1
Q
Give some properties as to why O2 is good for energy generating capacity?
A
- Oxygen is found almost everywhere on the earth’s surface
- oxygen diffuses easily across cell membranes
- under certain circumstances oxygen is highly reactive so it can readily accept electrons. This capacity is also responsible for another property of oxygen, its tendency to form highly destructive metabolites called reactive oxygen species ( ROS).
2
Q
What is the terminal electron acceptor extracted from fuel molecules?
A
O2
3
Q
ETC is a series of what?
A
- electron carriers in the inner membrane of the mitochondria of eukaryotes and the plasma membrane of aerobic prokaryotes
4
Q
ETC is a series of electron carriers arranged in the inner membrane in order of what?
A
- increasing electron affinity; it is these molecules that transfer the electrons derived from reduced coenzymes to oxygen.
5
Q
During the transfer of electrons there is a ___ in reduction potential that occurs.
A
decreease
6
Q
When NADH is the electron donor and oxygen is the electron acceptor the change in standard reduction potential is what?
A
+0.82V-(-0.32V)= +1.14V
7
Q
The process in which oxygen is used to generate energy from food molecules is sometimes called what?
A
cellular respiration
8
Q
The energy released during electron transfer is coupled with what?
A
several ednergonic processes….prominently ATP synthesis
9
Q
What are the principle sources of electrons?
A
- reduced coenzymes from glycolysis, TCA and fatty acid oxidation
10
Q
Where are the components located for ETC in eukaryotes? What are they organized into?
A
- inner mitochondrial membrane
- four complexes
L> consisting of several proteins and prosthetic groups.
11
Q
Complex 1 is also called what?
A
NADH dehydrogenase complex
L> catalyzes the transfer electrons from NADH to UQ (ubiquinone)
12
Q
Sources of NADH?
A
TCA……….fatty acid oxidation
13
Q
Which complex is the largest?
A
Complex 1
L> made of 25 different polypeptides……
14
Q
What is complex 1 made up of?
A
- FMN, seven iron sulfer centres
15
Q
What are iron sulfur centres?
A
they mediate one electron transfer reactions…..proteins that contain these are called nonheme ion proteins.
16
Q
Function of complex 1?
A
- NADH reduces FMN to FMNH2…electrons are transferred from FMNH2 to an iron sulfur centre….1 electron at a time…….after the transfer from one IS center to another the electrons are eventually donated to UQ…
17
Q
What is UQ?
A
a lipid soluble mobile electron carrier capable of accepting/donating electrons one at a time.
18
Q
Electron transport is accompanied by the net movement of what?
A
protons from the matrix across the inner membrane and into the inter membrane space.
19
Q
What is the other name for Complex 2?
A
- succinate dehydrogenase complex
20
Q
What is the succinate dehydrogenase complex composed of?
A
- TCA enzyme succinate dehydrogenase and two iron sulfur proteins.
21
Q
Complex 2’s function?
A
- mediates the transfer of electrons from succinate to UQ. The oxidation site for succinate is located on the larger of the iron sulfur proteins…..it is covalently bound to FAD
22
Q
In some cells what doe glycerol-3-phosphate dehydrogenase do?
A
- located on the outer face of the inner mitochondrial membrane transferring electrons from cytoplasmic NADH to the ETC.
23
Q
Acetyl-CoA dehydrogenase ???
A
transfers electrons to UQ from the matrix side of the inner membrane.
* first enzyme in fatty acid oxidation
24
Q
Complex 3 is also called??
A
cytochrome b
25
What is complex 3 composed of?
11 subunits
| L> three cytochromes ( bL, bH and C1 ) and one iron sulfur centre
26
What are cytochromes?
- a series of electron transport proteins that contain a heme prosthetic group similar to those found in hemoglobin and myoglobin
L> electrons are transferred by cytochromes one at a time in association with a reversible change in the oxidation state of a heme ion.
(ex: btwn a reduced Fe 2+ and an oxidized Fe 3+)
27
Function of Complex 3?
transfer of electrons from reduced coenzyme Q (UQH2) go a protein called cytochrome C (cyt c)
28
Complex 3:
| Cytochrome c?
is a mobile electron carrier that is loosely associated with the outer face of the inner mitochondrial membrane.
29
The passage of electrons through complex 3 is referred to what?
Q cycle
30
Complex 3:
| What is the overall reaction for the process which each UQH2 donates two electrons to cytochrome C?
UQH2+ 2 cyt cox (Fe3+) + (2H+)-----> UQ + 2 cyt red (Fe2+) + 4H+ (cytosol)
31
Complex 3:
| During the Q cycle coenzyme Q molecules diffuse within the inner membrane between the electron donors in?
complex 1 or 2 and the electron acceptor in complex 3 ( the iron sulfur protein).
32
Complex 3:
| How many electrons does UGH2 donate?
two electrons one at a time
33
Complex 3:
| One electron flows to the _____, which then transfers it to ___ which it is then donated to ___.
Fe-S protein
cyt c1
cyt c
34
Complex 3:
-The second electron flows to ___ and then to ___ which then transfers this electron to an oxidized ____ to generate ______.
cyt bL
cyt bH
CoQ molecule (UQ)
UQ semiquinone (UQ-)
35
Complex 3:
| Where are the protons released to from the oxidation of UQH2?
inner membrane space.
36
Complex 3:
| -The other electron from the second UQH2 ??
- its transferred to cyt bL and b H and then its donated to UQ semiquinone . As UQ- accepts this electron it also binds two protons from the matrix to form UQH2.
37
Complex 3:
| give an overview for the products!
- two molecules of cyt c are reduced, four protons are released into the inner membrane space and a molecule of UQH2 is regenerated from UQ-
38
What is complex 4 called?
- cytochrome oxidase
39
complex four catalyzes?
- catalyzes the four electron reduction of O2 to form H2O
40
Complex 4:
| - made up of??
- membrane spanning complex
- 6-13 subunits
- cytochrom a and a 3.........and three copper ions.
- Two copper ions form CuA/CuA a binuclear Cu-Cu center and heme a3 and CuB from a binuclear Fe-Cu center.
L> both centres accept one electron at a time.
41
Complex 4:
| - Describe the electron flow!
- from cytochrome c to CuA/CuA to cytochrome a and then to a3-CuB and finally to O2.
42
Complex 4:
| - describe overall?
- Four protons and four electrons are shuttled through complex 4 from the outer face of the inner mitochondrial membrane o the matrix for delivery to the cytochrome a3-Fe(II)-bound dioxygen.
43
Complex 4:
| -How many molecules are made?
- two
| O2 + (4H+) + 4e- -----> 2H2O
44
Complex 4:
| - ATP binding regulatory site?
when ATP is high , ATP ACTS AS AN ALLOSTERIC INHIBITOR BINDING TO THE SITE AND CAUSES A DECREASE IN THE ACTIVITY OF CYTOCHROME OXIDASE
45
- NADH oxidation results in the release of a substantial amount of energy which is measured how?
- decreased reduction potential as electrons flow through complexes 1, 3 and 4
46
Electron transport inhibitors:
| - when ETC is inhibited what is reduced?
- oxygen consumption is reduced or eliminated.
47
Electron transport inhibitors:
| - Since oxygen consumption is reduced or eliminated what accumulates?(2)
- oxidized ETC components accumulate on the O2 reducing side of the site of inhibition.
- Reduced ETC components accumulate on the non oxygen side of the site inhibition.
48
Electron transport inhibitors:
| What inhibits cyt b in complex 3?
- antimycin A.......
49
Electron transport inhibitors:
If antimycin A is added to a suspension of the mitochondria, ___, ___ and ___ become more reduced. The ____ and ___ become more oxidized.
- NAD+, Flavins and cyt b
| - cytochromes c1 and c
50
Electron transport inhibitors:
| - Two examples that inhibit NADH dehydrogenase (complex 1)
- rotenone and amytal
51
Electron transport inhibitors:
| - three examples that inhibit cytochrome oxidase (complex 4)
carbon monoxide, azide (N3-) and cyanide (CN-)
52
What is oxidative phosphorylation?
energy is generated by the ETC is conversed by the phosphorylation of ADP to yield ATP.
53
Oxidative phosphorylation:
| Free energy released during electron transport drives ATP synthesis is called?? (theory?)
Chemiosmotic theory !
54
Oxidative phosphorylation:
| What are the features of the Chemiosmotic theory? (2)
1. as electrons pass through the ETC protons are transported from the matrix and released into the inter membrane space causing an electrical potential and a proton gradient arise across the inner membrane. (proton motive force)
2. Protons which are present in the inter membrane space in great excess asa result of the ETC process can pass through the inner membrane and back into the matrix down their concentration gradient only through special channels. (inner membrane is permeable to ions like protons)
L> AS the thermodynamically favourable flow of protons occurs through a channel each of which contains an ATP synthase activity, ATP synthesis occurs.
55
Oxidative phosphorylation:
| During OP free energy released from the ETC and ATP synthesis is coupled by what?
protonmotive force created by the ETC
56
Oxidative phosphorylation:
| What are three pieces of evidence for the chemiosmotic theory that supports it?
1. actively respiring mitochondria expel protons...pH drops when O2 is added to a weakly buffered suspension of mitochondria.
(ph norm= 0.05 of gradient)
2. ATP synthesis stops when the inner membrane is disrupted
L>ex: stops when mitochondria is in a hypertonic solution...=swelling and leakage of protons across the inner membrane...but ETC still happens.
3. Uncouplers and Ionophores.....dissipate the proton gradient....when a disruption occurs in the gradient...energy from food is released as heat
57
Oxidative phosphorylation:
| Uncouplers?
- ex: dinitrophenol collapses the proton gradient by quailing the [proton] on both sides of the membrane...(as they diffuse across the membrane uncouplers pick up protons from one side and release them on the other.
58
Oxidative phosphorylation:
| Ionophore?
hydrophobic molecules that dissipate osmotic gradients by inserting themselves into a membrane and forming a channel...ex: gramicidin: allowing H, K and Na to cross.
59
Oxidative phosphorylation:
| The proton gradients generated by ETC can be dissipated fro two general purposes what are they?
1. ATP is synthesized as patrons flow through the ATP synthase
2. regulated proton leakage is used to drive several other toes of biological work.
60
Oxidative phosphorylation:
| Where are proton translocating ATP synthases located?
- inner mito membrane
61
Oxidative phosphorylation:
| What are the two major components of ATP synthase?
```
1. F1 unit
L> active ATPase
L> 5 subunits: alpha3:beta3:y:o:e
L> three nucleotide binding catalytic sites
2. Fo unit
L> transmembrane channel for protons
L> three subunits: a:b2:c12
```
62
Oxidative phosphorylation:
| How many rotors are in ATP synthase?
two
63
Oxidative phosphorylation:
| ATP synthases rotors are linked by a strong flexible ____.
stator
| L> stationary component of a motor
64
Oxidative phosphorylation:
| In respiring organisms the Fo motor converts the ____ into a _____ that drives ATP synthesis catalyzed by the __.
protonmotive force
- rotational force
- F1 unit
65
Oxidative phosphorylation:
The revolving component of ATP synthase is called the c ring which is made up of? It is attached to a central shaft composed of the ___ and ___ subunits, rotates within the alpha,beta hexamer of the F1 unit. What does the stator do? (made up of as well)
-c subunits.
-e and y
prevents the aloha beta hexamer from rotating
( b and o)
66
Oxidative phosphorylation:
| The synthesis of each ATP requires the translocation of ___ protons through the ATP synthase.
3
L> an additional proton is required as well for the transport of ATP and OH out of the matrix in exchange for ADP and Pi.
67
Oxidative phosphorylation:
| As protons flow through Fo what occurs?
- rotation of the proton channel aka c ring is transmitted to the y subunit that projects into the core of the F1 unit. The rotation of the central shaft puts it in three possible positions relative to each alpha, beta dimer.
* protonmotive force cause three rotations (120 degrees) of the alpha, beta hexamer.
68
Oxidative phosphorylation:
| As rotation occurs each of the three nucleotide binding sites ??
undergoes conformational changes that result in ATP synthesis.
69
Oxidative phosphorylation:
| What happens in fermentative lactic acid bacteria or E.coli in anaerobic conditions?
- F1 acts in reverse....ATP is hydrolyzed....protons are pumped outward which makes a gradient aiding in cellular work like flagella rotation and nutrient transport.
70
Oxidative phosphorylation:
ATP Synthase :
- explain rotation.
- Fo:
L> each c subunit in the c ring consists of two transmembrane antiparallel helices. The c-terminal helix consist of c subunits contains an essential aspirate residue that upon protonation cause a swivelling motion that in turn triggers the rotation of the entire sub unit.
71
Oxidative phosphorylation:
ATP Synthase :
- Where do protons enter the c ring?
- channel in a subunit.
L> at the end of it....at the interface of the a subunit and the proximal of the c subint.... a basic residue (Arg) transfers the incoming protons to the Asp residue in the c subunit.
72
Oxidative phosphorylation:
ATP Synthase :
- what direction does the c ring rotate?
counterclockwise
73
Oxidative phosphorylation:
ATP Synthase :
- As each c subunit reaches a channel on the a subunit what occurs?
deprotonation
L>proton exits into the mitochondrial matrix
L> the torque causes the asymmetric central shift to rotate within a sleeve inside the alpha, beta hexamer.
74
Oxidative phosphorylation:
ATP Synthase :
- The catalytic sites in the alpha, beta hexamer occur on the beta subunits....they occur n three conformations in terms of affinity for adenine nucleotide ligands, what are they?
L> interconversion between these happens via?
1. open (O)..inactive with low affinity
2. tight (T).... active with high affinity
3. loose (L) also inactive.
L>interaction with the rotating y subunit
75
Oxidative phosphorylation:
What are essentially the three steps to ATP synthesis?
L> what happens as the y subunit rotates and sequentially interacts with each beta subunit?
1. ADP and PI bind to L site
2. ATP is synthesized when the L conformation is transformed to a T conformation
3. ATP is released as the T conformation converts to O conformation.
L> each active site is formed through the O, T and L conformations.
76
Control of Oxidative phosphorylation:
| - P/O ratio?
- the number of moles of Pi consumed for each oxygen atom reduced to H2O....it reflects the degree of coupling observed between the proton motive force created by the ETC and ATP synthesis
77
Control of Oxidative phosphorylation:
| - Respiratory control?
oxygen consumption increases dramatically via ADP being supplied
78
Control of Oxidative phosphorylation:
| - [ATP]/ [ADP][Pi]
- ATP mass action ratio
| - ATP synthase is inhibited by high ATP...activated when ADP and Pi are high
79
Control of Oxidative phosphorylation:
- The amount of ATP and ADP within the mitochondria is largely regulated by two transport proteins in the inner membrane. What are they?
1. ADP-ATP translocator
| 2. Phosphate carrier
80
Control of Oxidative phosphorylation:
| 1. ADP-ATP translocator?
dimeric protein responsible for the 1:1 exchange of intra mitochondrial ATP for the ADP produced in the cytoplasm.
81
Control of Oxidative phosphorylation:
| - Explain why the outward transport of ATP and inward transport of ADP is favoured?
- ATP is more negative than ADP
82
Control of Oxidative phosphorylation:
| 2. Phosphate Translocase ?
transport of H2PO4- along with a proton is mediated by this
83
Control of Oxidative phosphorylation:
| 2. Phosphate Translocase ...also called?
- H2PO4-/H+ symporter
84
Symporter??
- transmembrane transport proteins that move solutes across a membrane in the same direction
85
Control of Oxidative phosphorylation:
2. Phosphate Translocase
L> the inward transport of __ protons is required for the synthesis of each ATP molecule: __ to drive the ATP synthase rotor and __ to drive the inward transport of phosphate.
4
3
1
86
The inner mitochondrial membrane is impermeable to??
NADH
| L> from cyto..from glycolysis
87
Glycerol phosphate shuttle?
- DHAP is reduced by NADH to form glycerol-3-phosphate.....this is followed by the oxidation of it by mitochondrial glycerol-3-phosphate dehydrogenase;
L> uses FAD as an e- acceptor....
L> FADH2 produced is then oxidized by ETC.
= 1.5 ATP per cytoplasmic NADH
88
Malate-asparate shuttle?
- more energy efficient
- cytoplasmic oxaloacetate is reduced to malate via NADH.
- Malate passes into the mitochondrial matrix and is reoxidized.... The NADH produced is oxidized by the ETC.
L> for the shuttle to continue again....oxaloacetate must return to the cytoplasm....but the inner membrane of the mitochondria is impermeable to it.
L> its converted to aspartate in a transamination reaction involving glutamate.
(glutamate results in alpha ketoglutarate)
L> aspartate goes back through the glutaamte-aspartate transport protein.(alpha ketoglutarate goes through the malate-alpha-K TP)..into the inter membrane space and is converted back to oxaloacetate with the help of alpha ketoglutarate (reconverted back to glutamate after the the rxn)
89
Malate-asparate shuttle?
| L> Value of NADH for ATP?
- for each NADH = 2.25
| glycolysis produced NADH
90
Two molecules of ATP are produced in the Citric Acid Cycle via GTP but what is the price to transport them into the cytoplasm?
- uptake of two protons into the matrix.......ATP is reduced by half an ATP molecule..
0. 75 per GTP= 0.75 ATP
91
Assuming the total number of ATP produced is 30 what is the overall equation for the complete oxidation of glucose?
C6H12O6 + 6O2 + 30 ADP = 30Pi ---> 6CO2 + 6H2O + 30 ATP
92
How much ATP is per 1 NADH from Oxidative phosphorylation of glycolytic NADH?
2.25 ATP = Asp-Mal shuttle
or
1.5 ATP for 1 FADH2 via Glycerol-3-p shuttle
93
How much ATP is per 1 NADH from Oxidative phosphorylation of NADH produced from pyruvate ---> Acetyl.CoA?
1 NADH =2.5 ATP
94
How much ATP is per 1 NADH from Oxidative phosphorylation of NADH from TCA?
1 NADH= 2.5 ATP
95
How much ATP is per 1 FADH2 from Oxidative phosphorylation of 1 FADH2 from TCA?
1.5 ATP = 1 FADH2
96
Uncoupling proteins?
partially dissipate oxidative energy by translocating protons across the mitochondrial inner membrane without involving ATP synthase.
97
Example of an uncoupling protein?
- Uncoupling Protein 1 (UCP1)
L> a dimer that forms a proton channel
also called thermogenin
98
UCP1 is found only where?
mitochondria of brown fat
99
when is UCP1 activated?
when it is bound to fatty acids
| L> during the reduction of the proton gradient by UCP1 the energy captured during ETC is dissipated as heat.
100
Nonshivering thermogenesis?
process of generating heat from brown fat...its regulated by norepinephrine !
101
Briefly explain Nonshivering thermogenesis!
heat is produced by non voluntary muscle contrition.
| L> NE initiates a cascade mech that hydrolyzes fat molecules. The fatty acid products activate UCP1
102
What are the other two uncoupling proteins besides UCP1?
1. UCP2: in most mamalian tissue..believed to be linked to body weight regulation
2. UCP3: linked to thermogenic effect of thyroid hormone...detected in skeletal muscle as well as brown adipose tissue.
Introductory Biochemistry
flashcards
Decks in class (13)
# Cards
-
Chapter 1: An Introduction to Biochemistry104
-
Chapter 2: Living Cells0
-
Chapter 3- Water: The Matrix of life41
-
Chapter 4: Energy28
-
Chapter 5: Amino acids, Peptides and Proteins50
-
Chapter 6: Enzymes72
-
Chapter 7: Carbohydrates7
-
Chapter 8: Carbohydrate Metabolism101
-
Chapter 9: The Citric Acid Cycle62
-
Chapter 10: Electron Transport Chain and Oxidative Phosphorylation102
-
Lab 1:Separation and Identification of AA's via Paper chromatography17
-
Lab2: Determination of Protein Concentration17
-
Lab 3: Qualitative and Quantitative Tests for the Analysis of Carbohydrates28
