Chapter 5: Aerobic Respiration and Mitochondrion

9/24/15
1.
a.
b.
c.
d.
e.
i.
2.
a.
i.
ii.
b.
3.
a.
b.
c.
i.
4.
a.
i.
ii.
b.
i.
ii.
5.
a.
i.
ii.
iii.
b.
i.
ii.
iii.
1.
6.
a.
b.

Intro
mitochondria dont have characteristic bean shape always
Krebs cycle and electron transport
early earth not a lot of oxygen in the atmosphere: earliest animals were anaerobic
get air flow and circulation if there is a wound, bacteria will consume flesh if no oxygen present
cyanobacteria started anaerobic then switched to aerobic
aerobes can extract more oxygen
Mitochondrial Shape May Vary
long strings with branches, beans, elongated
tail and neck of sperm fall off, which is why you dont get any mitochondria from your father
because its falls off
enzyme on head of sperm that breaks down the egg membrane
size and number reflect the energy requirements of the cell
Mitochondria can fuse with another, or split in two
the balance between fusion and fission is a major determinant of mitochondrial number, length,
and interconnection
constantly changing process
DRP 1( protein) goes around central part of mitochondria, and contracts and squeezing to make 2
mitochondrial
how many, how long
The Structure of Mitochondrion
2 membranes: outer and inner
inner folded up and waded and forms layers called cristae: used for glycolysis stuff?
outer serves as the outer boundary
Mitochondrial matrix (like cytosol): contains circular DNA, ribosomes, and enzymes
genome has 36ish genes
some constantly leaking into nuclear DNA via horizontal gene transfer
Mitochondrial Membranes
Outer
50% protein
large pore-forming called porin
permeable to come proteins
Inner
75% protein
contains cardiolipin but not cholesterol (both true of bacteria)
impermeable to small molecules: a proton cant go through the membrane
because it is MORE DENSE
Carbohydrate Metabolism in Eukaryotic Cells
glycolysis: pyruvate out, goes into mitochondria as acetyl coA
NAD+ have to make more NADH, do in mitochondria or fermentation (lactic acid)

c.
d. layer that bubbles in, what happens in the mitochondria, more folding will make it easier to
process NAD+
7. Glycolysis Review
a. glucose is phosphorlated
i.
lose 1 ATP
ii.
enzyme: hexokinase
b. rearrange glucose 6-phosphate Fructose 6 Phosphate
c. Fructose 6-phosphate is phosphorylated
i.
LOSE 1 ATP
ii.
enzyme: phosphofructokinase
iii.
RATE DETERMINING
d. cleave into 2 isomers
e. rearrange dihydroxyavetone
f. dump
g. remove
h. rearrange
i. dehydrate
j. remove
8. Tricarboxylic acid (TCA) cycle
a. stepwise cycle where substrate is oxidized and its energy is conserved
b. 2 carbon acetyl group from acetyl CoA is condensed with 4-carbon oxaloacetate to form a sixcarbon citrate
c. during the cycle, two carbons are oxidized to CO2, regenerating the four-carbon oxaloacetate
needed to continue the cycle
9. The TCA Cycle
a. pyruvate from Krebs binds to coenzyme A, forming acetyl-CoA

i.
ii.

generated 1 NADH and 1 CO2

pyruvate dehydrogenase pulls off a CO2, stick those hydrogen on NAD+
b. acetyl CoA enters the Kreb cycle and binds to oxaloacetate to generate 6-carbon molecule: citrate
i.
CoA is released
ii.
3 COO- in citrate = tricarboxylic acid
c. citrate is rearranged to isocitrate
d. isocitrate is dehydrogenated in a rapid rxn with oxalosuccinate as an intermediate.
i.
then make a-ketoglutarate
ii.
make CO2?? you also make an NADH
iii.
RATE DETERMINING
e. a-ketoglutarate is dehydrogenated to Succinyl-CoA
i.
1 NADH and 1 CO2
f. Succinyl-CoA is converted to succinate
i.
generates 1 GTP
ii.
GTP: drives proteins and stuff because not enough energy in GTP has to have conformational
changes
g. succinate is dehydrogenated to fumatate
h. fumarate is re-hydrated to form malate
i. malate is dehydrogenated to form oxaloacetate
i.
Forms 1 NADH
j. OVERALL
i.
generate 4 electron carriers, any combo of NAD+ to form NADH or FAD+ to form FADH2
ii.
form 1 GTP to substrate-level phosphorylation
1. low energy phosphate and stick is back on a compound, not generating by electron transport
iii.
release 3 CO2
iv. electron transport is the important thing! we dont generate a bunch of ATP :[
10. TCA Cycle
a. central metabolic pathway of the cell
b. everything you eat feeds in there somehow
i.
bacon contains fat, which gets transformed into acetyl CoA
ii.
protein contains amino acids that can be converted into a number of things that feed into the the
Krebs cycle
1. energetically unfavorable
2. body turns to your muscles first because it is easier to get into the Krebs cycle compared to the
fat
iii.
easiest way is carbs which is why we like them!
1. glucose is only thing your brain can use
2. liver can convert fats back into glucose (but also makes ketones)
a. high level of ketones can become impairing
11. Glycerol Phosphate Shuttle
a. reduced coenzymes in the formation of ATP
b. reduced coenzymes FADH2 and NADH primary products of Krebs
c. NADH forms enters mitochondria via malate-aspartate or glycerol phosphate shuttles
i.
oxidize NADH NAD+ to continue glycolysis
12. Summary of Oxidative Phosphorylation
a. reduced coenzymes carry energy that power making ATP

b. getting electrons off NADH and harvesting energy, then using the energy to make ATP
i.
remove some energy by making it do work, mitochondria will use enrgy to pump H+ ions across
the membrane, ahve to have a pump to do this because the membrane is impermeable, system
designed to moved the H ions across to power the pump
ii.
get H ions on one side and get all the energy we can, Oxygen will bind to the electrons and bind
with the H to make water
iii.
ATP is made in separate step because H ions on one side so they will flow
chemiosmosis
9/29/15
How many electron carriers (NADH, NADPH, FADH2) are reduced during the Kreb's cycle?
ANSWER: 3 uring the Krebs, 1 right before Krebs
Rate limiting step of KRebs- enzyme
isocitrate dehydrogenase is the enzyme
13. Summary of Oxidative Phosphorylation
a. reduced coenzymes are important
i.
as e- move through the electron-transport chain, H+ pumped out across the inner membrane
ii.
ATP formed by controlled movement of H+ back across the membrane through ATPsynthesizing enzyme
iii.
coupling H+ translocation to ATP synthesis is called chemiosmosis
iv. 3 molecules of ATP formed each pair of electrons donated by NADH and 2 molecules of AATP
formed from each pair of electrons donated by FADH2
14. Electron Transport
a. electrons move thorugh the inner membrane via a series of carriers of decreasing redox potential
b. electrons associated with NADH or FADH2 transferred through specific electron carriers that
make up the election transport chain
i.
has to get more and more positive and use the engergy of those electrons
ii.
get 1 +, then 2 +, then 3 +
15. Types of Electron Carriers
a. Flavoproteins
i.
polypeptides bound to FAD or FMN
b. Cytochromes
i.
contain heme groups bearing Fe or Cu metal ions
ii.
heme: flower shape
c. Three copper atoms
i.
located within single protein complex and alternate between Cu2+/Cu3+
d. Ubiquinone
i.
coenzyme Q
ii.
is lipid soluble mlecule made of 5-carbon isoprenoid units
e. iron-sulfur proteins contain Fe in association with inorganic sulfur
i.
carriers arranged in order of increasingly positive redox potential.
ii.
important: energy level of negatively charged electrons decreases with each step
iii.
hold in line by cysteine residues, and stay put
iv. sequence of carriers was determines by use of inhibitors

v.

enter electron transport chain, release energy step by step, NADH have high energy compared to
FADH2, each step the electron loses energy until you get to he end of the process and make
water
16. THe electrno transport chain of the inner mitocondrial membrane
a. arranged in a sequence of less positive to more positive
b. complex 1: less positive
i.
NADH dehydrogenase
ii.
catalyzes transfer of e- from NADH to ubinoquinone and transports 4 H+ per pair
c. complex 3
i.
cytochrome bc1
ii.
catalyzes the transfer of e- from ubiquinone to cytochrome c and transports 4 H+ per pair
d. complex 2
i.
succinate dehydrogenase
ii.
catalyzes transfer of electrons from succinate to FAD to ubiquinone without transport of H+
e. complex 4: very positive
i.
cytocrhome c oxidase
ii.
catalyzes transfer of e- to O2 and transports H+ across across the inner membrane
1. cytochrome oxidase is a large complex that adds 4 electrons to O2 to form 2 molecules of H20
2. metabolic poisons CO, N3-, CN- bind catalytic sites in complex 4 to block it

17.
18. How Complex 1 Works
a. contains peripeheral hydrophilic domain and membrane-embedded hydrophobic domain
b. electron tranfer in peripheral hydrophillic arm is coupled by conformational changes to proton
trnaslocation across the membrane domain
i.
elbow is like a gate
c. unprotonated glutamic acid and protonated lysine residues, driven by transmembrane helix
conformational changes, promotes proton translocation
19. How Complex 4 Works

a. cytochrome oxidase is a proton pump in synthetic liposomes that adds 4 electrons to O2 to form
two molecules of H20
b. core is an iron or a copper (cytosome b)
c. electrons jump between different metal atoms, protons move through the system
d. changes promote H+ ions movement
20. Electron Transport and Tunneling
a. tendency for electrons to be transferred from one carrier to the next depends on the energy
potential differences between the two redox centers
b. rate of transfer depends on catalytic activities of the proteins involved
c. electrons may travel considerable distances (10-20 A) between adjacent redox centers
d. electrons probably flow through special tunneling pathways consisting of a series of covalent
and H bonds that stretch across parts of several amino acid residues
e. if an electron gets loose in the electron transport chain then it becomes a free radical
21. Translocation of Protons and the Establishment of Proton-Motive Force
a. use this force to do more work
b. chemical dinitrofenal uncouples glucose oxidation and ATP formation by increasing the
permeability of the inner membrane to H+ this elminating the proton gradient
22. Machinery for ATP Formation
a. isolation of coupling fctor 1 or F1, showed that it hydrolyzed ATP
i.
behaves as an ATP synthase
ii.
led to conclusion that an ionic gradient establishes a proton-motive force to phosphorylate ADP
23. Structure of ATP Synthase
a. looks like a tree
b. globby part at the top ocurs in 3 pairs
c. form an active site as 2 proteins oair togeher
d. hole that the protons pass through, and the flow of the charged particles makes electricty which
powers ATP synthesis
e. Fo
i.
number of subunits in the c ring is 10-14
ii.
yeast and bacteria have less subunits
f. aspartic acid forms part of the active site for H+ ions to flow from inner mitohcondria then
causes the bottom unit to spin like merry go round, then the stalk and the top rotates
g. synthase F1occur as dimers (pairs) to make 3 active sites and go through 3 different
conformaitonal changes
i.
open phase and wants ATP
ii.
LOOSE:when ATP diffuses on the active site, it rotates
1. ATP and inorganic phosphate now bound
iii.
TIGHT: tightens up even more, and puts the lat phosphate group back on just because of physical
squeezing
24. Experimental Evidence of F1 mechanism
a. see that the thing spins
25. Other roles
a. more ADP, faster metabolism needs to be
26. Peroxisomes
a. instead od taking O2 and making water, sometime you make free radicals

b. peroxisomes get the free radicals and make hydrogen peeroxide and store it, use it to kill
invading bacteria or chew up long fatty acids
27. Glyoxysomes
a. convert fats in plants into glucose to make seeds, seeds needs nutrients in the seed, oils are
degraded and power the seed through the first stages of growth