catabolism

anabolism?

• breakdown of molecules to produce energy
• formation of macromolecules that requires an input of energy

• glucose to glucose 6 phosphate with hexokinase
• removes glucose from solute pool
• uses ATP to prepare glucose for E extraction

• fructose 6 phosphate to fructose 1,6-biphosphate
• phosphofructokinase
• uses second ATP; ends E investment

• glyceraldehyde 3 phosphate to 1,3-bisphosphoglycerate 
• glyceraldehyde phosphate dehydrogenase
• NAD+ to NADH and Pi added
• reaction made favorable by steady state conditions

• 1,3-bisphosphoglycerate to 3 phosphoglycerate
• phosphoglycerate kinase
• 2 ATP made for each glucose that recoups invested ATP

• Phosphoenolpyruvate to pyruvate
• pyruvate kinase 
• 2 more ATP /glucose

• substrate-level phosphorylation - direct transfer of Phosphate from an organic molecule to ADP
• oxidative level phosphorylation - indirect transfer of phosphate from an inorganic molecule to ADP (NADH used to make H+ gradient to make ATP)

• payout phase molecules have a lower affinity for the phosphate group than does ATP
• investment phase molecules have a higher affinity for phosphate than does ATP

2 ATP 

2 NADH

2 pyruvate that can be metabolized further or anaerobically be turned to lactic acid to recycle NADH to NAD+ for further glycolysis

allosteric activators?

allosteric inhibitors?

examples of both?

A - increase binding affinity

ADP

AMP

I - decrease binding affinity

ATP

citrate

• outer - 1:1 protein lipid ratio; permeable with porins
• inner - 3 to 1 protein lipid ratio; highly impermeable

• contain some DNA (from moms)
• double membrane
• can replicate themselves; fusion and fission
• powerhouse of cell
• contain ribosomes so they can do their own protein synthesis

• pyruvate to Acetyl CoA
• pyruvate dehydrogenase
• NADH produced
• CoA added; CO2 released

4 NADH (1 from Acetyl CoA production)

1 GTP 

1 FADH2

• carbon rings
• ubiquinone
• metal ions (Cu)
• hemes
• FE-S centers

• 2e-s are transfered from NADH to complex 1; E released used to pump 4H+ to intramembrane space
• they join Q along with 2H+ to balance out the charge on the matrix side of the membrane and float across the membrane to the intramembrane side of complex 3.
• they are released to complex 3 without the 2 H+ which are released outside the membrane

• in the oxidation of succinate to fumarate FAD is reduced to FADH2
• FADH2 is oxidized by complex 2 and the electrons are taken by Q along with 2H+ to balance the charge
• Q binds to complex 3 and gives it its e-s and releases its 2H+

• E released to move e-s through complex 3 releases 2H+
• one e- at a time is acquired by cyt c at the IM side of complex 3 and moves through the intermembrane space to complex 4
• Cu accepts one e- at a time until it gets 4e-
• for every e- pair 2H+s move to IMS
• then Cu moves to the matrix side and releases e-'s to oxygen and 4H+ to form 2 H20's

• a steep proton gradient that generates a electrochemical gradient
• depends on impermability of inner mito membrane

• Fo stalk - made of 12 c subunits and A. rotates around gamma structure
• F1 ball - 3 beta subunits that catalyze ATP synthesis; 3 alpha subunits provide structural support. stationary by s subunit held by b and a.

• Loose - medium affinity for ADP and Pi as they bind loosely
• Tight - high affinity for ADP and Pi as they join to form ATP
• Open - releases ATP and low affinity for ADP and Pi as it binds very loosely

1. ATP synthesis
2. exchange ATP for ADP (antiport)
3. bring in Pi (symport)

• the H+ gradient becomes so steep that the energy to pump out H+ is too great.

• ADP levels are low
• H+s are blocked from the ATP synthase
• chemicals can block e- transport in complexes

• allow H+ to diffuse back into mito matrix
• therefore more glucose will have to be oxidized in order to produce a steep H+ gradient

1. outer envelope - double membrane; permeable
2. thylakoid membrane - impermeable

2 sets of rxns taht make up photosynthesis?

products? location?

• light dependent - converts light and water into oxygen while producing ATP and NADPH in thylakoid membrane
• light independent - converts CO2 to carbohydrates in stroma using ATP and NADPH

1. photosystem II
2. cytochrome b6f
3. photosystem I

1. P-ring - porphyrin ring 
2. phytol tail 

• looks like a lilly pad

1. fluorescence - photon of longer wavelength emitted
2. resonance energy transfer (RET) - energy is transfered to another molecule
3. Electron transfer - electron is donated to another molecule

• light E is absorbed by reaction center cholorphyll starting e- transport
• H2O is ripped apart by oxygen evolving complex and 4e-s enter as 4H+s contribute to H+ gradient and oxygen is produced
• e-s go through PSII and exit in plastoquinone

• e-s leave PSII in PQ and go through cytochrome b6f pumping H+s into TK lumen
• e-s then leave in plastocyanin (PC) to PSI
• e-s used to reduce NADP+ to NADPH

• uses a lot of energy (ATP and NADPH) to convert CO2 into RuBP
• uses RUBP carboxylase (Rubisco)

• cytoplasmic proteins
• imported mito proteins
• nuclear proteins

made in RER

• secretory proteins
• IMPS at PM, ER, golgi, nuclear envelope, lysozymes
• lumenal proteins of ER, golgi, lysozymes

1. cis golgi network
2. cis cisternae
3. medial golgi
4. trans cisternae
5. trans golgi network

• attach GFP to a chimeric gene

• set of signal codons at the 5' end of mRNA
• as singal codon is translated its signal peptide product causes the mRNA/ribosome/protein to go to the RER
• protein is inserted into RER through pore
• signal peptide is cleaved off once inside the RER.

1. advantages of radioactivity tracing?

1. traceable
2. quantifiable
3. sensitive

• IMP - goes through TOM complex, then TIM 22 complex where it is integrated into the inner membrane. has internal targeting sequence
• Matrix - has presequence at N terminus. goes through TOM complex, then through TIM 23 complex. MPP chops off presequence

• hormone synthesis
• detoxification (liver)
• Ca sequestering (sarcoplasmic reticulum)
• lipid synthesis

• chaperone proteins like BiP, calnexin and calreticulin
• protein disulfide isomerase (PDI)
• serve as quality control

1. last 2 glucose removed from oligoscde
2. calnexin recognizes it and binds
3. chaperone part binds and last glucose removed by glucosidase II
4. Glucosyltransferase looks over and if is unfolded improperly adds glucose back
5. then binds back to calnexin for another try
6. if no glucose added then protein goes on its designated pathway