Bioenergetics Flashcards

(249 cards)

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
Why is control necessary in metabolic processes (3)
1. To avoid uncontrolled substrate (futile) cycles 2. To link energy production to energy usage 3. To respond to physiological changes
26
How are enzyme activities controlled
Change in the amount of enzyme Metabolic control of enzyme
27
How can you change the amount of enzyme
Altering rate of synthesis or rate of destruction | Slow long term response
28
Describe metabolic control of an enzyme
Rapid response for quick control of a pathway eg when products of a pathway inhibit steps at the start preventing accumulation of intermediates
29
What are the mechanisms for controlling enzyme reaction rates
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
30
Catabolic vs anabolic
Catabolic is degradation | Anabolic is biosynthesis
31
What are the 3 pathways required to completely oxidise glucose and produce ATP Sum these processes up in an equation
Glycolysis Krebs Cycle Oxidative phosphorylation Glucose + 6O2 —-> 6CO2 + 6H2O + ATP
32
How is glucose usually transported into cells
Via GLUTs
33
Name 3 insulin independent transporters
GluT1,2, and 3
34
How is entry of glucose into fat controlled by How does insulin control this
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
35
What are the 2 fates of NADH produced in glycolysis
It can be transported into the mitochondria for oxidation or can be used to reduce pyruvate to lactate, thus regenerating NAD+
36
What is another function of glycolysis other than making pyruvate for Krebs cycle Where is this important
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
37
How is the oxygen debt repaid
Increasing krebs cycle rate to oxidise lactate produced
38
What are the 2 halves of the citric acid cycle
Pruning and energy generation
39
2 ways to regenerate NAD+
NADH oxidation in mitochondria | NADH can also be oxidised by lactate dehydrogenase during the conversion of pyruvate to lactate (anaerobic)
40
Are white muscles fast twitch or slow twitch
Fast twitch
41
Where does fast twitch muscle derive most of its energy
Anaerobic glycolysis
42
What is the normal blood level of lactate What happens if it exceeds 5mM How does this occur
1mM Blood pH drops to pH ~7 Tissue hypoxia
43
What are the 3 stages of the control of glycolysis
Transport of glucose into the cell Phosphorylation of glucose PFK-1
44
What happens when glucose is transported into the cell during glycolysis control
GLUT4 transports it into muscle cells and adipocytes GLUT2 are found in the liver and are non insulin dependent
45
How is glucose phosphorylated in the liver and in muscle Why is there a difference and why is it important
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
46
Are both hexokinase and glucokinase inhibited by glucose-6-phosphate Why
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
47
How is PFK-1 inhibited How is it reactivated
ATP is both a substrate and allosteric inhibitor of PFK-1 AMP overcomes this inhibition
48
2ADP↔️? What does this What is the value of its equilibrium constant and what does this mean?
ATP+AMP Adenylate kinase (catalyst) ~1 [AMP]~[ADP]^2/[ATP]
49
What will a 10% decrease in [ATP] result in for [AMP] What does this mean about AMP
~400% increase because [AMP] are only 2% of [ATP] It is a very sensitive indicator of energy status in the cell
50
How does an increase in AMP affect glycolysis
Increases glycolysis via control of PFK-1
51
How is PFK-1 controlled in the liver
By fructose-2,6-bisphosphate (as F-2,6-B increases glycolysis increases and gluconeogenesis decreases) which is a potent activator of PFK-1
52
How is fructose-2,6-bisphosphate formed
Phosphorylation of fructose-6-phosphate by PFK-2
53
What is the key ‘futile cycle’ associated with glycolysis
Fructose-6-phosphate to fructose-1,6-bisphosphate by the action of PFK-1 and fructose-1,6-bisphosphatase
54
What is the importance of substrate cycles
They serve the regulatory purpose of signal amplification: at the cost of ATP, the system is made more sensitive to small changes
55
How is pyruvate kinase activated
By fructose-1,6-bisphosphate
56
Give the 3 key fates of pyruvate
Ethanol Lactate Becomes Acetyl-CoA for Krebs Cycle
57
Why is glycogen a good storage molecule
Reduced osmotic potential of glucose which would otherwise damage cells in the body and avoids glycosylation of proteins as occurs in diabetes
58
Give the stages of glycogen synthesis
Glucose—> glucose-6-phosphate —-> glucose-1-phosphate —-> (glucose)n+1
59
Give the stages for the degradation of glycogen
Glycogen-> glucose-1-phosphate-> glucose-6-phosphate (which then becomes glucose in the liver, or to pyruvate after glycolysis)
60
Why is UTP used in the synthesis of glycogen Give equations
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
61
What happens to glycogen during exercise
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
62
How Is cAMP broken down What stimulates and inhibits this
By cAMP phosphodiesterase to AMP Activated by insulin Inhibited by caffeine
63
Why does the AMP formed when cAMP is broken down not affect metabolism
They are in tiny amounts
64
How else can phosphorylase b be stimulated
5’AMP allosterically stimulates it ATP opposes this In muscle Ca2+ activates it
65
What happens to glycogen in the well fed state
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
66
How do glucose pens work
Glucose oxidase is entrapped at a Clark oxygen electrode using a dialysis membrane The decrease in [O2] was proportional to [glucose]
67
What are the 2 fates of lactate
Either oxidised in Krebs cycle or converted back to glucose
68
Which 3 reactions in glycolysis are NOT readily reversible
Phosphorylation of glucose using ATP Phosphorylation of fructose-6-phosphate using ATP Conversion of phosphoenolpyruvate to pyruvate
69
What is required to form oxaloacetate from pyruvate
ATP and bicarbonate | Enzyme= pyruvate carboxylase
70
How does oxaloacetate become PEP
``` GTP + PEP carboxylase (enzyme) ```
71
What is the reverse action for the action of a kinase
Hydrolysis of the phosphate
72
In the liver how is the balance between glycolysis and gluconeogenesis controlled
Through [fructose-2.6-bisphosphate] produced by PFK-2 and recycled to F-6-P by F-2,6-B-ase
73
When does glucagon act in the liver? What does glucagon do?
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
74
What does fructose-2,6-bisphosphate activate and inhibits
Activates: PFK-1 Inhibits: Fructose-1,6-bisphosphate
75
Do muscles have the same Janus enzymes as the liver for glycolysis What happens in cardiac muscles under exercise
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
76
What happens the PFK-2 in skeletal muscle in exercise
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
77
When is large amounts of lactate produced What happens to it after and why
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
78
During T2 diabetes what does adipose and skeletal muscle tissues produce in excess
Lactate Alanine Glycerol
79
Under normal circumstances how is gluconeogenesis controlled What happens in T2 diabetes
Via expression of PEPCK which is negatively regulated by insulin This is lost so PEPCK expression rises and glucose production rises adding to hyperglycaemia
80
What is metformin
T2 diabetes treatment | It suppresses gluconeogenesis
81
Give the other two names of the citric acid cycle
Krebs cycle | Tricarboxylic acid cycle
82
What conditions does the Krebs cycle occur under
Oxidative, taking place in the mitochondria
83
How NADH and FADH2 is generated in each cycle of the Krebs cycle What happens to these What else is produced
3NADH 1 FADH2 To generate ATP in oxidative phosphorylation GTP (which is readily converted unto ATP) and CO2
84
What must happen to pyruvate to start the Krebs cycle
Conversion to Acetyl - CoA which is catalysed by pyruvate dehydrogenase
85
Talk briefly about the structure of pyruvate dehydrogenase and the advantage of it
A complex of 3 enzymes | Co-localising these reduces side reactions and increases overall rate
86
What metabolic processes are in the mitochondria
Citrix acid cycle β oxidation Respiratory chain
87
Which metabolic processes are in the cytosol mostly
Enzymes of glycolysis The pentode phosphate pathway Fatty acid synthesis
88
What is the problem with the citric acid cycle
If we use the cycle to generate new compounds we lose carbon so an anaplerotic (filling up) pathway is needed
89
Give an equation for an anaplerotic pathway
Pyruvate+CO2+ATP+H2O—-> oxaloacetate + ADP + Pi+ 2H+
90
How much ATP is generates from oxidative glycolysis What if it is under anaerobic conditions
5ATP 2ATP
91
How many ATP are produced from the citric acid cycle
25
92
How much ATP is produced from aerobic respiration and the citric acid cycle
30 ATP
93
What are the two regulatory enzymes for PDH
PDH kinase deactivates | PDH phosphatase activates
94
What is PDH kinase inhibited by and why
Pyruvate Ensures PDH is ‘on’ when there’s lots of pyruvate
95
How is PDH phosphatase activated
Ca2+ and insulin in adipocytes Stimulates PDH during exercise and feeding
96
How is citrate synthase regulated
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
97
When is isocitrate dehydrogenase activated and inhibited
Inhibited: High NADH/NAD+ ratio and by ATP | StimulateD by ADP
98
When is α-ketoglutarate dehydrogenase activated and inhibited
Stimulated by Ca2+ | Inhibited by its products (succinyl CoA and NADH)
99
3 ways to measure the rate of the citric acid cycle
Monitoring O2 consumption with an O2 electrode Both carbon-14 and -13 experiments can be used to chase the label around the cycle fMRI
100
What does MRI rely on
``` Detecting hydrogen nuclei in water Paramagnetic substances (such As deoxyhaemoglobin) modify this signal ```
101
What does it mean to have a high oxidative glycolytic rate Where is this usually found
The rate of glycolysis is high despite O2 being present In tumours
102
Why do tumours generate energy by such an inefficient means as glycolysis when there is oxygen available??
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
What does the body initially burn for energy? When does it burn ‘fats’?
Sugars When utilisation outstrips supply
104
How are fats stored What are the other names for this Where is it stored
As triglycerides Neutral fats or triacylglycerols In adipocytes or in the liver
105
How are TAGs mobilised
Converted into glycerol and FFA by lipases, which hydrolyse Ester bonds to DAG then MAG and finally to FFA
106
How is hormone sensitive lipase HSL activated
Phosphorylation by protein kinase A
107
Where do FFA go In what proportion?
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
What is β oxidation Where does it occur
Oxidation of fats: it converts aliphatic fat into acetyl CoA for the citric acid cycle Mitochondria
109
What are the steps of β oxidation
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
How is the overall reaction of β oxidation made favourable
The PPi formed is hydrolysed to Pi
111
Where does activation of β oxidation occur What happens to the resulting product
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
What happens once the acyl-CoA is inside the mitochondrion
It is transferred back to CoASH in a reaction catalysed by acyltransferase 2 and the carnitine travels back out of the mitochondrion
113
Why is an activated fatty acid oxidised....
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
What is thiolysis How many times is it repeated
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
Give the structure of acetyl CoA
O || H3C-C-S-CoA
116
What is produced from β oxidation (3) and what processes do they contribute to
FADH2 and NADH (oxidative phosphorylation) | Acetyl-CoA (citric acid cycle)
117
How do mammals generate glucose from fat-derived acetyl CoA
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
What happens when oxaloacetate levels drop during gluconeogenesis
More acetyl CoA is produced than can be metabolised so ketone bodies are formed in the liver
119
What are the four FAD dependent acyl CoA dehydrogenases
Very long chain acyl CoA dehydrogenase Long chain “ “ “ Medium chain “”” Short chain “””
120
Why does oxidising fats require more O2 than for carbs
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
Why is MCAD a cause of cot death
Babies cannot oxidise fatty acids so readily and die at night when glycogen is depleted
122
What causes Jamaican vomiting sickness
Unripe ackee contains an inhibitor of acyl-CoA dehydrogenases, depleting glycogen supplies
123
What are the 3 ketone bodies
Acetoacetate β-hydroxybutyrate Acetone
124
What happens to acetoacetate in muscle mitochondria What about in liver
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
Can glycerol from TAGs be recycled?
Yes via gluconeogenesis
126
How is β oxidation regulated
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
Explain how re-esterification regulates β oxidation
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
What are GPATs
Reesterification enzymes
129
How is transport into the mitochondria controlled Why is it controlled
Carnitine shuttle is inhibited by malonyl-CoA (produces during fatty acid synthesis) In liver To prevent synthesis and degradation occurring alongside one another
130
What does malonyl CoA do in muscle
Mostly regulatory
131
Where are fatty acids >22 oxidised
In peroxisome Mitochondria cannot import such long chains
132
What is peroxisomal synthesis controlled by
Ligand induces transcription factors
133
What is a PPAR
Peroxisomal Proliferation Activated Receptors
134
What is the target of fibrate drugs
PPAR α These tackle hyperglycaemia
135
What does PPAR γ control
Adipogenesis and improves insulin sensitivity
136
What does PPAR δ
Expressed everywhere and drives fatty acid oxidation
137
Why is it easier to store fat than glycogen What does this mean for excess glycogen Where does this happen
Les what is necessary and fat is more energy rich Excess glycogen is converted to fat This happens in the mitochondria
138
Where are acetyl CoA and fatty acids synthesised
Acetyl CoA is in the mitochondria | Fatty acid is in the cytosol
139
What does fatty acid synthase do
Adds acetyl CoA to a growing strand of fatty acid | Reduces -CH2CO- to -CH2CH2-
140
How is acetyl CoA removed from the mitochondrion
It combines with oxaloacetate (C4) to make citrate (C6) and CoA Via the action of citrate synthase in the mitochondrion
141
What happen to citrate once is ends up in the cytosol
It reacts with ATP and CoA to form oxaloacetate and acetyl CoA
142
Which step in fatty acid synthesis is regulated and why Is it allosteric or hormonal regulation
Conversion of Acetyl CoA to Malonyl CoA using acetyl CoA carboxylase This is the rate limiting step Both
143
What causes acetyl CoA carboxylase to activate Inhibits?
Citrate (allosteric) and insulin (hormonal) Fatty acids (allosteric) and glucagon (hormonal)
144
How do insulin and glucagon control malonyl CoA
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
What does 5’AMP do for ACC
Increases phosphorylation of ACC via AMPK
146
What is 5’AMP important
It acts as a fuel gauge to mark the breakdown of ATP
147
Give the general equation to make a TAG Where does this occur
Fatty acid- CoA + glycerol-3-phosphate —-> TAG Liver, adipose and lactating mammary glands
148
Why is glucose needed to make TAGs from fatty acyl-CoA
A regular supply of glycerol 3 phosphate is needed from glycolysis
149
Where is amino acid metabolism most intensive
Liver where the urea cycle is focussed
150
What kind of amino acids does muscle tissue produce
Branched chain
151
How is the NH3 produced from amino acid metabolism captured
As glutamate and glutamine
152
How is nitrogen exported
As urea
153
Give the formula of urea
NH2CONH2
154
Why is urea ideal
It is water soluble, neutral, and ideal for detoxification
155
What transfers amino groups between amino acids
2-oxo acids via amino transferases
156
What is vitamin B6
Pyridoxal Phosphate | A prosthetic group of amino transferase, acting as a temporary parking spot for amine groups
157
What does alanine do
Carrier of ammonia and of the carbon skeleton of pyruvate from skeletal muscle to liver
158
How is glutamine formed
As excess ammonia is added to glutamate | Catalysed by glutamine synthase and requires ATP
159
What happens to glutamine
Is it exported to the liver where NH4+ is liberated by glutaminase
160
What does glutamate dehydrogenase do Why is this enzyme unusual How is it regulated
Releases Nitrogen from glutamate as NH3 via oxidative deamination It will use NAD+ or NADP+ Allosterically by GTP and ADP
161
What form is the nitrogen that is put into the urea cycle
Aspartate and ammonia
162
What’s wrong with Xs ammonia
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
Explain the chemiosmotic hypothesis
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
What do Cristae do in the mitochondria
Increase surface area
165
What does the PMF do
The proton motive force pumps protons uphill out of the mitochondrion
166
What are the two gradients the PMF works against
``` pH difference (courtesy of [H+]) Charge ```
167
Give the PMF equation
PMF=ΔΨ-(2.303RT/F)ΔpH
168
What is ΔΨ
Difference in charge
169
What must protons travel through as ATP is formed
ATP synthase
170
What measures oxygen consumption in the mitochondria
Oxygen electrode Mitochondria placed in buffer and oxygen electrode measures decrease in O2 level
171
When does O2 consumption increases in the mitochondria
When ADP is present Only then are protons allowed to flow across the membrane as oxygen is used to oxidise reducing agents
172
What do uncouplers do?
Promote H+ re-entry | When they are present, O2 is burnt without ATP being produced
173
Give examples of uncouplers
Ionophores | 2,4- dinitrophenol
174
Why can’t O2 be directly reduced to H2
It would be too explosive
175
How many supramolecular complexes exist in the e- transfer chain How are e shuttles between them
4 By ubiquinone and cytochrome C
176
What does QH2 do
Serves as a mobile carrier of e- and H+
177
How is ubiquinone adapted
Has a long lipophilic side chain to make it membrane soluble
178
How is Q reduced to QH2
Transports electrons from complex 1 and 2 to 3 | For complex 3 this involves H+ pumping using the Q cycle
179
What do cytochromes do
Transfer single e- by Fe2+/3+ redox
180
Where can different types of cytochrome be found
b and c1: complex 3 a and a3: complex 4 C: ferries e- from 3 to 4
181
For each complex give its donor
1: NADH 2: Succinate 3: reduced Q 4: reduced cytochrome c
182
For each complex give the acceptor
1: ubiquinone 2: ubiquinone 3: cytochrome c 4: O2
183
Discuss complex 1
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
Discuss complex II
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
How many protons are pumped out for each package of 2 e- that passes from NADH to oxygen? Show the maths
10 4 protons by complex 1 4 protons by Q 2 protons by complex 4
186
Discuss complex 3
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
What is the important role of complex 3 In apoptosis
It is released either via a pore or when mitochondria rupture as part of the apoptosis cascade that ultimately results in cell suicide
188
Describe the structure of cytochrome b in complex 3
Spans mitochondrial membrane | 2 harms at opposite sides of protein
189
Discuss complex 4
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
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Are the 4H+ pumped along proton wires used to make water in complex 4
No
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What happens if complex 4 is impaired
Alzheimer’s T2 diabetes Ageing
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What reaction does ATP synthase catalyse
ADP + Pi —-> ATP + water
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Describe the structure of ATP synthase
``` 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 ```
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What happens If F0 is separates from F1
It just hydrolyses ATP using water
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What blocks the F0 channel
Oligomycin
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How many subunits does F0 have What do these do
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
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How many protons are used for each ATP produced
3
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What are the 3 conformations that each site in complex 4 cycles through Give a brief description of each
Open - low affinity for ADP and P Loose - bonds ADP and P loosely Tight - squeezes out water
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Give the 3 steps involving L, T, and O sites
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
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2 ways to provide energy to drive metabolites through particular channels Give examples
Difference in charge or pH between compartments ATP and ADP exchange courtesy of charge Phosphate enters courtesy of pH
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What happens if rate of e- entry in the respiratory chain is greater than the rate of e- transfer through the chain
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
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Structure of aconitase
4Fe-4S protein
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What opposes formation of •OH
Reduced glutathione (GSH)
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What is the number one role of the liver in metabolism
A buffer of blood glucose
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What happens when 2ATPs are broken down? How can this be made more useful?
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
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What happens to lactate Why is it in different organs
It is taken to the liver Gluconeogenosis occurs generating more glucose for the muscles To avoid a futile cycle
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How are fatty acids released from adipose When
Hormone sensitive lipase or ATGL During endurance exercise
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How do you balance oxaloacetate if there is excess acetyl CoA
Convert isoleucine and valine to succinyl-CoA then oxaloacetate
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What is the ‘wall’ in endurance exercise Why
Depletion of glycogen It is priming TCA cycle
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What inhibits hexokinase
Raised G6P
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How is AMPK turned on What does AMPK do
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
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What is marasmus
Deficiency in calories
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Kwashiorkor
Exclusively carb diet with severe protein deficiency in children
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3 negative effects of obesity
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
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What are some consequences of the metabolic alterations in muscle due to insulin resistance (4)
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
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Give the benefits of exercise
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
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What is necessary for synthesis of ATP from ADP and Pi in the mitochondrial matrix
The entry of H+ from the inter membrane space
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Does β oxidation involve cleavage of a phosphoanhydride bond? What about synthesis of fatty acids from acetyl CoA and malonyl CoA
No No
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Can ketogenic amino acids contribute nitrogen to the urea cycle
Yes
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Which micronutrient is needed for maintaining cell membrane integrity
Vitamin E
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Name 1 thing that activates pyruvate carboxylase
Acetyl CoA
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What is activated in response to PIP3
PKD
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What kind of receptor is the glucagon receptor
A GPCR
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Name an intermediate in both the TCA cycle and gluconeogenesis
Oxaloacetate
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How does F-2,6-B affect PFK-1
Increases PFK-1 activity, driving glycolysis
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How is PDH affected by NADH and acetyl CoA
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
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What inhibits complex 3
Antimycin
228
What is the pathway for the effect of adrenaline on glycogen
Adrenaline->cAMP->PKA->inhibits glycogen synthase and activates phosphorylase kinase (which activates glycogen phosphorylase)
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What is the intermediate between G-1-P and glycogen in glycogen synthesis
UDP-glucose using glycogen synthase
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How does insulin encourage glycogen formation
Inhibits Glycogen Synthase Kinase 3, allowing glycogen synthase to become active
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How is pyruvate concerted back to phosphoenolpyruvate (PEP) in gluconeogenesis? Do they use ATP?
Converted to oxaloacetate (by pyruvate carboxylase) - Uses ATP Then oxaloacetate is converted to PEP by PEP carboxykinase - uses GTP
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Name a metabolic Conversion that doesn’t involve cleavage of a phosphoanhydride bond
Fatty acid synthesis from acetyl CoA and malonyl CoA
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Name a substance that actives pyruvate carboxylase
Acetyl CoA
234
Name a micronutrient that is involved in maintaining the integrity of cell membranes
Vit E
235
Which kinase is activated by PIP3
PKB
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Which metabolic receptor is a GPCR
Glucagon receptor
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Which experimental approach should be used to identify all of the DNA binding site for a specific DNA binding protein in the genome
ChIP
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What does PDH do What controls PDH
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
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What does citrate synthase do How is it controlled
Converts Acetyl CoA and OAA to citrate Inhibited by citrate and allosterically inhibited by ATP
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How is isocitrate dehydrogenase controlled What does it do
Inhibited by high NADH and ATP Stimulated by ADP and Ca2+ Converts Isocitrate and NAD to α ketoglutarate and NADH
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What does α ketoglutarate do How is it controlled
α ketoglutarate and NADH to succinyl CoA and NADH Inhibited by high NADH and succinyl CoA Stimulated by Ca2+
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What are all the TCA cycle dehydrogenases inhibited and stimulated by
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
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What causes inactivation of HSL
De phosphorylation (P naturally falls off over time)
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Why is carnitine needed
CoA cannot pass mitochondrial membrane
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What converts acyl-CoA to acyl-carnitine? Where is this found
Carnitine acyl transferase 1 Physically bound to the outer mitochondrial membrane
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How does acyl-carnitine enter the mitochondria
Down its concentration gradient through a channel called translocase
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How is acyl carnitine converted to acyl CoA Where is this found
Carnitine acyl transferase II Free in the mitochondria
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Where is cytochrome c found
Loosely associated with the INNER membrane of the mitochondrion
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How is PKA activated
When cAMP binds to the regulatory subunits of PKA, the catalytic subunits dissociate and become active