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EMC > Powering Biology L1-5 > Flashcards

Powering Biology L1-5 Flashcards

1
Q

Where is the site of ATP synthesis in Mitochondria?

A

INNER compartment (MATRIX)

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2
Q

Where is the site of ATP synthesis in Chloroplasts?

A

OUTER compartment (STROMA)

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3
Q

Where is the site of ATP synthesis in Purple Photosynthetic Bacteria?

A

INNER compartment (CYTOPLASM)

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4
Q

What is the energy transducing intermediate?

A

The Chemiosmotic hypothesis

Chemiosmosis-movement of ions across a selectively permeable memb. down their electrochemical gradient

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5
Q

Bacteria streptococcus faecalis doesn’t have a functional electron transport chain. How does it power the transfer of metabolites?

A

It is grown on glucose.

It uses the ATP generated from glycolysis to generate a PMF and so power the transfer of metabolites

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6
Q

What is the equation for Gibbs free energy of concentration?

A chemical in two compartments

A

ΔG (in-out) = RT ln( [A]in / [A]out)
units J.mol-1
R=gas constant=8.314J.k-1.mol-1

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7
Q

What is the equation for Gibbs free energy of ions?

An ion in two compartments

A 
ΔG (in-out) = n.F.ΔΨ
F=Faraday constant=96500J.V-1.mol-1
(When performing calculations make sure all values are in VOLTS not mV or anything else)
n=1 for N+/H+
n=-1 for Cl-
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8
Q

What is the equation for Gibbs free energy?

Free energy of an ion in two compartments

A

ΔG A n+ (in-out) = n.F.ΔΨ + RT ln( [A]in / [A]out)

NB/ for H+ (P-N) is equivalent to (in-out) in the other equation

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9
Q

Name a use of the ion gradient Na+/K+

A

Nerve impulse propagation in neurones

K+ and Ca2+ are involved in insulin release

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10
Q

Some bacteria use a different type of PMF for the ATP synthase. What is it?

A

Sodium motif force

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11
Q

Whats the equation for the proton electrochemical gradient?

Consists of a membrane potential and pH gradient

A

ΔG H+ (P-N) = n.F.ΔΨ - 2.303RT.ΔpH(P-N)

NB/ negative sign comes from negative nature of the pH scale

  1. 303 is used since natural logs=log10
    units: J.mol-1
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12
Q

If we want the entire free energy difference to be expressed as a VOLTAGE what do we do to the equation?

A

DIVIDE BY F
PMF=Δp= ΔGH+/F = n.ΔΨ - (2.303RT/F).ΔpH(P-N)
units:volts

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13
Q

Which out of mitochondria, choloplasts and e.coli have the largest PMF?

A

Mitoch ΔΨ=0.168 > Chloroplasts ΔΨ=0 > E.coli ΔΨ=0.140
Mitoch ΔGH+ = 20,777
If you increase this value over 21,000 the membrane becomes leaky

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14
Q

Why is there no ΔΨ in chloroplasts?

A

The ΔΨ does not build up in chloroplasts because of compensating co translocation of Cl- ions or counter translocation of Mg2+
(Cl- in and Mg2+ out)

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15
Q

What is the direction of proton pumping in mitochondria, chloroplasts and bacteria?

A

Mitoch/Bact: Protons pumped inside to outside
N will be on the inside and P on the outside
Protons want to flow down its conc gradient into the N compartment through the ATP synthase

Chloroplasts: Protons are pumped from the outside to the inside. The N compartment is on the outside and the P on the inside
The lumen (P inside) are kept at pH 4
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16
Q

What type of sym/anti/uniporter is lactose transported into E.coli?

A

Electrogenic lactose:proton SYMPORTER
Electrogenic=involves net movement of charge
Lactose is transported into the N cytoplasm
It is powered by both the proton conc and electrical gradient of the PMF

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17
Q

What type of sym/anti/uniporter is mitochondrial H+/Na+ transport?

A

ANTIPORTER
It is only powered by the ΔpH/conc gradient of protons component of the proton motive force
Electroneutral (one positive for one positive charge therefore no net movement of charge)

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18
Q

What type of sym/anti/uniporter is the mitochondrial transport of calcium?

A

Electrogenic uniporter powered by the ΔΨ component of the PMF
Calcium is driven into the matrix (inner compartment) against its conc gradient by the ΔΨ
ETC maintains the ΔΨ by pumping more protons into the IMS in order to restore it.

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19
Q

What type of sym/anti/uniporter is glucose sodium transport?
NB/ It uses this in conjunction with an ATP powered 3sodium/2potassium antiporter to avoid equilibration of the sodium gradient across the membrane which would stop the transport of glucose

A

SYMPORTER
This is found in the cytoplasmic membrane of cells that line your gut/small intestine.
It uses the transmembrane sodium gradient to power glucose into the cell AGAINST its conc gradient
One sodium moves for every glucose

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20
Q

Although ATP is used as the energy currency in cells there are other small molecules with much high energies of phosphate bonds hydrolysis. Name one.

A

Phosphoenolpyruvate (PEP) -61.9 (twice ATP)
Phosphocreatine -43.1
Phosphate -33.5
ATP -30.5

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21
Q

Why is ATP useful as an energy currency?

A
  1. It is relatively stable in aqueous solution
    ATP hydrolysis has activation energy (Ea) and so is kinetically slow (although thermodynamically stable since products are lower energy than reactants)
    Enzymes speed reaction up by lowering the activation energy barrier.
    We want ATP to be relatively stable so that we can utilise it at a different place to where its being made.
    Given enough time ATP in solution will reach an equilibrium where almost all of it will by hydrolysed to ADP and Pi with a ratio of ten million ADPs for every ATP at equilibrium.
  2. Cell maintains a very high ATP/ADP ratio so that when ATP is hydrolysed you get a big amount of energy out of it for every moles you convert to ADP
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22
Q

What ratio of ATP:ADP is maintained in living cells?

A

1000ATP for every ADP
This displacement from equilibrium means that cellular hydrolysis releases a large amount of free energy(why ATP is used as energy currency). Energy is burnt in order to maintain the system in the out of equilibrium state

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23
Q

What is ATP used for?

A
  1. synthesis of macromolecules such as DNA/RNA/proteins
  2. transport of molecules across membs through ATP-like transporters
  3. phosphorylation reactions in metabolic pathways
  4. phosphorylation by kinases in signalling cascades
  5. cell to cell receptor signalling in the Nervous System in mammals
  6. maintenance of cell structure through assembly and disassembly of the cytoskeleton
  7. powering of muscle contraction through shortening of actin and myosin filament crossbridges
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24
Q

What is the typical ATP conc inside a cell?

A

1-10mM

It is constantly being turned over

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25
Q

What are uncouplers/protonpores?

A

They short circuit the PMF and uncouple the substrate oxidation reactions that are running the ETC from energy utilising reactions like ATP synthesis.
These are small molecules that are soluble in the membrane interior in both protonated and deprotonated forms with pKa close to 7.
They make membranes leaky and shuttle protons across to dissipate the proton gradient.
This short circuits the cycle of proton flow, uncoupling PMF generation from ATP synthesis, the energy being lost as HEAT.

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26
Q

What is the pKa?

A

pKa is a measure of affinity for a proton.

It is the pH with 1/2 protonated and 1/2 deprotated

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27
Q

Give an example of an uncoupler.

A

1.CCCP (carbonyl cyanide m-chlorophenyl hydrazone)
Protonated form of CCCP is neutral/deprotonated form=anion
2.FCCP (p-trifluoromethoxy carbonyl cyanide phenyl hydrazone)
This are LIPID SOLUBLE WEAK ACIDS, the negative charge of which is DELOCALISED/distributed over the molecule allowing the anion to diffuse through the phospholipid membranes. This is also why it can remain soluble in the membrane despite it is negatively charged.
3.DNP (2-4 dinitrophenol) associates with a proton in the cytosol and releases it in the matrix. Was once before used for weight loss.

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28
Q

What reaction occurs in brown adipose tissue?

A

Non-shivering thermogenesis
It is found in small mammals (rodents), mammals that hibernate and young mammals
In human infants BAT contributes 5% of body weight

29
Q

How is the energy of an electrical gradient is dissipated in brown adipose tissue?

A

Uncoupling protein 1 (UCP1 once called thermogenin) by-passing the ATP synthase and generating heat.
ATP synthase acts like an uncoupler

30
Q

What is uncoupling protein 1?

A

UCP1 is a membrane spanning protein found exclusively in mammalian brown fat (5% of mitochondria protein) and it dissipates the proton gradient.
The protein consists of 3 REPEATS of 2 TM alpha helices linked by a long hydroPHILIC loop on the matrix side of the memb.
Is is thought that the bundle of helices form a hydrophilic channel in the core of UCP1 where protons can flow.
Access of this channel is controlled by gates formed by the loops.
Good proton carriers since there are some charged residues in the alpha helices.
UCP1 is involved in both keeping small babies/mammals warm but also involved in kick starting hibernation.

31
Q

In addition to the net transport of protons from the IMS to the matrix what other things does UCP1 transport?

A

It also catalyses the export of fatty acid anions from the mitochondrion as well as a range of other anions such as chloride.

32
Q

What are the characteristics of torpor/hibernation?

A

Low body temp
Low metabolic rate
Low heart rate
Total energy expenditure is as little as 2% of normal.
Body temp can drop as low as 4degrees Celsius\
UCP1 is important for the recovery of this state. (need energy boost form standby mode)

33
Q

How does an animal recover from hibernation?

A

In response to hormonal signals the animal will hyperventilate, increasing O2 levels and reducing CO2 in the blood starting its metabolism.
Body temp rises exponentially from non-shivering thermogenesis mediated by UCP1.
At this point the system doesn’t have enough energy for muscle movement to occur for the animal to shiver.
Shivering begins at temps above 20degrees where then body temp will increase further

34
Q

In an electron transfer reaction what is the electron donor and acceptor?

A

Donor=reductant
Acceptor=oxidant
Reductants tend to have more negative redox potentials than oxidants.
Electrons flow in the direction of increasingly positive redox potentials

35
Q

What is the Nernst equation-deals with the ratio of oxidised/reduced forms of a molecule of ion at a given redox potentail?

A

E=Em + (2.303RT/(nF)) log10([ox]/[red])

E=redox potential where [ox]=[red]
Using the Nernst equation gives you a linear plot

36
Q

What does the term “redox couple” mean?

A

Oxidised and reduced forms of a ion or molecule
NB/some redox reactions involved protons and some do not.
Also redox couples have to be connected as pairs since free electrons do not really exist.

37
Q

What is the reference standard in electrochemistry called?

A

The HYDROGEN ELECTRODE
The potential of a hydrogen electrode with hydrogen at 1atm pressure, H+ ions at unit activity (1mol.L-1) (pH 0) is assigned the value of 0 volts. Everything is measured relative to this.
A redox potential is the excess potential of a redox couple to the standard electrode at the START of the experiment.
The actual redox potential of a solution varies with the concentration of [oxidised] and [reduced]

38
Q

Are reactions written as reductions or oxidations?

A

REDUCTIONS

39
Q

What is the Faraday constant?

A

F is the amount of electric charge per mol of electrons and has the value of 96487C.mol-1 / 96487J.mol-1.volt-1

40
Q

What is the equation for the change in free energy of an individual REDOX reaction?

A

ΔG^o’=-n.F.E^o’
-n is negative since electrons are negative
n=number of electrons
F=faraday constant

If answer is NEGATIVE it is releases energy/exergenic and is ENERGETICALLY FAVOURABLE

41
Q

Free energy change differences from induvidual redox reactions to coupled redox reactions

A

Eg. first rxn in the mitochondrial ETC is an OXIDATION (normally written as reduction)
NADH–>NAD+ +2e- + H+

ΔG^o’=-n.F.E^o’
-296487+0.32=-62kJmol-1
Note use positive 0.32 as reduction reaction is actually an oxidation in this case (reverse sign)

For coupled reactions-difference in redox potetial
(both written as reductions)
NADH--->NAD+ + 2e- + H+
1/2O2 + 2e- + 2H+ ---> H2O
ΔG=-n.F.ΔV
-2*96487* (ΔE^o'(e- acceptor)-ΔE^o'(e- donor))
-2*96487* (+0.82-(-0.32))
-2*96487* +1.14 =-220kJ.mol-1
42
Q

At pH7 what is the actual change of free energy for a reaction? Equation?

A

ΔG=ΔG^o’ + RTln([prod]/[react])

43
Q

Redox potential of a non standard solution equation?

A

E=E^o’ + (RT(nF))ln([ox]/[red])

44
Q

Facts about the midpoint potential

A

At the midpoint [ox]=[red] so [ox]/[red]=1
Midpoint potential is also the standard redox potential
Em=E^o’
Em is a measure of strength of an oxidant or reductant
Em is the intercept on the y axis (E plotted against log10([ox]/[red])

45
Q

What is the slope for a graph determining the midpoint potential?

A

2.303RT/nF

46
Q

What is the expression for how Em,pH varies with pH?

A

Em,pH=E^o - (2.303RT/F).(m/n).pH

Em,pH depends on the numbers of electrons (n) and the numbers of protons (m)

47
Q

What is the number of electrons and protons for QUINONE?

A

The number of electrons is always 2 for quinone but the number of protons will be 2,1,0 depending on the pH the reaction takes place.
Quinone has 2 pKas
One is inb/w pH7andpH9
and one is inb/w pH9andpH13

48
Q

What is the value of -2.303RT/F at 298K?

A

-0.059

So at any point the slope is: -0.059(m/n)

49
Q

Why is the standard hydrogen electrode not always used to measure redox potentials? And what can be used as an alternative?

A

SHE is impractical (pH0=acidic and hydrogen gas=explosive)
In practice you use an alternative reference electrode with a known potential (known relative to the standard hydrogen electrode)
eg saturated calomel electrode which consists of mercury/mercurous chloride (calomel) which is in contact with a saturated solution of potassium chloride (offset E^o=+0.244V relative to the SHE)

50
Q

In Mitochondria what makes reactive oxygen species?

Formation of high levels of ROS are known as oxidative stress.

A

“Slippage” in the mitochondrial ETC leads to the formation of ROS at a level of 0.2-2% total oxygen consumption.
Oxidative stress can result from ROS in the environment, or ROS produced by ionising radiation, metal catalysed oxidation or dysfunction of normal metabolic activity

51
Q

Where are the major sites for ROS?

A

Major sites for ROS production are NADH dehydrogenase (complex I) and the cytochrome bc1 complex (complex III) where single electrons reduce oxygen to a superoxide ion

52
Q

What enzyme converts superoxide ion into hydrogen peroxide?

A

Superoxide dismutase
Hydrogen peroxide can be produced either spontaneously or by dismutation of the superoxide ion (involves 2 superoxide ions where an electron is removed from the first (forming oxygen) and then donated to a second superoxide ion)

53
Q

How is the hydroxyl radical produced?

A

Reduction of hydrogen peroxide by Fe2+ produces a HO- (hydroxide ion) and a hydroxyl radical which is highly reactive

54
Q

What do reactive oxygen species do?

A

Cause oxidative damage of biomolecules, particularly iron sulfur cluster proteins and SNA and formation of non-native disulphide bonds giving protein dysfunction/aggregation.
High levels=oxidative stress and this can cause cellular damage, apoptosis and necrosis.

55
Q

What can oxidative stress and associated biomolecule damage cause?

A

It is thought to play a role in aging and a number of disease states including cataract formation and macular degeneration, chronic heart failure, carcinogenisis and atherosclerosis.
Mitochondrial dysfunction arising form oxidative stress plays in several neurodegenerative diseases including Alzheimers, Parkinsons and Huntingtons

56
Q

How does your body deal with ROS?

A

Uses anti-oxidants to remove ROS and maintain the bodys redox homeostasis preventing mitochondrial and cellular damage

57
Q

What is the major small-molecule antioxidant in Eukaryotes and gram-negative bacteria is what sulphur containing molecule?

A

Glutathione-the major endogenous antioxidant produced by cells
A tripeptide of glutamate, cysteine and glycine with the glutamate linked by is side chain COO- group.
It exists in two forms, the reduced glutathione monomer (G-SH) and the oxidised glutathione dimer (G-S-S-G) linked by a disulfide bond

58
Q

Other than glutathione being important as an antioxidant what other ways is it important to the cell?

A

Maintains important exogenous (dietry) antioxidants such as water-soluble vitamin C (ascorbic acid) and lipid soluble vitamin E (tocopherol) in their reduced (active) forms

59
Q

How do plants produce damaging ROS?

A

Through reduction of oxygen they form during light-driven water oxidation
This is a particular problem when normal energy transfer and electron transfer are impaired

60
Q

What are the principle antioxidants in plants?

A

Carotenoids
Prevent oxidative protein damage.
In humans dietary carotenoids such as beta-carotene are precursors for vitamin A (retinal) and protect against a range of eye diseases, including macular degeneration

61
Q

A range of enzymes combat oxidative stress. How does catalase do this?

A

Catalase converts two H2O2 into two H2O and one O2
Two electrons are donated to the first H2O2 forming 2H2O, then two electrons are removed from the seconds H2O2 forming O2

62
Q

What is the role of theioredoxin?

Small redox protein with two cysteine thiol (-SH) groups in its active site

A

Thioredoxin’s main function is to maintain thiol groups of other proteins in the reduced state, preventing protein inactivation and aggregation through oxidative formation of unwanted disulfide bonds
It maintains a reducing environment in the cytoplasm, along with glutathione

63
Q

How are the reduced forms of glutathione and theioredoxin maintained?

A

By reductase enzymes using NADPH as the electron donor

Need electrons donated to reactive oxidative stress

64
Q

What type of White Blood Cells form part of the early inflammatory response to bacterial infection?

A

Neutrophils
These phagocytose invading bacteria, killing them through the production of ROS in a “respiratory burst” of oxygen consumption
On phagocytosis of bacterium, NADPH oxidase assembles in the phagocytic membrane and reduced oxygen to superoxide

65
Q

What do cytochrome P450 enzymes do?

A

Catalyse the metabolism of a wide range of biomolecules , including lipids, steroid hormones, and xenobiotics such as toxic chemicals and drugs
These enzymes are able to modify drug molecules, either to inactivate them, or in such a way that the drug is converted into the bioactive form.
Perform the monooxygenase reaction
In addition to hormone biosynthesis, these enzymes are involved in herbicide degeneration in plants, and insecticide resistance to insects.

66
Q

Many of the cytochrome P450 catalyse the monooxygenase reaction-what is this?

A

Where one atom of oxygen is inserted into an organic substrate (RH) while the other is reduced to water
RH + O2 + 2H+ + 2e- —> ROH + H2O

67
Q

ROS involved in signalling and gene control

A

A variety of ROS are involved in the modulation of intracellular signalling networks and the control of gene expression, modification or oxidation of the -SH group of cysteine residues playing a key role.

A simple example is the OxyR transcription factor from E.coli which helps to protect the organism from attack by ROS by inducing the expression of multiple genes for antioxidant proteins, detoxification proteins and factors that participate in DNA repair.
The reduced form of OxyR binds to DNA but cannot induce transcription.
Particular cysteines of OxyR undergo modification by H2O2, NO or oxidised glutathione, resulting in the formation of S-OH, S-NO and S-glutathionyl adducts, and disulphide bonds -S-S-
The modified forms of the OxyR are transcriptionally active but differ in structure, DNA binding affinity, and promoter activities, effecting gene expression in different ways.

68
Q

What type of integrin molecules are involved in focal adhesions and hemidesmosomes in the basement membrane?

A

Focal adhesions beta1/3

hemidesmosomes alpha6beta4

69
Q

What proteins exist in tight junctions b/w 2 neighbouring epithelial cells?

A

Occludin- 4TM domains and 2 loops, large cytoplasmic domain at C terminus
Claudin- 1-4TM domains and 2 loops
JAM- 1TM domain

EMC (12 decks)

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