The roles of ATP in living cells and the mechanisms of production of ATP Flashcards
1
Q
Define metabolism
A
Metabolism: integrated set of enzymatic reactions comprising both anabolic and catabolic reactions
2
Q
Define anabolism and catabolism
A
Anabolism: synthesis of complex molecules from simpler ones (necessary energy usually derived from ATP)
Catabolism: breakdown of energy- rich molecules to simpler ones (CO2 H2O and NH3)
3
Q
How is energy released from catabolism?
A
(energy released is ‘captured’ as adenosine triphosphate (ATP) and stored for later use in anabolic reactions
4
Q
Which processes make up metabolism?
A
Anabolism: synthetic reactions - the pathways end in ‘genesis’ e.g. glycogenesis (synthesis of glycogen from glucose)
Catabolism: breakdown reactions - the pathways end in ‘lysis’ e.g. glycolysis (breakdown of glucose to pyruvate)
5
Q
What is energy required for?
A
§Motion (muscle contraction)
§Transport (of ions/molecules across membranes)
§Biosynthesis of essential metabolites
§Thermoregulation
6
Q
Why is stored energy needed?
A
Timing of these energy-requiring processes does not necessarily coincide with feeding times so storage forms of food are required
7
Q
What is an isothermal system?
A
- Cells are isothermal systems
- Heat flow cannot be used as a source of energy (heat can only do work when it passes to an area or an object at a lower temperature)
- Free energy (energy available to perform work) is acquired from nutrient molecules
8
Q
Define
Gibbs free energy
Enthalpy
Entropy
A
- Gibbs free energy (G) – energy capable of doing work at constant temperature and pressure
- Enthalpy (H) – the heat content of the reacting system
- Entropy (S) – the randomness or disorder in a system
9
Q
What is the gibbs free energy equation?
A
10
Q
What is the gibbs free energy of a reaction?
A
Gibbs free energy of a reaction – maximum energy that can be obtained from a reaction at constant temperature and pressure
11
Q
For the reaction A -> B
State what will happen if -
If greater concentration of B than A at equilibrium:
If greater concentration of A than B at equilibrium:
A
12
Q
What is an exogernic reaction?
A
Products have less free energy than reactants and so are more stable than the reactants. Formation of product is “downhill” (spontaneous)
13
Q
What is an endogernic reaction?
A
Products have more free energy than reactants and so are less stable than the reactants. Formation of product is ‘uphill’
14
Q
What kind of reaction is this and is the gibbs free energy positive or negative?
A
15
Q
What kind of reaction is this and is the gibbs free energy positive or negative?
A
16
Q
What is coupling of reactions?
A
An endergonic reaction can be driven in the forward direction by coupling it to an exergonic reaction through a common intermediate
17
Q
How would these reactions be coupled?
A
18
Q
What is the role of ATP?
A
- ATP provides most of the free energy required for anabolism
- ATP is the energy currency of the cell
19
Q
What is gibbs free energy in relation to ATP?
A
•Gibbs free energy: the energy derived from the oxidation of dietary fuels to generate ATP
20
Q
Energy is conserved as _____ and is transduced into useful work
A
ATP
21
Q
Complete the diagram on the structure of ATP
A
22
Q
What is the role of Mg2+ in ATP?
A
- ATP in the cytosol is present as a complex with Mg2+
- Mg2+ interacts with the oxygens of the triphosphate chain making it susceptible to cleavage in the phosphoryl transfer reactions
23
Q
What is the result of a Mg2+ deficiency?
A
A Mg2+ deficiency impairs virtually all metabolism
24
Q
Label the compounds
A
25
What is Substrate level phosphorylation (SLP)?
* Formation of ATP by phosphate group transfer from a substrate to ADP
* Known as SLP to distinguish it from respiration-linked phosphorylation
26
How is the difference between substrate level phosphorylation and respiration-linked phosphorylation?
* SLPs require soluble enzymes and chemical intermediates
* Respiration-linked phosphorylations involve membrane-bound enzymes and transmembrane gradients of protons and require oxygen
27
Label the diagram on substrate level phosphorylation
28
What are enzymes and how do they work?
* Biological catalysts that accelerate the rate of chemical reactions
* Creates a new pathway for the reaction; one with a lower activation energy
29
Draw an energy profile with and without a catalyst
30
Do enzymes change the gibbs free energy?
31
Complete the table on enzyme classification
32
What are cofactors?
•Cofactors are non-protein molecules necessary for enzyme activity e.g. metal cations
33
What are coenzymes?
•Most coenzymes are organic molecules derived from vitamins
34
What is the role of coenzymes and cofactors?
* Participate in enzymatic reactions
* Cycle between oxidised and reduced forms
35
Complete the diagram on types of cofactors
36
How do coenzymes/cosubstrates work?
Have a loose association with their enzyme
Diffuse between enzymes carrying e-
37
What are prosthetic groups?
* Non-protein cofactor that is covalently bound to the enzyme
* Not released as part of the reaction
* Acts as a temporary store for e- or intermediates
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39
40
Name 2 vitamin precursers of imporant coenzymes/cofactors/prosthetic groups
B2 (Riboflavin)
Niacin
41
Complete the table on vitamin precursers
42
What are the major redox coenzymes/prosthetic groups?
•Major redox coenzymes/prosthetic groups involved in transduction of energy from dietary foods to ATP: NAD+ / FAD / FMN
43
How do redox coenzymes/prosthetic groups work?
* Electrons are transferred from dietary material to these carriers -\> coenzymes are reduced
* In each case two electrons are transferred but the number of H+ moved varies
e.g. NAD+ is reduced to NADH
FAD is reduced to FADH2
44
What is the role of Nicotinamide adenine dinucleotide (NAD+)?
NAD+ and NADP+ accept pairs of electrons to form NADH or NADPH
It is the nicotinamide that is the functional part of the molecule
i) NADH for ATP synthesis
ii) NADPH for reductive biosyntheses
45
What is the reduced and oxidised form of Nicotinamide adenine dinucleotide (NAD+)?
46
How does Re-oxidation of redox coenzymes occur?
* Recycling of NADH and FADH2 is via the respiratory chain in the mitochondria
* This is coupled to ATP synthesis - process of oxidative phosphorylation
47
Where does this happen?
48
Where does glycolysis occur?
Cell cytoplasm
49
Complete the diagram
50
Each reaction from G-3-P occurs ______ for every glucose molecule metabolised
Each reaction from G-3-P occurs twice for every glucose molecule metabolised
51
SLP: substrate level phosphorylation
52
Label the diagram of glycolysis
53
What reaction happens at the priming stage?
Priming stage
- uses 2 ATP and produces two C3 molecules which are interconvertible:
DHAP⇄ GAP
54
What is produced from the payoff stage?
Payoff stage
- generates 4 ATP and 2 NADH and various intermediates
55
56
What are the 2 possible fates of pyruvate?
* Under aerobic conditions, oxidation and complete degradation
* In hypoxic conditions, it can be reduced to lactate
57
58
Why has this system of lactate production evolved?
To allow glycolysis to continue in anaerobic conditions by oxidising NADH to NAD+ for use in glycolysis
59
What are the 4 roles of pyruvate in metabolism?
60
What happens to pyruvate under aerobic conditions?
•Under aerobic conditions, conversion to acetyl-CoA for oxidation and complete degradation
61
Where is pyruvate converted to acetyl-CoA?
* Where? In the mitochondria
* Glycolysis occurs in the cytosol (and can proceed in the presence and absence of O2) SO pyruvate is transported into the mitochondria for complete oxidation
62
Which mitochondrial membrane is selectively permeable?
IMM is highly selectively permeable
63
64
How does Transport of pyruvate into the mitochondrion occur?
* Occurs via specific carrier protein embedded in the mitochondrial membrane in aerobic conditions
* Pyruvate undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex to form Acetyl CoA:
65
How is pyruvate converted to acetyl CoA?
Pyruvate converted to acetyl-CoA by the PDH complex: consists of 3 enzymes and 5 coenzymes
66
Pyruvate either gets turned into _____ or enters \_\_\_\_\_
Lactate
Mitochondria
67
What is the Tricarboxylic acid (TCA) cycle?
* Also known as ‘citric acid’ or ‘Krebs’ cycle
* Final common pathway for the oxidation of fuel molecules
68
What happens in the TCA cycle?
* In 8 steps, acetyl residues (CH3-CO-) are oxidised to CO2
* Reducing equivalents transferred to NAD+ or FAD to form NADH and FADH2
A 4-carbon unit condenses with a 2-carbon unit. Eventually, 2 carbons leave the cycle as CO2 and the 4-C unit is regenerated.
69
Complete the diagram on the TCA cycle
70
The TCA cycle involves 4 _______ reactions (\_\_\_\_\_\_ & ______ production) and one molecule of ______ is produced directly for each round of the cycle.
Involves 4 oxidation-reduction reactions (NADH & FADH2 production) and one molecule of ATP is produced directly for each round of the cycle
71
Label the TCA cycle
72
What is a mnemonic to remember the TCA cycle?
After Class I Keep Some Specific Facts More Or-less
Acetyl CoA, Citrate, Isocitrate, a-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, Oxaloacetate
73
What are the 9 enzymatic steps in the TCA cycle?
74
Which enzyme in the TCA cycle is also part of the respiratory chain complex?
succinate dehydrogenase
Also part of the respiratory chain (complex II)
75
Label the enzyme used in each enzymatic step of the TCA cycle
76
Flow of carbon atoms from pyruvate into and through the TCA cycle is tightly regulated at which 2 levels?
1. Conversion of pyruvate to acetyl-CoA (PDH reaction)
2. Entry of acetyl-CoA into the TCA cycle (citrate synthase reaction)
77
How is the TCA cycle regulated?
•Flow of carbon atoms from pyruvate into and through the TCA cycle is tightly regulated at 2 levels:
1. Conversion of pyruvate to acetyl-CoA (PDH reaction)
2. Entry of acetyl-CoA into the TCA cycle (citrate synthase reaction)
•Also regulated at isocitrate dehydrogenase and a-ketoglutarate dehydrogenase reactions
78
What happens at regulatory points of the TCA cycle?
These reactions are irreversible and the main regulatory points
79
Which reactions are irreversible and the main regulatory points?
80
What other compounds feed into the TCA cycle?
Fatty acids and some amino acids can be a source of Acetyl-CoA
81
Why are Concentrations of TCA intermediates in dynamic balance?
Components of the TCA cycle are important biosynthetic intermediates - needed for other functions as well elsewhere in the cell but must be replenished for the TCA cycle.
Replenished by anaplerotic reactions (red arrows)
82
What does the red arrows represent?
TCA cycle components replenished by anaplerotic reactions (red arrows)
83
Complete the diagram on the products of the TCA cycle
84
What are the products of the TCA cycle?
Energy released from oxidations is conserved in the production of:
3 NADH, 1 FADH2, 1 GTP (ATP)
2 CO2 also produced
85
What are the products of glycolysis and the TCA cycle?
Glycolysis: pyruvate and NADH
TCA cycle: 3 NADH, 1 FADH2, 1 GTP (ATP)
86
How is the NADH produced from glycolysis oxidised?
NADH and FADH2 are oxidised by the mitochondrial ETC
BUT:
* The inner mitochondrial membrane is impermeable to NADH!
* There is no carrier in the membrane to transport it across
SO Electrons from NADH enter mitochondria via shuttles
87
What are the 2 shuttles that electrons from NADH use to enter mitochondria?
1. The glycerol-3-phosphate shuttle, especially prevalent in brain and muscle
2. The malate-aspartate shuttle, in liver and heart
88
What is the role of the shuttles which transport electrons from NADH into mitochondria?
Both shuttles act to regenerate NAD+ and make 1.5 or 2.5 moles of ATP
89
Complete the diagram on the the glycerol-3-phosphate shuttle in brain and muscle
90
Complete the diagram on the the malate-aspartate shuttle in liver and heart
91
Complete the diagram of a mitochondria
92
What is the difference in permeability between the outer and inner mitochondrial membrane?
Outer membrane - Freely permeable to small molecules and ions
Inner membrane - Impermeable to small molecules and ions, including H+
93
Where is the Location of electron transfer chain?
Inner mitochondrial membrane
94
What is the electron transport chain?
•Comprises four large multi-unit proteins intrinsic to the inner mitochondrial membrane
95
What is the role of the electron transport chain?
•Catalyse a series of reactions:
NADH + H+ + 1/2O2 = NAD+ + H2O
•Energy released from this reaction not released as heat but tightly coupled to the production of ATP
96
What are the componenets of the electron transport chain?
Four components: Complex I, II, III and IV
These are linked by 2 soluble proteins
1. Ubiquinone (coenzyme Q) – a lipid soluble benzoquinone with a long isoprenoid tail
2. Cytochrome c
These are free to move in the membrane by diffusion (they are not part of the complexes)
97
Complete the table on the protein components of electron chain complexes
98
Complete the diagram of the electron transport chain
99
100
What is complex I?
Complex I. NADH dehydrogenase
• It is a proton pump, moving protons from the matrix into the intramitochondrial space
101
What happens at complex I?
* Initially electrons are passed to FMN to produce FMNH2
* Subsequently transfer to a series of iron-sulphur clusters
* Then transfer to Coenzyme Q (ubiquinone)
102
What reaction happens at complex I?
•So, the enzyme catalyses the overall reaction:
NADH + H+ + Q = NAD+ + QH2
103
104
What is complex II?
Complex II. Succinate dehydrogenase
105
What happens at complex II?
* FAD within complex II is reduced to FADH2 by electrons gained from the conversion of succinate to fumarate in the TCA cycle
* Complex II passes electrons to ubiquinone
* Other substrates for mitochondrial dehydrogenases also pass on their electrons to ubiquinone but not through complex II – e.g. from the G-3-P shuttle
106
What are the sources of electrons entering the ETC?
107
108
What is complex III?
* Ubiquinone:cytochrome c oxidoreductase
* Second of three proton pumps in the respiratory chain
109
What is complex IV?
* Cytochrome oxidase
* Third and final proton pump
110
What does complex IV do?
* Carries electrons from cytochrome c to molecular oxygen
* Produces water
111
Draw the flow of electrons through the ETC
112
What is the purpose of the ETC?
Purpose of the whole process!
113
What is the equation for ATP production?
114
How is ATP transported in the mitochondria?
Inner mitochondrial leaflet is generally impermeable to charged species, BUT
3 specific systems in this membrane that:
1. Transport ADP and Pi into the matrix
2. Synthesise ATP
3. Transport ATP into the cytosol
115
What is Adenine nucleotide translocase?
* Integral protein of the inner mitochondrial membrane
* Known as an ‘antiporter’
116
What is this?
Adenine nucleotide translocase
117
How does adenine nucleotide translocase work?
* Transports ADP3- from the intramitochondrial membrane space into the matrix
* In exchange for an ATP4- molecule transported in the other direction (Favoured by the electrochemical gradient generated by proton pump)
118
What is an inhibitor of adenine nucleotide translocase?
Atractyloside, a glycoside isolated from a thistle, is a specific inhibitor of adenine nucleotide translocase
119
What is Phosphate translocase?
A second membrane transporter is essential for oxidative phosphorylation and synthesis of ATP
120
What is this?
Phosphate translocase
121
How does Phosphate translocase work?
Transports both phosphate and hydrogen ions into the matrix: a ‘symporter’
(favoured by the transmembrane proton gradient)
122
What is ATP synthase?
An F-type ATPase
123
What is ATP synthase made up of?
Two functional domains
1. Fo, an oligomycin-sensitive proton channel
2. F1, an ATP synthase
124
What is this?
ATP synthase
125
Label the transporters in the inner mitochondrial membrane
1. Phosphate translocase
2. ATP synthase
3. Adenine nucleotide translocase
126
What is the structure of ATP synthase?
* Fo comprises three different types of subunit: a, b, and c
* Forms a complex of 13-15 subunits
* Subunits c1-10 arranged in a circle
* F1 comprises five different types of subunit: a3, b3, g, d, and e
* Forms a complex of 9 subunits
The 3 b subunits have catalytic sites for ATP synthesis
127
Label the subunits of ATP synthase
128
How are the subunits in ATP synthase arranged?
129
What is the theory of rotational catalysis?
•3 β subunits take it in turns catalysing the synthesis of ATP
130
How does the theory of rotational catalysis work?
* Any given b subunit starts in a conformation for binding ADP and Pi
* Then changes conformation so the active site now binds the product ATP tightly
* Then changes conformation to give the active site a very low affinity for ATP (‘b-empty’ conformation) so ATP is released
131
What causes the properties of the b-catalytic unit to change?
132
What equation summarises the energy changes?
133
Summarise the energy changes in the ETC
* Energy released is coupled to the movement of H+ across the inner membrane
* Electrochemical energy generated represents temporary conservation of the energy of electron transfer
* Protons flow spontaneously down their electrochemical gradient releasing energy available to do work
134
What is the equation of respiration?
135
Complete the table on the products of respiration
136
How does uncoupling reagents work?
* Normally e- flow and phosphorylation of ADP are tightly coupled
* Uncouplers dissipate the pH gradient by transporting H+ back into the matrix of the mitochondria so bypassing the ATP synthase
* Thus an uncoupler (e.g. DNP) severs the link between e- flow and ATP synthesis, with the energy being released as heat
137
Where does uncoupling reagents happen naturally?
•Can occur naturally e.g. UCP1 (thermogenin) is found in brown adipose tissue and has a specific H+ channel through which the [H+] may be dissipated - energy released as heat
138
What are the features of brown adipose tissue?
* High numbers of mitochondria
* Mitochondria contain thermogenin (UCP-1)
* Specialized for heat generation
139
Which clinical scenarios is brown adipose tissue relevant for?
Important in new-borns, possible role in obesity/diabetes
140
What does this show?
Uncoupling and brown fat thermogenesis
141
What is DNP?
DNP – an exogenous uncoupler
•Weak acid that crosses membranes 'ferrying' H+ across
142
How does DNP work?
* Each DNP molecule collects a proton from the IMS (intermembrane space) and moves through the membrane with it, depositing it in the matrix
* Can then return though the membrane to collect another proton
143
What are the applications of DNP?
DNP achieved notoriety in the 1930’s in USA as a slimming drug with
disastrous results - several people died through overdosing on DNP
* 2013 - a medical student at Leeds suffering with bulimia took 2,4-DNP as a weight-loss aid with disastrous results
* 62 deaths due to DNP reported in the medical literature including body builders and slimmers (latest was a body builder in December 2017)
144
How does DNP overdose kill you?
• Toxicity arises from liver damage, respiratory acidosis and hyperthermia
145
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