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Biochem Exam 2, part 4
Overview of Metabolism, Krebs Cycle Function and Regulation, Oxidative Phosphorylation
59
Biochemistry
Graduate
09/20/2011

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Cards

Term
How is a human metabolism similar to a fire?
Definition
They both have the same general equation:

Carbon source + O2 -> CO2 + H2O + energy
Term
How much ATP is made in the body in one day in terms of weight?
Definition
About the same amount as body weight
Term
Why is ATP unstable and therefore a source of energy?
Definition
The phosphate groups repel each other
Term
Where does glycolysis take place?
Definition
The cytosol
Term
Where does the Krebs cycle take place?
Definition
The mitochondrial matrix
Term
Where does the Electron Transport chain take place?
Definition
On the innermembrane of the mitochondria
Term
Describe the gradient formed during the ETC. Where is it?
Definition
High proton concentration inside mitochondrial innermembrane space, lower concentration in the matrix
Term
How is the proton gradient for the ETC basically formed?
Definition
Electrons are carried through protein complexes that end up reducing O2 to H2O. This energy is used to pump protons into the innermembrane space.
Term
Under what sort of conditions does mitochondrial O2 consumption increase?
Definition
Any condition that would compromise the proton gradient

Ex. Uncouplers, ATP synthase issues, membrane destruction
Term
What does the Krebs cycle start with?
Definition
Acetyl CoA
Term
What is the only molecule that gets "used up" in the Krebs cycle?
Definition
Acetyl CoA
Term
From what is Acetyl CoA derived?
Definition
Pyruvate or fatty acids
Term
How many reactions in the Krebs cycle reduce coenzymes?
Definition
4
Term
Describe brown adipose tissue and why it uses a lot of O2
Definition
Brown adipose tissue is used for thermoregulation (babies have a lot of it)

Mitochondria is designed for heat generation, not ATP synthesis. Uncouplers are present that lead to increased O2 consumption without making ATP.
Term
Why, basically, do uncouplers increase the rate of O2 consumption?
Definition
Uncoupling proteins are designed to bring H+ back into the innermembrane space without making ATP. Therefore, O2 is consumed, but no ATP is produced.
Term
Is O2 consumption based on ATP production?
Definition
Not necessarily.

O2 consumption is directly based on electron and H+ transport rate, not ATP production.
Term
What is the mobile carrier of carbons between glycolysis in the cytosol and Krebs in the mitochondria?
Definition
Pyruvate
Term
Where is pyruvate converted to Acetyl-CoA?
Definition
The mitochondria
Term
What is the enzyme that converts pyruvate to Acetyl-CoA?
Definition
Pyruvate dehydrogenase, a huge enzyme
Term
What are some inhibitors of pyruvate dehydrogenase?
Definition
Acetyl-CoA, NADH
Term
What are the products of the pyruvate DH reaction?
Definition
Acetyl CoA, CO2, and 1 NADH
Term
What are the net products of the Krebs cycle?
Definition
2CO2, GTP, 3NADH, 1 FADH2
Term
What are some vitamins that are needed for the Krebs cycle?
Definition
Thiamine (vitamin B1) in TPP, Riboflavin in FAD, Niacin in NAD, Pantothenate in CoASH, Lipoic acid
Term
What enzymes in the Krebs cycle have a large -ΔG?
Definition
Citrate synthase
Isocitrate dehydrogenase
α-ketoglutarase dehydrognease
Term
What is notable about citrate synthase?
Definition
Large -ΔG, forms C-C bond
Term
What is notable about isocitrate dehydrogenase?
Definition
Large -ΔG, 2 isoforms

One isoform makes NADH, one isoform makes NADPH
Term
Generally speaking, what is the difference between the use of NADH vs NADPH?
Definition
NADH is used for the ETC
NADPH is used for anabolic and antioxidative reactions
Term
What is notable about α-ketoglutarase dehydrognease?
Definition
Large -ΔG, mechanically similar to pyruvate dehydrogenase
Term
What is notable about succinyl-CoA synthase?
Definition
It catalyzes the reaction in the Krebs cycle that makes an ATP
Term
What is notable about Succinate dehydrogenase?
Definition
It is also in the ETC
Term
What is notable about Malate dehydrogenase?
Definition
It has a large +ΔG
Term
How does NADH get from the cytosol to the mitochondria
Definition
Through shuttles:
Glycerol-3-phosphate shuttle and malate-aspartate shuttle
Term
For any general metabolic reaction, where could you find regulation points?
Definition
Entry points, exergonic steps, branch points, and substrate supply
Term
Why does Calcium activate the Krebs cycle?
Definition
Because ATP is needed for Ca-ATPase in muscles

95% of ATP produced is used for that purpose
Term
What is notable about aconitase?
Definition
4Fe-4S Cubane Cluster
Term
What directly activates pyruvate dehydrogenase?
Definition
The phosphorylated pyruvate dehydrogenase complex
Term
What are some inhibitors of pyruvate dehydrogenase?
Definition
ATP, NADH, Acetyl CoA, Fatty acids

(just think about what logically would inhibit)
Term
What are some activators of pyruvate dehydrogenase?
Definition
ADP/AMP, Calcium, Pyruvate, CoA, NAD+

(just think about what logically would activate)
Term
Describe "substrate channeling"
Definition
Krebs cycle enzymes are physically linked so the substrates move through quickly and with more regulation
Term
Define amplerosis
Definition
Replenishment of Krebs cycle intermediates

Ex. Pyruvate carboxylase converts pyruvate to oxaloacetate
Term
Describe thiamine pyrophosphate
Definition
A coenzyme in pyruvate dehydrogenase that cleaves C-C bonds
Term
Define biotin
Definition
A coenzyme in pyruvate carboxylase that forms C-C bonds
Term
What does a (+) E(v) indicate?
Definition
The element wants to accept electrons
Term
What kind of E(v) value does O2 have? What sort of E(v) value does NAD+ have?
Definition
O2 has a very (+) E(v) value, NAD+ has a (-) value
Term
What forms FMNH2 in the electron transport chain?
Definition
The electrons given off from NADH
Term
What forms FADH2 for the electron transport chain?
Definition
Succinate dehydrogenase (converting succinate to fumarate)
Term
From where does Coenzyme Q get electrons?
Definition
FMNH2,
FADH2,
Glyceraldehyde-3-phosphate
β-oxiation flavoprotein
Term
Describe the path of electrons in the electron transport chain from Coenzyme Q to the final electron acceptor
Definition
Coenzyme Q -> Complex III -> Cytochrome C -> Complex IV -> O2 -> H20
Term
Are the complexes in the electron transport chain as simple as they appear in the diagrams?
Definition
No, the complex are complex. :)

There are many subunits and actually over 40 redox reactions in the ETC
Term
Give four examples of an electron transport chain inhibitor
Definition
Roterone, antimycin A, CN-, CO
Term
What is the result of an electron transport chain inhibitor?
Definition
All molecules become reduced upstream, all molecules become oxidized downstream.

No proton gradient, no ATP= death
Term
Describe mitochondria DNA
Definition
It has its own genome, but very limited.
Can only make 13 proteins
Susceptible to genetic diseases
Term
How many electrons can Ubiquinone/Coenzyme Q carry?
Definition
1 or 2
Term
List three electron carriers in the electron transport chain
Definition
  1. Ubiquinone/Coenzyme Q
  2. Cytochromes
  3. Iron-sulfur proteins
Term
Describe the structure of ATP synthase
Definition

F1 unit makes ATP with α, β,and γ subunits

 

F0 unit is the proton transporter submerged in the lipid bilayer which rotates

Term
Describe what the α, β,and γ subunits in ATP synthase do
Definition
α and β change configuration, each with a catalytic site

γ stalk touches the active sites and makes the Enzyme-ATP complex less stable so ATP can be removed
Term
What is the H+ proton gradient energy ultimately used for?
Definition
Removal of ATP from ATP synthase
Term
What are four regulators Dr. Szwedna listed for Oxidative Phosphorylation?
Definition
Thermodynamic
Energy charge
Protein inhibitor IF1
Uncoupling Proteins
Term
List some functions of mitochondria
Definition
Choose from:

ATP synthesis, gluconeogenesis, thermogenesis, Amino acid production/consumption, Ureagenesis, prophryrin biosynthesis, apoptosis, Ca++ hoarding, free radical production
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