Biochem Block 2 Week 4

Front 1

In the TCA cycle, Isocitrate (with alcohol group) is converted to alpha-ketoglutarate (a ketone). What kind of rxn is this - oxidation or reduction? And as a result of this, what is gained energy-wise? What enzyme mediates this rxn?

Back 1

It is an oxidation - meaning that there's a reduction of something else - namely NAD+ to NADH for use as an energy store. CO2 is released. Isocitrate dehydrogenase mediates this rxn. (p136)

Front 2

In TCA, alpha-ketoglutarate is converted to Succinyl CoA by alpha-ketoglutarate dehydrogenase complex. What is the product of this rxn?

Back 2

NADH and CO2

Front 3

What does Citrate Synthase do? How/why is this rxn driven to completion? (p137)

Back 3

It condenses oxaloacetate and acetyl-CoA. Driven to completion bc the high energy thioester bond it produces is harvested.

Front 4

In TCA, what is the purpose of Aconitase? What is unique about this enzyme?

Back 4

To move the hydroxyl group of citrate to a position where it can be oxidized to a ketone and produce NADH (p137). This enzyme has an iron-sulfur center that helps position the substrate in the active site.

Front 5

What are iron-sulfur centers vulnerable to oxidative stress? What does this mean for the TCA cycle?

Back 5

Under oxidative stress, iron-sulfur centers will get their Fe's ripped out - leaving the enzyme useless. Since TCA uses Aconitase - an iron-sulfur center enzyme, a high oxidative stress environment will shut this cycle down.

Front 6

In TCA, Succinate is converted to Fumarate in a ?? rxn. What is the enzyme that catalyzes this rxn? How is this enzyme different than the others in the TCA cycle and what does the rxn yield?

Back 6

Conversion is a dehydrogenation rxn (removal of H2). The enzyme catalyzing this rxn is Succinate dehydrogenase that is located OUTSIDE of the mitochondria. Rxn yields an FADH2. p136

Front 7

Note: On my TCA diagram on pg136, I track the 2C from acetyl-CoA using yellow highlight. However, this can only be done until succinyl CoA - at which point you can't distinguish the original 2C's due to succinate's symmetry.

Back 7

Note: On my TCA diagram on pg136, I track the 2C from acetyl-CoA using yellow highlight. However, this can only be done until succinyl CoA - at which point you can't distinguish the original 2C's due to succinate's symmetry.

Front 8

As discussed on a previous notecard, Succinate Dehydrogenase is embedded in the inner membrane facing the matrix. Also, it's the exact same thing as Complex II in the electron transport chain.

Back 8

As discussed on a previous notecard, Succinate Dehydrogenase is embedded in the inner membrane facing the matrix. Also, it's the exact same thing as Complex II in the electron transport chain.

Front 9

review 55:00 maybe - re prochirality and how that works. (9/26 8a)

Back 9

review 55:00 maybe - re prochirality and how that works. (9/26a)

Front 10

In TCA what are the three enzymes subjected to regulation?

Back 10

1. Citrate Synthase
2. Isocitrate Dehydrogenase
3. alpha-Ketoglutarate Dehydrogenase

Front 11

In TCA, what inhibits Citrate Synthase?

Back 11

ATP, NADH, and succinyl-CoA

Front 12

In TCA, what inhibits Isocitrate Dehydrogenase? What activates it.

Back 12

Inhibitors: ATP, NADH
Activation: ADP, AMP

Front 13

In TCA, what inhibits alpha-Ketoglutarate dehydrogenase? In some tissues, this ?? activates it.

Back 13

Inhibitors: ATP, GTP, NADH, and succinyl-CoA
Activator in some tissues: Ca2+

Front 14

Citrate is a pre-cursor for fatty acid storage. In TCA, isocitrate dehydrogenase is inhibited by ATP. If that happens bc the cell is in the fed state, citrate will accumulate and be shunted toward fatty acid synthesis. p142

Back 14

Citrate is a pre-cursor for fatty acid storage. In TCA,isocitrate dehydrogenase is inhibited by ATP. If that happens bc the cell is in the fed state, citrate will accumulate and be shunted toward fatty acid synthesis. p142

Front 15

What does this graph show you re the activity of isocitrate dehydrogenase relative the concentration of ADP and isocitrate.

Back 15

When the cell has plenty of energy, it requires really high concentrations of isocitrate before it will begin to metabolize it. However, when the concentration of ADP is high, even a small amount of isocitrate will activate the enzyme.

Front 16

See clinical correlation on 9/26 around 1:06.
Why do alcoholics tend to be hypoglycemic?

Back 16

Alcohol dehydrogenase consumes NAD+ as it metabolizes alcohol. Gluconeogenesis requires NAD+ to convert lactate to pyruvate.

Front 17

It is essential that each TCA intermediate is available otherwise the cycle stops. What are the rxns called that replenish TCA intermediates?

Back 17

Anaplerotic rxns (greek for: Ana (up) plerotikos (to fill).

Front 18

Of the anaplerotic rxns, which one is the most important? What does it make?

Back 18

Pyruvate carboxylase. It makes oxaloacetate by combining pyruvate with CO2

Front 19

What activates pyruvate carboxylase? Why does this make sense?

Back 19

Pyruvate carboxylase is an anapleroitic rxn enzyme that is activated by acetyl-CoA. This makes sense bc if acetyl-CoA is accumulating, that means oxaloacetate is not around and needs to be increased. p144

Front 20

Important: Review how pyruvate carboxylase is regulated on p144 and 1:13 and earlier on 9/26 8a lecture. He said it's important that we know this stuff.

Back 20

Important: Review how pyruvate carboxylase is regulated on p144 and 1:13 and earlier on 9/26 8a lecture.

Front 21

How many electrons are required to turn O2 to water?

Back 21

4

Front 22

How does the reducing potential of NADH get into the matrix? (seep 149)

Back 22

Dihydroxyacetone phosphate is converted to glycerol 3-phosphate mediated by CYTOPLASMIC glycerol 3-P dehydrogenase. Then MITOCHONDRIAL glycerol 3-P dehydrogenase mediates glycerol 3-phosphate back to dihydroxyacetone phosphate in a E-FAD to E-FADH2 reduction in the membrane. This is transferred to Q to QH2 in the matrix.

Front 23

Recall that the Glycerol-Phosphate and Malate-Aspartate shuttles are charged with transferring energy equivalents into the matrix. How do the final equivalents differ?

Back 23

Glycerol-Phosphate leads to a QH2 inside the matrix while the Malate-Aspartate leaves NADH inside the matrix (note: Both start with NADH)

Front 24

Complex IV has a common name that he wants us to know. What is it?

Back 24

Cytochrome c oxidase.

Front 25

It seems important to practice calculating reduction potential. See qs on p154, and 9/27 1:03 for info and Angel for more examples

Back 25

It seems important to practice calculating reduction potential. See qs on p154, and 9/27 1:03 for info and Angel for more examples

Front 26

He asked us to know mitochondrial states 3 and 4. What is the difference and what is the limiting factor in each?

Back 26

State 3 is "working" mitochondria whereas State 4 is resting. Limiting factor in 3 is the electron transport chain. The limiting factor in State 4 is ADP.(review 9/27 lecture at about 1:24)

Front 27

Where does cyanide and CO exert their effects?

Back 27

A3 of Cytochrome oxidase Complex IV

Front 28

Review p163 graph and what is happening there. (opposite side explains)

Back 28

1. State 4: no consumption of O2 bc no ADP avail to make ATP and therefore allow influx of H+. Bc of this, the system cannot pump any more H+ out of the cell and the electrons in the system are stuck.
2. State 3: An influx of ADP occurs (as in exercising) and now H+ can flow in to make more ATP, therefore allowing electrons to flow as system pumps H+ out.

Front 29

How do you calculate RCI?

Back 29

RCI = respiratory control index = Slope A (steep) / Slope B (flat-ish)

Front 30

What does Brown adipose tissue (BAT) have a lot of compared to other tissue? What is its major role?

Back 30

It has high Uncoupling Protein-1 (UCP1). Its role is to dissipate the proton gradient without doing work and thereby creating heat.

Front 31

How does UCP1 work to increase heat?

Back 31

It allows protons to flow back into the matrix without going through the ATPase. Without doing work, it releases its energy via heat.

Front 32

How can 18^Fluorodeoxyglucose be used to detect cancer? What must usually be co-administered? (something he wants us to know) (see pt 168)

Back 32

18-FDG is a PET probe that can enter the cell like glucose and be phosphorylated to get stuck in cells. Moreover, it is metabolically a dead end molecule so it stays there. In tumors that are metabolically active, it accumulates. However, since BAT is active, Propranolol must be co-administered to block sympathetic NS stimulation and prevent 18-FDG from entering BAT and showing up as false-positive tumors.

Front 33

See pg 170 for a table that he said we should be able to reproduce. What yields more ATP? Glycerol-phosphate shuttle or the malate-aspartate shuttle?

Back 33

Malate-asparate shuttle. (+3 vs +5 for malate)

Front 34

Where does fatty acid synthesis take place?

Back 34

In the cytosol.

Front 35

What are the four major physiological roles of fatty acids?

Back 35

1. Building blocks of phospholipids and glycolipids which are amphipathic molecules important to membranes.
2. They are covalently attached to proteins via post-translational modifications that target membrane locations
3. Important source of energy and stored primarily in adipose tissue in the form of triglycerides
4. Serve ase hormones and intracellular messengers.

Front 36

From CHO's to FA synthesis, what are the basic steps? I.e. CHO --> glycolysis -->...--> FA synthesis

Back 36

CHOs --> glycolysis --> pyruvate --> acetyl CoA --> citrate --> FA synthesis.

Front 37

Some common fatty acid characteristics:
1. Consist of an ? chain with a terminal ? group.
2. Unsaturated FA occur commonly in man with up to ? double bonds per chain.
3. Most common fatty acids in biological systems have an ? number of carbon atoms.
4. Most FA in humans are C?, C?, or C? but several with longer chains occur in lipids of nervous system.

Back 37

1. Consist of an ALKYL chain with a terminal CARBOXY group2. Unsaturated FA occur commonly in man with up to 6 double bonds per chain.
3. Most common fatty acids in biological systems have an EVEN number of carbon atoms.
4. Most FA in humans are C16, C18, or C20 but several with longer chains occur in lipids of nervous system.

Front 38

In FA, C-1 is determined by which carbon? The omega carbon is where?

Back 38

The carboxyl carbon. Omega carbon is the methyl group at the end of the alkyl chain.

Front 39

How are double bond locations designated in FA?

Back 39

They are listed in parentheses based on the C-number closest to the carboxy side of the carbon atom and also by the number of C from the omega side of the molecule.

Front 40

What are the double bond designations for:
CH3(CH2)5CH=CH(CH2)7COOH

Back 40

(w7) and (9)

Front 41

FA that are essential have an omega designation that is ?? and below?

Back 41

omega 6 and below. I.e. anything that is below w7 cannot be made by the body and required in the diet.

Front 42

What are the 7 FA he asked us to memorize? And their formulas.

Back 42

1. Palmitic 16:0
2. Palmitoleic Acid 16:1(9)
3. Stearic Acid 18:0
4. Oleic Acid 18:1(9)
5. Linoleic Acid 18:2(9,12)
6. alpha-Linoleic Acid 18:3(9,12,15)
7. Arachidonic acid 20:4(5,8,11,14)

Front 43

Of the 7 FA he wants us to know, which are essential?

Back 43

Linoleic, alpha-Linolenic, Arachidonic acid.

Front 44

Why is arachidonic acid so important to the diet?

Back 44

BC it's a precursor for prostaglandins and other hormones.

Front 45

As FA get longer, what happens to their MP? What happens to the MP as you add cis-double bonds? (use Palmitic acid and Palmitoleic acid as an example)

Back 45

It gets higher. For FA with double bonds, the MP drops. For example, Palmitic Acid 16:0 and Palmitoleic Acid 16:1(9), the MP drops from 63C to -0.5C with just one double bond.

Front 46

What makes linoleic and alpha-linolenic acid so essential?

Back 46

They have double bonds at the 9 and 12 position (AKA w6 and w3 position) and can be used to build longer FA (eg essential prostaglandins). We cannot add double bonds to the w6 or w3 positions and this is why linoleic and linolenic acid is essential (ss pt 175)

Front 47

Review the FA synthesis pathway on pg 177. The level of detail he wants us to know is on the back:

Back 47

1. Know that you start with Acetyl-CoA
2. It undergoes a rxn with Malonyl-CoA that leads to a product with at ketone (Ketone-ACP)
3. This ketone needs to be removed by being reduced to an -OH, then a hydrocarbon
4. This cycle repeats until you reach Palmitic acid 16:0

Front 48

In FA synth, what does thioesterase do?

Back 48

When the growing FA becomes at least 16 C long, thioesterase cleaves the ACP from the complex (i.e. C16-acyl-ACP), leaving ACP and Palmitate.

Front 49

What is the storage form of fatty acids?

Back 49

Triglycerides

Front 50

Describe what end FA's are added to WHAT backbone via WHAT bond?

Back 50

The carboxyl end is added to a glycerol backbone via ester bond.

Front 51

In a triglyceride, what kind of FA is typically at the R1 position and what about the R2?

Back 51

R1 is typically saturated and R2 is unsaturated.

Front 52

From what does the triglyceride backbone originate from?

Back 52

It originates from the reduction of dihydroxyacetone phosphate to glycerol-3-phosphate. You should recognize that from the glycolytic cycle.

Front 53

Review how triglycerides are synthesized on pg 181-2

Back 53

w

Front 54

What is the commitment step for FA synthesis?

Back 54

Acetyl-CoA carboxylase - it converts Acetyl-CoA to Malonyl-CoA

Front 55

Acetyl-CoA is ?? when phosphorylated and ?? when dephosphorylated

Back 55

P = Inactive
de-P = Active

Front 56

What phosphorylates Acetyl-CoA and what regulates it?

Back 56

AMP-Activated protein kinase. Regulated by AMP levels.

Front 57

Why is AMPK consider to be a fuel gauge in the cell?

Back 57

BC it is activated by AMP and inhibited by ATP

Front 58

What dephosphorylates inactive Acetyl-CoA carboxylase?

Back 58

Protein phosphatase 2A

Front 59

There will be four questions from the CBD group.

Back 59

There will be four questions from the CBD group.