Section 1: Bioenergetics Flashcards
1
Q
Formation of polymers
A
Forms through dehydration (- H2O)
Breaks through hydrolysis (+ H2O)
Constructed of monomers
2
Q
How much of the body is occupied by polymers?
A
~80%
The remaining 20% of a cell are monomers and other small molecules
3
Q
Types of polymers
A
Lipids
Polysaccharides (carbohydrates)
Proteins
Nucleic acid
4
Q
Building block of lipids
A
Acetates, which join tgt to form acyl chains
5
Q
Lipids and phosphate
A
Lipids can grow to form hydrophobic fatty acid (acyl) chains
Addition of phosphate makes fatty acids amphipathic
6
Q
Acyl chains can be…
A
Saturated or unsaturated
7
Q
Lipids - functions
A
Energy storage (mass, energy of glycogen, a complex storage sugar) Structural molecules (membranes) Steroids (all from cholesterol, some further made into electron carriers and vitamins)
8
Q
Lipids: Structure of a fat molecule
A
Ester linkages, which link glycerol and acyl chains together
9
Q
The cell membrane is formed of a…
A
Phospholipid bilayer
10
Q
Phospholipids - replication
A
No genetic info required, just physical laws of stability of vesicle size
Could have been the first form of replication
11
Q
How are sugars formed
A
From central pathways (trioses)
12
Q
Monosaccharides
A
Single sugars
Different types
13
Q
Disaccharides and oligosaccharides
A
Form from several mixed sugar types
Disaccharide: 2 sugar molecules
14
Q
How are polysaccharides formed
A
Formed from many repeated sugar units connected by glycosidic bonds
Specific glycosidic bonds determine flexibility
15
Q
Polysaccharides - function
A
Energy storage (starch and glycogen) Structural molecules - used by plants and animals to form structures, e.g. cellulose, chitin Carbohydrate residues can be joined to proteins or lipids (glycoproteins/lipids)
16
Q
Starch
A
A storage polysaccharide in plants
Polymer of glucose monomers
Stored as granules in plastids, e.g. chloroplasts
17
Q
Glycogen
A
Sugar storage in animals
Polymer of glucose monomers - more extensively branched than starch –> more flexible with α 1-4 bonds
Large stores in liver and muscle cells
18
Q
Cellulose
A
Structural polysaccharide in plants
Polymer of glucose (not branched)
Stored in cell wall
Most abundant organic compound on Earth
19
Q
α vs β glycosidic bonds
A
α1–>4: starch and glycogen
β1–>4: chitin and cellulose
Subtle difference, but profound effect
20
Q
Chitin
A
Structural polysaccharides in animals
Polymer of glucose, but glucose monomer has a N containing appendage
Forms exoskeleton of arthropods and fungi cell walls
21
Q
Nucleic acids (RNA and DNA) - function
A
Involved in all informational processes
Storage of chemical energy in ATP
Intracellular signalling cAMP
22
Q
Phosphodiester bond
A
PO4 3-
Formation leads to elimination of H2O (i.e. dehydration)
23
Q
Components of nucleic acids
A
Sugar-phosphate backbone (phosphate group and sugar)
Nitrogenous base
5’ and 3’ end
24
Q
Types of nitrogenous bases
A
Pyrimidines:
Cytosine (C)
Thymine (T in DNA)
Uracil (U in RNA)
Purines:
Adenine (A)
Guanine (G)
25
Sugars - DNA vs RNA
One of the Hs in deoxyribose (in DNA) is replaced by OH in ribose (in RNA)
26
How are proteins formed
Formed from amino acids connected through peptide bonds
| Bonds formed through dehydration and break through hydrolysis
27
Properties of proteins determine...
Protein structure and function
28
Parts of an amino acid
Amine group
Carboxy terminus
R side group
29
Life and order
Life generates order (decreases entropy) and drives itself away from equilibrium, but at the expense of making more disorder (increasing entropy)
30
Passage of energy
Photoautotrophs capture electromagnetic energy of light and converts this to chemical energy
Heterotrophs consume, use and store chemical energy and pass energy onto carnivores
At each passage of energy, some is lost to the universe as heat
31
Stored energy (via anabolic processes)
Occurs through synthesis of carbohydrates, fats, and proteins
These are then catabolised (oxidised) to release energy
O2 required to completely oxidise foodstuffs to CO2 and H2O
32
Where is energy conserved from oxidation reactions
Within phosphate bonds of ATP
33
What does ATP stand for
Adenosine triphosphate
34
Excess dietary fuel
Exceeds body's immediate energy needs
Stored mainly as glycogen and fat
Provides energy when fasting
Oxidation of these fuels release energy, which often use Acetyl-Co Enzyme A
35
Gibb's free energy - equation
ΔG = ΔH - TΔS
ΔH (enthalpy) = q + w (aka heat + work done)
T (temperature)
ΔS (entropy)
36
ATP
Almost universal - cells also use GTP, UTP and creatine phosphate
Likely ancestral
High ΔG --> can make the unfavourable favourable (spontaneous)
Much higher tendency for ATP --> ADP + Pi than the other way around
37
How does ATP release energy
From electrically charged phosphates, which change molecular properties and do work
38
ATP phosphates
Electrical charges are crowded among phosphates, especially the terminal phosphate --> leaves more easily and can bind and carry with it the electrical charge
This charge can then alter the conformation of a protein, altering the protein elsewhere
In the cell, most hydroxyl groups of phosphates are ionised (O-)
39
Two fundamental laws of thermodynamics
1. Energy is not created nor destroyed, it just changes form
2. The overall entropy of the universe is increasing
These laws are the foundation of Gibb's equation
40
Universe tends toward...
Disorder
More disorder --> increased entropy (rotting apple) - exothermic
More disorder --> going towards equilibrium
41
When a reaction reaches equilibrium...
They go no further
42
Anabolic processes
Build things up
43
Heat
The end result of all processes
| Dissipates into the universe
44
Negative ΔG
The more -ve the ΔG, the greater the likelihood a reaction occurs
45
When is most ΔG in ATP released
Hydrolysis of ATP to ADP and inorganic phosphate
ΔG of ATP is greater than the sum of 'products of formation' of ADP + Pi --> can drive rxns that would otherwise go too slowly or not at all
46
Anabolic vs catabolic processes
Anabolic: creates molecules the body needs for functionality and uses energy in the process
Catabolic: breaks down complex molecules and releases energy which is available for the body to use
47
Example of anabolic vs catabolic processes
Anabolic: photosynthesis in chloroplasts ---organic molecules + O2---> cellular respiration in mitochondria
Catabolic: cellular respiration in mitochondria ---CO2 + H2O---> photosynthesis in chloroplasts
48
Combustion of different food sources
Diff food sources release diff amounts of energy when combusted
```
Least to most:
Carbohydrate
Protein
Alcohol
Fat
```
49
Metabolism of different food sources
```
Least to most:
Alcohol
Fat
Protein
Carbohydrate
```
50
Why is combustion different to metabolism
Access to C-C bonds, internal and not easily accessed
Metabolic enzymes work on C-H and O-H bonds
Molecules must be rearranged
51
Fat
May have less energy for outright mass, but stores well and has no associated water
Can't be metabolised without O2
52
Stages of catabolism
1. Hydrolysis of complex molecules to their building blocks
2. Conversion of building blocks to Acetyl CoA
3. Oxidation of acetyl CoA - oxidative phosphorylation
53
Acetyl-CoA
Hub molecule
54
ATP - structure
Phosphoanhydride bond - relatively stable in water
| Phosphate group has resonance / charge delocalisation
55
Equilibrium vs non-equilibrium
```
Equilibrium = less order = higher entropy
Non-equilibrium = ordered = low entropy
```
Life fights equilibrium/entropy
56
ΔG - purpose
Predicts whether a rxn occurs spontaneously
Predicts max possible change in conc between reactants and products
Does NOT predict rate at which reactions will occur
57
What does the ° mean in ΔG°
Standard conditions
1 mol/L, pH 7, 25°C
In real life, these conditions are quite different - ΔG is maybe -50-60 kJ/mol
58
Exergonic reactions
Releases energy
59
Hydrolysis is dependent on..
Ratio of reactants to products
| So, ATP is held at a high conc, and there is more reserve ATP
60
Human heart - ATP
Contains approx 700mg of ATP - enough to fuel one heartbeat per second for 10s
61
Formation of glutamine
1. ATP phosphorylates glutamic acid, making the amino acid less stable
2. Ammonia displaces phosphate group, forming glutamine
Note: enzyme glutamine synthetase required
Net ΔG is -ve
62
Does glycolysis require oxygen
No
It is an initial component of aerobic metabolism, but can also operate without oxygen by fermentation to produce lactate or ethanol, but inefficient
63
Glycolysis enzymes
Enzymes of glycolysis are arranged to form pathways, which increases efficiency of reactions
10 enzymes produce 2 ATP net
64
Two phases of glycolysis
```
Energy investment (-2 ATP):
- Hexo/Glucokinase
- PFK
Energy harvesting (+4 ATP):
- Phosphoglycerate kinase
- Enolase
```
65
Important features of glycolysis
Sugar-splitting reaction
Oxidative event that generates reduced NADH
Two specific steps where the reaction sequence is coupled to ATP generation by substrate-level phosphorylation
66
Glycolysis - steps
1. Conversion of glucose to glucose-6-phosphate (G6P) --> traps glucose --> can't be transported out of cells - irreversible
Catalysed by hexokinase and glucokinase
Requires energy (2 ATP invested)
2. G6P rearranged, and another phosphate is invested
3. Resulting intermediate then split into 2 molecules of the 3-carbon compound glyceraldehyde 3-phosphate
4. Each glyceraldehyde 3-phosphate molecule has an additional phosphate added alongside the formation of NADH (by reduction of NAD+)
5. 1, 3-bisphosphoglycerate is formed
In following reactions, 4 ATP are recaptured by substrate level phosphorylation and 2 pyruvate molecules are formed
67
Glycolysis - Hexokinase vs glucokinase
Both interact with glucose, but in slightly diff ways
Puts a phosphate on the glucose
Hexokinase:
Expressed in all tissues
High affinity (low Km) for glucose
At very low glucose conc, will already start to add a phosphate to it to form G6P (very sensitive to glucose)
Glucokinase:
Found predominantly in liver (takes up glucose and stores) and pancreatic beta cells (regulates insulin)
Lower affinity (higher Km by ~100x)
Must get up to a reasonable (higher) conc of glucose for it to work - high Vmax
68
Glycolysis - net reaction
Glucose + 2NAD+ + 2Pi + 2ADP --> 2pyruvate + 2NADH + 2H+ + 2ATP + 2H2O
69
Stages of cellular respiration
Glycolysis - breaks down glucose into 2 pyruvate molecules
Citric Acid Cycle - completes breakdown of glucose
Oxidative phosphorylation - accounts for most of the ATP synthesis
70
Lactate
End product of glycolysis during strenuous exercise
| Lactate produce in muscle and other tissues can return to liver where it is reconverted to glucose - Cori cycle
71
For sustained flow of glycolysis...
NAD+ must be regenerated
Anaerobic: NAD is regenerated by LDH (lactate dehydrogenase)
72
Glycolysis: Re-oxidation of NADH
Cells with O2: accomplished by oxidative phosphorylation
Aerobic conditions: O2 may be limiting and ATP demands can exceed capacity of mitochondria
Pyruvate is reduced to lactate by lactate dehydrogenase in cytosol
73
Glycolysis: Speed and efficiency
Can form ATP very quickly, but not very efficient as it only forms 2 ATP net per glucose (3 ATP if it comes from glycogen
74
Redox reactions
Oxidation: loss of electrons
Reduction: gain of electrons
75
Oxidation of C bonds
Energy from C-C = C-H bonds, but C-C can't be oxidised directly
Must be rearranged to C-OH for oxidation --> electrons ultimately flow to oxygen
76
Redox reactions use...
Dehydrogenases
77
Energy release must be...
Controlled, otherwise explosions!
| Thus cellular respiration is controlled energy captured in ATP
78
Glycolysis: NAD+
Acts as an electron shuttle
| Water soluble
79
Glycolysis: Irreversible enzymes
Hexokinase or glucokinase
Phosphofructokinase
Pyruvate kinase
Highly regulated and irreversible in vivo
80
Glycolysis: At which point is glucose fully committed?
Phosphofructokinase (PFK)
Highly regulated point in pathway (most important regulator)
Another ATP invested
81
Glycolysis: What is PFK regulated by
High ATP slows down
(ATP --> ADP -->) AMP activates PFK
Citrate inhibits PFK from CAC
Moderately low pH turns PFK on, but when too acidic inhibits PFK --> tight control
82
Energy yield of glycolysis vs aerobic glucose oxidation
Energy yield of aerobic glucose oxidation much greater
83
Main functions of CAC cycle
Oxidise acetyl-CoA
Reduce co-enzymes NADH and FADH2
Form ATP (and decrease ADP)
Therefore, principle driving forces for CAC is due to amount of reduced coenzymes and ADP abundance
84
CAC: Pyruvate (from glycolysis) is converted to...
Acetyl CoA, in an oxidative decarboxylation reaction by the pyruvate dehydrogenase complex
Then further oxidised to CO2
85
CAC: Acetyl CoA is produced in most pathways of...
Fuel oxidation
86
Coenzymes
Complex organic structures, which participate in enzymatic reactions
87
CAC: Coenzymes
Coenzyme A, NAD+ and FAD
88
CAC: NAD+ vs FAD
Both are oxidation reduction coenzymes
Both act as electron acceptors
FAD able to accept single electrons and bound
NAD+ is mobile in aqueous environment and accepts 2 e- in one step
FAD has less reducing power
89
Where do most enzymatic reactions of CAC cycle occur
Mitochondrial matrix or bacterial cytosol
90
CAC: Oxidation reactions
4, which transfer electrons to NAD+ or FAD by binding Hs to form NADH + H+ and FADH2
Other reactions in the pathway result in rearrangements to facilitate REDOX reactions with NAD+ or FAD
91
CAC: Oxaloacetate
Regenerated in CAC after oxidation of NAD+ and FAD
| Available to react with another molecule of acetyl CoA
92
Net energy yield from CAC and oxidative phosphorylation
High
| ~10ATP for each acetyl group oxidised
93
Energy yield from oxidation of NADH and FADH2 by electron transport and phosphorylation systems
~2.5 ATP per NADH oxidised
| ~1.5 ATP per FADH2 oxidised
94
The high-energy phosphate bond of GTP is generated by...
Substrate level phosphorylation
95
How does CAC 'control' ATP utilisation
ATP:ADP ratio
Reduction state as per the NADH/NAD+ ratio (REDOX state) - high NADH = lots of reducing power
Calcium (signal that indicates cells are depolarised/activated and need ATP)
96
CAC: Examples of key regulatory enzymes
```
Isocitrate dehydrogenase (IDH)
α-ketoglutarate dehydrogenase (αKDH)
```
97
CAC: During oxidation of each molecule of acetyl CoA...
Only one molecule of high-energy phosphate (GTP/ATP) is produced
98
CAC equation for 2 pyruvates
6CO2, 8NADH, 2FADH2, 2GTP (or 2ATP)
99
Endosymbiosis
A symbiotic relationship where one organism lives inside the other
100
Mitochondria
Permits an existence with oxygen (quite toxic and in effect ages us)
Allowed larger cells - cristae increase efficiency of ATP synthesis --> increases cell's capacity to make ATP --> more complex genomes --> increased gene copy numbers --> possibly drove rapid diversification of genes, cell structures, types and body plans
101
Junction between glycolysis and CAC
Irreversible step
| Very large -ΔG and regulated
102
Vitamin B1 - Thiamine
Has thiamine pyrophosphate found within pyruvate dehydrogenase
TPP is within E1 - acts to remove CO2
103
CAC: GTP vs ATP
Liver makes GTP, muscle makes ATP
104
CAC: Succinate dehydrogenase (SDH)
Part of ETS Complex II
FAD+ bound within it
Sits in inner mitochondrial membrane
Directly connects oxidation to electron transfer
105
CAC: Amphibolic
Involves both catabolism and anabolism
106
CAC: If there is too much succinyl-CoA or acetyl-CoA...
CoA becomes limiting and CAC slows
107
CAC: ADP/ATP ratio regulates...
IDH activity
10/2 goes faster
2/10 goes slower
108
CAC: Ca2+ regulates...
PDH, aKDH and IDH
109
Cholesterol is an important component of...
Animal cell membranes
110
Glucose + glucose -->
Maltose + water (via dehydration)
111
Enzymatic reactions involved in glycolysis fatty acid breakdown and CAC cycle conserve most energy into _____
NADH and FADH2, which can transfer their electrical power into usable energy by transferring H+ across membranes
112
Respiratory complexes
Enzymes that sit on membranes and mediate H+ transfer as electrons from NADH and FADH2 ultimately flow to O2 and reduce it to form H2O
113
Electron transport system - gradients
H+ accumulates on one side of membrane --> generates gradient, which is harnessed to synthesize ATP
114
Oxidation of NADH and FADH2 results in...
Release of electrons
115
What is the electron transport system (ETS)
A sequence of electron-transfer carriers involving electrophilic molecules, e.g. flavins, haeme and iron-sulfur complexes, which transfer electrons in a step-wise manner to O2
116
ETS: The flow of electrons changes...
The charges of ETS protein complexes so they pump H+ or promote chemical reactions that transfer
117
ETS: Where are protons transferred
Across the inner mitochondrial membrane (IMM) from matrix to intermembrane space (IMS) --> raises pH in matrix and lowers it in IMS
Therefore, there is a pH gradient and electrical potential
118
Electron transport carriers that oxidise NADH
```
Organised into three large membrane spanning complexes:
Complex I (CI, aka NADH dehydrogenase)
Complex III (aka cytochrome b-c1)
Complex IV (aka cytochrome oxidase)
```
Together form super-complexes / respirosome
Arranged as 3 separate units, but linked functionally by two additional electron carriers; co-enzyme Q and protein cytochrome C
119
Co-enzyme Q
A lipid soluble molecule (not a protein)
120
Electrons flowing through the NADH pathway drive...
Proton pumps of complex I and IV, and the chemical transfer of protons at complex III
All develop a H+ gradient
121
Electron transport carriers that oxidise FADH2
Mediated by a second electron transport linked to CII
Part of CII is succinate dehydrogenase (SDH), which is what FADH2 is bound to and most likely stops dangerous free radical production
Flow from FADH2 (oxidised to FAD) and are transferred to co-enzyme Q --> electrons flow through complexes III and IV
122
ETS: Do electrons flow from CI to CII
No
123
Succinate dehydrogenase (SDH)
An enzyme of CAC
124
NADH vs FADH2 - redox potential
FADH2 has lower redox potential / reducing power
| This means that CII itself doesn't pump protons, but CIII and CIV (downstream) still contribute to proton gradient
125
ETS: Flavin mononucleotide (FMN)
Specific molecule found within complexes I-IV which act as electron acceptors
Made from vitamin B2
Top part similar to FAD (alloxan rings)
Other e.g. FeS centres, Fe-haeme and Cu2+
Accepts Hs --> accepts electrons, which come from NADH
126
ETS: Poisons
Several poisons can react with molecules and blockage of ETC at any point prevents formation of ATP
e.g. cyanide
127
Ubiquinone vs ubiquinol
Ubiquinone has 2 C=O bonds
Ubiquinol replaces those carbonyl groups with two OH groups
Changes conformation
128
Cytochrome C
Little protein with a haeme in it
Unlike Q, carries e- one at a time
Iron atom changes colour when reduced/oxidised
Found in all aerobic organisms
129
NADH has a much higher ____ than FADH2
Driving capacity
130
The energy from fuel oxidation is converted to ATP by the process of...
Oxidative phosphorylation
| But, this requires transfer of electrons to oxygen and the coupling of this power to synthesize ATP
131
Mitochondria and energy demands
The location and number of mitochondria is correlated with a tissue's energy demands
132
Complex I (NADH oxidase)
```
Works as a proton pump
Pumps 4 protons per NADH
Large L-shaped protein
Contains FMN
7 FeS clusters
```
133
ΔG for NADH and FADH2
More negative for NADH
134
Iron-sulphur clusters
e- can effectively flow through these molecules as the Fe atoms can change oxidation state between Fe3+ and Fe2+
135
Complex I and II both...
Use Q10
| Converge on CIII
136
Complex III
Transfers 4 protons, 2x from reduced QH2, 2x from matrix by Q cycle
Protons deposited on intermembrane space due to chemical reactions, NOT by pumps (technically transferred, not pumped)
137
Complex III: The complexity of the Q cycle is likely because...
Cytochrome C can only carry one e- at a time (aka cytochrome c oxidase) to CIV
138
Complex IV - overall
2 protons are pumped and the electrons flow to O2 to form H2O
139
Complex I - poisons
Blocked by some anesthetics and poison (rotenone)
| Blocks binding point for ubiquinone
140
Complex III - poisons
Antimycin a - binds to CIII and disrupts e- flow and locks it down
141
Cytochrome C oxidase (CIV) - poisons
NO, H2S, CO and cyanide - bind to haeme groups --> stops oxygen flowing
142
Complexes I, III and IV transfer __ protons
| Complexes II, III and IV transfer __ protons
10 protons
| 6 protons
143
NADH moves ____ hydrogens than FADH2
4 more
144
What do flowing electrons power
Pumps and chemical transfer of H+ to form an electrochemical gradient (proton motive force / PMF), which is harnessed to drive ATP synthesis
145
What is the ATP synthase
A molecular machine
Mirrors concept of water turbine of a hydrodam
H+ flowing through the complex provide the force to push ADP and Pi tgt to form ATP
146
Complete oxidation of one molecule of glucose to six molecules of CO2 and H2O yields...
Approx 30-32 molecules of ATP
147
What is the most important regulator of oxidative phosphorylation
ADP
148
Net yield of oxidative phosphorylation - NADH and FADH2
~2.5 moles of ATP per mole of NADH oxidised
| ~1.5 moles of ATP per mole of FADH2 oxidised
149
Overall, how much ATP does 1 glucose produce
28-38
| Variable
150
What is the bacterial rhodopsin?
A light-driven proton pump
| Pumps protons into vesicle (inside out?)
151
What chemicals stop ATP synthesis
Chemicals that disrupt or 'uncouple' the proton gradient
| Chemicals that poison electron flow
152
Proton motive force - components
```
2 components in mitochondria;
Conc gradient (ΔpH) and an electrical charge in mV
```
Both have an effect and can provide power --> electrochemical gradient
Inside of mitochondria -vely charged, outside +vely charged
153
Where are ATP synthases located
All over ridges of cristae
Appear to form lines
Tightly arranged
Proteins arranged in a V-shape for mitochondria
154
OXPHOS: How do protons flow?
Directly towards ATP synthases
Since V-shaped, they shape the membrane and drag electrical charges on the phospholipids --> concentrated -ve charge around ATP synthases --> attracts protons --> localised conc of H+ --> low pH --> can turn ATP synthases = microdomain
155
ATP synthase - steps
1. H+ ions flowing down their gradient enter a half channel in a stator anchored in the membrane
2. H+ ions enter binding sites within a rotor (C-ring), making it click and changing shapes of each subunit so the rotor spins within the membrane
3. Each H+ makes one complete turn before leaving the rotor and passing through a second half channel in the stator into the mitochondrial matrix
4. Spinning of rotor causes an internal rod to spin, which extends like a stalk into the knob below it
5. Turning of rod activates catalytic sites in knob (held still by a stator) that produce ATP from ADP and Pi
156
Internal rod - shape and function
Not straight - slightly helical shape
As it spins, it places forces against the alpha and beta F1 sub-units of catalytic region --> changes conformation
This power is used to transform ADP and Pi to ATP
157
For each rotation of the internal rod...
3 ATP are made (because 3 sites) and protons drive the rotation
158
Helicases - function
As they move down, they...
Split DNA
Hydrolyse ATP
Physically move strands of DNA
Have 6 units working tgt - very similar to catalytic region
159
Catalytic knob sub-units
Effectively are a helicase working in reverse with the gamma sub-unit in the centre
160
NADH getting into mitochondria
Can't get into mitochondria by itself - two systems effectively transfer the electrons:
- malate aspartate shuttle makes ~2.5 ATP
- G3PDH shuttle makes ~1.5 ATP
161
Malate aspartate shuttle
Slow, complicated, but efficient
162
G3PDH shuttle
```
Less efficient (because FADH2, which means loss of ~1 ATP), but fast
Multiple enzyme pathway
```
163
Summing up - 1 glucose
Net glycolysis makes 2 ATP and 2 NADH
2 x pyruvate --> acetyl-CoA makes 2x NADH
2 CAC makes 2 GTP/ATP, 6 NADH and 2 FADH2
OXPHOS converts 1 NADH --> ~2.5 ATP, or 1 FADH2 --> ~1.5 ATP
164
Why is the ATP yield (28-38) vague?
1. Temp - membranes leak H+ more when warm hot (less efficient), early expt done at only 25°C
2. NADH from glycolysis has 2 fates; malate aspartate shuttle or G3PDH shuttle
3. H+ are also used for other processes
165
Leigh's disease
Mutation in C-ring of ATP synthase
Results in proton slippage
Complex I appears to commonly fail / be impaired in disease states
End up with aberration in brain
166
Damaged inner mitochondrial membranes - consequence
Increases leakiness to protons and structure changes
| Consequences on ATP synthesis?
167
How can uncoupling ATP synthesis be useful
Makes heat
As electrons flow through ETS, they make heat
If flow faster through respiratory complexes, make more heat
Protons pump faster
Makes heat in lean people, obese people already have fat to keep them warm
168
K(M) and affinity
High Km = need lots of glucose = low affinity
169
NADH has ____
Energy
| NAD+ can float through cell and carry energy from A to B (water soluble)
170
Nicotinamine
Oxidised form - has a positive charge
| Can add electron, which is added with an H+
171
Glycolysis - substrate level phosphorylation
Capture ATP
Phosphoglycerate kinase and pyruvate kinase
Binds phosphate which has energy in it --> changes shape of enzyme --> grabs an ADP --> ATP
172
PFK - properties
Quite slow working
Easy to turn on and off
Amount of PFK is not huge - controls how fast the reaction goes
173
Two fates of glucose
Can feed into aerobic pathways
| Can feed into anaerobic pathway - much less efficient but much faster
174
Anaerobic - no O2
Can't get rid of NADH at G3P
175
Pyruvate - acidity
Quite acidic
176
Production of lactate during anaerobic glycolysis
Lactate dehydrogenase - takes the Hs and passes it onto pyruvate that generates lactate
NADH oxidised back to NAD and glycolysis can continue
Lactate accumulates --> muscles hurt
177
Recycling of lactate
Still has energy in it, so is recycled through Cori cycle
Exported into blood --> into liver --> turn lactate back into pyruvate --> turned back into glucose
Process uses lots of ATP
178
CAC: Amino acids
Some amino acids can be fed directly into CAC
179
Where are CAC enzymes found
In matrix of mitochondria
180
Pyruvate breaks down into...
Acetate and CO2
181
Pyruvate structure
Has a carboxylate at the end --> removed to form CO2
182
Pyruvate dehydrogenase
A trifunctional enzyme (3 enzymes all arranged tgt)
183
Vitamin B1 (thiamine) - process
Pyruvate comes in with 3 Cs
Thiamin diphosphate binds the acetate group and CO2 is removed
Acetate binds to thiamine group --> passed onto lysine lipoamide (has S on end)
Acetyl CoA (also contains a S) picks up the acetate, and lipoamide becomes reduced
E3 containing FAD takes e- from lipoamide and becomes reduced --> FADH2
E3 donates extra e- to NAD --> NADH
184
FADH - reactivity
Quite reactive - always found bound within proteins (never floating around)
185
What does the A stand for in acetyl-CoA
Acetate
186
Acetyl CoA
Has sulfur and acetate in it
| Acetate can be fed into CAC
187
CAC - carbons
Cs get shuffled through the intermediates and some get pulled off as it goes
Takes ~4 cycles for the C that's been injected to get spat out again as CO2
188
α-KDH vs PDH
Very similar - similar ancestral origins
Both poisoned by arsenic - binds to E2 and shuts it down
Same process, but recognise diff substrates
189
Succinate dehydrogenase (SDH) - process
Electrons flow to molecule Q
Succinate comes in and a redox rxn takes place where a FAD is involved with dehydrogenation of C-H bonds
Becomes a double bond (lose 2H)
E- make their way down through Fe-S complex, and there is a heme where e- sit waiting
Ubiquinone comes in and accepts e- and Hs
190
FAD / FADH2 - structure
Have alloxan rings which can accept 2 Hs and thus carry e-
191
CAC: Amphibolic - reactants and products
```
Acetyl-CoA --> ACh
Citrate --> fatty acids
α-ketoglutarate --> glutamate
Succinate-CoA --> porphyrin (haemoglobin, cytochromes, chlorophyll)
Malate -> glucose (gluconeogenesis)
Oxaloacetate --> amino acid syntehsis
```
192
Control of CAC - what slows down CAC
High ATP, acetyl-CoA, succinyl CoA and NADH
| High NADH = lots of reducing power --> may drive unwanted rxns
193
Pyruvate dehydrogenase (PDH) - regulation
Regulated allosterically
Pyruvate, AMP, NAD, Ca2+ speeds it up
Acetyl-CoA slows it down
194
What does Ca2+ regulate
PDH, α-KDH and IDH
When cells are polarised, Ca2+ floods in --> makes heart beat faster --> cell needs ATP --> turns enzymes on and makes them go faster
195
Role of ETS
Take e- from NADH and FADH2 and transfer them through a series of e- carriers and other respiratory proteins/complexes
Some move protons from matrix to IMS --> accumulate on one side --> chemiosmotic gradient
Flows back through ATP synthase to make ATP
196
ETS: Location of NADH and FADH
FADH situated lower, so packs less punch
| NADH has a slightly higher potential (~1.135V) than FADH2 (~0.815V)
197
ETS: Voltage
Voltage diff between top and bottom of ETS
198
Complex I - where are the parts most likely from
Part in matrix likely from a primitive dehydrogenase
| Part in membrane likely from ion pumps
199
FMN vs NADH
FMN has greater reducing power --> can pull e- from NADH
200
Complex I - cavities
To start with, cavities are facing down (into IMS)
As charge is imparted, ubiquinone comes in and cavities open up to matrix
Lining of these cavities have amino acids that attract protons
Protons come into cavity and channel down
201
ETS: Quinones
Can accept 2e- by binding 2Hs to form 2 OH groups
Q10 = ubiquinone
Q9 = ubiquinol
Ubiquinone --accepts 1H--> semiquinone --accepts another H--> ubiquinol
202
Complex II
Doesn't have power to pump, but does contribute to proton pumping overall
Only part of CAC found in inner membrane
FAD found within complex II (not floating around)
203
Heme molecule
Iron atom surrounded by a porphyrin ring
204
Which similar system is found in photosynthesis
Complex III
205
How does rotenone work
Ubiquinone and rotenone have similar groups, so it can get into cleft and jams in there - irreversible
206
Cytochromes
CII, III, IV and cytochrome c have metals bound within them
Change colour as they are reduced/oxidised
Mainly CIII, IV and cytochrome C
207
If add rotenone, what happens to e- in ETS
Stops e- flowing at complex I --> run out of e- at end of chain
Cytochromes / ETS becomes oxidised
208
If add antimycin, what happens to e- in ETS
Poisons CIII
End of ETS loses e- --> becomes oxidised
Start of ETS (CI and Q) - accumulation of e- at CIII --> start becomes reduced
209
If add cyanide, what happens to e- in ETS
Blocks CIV
| E- stops at CIV --> builds up --> whole chain is reduced
210
If hypoxia (low) or anoxia (no) oxygen, what happens to e- in ETS
E- builds up (can't bind with water) --> ETS reduction
211
ETS: How many protons do the complexes pump
CI: 4
CIII: 4
CIV: 2
CII: 0
212
NADH vs FADH - how many Hs do they move
NADH moves 4 more Hs than FADH (FADH less reducing power)
213
Proton motive force - charge
Net -ve charge on inside of inner membrane of mitochondria
Pushes equilibrium into more ordered state where we've generated a partition across the membrane
As protons come back, they use the turbine to produce ATP
214
pH difference across mitochondria
Not that large, and for ATP synthase to turn, needs a pH difference of 2 (quite large)
215
Cristae work as...
A lightning conductor rod - focus electrical charges of protons towards the ATP synthase
If proton flow is turned on, protons go through respiratory complexes - not randomly, but towards the ATP synthase
216
Protons flowing through ATP synthases - steps
ATP synthases move into membrane
Since V-shaped, they shape the membrane and drag electrical charges around the phospholipid --> concentrated -ve charge around ATP synthases --> attracts protons --> localised conc of protons --> very low pH at ATP synthases, which activates it
Results in a microdomain near ATP synthases
217
ATP synthase: Catalytic region is made from...
3 alpha and 3 beta subunits
218
Brown adipose tissues
Uncoupling of ATP synthesis
Allows protons to flow back through the protein
Short circuits the ETS
219
Cellular respiration: Adding succinate (substrate for CII)
Succinate provides e- that gets ETS to pump protons
| MP increases
220
Cellular respiration: Adding succinate then ADP and Pi
Addition of Pi drops MP a bit, but not all the way to baseline
Still maintains a MP
221
Cellular respiration: Adding succinate, ADP and Pi, then oligomycin (inhibitor of ATP synthase)
Oligomycin creates a block on ATP synthase
ETS pumps a lot and starts to fill IMS with protons --> MP increases
Decreases respiration rate
222
Cellular respiration: Adding succinate, ADP and Pi, then dinitrophenol (DNP)
DNP allows respiration to accelerate and become maximal
DNP drops ATP synthesis rates until zero because no more MP to drive ATP synthesis, and decreases pH gradient
223
What is photosynthesis
The process of capturing and converging solar (electromagnetic) energy into chemical energy by plants, algae and bacteria
224
Photosynthesis equation
6CO2 + 6H2O -->LIGHT--> C6H12O6 + 6O2
225
Photosynthesis - What is reduced and what is oxidised
CO2 is reduced
| H2O is oxidised - this is the only process in the whole of biology where water is oxidised
226
Photosynthesis can be broken down into...
2 processes;
1. Light reactions
2. Calvin Cycle (dark reactions)
227
Where does photosynthesis take place
Chloroplasts, mostly found in cells located just below the surface of the leaf
228
Chloroplasts - structure
Highly organised internal structures
| Contain pigments which can absorb visible light, generally referred to as chromophores
229
Best known chromophore
Chlorophyll
230
Chlorophyll - structure
Arranged in antennae within photosystems
Perforin ring
Long hydrophobic chain - keeps it embedded within photosystems
Absorb light and become energised and resonate within PSs
231
Photosystem names
PSII and PSI (in this order!)
232
Photosynthesis: Light reactions - how is energy transferred between chlorophyll molecules
Via quantum tunnelling towards a special acceptor chlorophyll, which will lose an e-
This e- is used to reduce a receptor molecule
Light energy has become chemical energy
233
Photosynthesis: Light reactions - what happens to the electron-deficient chlorophyll
It extracts an e- from another donor and cycle can be repeated
234
Electron donors for PSI and PSII
Water is ultimate electron donor for PS2
| Plastocyanin (a special e- carrier) is e- donor for PSI
235
Photosynthesis: Light reactions - equation
2H2O + 2NADP --> Light --> 2H+ + O2 + 2NADPH2 (+ ATP)
236
Photosynthesis: Non-cyclic / linear photophosphorylation
The production of ATP and NADPH using the flow of e- from PSII to PSI
237
Cyclic electron flow
Under certain conditions, photoexcited e- within PSI can take an alternative path called cyclic electron flow, which makes only ATP
238
What is produced in light reactions that is used in the Calvin cycle
Calvin cycle uses NADPH and ATP from light reactions to fix CO2 from air to form G3P
Consumption of ATP and NADPH by dark reactions is sustained by the light reactions
239
Calvin cycle - input of light
Does not require direct input of light
| But, do require products of light reactions; ATP and NADPH which are used in fixation of CO2 to produce sugars
240
Calvin cycle - phases
Carbon fixation
Reduction
Regeneration of carrier (RBP)
241
Calvin cycle - carrier
```
Ribulose bisphosphate (RuBP)
CO2 is fixed to RuBP by enzyme ribulose bisphosphate carboxylase (RiBisCo)
```
242
Product of Calvin cycle
A molecule of G3P, which requires input of 3CO2, 9ATP and 6NADPH
243
How is glucose stored in plants
As starch and sucrose, which act as an energy source for plants
244
Photorespiration
Where O2 competes with CO2 at RuBisCo
| Undesirable for farmers
245
Photorespiration - C4 plants
C4 plants have a solution to photorespiration and concentrate CO2 within adjoining cells within leaves
This uses addition ATP which may come from cyclic e- flow
246
Why does RuBisCo bind oxygen
While affinity for O2 is low, with intense light, photosynthesis can generate large amounts of O2, which is then incorporated into metabolites
For plant, may eliminate harmful O2, thus C is not fixed and water is wasted
247
How do C4 plants capture CO2
Using enzymes associated with other common pathways, e.g. phosphoenolpyruvate carboxylase
248
C4 plants - Phosphoenolpyruvate carboxylase
Has a v high affinity for CO2, incorporates CO2 into a 4C intermediate in mesophyll cells where the Calvin cycle is less active
C4 intermediates then pass into the bundle-sheath cells where CO2 is released to the Calvin cycle
ATP required to drive this process, but chloroplasts of the bundle-sheath cells lack PSII, so all photosynthesis in this layer is cyclic, which makes addition ATP
249
Main types of chlorophyll
Chlorophyll a and b
250
Photoreceptive componds within the chloroplast are grouped tgt with other compounds to form...
Photosystems, and it is these complexes which absorb light
251
Processes within photosystems are called the... and include...
Light reactions
- splitting of water
- NADP+ reduction
- H+ gradient generation
252
Thylakoid membrane - permeability
Impermeable to most ions and molecules, but not Mg2+ and Cl-
253
Where do light reactions take place
Molecules in the thylakoid membrane
254
Where do dark reactions (Calvin cycle) take place
Stroma
255
Photosynthesis uses mostly _____ light
Blue and red
i.e. these are the colours primarily absorbed and green is reflected
Lack of absorbance at 500-600nm
256
Excitation of isolated chlorophyll molecule
Electrons jump up to another orbital --> gain energy
Comes back down and releases energy in two ways:
- heat
- gives off light at a shorter light, e.g. if hit by blue light, drops back down and gives a red fluorescnece
257
Photosystem II structure
Chlorophyll molecules juxtaposed very closely tgt
258
Photosystem II - process
Light hits PSII and makes its way to special chlorophylls (P680)
As energy is imparted, e- jump up to special chlorophyll molecules that are missing Mg --> accepts e- and passes them onto quinones bound within PSII --> Pq
Pq floats through cytochrome complex and unloads its protons and drags 2 protons from stroma into thylakoid space
E- passed onto plastocyanin
259
How a photosystem harvests light
Light strikes chlorophyll molecules and energy is transferred between them and gets trough special chlorophyll a molecule
E- is excited and jumpts up into reaction centre
That energy is then passed down through Pq then through a cytochrome complex which can contribute to ATP synthesis and e- passed to Pc
260
Pq and Pc
Plastoquinone
| Plastocyanin - has copper so blue in colour
261
Chain of linear e- flow
PSII --cytochrome complex--> PSI
262
Splitting of water and O2 release at O2 (e- holes)
Initial e- donor is chlorophyll molecules
Protons knock e- out of orbits and form e-holes within atoms so must get e-
There are 4 Mn atoms arranged tgt in PSII, which can grab water and rip protons from O and e- from within to fill holes of chlorophyll molecules
Ultimate e- donor is water
263
Photosystem I - process
Light hits PSI
E- flow up to special acceptor molecules then to Fe-S complexes and reach ferrodoxin, which passes e- to NADP reductase
E- are used by NADP reductase and passed onto NADP+ --> NADPH (e- carrier) - has reducing power
Creates e- holes - Pc is carrying e-, which donates e- to fill the holes
264
Where does photosystem I occur
Stroma
265
Chloroplast ATPase (vs mitochondria ATPase)
Has 14 c-ring subunits compared to 8 in mitochondria - 6 more protons required to make ATPase turn than in mitochondria
Are dimers in mitochondria
266
Light reactions - there is a proton gradient developed by...
1. The splitting of water --> H+ released in thylakoid space
| 2. Cytochrome complex transfers 4 H+ into thylakoid space
267
Mitochondria vs chloroplasts - similarities
Have ETS
Create gradient
Make ATP through diffusion of H+ through ATPase
268
Chloroplasts vs mitochondria - focal points
Chloroplasts don't have focal points to create a microdomain
Mitochondria has MP that has electrical potential AND pH (conc of protons)
Chloroplasts are permeable to Mg2+ and Cl- --> lose electrical potential --> must pump more protons into thylakoid space to generate gradient --> low pH - doen't need focal points since pH diff quite large
269
Why are PSII and I separated
To do with cyclic electron flow
270
What is cyclic electron flow
The other route of PSI
271
Cyclic electron flow - process
Light hits chlorophyll (photon)
E- jump up and pass down to PQ (not NADPH) which passes e- to Q cycle --> plastocyanin and feed back
Fills its own holes
Can generate proton gradient without splitting water
272
Why is there structure in thylakoid membranes
Must separate linear and cyclic flow / pathways
273
Why have cyclic electron flow
Produces ATP only (no NADPH)
| C4 plants - require ATP
274
Why is Calvin cycle confined to stroma
Stops intermediates and products being metabolised, as some intermediates feed directly into glycolysis
Cell's normal pathway is full of glycolytic pathways so much keep separate or won't make sugar
275
Calvin cycle: Phases - fixation
Done by RuBisCo
3x 5C molecules --> 3x 6C molecules (unstable) --> 6x 3C molecules
Note: multiple molecules pass through the reactions so 6x ATP and NADPH
276
RuBisCo
Most abundant protein
Works / oxidised v slowly and v sensitive to changes in pH
Highly concentrated in chloroplasts
277
NADP vs NAD
As a rough rule, NADP/NADPH is involved in reducing reactions and NAD/NADH in oxidation reactions
NADPH tends to be used for biosynthesis/regeneration
278
Calvin cycle: Phases - reduction
Adds another phosphate and reduces it
| Enzymes involved are phosphoglycerate kinase (takes ATP) and G3P dehydrogenase
279
Calvin cycle: Phases - regeneration
After loss of 1x C3, 5x C3 are left
| These are rearranged to 3x C5 and RuBP is regenerated
280
Calvin cycle: To bind 3CO2...
Needs 6NADPH and 9ATP to give 6G3P (energetically expensive)
One is removed to make sugar
So 2 cycles required to make 1 glucose
281
Calvin cycle: Only 1 G3P available for subsequent conversion to...
Half a hexose
282
What is G3P
A simple triose sugar
283
Regulation of Calvin cycle
pH - more alkaline stroma = faster Calvin cycle rate. stromal pH rises when light reactions are working
Ferrethio reductase - needs NADPH to reduce/stabilise RuBisCo
Explains why RuBisCo doesn't work well in isolation and needs light
284
RuBisCo - issues?
Slow
Makes a useless/toxic product (2-phosphoglycolate) and wastes water
The faster it works, the more errors it makes (high temp increases rxn rate and error)
When O2 si high (low CO2), up to 20-30% of photosynthesis is wasteful
285
Evolution of a solution for photorespiration
```
Some plants (hot climates) can concentrate CO2 into oxaloacetate (4C plants)
Partitioning of specific cycle into diff leave cells
4C oxaloacetate used as a CO2 shuttle
```
286
C4 vs C3 plants
C4 have more spaces for gases
Diff arrangement of cells and how they feed into each other, e.g. how water is delivered
If temp high, stroma closes and regulates water loss and accumulates oxygen in leaves
287
C4 vs C3 plants - photorespiration
C4 plants don't photorespire as much as C3 plants
288
If C3 plants photosynthesise at a high rate...
O2 accumulates --> results in photorespiration - wasteful use of H2O and C already in CAC
289
Since C4 system concentrates CO2...
It decreases photorespiration
| C4 plants use more ATP, which comes from cyclic e- flow and sunlight is cheap
290
When do C4 plants work more efficiently
Ultimately C4 plants use water more efficiently and function better in warmer climates
291
Net reaction for glycogen synthesis
(glucose)n + glucose + 2UTP --> (glucose)n+1 + 2UDP + 2Pi
292
Net reaction for glycogen breakdown
(glucose)n + Pi --> (glucose)n-1 + glucose-P
293
Where is glycogen stored in most tissues
Cytosol
294
Glycogen - solubility
Insoluble
295
What is synthesis and breakdown of glycogen driven by
Synthesis driven by insulin
| Breakdown driven by glucagon
296
Which glycogen can release glucose to other tissues
Only glycogen in liver and a bit in kidney
297
Mass of glycogen in liver and muscles
Liver can store 8-10% of wet mass as glycogen
| Muscles can store 1-2% only - space limits in muscle
298
Types of bonds in glycogen
α-1,4-glycosidic bonds
| α-1,6-glycosidic bonds
299
What is glycogen synthesis called
Glycogenesis
300
Glycogenesis - process
Glucose goes through glucose transporter into hepatocyte but can equally go back, so must phosphorylate it to become G6P which is trapped by glucokinase in liver and hexokinase in muscle
G6P becomes G1P to be committed to glycogenesis
Pyrophosphorylase uses UTP
UDP glucose now visible to glycogen synthase --> makes glycogen - grows long chain
Gets to ~11 subunits long then a branching enzyme moves the sugars up 4 glycosyl units towards core and builds more to become more dense
301
Glycogenesis - energy
Uses energy - endergonic
302
Glycogenesis - where does the glycosyl group bind
The non-reducing ends, NOT the reducing end
| α-1-4 glycosidic bonds and α 1-6 glycosidic bonds
303
Branching of glycogen
Makes many termini = efficient storage and breakdown
Created by transfer of ~7 glycosyl residues
Each branch must grow to ~11 residues before transfer
New branches are exactly 4 residues away and move in towards core
304
What is glycogen breakdown called
Glycogenolysis
305
Adrenaline drives glucose _____
Release
If release is sustained, hypothalamus releases adrenocorticotropic hormone, which stimulates further release of adrenaline and cortisone --> enhances generation of glucose by liver and breakdown of glycogen
306
Glycogenolysis - enzymes
Glycogen phosphorylase
Glycogen de-branching enzyme (made of 2 enzymes)
Phosphoglucomutase
307
Glycogenolysis: Glycogen phosphorylase - energy requirement
Doesn't require ATP - uses Pi
308
Glycogenolysis: Glycogen phosphorylase - process
Uses Pi in cytosol and adds to glucose molecule - not a hydrolysis, but breaks bond by phosphorolysis
Forms G1P which is free into cytosol
Works until we get to 5th glycosyl units leaving 4 left
309
Glycogenolysis: Glycogen phosphorylase - why does it only reach the 5th glycosyl units
Due to steric hindrance - can't get all the way, but debranching enzyme can act as a transferase which transfers the 3 glycosyl units and leaves one, which is broken and hydrolysed (alpha-1,6) and glucose is free in cytosol
Remaining glucose is trapped using an ATP and hexokinase
310
Glycogenolysis: Glycogen phosphorylase - what is phosphoryolysis (not hydrolysis) important for
Hydrolysis will leave an un-phosphorylated glucose
Ensures released glucose is charged and trapped in cells - important in muscles
Saves an ATP each time - Pi is used directly, i.e. hexokinase isn't used
311
Glycogenolysis: Phosphoglucomutase
Phosphate rearranged so G1P --> G6P
Can be used for metabolism in cell
Bypasses first step of glycolysis --> *glycolysis of G6P will yield 3ATP*
312
Glycogenolysis: Glucose-6-phosphatase
Converts G6P to glucose, which can be used by blood and other tissues
Only in liver and kidneys
313
Coordinated control of glycogen metabolism
Stimulated/inhibited by glucagon or epinephrine (adrenaline)
2 cascades are activated by adrenaline - one switches glycogenolysis on, the other switches it off
Ensures glycogen is not being made as it's being broke down
314
Coordinated control of glycogen metabolism - cascade
A few molecules of adenylate kinase can make many molecules of cAMP (continuously for a while) which then interact with protein kinase A --> can have thousands which start to work on phosphorylase molecules and amplify the signal
315
Glycogen storage diseases
11 known types
Incidence ~2.5/100,000 births
7 result in muscle weakness or wastage
5 result in enlarged livers
316
Von Gierke's disease (type I GSD)
G6Pase mutation or deficiency (can't release glucose from liver)
Hypoglycaemia
Excess G6P in liver shunted to triglycerides --> hyperlipidaemia (high levels of blood lipids / fats)
Elevated lactate during fasting
G6P can be shunted into diff pathways, one of them being pentose phosphate pathway, which can be converted into uric acid - forms crystal in joints - gout (hyperuricaemia)
Enlarged liver and kidneys due to accumulated glycogen
Treatment fructose and other carbs
317
McArdle's disease
Glycogen in muscle but not released, but severe muscle cramps
Lack of glucose release, little glycogen (myo)phosphorylase activity in muscle
318
McArdle's disease: ADP level
Normal person: level of ADP doesn't change much from light exercise to heavy exercise
McArdle's disease: dramatic increase in ADP with light exercise (inhibits lots of processes in cells, e.g. muscle cramps)
- but if keep exercising and gain a second wind effect, ADP levels drop back down - shows the liver starts to release glucose but takes longer to occur
319
McArdle's disease: what can also be used to support glycolysis / respiration
Proteins
| Lipid by mitochondria, but not to same efficiency as glycolysis
320
What is the word for 'to make glucose'
Gluconeogenesis
321
Sources of building blocks for gluconeogenesis
```
Lactate --> pyruvate (Cori cycle)
Amino acids (except leucine and lysine)
Glycerol can be converted into glyceraldehyde and fed back up through gluconeogenic pathway (remainder of fats can't be used in animals to make glucose)
TCA/CAC intermediates fed around and out mitochondria and into gluconeogenic pathway(conversion to citrate/oxaloacetate/malate)
```
322
Cori cycle
Lactate is sent out to liver, which converts it back into glucose
323
Where does gluconeogenesis occur
Only occurs in liver
324
Overall gluconeogenesis equation
2pyruvate + 4ATP + 2GTP + 2NADH + 6H2O --> glucose 4ADP + 2GDP + 2NAD+ + 2H+ + 6Pi
325
Gluconeogenesis - reversing glycolysis?
If glycolysis is simply reversed, ΔG is +ve
| Using glyconeogenesis has -ve ΔG
326
Gluconeogenesis - ATP usage?
Overall uses 11-12 ATP equivalents
327
Gluconeogenesis - bypasses
```
3 bypasses required for kinases as they don't reverse:
Pyruvate kinase (bypass I)
PFK (bypass II)
Hexo/glucokinase (bypass III)
```
328
Gluconeogenesis - Bypass I
Enzymes: pyruvate carboxylase, phosphoenolpyruvate carboxykinase (PEPCK)
2 ATP equivalents used
NADH used = ~2.5-3 ATP
NADH used at GAPDH - more ATP
329
Gluconeogenesis - Bypass II
Enzyme: fructose 1,6-biphosphatase
ATP is not reformed - the phosphate is lost
330
Gluconeogenesis - Bypass III
Enzyme: glucose 6-phosphatase
ATP is not reformed - the phosphate is lost
331
Control of gluconeogenesis and glycolysis
Gluconeogenesis consumes ~12 ATP
GLycolysis makes +2 ATP (or +3 from glycogen)
--> mis-match of ~10 ATP
Thus the 2 pathways must not run at the same time or net effect will be we burn lots of ATP
Often will have opposite reaction from same metabolite on other side of pathway
332
After 3 days of starvation, the brain’s energetic requirements are met by...
β-hydroxybutyrate
Acetoacetate
Limited glucose
333
Why is anaerobic glycolysis very fast
Glycogen present in the cell can be rapidly mobilised
Doesn't rely on O2 diffusion into cell
Has fewer enzymatic steps than does the full oxidation of glucose to CO2 and H2O
334
In absence of O2, glycolysis only proceeds if...
NADH can be oxidised and pyruvate is reduced
335
The Cori cycle stores energy in the form of ____
Lactate
336
What compound delivers ATP to hardworking muscles at the fastest and slowest rate
Fastest: Creatine phosphate
Slowest: Stored fats oxidised to CO2
337
Which enzyme occurs in the liver and permits glucose release to the blood
G6Pase
338
Following intense exercise, blood lactate increases. This lactate is...
Oxidised by the heart and brain, or cleared through the liver by the Cori cycle
339
What method did Melvin Calvin and Andrew Benson to resolve the Calvin cycle?
Paper chromatography with radioisotopes
340
How many turns of the Calvin cycle is/are required to make a glucose molecule?
2
341
Mitochondria vs chloroplast ATPase - number of subunits
ATPase of chloroplast has more subunits in its C-ring --> requires a greater proton gradient to drive ATP synthase
342
Oxidised / reduced inorganic compounds can ultimately power life
Reduced
343
H+ inhibits/stimulates glycolysis
Inhibits
344
What process can C4 plants avoid
Photorespiration, but requires ATP
345
Dinitrophenol
Acts as an ionophore
| Dissipates the MP across the inner mitochondrial membrane
346
The cytochrome complex of photosynthetic organisms shows strong similarities to which complex within mitochondria
Complex III
347
It's hypothesised that e- move from each component of the Cyclic electron flow pathway in the following order...
Photosystem I --> ferredoxin --> cytochrome complex --> plastocyanin
