chase the label around the cycle

fMRI

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100
Q

What does MRI rely on

A 
Detecting hydrogen nuclei in water 
Paramagnetic substances (such As deoxyhaemoglobin) modify this signal
101
Q

What does it mean to have a high oxidative glycolytic rate

Where is this usually found

A

The rate of glycolysis is high despite O2 being present

In tumours

102
Q

Why do tumours generate energy by such an inefficient means as glycolysis when there is oxygen available??

A

By running glycolysis at a higher flux helps promote flux through the pe rose phosphate pathway. The PPP produces ribose for nucleotide synthesis and NADPH for fatty acid synthesis and glutathione reduction, along with reducing effects of reactive oxygen species.

This all gives cancer a competitive advantage in terms of replication

103
Q

What does the body initially burn for energy?

When does it burn ‘fats’?

A

Sugars

When utilisation outstrips supply

104
Q

How are fats stored

What are the other names for this

Where is it stored

A

As triglycerides

Neutral fats or triacylglycerols

In adipocytes or in the liver

105
Q

How are TAGs mobilised

A

Converted into glycerol and FFA by lipases, which hydrolyse Ester bonds to DAG then MAG and finally to FFA

106
Q

How is hormone sensitive lipase HSL activated

A

Phosphorylation by protein kinase A

107
Q

Where do FFA go

In what proportion?

A

After being released from adipose tissue they are taken up by liver and muscle where they inhibit utilisation of glucose as fuel

Most go to heart and skeletal muscle during sustained exercise

108
Q

What is β oxidation

Where does it occur

A

Oxidation of fats: it converts aliphatic fat into acetyl CoA for the citric acid cycle

Mitochondria

109
Q

What are the steps of β oxidation

A

Fatty acids cleaved from the glycerol back bone are activated using CoA to form acetyl CoA by acyl CoA synthase.
Formation of high energy bond between CoASH and fatty acid result in ATP becoming AMP

110
Q

How is the overall reaction of β oxidation made favourable

A

The PPi formed is hydrolysed to Pi

111
Q

Where does activation of β oxidation occur

What happens to the resulting product

A

At the outer mitochondrial membrane

The acyl-CoA cannot diffuse across the barrier so after modification by carnitine acyltransferase 1, the fatty acid is carried across attached to the carnitine

112
Q

What happens once the acyl-CoA is inside the mitochondrion

A

It is transferred back to CoASH in a reaction catalysed by acyltransferase 2 and the carnitine travels back out of the mitochondrion

113
Q

Why is an activated fatty acid oxidised….

A

It is oxidised to introduce a double bond
The double bond is hydrated to introduce water and the resulting alcohol is oxidised to a ketone
The 4 carbon fragment is cleaved by CoA to yield acetyl CoA and a fatty acid chain that is 2 C’s shorter

114
Q

What is thiolysis

How many times is it repeated

A

Conversion of a ketone to acetyl CoA and a fatty acid

It is repeated until the fatty acid is completely converted into acetyl CoA

115
Q

Give the structure of acetyl CoA

A

O
||
H3C-C-S-CoA

116
Q

What is produced from β oxidation (3) and what processes do they contribute to

A

FADH2 and NADH (oxidative phosphorylation)

Acetyl-CoA (citric acid cycle)

117
Q

How do mammals generate glucose from fat-derived acetyl CoA

A

It can’t as it is past the point of no return to pyruvate

Instead this Acetyl CoA is completely oxidised to CO2 which can lead to muscle break down in long term starvation

118
Q

What happens when oxaloacetate levels drop during gluconeogenesis

A

More acetyl CoA is produced than can be metabolised so ketone bodies are formed in the liver

119
Q

What are the four FAD dependent acyl CoA dehydrogenases

A

Very long chain acyl CoA dehydrogenase
Long chain “ “ “
Medium chain “””
Short chain “””

120
Q

Why does oxidising fats require more O2 than for carbs

A

Carbs (1 oxygen molecule) has the basic structure of H-C-O-H
So requires 2 O2 to go to CO2 and water

Fat has the basic unit H-C-H so needs 1.5 molecules of O2 to get to the same products

121
Q

Why is MCAD a cause of cot death

A

Babies cannot oxidise fatty acids so readily and die at night when glycogen is depleted

122
Q

What causes Jamaican vomiting sickness

A

Unripe ackee contains an inhibitor of acyl-CoA dehydrogenases, depleting glycogen supplies

123
Q

What are the 3 ketone bodies

A

Acetoacetate
β-hydroxybutyrate
Acetone

124
Q

What happens to acetoacetate in muscle mitochondria

What about in liver

A

It is cleaved to 2x acetyl CoA for Krebs cycle

It cannot happen in the liver as it lacks the transferase needed to move CoA from succinyl-CoA to form acetoacetyl-CoA

125
Q

Can glycerol from TAGs be recycled?

A

Yes via gluconeogenesis

126
Q

How is β oxidation regulated

A

Reesterification of fatty acids

Transport of fatty acid into mitochondria

Availability of NAD+ and FAD (competition with citric acid cycle for these co-factors)

127
Q

Explain how re-esterification regulates β oxidation

A

In fasting glucose is in short supply and there will not be spare glucose phosphate available to provide reesterification. This is because insulin is low so GluT4 is not recruited, thus there is little glucose uptake
FFA are not reesterified and circulate instead

128
Q

What are GPATs

A

Reesterification enzymes

129
Q

How is transport into the mitochondria controlled

Why is it controlled

A

Carnitine shuttle is inhibited by malonyl-CoA (produces during fatty acid synthesis) In liver

To prevent synthesis and degradation occurring alongside one another

130
Q

What does malonyl CoA do in muscle

A

Mostly regulatory

131
Q

Where are fatty acids >22 oxidised

A

In peroxisome

Mitochondria cannot import such long chains

132
Q

What is peroxisomal synthesis controlled by

A

Ligand induces transcription factors

133
Q

What is a PPAR

A

Peroxisomal Proliferation Activated Receptors

134
Q

What is the target of fibrate drugs

A

PPAR α

These tackle hyperglycaemia

135
Q

What does PPAR γ control

A

Adipogenesis and improves insulin sensitivity

136
Q

What does PPAR δ

A

Expressed everywhere and drives fatty acid oxidation

137
Q

Why is it easier to store fat than glycogen

What does this mean for excess glycogen
Where does this happen

A

Les what is necessary and fat is more energy rich

Excess glycogen is converted to fat
This happens in the mitochondria

138
Q

Where are acetyl CoA and fatty acids synthesised

A

Acetyl CoA is in the mitochondria

Fatty acid is in the cytosol

139
Q

What does fatty acid synthase do

A

Adds acetyl CoA to a growing strand of fatty acid

Reduces -CH2CO- to -CH2CH2-

140
Q

How is acetyl CoA removed from the mitochondrion

A

It combines with oxaloacetate (C4) to make citrate (C6) and CoA
Via the action of citrate synthase in the mitochondrion

141
Q

What happen to citrate once is ends up in the cytosol

A

It reacts with ATP and CoA to form oxaloacetate and acetyl CoA

142
Q

Which step in fatty acid synthesis is regulated and why

Is it allosteric or hormonal regulation

A

Conversion of Acetyl CoA to Malonyl CoA using acetyl CoA carboxylase

This is the rate limiting step

Both

143
Q

What causes acetyl CoA carboxylase to activate

Inhibits?

A

Citrate (allosteric) and insulin (hormonal)

Fatty acids (allosteric) and glucagon (hormonal)

144
Q

How do insulin and glucagon control malonyl CoA

A

Insulin activated pyruvate dehydrogenase to make more acetyl CoA by promoting the dephosphorylation of of PDH
Insulin also activates acetyl CoA carboxylase by stimulating its dephosphorylation to increase malonyl CoA supply

Glucagon opposes this by raising phosphorylation of ACC

145
Q

What does 5’AMP do for ACC

A

Increases phosphorylation of ACC via AMPK

146
Q

What is 5’AMP important

A

It acts as a fuel gauge to mark the breakdown of ATP

147
Q

Give the general equation to make a TAG

Where does this occur

A

Fatty acid- CoA + glycerol-3-phosphate —-> TAG

Liver, adipose and lactating mammary glands

148
Q

Why is glucose needed to make TAGs from fatty acyl-CoA

A

A regular supply of glycerol 3 phosphate is needed from glycolysis

149
Q

Where is amino acid metabolism most intensive

A

Liver where the urea cycle is focussed

150
Q

What kind of amino acids does muscle tissue produce

A

Branched chain

151
Q

How is the NH3 produced from amino acid metabolism captured

A

As glutamate and glutamine

152
Q

How is nitrogen exported

A

As urea

153
Q

Give the formula of urea

A

NH2CONH2

154
Q

Why is urea ideal

A

It is water soluble, neutral, and ideal for detoxification

155
Q

What transfers amino groups between amino acids

A

2-oxo acids via amino transferases

156
Q

What is vitamin B6

A

Pyridoxal Phosphate

A prosthetic group of amino transferase, acting as a temporary parking spot for amine groups

157
Q

What does alanine do

A

Carrier of ammonia and of the carbon skeleton of pyruvate from skeletal muscle to liver

158
Q

How is glutamine formed

A

As excess ammonia is added to glutamate

Catalysed by glutamine synthase and requires ATP

159
Q

What happens to glutamine

A

Is it exported to the liver where NH4+ is liberated by glutaminase

160
Q

What does glutamate dehydrogenase do

Why is this enzyme unusual

How is it regulated

A

Releases Nitrogen from glutamate as NH3 via oxidative deamination

It will use NAD+ or NADP+

Allosterically by GTP and ADP

161
Q

What form is the nitrogen that is put into the urea cycle

A

Aspartate and ammonia

162
Q

What’s wrong with Xs ammonia

A

It can accumulate in the brain, drawing in water and damaging the brain as it tries to expand within a finite container (the skull). This is hepatic encephalopathy

It can also deplete the Krebs cycle of α ketaglutarate by converting it first to glutamate then to glutamine

163
Q

Explain the chemiosmotic hypothesis

A

NADH and FADH2 are oxidised by O2 to produce water
This pumps protons across the mitochondrial membrane
This generates force which can be used to make ATP from ADP and Pi, fuelling the cell

164
Q

What do Cristae do in the mitochondria

A

Increase surface area

165
Q

What does the PMF do

A

The proton motive force pumps protons uphill out of the mitochondrion

166
Q

What are the two gradients the PMF works against

A 
pH difference (courtesy of [H+])
Charge
167
Q

Give the PMF equation

A

PMF=ΔΨ-(2.303RT/F)ΔpH

168
Q

What is ΔΨ

A

Difference in charge

169
Q

What must protons travel through as ATP is formed

A

ATP synthase

170
Q

What measures oxygen consumption in the mitochondria

A

Oxygen electrode

Mitochondria placed in buffer and oxygen electrode measures decrease in O2 level

171
Q

When does O2 consumption increases in the mitochondria

A

When ADP is present

Only then are protons allowed to flow across the membrane as oxygen is used to oxidise reducing agents

172
Q

What do uncouplers do?

A

Promote H+ re-entry

When they are present, O2 is burnt without ATP being produced

173
Q

Give examples of uncouplers

A

Ionophores

2,4- dinitrophenol

174
Q

Why can’t O2 be directly reduced to H2

A

It would be too explosive

175
Q

How many supramolecular complexes exist in the e- transfer chain

How are e shuttles between them

A

4

By ubiquinone and cytochrome C

176
Q

What does QH2 do

A

Serves as a mobile carrier of e- and H+

177
Q

How is ubiquinone adapted

A

Has a long lipophilic side chain to make it membrane soluble

178
Q

How is Q reduced to QH2

A

Transports electrons from complex 1 and 2 to 3

For complex 3 this involves H+ pumping using the Q cycle

179
Q

What do cytochromes do

A

Transfer single e- by Fe2+/3+ redox

180
Q

Where can different types of cytochrome be found

A

b and c1: complex 3
a and a3: complex 4
C: ferries e- from 3 to 4

181
Q

For each complex give its donor

A

1: NADH
2: Succinate
3: reduced Q
4: reduced cytochrome c

182
Q

For each complex give the acceptor

A

1: ubiquinone
2: ubiquinone
3: cytochrome c
4: O2

183
Q

Discuss complex 1

A

Uses NADH to reduce ubiquinone
Largest complex with ~40 polypeptides
NADH reduces FMN, e- pass through 8-9 FeS centres and this reduces Q to QH2
Pumping is driven by conformational changes

184
Q

Discuss complex II

A

It is succinate dehydrogenase and thus part of the Krebs cycle
It had bound FAD that is reduced by succinate
3 FeS centres pass electrons to Q to produce QH2

185
Q

How many protons are pumped out for each package of 2 e- that passes from NADH to oxygen?

Show the maths

A

10

4 protons by complex 1
4 protons by Q
2 protons by complex 4

186
Q

Discuss complex 3

A

This uses ubiquinone to reduce cytochrome c
It contains FeS protein, cytochrome c1 and b. It is therefore referred to as the bc1
Cytochrome c1 receives e- from FeS centre and transfers them to c which is loosely associated with the outer surface of the mitochondrion

Antimycin inhibits this complex

187
Q

What is the important role of complex 3 In apoptosis

A

It is released either via a pore or when mitochondria rupture as part of the apoptosis cascade that ultimately results in cell suicide

188
Q

Describe the structure of cytochrome b in complex 3

A

Spans mitochondrial membrane

2 harms at opposite sides of protein

189
Q

Discuss complex 4

A

Uses cytochrome c to reduce oxygen to water
4 redox centres: cyt a, a3, CuA centre with two Cu ions, and CuB
These work together to ensure oxygen is reduced to O2^2-, avoiding production ot superoxide
2 more e- cleave O-O and with 4H+ we make water

190
Q

Are the 4H+ pumped along proton wires used to make water in complex 4

A

No

191
Q

What happens if complex 4 is impaired

A

Alzheimer’s
T2 diabetes
Ageing

192
Q

What reaction does ATP synthase catalyse

A

ADP + Pi —-> ATP + water

193
Q

Describe the structure of ATP synthase

A 
2 parts (F0 and F1)
F0 forms the channel for the return of protons to the mitochondrial complex 
F1 is linked to F0 by a stalk 
PMF drives shape changes in F1 and so ADP and Pi are squashed together forming ATP
194
Q

What happens If F0 is separates from F1

A

It just hydrolyses ATP using water

195
Q

What blocks the F0 channel

A

Oligomycin

196
Q

How many subunits does F0 have

What do these do

A

10

Translocate H+s to the γ subunit other the F1 core. Protons flow through F0 generating a torque which rotates the c subunits and drives the γ subunit

197
Q

How many protons are used for each ATP produced

A

3

198
Q

What are the 3 conformations that each site in complex 4 cycles through

Give a brief description of each

A

Open - low affinity for ADP and P
Loose - bonds ADP and P loosely
Tight - squeezes out water

199
Q

Give the 3 steps involving L, T, and O sites

A

1) ADP and P bind to L
2) energy in to convert L to T
ADP+P —-> ATP + water
3) energy to convert T to O
ATP is released

200
Q

2 ways to provide energy to drive metabolites through particular channels

Give examples

A

Difference in charge or pH between compartments

ATP and ADP exchange courtesy of charge
Phosphate enters courtesy of pH

201
Q

What happens if rate of e- entry in the respiratory chain is greater than the rate of e- transfer through the chain

A

Partially reduced ubiquinone radical can be produced which donates an e- to oxygen

Superoxide acts on aconitase to release Fe2+ which leads to •OH formation

202
Q

Structure of aconitase

A

4Fe-4S protein

203
Q

What opposes formation of •OH

A

Reduced glutathione (GSH)

204
Q

What is the number one role of the liver in metabolism

A

A buffer of blood glucose

205
Q

What happens when 2ATPs are broken down?

How can this be made more useful?

A

2ADP+2Pi

2ADP can become ATP+AMP via adenylate kinase
AMP can become IMP which stimulates glycogenolysis

IMP is further degraded to adenosine which stimulates vasodilation

206
Q

What happens to lactate

Why is it in different organs

A

It is taken to the liver
Gluconeogenosis occurs generating more glucose for the muscles

To avoid a futile cycle

207
Q

How are fatty acids released from adipose

When

A

Hormone sensitive lipase or ATGL

During endurance exercise

208
Q

How do you balance oxaloacetate if there is excess acetyl CoA

A

Convert isoleucine and valine to succinyl-CoA then oxaloacetate

209
Q

What is the ‘wall’ in endurance exercise

Why

A

Depletion of glycogen

It is priming TCA cycle

210
Q

What inhibits hexokinase

A

Raised G6P

211
Q

How is AMPK turned on

What does AMPK do

A

Muscle contraction

Switches on catabolic processes that generate ATP and switch off anabolic storage processes

It activates glucose uptake and fatty acid oxidation by inhibiting ACC and relieving inhibition of CPT-1 by malonyl CoA

212
Q

What is marasmus

A

Deficiency in calories

213
Q

Kwashiorkor

A

Exclusively carb diet with severe protein deficiency in children

214
Q

3 negative effects of obesity

A

Lipotoxicity- antagonism of insulin signalling by lipid regulated kinases

Inflammation- enlarges adipocytes attract macrophages which secret cytokines that antagonise insulin receptor signalling by activating inhibitory cascades

Oxidative stress - abnormal oxidation gives ROS which damages proteins and membranes

215
Q

What are some consequences of the metabolic alterations in muscle due to insulin resistance (4)

A

GluT 4 is not recruited to membrane due to changes in insulin pathway

Faulty insulin signalling increases glycogen breakdown

Rate of glycolysis is low due to failure to recruit GluT 4

Acetyl CoA and NADH from β oxidation inhibit pyruvate dehydrogenase turning off entry into TCA cycle

216
Q

Give the benefits of exercise

A

Training decreases size and fat content of adipocytes

Muscle contraction stimulates glucose uptake via GluT 4 by non-insulin dependant mechanisms

Post exercise, glucose uptake via GluT 4 is more insulin sensitive

Exercise immediately after stress accelerates removal of harmful levels of FFA

217
Q

What is necessary for synthesis of ATP from ADP and Pi in the mitochondrial matrix

A

The entry of H+ from the inter membrane space

218
Q

Does β oxidation involve cleavage of a phosphoanhydride bond?

What about synthesis of fatty acids from acetyl CoA and malonyl CoA

A

No

No

219
Q

Can ketogenic amino acids contribute nitrogen to the urea cycle

A

Yes

220
Q

Which micronutrient is needed for maintaining cell membrane integrity

A

Vitamin E

221
Q

Name 1 thing that activates pyruvate carboxylase

A

Acetyl CoA

222
Q

What is activated in response to PIP3

A

PKD

223
Q

What kind of receptor is the glucagon receptor

A

A GPCR

224
Q

Name an intermediate in both the TCA cycle and gluconeogenesis

A

Oxaloacetate

225
Q

How does F-2,6-B affect PFK-1

A

Increases PFK-1 activity, driving glycolysis

226
Q

How is PDH affected by NADH and acetyl CoA

A

PDH is turned off if lots of NADH and acetyl CoA are present so it is regulated by ratio of NADH/NAD+ and acetyl CoA/ CoA

227
Q

What inhibits complex 3

A

Antimycin

228
Q

What is the pathway for the effect of adrenaline on glycogen

A

Adrenaline->cAMP->PKA->inhibits glycogen synthase and activates phosphorylase kinase (which activates glycogen phosphorylase)

229
Q

What is the intermediate between G-1-P and glycogen in glycogen synthesis

A

UDP-glucose using glycogen synthase

230
Q

How does insulin encourage glycogen formation

A

Inhibits Glycogen Synthase Kinase 3, allowing glycogen synthase to become active

231
Q

How is pyruvate concerted back to phosphoenolpyruvate (PEP) in gluconeogenesis?

Do they use ATP?

A

Converted to oxaloacetate (by pyruvate carboxylase) - Uses ATP

Then oxaloacetate is converted to PEP by PEP carboxykinase - uses GTP

232
Q

Name a metabolic Conversion that doesn’t involve cleavage of a phosphoanhydride bond

A

Fatty acid synthesis from acetyl CoA and malonyl CoA

233
Q

Name a substance that actives pyruvate carboxylase

A

Acetyl CoA

234
Q

Name a micronutrient that is involved in maintaining the integrity of cell membranes

A

Vit E

235
Q

Which kinase is activated by PIP3

A

PKB

236
Q

Which metabolic receptor is a GPCR

A

Glucagon receptor

237
Q

Which experimental approach should be used to identify all of the DNA binding site for a specific DNA binding protein in the genome

A

ChIP

238
Q

What does PDH do

What controls PDH

A

Pyruvate + NAD + CoASH-> acetyl CoA + NADH + CO2

PDH kinase inhibits PDH:
•Inhibited by pyruvate
• activated by high NADH and Acetyl CoA

PDH phosphatase activates PDH
•activated by Ca2+ and insulin

239
Q

What does citrate synthase do

How is it controlled

A

Converts Acetyl CoA and OAA to citrate

Inhibited by citrate and allosterically inhibited by ATP

240
Q

How is isocitrate dehydrogenase controlled

What does it do

A

Inhibited by high NADH and ATP
Stimulated by ADP and Ca2+

Converts Isocitrate and NAD to α ketoglutarate and NADH

241
Q

What does α ketoglutarate do

How is it controlled

A

α ketoglutarate and NADH to succinyl CoA and NADH

Inhibited by high NADH and succinyl CoA
Stimulated by Ca2+

242
Q

What are all the TCA cycle dehydrogenases inhibited and stimulated by

A

Inhibited by high NADH
Stimulated by Ca2+

This is done indirectly in PDH: high NADH stimulates PDH kinase (inhibits PDH) and Ca2+ activates PDH phosphatase

243
Q

What causes inactivation of HSL

A

De phosphorylation (P naturally falls off over time)

244
Q

Why is carnitine needed

A

CoA cannot pass mitochondrial membrane

245
Q

What converts acyl-CoA to acyl-carnitine?

Where is this found

A

Carnitine acyl transferase 1

Physically bound to the outer mitochondrial membrane

246
Q

How does acyl-carnitine enter the mitochondria

A

Down its concentration gradient through a channel called translocase

247
Q

How is acyl carnitine converted to acyl CoA

Where is this found

A

Carnitine acyl transferase II

Free in the mitochondria

248
Q

Where is cytochrome c found

A

Loosely associated with the INNER membrane of the mitochondrion

249
Q

How is PKA activated

A

When cAMP binds to the regulatory subunits of PKA, the catalytic subunits dissociate and become active

MIMS (12 decks)

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