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BIOSCI 101 > Section 1: Bioenergetics > Flashcards

Section 1: Bioenergetics Flashcards

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1
Q

Formation of polymers

A

Forms through dehydration (- H2O)
Breaks through hydrolysis (+ H2O)

Constructed of monomers

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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

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3
Q

Types of polymers

A

Lipids
Polysaccharides (carbohydrates)
Proteins
Nucleic acid

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4
Q

Building block of lipids

A

Acetates, which join tgt to form acyl chains

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5
Q

Lipids and phosphate

A

Lipids can grow to form hydrophobic fatty acid (acyl) chains

Addition of phosphate makes fatty acids amphipathic

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6
Q

Acyl chains can be…

A

Saturated or unsaturated

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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)
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8
Q

Lipids: Structure of a fat molecule

A

Ester linkages, which link glycerol and acyl chains together

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9
Q

The cell membrane is formed of a…

A

Phospholipid bilayer

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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

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11
Q

How are sugars formed

A

From central pathways (trioses)

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12
Q

Monosaccharides

A

Single sugars

Different types

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13
Q

Disaccharides and oligosaccharides

A

Form from several mixed sugar types

Disaccharide: 2 sugar molecules

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14
Q

How are polysaccharides formed

A

Formed from many repeated sugar units connected by glycosidic bonds
Specific glycosidic bonds determine flexibility

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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)
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16
Q

Starch

A

A storage polysaccharide in plants
Polymer of glucose monomers
Stored as granules in plastids, e.g. chloroplasts

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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

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18
Q

Cellulose

A

Structural polysaccharide in plants
Polymer of glucose (not branched)
Stored in cell wall
Most abundant organic compound on Earth

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19
Q

α vs β glycosidic bonds

A

α1–>4: starch and glycogen
β1–>4: chitin and cellulose

Subtle difference, but profound effect

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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

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21
Q

Nucleic acids (RNA and DNA) - function

A

Involved in all informational processes
Storage of chemical energy in ATP
Intracellular signalling cAMP

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22
Q

Phosphodiester bond

A

PO4 3-

Formation leads to elimination of H2O (i.e. dehydration)

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23
Q

Components of nucleic acids

A

Sugar-phosphate backbone (phosphate group and sugar)
Nitrogenous base
5’ and 3’ end

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24
Q

Types of nitrogenous bases

A

Pyrimidines:
Cytosine (C)
Thymine (T in DNA)
Uracil (U in RNA)

Purines:
Adenine (A)
Guanine (G)

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25
Q

Sugars - DNA vs RNA

A

One of the Hs in deoxyribose (in DNA) is replaced by OH in ribose (in RNA)

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26
Q

How are proteins formed

A

Formed from amino acids connected through peptide bonds

Bonds formed through dehydration and break through hydrolysis

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27
Q

Properties of proteins determine…

A

Protein structure and function

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28
Q

Parts of an amino acid

A

Amine group
Carboxy terminus
R side group

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29
Q

Life and order

A

Life generates order (decreases entropy) and drives itself away from equilibrium, but at the expense of making more disorder (increasing entropy)

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30
Q

Passage of energy

A

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

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31
Q

Stored energy (via anabolic processes)

A

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

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32
Q

Where is energy conserved from oxidation reactions

A

Within phosphate bonds of ATP

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33
Q

What does ATP stand for

A

Adenosine triphosphate

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34
Q

Excess dietary fuel

A

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

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35
Q

Gibb’s free energy - equation

A

ΔG = ΔH - TΔS
ΔH (enthalpy) = q + w (aka heat + work done)
T (temperature)
ΔS (entropy)

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36
Q

ATP

A

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

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37
Q

How does ATP release energy

A

From electrically charged phosphates, which change molecular properties and do work

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38
Q

ATP phosphates

A

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-)

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39
Q

Two fundamental laws of thermodynamics

A
  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

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40
Q

Universe tends toward…

A

Disorder
More disorder –> increased entropy (rotting apple) - exothermic
More disorder –> going towards equilibrium

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41
Q

When a reaction reaches equilibrium…

A

They go no further

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42
Q

Anabolic processes

A

Build things up

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43
Q

Heat

A

The end result of all processes

Dissipates into the universe

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44
Q

Negative ΔG

A

The more -ve the ΔG, the greater the likelihood a reaction occurs

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45
Q

When is most ΔG in ATP released

A

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

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46
Q

Anabolic vs catabolic processes

A

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

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47
Q

Example of anabolic vs catabolic processes

A

Anabolic: photosynthesis in chloroplasts —organic molecules + O2—> cellular respiration in mitochondria
Catabolic: cellular respiration in mitochondria —CO2 + H2O—> photosynthesis in chloroplasts

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48
Q

Combustion of different food sources

A

Diff food sources release diff amounts of energy when combusted

Least to most:
Carbohydrate
Protein
Alcohol
Fat
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49
Q

Metabolism of different food sources

A 
Least to most:
Alcohol
Fat
Protein
Carbohydrate
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50
Q

Why is combustion different to metabolism

A

Access to C-C bonds, internal and not easily accessed
Metabolic enzymes work on C-H and O-H bonds
Molecules must be rearranged

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51
Q

Fat

A

May have less energy for outright mass, but stores well and has no associated water
Can’t be metabolised without O2

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52
Q

Stages of catabolism

A
  1. Hydrolysis of complex molecules to their building blocks
  2. Conversion of building blocks to Acetyl CoA
  3. Oxidation of acetyl CoA - oxidative phosphorylation
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53
Q

Acetyl-CoA

A

Hub molecule

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54
Q

ATP - structure

A

Phosphoanhydride bond - relatively stable in water

Phosphate group has resonance / charge delocalisation

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55
Q

Equilibrium vs non-equilibrium

A 
Equilibrium = less order = higher entropy
Non-equilibrium = ordered = low entropy

Life fights equilibrium/entropy

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56
Q

ΔG - purpose

A

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

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57
Q

What does the ° mean in ΔG°

A

Standard conditions
1 mol/L, pH 7, 25°C

In real life, these conditions are quite different - ΔG is maybe -50-60 kJ/mol

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58
Q

Exergonic reactions

A

Releases energy

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59
Q

Hydrolysis is dependent on..

A

Ratio of reactants to products

So, ATP is held at a high conc, and there is more reserve ATP

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60
Q

Human heart - ATP

A

Contains approx 700mg of ATP - enough to fuel one heartbeat per second for 10s

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61
Q

Formation of glutamine

A
  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

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62
Q

Does glycolysis require oxygen

A

No
It is an initial component of aerobic metabolism, but can also operate without oxygen by fermentation to produce lactate or ethanol, but inefficient

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63
Q

Glycolysis enzymes

A

Enzymes of glycolysis are arranged to form pathways, which increases efficiency of reactions
10 enzymes produce 2 ATP net

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64
Q

Two phases of glycolysis

A 
Energy investment (-2 ATP):
- Hexo/Glucokinase
- PFK
Energy harvesting (+4 ATP):
- Phosphoglycerate kinase
- Enolase
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65
Q

Important features of glycolysis

A

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

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66
Q

Glycolysis - steps

A
  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
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67
Q

Glycolysis - Hexokinase vs glucokinase

A

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

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68
Q

Glycolysis - net reaction

A

Glucose + 2NAD+ + 2Pi + 2ADP –> 2pyruvate + 2NADH + 2H+ + 2ATP + 2H2O

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69
Q

Stages of cellular respiration

A

Glycolysis - breaks down glucose into 2 pyruvate molecules
Citric Acid Cycle - completes breakdown of glucose
Oxidative phosphorylation - accounts for most of the ATP synthesis

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70
Q

Lactate

A

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

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71
Q

For sustained flow of glycolysis…

A

NAD+ must be regenerated

Anaerobic: NAD is regenerated by LDH (lactate dehydrogenase)

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72
Q

Glycolysis: Re-oxidation of NADH

A

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

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73
Q

Glycolysis: Speed and efficiency

A

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

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74
Q

Redox reactions

A

Oxidation: loss of electrons
Reduction: gain of electrons

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75
Q

Oxidation of C bonds

A

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

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76
Q

Redox reactions use…

A

Dehydrogenases

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77
Q

Energy release must be…

A

Controlled, otherwise explosions!

Thus cellular respiration is controlled energy captured in ATP

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78
Q

Glycolysis: NAD+

A

Acts as an electron shuttle

Water soluble

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79
Q

Glycolysis: Irreversible enzymes

A

Hexokinase or glucokinase
Phosphofructokinase
Pyruvate kinase

Highly regulated and irreversible in vivo

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80
Q

Glycolysis: At which point is glucose fully committed?

A

Phosphofructokinase (PFK)
Highly regulated point in pathway (most important regulator)
Another ATP invested

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81
Q

Glycolysis: What is PFK regulated by

A

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

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82
Q

Energy yield of glycolysis vs aerobic glucose oxidation

A

Energy yield of aerobic glucose oxidation much greater

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83
Q

Main functions of CAC cycle

A

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

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84
Q

CAC: Pyruvate (from glycolysis) is converted to…

A

Acetyl CoA, in an oxidative decarboxylation reaction by the pyruvate dehydrogenase complex
Then further oxidised to CO2

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85
Q

CAC: Acetyl CoA is produced in most pathways of…

A

Fuel oxidation

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86
Q

Coenzymes

A

Complex organic structures, which participate in enzymatic reactions

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87
Q

CAC: Coenzymes

A

Coenzyme A, NAD+ and FAD

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88
Q

CAC: NAD+ vs FAD

A

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

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89
Q

Where do most enzymatic reactions of CAC cycle occur

A

Mitochondrial matrix or bacterial cytosol

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90
Q

CAC: Oxidation reactions

A

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

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91
Q

CAC: Oxaloacetate

A

Regenerated in CAC after oxidation of NAD+ and FAD

Available to react with another molecule of acetyl CoA

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92
Q

Net energy yield from CAC and oxidative phosphorylation

A

High

~10ATP for each acetyl group oxidised

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93
Q

Energy yield from oxidation of NADH and FADH2 by electron transport and phosphorylation systems

A

~2.5 ATP per NADH oxidised

~1.5 ATP per FADH2 oxidised

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94
Q

The high-energy phosphate bond of GTP is generated by…

A

Substrate level phosphorylation

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95
Q

How does CAC ‘control’ ATP utilisation

A

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)

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96
Q

CAC: Examples of key regulatory enzymes

A 
Isocitrate dehydrogenase (IDH)
α-ketoglutarate dehydrogenase (αKDH)
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97
Q

CAC: During oxidation of each molecule of acetyl CoA…

A

Only one molecule of high-energy phosphate (GTP/ATP) is produced

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98
Q

CAC equation for 2 pyruvates

A

6CO2, 8NADH, 2FADH2, 2GTP (or 2ATP)

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99
Q

Endosymbiosis

A

A symbiotic relationship where one organism lives inside the other

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100
Q

Mitochondria

A

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

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101
Q

Junction between glycolysis and CAC

A

Irreversible step

Very large -ΔG and regulated

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102
Q

Vitamin B1 - Thiamine

A

Has thiamine pyrophosphate found within pyruvate dehydrogenase
TPP is within E1 - acts to remove CO2

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103
Q

CAC: GTP vs ATP

A

Liver makes GTP, muscle makes ATP

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104
Q

CAC: Succinate dehydrogenase (SDH)

A

Part of ETS Complex II
FAD+ bound within it
Sits in inner mitochondrial membrane
Directly connects oxidation to electron transfer

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105
Q

CAC: Amphibolic

A

Involves both catabolism and anabolism

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106
Q

CAC: If there is too much succinyl-CoA or acetyl-CoA…

A

CoA becomes limiting and CAC slows

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107
Q

CAC: ADP/ATP ratio regulates…

A

IDH activity
10/2 goes faster
2/10 goes slower

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108
Q

CAC: Ca2+ regulates…

A

PDH, aKDH and IDH

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109
Q

Cholesterol is an important component of…

A

Animal cell membranes

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110
Q

Glucose + glucose –>

A

Maltose + water (via dehydration)

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111
Q

Enzymatic reactions involved in glycolysis fatty acid breakdown and CAC cycle conserve most energy into _____

A

NADH and FADH2, which can transfer their electrical power into usable energy by transferring H+ across membranes

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112
Q

Respiratory complexes

A

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

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113
Q

Electron transport system - gradients

A

H+ accumulates on one side of membrane –> generates gradient, which is harnessed to synthesize ATP

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114
Q

Oxidation of NADH and FADH2 results in…

A

Release of electrons

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115
Q

What is the electron transport system (ETS)

A

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

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116
Q

ETS: The flow of electrons changes…

A

The charges of ETS protein complexes so they pump H+ or promote chemical reactions that transfer

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117
Q

ETS: Where are protons transferred

A

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

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118
Q

Electron transport carriers that oxidise NADH

A 
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

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119
Q

Co-enzyme Q

A

A lipid soluble molecule (not a protein)

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120
Q

Electrons flowing through the NADH pathway drive…

A

Proton pumps of complex I and IV, and the chemical transfer of protons at complex III
All develop a H+ gradient

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121
Q

Electron transport carriers that oxidise FADH2

A

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

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122
Q

ETS: Do electrons flow from CI to CII

A

No

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123
Q

Succinate dehydrogenase (SDH)

A

An enzyme of CAC

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124
Q

NADH vs FADH2 - redox potential

A

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

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125
Q

ETS: Flavin mononucleotide (FMN)

A

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

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126
Q

ETS: Poisons

A

Several poisons can react with molecules and blockage of ETC at any point prevents formation of ATP
e.g. cyanide

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127
Q

Ubiquinone vs ubiquinol

A

Ubiquinone has 2 C=O bonds
Ubiquinol replaces those carbonyl groups with two OH groups
Changes conformation

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128
Q

Cytochrome C

A

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

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129
Q

NADH has a much higher ____ than FADH2

A

Driving capacity

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130
Q

The energy from fuel oxidation is converted to ATP by the process of…

A

Oxidative phosphorylation

But, this requires transfer of electrons to oxygen and the coupling of this power to synthesize ATP

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131
Q

Mitochondria and energy demands

A

The location and number of mitochondria is correlated with a tissue’s energy demands

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132
Q

Complex I (NADH oxidase)

A 
Works as a proton pump
Pumps 4 protons per NADH
Large L-shaped protein
Contains FMN
7 FeS clusters
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133
Q

ΔG for NADH and FADH2

A

More negative for NADH

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134
Q

Iron-sulphur clusters

A

e- can effectively flow through these molecules as the Fe atoms can change oxidation state between Fe3+ and Fe2+

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135
Q

Complex I and II both…

A

Use Q10

Converge on CIII

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136
Q

Complex III

A

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)

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137
Q

Complex III: The complexity of the Q cycle is likely because…

A

Cytochrome C can only carry one e- at a time (aka cytochrome c oxidase) to CIV

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138
Q

Complex IV - overall

A

2 protons are pumped and the electrons flow to O2 to form H2O

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139
Q

Complex I - poisons

A

Blocked by some anesthetics and poison (rotenone)

Blocks binding point for ubiquinone

140
Q

Complex III - poisons

A

Antimycin a - binds to CIII and disrupts e- flow and locks it down

141
Q

Cytochrome C oxidase (CIV) - poisons

A

NO, H2S, CO and cyanide - bind to haeme groups –> stops oxygen flowing

142
Q

Complexes I, III and IV transfer __ protons

Complexes II, III and IV transfer __ protons

A

10 protons

6 protons

143
Q

NADH moves ____ hydrogens than FADH2

A

4 more

144
Q

What do flowing electrons power

A

Pumps and chemical transfer of H+ to form an electrochemical gradient (proton motive force / PMF), which is harnessed to drive ATP synthesis

145
Q

What is the ATP synthase

A

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
Q

Complete oxidation of one molecule of glucose to six molecules of CO2 and H2O yields…

A

Approx 30-32 molecules of ATP

147
Q

What is the most important regulator of oxidative phosphorylation

A

ADP

148
Q

Net yield of oxidative phosphorylation - NADH and FADH2

A

~2.5 moles of ATP per mole of NADH oxidised

~1.5 moles of ATP per mole of FADH2 oxidised

149
Q

Overall, how much ATP does 1 glucose produce

A

28-38

Variable

150
Q

What is the bacterial rhodopsin?

A

A light-driven proton pump

Pumps protons into vesicle (inside out?)

151
Q

What chemicals stop ATP synthesis

A

Chemicals that disrupt or ‘uncouple’ the proton gradient

Chemicals that poison electron flow

152
Q

Proton motive force - components

A 
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
Q

Where are ATP synthases located

A

All over ridges of cristae
Appear to form lines
Tightly arranged
Proteins arranged in a V-shape for mitochondria

154
Q

OXPHOS: How do protons flow?

A

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
Q

ATP synthase - steps

A
  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
Q

Internal rod - shape and function

A

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
Q

For each rotation of the internal rod…

A

3 ATP are made (because 3 sites) and protons drive the rotation

158
Q

Helicases - function

A

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
Q

Catalytic knob sub-units

A

Effectively are a helicase working in reverse with the gamma sub-unit in the centre

160
Q

NADH getting into mitochondria

A

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
Q

Malate aspartate shuttle

A

Slow, complicated, but efficient

162
Q

G3PDH shuttle

A 
Less efficient (because FADH2, which means loss of ~1 ATP), but fast
Multiple enzyme pathway
163
Q

Summing up - 1 glucose

A

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
Q

Why is the ATP yield (28-38) vague?

A
  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
Q

Leigh’s disease

A

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
Q

Damaged inner mitochondrial membranes - consequence

A

Increases leakiness to protons and structure changes

Consequences on ATP synthesis?

167
Q

How can uncoupling ATP synthesis be useful

A

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
Q

K(M) and affinity

A

High Km = need lots of glucose = low affinity

169
Q

NADH has ____

A

Energy

NAD+ can float through cell and carry energy from A to B (water soluble)

170
Q

Nicotinamine

A

Oxidised form - has a positive charge

Can add electron, which is added with an H+

171
Q

Glycolysis - substrate level phosphorylation

A

Capture ATP
Phosphoglycerate kinase and pyruvate kinase
Binds phosphate which has energy in it –> changes shape of enzyme –> grabs an ADP –> ATP

172
Q

PFK - properties

A

Quite slow working
Easy to turn on and off
Amount of PFK is not huge - controls how fast the reaction goes

173
Q

Two fates of glucose

A

Can feed into aerobic pathways

Can feed into anaerobic pathway - much less efficient but much faster

174
Q

Anaerobic - no O2

A

Can’t get rid of NADH at G3P

175
Q

Pyruvate - acidity

A

Quite acidic

176
Q

Production of lactate during anaerobic glycolysis

A

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
Q

Recycling of lactate

A

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
Q

CAC: Amino acids

A

Some amino acids can be fed directly into CAC

179
Q

Where are CAC enzymes found

A

In matrix of mitochondria

180
Q

Pyruvate breaks down into…

A

Acetate and CO2

181
Q

Pyruvate structure

A

Has a carboxylate at the end –> removed to form CO2

182
Q

Pyruvate dehydrogenase

A

A trifunctional enzyme (3 enzymes all arranged tgt)

183
Q

Vitamin B1 (thiamine) - process

A

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
Q

FADH - reactivity

A

Quite reactive - always found bound within proteins (never floating around)

185
Q

What does the A stand for in acetyl-CoA

A

Acetate

186
Q

Acetyl CoA

A

Has sulfur and acetate in it

Acetate can be fed into CAC

187
Q

CAC - carbons

A

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
Q

α-KDH vs PDH

A

Very similar - similar ancestral origins
Both poisoned by arsenic - binds to E2 and shuts it down
Same process, but recognise diff substrates

189
Q

Succinate dehydrogenase (SDH) - process

A

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
Q

FAD / FADH2 - structure

A

Have alloxan rings which can accept 2 Hs and thus carry e-

191
Q

CAC: Amphibolic - reactants and products

A 
Acetyl-CoA --> ACh
Citrate --> fatty acids
α-ketoglutarate --> glutamate
Succinate-CoA --> porphyrin (haemoglobin, cytochromes, chlorophyll)
Malate -> glucose (gluconeogenesis)
Oxaloacetate --> amino acid syntehsis
192
Q

Control of CAC - what slows down CAC

A

High ATP, acetyl-CoA, succinyl CoA and NADH

High NADH = lots of reducing power –> may drive unwanted rxns

193
Q

Pyruvate dehydrogenase (PDH) - regulation

A

Regulated allosterically
Pyruvate, AMP, NAD, Ca2+ speeds it up
Acetyl-CoA slows it down

194
Q

What does Ca2+ regulate

A

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
Q

Role of ETS

A

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
Q

ETS: Location of NADH and FADH

A

FADH situated lower, so packs less punch

NADH has a slightly higher potential (~1.135V) than FADH2 (~0.815V)

197
Q

ETS: Voltage

A

Voltage diff between top and bottom of ETS

198
Q

Complex I - where are the parts most likely from

A

Part in matrix likely from a primitive dehydrogenase

Part in membrane likely from ion pumps

199
Q

FMN vs NADH

A

FMN has greater reducing power –> can pull e- from NADH

200
Q

Complex I - cavities

A

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
Q

ETS: Quinones

A

Can accept 2e- by binding 2Hs to form 2 OH groups
Q10 = ubiquinone
Q9 = ubiquinol
Ubiquinone –accepts 1H–> semiquinone –accepts another H–> ubiquinol

202
Q

Complex II

A

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
Q

Heme molecule

A

Iron atom surrounded by a porphyrin ring

204
Q

Which similar system is found in photosynthesis

A

Complex III

205
Q

How does rotenone work

A

Ubiquinone and rotenone have similar groups, so it can get into cleft and jams in there - irreversible

206
Q

Cytochromes

A

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
Q

If add rotenone, what happens to e- in ETS

A

Stops e- flowing at complex I –> run out of e- at end of chain
Cytochromes / ETS becomes oxidised

208
Q

If add antimycin, what happens to e- in ETS

A

Poisons CIII
End of ETS loses e- –> becomes oxidised
Start of ETS (CI and Q) - accumulation of e- at CIII –> start becomes reduced

209
Q

If add cyanide, what happens to e- in ETS

A

Blocks CIV

E- stops at CIV –> builds up –> whole chain is reduced

210
Q

If hypoxia (low) or anoxia (no) oxygen, what happens to e- in ETS

A

E- builds up (can’t bind with water) –> ETS reduction

211
Q

ETS: How many protons do the complexes pump

A

CI: 4
CIII: 4
CIV: 2
CII: 0

212
Q

NADH vs FADH - how many Hs do they move

A

NADH moves 4 more Hs than FADH (FADH less reducing power)

213
Q

Proton motive force - charge

A

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
Q

pH difference across mitochondria

A

Not that large, and for ATP synthase to turn, needs a pH difference of 2 (quite large)

215
Q

Cristae work as…

A

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
Q

Protons flowing through ATP synthases - steps

A

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
Q

ATP synthase: Catalytic region is made from…

A

3 alpha and 3 beta subunits

218
Q

Brown adipose tissues

A

Uncoupling of ATP synthesis
Allows protons to flow back through the protein
Short circuits the ETS

219
Q

Cellular respiration: Adding succinate (substrate for CII)

A

Succinate provides e- that gets ETS to pump protons

MP increases

220
Q

Cellular respiration: Adding succinate then ADP and Pi

A

Addition of Pi drops MP a bit, but not all the way to baseline
Still maintains a MP

221
Q

Cellular respiration: Adding succinate, ADP and Pi, then oligomycin (inhibitor of ATP synthase)

A

Oligomycin creates a block on ATP synthase
ETS pumps a lot and starts to fill IMS with protons –> MP increases
Decreases respiration rate

222
Q

Cellular respiration: Adding succinate, ADP and Pi, then dinitrophenol (DNP)

A

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
Q

What is photosynthesis

A

The process of capturing and converging solar (electromagnetic) energy into chemical energy by plants, algae and bacteria

224
Q

Photosynthesis equation

A

6CO2 + 6H2O –>LIGHT–> C6H12O6 + 6O2

225
Q

Photosynthesis - What is reduced and what is oxidised

A

CO2 is reduced

H2O is oxidised - this is the only process in the whole of biology where water is oxidised

226
Q

Photosynthesis can be broken down into…

A

2 processes;

  1. Light reactions
  2. Calvin Cycle (dark reactions)
227
Q

Where does photosynthesis take place

A

Chloroplasts, mostly found in cells located just below the surface of the leaf

228
Q

Chloroplasts - structure

A

Highly organised internal structures

Contain pigments which can absorb visible light, generally referred to as chromophores

229
Q

Best known chromophore

A

Chlorophyll

230
Q

Chlorophyll - structure

A

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
Q

Photosystem names

A

PSII and PSI (in this order!)

232
Q

Photosynthesis: Light reactions - how is energy transferred between chlorophyll molecules

A

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
Q

Photosynthesis: Light reactions - what happens to the electron-deficient chlorophyll

A

It extracts an e- from another donor and cycle can be repeated

234
Q

Electron donors for PSI and PSII

A

Water is ultimate electron donor for PS2

Plastocyanin (a special e- carrier) is e- donor for PSI

235
Q

Photosynthesis: Light reactions - equation

A

2H2O + 2NADP –> Light –> 2H+ + O2 + 2NADPH2 (+ ATP)

236
Q

Photosynthesis: Non-cyclic / linear photophosphorylation

A

The production of ATP and NADPH using the flow of e- from PSII to PSI

237
Q

Cyclic electron flow

A

Under certain conditions, photoexcited e- within PSI can take an alternative path called cyclic electron flow, which makes only ATP

238
Q

What is produced in light reactions that is used in the Calvin cycle

A

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
Q

Calvin cycle - input of light

A

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
Q

Calvin cycle - phases

A

Carbon fixation
Reduction
Regeneration of carrier (RBP)

241
Q

Calvin cycle - carrier

A 
Ribulose bisphosphate (RuBP)
CO2 is fixed to RuBP by enzyme ribulose bisphosphate carboxylase (RiBisCo)
242
Q

Product of Calvin cycle

A

A molecule of G3P, which requires input of 3CO2, 9ATP and 6NADPH

243
Q

How is glucose stored in plants

A

As starch and sucrose, which act as an energy source for plants

244
Q

Photorespiration

A

Where O2 competes with CO2 at RuBisCo

Undesirable for farmers

245
Q

Photorespiration - C4 plants

A

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
Q

Why does RuBisCo bind oxygen

A

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
Q

How do C4 plants capture CO2

A

Using enzymes associated with other common pathways, e.g. phosphoenolpyruvate carboxylase

248
Q

C4 plants - Phosphoenolpyruvate carboxylase

A

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
Q

Main types of chlorophyll

A

Chlorophyll a and b

250
Q

Photoreceptive componds within the chloroplast are grouped tgt with other compounds to form…

A

Photosystems, and it is these complexes which absorb light

251
Q

Processes within photosystems are called the… and include…

A

Light reactions

  • splitting of water
  • NADP+ reduction
  • H+ gradient generation
252
Q

Thylakoid membrane - permeability

A

Impermeable to most ions and molecules, but not Mg2+ and Cl-

253
Q

Where do light reactions take place

A

Molecules in the thylakoid membrane

254
Q

Where do dark reactions (Calvin cycle) take place

A

Stroma

255
Q

Photosynthesis uses mostly _____ light

A

Blue and red
i.e. these are the colours primarily absorbed and green is reflected

Lack of absorbance at 500-600nm

256
Q

Excitation of isolated chlorophyll molecule

A

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
Q

Photosystem II structure

A

Chlorophyll molecules juxtaposed very closely tgt

258
Q

Photosystem II - process

A

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
Q

How a photosystem harvests light

A

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
Q

Pq and Pc

A

Plastoquinone

Plastocyanin - has copper so blue in colour

261
Q

Chain of linear e- flow

A

PSII –cytochrome complex–> PSI

262
Q

Splitting of water and O2 release at O2 (e- holes)

A

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
Q

Photosystem I - process

A

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
Q

Where does photosystem I occur

A

Stroma

265
Q

Chloroplast ATPase (vs mitochondria ATPase)

A

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
Q

Light reactions - there is a proton gradient developed by…

A
  1. The splitting of water –> H+ released in thylakoid space

2. Cytochrome complex transfers 4 H+ into thylakoid space

267
Q

Mitochondria vs chloroplasts - similarities

A

Have ETS
Create gradient
Make ATP through diffusion of H+ through ATPase

268
Q

Chloroplasts vs mitochondria - focal points

A

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
Q

Why are PSII and I separated

A

To do with cyclic electron flow

270
Q

What is cyclic electron flow

A

The other route of PSI

271
Q

Cyclic electron flow - process

A

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
Q

Why is there structure in thylakoid membranes

A

Must separate linear and cyclic flow / pathways

273
Q

Why have cyclic electron flow

A

Produces ATP only (no NADPH)

C4 plants - require ATP

274
Q

Why is Calvin cycle confined to stroma

A

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
Q

Calvin cycle: Phases - fixation

A

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
Q

RuBisCo

A

Most abundant protein
Works / oxidised v slowly and v sensitive to changes in pH
Highly concentrated in chloroplasts

277
Q

NADP vs NAD

A

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
Q

Calvin cycle: Phases - reduction

A

Adds another phosphate and reduces it

Enzymes involved are phosphoglycerate kinase (takes ATP) and G3P dehydrogenase

279
Q

Calvin cycle: Phases - regeneration

A

After loss of 1x C3, 5x C3 are left

These are rearranged to 3x C5 and RuBP is regenerated

280
Q

Calvin cycle: To bind 3CO2…

A

Needs 6NADPH and 9ATP to give 6G3P (energetically expensive)
One is removed to make sugar
So 2 cycles required to make 1 glucose

281
Q

Calvin cycle: Only 1 G3P available for subsequent conversion to…

A

Half a hexose

282
Q

What is G3P

A

A simple triose sugar

283
Q

Regulation of Calvin cycle

A

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
Q

RuBisCo - issues?

A

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
Q

Evolution of a solution for photorespiration

A 
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
Q

C4 vs C3 plants

A

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
Q

C4 vs C3 plants - photorespiration

A

C4 plants don’t photorespire as much as C3 plants

288
Q

If C3 plants photosynthesise at a high rate…

A

O2 accumulates –> results in photorespiration - wasteful use of H2O and C already in CAC

289
Q

Since C4 system concentrates CO2…

A

It decreases photorespiration

C4 plants use more ATP, which comes from cyclic e- flow and sunlight is cheap

290
Q

When do C4 plants work more efficiently

A

Ultimately C4 plants use water more efficiently and function better in warmer climates

291
Q

Net reaction for glycogen synthesis

A

(glucose)n + glucose + 2UTP –> (glucose)n+1 + 2UDP + 2Pi

292
Q

Net reaction for glycogen breakdown

A

(glucose)n + Pi –> (glucose)n-1 + glucose-P

293
Q

Where is glycogen stored in most tissues

A

Cytosol

294
Q

Glycogen - solubility

A

Insoluble

295
Q

What is synthesis and breakdown of glycogen driven by

A

Synthesis driven by insulin

Breakdown driven by glucagon

296
Q

Which glycogen can release glucose to other tissues

A

Only glycogen in liver and a bit in kidney

297
Q

Mass of glycogen in liver and muscles

A

Liver can store 8-10% of wet mass as glycogen

Muscles can store 1-2% only - space limits in muscle

298
Q

Types of bonds in glycogen

A

α-1,4-glycosidic bonds

α-1,6-glycosidic bonds

299
Q

What is glycogen synthesis called

A

Glycogenesis

300
Q

Glycogenesis - process

A

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
Q

Glycogenesis - energy

A

Uses energy - endergonic

302
Q

Glycogenesis - where does the glycosyl group bind

A

The non-reducing ends, NOT the reducing end

α-1-4 glycosidic bonds and α 1-6 glycosidic bonds

303
Q

Branching of glycogen

A

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
Q

What is glycogen breakdown called

A

Glycogenolysis

305
Q

Adrenaline drives glucose _____

A

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
Q

Glycogenolysis - enzymes

A

Glycogen phosphorylase
Glycogen de-branching enzyme (made of 2 enzymes)
Phosphoglucomutase

307
Q

Glycogenolysis: Glycogen phosphorylase - energy requirement

A

Doesn’t require ATP - uses Pi

308
Q

Glycogenolysis: Glycogen phosphorylase - process

A

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
Q

Glycogenolysis: Glycogen phosphorylase - why does it only reach the 5th glycosyl units

A

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
Q

Glycogenolysis: Glycogen phosphorylase - what is phosphoryolysis (not hydrolysis) important for

A

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
Q

Glycogenolysis: Phosphoglucomutase

A

Phosphate rearranged so G1P –> G6P
Can be used for metabolism in cell
Bypasses first step of glycolysis –> glycolysis of G6P will yield 3ATP

312
Q

Glycogenolysis: Glucose-6-phosphatase

A

Converts G6P to glucose, which can be used by blood and other tissues
Only in liver and kidneys

313
Q

Coordinated control of glycogen metabolism

A

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
Q

Coordinated control of glycogen metabolism - cascade

A

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
Q

Glycogen storage diseases

A

11 known types
Incidence ~2.5/100,000 births
7 result in muscle weakness or wastage
5 result in enlarged livers

316
Q

Von Gierke’s disease (type I GSD)

A

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
Q

McArdle’s disease

A

Glycogen in muscle but not released, but severe muscle cramps
Lack of glucose release, little glycogen (myo)phosphorylase activity in muscle

318
Q

McArdle’s disease: ADP level

A

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
Q

McArdle’s disease: what can also be used to support glycolysis / respiration

A

Proteins

Lipid by mitochondria, but not to same efficiency as glycolysis

320
Q

What is the word for ‘to make glucose’

A

Gluconeogenesis

321
Q

Sources of building blocks for gluconeogenesis

A 
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
Q

Cori cycle

A

Lactate is sent out to liver, which converts it back into glucose

323
Q

Where does gluconeogenesis occur

A

Only occurs in liver

324
Q

Overall gluconeogenesis equation

A

2pyruvate + 4ATP + 2GTP + 2NADH + 6H2O –> glucose 4ADP + 2GDP + 2NAD+ + 2H+ + 6Pi

325
Q

Gluconeogenesis - reversing glycolysis?

A

If glycolysis is simply reversed, ΔG is +ve

Using glyconeogenesis has -ve ΔG

326
Q

Gluconeogenesis - ATP usage?

A

Overall uses 11-12 ATP equivalents

327
Q

Gluconeogenesis - bypasses

A 
3 bypasses required for kinases as they don't reverse:
Pyruvate kinase (bypass I)
PFK (bypass II)
Hexo/glucokinase (bypass III)
328
Q

Gluconeogenesis - Bypass I

A

Enzymes: pyruvate carboxylase, phosphoenolpyruvate carboxykinase (PEPCK)

2 ATP equivalents used
NADH used = ~2.5-3 ATP
NADH used at GAPDH - more ATP

329
Q

Gluconeogenesis - Bypass II

A

Enzyme: fructose 1,6-biphosphatase

ATP is not reformed - the phosphate is lost

330
Q

Gluconeogenesis - Bypass III

A

Enzyme: glucose 6-phosphatase

ATP is not reformed - the phosphate is lost

331
Q

Control of gluconeogenesis and glycolysis

A

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
Q

After 3 days of starvation, the brain’s energetic requirements are met by…

A

β-hydroxybutyrate
Acetoacetate
Limited glucose

333
Q

Why is anaerobic glycolysis very fast

A

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
Q

In absence of O2, glycolysis only proceeds if…

A

NADH can be oxidised and pyruvate is reduced

335
Q

The Cori cycle stores energy in the form of ____

A

Lactate

336
Q

What compound delivers ATP to hardworking muscles at the fastest and slowest rate

A

Fastest: Creatine phosphate
Slowest: Stored fats oxidised to CO2

337
Q

Which enzyme occurs in the liver and permits glucose release to the blood

A

G6Pase

338
Q

Following intense exercise, blood lactate increases. This lactate is…

A

Oxidised by the heart and brain, or cleared through the liver by the Cori cycle

339
Q

What method did Melvin Calvin and Andrew Benson to resolve the Calvin cycle?

A

Paper chromatography with radioisotopes

340
Q

How many turns of the Calvin cycle is/are required to make a glucose molecule?

A

2

341
Q

Mitochondria vs chloroplast ATPase - number of subunits

A

ATPase of chloroplast has more subunits in its C-ring –> requires a greater proton gradient to drive ATP synthase

342
Q

Oxidised / reduced inorganic compounds can ultimately power life

A

Reduced

343
Q

H+ inhibits/stimulates glycolysis

A

Inhibits

344
Q

What process can C4 plants avoid

A

Photorespiration, but requires ATP

345
Q

Dinitrophenol

A

Acts as an ionophore

Dissipates the MP across the inner mitochondrial membrane

346
Q

The cytochrome complex of photosynthetic organisms shows strong similarities to which complex within mitochondria

A

Complex III

347
Q

It’s hypothesised that e- move from each component of the Cyclic electron flow pathway in the following order…

A

Photosystem I –> ferredoxin –> cytochrome complex –> plastocyanin

BIOSCI 101 (4 decks)

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