Proteins and enzymes

probability of going to S to P at the top of the energy barrier where the reaction intermediate is?

equal probability, thats why enzymes rearrange bonds and change position of chemical groups to push the reaction towards products

methyl group

carbonyl group

glycogen chain synthesis steps

1. Use ATP to phosphorylate glucose on C-6

   1. catalyzed by hexokinase in muscle and glucokinase in the liver

2. Move phosphate from C6 to C1 —> glucose 6-P to glucose 1-P

3. React with UTP to form UDP-glucose and 2 phosphates

   1. this activates it

4. Glycogenin is an enzyme that has a tyrosine residue and UDP-glucose attaches to the residue

5. Glycogen synthase is recruited and glycogenic fits attaches to it

   1. PP1 binds to R5 which activates it which then the PP1-R5 complex dephosphorylates GS which activates GS for chain elongation

6. Glycogenin adds another UDP-glucose at the C4 non reducing end to produce UDP and a 1-4 linkage which adds to the non-reducing end of a chain

   

7. Glycogen synthase takes over the elongation by adding more UDP-glucose to form a long chain

   

8. Branches get added by glycogen synthase and branching enzyme working together to form a highly branched chain

9. Regulation inactivates glycogen synthase and releases it from glycogenin but the reducing end of glycogen stays connected to glycogenin

branching enzyme function

cleaves 1-4 linkage in a glycogen chain and attaches broken chain to another chain to form a 1-6 bond to form a branch

glycolysis steps

1. Glucose converted to glucose-6-phosphate by hexokinase

   1. uses 1 ATP

   2. irreversible

2. G6P converted to fructose-6P (furanose) by phosphoglucose isomerase

3. F6P converted to Fructose 1-6-biphosphate by phosphofructokinase

   1. uses 1 ATP

   2. irreversible

4. F1-6BP converted into DHAP and glyceraldehyde 3 phosphate by aldolase

5. DHAP and G3P in equilibrium but DHAP is converted into G3P by triose phosphate isomerase

6. G3P converted into 1,3 biphosphoglycerate by glyceraldehyde 3-phosphate dehydrogenase x2

   1. reduces NAD+ to NADH (exergonic)

   2. uses P to phosphorylate (endergonic)

7. 1,3 BPG converted to 3 phosphoglycerate by phosphoglycerate kinase x2

   1. high energy —> converts ADP to ATP

8. 3PG converted to 2PG by phosphoglycerate mutase x2

9. 2PG converted to phosphoenolpyruvate by enolase x2

   1. hydrolyses it so H2O is formed in the process

10. PEP converted to pyruvate by pyruvate kinase x2

    1. super high energy —> converts ADP to ATP

    2. irreversible

bypass steps of gluconeogenesis (converting pyruvate to PEP)

First bypass

1. Pyruvate transported from cytosol to mitochondria and alanine (product of pyruvate) transported into mitochondria and then converted to pyruvate

2. Pyruvate converted into oxaloacetate by pyruvate carboxylase

   1. uses 1 ATP

   2. uses CO3- as source of carbon

3. Oxaloacetate converted into malate by malate dehydrogenase

   1. uses oxidation of NADH to NAD+

4. Malate exported to cytosol where it is converted to oxaloacetate

   1. reduces NAD+ to NADH

5. Oxaolacetate converted to PEP by PEP carboxykinase

   1. Uses 1 GTP

• In cells with lactate after fermentation (muscle and red blood cell)

  1. Lactate converted to pyruvate in cytosol

     1. by lactate dehydrogenase

     2. NAD+ to NADH

  2. Pyruvate goes to mitochondria where it gets converted to oxaloacetate

     1. pyruvate carboxylase

     2. 1 ATP, CO3-

  3. Oxaloacetate converted into PEP

     1. mitochondrial PEP carboxykinase

  4. PEP transported out of cell into cytoplasm

Second bypass (one step)

1. Fructose 16BP converted to F6P

   1. F16biphosphatase

   2. exergonic, but not coupled with ATP synthesis

2. Coupled with regulation of PFK1 which is the exergonic reverse bc u cant have both exergonic reverse reactions running at the same time in the cytosol

Third bypass (one step)

1. Glucose6P to glucose

   1. glucose-6-phosphatase which is only found in liver and kidneys

   2. Exergonic and irreversible but step in glycolysis is more exergonic

pyruvate dehydrogenase steps

1. decarboxylation

   1. E1 which has TPP attached to it and it reacts with pyruvate forming CO2 and hydroxyethyl TPP

2. Oxidation

   1. Lipoamide arm bound to E2 goes into E1 where the transfer of acetyl group from TPP to lipoamide arm

   2. thioester (big energy of hydrolysis) between lipoamide and acetyl group is formed and TPP back in its original state

3. Tranfer

   1. arm goes into second E2 unit and the thioester bond is broken but a new one is formed between acetyl group and coenzyme A to form acetyl-CoA

4. Regeneration

   1. The disulfide bond on the arm has to be regenerated again so it goes into E3 which has FAD which will accept 2 electrons and 2 protons released when disulfide bond is formed to form FADH2

   2. FAD needs to be regenerated so give protons to NAD+ to form NADH which will be used in oxidative phosphorylation

5. 

Citric Acid cycle step 1

• Acetyl-CoA + Oxaloacetate to Citrate

• Citrate Synthase

• Uses H2O and produces CoA-SH

• Irreversible

Cycle Step 2A and B

• A: Citrate to cis-Aconitate

• B: cis-Aconitate to Isocitrate

• Aconitase

• removes an OH and H to form H2O in 2A, adds in water in 2B to reposition OH

• reversible

Cycle Step 3

• Isocitrate to a-Ketoglutarate

• Isocitrate Dehydrogenase

• Forms CO2 and NADH

• irreversible

Cycle Step 4

• a-Ketoglutarate to Succinyl Co-A

• a-Ketoglutarate dehydrogenase complex

• reacts with CoA-SH to form CO2 and also formed NADH

• irreversible

Cycle Step 5

• Succinyl Co-A to Succinate

• Succinyl Co-A synthetase

• GDP to GTP, and CoA-SH produced

• reversible

• high energy

Cycle Step 6

• Succinate to Fumarate

• succinate dehydrogenase

• Produces FADH2 and removes and H

Cycle Step 7

• Fumarate to Malate

• fumarase

• uses water to add an OH group

• reversible

Cycle Step 8

• Malate to Oxaloacetate

• malate dehydrogenase

• removed 2 H and produced NADH

• reversible

Complex 1

• NADH-ubiquinone oxidoreductase

• FMN accepts 2e and 2H+ from NADH + H in the matrix

• FMNH2 gives 2e to Fe-S

• Fe-S gives 2e to Q and matrix gives 2H+ to Q

• QH2 is formed

• 4 H+ get pushed into intermembrane space

Complex II

• Succinate dehydrogenase

• this protein in step 6 of the TCA cycle produced FADH2

• Then it gives 2e- to Fe-S

• gives 2e- to Q

• forms Q2

Complex III

• Q cytochrome c oxidoreductase

• gets 2e- from QH2

• Gives 4H+ into the inter membrane space

• Through the Q cycle 2 cytochrome Cs each shuttle 1 electron to Complex IV

Q cycle

• • Q has 3 states

    • Ubiquinone 

      • Q

    • Radical Semiquinone → gains an e- and p

      • QH

    • Ubiquinol → 2e- and 2p (fully reduced)

      • QH2

  • QH2 from Complex I and Complex II goes to Complex III to become Q again but cytochrome C in Complex III can only accept 1 e- at a time

  • How it works

    • Has 2 binding sites: Q0 and Qi

    • QH2 binds to Q0 and a Q binds to Qi

    • 2 H+ protons from QH2 get sent into intermembrane space

      • Has 2e- left

    • One e- is transported to Fe-S, then cyt C1, then cyt C to accept 1e- which is on the intermembrane side of Complex III

    • Cyt C dissociates from Complex III

    • Other e- from QH2 is given to cyt BL, cyt BH, and then to Q at site Qi

    • This forms a Qe- at the Qi site and a Q at the Q0 site

    • The Qe- takes one H+ from the matrix to form QH

    • The Q at the Q0 site is replaced by another QH2 and cytochrome C is replaced

    • The QH2 releases its 2H+ into intermembrane space

    • 1e- is sent to cyt C

    • The other e- is given to QH at Qi site and it also takes another H+ from matrix to form a QH2 at the Qi site

    • Qi releases QH2 and Q0 releases Q

    • Complex III can start a new cycle

  • So one round in total releases 4H+ into intermembrane and takes 2 H+ from matrix

  • 

Complex IV

• cytochrome oxidase

• Step 1

  • takes 1 e- from the first cyt C

  • gives it to Cu-A, then Heme A, then Heme A3, then Cu-B

• Step 2

  • takes 1 e- from second cyt C

  • gives it to Cu-A, then Heme A, then Heme A3

  • O2 is put in between reduced Heme A3 (which is now Fe2+) and reduced Cu-B (which is now Cu+)

  • Forms a bridge: Fe2+-O2-Cu+

• Step 3

  • takes an e- from another cyt C

  • gives it to Cu-A, then Heme A, then bridge

  • One H+ is extracted from matrix

  • H+ breaks bridge by formed an OH

  • Left with: Fe2+-O and OH-Cu+

• Step 4

  • takes e- from another cyt C

  • gives it to Cu-A, then Heme A, then Fe2+-O

  • take another H+ from matrix

  • Form: Fe2+-OH and OH-Cu+

• Step 5

  • take 2 more H+ from matrix to form 2 H2O molecules from the 2 OH groups

  • Left with: H2O, Fe3+, and Cu2+

• Shuttles 4 protons into inter membrane space (total of 8 protons lost from matrix), 2 protons per molecule of H2O