lect 5: mitochondria & aerobic respiration

Question 1

what are the learning objectives?

Answer 1

-describe the structure and functions of the membranes and matrix of the mitochondrion
-outline the function of glycolysis, fermentation, the TCA cycle and oxidative phosphorylation
-explain how the transport of electrons down the respiratory chain leads to the formation of a proton gradient
-explain how translocation of protons can establish a proton-motive force

Question 2

what are aerobes and anaerobes?

Answer 2

-anaerobes: capture and utilize energy by oxygen-independent metabolism like glycolysis and fermentation
-aerobes: use oxygen to extract more energy from organic molecules (oxidative phosphorylation)

-in eukaryotes, the utilization of oxygen as a means of energy extraction takes place in a specialized organelles, the mitochondrion (prokaryotes don’t have mitochondria)

Question 3

what is the structure of the mitochondria?

Answer 3

-different overall structure depending on cell (and metabolic activity)
-typically bean-shaped organelles but may be round or threadlike
-size/number of mitochondria reflect the energy requirements of the cell

Question 4

what are the 5 roles that mitochondria play in cells?

Answer 4

Question 5

what is the graph of mitochondrial functions?

Answer 5

Question 6

what are the membranes and aqueous compartments of the mitochondria?

Answer 6

Question 7

what is the mitochondrial genetic organization?

Answer 7

mitochondria have a genome and can synthesize proteins

MtDNA (mitochondrial DNA):
-synthesizes for 13 protein (which is only 18% that is need, so gets other from nucleus)
-get it from your mother (maternally contributed)

what about the other proteins it needs?
-they must travel through TOM and TIM
-translocase of the outer membrane (TOM)
-translocase of the inner membrane (TIM)

Question 8

what are the steps of aerobic respiration?

Answer 8

1. glycolysis occurs in cytoplasm
   -glucose to acetyl CoA
2. acetyl CoA travels into mitochondria
   -citric acid cycle (occurs in matrix)
3. oxidative phosphorylation
   -occurs inside inner mito membrane
   -where ETC is

Question 9

what is the first step in oxidative metabolism?

Answer 9

glycolysis
-occurs in the cytosol, so doesn’t occur in organelles
-no oxygen is needed for it to take place
-energy input of 2 ATP

products:
-2 pyruvate
-4 ATP
-2 NADH

the net gain is 2 ATP

Question 10

what is the structure and function of ATP?

Answer 10

ATP (adenosine triphosphate) is the energy currency of cell

ATP has 3 components
-adenine
-ribose (sugar; also in RNA)
-3 phosphate groups

dephosphorylation (removes a phosphate group) releases energy
-ATP becomes ADP (adenosine di-phosphate) which releases energy
-ATP to ADP to AMP

therefore the addition of a phosphate group (phosphorylation) to AMP and ADP requires energy

Question 11

what are electron carriers?

Answer 11

electron “shuttles”
-nicotinamide adenine dinucleotide (NAD+), derived from B vitamin group and are derivative of nucleotides
-flavin adenine dinucleotide (FAD+)

NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule
-oxidation is removing electrons from a molecule
-reduction is adding electrons to a molecule

Question 12

what is the graph of the fates of pyruvate?

Answer 12

multiple different different paths that it can take depending on the environment and needs of the cell

Question 13

when do the fates of pyruvate happen?

Answer 13

aerobic conditions
-pyruvate transported across inner membrane
-decarboxylated to acetyl CoA
-acetyl CoA enter the next stage which is the kreb’s cycle

anaerobic conditions
-fermentation

Question 14

what is fermentation?

Answer 14

-anaerobic process in which NAD+ is regenerated from glucose
-occurs in cytosol
-occurs in muscle when you have an insufficient oxygen supply, which forms lactate

kreb cycle cannot occur
-doesn’t directly require oxygen but the electron shuttles it produces need oxidative phosphorylation which needs O

Question 15

what is the second step in oxidative phosphorylation?

Answer 15

citric acid cycle
-occurs in mitochondria
-needs oxygen indirectly
-main source of energy for cells

input
-acetyl CoA (oxidized)

products
-3 NADH
-1 FADH2
-1 GTP
net gain is 12 ATP

Question 16

what is the massive graph of the citric acid cycle?

Answer 16

-different reactions and enzymes used
-diff locations
-oxaloacetate gets recycled and reused

Question 17

does the citric acid cycle only act alone?

Answer 17

citric acid cycle is a critically important metabolic pathway

other catabolic pathways generate compounds that are fed into TCA cycle
-fatty acid cycle
-catabolism of amino acids

depend and rely on eachother for substrates
-in fasted states, we can use fatty acid for creb cycle

Question 18

what are the reduced coenzymes and ATP formation?

Answer 18

primary products of TCA cycle
-FADH2 and NADH which contain high energy electrons

-electrons are fed into mitochondrial electron-transport chain to generate ATP

what about the NADH formed in the cytosol during glycolysis?
-solution is the glycerol phosphate shuttle
-NADH needs a way to move into cell
-DHAP takes electrons from NADH to create NAD+ and glycerol 3 phosphate which can cross membranes

Question 19

what is the glycerol phosphate shuttle?

Answer 19

-cytosolic NADH
-electron transferred to dihydroxyacetone (DHAP) -> glycerol-3P
-glycerol 3P shuttles the electron into intermembrane space
-GSPDH transfer election to FAD+ to create FADH2

Question 20

what are the steps of oxidative phosphorylation?

Answer 20

1. electron transport chain
2. chemiosmosis

Question 21

what is oxidative phosphorylation in simple terms?

Answer 21

process of ATP formation
-electron transport chain: high energy electrons passed from NADH and FADH2 through a series of carriers
-chemiosmosis: controlled movements of H+ back across the membrane coupled to ATP synthesis

Question 22

what is the role of mitochondria in ATP formation of oxidative reduction potentials?

Answer 22

reducing agents ranked according to electron-transfer potential
-strong oxidizer=high electron affinity
-strong reducer= weak electron affinity

oxidizer/reducer occur as pairs
-e.g. NAD+ and NADH
-differ in electron number

the transfer of electrons between a pair causes a charge separation that can be measured
-called the oxidative-reduction (redox) potential

NADH is a strong reducing agent (so it has a weak electron affinity bc its good at giving electrons)

Question 23

what is the role of mitochondria in ATP formation in electron transport?

Answer 23

reactions in TCA transfer pairs of electrons from substrates to cofactors (NAD+, FAD+) which become NADH and FADH2

high energy electron from cofactors transferred through series specific electron carriers that make up electron transport chain
-complexes I, II, III and IV
-occurs in the inner membrane

Question 24

what are the types of electron carriers?

Answer 24

found within complexes
-flavoproteins
-cytochromes
-copper atoms
-ubiquinone
-iron-sulfur proteins

Question 25

what are flavoproteins?

Answer 25

type of electron carrier flavoproteins are polypeptides bound to flavin adenine dinucleotide (FAD) which forms flavin mononucleotide (FMN) major flavoproteins of the mitochondria: -NADH dehydrogenase (electron-transport chain) -succinate dehydrogenase (TCA cycle)

Question 26

what are cytochromes?

Answer 26

type of electron carrier cytochromes contain heme groups with Fe or Cu metal ions -reversible transition between the Fe+3 (acceptance of electron) and Fe+2 (loss of electron) (so changes in oxidation state) the electron transport chain has three cytochrome types (a b and c)

Question 27

what are copper atoms?

Answer 27

type of electron carrier -copper atoms: three located within single protein complex and alternate between Cu+2/Cu+3

Question 28

what is ubiquinone?

Answer 28

type of electron carrier -also called coenzyme Q -is a lipid soluble molecule (not fixed in one place in membrane) of five-carbon isoprenoid units

Question 29

what are iron-sulfur proteins?

Answer 29

type of carrier protein -Fe atoms linked to inorganic sulfide ions as part of an iron-sulfur center -not located within a heme group

Question 30

what is the role of electron carriers in ATP formation?

Answer 30

-carriers arranged in order of increasingly positive redox potential -electron lose energy along chain -each carrier is reduced by the preceding carrier and then oxidized by carrier following it -final electron acceptor is O2 (reduced to H2O)

Question 31

what are do the electron transport complexes do?

Answer 31

-4 distinct, asymmetric, membrane-spanning complexes (I, II, III, IV) -within a complex, electron travel between adjacent redox centers -3 places where electron transfer is associated with increased free energy -free energy conserved by translocation of H+ from matrix to the intermembrane space

Question 32

what is complex I?

Answer 32

complex 1 (NADH dehydrogenase) -NADH electron pair is given to ubiquinone (CoQ) which forms ubiquinol (UQ) -has hydrophilic domain which lies in the matrix -hydrophobic portion in inner membrane -electron transfer and 1 H+ translocation

Question 33

what is complex 2?

Answer 33

complex 2 (succinate dehydrogenase) consists of -2 hydrophobic subunits which anchor protein in membrane -2 hydrophilic subunits made up of succinate dehydrogenase (also in TCA cycle) -lower energy electron from succinate is transfer to FADH2 to CoQ to ubiquinol (UQ) contain heme group -traps escaped electrons so prevents formation of destructive superoxide radicals -there is NO H+ TRANSLOCATION

Question 34

what is complex 3?

Answer 34

complex 3 (cytochrome bc1) -UQ electron pair is transferred to cytochrome c -4 H+ translocation for every electron pair (greater than complex 1) H+ release in two separate steps 1. two protons are derived from the molecule of ubiquinol that entered the complex 2. two protons are removed from the matrix and translocation as part of a second molecule of ubiquinol

Question 35

what is complex 4?

Answer 35

complex 4 (cytochrome oxidase) final step of ETC -electron transferred from cytochrome c to molecular O2 -complex 4 is a huge assembly of subunits that act as redox-driven proton pump for every molecule of O2 reduced, 8 H+ are taken up from the matrix -4 are consumed to form two molecules of water -4 are translocated to the intermembrane space

Question 36

what is the establishment of a proton-motive force?

Answer 36

two components of H+ gradient (more H+ in inner membrane space than in matrix) -concentration gradient between matrix and intermembrane space creates a pH gradient -separation of charge across the membrane creates an electric potential (voltage) -energy present in both components (add together above) of the gradient is proton-motive force -fluorescent dye JC-1 green-orange in response to membrane potential increasing

Question 37

what is the structure of ATP synthase?

Answer 37

protein complex with 2 parts: F1 particles=catalytic subunit -3 catalytic sites for ATP synthesis F0 particle=embedded in inner membrane -base contains channel moving protons from intermembrane space to matrix

Question 38

what are other roles for proton motive force?

Answer 38

creates ATP but also facilitates other functions mitochondria engaged in other processes that rely on the proton-motive force for energy -drives the uptake of ADP and inorganic phosphate into mitochondria in exchange for ATP and H+ respectively -used to "pull" calcium ions into the mitochondrion; to drive the events of mitochondrial fusion

Question 39

what is mitochondrial dynamics?

Answer 39

fusion and fission -allow to adjust to metabolic environmental stress -share organelles components to replace damaged or lost components (ways for mito to repair itself)