Metabolism Flashcards
Lectures 21-26 (Declan Doyle)
1
Q
What is the meaning of catabolic?
A
A reaction that releases energy.
2
Q
What is the meaning of anabolic?
A
A reaction that uses energy.
3
Q
What are the two functions of the oxidative catabolism of glucose?
A
- Production of ATP
- Production of intermediates from glycolysis and TCA cycle (for other metabolic pathways)
4
Q
What is the equation for Gibbs free energy?
A
Enthalpy - temperature x entropy (ΔH-TΔS)
5
Q
What is ΔG∘’?
A
Gibbs free energy at pH 7, also known as gibbs free energy during reactions.
6
Q
What is ΔG∘?
A
Gibbs free energy at pH 0.
7
Q
What does a negative ΔG∘ tell you about a reaction?
A
Reaction is exergonic meaning free energy is released during it.
8
Q
What does a positive ΔG∘ tell you about a reaction?
A
The reaction is endergonic and free energy is absorbed during it.
9
Q
What is Kc?
A
An equilibrium constant, otherwise known as the ratio of concentration of products to reactants.
10
Q
What does a small Kc tell you about a reaction?
A
It lies to the left, meaning the reactants are much smaller than the products.
11
Q
What is the Van’t Hoff Isotherm equation?
A
ΔG = ΔG∘’ + R(Gas constant)T InQ
12
Q
What is the Van’t Hoff Isotherm used for?
A
It can be used to predict if a reaction is spontaneous or not.
13
Q
What are the two things the ΔG is dependant on?
A
Constant term: Value depends only on if reaction happens or not.
Variable term: Dependent on concentrations of reactants and products.
14
Q
What is the importance of ΔG being additive?
A
Throughout a metabolic pathway, ΔG of any one reaction can be positive and the pathway can still occur as long as the overall ΔG is negative.
15
Q
Why are metabolic pathways irreversible?
A
They are highly exergonic so the reverse would be highly endergonic which doesnt work.
16
Q
What is feedback inhibition and how does it prevent metabolic pathways?
A
It is when the product of a pathway stops the pathway occurring again by switching on/off the gene for the first enzyme, so not too much product is made.
17
Q
Why is glycolysis irreversible?
A
It has a large positive ΔG.
18
Q
What is the first main step of glycolysis?
A
D glucose → Glucose 6 Phosphate (via Hexokinase reaction that requires ATP)
19
Q
What is the second main step of glycolysis?
A
Fructose 6 phosphate → Fructose 1,6 Biphosphate (via phosphofructokinase that requires ATP)
20
Q
What s the third main step of glycolysis?
A
PEP → Pyruvate (Via pyruvate kinase that requires ATP)
21
Q
What is a cofactor?
A
A non protein component of an enzyme.
22
Q
What is a coenzyme?
A
An organic cofactor.
23
Q
What is oxidation?
A
A loss of electrons/hydrogen. Results in many C-O bonds and lower potential energy.
24
Q
What is reduction?
A
Gain of electrons and hydrogen. Results in many C-H bonds and higher potential energy.
25
Are phosphorylation reactions ender or exogonic?
They are endergonic. They are also irreversible because to take the phosphate and add it to ADP is highly endergonic.
26
What are the 3 reasons the kJ/mol from glucose isn't simply released as heat?
1. Biological systems do not utilise heat as a source of energy.
2. No single energy requires that much energy to be released.
3. The activation energy needs to be overcome and enzymes only act on small changes
27
How is glucose energy released?
Glucose is catabolised in small steps and energy is released in usable bouts of ATP. These are 30kJ/mol.
28
What is ATP coenzyme used for?
Phosphate transfer.
29
What is NAD+/NADH used for?
Oxidation/reduction
30
What is the use of glycerol?
Readily metabolised into an intermediate glycolysis. Either converted into pyruvic acid or used in gluconeogenesis.
31
What is the first of ten steps of glycolysis?
Facilitated diffusion via transport proteins, moving from a high to low concentration of glucose.
- Needs no energy
32
What is the second of ten steps of glycolysis? Is this reversible?
G6P → F6P via phosphoglucose isomerase.
- Done because it needs to phosphorylate a hydroxyl group so that after lysis both 3 carbons are phosphorylated.
- Reversible.
33
What is the third of ten steps of glycolysis? Is this reversible?
F6P → F-1,6-Biphosphate via phosphofructokinase.
- Two phosphate groups added.
- Irreversible
34
What is the fourth of ten steps of glycolysis? Is this reversible?
F-1,6-BP → DHAP and GAP via aldolase.
- Reversible.
35
What is the fifth of ten steps of glycolysis? Is this reversible?
DHAP → GAP via triose phosphate isomerase.
- Reversible
36
What is the sixth of the ten steps of glycolysis? Is this reversible?
Gap ↔ 1,3BP via GAP hydrogenase.
- Uses NAD⁺ or NADH + H⁺
- Reversible
- Oxidation step, converting an aldehyde to a carboxylic acid.
37
What is the seventh of the ten steps of glycolysis? Is this reversible?
1,3BP ↔ 3 phosphoglycerate via phosphoglycerate kinase.
- Uses ADP or ATP as it is reversible.
- Acid from phosphate leads to greater negative ΔG.
38
What is the eighth of the ten steps of glycolysis? Is this reversible?
3P (Phosphoglycerate) ↔ 2P via phosphoglycerate mutase.
- Reversible.
- Not exergonic enough to produce ATP.
39
How is 2P transformed into PEP in Glycolysis?
| 2P = 2 phosphoglycerate
PEP = Phosphoenol Pyruvate
2 Phosphoglycerate ↔ Phosphoenol pyruvate via enolase.
- Reversible, H₂O produced when forward.
- Highly exergonic.
40
Why is the ninth step of glycolysis so exergonic?
The phosphoryl group traps the molecule in an unstable enol (alkaline with hydroxyl group) form.
- Enol converts into more stable ketone (pyruvate)
41
What is the tenth of the ten steps of glycolysis? Is this reversible?
Phosphoenol pyruvate → pyruvate via pyruvate kinase.
- Produces ATP
- Irreversible
42
What are the two types of coenzymes?
Apoenzyme: Becomes active by binding of coenzymes to enzyme
Holoenzyme: Formed when associated cofactor binds to enzymes active site.
43
What happens to pyruvate in aerobic conditions?
Enters the mitochondria via the porins and MPC, to be consumed in the TCA cycle.
There is enough NAD+ for this because of the electron transport chain.
44
What happens to pyruvate in anaerobic conditions?
- No NAD+ :(
- Converted into stuff like lactate. All of it has to be converted for ATP synthesis to continue.
45
Where does glycolysis take place in prokaryotic and eukaryotic cells?
Both in the cytoplasm.
46
Where does the TCA cycle take place in prokaryotic and eukaryotic cells?
Prokaryotic: Cytoplasm
Eukaryotic: Mitochondria
47
Where does ETC take place in prokaryotic and eukaryotic cells?
Prokaryotic: Cell membrane
Eukaryotic: Mitochondrial membrane
48
Why do eukaryotes separate glycolysis and TCA but prokaryotes don't?
Eukaryotes are huge compared to prokaryotes and therefore don't rely on diffusion so they are compartmentalised. One TCA enzyme is an integral membrane protein so cell has to select 1 membrane (close between TCA and ETC)
49
How is pyruvate transported in the mitochondria?
- MPC (Mitochondrial pyruvate carrier)
Enters through pores, through intermembrane space, into outer then inner membrane and then through MPC.
50
How is NADH transported in the mitochondria?
No specific transporter needed, porins allow NADH access to the inter mitochondrial space.
51
Describe the link reaction.
Pyruvate → Acetyl CoA. Uses enzyme pyruvate dehydrogenase complex, which produces NADH and CO2 out of NAD+ and CoA-SH.
52
What is CoA?
A coenzyme. It carries acetyl to active sites.
- It is a thiol (Have SH) and can react with carboxylic acid to form thioesters.
- Used in synthesis of fatty acids when there is excess glucose
- Contains unit of ADP
53
What evidence is there for mitochondria being derived from symbiotic bacteria?
- Bacillus rod shape
- Both replicate via fission
- Both contain circular DNA plasmids
- Mitochondrial ribosomes are more similar to bacterial ribosomes than ours, same with their membrane proteins.
54
What is a prosthetic group?
A tightly bound non polypeptide unit required for enzyme activity.
55
What is the point of an enzyme complex?
Speeds up reactions because the products of a reaction can continue to the next one without having to go through diffusion. Also prevents other unfavourable reactions.
56
How is Citrate produced in the TCA cycle?
## Footnote
1st Step
Oxaloacetate and Acetyl → Citrate via citrate synthase.
- Produces CoA-SH.
- Irreversible due to very negative ΔG'∘.
57
How is Citrate transformed into Isocitrate in the TCA cycle?
## Footnote
2nd step
Citrate →Cis-Aconitate → Isocitrate via aconitase.
Citrate: Tertiary alcohol due to HO-C
Isocitrate: Secondary alcohol due to HO-CH
- Irreversible
58
What is the 3rd step in the TCA cycle?
Isocitrate →(+ NADH and H+) Oxalosuccinate → α-Ketoglutarate (+ Co2).
- Both reactions via isocitrate dehydrogenase
- 1 of 4 oxidative decarboxylation reactions
59
How is α-ketoglutarate transformed into Succinyl CoA in the TCA cycle?
## Footnote
Step 6
α- Ketoglutarate (5C) → Succinyl CoA (5C).
- Via α- Ketoglutarate dehydrogenase
- Produces Co2, NADH and H+.
- 2 of 4 oxidative decarboxylation reactions
60
What is the 5th step in the TCA cycle?
Succinyl CoA → Succinate via succinyl CoA-synthetase.
- Reversible, when forward produces GTP and CoA-SH.
- Energy from GTP released from hydrolysis of a thioester bond, providing energy for substrate level phosphorylation.
61
What is the 6th step in the TCA cycle?
Succinate → Fumarate via succinate dehydrogenase.
- Reversible, when forward produces FADH₂
- Only enzyme of TCA in the inner mitochondrial membrane
- 3rd of 4 oxidative decarboxylation reactions
62
What is the 7th step in the TCA cycle?
Fumarate → L-Malate via fumarase.
- Reversible, when forward produces H₂O
- Catalyses a trans addition of a hydrogen atom and hydroxyl group
63
What is the 8th step of the TCA cycle?
L-Malate → Oxaloacetate via malate dehydrogenase.
- Reversible, when forward produces NADH and H+
- 4th of 4 oxidative decarboxylation reactions.
64
What restarts the TCA cycle?
Step 1 is incredibly exergonic so oxaloacetate used up immediately again.
65
What is the net gain of ATP from glycolysis?
8 ATPs. Comes from:
- 2 ATPs used to prime glycolysis,
- 4 ATPS produced from substrate level phosphorylation
- 2 NADH produced ( = 3 ATP each)
66
How much energy is produced from the catabolism of pyruvate?
- 4 NADHs (1 from Acetyl CoA production, 3 from TCA cycle)
- 1 FADH₂ from TCA
- 1 GTP/ATP from TCA
67
How much energy is produced from the complete oxidation of glucose?
- 8 ATP (Glycolysis)
- 30 ATP (15 x 2, TCA cycle)
68
Why doesn't NADH have a transporter into the mitochondria?
It would move with the concentration gradient out of the mitochondria which is not wanted.
69
How does NADH get into the matrix?
A Malate Aspartate Shuttle or the Glycerol-Phosphate Shuttle.
70
How does the MAS transfer NADH?
| MAS = Malate Aspartate Shuffle
- Two specific inner mitochondrial transporters
- Electrons and proteins from cytoplasmic NADH transferred to NAD+ in mitochondrial matrix.
- NADH made here results in 3 ATP
71
Where are MAS found? Why?
Low energy requirement tissue like the liver.
- Because if too much NAD+ was produced in the tissue the shuttle would reverse itself.
72
How does the Glycerol-Phosphate Shuttle transfer NADH?
1. Transfers electrons from NADH to Dihydroxyacetone Phosphate creating Glycerol 3 Phosphate.
2. Transfers electrons from G3P into mitochondrial ETC.
- 2 types of glycerol 3 phosphate dehydrogenases: Cytoplasmic (1st step) and mitochondrial (2nd step)
73
What stops the GPS from reversing?
One less ATP as it decouples matrix NADH from cytoplasmic NADH.
74
How much ATP does the GPS produce?
2, because the cycle of oxidation/reduction produced FADH₂.
75
Where is the GPS found?
Metabolically high active tissue such as neurons.
76
What is the difference between the permeability of the inner and outer mitochondrial membrane?
The inner is highly impermeable and requires specific transporters. The outside doesn't.
77
Where is FADH₂ produced?
Inner membrane.
- From the reaction of Succinate → Fumarate via succinate dehydrogenase.
78
Are oxidation reactions exer or endergonic?
Exergonic, due to very large negative ΔG∘ (-220kj/mol for NADH and -150kj/mol for FADH₂)
- Therefore spontaneous
79
What is the basic function of the ETC?
- NADH and FADH₂ pass their electrons to transmembrane protein complexes in the inner membrane
- Carrier affinity for electrons slowly increases
- Eventually electrons passed to oxygen to produce water.
80
How is ATP generated from the energy of coenzymes?
- Indirectly
- Energy is coupled to proton transport from matrix to intermembranous space
- Generates an electrochemical gradient across the inner membrane that produces ATP
81
What are the two parts of the electrochemical gradient?
1. Chemical gradient: Difference in solute concentration across a membrane
2. Electrical gradient: Difference in charge across a membrane
82
Why are electrons transferred from NADH to oxygen in stages? How does it do this?
It is too much to be released all at once.
- Electrons are transferred between acceptors, releasing energy at each stage.
- Proton gradient formed generates ATP.
83
Why must electrons be moved in a H+ pump?
It provides energy that destabilises the proton in the negative binding site at the top of the pump. The proton is pretty cushty so it needs some help in moving.
84
What are the main parts of a H+ pump?
A rotor part in the IMS and a non moving head part where ATP is hydrolysed in the matrix. This non moving part is a heterohexamer made of 3α and 3β subunits.
85
How many H+ are needed for a pump to produce an ATP?
3
86
How does the movement of electrons in a H+ pump cause movement of protons?
The electron transfer drives the H+ affinity to decrease, alongside the opening of the gates and the conformational change required to release the proton.
87
What are α subunits in H+ pumps used for?
Can bind ATP, but do not participate in catalysis.
88
What are the 3 types of β subunits in the H+ pump, and what do they do?
L = Loose state, binds to ATP and Pi tightly.
T = Tight state, favours ATP binding + formation.
O = Open state favours ADP binding + disassociation of ATP.
89
How does rotation drive ATP synthesis?
Causes confirmational changes in the head groups subunits of the stator, driving ATP synthesis from ADP and Pi.
- Unbinding requires energy
90
What is the name and function of NADH oxidation Complex I?
It is called NADH Q Reductase.
- Oxidises NADH by transferring 2 electrons to mobile carrier ubiquinone and 4 protons across the inner mitochondrial membrane
91
Where does reduced ubiquinone(QH₂) travel to?
## Footnote
Reduced ubiquinone is called ubiquinol, or QH₂.
Through the mitochondrial membrane, where QH₂ delivers its electrons to complex III.
92
What is the name and function of NADH oxidation Complex III?
Q cytochrome- c oxidoreductase.
- Transfers two electrons (from QH₂) between two mobile electron carriers o soluble cytochrome-c in IM.
93
How many protons are transferred by complex III? Where to?
1 transferred to cytochrome-c with two protons.
- 2nd is stored internally and then moved to second cytochrome-c, resulting in 2 more being transferred from the matrix to IMS.
4 in total transferred.
94
What is the name and function of NADH oxidation Complex IV?
It is called Cytochrome oxidase.
- Transfers 2 electrons from cytochrome-c proteins to mitochondrial matrix.
- Accompanied by 2H+ to IM space and reduction of oxygen in the matrix to produce H20.
95
How many protons are transferred from all complexes from one NADH?
10.
- 4 from complex I
- 4 from complex III
- 2 from complex IV
All go to the IM space.
96
Where does the oxidation of FADH₂ take place? What enzyme is used?
Complex II, III and IV.
- Succinate dehydrogenase
97
How much ATP and H+ does one FADH₂ produce?
2 ATP.
6 protons (4 from Complex III and 2 from Complex IV) into the IMS.
98
Is ATP stored?
No. It has to be made on demand. Specific transporters are required to make ATP on command. These only work if ADP is on the other side.
99
How are ATP transporters driven?
- Voltage gradient
-4 charge on ATP means it prefers to move out, but -3 charge on ADP moves it into the matrix.
100
What happens if there is no ADP?
H+ cannot return to the matrix.
- Proton gradient will be matched by NADH oxidation.
- Electron transport will stop and so will ATP.
