bichem exam 2

oxidative phosphorylation and light rxn

where does oxidative phosphorylation occur and complete rxn

What is it

mitochondria- double membrane; oxidative phosphorylation occurs in inner membrane- fuel and O2 deliver via blood

C6H12O6 +6O2→ 6CO2 +6H2O

complete oxidation of glucose to O2 which gets reduced to H2O, used to get ATP

glucose oxidize

O2 reduce

cellular respiration ultimate e donor/acceptor and how many ATP gen throght oxidative phosphorylation

donor- can be either organic or inorganic compound

acceptor is O2

this process gen 26/30 ATP

sequence of the e- transport chain

1. NADH pssaes e- to Complex 1(NADH-Q reductase) and it pumps protons back to the matrix through ATP synthase to generate ATP and then passes the e- which passes to Q enzyme(ubiquinone)

2. ubiquinone passes to complex 3(cytochrome c reductase) and it pumps protons back to the matrix through ATP synthase to generate ATP and then passes the e- which gets passed to coenzyme C (cytochrome)

3. cytochrome passes e- to complex 4 (cytochrome c oxidase) and it pumps protons back to the matrix through ATP synthase to generate ATP and then passes the e-

4. complex 4 passes e- to O2 acceptor in the form of H20

if the e- donor is FADH2

1. FADH2 passes e- to Complex 2(Succinate dehydrogenase) which passes to Q enzyme(ubiquinone)

2. ubiquinone passes to complex 3(cytochrome c reductase) and it pumps protons back to the matrix through ATP synthase to generate ATP and then passes the e- which gets passed to coenzyme C (cytochrome)

3. cytochrome passes e- to complex 4 (cytochrome c oxidase) and it pumps protons back to the matrix through ATP synthase to generate ATP and then passes the e-

4. complex 4 passes e- to O2 acceptor in the form of H20

Needs to go through this process because if it didn’t too much energy would be release and be damaging to the cell. All of the steps are exogenic allowing a little bit of energy to be released at a time

ubiquinone and cytochrome

ubiquinone- gets reduced to QH2 through various oxidation steps. the oxidized Q and reduced QH2 are present in the mitochondrial membrane are is called the Q pool

cytochrome- contains a heme iron that cycles through +2 and +3 charges as it accepts and donates e-

prosthetic groups of complex 1 and 2

e- carriers; that can accept/donate 2H and 2e-. they accept the e- from NADH and FADH2.

FAD- complex 2

Flavoprotein (FMN)- complex 1

what does a strong oxidizing agent tend to do

accept e-

what does a strong reducing agent tend to do

donate e-

what is the ETC made up of

e- carriers with a high tendency to gain e- (meaning having a high redox potential)_

Reactive oxygen species

reactive chemical species generated in aerobic respiration as a byproduct

ROS attach different cells and damage DNA, protein, and other biomolecules.

Include: O2-, O2-2, OH-

ways to expel the ROS

superoxide dismutase (SOD) and catalase a super-efficient (near diffusion rate) enzyme that changes O2- to H2O using metals. SOD: forms H202 which is still free radical catalase → H2O

Anti-oxidants- helps to keep a good number of free radicles (vit C and E)

Glutathione- acts as an O2 scavenger

Endogenous ROS scavengers are molecules your body produces, like superoxide dismutase, catalase, and glutathione, while exogenous ROS scavengers come from the diet, such as vitamins C and E and plant-derived antioxidants, all of which neutralize reactive oxygen species to protect cells from oxidative damage

iron-sulfate clusters

e- carriers that accept an e- from flavoprotein and donate it to the corresponding complex

they are non-heme complexes; use the same iron 2+ → 3+ that flavoprotein use

frataxin is a protein needed for the synthesis of the iron sulfate clusters- deficiency causes Friedreich’s ataxia

effectors of rate of the ETC

rate decreases rapidly when the e-donors and acceptors move far apart

being coupled with ATP synthesis; e- can’t go through ETC unless ADP→ATP. therefore when [ADP] is high the rate of oxidative phosphorylation is high as well (known as respiratory control)

different protein pumps/channels

uniport

symport

antiport

ionophores

pumps-need energy

channels-no energy needed

uniport-protein moves 1 mol across meb

symport- protein moves2 mol in same direction across meb

antiport- protein moves 2 mol in opposite direction across meb

ionophores-proteins move ions across a membrane

proton gradient

a proton gradient is formed from the ETC pumping e- into the inner membrane space

the proton gradient (aka proton motive force) which consists of a chemical gradient and a charge gradient.

the proton pumps of the ETC dont need ATP they use the energy released by the e- to power the movement of the protons.

structure of ATP synthase

ATP synthase is made of proton conducting unit (f0) and catalytic unit (F1)

F0 is embedded in the inner mitochondrial membrane and has a proton channel

F1 is made of 3 active sites located on 3 B subunits protruding into the matrix

the y subunit connects the f0 and F1

how the F1 is composed

Equal amounts of bound ATP and ATP are found at the catalytic site

Absence of a proton gradient can form ADP and inorganic phosphate but can't release from the active site pocket

Binding change mechanism accounts for synthesis of ATP in response to proton flow

There are three catalytic beta subunits of the F1 component existing in three confirmations:

O form (open)-nucleotides bind or be released from the beta subunit (release of ATP)

L form (loose)- Nucleotides are trapped in beta subunit (binding of ADP and Pi)

T form (tight)- ATP is synthesized

alpha-structural B-chem occurs, y-conformational change

Proton flow causes the release of the newly synthesized ATP When the gamma rotates 120 degrees counterclockwise ATP is synthesized. One full rotation causes the synthesis of three ATP molecules

binding change mechanism

ATP synthesis Works by changing confirmations of the beta subunit. Rotation of the Gamma subunit caused by proton flow causes the beta subunit to change confirmations. It rotates between the O L and T form Which causes the release of ATP the binding of A or the synthesis of ATP

regeneration of FADH2

NADH can't enter the mitochondria by itself, so it transfers electron to DHAP to form glycerol-3-phosphate in the cytoplasm. Once the glycerol-3-phosphate travels into the surface of the inner mitochondrial membrane (complex 2) it converts back to DHAP with the help of glycerol-3-phosphate dehydrogenase. The e- is transferred to FAD to form FADH2

this helps to regenerate the NAD+ used in glycolysis

occurs in skeletal muscles

Maltate-Aspartate shuttle

occurs in the heart and liver

Brings NADH to the inner mitochondrial matrix

the e- NADH transfers to oxaloacetate which forms malate. the malate is moved into the mitochondrial membrane. the e- from malate transfers to NAD+ to form NADH transforming the malate to oxaloacetate. Glutamate (changes to aspartate) donates an amino group to oxaloacetate to form alpha-ketoglutamate . both the alpha-keto and aspartate pass back to the cytoplasm and aspartate takes the amino group back to form oxaloacetate and glutamate

ATP/ADP translocase

moves ATP/ADP across matrix. contains a single nucleotide binding site

faces cytoplasm ADP binds causing a conformational change and brings to matrix/release. ATP then binds causing conformational change to the cytoplasm/release

since ATP has a - charge and positive membrane potential, this process is favored during active respiration

inhibition of this process leads to inhibition of cellular respiration

what do transmembrane proteins do

there are many that bring many metabolites in and out of the cell

How much ATP is produced from ETC FADH2 and NADH in the matrix and cytoplasm

NADH (matrix)-2.5

FADH2(matrix)/NADH (cytoplasm)-1.5; NADH reasoning is it needs to go through glycerol-3-phosphate

uncouplers and what is brown fat/ examples

make heat from forming a pathway to disrupt the proton gradient

brown fat-tissues with high UPC-1

2-4 DNP (dinitrophenol): caused NADH→ O2 like normal but no ATP made since proton gradient is disrupted- the energy made is released as heat

how energy charges are regulated with ATP synthesis

as [ADP] decreases in resting muscle cells, NADH/FADH2 aren’t as consumed by the ETC therefore TCA cycle slows

as ADP increases, phosphorylation speeds up as well as TCA cycle

inhibitors of ETC

CO: inhibits ferrous (Fe2+) form

CN- and N3-:reacts with ferric (Fe3+) to form heme a3

rotenone and amytal: prevents using NADH as substrate

oligomycin DCC: prevents influx of protons

Atractyloside (cytoplasm) and Bongkerkic (matrix): inhibits ADP/ATP translocase

ATP synthase chem formula

ADP 3- + HPO4-2 + H+ → ATP -4 + H2O

how is energy for ATP synthesis generated

by movement of proton from intermembrane space to matrix establishing a electrical potential gradient

is oxidative phosphorylation reversable

NO

photosynthesis rxn and where light rxn occurs

6co2+ 6H2O + energy→ C6H12O6 + 6O2

this reaction is not thermodynamically favored and needs light energy to proceed.

happens in the chloroplasts, specifically the thylakoid membrane

2 parts of photosynthesis

light reaction- make NADH and ATP

dark reaction- use NADH and ATP

photoinduced charge separation

an excited e- moves to an acceptor, occurs in the reaction center

this process occurs in chlorophyll a (4N around mg )- effective because of the alternative double and single bonds

pigment and absorbance

different pigments absorb at different wavelengths can then use electron transfer to get these electrons to the reaction center

PSII happens at 680nm

PSI happens at 700nm

light is captured by antenna chlorophyl

what does the oxidation of chlorophyll do

created a radical Chl+ which is important to photosynthesis

ultimate e- acceptor and donor of photosynthesis

acceptor- NADP+

donor-H20

separate rxn of PSI and II

light: NADP+ + H+ +2e- → NADPH gen reducing power

dark: h20→1/2 O2 +2H- +2e- generates oxidizing power

PSII

made of 30 plus chlorophyll a molecules with 2 of them being the reaction center (D1/d2)

Mn center used to help transfer e-

light catalizes transfer of e- from H2o (creates a ROS)→ pheophtin →plastoquinone QA → plastoquinone QB. once plastoquinone QB has 2e- and get 2H from the stroma it turns into plastoquine which gets transported to cytochrome bf

this reaction leave the extra H from H20 in the thylakoid lumen generating a proton gradient

Tyrosine in subunit D1is the electron donor!

How Mn center of PSII works

Mn helps with the binding and release of e- by the differing oxidation states. 4photons are needed

Tyrosine in subunit D1is the electron donor!

cytochrome bf

links PSI/II

catalizes rxn of plastoquinol→plastocyanin in thylakoid membrane

at the same time 2 H are being pumped into the thy. membrane further expanding the proton gradient