Bioenergetics Flashcards
(249 cards)
1
Q
What are the standard conditions for ΔG
A
pH 7
One atmosphere
298K
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
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
4
Q
What is phosphorylation potential
A
The free energy of ATP hydrolysis
5
Q
What is the ATP turnover in humans during exercise
A
0.5kg/min
6
Q
What is ATP often buffered by in mammals
A
Phosphocreatine
7
Q
Give 3 examples of ATP hydrolysis
A
- Phosphorylate glucose to provide enough energy to prime the molecule to be broken down to pyruvate
- Peptides are unstable thermodynamically so ATP can be used to build long chains
- To join 2 nucleic acids at the start of DNA synthesis
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
9
Q
What do biotin and uridine diphosphate glucose carry respectively
A
B: CO2
UDG: glucose
10
Q
What is the main redox system for energy producing pathways
What is it for biosynthesis
A
NAD+/NADH
NADP+/NADPH
11
Q
What does the phosphate group act as in NADP+
A
A tag allowing recognition of this redox system by biosynthetic enzymes
12
Q
What does Coenzyme A provide
A
The activated form of acetate
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
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
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
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
17
Q
Why is adipose tissue important for fuel economy
A
Fat storage and energy store
Secretes hormones etc
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
19
Q
What are the beginning and end products of gluconeogenesis
A
Pyruvate to glucose-6-phosphate
20
Q
What are the beginning and end products of glycolysis
A
Glucose 6 phosphate to pyruvate
21
Q
What are the beginning and end products of glycogen synthesis
A
Glucose 1 phosphate to glycogen
22
Q
What are the beginning and end products of fat synthesis
A
Acetyl CoA to fatty acid
23
Q
What are the beginning and end products of glycogen breakdown
A
Glycogen to glucose 1 phosphate
24
Q
What are the beginning and end products of fat breakdown
A
Glycogen to glucose-1-phosphate
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
190
Are the 4H+ pumped along proton wires used to make water in complex 4
No
191
What happens if complex 4 is impaired
Alzheimer’s
T2 diabetes
Ageing
192
What reaction does ATP synthase catalyse
ADP + Pi —-> ATP + water
193
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
```
194
What happens If F0 is separates from F1
It just hydrolyses ATP using water
195
What blocks the F0 channel
Oligomycin
196
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
197
How many protons are used for each ATP produced
3
198
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
199
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
200
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
201
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
202
Structure of aconitase
4Fe-4S protein
203
What opposes formation of •OH
Reduced glutathione (GSH)
204
What is the number one role of the liver in metabolism
A buffer of blood glucose
205
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
206
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
207
How are fatty acids released from adipose
When
Hormone sensitive lipase or ATGL
During endurance exercise
208
How do you balance oxaloacetate if there is excess acetyl CoA
Convert isoleucine and valine to succinyl-CoA then oxaloacetate
209
What is the ‘wall’ in endurance exercise
Why
Depletion of glycogen
It is priming TCA cycle
210
What inhibits hexokinase
Raised G6P
211
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
212
What is marasmus
Deficiency in calories
213
Kwashiorkor
Exclusively carb diet with severe protein deficiency in children
214
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
215
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
216
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
217
What is necessary for synthesis of ATP from ADP and Pi in the mitochondrial matrix
The entry of H+ from the inter membrane space
218
Does β oxidation involve cleavage of a phosphoanhydride bond?
What about synthesis of fatty acids from acetyl CoA and malonyl CoA
No
No
219
Can ketogenic amino acids contribute nitrogen to the urea cycle
Yes
220
Which micronutrient is needed for maintaining cell membrane integrity
Vitamin E
221
Name 1 thing that activates pyruvate carboxylase
Acetyl CoA
222
What is activated in response to PIP3
PKD
223
What kind of receptor is the glucagon receptor
A GPCR
224
Name an intermediate in both the TCA cycle and gluconeogenesis
Oxaloacetate
225
How does F-2,6-B affect PFK-1
Increases PFK-1 activity, driving glycolysis
226
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
227
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)
229
What is the intermediate between G-1-P and glycogen in glycogen synthesis
UDP-glucose using glycogen synthase
230
How does insulin encourage glycogen formation
Inhibits Glycogen Synthase Kinase 3, allowing glycogen synthase to become active
231
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
232
Name a metabolic Conversion that doesn’t involve cleavage of a phosphoanhydride bond
Fatty acid synthesis from acetyl CoA and malonyl CoA
233
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
236
Which metabolic receptor is a GPCR
Glucagon receptor
237
Which experimental approach should be used to identify all of the DNA binding site for a specific DNA binding protein in the genome
ChIP
238
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
239
What does citrate synthase do
How is it controlled
Converts Acetyl CoA and OAA to citrate
Inhibited by citrate and allosterically inhibited by ATP
240
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
241
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+
242
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
243
What causes inactivation of HSL
De phosphorylation (P naturally falls off over time)
244
Why is carnitine needed
CoA cannot pass mitochondrial membrane
245
What converts acyl-CoA to acyl-carnitine?
Where is this found
Carnitine acyl transferase 1
Physically bound to the outer mitochondrial membrane
246
How does acyl-carnitine enter the mitochondria
Down its concentration gradient through a channel called translocase
247
How is acyl carnitine converted to acyl CoA
Where is this found
Carnitine acyl transferase II
Free in the mitochondria
248
Where is cytochrome c found
Loosely associated with the INNER membrane of the mitochondrion
249
How is PKA activated
When cAMP binds to the regulatory subunits of PKA, the catalytic subunits dissociate and become active
