biochem exam 2 - citric acid cycle Flashcards
Which of the following is not a cofactor in the Pyruvate Dehydrogenase Complex?
A
TPP
B
Biotin
C
FAD
D
NAD
E
Lipoate
B
Biotin
From what vitamin is NAD derived?
A
Thiamine
B
Niacin
C
Riboflavin
D
Pantothenate
E
Folate
B
Niacin
Which CAC reaction requires the same 5 cofactors as the pyruvate dehydrogenase reaction?
A
3 (Formation of α-KG)
B
4 (Formation of Succinyl-CoA)
C
5 (Formation of Succinate)
D
6 (Formation of Fumarate)
E
7 (Formation of L-malate)
B
4 (Formation of Succinyl-CoA)
In which CAC reaction is GTP (or ATP) formed?
A
3 (Formation of α-KG)
B
4 (Formation of Succinyl-CoA)
C
5 (Formation of Succinate)
D
6 (Formation of Fumarate)
E
7 (Formation of L-malate)
C
5 (Formation of Succinate)
Which intermediates of the CAC are formed in anaplerotic reactions?
A
Citrate and isocitrate
B
Citrate and malate
C
Malate and oxaloacetate
D
Succinate and oxaloacetate
E
Succinate and fumarate
C
Malate and oxaloacetate
What effect does an elevated level of ADP have on the activity of isocitrate dehydrogenase (Rxn #3)?
A
ADP activates the enzyme
B
ADP inhibits the enzyme
A
ADP activates the enzyme
and indicators of high energy inhibit the citric acid cycle
and indicators of low energy promote the citric acid cycle
Notes:
Isocitrate is oxidized and then decarboxylated (CO2 formed) to form α-ketoglutarate Exergonic; Regulated [ATP] – energy inhibitor, NADH - product inhibitor NAD(P)H is an electron carrier that will help make ATP (~2.5) in the ETC (later)
Fates of Glucose: Glycolysis…and more?
in glycolysis
- glucose to pyruvate
in full oxidation
- glucose to 6CO2 + 6H2O
Glycolysis captures only a small amount of the available energy in glucose… How do we get the rest out? Cellular respiration!
Cellular Respiration
Process in which cells consume O2 and produce CO2
Provides more energy (ATP) from glucose than glycolysis
Captures energy stored in lipids and amino acids
produces 32-38 ATP rather than 2 ATP which is what glycolysis produces
Three Steps:
1. Acetyl CoA production (Now - from pyruvate (sometimes not))
2. Acetyl CoA oxidation (Citric Acid Cycle – Now)
3. Electron transfer and oxidative phosphorylation
The CAC Occurs in Mitochondria in Eukaryotes
Glycolysis occurs in the cytoplasm
CAC occurs in the mitochondrial matrix *succinate dehydrogenase is in the inner membrane
oxidative phosphorylation occurs in the inner membrane
glycolysis: 2 ATP
CAC: 2 ATP
Oxidative phosphorylation: 34 ATP
Step 1: Pyruvate to Acetyl-CoA
Net Reaction: Completely irreversible!
Oxidative decarboxylation of pyruvate (remove CO2)
the 5 co-factors of pyruvate dehydrogenase
- TPP - thiamine pyrophosphate from thiamine
- FAD - from riboflavin
- coenzyme A (COA; from pantothenate)
- NAD (from niacin)
- lipoate
pyruvate is transported from the cytosol into the mitochondria via the pyruvate carrier
pyruvate + CoA-SH + NAD+ + pyruvate dehydrogenase complex (E1 + E2 + E3) = NADH + Acetyl-CoA + CO2
- the thioester in the acetyl-CoA is high-energy storage! coupling
pyruvate dehydrogenase complex
- is a 3-enzyme complex
- has 5 cofactors for the 3-enzyme complex
vitamin deficiencies?
- B1 (beriberi)
- B2, B5
- B3 (pellagra)
Step 1: Pyruvate Dehydrogenase Complex
very large complex with multiple copies of
E1 - pyruvate dehydrogenase w TPP
E2 - dihydrolipoyl transacetylase with lipoate
E3 - dihydrolipoyl dehydrogenase with FAD
- 2 regulatory proteins:
- protein kinase
- phosphoprotein phosphatase
Advantages of multienzyme complexes:
- Short distance b/t catalytic sites allows for channeling of substrates b/t catalytic sites
- Channeling minimizes side-reactions
- Regulation of activity of one subunit affects the entire complex (everything is so close!)
Step 1: So what happens?
Five Steps:
1. Pyruvate ox.→CO2. Remaining 2-C molecule binds to TPP.
- 2-C molecule is oxidized and transferred to lipoic acid→ acetyl group created.
- Acetyl group transferred to CoA. Lipoic acid is left reduced.
- FAD can reoxidize lipoic acid (FAD→FADH2) so everything can go again.
- NAD+ oxidizes FADH2 → FAD. NADH created (electrons!)
Lipoate or lipoic acid is also known as a biological tether
focus on the 3 enzyme and 5 cofactors
Step 1 of CAC: Citrate Formation
Notes:
Only reaction with C-C bond formation
Acetyl from the CoA is added to the oxaloacetate → citrate
CoA-SH is lopped off…and energy is released…what does that mean? Forward!
Exergonic; Regulated – citrate – product inhibition; [ox] substrate availability; covalent (later) Activity depends on [oxaloacetate] (required for Acetyl-CoA binding to the enzyme)
acetyl-COA + oxaloacetate + citrate synthetase = citrate
delta G = -32.2 kJ/mol
Step 2 of CAC: Citrate→Isocitrate
Notes:
Enzyme in the next reaction only binds isocitrate
Dehydration and then rehydration isomerizes citrate to isocitrate Endergonic: delta G = 13.3 kJ/mol
Coupled exergonic reactions to make it go
citrate + aconitase - remove water
cis-aconitate + aconitase - add water
= isocitrate
H + OH effectively reversed
Step 3 of CAC: α-Ketoglutarate and CO2 Formation!
Notes:
- Isocitrate is oxidized and then decarboxylated (CO2 formed) to form α-ketoglutarate
- Exergonic; Regulated [ATP] – energy inhibitor, NADH - product inhibitor
NAD(P)H is an electron carrier that will help make ATP (~2.5) in the ETC (later)
isocitrate + NAD(P) + isocitrate dehydrogenase = NAD(P)H + H+ = a-ketoglutarate
notes:
NAD(P)H formed
CO2 released
Step 4 of CAC: Succinyl-CoA and CO2 Formation!
Notes: Similar enzyme complex as pyruvate dehydrogenase!
α-ketoglutarate is oxidized, decarboxylated, and CoA-S is added to store energy as Succinyl-CoA This stored energy (thioester) will be used later…NADH→ATP (~2.5) ETC
Exergonic; Regulated by product inhibition
Step 5 of CAC: Succinate Formation
Notes: Substrate-level phosphorylation (ADP + Pi→ATP)
Only time in the entire CAC where ATP is produced directly
That CoA-S that was added to store energy as Succinyl-CoA was used to make ATP
Step 6 of CAC: Formation of Fumarate
Notes: Oxidation of an alkane to alkene by dehydrogenation
Succinate dehydrogenase is bound to the mitochondria inner membrane (flavoprotein (FAD)) Acts in the ETC to take electrons from FADH2 → ATP (~1.5)
Step 7 of CAC: Formation of Malate
Notes: Very stereospecific – only L-malate is formed
Why? Addition of water is always trans- (-OH and H added across the double bond) making L- malate
Step 8 of CAC: Oxaloacetate Formed (Cycle!)
Notes: Final step – regenerates oxaloacetate.
Very Endergonic; [oxaloacetate is kept very low by citrate synthase helping pull reaction forward). This is coupled to the next (first) reaction.
More NADH
summary of CAC products
Notes:
1. Where is CO2 released?
2. Where is energy released?
3. How do exergonic reactions pull endergonics?
products:
NADH
ATP
FADH2
Summary: Energy Transformation
aerobic metabolism of glucose yields about 5x as much ATP as anaerobic (30-32 vs 5-7)
acetyl-COA + 3NAD+ + FAD + GDP + Pi + 2 H2O to 2CO2 + 3NADH + FADH2 + GTP + CoA + 3H+
energy production summary for glycolysis, pyruvate dehydrogenase, and the CAC
- assumption:
NADH makes 2.5 ATP
FADH makes 1.5 ATP
per 1 glucose molecule
glycolysis
- 2 ATP
- NADH
ultimate ATP: 3-5
pyruvate to acetyl-CoA
- 2 NADH
ultimate ATP: 5
CAC
- 2 ATP
- 6 NADH
- 2 FADH2
ultimate ATP’s: 30-32
role of CAC in anabolism
lipid synthesis
- fatty acids and sterols give rise to citrate
amino acid synthesis and nucleic acid synthesis
- glutamate gives rise to alpha-ketoglutarate
hemoglobin
- porphyrins & heme give rise to succinyl-CoA
PEP goes to glucose
oxaloacetate is made into asparagine
PEP
- can be made into S, G, C, F, Y, W
central role of CAC
an amphibolic pathway
anaplerotic rxns replenish intermediates when they are removed to become precursors of other molecules
any intermediate-replenishing rxn can be called anaplerotic
