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Year 2: Semester 1 > Biostructures, Synthesis, energetics > Flashcards

Biostructures, Synthesis, energetics Flashcards

1
Q

What is the tendency of entropy?

A

To always increase.

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2
Q

What is the “central dogma of energy conversion”?

A

Release -> Transfer -> Trapping

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3
Q

What is delta P?

A

The proton motive force.

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4
Q

What are reductants?

A

Molecules broken down via metabolism to release electrons -> transferred via coupled reaction with protons pumps (redox) -> force to synthesise ATP

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5
Q

What causes a motive force?

A

Displacing reactions from equilibrium.

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6
Q

What is the function of Transhydrogenase?

A

Synthesise reductants

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7
Q

What photosystems are used by phototrophs?

A

Photosystems 1 + 2

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8
Q

What are the 3 pieces of evidence for Chemiosmotic Theory:

A

-Jagendorf Acid Bath
-DNP addition
-Isolated Bacteriorhodopsin with Beef Heart ATP Synthase.

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9
Q

Jagendorf Bath Experiment.

A

thylakoid incubated a pH 4 in dark (using weak permeable acid e.g. succinate) -> Transferred to high pH medium -> forms deltaP -> Allows for ATP synthesis when ADP and Pi are added.

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10
Q

DNP as evidence for chemisomosis:

A

DNP acts as an uncoupler, it facilitates the diffusion of protons across the membrane -> prevent formation of pmf -> abolishing ATP synthesis.

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11
Q

Bacteriorhodopsin reconstitution as evidence for chemiosmosis:

A

The pump is isolated and reconstituted onto a lipid vessicle with ATP synthase from beef heart -> in presence of ADP and Pi -> ATP synthesis can occur.

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12
Q

Where do dark reactions occur?

A

In the stroma.

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13
Q

What is the generic role of chlorophyll?

A

Light Harvesting

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14
Q

Similarity between chlorophyll and Haem?

A

-Both have a tetrapyrrole ring (similar to benzene ring having a conjugate pi electron system)
- Both have a prosthetic group (Mg2+ and Fe2+)

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15
Q

What structure in chlorophyll is responsible for light absorption?

A

The tetrapyrrole ring tuned by Mg2+

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16
Q

Where do the light reactions take place?

A

In the Thylakoid Membrane (ATP synthase, PSII, PSI, Cytochrome b6f)

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17
Q

What occurs in a chlorophyll pigment upon absorption of light?

A

An electron in the tetrapyrrole ring is excited to a higher energy level.

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18
Q

What is the Q cycle process?

A

The two different routes of electrons from Plastoquinol in the cytochrome b6f complex.

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19
Q

Where is plastoquinone and ubiquinone

A

Plastoquinone is in the thylakoid, Ubiquinone is in the mitochondria.

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20
Q

What does endergonic mean?

A

“uphill” reaction requiring an input of energy.

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21
Q

What is the special pair of chlorophylls called in PSII?

A

P680

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22
Q

What is the special pair of chlorophylls called in PSI?

A

P700

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23
Q

What does PSII oxidise and reduce?

A

Oxidises Water
Reduces Plastoquinone into plastoquinol

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24
Q

What does PSI oxidise and reduce?

A

Oxidises plastocyanin and reduces ferrodoxin -> which donates electrons to NAD+ -> NADPH

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25
Q

What are the products of water oxidisation?

A

2H2O -> O2 + 4H+ + 4e-

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26
Q

What is the effect of exciting the special chlorophyll pair?

A

Gives it a more negative redox potential, allowing it to donate its electron to downstream components in the electron transport chain.

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27
Q

What is the order of components in PSII?

A

P680 -> Plastoquinone (reduction) -> Cytochrome b6f -> Photosynthetic complex -> P700 (PSI) -> ferrodoxin -> NADP+

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28
Q

What is the structure of a photosystem?

A

An antenna complex of hundreds of accessory chlorophyll pigments that transfer light energy to the reaction centre to a special pair of redox active chlorophyll.

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29
Q

What is the purpose of oxidising in PSI and PSII?

A

To restore the electron lost by the photosystem.

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30
Q

What is the purpose of the antenna complex within photosystems?

A

To concentrate light in the reaction centre to maximise electron excitation within turnover capacity. (despite shade)

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31
Q

How does the R-group on the tetrapyrrole ring differ between Chlorophyll a and chlorophyll b?

A

A has a methyl group and B has a CHO (aldehyde) group

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32
Q

What is the effect of the differing R-groups on chlorophyll a and chlorophyll b?

A

They affect the electron environment, affecting the absorbance spectrum, therefore the combination of both allows for the absorption of a wider range of wavelengths.

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33
Q

What is the antenna structure of PSII?

A

PSII forms a dimeric super structure with Light Harvesting Complex II (LHCII) -> multiple antenna proteins provide large spatial cross-section for light absorption.

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34
Q

What is the antenna structure of PSI?

A

PSI forms a monomeric supercomplex with Light Harvesting Complex I -> multiple antenna proteins provide large spatial cross-section for light absorption.

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35
Q

What is meant by photosystem antenna structures being modular?

A

The LHC can grow more/less depending on the conditions. (more under low light, less under high light).

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36
Q

What do shapes on light spectra correspond to?

A

The jumps electrons make between orbitals (energy levels)

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37
Q

What is the oxygenic evolving complex?q

A

Site of water oxidation attached to reaction centre of PSII

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38
Q

What causes plants to fluoresce?

A

After time excited electrons will re-enter the ground centre, emitting light.

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39
Q

What photons are absorbed by molecules?

A

Photons with energy equal to that of the energy gap between electronic states.
(Blue S0 -> S2 and Red S0 -> S1)

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40
Q

How quickly does light absorption occur?

A

On a femtoseconds (10^-15s)

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41
Q

What is FRET?

A

Forster Resonance Energy Tranfer

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42
Q

What is the process of FRET?

A

When two chlorophylls are in close proximity, excited electrons in overlapping energy levels -> allow for electron in S1 to donate energy to a neighbouring chlorophyll molecule, exciting its electron to S1.

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43
Q

In what forms is energy lost as in chlorophyll after electron excitation?

A

Lost as heat (S2 -> S1) or as vibration or fluorescence emission (S1 -> S0) (stoke shift as light emission is more red than light absorbed)

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44
Q

Over what distances is FRET efficient?

A

Short distances of 7nm<

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45
Q

What is resonance?

A

Overlapping energy levels causing a transfer of energy.

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46
Q

What is the purpose of FRET?

A

Provides a downhill pathway for electron excitation to be directed to the Reaction Centre whilst minimising energy loss.

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47
Q

What is responsible for the directionality of the attenae complex?

A

The environment surrounding the chlorophyll and their bound r-groups affects the energy of their S1 excitation levels, pigments with lower energy levels are positioned closer to the RC.

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48
Q

Light Harvesting Complex 2: Structure

A

-Hydrophobic and Uniform.
-4x carotenoids
-6x Chlorophyll b
-8x chlorophyll a

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49
Q

What is the redox potential required for the oxidation of water?

A

Atleast +820mV

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50
Q

What is the reaction that occurs at Photosystem II?

A

2H2O + 2PQ + 4H+(stroma) -> O2 + 2PQH2 + 4H+(lumen)

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51
Q

What is the primary electron donor in the reaction at PS II?

A

The special pair chlorophyll P680

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52
Q

What is efficiency of the PSII reaction?

A

40%

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53
Q

What are the key co-factors that take part in the electron transfer reactions from water to plastoquinone? (PSII)

A

Chlorophyll aa and chlorophyll ab -> pheophytin (a + b), plastoquinone (Qa + Qb), tyrosine 161, manganese cluster.

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54
Q

How does the electron travel to reduce plastoquinone in PSII?

A

A chlorophyll a undergoes charge separation upon the induction of light energy at the reaction centre -> the electron moves towards stromal side across the co-factors onto plastoquinone Qb. The electron hole on the chlorophyll a is filled by water bound to the manganese cluster. -> process repeats -> and once two electrons have attached to plastoquinone Qb -> plastoquinol will dissociate.

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55
Q

What is the purpose of the manganese cluster in PSII?

A

To catalyse the oxidation of water (hydrolysis)

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56
Q

What is the role of tyrosine 161?

A

To transfer an electron from the manganese cluster to the RC to fill the electron hole.

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57
Q

How does the manganese cluster oxidate water?

A

It accumulates a +4 charge as it donates electrons to the P680* ->

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58
Q

What groups of plastoquinone are reduced?

A

Two carbonyl groups either side of a hex-2,5-diene

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59
Q

What is the function of plastoquinone’s large tail?

A

to aid its lipid solubility.

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60
Q

How many turnovers of the PSII are required for one full reaction?

A

2 turnovers (4 photons)

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61
Q

Other than the reduction of Plastoquinone into Plastoquinol, what is the additional function of PSII?

A

The pumping of H+ from the stroma into the lumen.

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62
Q

What is the shape/arrangement of cofactors in PSII?

A

A horse shoe arrangement.

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63
Q

What is the name of the combination of a photosystem and light harvesting complex?

A

a supercomplex.

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64
Q

What structural feature of PSI prevents the escape of electrons from the RC?

A

Neutral zone surrounding the RC.

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65
Q

What is the efficiency of the PSI reaction?

A

44%

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66
Q

What is the overall reaction of PSI?

A

Pc(red) + Fd(ox) -> Pc(ox) + Fd(red)

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67
Q

What is the electron donor in PSI?

A

Plastocyanin.

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68
Q

Structure of Plastocyanin:

A

2x Histeine, Cysteine, and methionine residues coordinate the active site

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69
Q

What is the redox potential of the P700* centre in PSI?

A

-1320 mV -> sufficient to reduce 2Fe-2S cluster of ferredoxin (-420 mV)

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70
Q

What are components of PSI?

A

The special pair of chlorophylls, Phylloquinone, and iron-sulphur clusters.

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70
Q

What is the role of reduced ferredoxin?

A

Acts as a powerful reductant that can reduce NADP+ into NADH and NO3 into NH4.

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70
Q

What is Marcus Theory:

A

An explanation of the rates of ET reactions where participants don’t undergo large changes -> smaller gradual changes less thermodynamically feasible occur more quickly than one very feasible larger step.

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71
Q

What is the redox potential of the P700 centre in PSI?

A

+480mv -> this is insufficient to oxidise water.

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72
Q

What is reorganisation energy?

A

When an electron is transferred the molecules around the donor/acceptor have to move to accommodate the change of charge -> energy is used to do this.

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73
Q

When is the rate of electron transfer optimal?

A

When reorganisation energy = delta G

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74
Q

How is energy loss by heat minimised in reaction centres?

A

The e- and +ve hole are quickly separated physically and energetically to prevent their recombination and ensuing heat loss.

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75
Q

Water oxidation cycle:

A

2H2O -> HO + H2O -> HO + H2O -> HO + HO -> HO + HO -> H2O + H2O

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76
Q

What occurs at each step of the water oxidation cycle? (to the manganese cluster)

A

The manganese cluster loses an electron each step, until it’s regenerated via the oxidation of Water.

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77
Q

What is inputted to the water oxidation cycle to regenerate it?

A

2 H2O molecules.

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78
Q

How many electrons are released in one cycle of the water oxidation cycle?

A

4 electrons.

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79
Q

What are components of Cytochrome b6f?

A

(2x plastaquinone, 1x carotenoid, 1x chlorophyll, 4 haem groups, 1 2Fe2S cluster } Per monomer in complex dimer

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80
Q

What is cytochrome b6f similar to?

A

Cytochrome in mitochondria.

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81
Q

What is the purpose of the carotenoid and chlorophyll portion of cytochrome b6f?

A

No clear purpose as cytochrome doesn’t use light harvesting.

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82
Q

What are the redox active cofactors in Cytochrome b6f?

A

Haem groups and 2Fe”S clusters.

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83
Q

What is the function of redox active cofactors in an electron transfer chain?

A

To carry the electron across through complexes.

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84
Q

What are the two types of haem groups in cytochrome b6f?

A

c-types (covalently linked to proteins via cysteine side chains)
b-types(linked via coordination bonds usually from histidine lone pair on nitrogen ligates to central Fe iron of haem group)

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85
Q

What is Bifurcated electron transfer?

A

The electrons are transferred but take two different paths, occurs in cytochrome b6f.

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86
Q

What type of electron carrier is plastoquinol?

A

A 2 electron 2 proton carrier.

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87
Q

At cytochrome b6f what and where does plastoquinol reduce?

A

Plastoquinol reduces the 2Fe2S cluster and the Haem Bp

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88
Q

What is the destination of the electron transferred to the 2FE2S cluster in cytochrome b6f?

A

Haem f (c-type)and then reduces Plastocyanin (ox) into Plastocyanin (red)

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89
Q

What type of electron carrier is plastocyanin?

A

A 1 electron carrier.

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90
Q

What is the high potential chain of cytochrome b6f?

A

The reduction of plastocyanin.

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91
Q

What is the low potential chain of cytochrome b6f?

A

The reduction of a stromal plastoquinone molecule into platoquinol (occurs after two runs)

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92
Q

What molecule in plastocyanin allows for it to accept electrons?

A

Cu centre.

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93
Q

What is the destination of the electron transferred to the Haem Bp in cytochrome b6f?

A

The electron is then transferred to Haem Bn and then Haem C -> Will then transfer to stromal plastoquinone after two runs.

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94
Q

What is the function of recycling one of the electrons from Plastoquinol to form plastoquinol at cytochrome b6f?

A

It doubles the number of protons transferred from the stroma to the lumen per PQH2 oxidised -> boosting its contribution to the pmf.

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95
Q

What the Ferredoxin-NADP+ reductase’s 2 domains?

A

-FAD binding domain
-NADP+ binding domain

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96
Q

What is an FAD domain?

A

A flavin adenine dinucleotide.

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97
Q

What is the name of the 3rd protein complex in the electron transport chain in the thylakoid membrane?

A

Ferredoxin-NADP+ reductase (FNR)

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98
Q

What are the steps of NADP reduction at the FNR?

A
  • Binding of NADP+ and Fd to binding domains
  • Fd donates electron to FAD and disociates x2
    -The two electrons reduce NADP+ -> recruits a proton to form NADPH -> disociates.
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99
Q

What is the proton/ATP ratio in the chloroplast?

A

4.67

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100
Q

How many ATPs are formed per NADPH in photosynthesis?

A

1.28, however this needs to be 1.5 for the efficient functioning of photosynthesis.

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101
Q

How is the redox imbalance of photosynthesis (ATP/NADPH) corrected?

A

Redox balance -> a second type of electron transport takes place (cyclic electron transport).

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102
Q

What are the two complexes that participate in cyclic electron transport?

A

PGR5 and the photosynthetic complex 1.

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103
Q

What is the function of Photosynthetic complex 1 in redox balance?

A

allows for electrons from ferredoxin to re-enter the electron transfer chain; this is coupled with the pumping of protons into the lumen.

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104
Q

How do electrons on ferredoxin re-enter the electron transport chain?

A

The electrons are used to reduced plastoquinone into plastoquinol.

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105
Q

What type of enzyme does photosynthetic complex I operate as?

A

A ferredoxin-plastoquinone reductase.

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106
Q

How does photosynthetic complex I transfer electrons from ferredoxin to Plastoquinone?

A

Photosynthetic Complex I has 4 4FE4S clusters which are used to shuttle electron from the ferredoxin to plastoquinone.

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107
Q

What are the two components that form ATP synthase?

A

Water soluble F1 and membrane integral F0.

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108
Q

What is delta psi?

A

The difference in membrane potential across a membrane.

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109
Q

What equation relates delta psi, delta p, and delta pH?

A

Delta p = Deta psi - 60 x delta pH.

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110
Q

How is the membrane potential maintained despite proton pumping?

A

The pumping of counter ions to partition/change. (This will negatively effect the proton motive force)

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111
Q

What is the function of the peripheral stalk in ATP synthase?

A

Acts as a dynamic scaffold to hold the F1 head in place around the central rotating shaft.

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112
Q

purpose of the 8-15c subunits in F0 of ATP synthase?

A

Act as the proton driven rotor embedded in the membrane

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113
Q

What is the gamma subunit of ATP synthase?

A

The central shaft that transmits toque from F0 to F1, changing the conformation of the beta subunits.

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114
Q

What are the 3 conformations of Beta subunits on F1 head of ATP synthase?

A

Open, Tight, and Loose.

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115
Q

What subunits form the F1 head of atp synthase?

A

3 alpha and 3 beta subunits.

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116
Q

What is the difference between a and b subunits on ATP synthase?

A

They are structurally similar however only B units are catalytically active.

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117
Q

What is the function of alpha subunits in F1 ATP synthase?

A

Structural role in the F1 head.

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118
Q

What forms the peripheral stalk of ATP synthase?

A

B2 and sigma subunits.

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119
Q

What is the function of alpha subunits in F0:

A

Act as a barrier.

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120
Q

What is the function of c subunits in the F0 of ATP synthesis:

A

Acts as a water wheel, each subunits has a glutamate which binds to protons and translocates them across the membrane.

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121
Q

What is the function of arginine residues in the alpha subunits in F0 of ATP synthase?

A

Has an amine froup that can bind to protons, when in proximity to a glutamate it stabilises it, allowing for it to unprotonate the glutamate, allowing for the release of protons in the low high pH region.

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122
Q

What process is coupled in the F0 region of the ATP synthase?

A

the resolving concentration gradient with the generation of torque.

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123
Q

How many ATP molecules are synthesised by full rotation of the c-ring in ATP synthase?

A

3 ATP molecules.

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124
Q

What does the rotation of the gamma shaft cause in the F1 head?

A

It causes changes in conformation of the B-subunits.

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125
Q

ATP Synthase: Open State

A

ATP is released and ADP and Pi bind to the b subunit

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126
Q

ATP synthase: Tight State

A

ADP + PI is converted to ATP

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127
Q

ATP Synthase: Loose State

A

ADP + Pi interact with eachother

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128
Q

Why do animals have smaller c rings than plants?

A

Animals have a regulated energy input, whereas plants energy input varies massively, therefore plants have larger c-rings to prioritise efficiency over speed.

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129
Q

How can the work of ATP synthase be reversed?

A

Supply the enzyme with a large conc. of ATP -> dependent on balance between deltaG ATP and delta P.

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130
Q

What are the 3 parts of the calvin cycle?

A

Carboxylation, reduction, regeneration.

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131
Q

What is the net output of the calvin cycle?

A

1 x GAP per 3 x CO2.

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132
Q

What is the main output of the Calvin cycle?

A

Glyceraldehyde-3-phosphate

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133
Q

What is the function of GAPs?

A

Used as the starting point of multiple metabolic pathways in plants

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134
Q

What residue is at rubisco’s active site?

A

lysine

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135
Q

How is rubisco regenerated?

A

Lysine reacts with another non-substrate molecule of C2 to form a carbamate anion which can then bind to Mg2+ ->

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136
Q

What is the function of the Mg2+ group in rubisco?

A

Activates ribulose -1,5-bisphosphate so it can react with CO2.

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137
Q

Thioredoxin: function

A

Regulates the activity of several calvin cycle enzymes, ensuring the activity of the light and dark reactions is closely regulated.

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138
Q

How many regulatory subunits are within rubisco?

A

8 subunits.

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139
Q

What is the product of carboxylation?(Calvin cycle)

A

2 3-phosphoglycerates per ribulose.

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140
Q

What is reacted in carboxylation?

A

Ribulose with CO2 and H2O.

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141
Q

What is stage of Calvin cycle involves rubisco?

A

Carboxylation

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142
Q

What occurs in the 1st reaction of the reduction stage of the Calvin Cycle:

A

3-phosphoglycerate is phosphorylated by phosphoglycerate kinase -> form 1,3-bisphosphoglycerate.

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143
Q

Where are the ATP molecules in the reduction stage of the Calvin cycle sourced from?

A

The light dependent reactions.

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144
Q

What occurs in the 2nd reaction of the reduction stage of the Calvin Cycle:

A

NADPH reduces 1,3-bisphophoglycerate to glyceraldehyde 3-phosphate (GAP)

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145
Q

What enzyme mediates the reduction stage of the Calvin Cycle:

A

glyceraldehyde-3-phosphate dehydrogenase.

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146
Q

What occurs in regeneration of the Calvin cycle?

A

-3 molecules of 5C sugar ribulose 5-phosphate formed
-Ribulose 5-phosphate is phosphorylated by phosphoribulose kinase to regenerate 1,5-bisphosphate.

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147
Q

Why are enzyme active sites are in hydrophobic pockets?

A

To allow for the force/power of the charged residues to have an effect on the substrate. -

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148
Q

Threshold enzymes:

A

Enzymes that bring key elements to a reaction.

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149
Q

Example of threshold enzyme:

A

Pyruvate carboxylase.

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150
Q

Primary metabolism:

A

-Essential compounds
-Basic housekeeping functions present in all cells
-Synthesised all the time (constitutive)

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151
Q

Secondary Metabolism:

A

-Specialised functions
-Present in differentiated cells
-Inducible
-E.g. antibiotics

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152
Q

X-ray crystallography:

A

-Equally spaced protein isomers
-laser -> scatters through crystal
-shows amplitude but not phase
-Uses Fournier Equation

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153
Q

What is phase?

A

Phase is the spatial information of a protein

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154
Q

What is the fournier transformation?

A

An equation that can be used to deduce structure from amplification.

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155
Q

What is Catabolism?

A

Breakdown of biomolecules. -> release energy

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156
Q

What is anabolism?:

A

Build up of new biomolecules. -> use up energy

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157
Q

What is the effect of phosphorylation on a molecule?

A

Addition of Pi group -> molecule becomes a higher energy form.

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158
Q

Why should glycolysis and gluconeogenesis occur at the same place?

A

It would be an energy sink/waste, because glycolysis doesn’t produce enough ATP for gluconeogenesis.

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159
Q

What is one benefit of energy lost by glycolysis?

A

Energy released as heat.

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160
Q

What occurs during resting metabolism?

A

A mixture of glycolysis and gluconeogenesis -> occurs despite energy wastage to conserve atom economy.

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161
Q

Why do reactions generating CO2 tend to be energetically favourable?

A

Co2 is very stable. CO2 readily escapes the site of reaction, Loss of CO2 from reaction is irreversible.

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162
Q

How do humans fix carbon and nitrogen?

A

From food/consumption.

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163
Q

CO2 can be fixed by what reaction?

A

Pyruvate with ATP and oxaloacetate.

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164
Q

What are group carriers?

A

Groups linking metabolic intermediates into larger molecules to prevent the loss of intermediates and increase energy efficieny.

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165
Q

What can be used to observe the metabolic activity of organisms?

A

Metabolic flux analysis.

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166
Q

COO carrier:

A

Biotin

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167
Q

C5 carrier:

A

Isopentenyl pyrophosphate

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168
Q

C1 (methyl) carrier:

A

S-adenosyl methionine

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169
Q

NH2 carrier:

A

Glutamine

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170
Q

C1 (CH, Ch2) carrier:

A

Folic Acid

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171
Q

C2 carrier:

A

Coenzyme A

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172
Q

[ATP] in cell?

A

10mM

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173
Q

What are the functions of vitamins?

A

B vitamins -> carriers
A - Vision
C + E - Antioxidant
D - Bones
K - Blood coagulant.

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174
Q

Why is biotin a good carrier of CO2?

A

It’s nitrogen 1 is very reactive and can react with the CO2 easily. Furthermore it can be covalently linked to proteins and-so can be used to transport CO2 directly to enzymes or proteins,

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175
Q

What enzyme in Krebs is biotin essential for?

A

Pyruvate carboxylase in link reaction, biotin is essential as a CO2 carrier.

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176
Q

How to activate Biotin?

A

Biotin is reacted with a carboxyphosphate to form biotin-COO-

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177
Q

Why is serine an important amino acid?

A

It’s a key precursor amino acid in the synthesis of many other, e.g. glycine.

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178
Q

Purpose of Folate:

A

Converts dUMP inton dTMP

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179
Q

What is homocysteine?

A

Similar to cysteine but has an extra methyl group.

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180
Q

Epigenetics:

A

All cells have the same DNA however portions are silenced to differentiate function.

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181
Q

What is SAM?

A

S-adenosylmethionine.

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182
Q

What is a key role of SAM?

A

The DNA methylation of cytosine and Histones (lysines and arginines)

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183
Q

What groups does Acetyl Coenzyme A have?

A

An adenosine and a phosphate group, contains pathothenic acid, and a thioester.

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184
Q

Purpose of the thioester bond in Acetyl Coenzyme A?

A

Makes it easier to transfer the acetyl group.

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185
Q

What is Patothenate (B5)?

A

A vitamin that carries C2 units in the link reaction of glycolysis.

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186
Q

What vitamin is found in retinol?

A

Vitamin A.

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187
Q

C5 unit assembly:

A

Steroid carbon skeleton -> 4 C5 chains -> form 20 carbon chain that folds into skeleton -> form steroids.

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188
Q

C5 units:

A

3x acetyl groups are joined together and one carbon is lost as CO2.

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189
Q

What are C5 units often used to synthesise?

A

Steroids

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190
Q

What is released when glutamine is hydrolysed?

A

NH2 and glutamate.

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191
Q

What are the Key roles of the TCA (Krebs) cycle?

A

Feeds into the ETC as source of energy but also makes key intermediates for biosynthesis.

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192
Q

Why is fat not used as a source of energy usually?

A

It’s an awkward and not straightforward pathway.

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193
Q

What kind of process is glycolysis?

A

An aerobic process.

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194
Q

How is glucose converted into fat?

A

Via the addition of acetly CoA.

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195
Q

Why is fat a better long-term store of energy?

A

Has higher energy content per gram and is not soluble in water and-so therefore not easily hydrolysed.

196
Q

What are the reactants in stage 1 of glycolysis?

A

Glucose and ATP

197
Q

Where do red blood cells (erythrocytes) get their energy?

A

Glycolysis.

198
Q

What are the products of stage 1 of glycolysis?

A

Two C3 units ( Glyceraldehyde 3-phosphate)

199
Q

What are the intermediates in Glycolysis stage 1?

A

Glucose-6-phosphate (hexokinase) -> Fructose-6-phosphate (phosphoglucose isomerase) -> Fructose-1,6-bisphosphate
(phosphofructokinase) -> Glyceraldehyde-3-phosphate (Aldolase)

200
Q

What do most muscles do to provide energy when not active?

A

Use glycolysis.

201
Q

Stage 2 of glycolysis?

A

Pyruvate is converted to lactate (Oxidises NADH) -> liver turns lactate back into glucose.

202
Q

What is a key feature of the organisation of glycolysis enzymes?

A

They are associated in one large complex, allowing for substrate channelling to directly transfer intermediates between enzymes.

203
Q

What is an important use of glycolysis intermediates?

A

Used as the start of many anabolic pathways in the synthesis of amino acids.

204
Q

Why is the conversion of Pyruvate into Acetyl CoA irrversible in the link reaction?

A

The loss of CO2 is irreversible and therefore this provides the reaction with directionality.

205
Q

What is the function of Acetyl CoA?

A

It’s fed into the Krebs cycle (for energy production or anabolic intermediates) or converted into fatty acids.

206
Q

What is the species reduced when Pyruvate is converted to lactate?

A

A ketone group.

207
Q

Where does gluconeogenesis mainly occur?

A

In the liver

208
Q

Are glycogen stores limited?

A

Yes, can run down after 90minutes of moderate activity.

209
Q

What is the start point of gluconeogenesis?

A

Pyruvate/lactate.

210
Q

What are the two sources of Pyruvate?

A

The transamination of alanine with alpha-ketoglutarate and glycolysis

211
Q

Glutamate is a key carrier for what?

A

A key carrier carrier for amino groups, having an amine group that can be traded for a ketone.

212
Q

In which organisms is pyruvate converted into acetaldehyde?

A

Yeast.

213
Q

Function of the Pentose Phosphate Pathway:

A

Pathway that occurs in parallel to glycolysis, however has many unique intermediates that are used for biosynthesis.

214
Q

What is the key functional difference between NADH and NADPH?

A

NADPH is a much stronger reducing agent.

215
Q

Why is the used of NADH favoured in metabolism?

A

NADH releases less energy than NADPH, however less energy is required -> therefore less wastage.

216
Q

What is an example of a key biomolecule synthesised using PPP intermediates?

A

Ribose sugars.

217
Q

Steps of the pentose phosphate pathway?

A

Pentose-6-phosphate forms ribulose (loses CO2 and reduces 2NADP+ into 2NADPH) -> converted into 2 5C sugars -> 3C and 7C -> 6C and 4C -> 4C reacts with a 5C -> to form 6C and 3C.

218
Q

What is the PPP?

A

The pentose phosphate pathway

219
Q

What is the starting molecule of the PPP?

A

Pentose-6-phosphate

220
Q

What is the irreversible step of the PPP?

A

The decarboxylation of pentose-6-phosphate

221
Q

What enzyme catalyses link reaction?

A

pyruvate dehydrogenase

222
Q

What cofactors are used in link reaction?

A

Thiamine Pyrophosphate, lipoic acid , FAD, Coenzyme A, NAD+

223
Q

What does the Krebs Cycle generate?

A

ATP, NADH, and FADH2

224
Q

What are anaplerotic mechanisms?

A

Mechanisms used to top-up the carbon count within the Krebs cycle, upon loss of intermediates for biosynthesis.

225
Q

Example of an anaplerotic?

A

Carboxylation of Pyruvate into Oxaloacetate by pyruvate carboxylase.

226
Q

What is the reaction equation of the carboxylation of pyruvate into oxaloacetate?

A

Pyruvate + CO2 + ATP + H2O -> Oxaloacetate + ADP.

227
Q

Why do photosynthetic organisms do Krebs cycle backwards?

A

Because they incorporate CO2 into molecules

228
Q

Can certain organisms not use the entire krebs cycle?

A

Yes

229
Q

What is the benefit of an organism being able to use the Krebs cycle in both directions?

A

Allows for a balance of reduction and oxidation.

230
Q

Why don’t anaerobic bacteria use the full Krebs cycle?

A

They don’t need it for the oxidative cycle or for metabolic precursors -> therefore run it backwards or split it into two arms.

231
Q

How can fatty acids catabolism feed into the Krebs cycle?

A

the beta-oxidation of fatty acids.

232
Q

What occurs in the beta-oxidation of fatty acids?

A

Faty acids are broken up into 2-carbon pieces forming acetyl Coa -> producing NADH and FADH2 for each 2-carbon piece.

233
Q

What oxidation reaction occurs in beta-oxidation of fatty acids?

A

oxidises 2 carbon atoms furthest away from the acyl headgroup -. occurs repeatedly.

234
Q

What enzyme is used for beta-oxidation of fatty acids?

A

Beta-carbon oxidase.

235
Q

What is meant by Omega-3 fatty acid?

A

The alkene group is only 3 carbons from the end.

236
Q

How is fatty acid biosynthesis the opposite of beta-oxidation?

A

Each addition produces a ketone group, that is then reduced in two stages.

237
Q

What is the enzyme that catalyses the process of fatty acid synthesis?

A

Fatty acid synthase:

238
Q

Features of fatty acid synthase?

A

Fatty acid synthase forms a dimeric protein that has 7 different enzyme functions in one polypeptide chain -> the fatty acid passes round the active sites in a cyclic process.

239
Q

What occurs fatty acid synthesis to halt?

A

The fatty acid will become to large and be displaced from the enzyme.

240
Q

Can ammonia be fixed by humans?

A

Yes, but not efficiently

241
Q

Where is nitrogen sourced from in humans?

A

The consumption of plants and animals.

242
Q

How is glutamate synthesised?

A

Alpha-ketogluatarate + Nh4+ -> Schiff base + H2O
Schiff base is reduced into glutamate by NAD(P)H

243
Q

What is the coenzyme for amino acid biosynthesis?

A

Pyridoxal phosphate (B6)

244
Q

How can nitrogen be passed between amino acids?

A

Transamination (glutamate can donate its amine to form alpha-ketoglutarate, a keto acid)

245
Q

What are the essential amino acids:

A

Amino acids that are synthesised by the human body but are necessary for function.

246
Q

Is making bases more or less complicated than aminoacids?

A

More complicated

247
Q

Pyrimidine Nucleotide synthesis: Order

A

-Base assembled first -> ribose attached.

248
Q

How is the pyrimidine ring formed in nucleotide synthesis?

A

The ring is formed by reacting aspartate with carbamoyl phosphate.

249
Q

Where is carbamoyl phosphate sourced from in nucleotide synthesis?

A

A reaction between bicarbonate, NH3, and 2ATP.

250
Q

Purine Nucleotide Synthesis:

A

-Ribose-5-phosphate forms 5-phosphorybosyl-1-pyrophosphate -> uses 2ATP
-> Intermediate atoms then added one at a time.

251
Q

Why is ATP converted into AMP during the synthesis of purines?

A

This is because it’s a large energy change than that of the formation of pyrimidines -> therefore more energy released to ensure it occurs.

252
Q

What is the committed step?

A

An irreversible step that commits to a reaction pathway.

253
Q

What are the two ways metabolic pathways are usually controlled?

A

-Committed steps
-The end-product causing feedback inhibition of the first step

254
Q

What molecule acts as an end-product allosteric inhibitor of glycolysis?

A

ATP -> inhibits the first step of glycolysis.

255
Q

Why are lots of pathways often inhibited by ADP?

A

if ADP levels are high the cell likely doesn’t have the ATP required for the pathway.

256
Q

How do most allosteric inhibitors work?

A

Most bind within the hydrophobic cleft -> influences how easy it is for active site to form.

257
Q

How can allosteric inhibition be used as a switch?

A

It can downregulate one metabolic pathway, therefore upregulating alternative using the same starting molecule.

258
Q

What are isozymes:

A

When there are more than one enzyme that do the same job; found in different conditions.

259
Q

How are isozymes formed?

A

Often derived from the same gene but are differentially spliced (in eukaroytes)
Or are the same protein-coding domain but attached to differetn regulatory domains (in proakryotes)

260
Q

Example of isozyme in E.coli?

A

Aspartokinase

261
Q

What is the function of lactate dehydrogenase?

A

Enzyme that converts pyruvate into lactate.

262
Q

Example of allosteric inhibition in eukaryotes:

A

aspartate transcarbamoylase, ATcase ->Nucleotide synthesis -> inhibited by the binding of CTP

263
Q

Key feature of lactate dehydrogenase structure:

A
  • has 4 subunits made of 2 different isozymes
  • has H(heart) isozymes and M(muscle) isozymes
    -H wants to convert lactate into pyruvate -> inhibited by pyruvate
    -M wants to convert pyruvate into lactate -> inhibited by lactate
264
Q

What is meant by the cumulative control of a single enzyme?

A

One single enzyme is inhibited independently by several products.

265
Q

Example of enzyme controlled cumulatively:

A

Glutamine synthase (AMP, Histidine, Glycine, Alanine + more)

266
Q

What is the effect of reversible phosphorylation on an enzyme?

A

Causes a regulated covalent modification -> Alters function

267
Q

What is an example of an enzyme that is regulated by reversible phosphroylation?

A

Glycogen phosphorylase:

268
Q

How does glycogen phosphorylase function?

A

-Removes glucose units from glycogen
-It’s activity is regulated by phosphorylation (enzyme that mediates this is regulated by glucagon)

269
Q

What are the two methods of regulation by enzyme expression?

A

An end product downregulates expression of the first enzyme of a pathway.
Or a substrate acts to remove the repression of gene expression pathway needed to process it.

270
Q

Example of regulation by enzyme expression? (prokaryotes)

A

Lac Operon.

271
Q

Example of regulation by enzyme expression? (eukaryotes)

A

Trp Repressor -> trp operon encodes genes for the biosynthesis of tryptophan -> if there’s tryptophan already it binds to repressor and shuts down pathway.

272
Q

Key difference between gene regulation and allosteric control:

A

Gene regulation is much slower taking hours, whereas allosteric can happen in milliseconds

273
Q

What does metabolic flux analysis show?

A

That increasing the amount of regulatory enzyme doesn’t make that much difference -> overall rate much more dependent on the entire pathway.

274
Q

What is the flux coefficient of an enzyme in a pathway?

A

How much each enzyme controls the entire pathway.

275
Q

What are the three types of fibres in the Cytoskeleton?

A

Microtubules, Actin filaments, and intermediate filaments.

276
Q

Difference between Sphingolipids and Phospholipids:

A

Sphingolipids contain Nh instead of O, often more saturated than phospholipids, and are mainly trans double bonds rather than cis.

276
Q

Microtubules:

A

Forms pathways for intracellular transport - made from tubulin and span from nucleus to cell surface.

276
Q

Intermediate filaments:

A

Made of fibrous proteins that crissscross the cell to hold it together to maintain structural integrity.

277
Q

What are the 3 types of lipids in the membrane:

A

Phospholipids, Sphingolipids, and Sterols.

277
Q

Actin filaments:

A

Made from actin -> runs around the inside of the cell membrane -> has multiple functions

278
Q

what kind of linkage joins a lipid headgroup and tail?

A

An ester linkage.

279
Q

How can membranes transition through phases?

A

By altering the external environment.

280
Q

Why are phospholipid bilayers thinner than ordinary

A

The headgroups are closer together because the membrane is less ordered.

281
Q

What can be added to a membrane to increase its width?

A

Cholesterol, by increasing the order of the membrane.

282
Q

What is the benefit of membrane fluidity?

A

Allows for movement within the bilayer to occur.

283
Q

Phosphatidylcholine:

A

Cylindrical phospholipid that packs well into flat bilayers.

284
Q

Phosphatidylethanolamine:

A

Phospholipid with a smaller headgroup than fatty acid tail, causes curving of the bilayer.

285
Q

What is the effect of different lipids of the surface membrane shape?

A

Different lipids can alter the shape/curvature of the membrane depending on their distribution between the two leaflets.

286
Q

What is scaffolding?

A

Extracellular proteins interacting with the membrane, affecting its shape (e.g. clathrin)

287
Q

How do membrane proteins affect cell membrane shape?

A

-Cylindrical membranes will keep membrane flat.
-Conical membranes will cause the membrane to curve.
-If protein inserts into single leaflet -> will increase its surface area -> causing curvature.

288
Q

Are lipid anchored proteins in a fixed position?

A

No they will move with their anchor,

289
Q

Why is the fluid mosaic model not completely correct?

A

-Membrane is less fluid
-Components localise into the membrane in specific membrane rafts -> rigid regions with cholesterol and sphingolipids.

290
Q

What kind of membrane proteins tend not to be in membrane rafts?

A

Prenyl-anchored proteins

291
Q

What is flipase?

A

An ATP-dependent enzyme which flips lipids between bilayer leaflets.

292
Q

What is phase separation?

A

The driving force of the two leaflets having different lipid compositions -> creates different sub regions in the memrbane.

293
Q

What does Atomic Force microscopy (AFM)show?

A

The height of different components and shows proteins embedded in the membrane

294
Q

How does atomic force microscopy work?

A

laser reflects light on cantilever arm that taps the membrane surface.

295
Q

What structures are proteins packaged into for transport?

A

Vesicles

296
Q

How can the lateral mobility of proteins be measured?

A

FRAP (fluorscence) recovery after photobleaching.

297
Q

What is the function of membrane rafts?

A

To bring membrane proteins together of keep them apart.

298
Q

What modifications can be made to membrane rafts to organise the attachment of proteins?

A

Covalent modifications, e.g. prenylation and the attachment of GPI anchors.

299
Q

Endocytosis:

A

The invagination of membrane to bring a membrane protein to the membrane or bound ligand molecule inside the cell. e.g. used to control number of aquaporins

300
Q

What is often used to congregate lipid rafts together to form larger rafts?

A

Dimerisation.

301
Q

What is the process of ligand-mediated endocytosis:

A

-> ligand binds to receptor -> leads to formation of raft -> proteins bind to the raft (Caveolin) -> cause inward curvature (invagination) -> Scaffolding proteins accentuate curvature -> Caveolae are pinched off at the top and moved into the cell.

302
Q

What is patch clamping?

A

A technique used to investigate the conductance through ion channels

303
Q

What does patch clamping show?

A

Membranes are insulated and charged particles can’t passively cross without channel/carriers.

304
Q

What do fixed excited levels tell us about ion channels?

A

All channels have the same current when open.

305
Q

What is the resting potential of the cell?

A

-60mV

306
Q

At what voltage are channels open?

A

0Mv.

307
Q

What is the Na+/K+ pump?

A

-ATP dependent pump which constantly pumps 3Na+ out of the cell and 2K+ in -> this is active because both ions are moving up their conc. gradients.

308
Q

What are resting K+ channels:

A

-Open when cell is at rest
-not gated
-Allows K+ to leak out the cell all the time -. to make membrane potential negative
-Leakage occurs untill localised [K+] is equalised -> not major problem

309
Q

What is a channel-inactivating segment?

A

A molecule that is attached to channels that reversibly plugs them to prevent over action.

310
Q

What are the two types of nerve cells:

A

Motor neurones (Spinal cord to muscle)and Sensory neurones (tissue to spinal cord)

311
Q

What occurs at a synpase?

A

An electrical signal is converted into a chemical signal at the synapse.

312
Q

What is transient charge?

A

A temporary membrane potential

313
Q

What is a nerve impulse?

A

A transient charge in the membrane potential.

314
Q

How is a stronger nervous signal produced?

A

More rapid (increased freq) of action potentials.

315
Q

What triggers the opening of voltage-gated Na+ channels?

A

The depolarisation of the membrane to -40mv.

316
Q

What is the benefit of Na+ channel plughs?

A

They prevent the signal from travelling backwards.

317
Q

What is the refractory period?

A

Time where the Na+ channels are plugged and cannot transmit an action potential.

318
Q

What makes depolarisation of neurones an energy efficient process?

A

Not much work is needed to restore ion/concentration because only small change in concentrations (and therefore potential).

319
Q

How does tetrodotoxin work as a poison in fugu?

A

blocks voltage-gated Na+ channels.

320
Q

Myelin Sheathes:

A
  • Insulate regions of nerve cells
    -Lipid membranes insulates ions from cross across large regions
    -Allows nerve impulses to travel faster (potentials can jump)
    -Gaps even 100Micro m
321
Q

What condition is caused by loss in myelin regions in the brain and spinal cord?

A

MS (multiple sclerosis)

322
Q

The Nernst Equation:

A

2 Equations that calculate the energy produced by ion gradients across a membrane.

323
Q

What is Equation 1 of Nernst?

A

Delta G = charge on ion x membrane potential (in V) x Faraday constant. -> relates membrane potential to free energy difference.

324
Q

What is the faraday constant?

A

96485 J mol^-1 V^-1

325
Q

What is the Equation 2 of Nernst:

A

membrane potential = (RT/charge on ion x Faraday) x ln ([out]/[in]) -> relates membrane potential to concentrations

326
Q

What cells make up the myelin sheathe?

A

Schwann cells.

327
Q

What equation is obtained by combining equation 1 and 2 in Nernst?

A

Delta G = RT x ln([out]/[in]) - zFE

328
Q

What is the name for how the potential “jumps” between gaps in the myelin sheathe?

A

Saltatory conduction.

329
Q

What is the basic problem with signalling?

A

The membrane is quite thick and proteins are fluid -> makes it difficult to transmit signals over large distances.

330
Q

What is signalling vital response for?

A

Hormones, growth factors, infection, neural synapses, bacterial response to environment

331
Q

What is signalling?

A

A method of how an extracellular change to the environment leads to a signal which will cause the cell the change its behaviour/expression

332
Q

What are the common effects of signalling?

A

They often effect enzyme activation and gene expression.

333
Q

What are the 4 major pathways for signals to enter a cell?

A
  • Ligand binds to a receptor
    -Ligand binds to GPCR
    -Ligand binds to ligand-gated ion channel
    -bind to intracellular receptor.
334
Q

GPCR: Ras Protein how it works

A

Ras is an adaptor protein that binds to 3 GTP molecules, the third forms hydrogen bonds with two loops on the protein surface (One is threonine and other is glycine) -> When the GTP is hydrolysed -> causes switch regions to move inwards (off)

335
Q

GPCR: How are changes to G-protein structure amplified?

A

The switches are associated with other proteins -> which amplify the change by moving aswell.

336
Q

What enzymes turn G proteins on?

A

GEFs (guanine exchange factors)

337
Q

Receptor-linked kinases are an example of which signalling pathway?

A

Ligand binding to a receptor.

338
Q

What do receptor linked kinases often control?

A

Transcription -> therefore defects can lead to cancer.

339
Q

How do Receptor tyrosine kinases work?

A

Use dimerisation mechanism to transduce signal.

340
Q

How does the dimerisation of receptor tyrosine kinases function?

A

Each receptor has an inactive kinase, when pulled together by the substrate -> kinases activate eachother (via autophosphorylation) -> the kinases can then activate secondary messengers.

341
Q

How do kinases work?

A

-> kinases have 2 domains -> N-terminal domain binds to ATP and C-terminal domain binds to the substrate -> upon binding to both the domains become closer and the substrate is phosphorylated.

342
Q

How are kinases activated?

A

Kinase binding to protein is weak -> upon binding the C-terminal domain to a phosphate (via the tyrosine residue) loop becomes more structured -> allowing for stronger binding to substrate. -> activating the kinase.

343
Q

What is the function of modular adaptor molecules in cell signalling?

A

They connect specific phosphorylated receptors to a more general signalling molecule.

344
Q

Grb2 Sos mechanism: Adaptor signalling

A

Grb2 -> has two SH3 domains which recognise polyproline helices (binds SOS)
Has SH2 domain that binds to phosphotyrosine
SOS has GEF domain that activates G-protein

345
Q

What does Ras activate?

A

Activates a kinase cascade Ras -> MEK -> ERK -> phosphorylates TFs.

346
Q

What is the general kinase cascade?

A

MAPKKK -> MAPKK -> MAPK -> phosphorylates TFs.

347
Q

GPCR signalling pathway summary:

A

Signal binds to GPCR -> activates G-protein -> activates adenylyl cyclase -> synthesis cAMP -> cAMP protein kinase A -> activation of protein kinase A -> subunits to diffuse into nucleus -> phosphorylate a CREB -> recruits CBP -> activates transcription.

348
Q

What is a CREB?

A

cAMP-response element binding protein

349
Q

GaS: GPCR

A

Stimulatory GCPR

350
Q

GaI: GPCR

A

inibitory -> inhibits cAMP pathway

351
Q

GaT: GPCR

A

involved in vision -> stimulates phosphodiesterase 6 -> breaks down cGMP

352
Q

GaQ: GPCR

A

Stimulates phospholipase Cbeta -> splits into PIP2, DAG, and IP2

353
Q

Inositol phosphates:

A

Used to make signal and are released upon lipase activity cleaves internal lipid bilayer.

354
Q

Examples of diseases that affect GPCR signalling:

A

Cholera -> G-protein not deactivated -> over excretion of Cl- and water
Whooping cough -> block GaI -> over expression of adenylyl cyclase -> excess cAMP.

355
Q

What is the role of arrestin?

A

Performs mechanism for turning off GPCR signalling by lysosome action.

356
Q

Outline arrestin-mediated signalling by GPCRs:

A

GRK phosphorylates receptor -> receptor binds to arrestin -> induces invagination of the protein (via AP2 clathrin) -> forms endosome -> then there are 3 different outcomes.

357
Q

What are the 3 outcomes of arrestin-mediated signalling by GPCRs?

A

-Internalised receptor
-Receptor hydrolysed
-Receptor recycled.

358
Q

What is NAChr?

A

Nicotinic acetyl choline receptor.

359
Q

What causes ion channels to open?

A

The rotation of alpha helices (like an iris)

360
Q

Ion channel properties:

A

-Rapid
-Reversing signal requires removal of all the ions -> requires a lot of energy.

361
Q

What pathway is best suited for specificity and regulation?

A

Tyrosine Kinases

362
Q

Signalling by hydrophobic ligands:

A

-> usually steroids
-> Receptors are in the cytoplasm
-> Receptors have 3 defined domains, DBD, AD, and LBD
-> Upon ligand binding conformationcal change occurs -> releases receptor from inhibitor + activate the receptor -. travels to DNA and triggers transcription

363
Q

How do proteins associate with the membrane?

A

-Integral Membrane Proteins: Associate with hydrophobic environment
-Lipid-anchored Proteins: Associate with lipid anchors on the membrane surface
-Peripheral Membrane Proteins: associate with other membrane proteins

364
Q

What interactions occur between peripheral membrane proteins and the membrane?

A

electrostatic forces and hydrogen-bonding with head groups -> polar interactions that are easily disrupted.

365
Q

What is a hydropathy plot?

A

A window of 19 residues used to calculate the hydropathy of the polypeptide stretch.

366
Q

What is the hydropathy index threshold for a transmembrane helix region?

A

+84

367
Q

What residue is affected by acylation?

A

Glycine -> N-terminal methionine is removed -> forms amid bond with C14 carboxylic acid

368
Q

What is the effect of acylation on membrane proteins?

A

Prevents the proteins from moving back into the cytoplasm.

369
Q

What residue is affected by prenylation?

A

Cysteine -> unsaturated anchor binds to C-terminus of the protein -> forms thioester link

370
Q

Structure of porins:

A

-Beta strands form large beta sheet -> rolled into a cylinder and pushed into membrane to form a tunnel
-Each strand is arranged in an anti-parallel arrangement.

371
Q

What is the role of aromatic side chains on porins?

A

To dampen the cylinder at the point between different environments.

372
Q

What type of interaction is important in making protein arrangements energetically feasible?

A

Hydrogen bonding

373
Q

Where are porins found?

A

ONLY on the outer-membrane of bacteria -> to prevent protons from entering the cell interior and inhibiting ATP synthesis.

374
Q

How does the polarity of an amino acid affect its hydrophobicity?

A

More positive transfer free energy = less hydrophilic/
More negative = hydrophobic.

375
Q

Why can’t hydropathy plots be used for porins?

A

Because porins aren’t alpha-helical

376
Q

Phenylalanine:

A

residue with single aromatic ring

377
Q

Tryptophan:

A

Residue with two aromatic rings.

378
Q

What is the width of Bacteriorhodopsin?

A

45 Angstroms

379
Q

Where does the structure of bacteriorhodopsin derive from?

A

Archaea

380
Q

Function of Bacteriorhodopsin:

A

To use light energy to transport protons from inside to outside the cell, generating a proton gradient to drive ATP synthesis.

381
Q

What type of proteins are most membrane proteins (In regards to their secondary structure)?

A

Alpha helical

382
Q

What do permeabilities correlate with?

A

Partition coefficients

383
Q

What is the membrane permeability equation?

A

Permeability = (Diffusion Coefficient within membrane x water-membrane partition coefficient)/Membrane thickness

384
Q

What factor other the partition coefficients is affects the ability of molecules to spontaneously cross the membrane?

A

The relative concentrations of the molecule across the membrane.

385
Q

What is a key example of a channel protein that allows for passive transport?

A

Aquaporins

386
Q

What are the key 3 features shared by channel proteins:

A

-Selectivity
-Filter
-Gate (optional)

387
Q

What are the shared components of Channel proteins?

A

->Selective tunnel
-> Hydrophobic interface (lots of phenylalanine) to protect pore from hydrophobic interior
-> Vestibule (cavity) on either side to collect the substrate.
->Gate (acts as a switch)

388
Q

Aquaporins:

A

Facilitate the movement of many more water molecules across the membrane in a given time.
-e.g. in the kidney for rapid diffusion back into the bloodstream after filtration

389
Q

How fast are aquaporins?

A

Operate near the diffusion limit.

390
Q

What are the 3 types of transport processes?

A

-Uniporters (typical channels + Passive)
-Symporters (Couple of two molecules in the same direction + Active)
-Antiporters (Couple of two molecules in the diff directions + Active)

391
Q

How do ATP pumps work?

A

Use chemical energy (ATP) to undergo large conformational changes to the pumps structure, allowing for the movement of molecules up the conc. grad.

392
Q

How does facilitated diffusion occur?

A

Facilitate diffusion down gradient by undergoing smaller conformational changes induced by the energy of binding with the molecule.

393
Q

What does the Jardetzky model depict?

A

A simple allosteric model for active carriers.

394
Q

What are the components of the Jardetzky model?

A

-An interior binding cavity that binds to transported species (high affinity)
-Channel protein can assume two different configurations -> provides alternating access.
-An energy input induces a conformational change that alternates access and decrease affinity of the interior binding cavity.

395
Q

Lac permease mechanism:

A

Ley amino-acids (aspartates and glutamates) in aq environment and _ve charged -> proton will bind to acidic amino acid -> causes change in binding site of lactose -> conformational change causes eversion -> loss of affinity of lactose -> lactose and H+ released -> lac permease returns to resting state.

396
Q

What is a word that can be used to describe a change between conformations in alternative access?

A

eversion

397
Q

What is the source of energy for the action of lac permease?

A

The proton gradient.

398
Q

What kind of active transport protein is lac permease?

A

A symporter (of lactose and H+)

399
Q

What family of proteins is lac permease part of?

A

Major facilitator family

400
Q

What do kinks in alpha helices suggest?

A

Flexibility of the protein.

401
Q

What does PSI reduce?

A

Ferredoxin

402
Q

What are the pigments in the reaction centre of PSI?

A

Chlorophylls (aA1 + aB2) + (aA2 +aB2) + Phylloquinone (QKA + QKB) and 4Fe4S clusters

403
Q

What resolves the charge at the special pair of electrons in PSI?

A

Plastocyanin

404
Q

Where is the reduced plastocyanin sourced from in PSI?

A

Cytochrome b6f.

405
Q

Structure of lac permease:

A

-12 transmembrane helices -> 2 separate 6 helices domains (pseudosymmetry)

406
Q

How was the structure of Lac permease found?

A

X-ray crystallography of a mutant locked in a single conformation.

407
Q

What energy does Bacteriorhodopsin use to drive its active transport?

A

Light energy

408
Q

How does the Light ensure the directionality of bacteriorhodopsin?

A

Input of light closes the gate, preventing the backflow of electrons .

409
Q

What bacteria is bacteriorhodopsin found in?

A

halophilic bacterium in brine lakes -> Halobacterium salinarum

410
Q

What responsible for bacteriorhodopsin’s colour?

A

Purple colour comes from covalently attached chromophore.

411
Q

What are the the important amino acids in bacteriorhodopsin?

A

D85 (aspartate -> near retinal), D96 (aspartate -> near cytoplasm), and Lys216 (schiff base)

412
Q

How many helices surround the retinal in bacteriorhodopsin?

A

7 helices

413
Q

Function of D85 in bacteriorhodopsin:

A

D85 acts as a counterion to stabilise the proton bound to lysine.

414
Q

What is the function of D96 in bacteriorhodopsin?

A

Forms a hydrophobic environment -> protonates because negative charge isn’t favourable in hydrophobic environment.

415
Q

What does the absorption of light cause in bacteriorhodopsin?

A

Isomerisation at C13 -> causes system to strain ->pushing against the protein.

416
Q

What are the stages of H+ pumping by bacteriorhodopsin?

A

-Light absorbed by retinal -> isomerisation -> allows access of cytoplasmic side to retinal -> lysine donates electron to D85 (is then released) and D96 donates electron to lysine-> proton form binds to D96 system restored.

417
Q

How does gating occur in bacteriorhodopsin:
(M stage)

A

Upon light absorption Helix F has a large movement outwards at the cytoplasmic end -> allows cytoplasm to fill half the channel -> allows for decrease D96 pKa -> dissociates H+ to retinal.
Retinal strain relaxes-> helix F closes -> makes half channel hydrophobic -> allows for protonates D96

418
Q

Why are K+ ions 100x more permeable in K+ channels than Na+?

A

Despite Na+ being smaller the energetic of its hydration require higher energy input to remove water

419
Q

What is the desolvation energy cost?

A

The energy cost of removing an ion from associated water molecules.

420
Q

What is KcsA?

A

A potassium ion channel found in streptomyces

421
Q

KcsA structure:

A

Tetrameric channel protein: Each subunit has 2 transmembrane helixes connected by a pore helix with a signature sequence.
has a selectivity filter formed by 4 pore helices.

422
Q

What is the purpose of the signature sequence on the pore helix of a pore protein (KcsA):

A

Carbonyl groups on the main chain in the pore lumen which provide selectivity by electronegativity

423
Q

Structure of KcsA subunits: Outer helix

A

Hydrophobic helix that forms outersurface of the pore

424
Q

Structure of KcsA subunits: Inner helix

A

Lines the vestibule and pore (helical pore has dipole that propels +ve forward)

425
Q

What force between ions helps aid the movement of K+ through KcsA?

A

Electrostatic repulsion

426
Q

What is KvaP?

A

Voltage gated K+ channel

427
Q

What links the pore domain and voltage domain in KvaP?

A

Linker domains

428
Q

Why does KvaP have 4 more helices than KcsA?

A

They are critical for the gating mechanism (contain the sensor for voltage change)

429
Q

KvaP: N-terminal Voltage Sensor

A

Moves up and down depending on the membrane potential (voltage) -> acts like a level mechanism which will push and pull by transient movement on inner helices in pore domain.

430
Q

KvaP: Subunits and purpose:

A

S5 and S6 -> analogues of the inner and outer helices of KcsA.
S1-4 -> form membrane embedded voltage sensor.

431
Q

KvaP: When the sensor are up is the channel open or closed?

A

Open

432
Q

What is the effect of glycine and prolines on transmembrane alpha helices?

A

They create a break in the helix -> indicating a hinge region.

433
Q

Where was rhodopsin initially harvested from?

A

Cows and squid

434
Q

How many Transmembrane helices does rhodopsin have?

A

7

435
Q

Is rhodopsin and bacteriorhodopsin releated?

A

No, but share similar structure.

436
Q

Role of retinal in rhodopsin?

A

Acts similar to a ligand on other GPCRs.

437
Q

Where is beta adrenergic receptor’s binding site?

A

The extracellular side

438
Q

What is the role of ligand binding on beta adrenergic receptors?

A

Energy of binding of ligand to binding site -> induces conformational change -> communicated to cytoplasmic side of receptor -> recognised by G-protein.

439
Q

What signalling cascade is rhodopsin involved in?

A

Sight.

440
Q

What membrane protein is activated by the activated alpha G protein subunit in Adrenaline receptors?

A

Adenylate cyclase

441
Q

Role of Adenylate Cyclase:

A

Converts ATP into cAMP for signalling cascade (activates protein kinase)

442
Q

At which steps of GPCR mechanisms does amplification occur?

A

For each ligand, multiple G proteins are activated -> binding of each results in multiple cAMP molecules.

443
Q

What happens to G protein when activated by GPCRs?

A

GDP dissociates and it replaced with GTP -> mediated by GEF.

444
Q

What are components of a heterotrimeric G protein?

A

Alpha, beta, and gamma subunits

445
Q

What is the effect on G alpha when bound to GTP?

A

It has a decreased affinity of the receptor and dissociates from the receptor and beta and gamma -> then associates with downstream proteins (e.g. adenylate cyclase)

446
Q

Adenylate cyclase structure:

A

12 transmembrane alpha helices and two large cytoplasmic extramembraneous domains.

447
Q

How do G-proteins deactivate:

A

-They can spontaneously reset through GTP hydrolysis via intrinsic GTPase activity
-> will the reassociate with gamma and beta subunits and form inactive heterotrimeric G-protein

448
Q

How does a GPCR receptor deactivate?

A

-The ligand will dissociate -> returning the receptor to its inactive state
- Or kinase will phosphorylate serines and threonines on the c-terminal end -> recruit beta-arrestin -> blocking recruitment of G-protein.

449
Q

What key group do threonines and serines have?

A

Hydroxyl group

450
Q

Where is the cis bond in rhodopsin’s retinal’s polyene tail?

A

11-cis carbon

451
Q

Where is the retinal ring in rhodopsin?

A

In the binding cavity

452
Q

What is the change that occurs in retinal of rhodopsin upon light absorption?

A

changes from 11-cis to all-trans .

453
Q

What is the mechanism by which rhosopsin conformational change occurs?

A

Upon isomerisation helix 6 and 3 are separated (possibly as a result of proton transfer from Schiff base to glu113) -> helix 6 relaxes and goes outwards, at the other end this causes conformation at the transducing complex.

454
Q

Visual signal transduction system post Rhodopsin:

A

G alpha subunit dissociates from rhodopsin and regulate phosphodiesterase -> decreases cGMP -> reduces binding to cGMP-gated ion channels -> prevents entry of cations -> membrane becomes hyperpolarised and neurotransmitters released.

455
Q

How is rhodopsin deactivated?

A

-Phosphorylation and recruitment of arrestin
-Or dissociation of retinal

456
Q

Why isn’t light used to observe molecules?

A

The wavelengths of visible light is too large to observe protein and biological molecules.

457
Q

What was the original method of observing proteins?

A

X-ray scattering -> scattering pattern and density analysed computationally to reverse engineer structure.

458
Q

X-ray crystallography issues with protein crystals:

A

Protein crystals are very fragile due to weakness of intermolecular interactions.

459
Q

Why were protein crystals used in X-ray crystallography?

A

They provided lots of copies and could be used despite the lack of lenses.

460
Q

What is the unit cell?

A

3D repeating unit that is the lattice structure repeated throughout the crystal.

461
Q

Why must the protein solution be very saturated?

A

To make sure the protein leaves as a crystal rather than a precipitate.

462
Q

What is X-ray crystallography resolution dependent on?

A

The quality of the crystals.

463
Q

Difficulties of crystallising proteins:

A

-Disruption of bilayers
-Aggregation of proteins occurs in water
->Detergent use must be very precise.

464
Q

Detergents:

A

Water-soluble surfactants that form micelles that separate hydrophobic species from the water.

465
Q

What is the resolution of recent CryoEM:

A

3 Angstroms

466
Q

Process of Cryo-EM:

A

Apply sample to EM grid -> blotted -> plunged into liquid ethane -> transferred to EM microscope -> at random orientations -> can build 3D shape.

467
Q

What are the benefits of Cryo-EM:

A

-No phase problems and pictures can be taken

468
Q

Why don’t crystals form in Cryo-EM?

A

the protein freezes so quickly in the ethane.

469
Q

SecYEG complex:

A

Membrane complex that acts as a pore that allows for the active transport of proteins out of the cytoplasm into the periplasm.

470
Q

What is an SRP?

A

A signal recognition particle

471
Q

What is the purpose of the FtsY:

A

Binds to SRPs (docking + hydrolysis of GTP) will trigger the ribosome forms a complex SecYEG pore -> protein will then be translated and fed through the pore simultaneously.

472
Q

What are the three ways of translocating a protein:

A

Co-translational translocation, Post-translational translocation (BiP or SecA ATPAse)

473
Q

What is the role of SecA:

A

->recognises unfolded protein -> binds together by polypeptide linking domain -> clamp around the protein and bringing it to the SecY complex -> will act as a seal whilst the ppeptide is fed through the pore -> cleaved after translocation is complete.

474
Q

Stages of Co-translational translocation:

A

Free ribosomal subunits assemble at a signal peptide -> mRNA is translated across the ribosome -> synthesised polypeptide is fed through translocator -> upon completion signal peptidase cleaves the signal peptide off the polypeptide.

475
Q

Which translocation mechanisms use the Sec61 complex?

A

Co-translational translocation and BiP

476
Q

What is the eukaryotic analogue of FtsY?

A

SRP receptor

477
Q

What are SAIs?

A

Signal Anchor I proteins

478
Q

What do SAI proteins indicate?

A

Indicate TM segments transfer into lipid during co-translational translocation.

479
Q

What is topogenesis:

A

The process by which proteins are integrated into the membrane.

480
Q

What are the 3 types of signals that initiate topogenesis in membrane proteins:

A
  • Cleavable proteins
  • Signal-anchor
  • Reversible-signal anchors
481
Q

Components of translocators:

A

-Hinge and Seam
-Plug
-Lipid-bilayer

482
Q

What factors effect the orientation of a membrane protein:

A

The number of positive and negative charges either side of the signal peptide + large globular domains don’t easily pass through the translocator + the hydrophobicity of the N-terminal domain.

483
Q

What occurs in single pass membrane protein integration:

A

Translocator binds to start-transfer sequence -> translocation occurs -> until stop-transfer sequence -> start-transfer seq. cleaved.

484
Q

What occurs in double pass membrane protein integration:

A

Similar to single pass except there’s polypeptide before the start-transfer seq. -> start-seq. is not cleaved -> forms loop.

485
Q

Example of modification of membrane proteins:

A

Glycosylation, phosphorylation, etc.

Year 2: Semester 1 (3 decks)

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