biochem citric acid cycle E3L3

citric acid cycle outputs:

1. for one acetyl-CoA

   1. 3 NADH, 1 FADH2, 1 GTP

2. 2 acetyl CoAs enter from 1 glucose → glycolysis → respiration → 2 acytyl

   1. so 6 NADH, 2 FADH2 and 2 GTP total

types of reactions:

1. condensation =

2. dehydration =

3. hydration =

4. oxidative decarboxylation

   1. decarboxylation =

   2. oxidative =

5. substrate level phosphorylation

6. dehydrogenation reaction

1. condensation = combining 2 mCs

2. removing water mC

3. add water

4. decarboxylation = remove CO2

5. oxidative = LEO loss of e-

6. substrate level phosphorylation = add Pi to ADP or GDP → ATP or GTP

7. dehydrogenation = removing e- w/ different carrier, hydration/dehydro steps

citric acid cycle:

1. amphibolic =

2. what enters

3. how many e- leave

4. how many decarboxylation rxns

5. how many substrate level phosphorylations

6. how many H20 are consumed

1. amphibolic = used in both anabolic and catabolic processes

   1. intermediates can enter/leave at different points

8 CAC steps

1. what to know for each

   1. incoming substrate/exiting products

   2. name of enzyme

   3. type of reaction

   4. know the pointed out structures in the lecture

   5. FOLLOW THE CARBONS

1. condensation

2. isomerization

3. oxidative decarboxylation

4. oxidative decarboxylation

5. substrate level phosphorylation (GTP)

6. oxidation/dehydrogenation (FADH2. all others NADH)

7. hydration

8. oxidation/dehydrogenation

CAC step 1:

1. what is it

2. what is regenerated

3. reversible?

4. oxaloacetate (OAA) substrate level/why?

5. how is rxn pushed forward if [OAA] is low

   1. why?

1. pic

2. CoA is regenerated and recycled

3. irreversible

4. OAA = substrate in 1st rxn that is constantly consumed by the CAC

   1. so, rxn concentration is low

5. driven forward by thioester hydrolysis

   1. recall acetyl CoA is an

citrate synthase (enzyme for CAC step 1: acetyl-CoA + OAA):

1. special function?

2. how does its structure ensure that it does that?

   1. 2 conformations

   2. when binding allowed?

3. thioester hydrolysis = ___

   1. why is that a problem?

4. how doe citrate synthase ensure acetyl-CoA transfers acetyl group to the correct place instead o?

1. prevents premature hydrolysis of acetyl-CoA

   1. dimer with open and closed conformations

      1. open = can bind acetyl-CoA

      2. closed = cannot bind acetyl- CoA

   2. has to bind OAA before it will enter closed conformation

      1. ensures acetyl group acceptor OAA is already in active site before it binds acetyl-CoA

2. thioester hydrolysis = release a lot of free E, (unstable (high G) bc no resonation)

   1. problem = acetyl CoA wants to give up acetyl group to anything even water

      1. solved by OAA binding conformation change of citrate synthase

CAC Step 2:

1. reaction (shown as 2 step, but memorize it as 1 step)

2. why is the purpose of this step?

3. DG’0 for this reaction?

   1. how driven forward?

1. d

2. why = convert citrate to better substrate for oxidation (the goal of CAC)

   1. citrate = tertiary alcohol (bad oxidation substrate)

   2. isocitrate = secondary alcohol (good oxidation substrate)

3. high DG but driven forward by rapid product removal in step 3

aconitase:

1. special structure

2. what’s the purpose

1. iron sulfur cluster = Fe-S crystal lactic w/ Cys residues in enzyme active site

2. purpose:

   1. allows e- to be taken 1 at a time

   2. Fe-S center center position reactants and enable removal/addition of water

CAC step 3:

1. rxn (drawn as 2 step memorize/structures as 1 step)

2. reaction

3. what is the strategy

4. why notable

5. structures remember necessary for all runs

1. d

2. notable = first oxidation

3. oxidative decarboxylation

   1. 2 step = oxidation then decarboxylation

4. strategy = generate unstable intermediate that readily loses CO2

CAC step 4:

1. reaction?

2. why notable/ 2 important things this reaction does

3. what is a-ketoglutarate

   1. what do we know about oxidative decarboxylation of a-ketoacids

4. where is CO2 leaving from?

1. oxidative decarboxylation

2. 2nd oxidation

   1. transfers e- to NAD+

   2. sets up reaction 5 by forming thioester (high group transfer potential)

3. a-keto acid

   1. similar to PDH pyruvate dehydrogenase complex

4. CO2 leaving from C4

a-ketoglutarate dehydrogenase complex (a-KDH):

1. 4 ways how similar to PDH

1. a-KDH is similar to PDH

   1. same structure

      1. E3 is identical

   2. same 5 cofactors

      1. NAD+ TPP lipoate FAD+, CoA-SH

   3. same type of reaction (oxidative decarboxylation of a-keto acid)

   4. EXACT SAME MECHANISM ALL STEPPS AS PDH