Study Guide

Question 1

What does “favorable” mean in terms of ΔG (aka: free energy)?

Answer 1

Delta G is negative

The glucose to G6P reaction is not favorable because there is more energy at the end of the reaction than at the beginning.

But, the reaction of ATP to ADP (releasing its 4th phosphate) is favorable because it helps offset reaction 1 (glucose to G6P).

G6P is less stable than glucose after ATP gave it a phosphate so there is potential energy stored in that G6P molecule

Question 2

Explain the process of reaction coupling to ATP

Answer 2

Reaction coupling can make an overall process spontaneous.

The individual Delta Gs are unchanged

Question 3

How does reaction coupling drive an unfavorable process or reaction?

Answer 3

Glucose → G6P is an unfavorable reaction
ATP → ADP is a favorable reaction

Combining the two creates a favorable reaction:
Glucose + ATP → G6P + ADP

Kinases require ATP coupling (adding a phosphate)

Question 4

Is ATP the only molecule in the cell considered to be a “high energy phosphate compound?”

Answer 4

Need a phosphate carrier at a higher level
1,3 BPG and PEP (but PEP is too much)
Have to couple with something with higher potential.
NADPH?

Question 5

In general, what does it mean to have high “phosphotransfer” potential energy?

Answer 5

A means of comparing the tendency of organic molecules to transfer a phosphoryl group to an acceptor molecule. For example transferring a phosphate

Question 6

Name the two major electron carrier molecules in the cell

Answer 6

NADH → NAD+ (mostly people)

FADH2 → FAD

Question 7

Explain how coupling to an electron carrier can drive an unfavorable reaction

Answer 7

Need to find things that have self-contained energy and couple them to together.

Glucose to G6P won’t happen. Too stable. But in the active site of an enzyme, slam them together, it will happen

In the electron chain, the carriers facilitate the transfer of electrons to an acceptor. This activity propagates down the chain and this vibration/humming energy forces protons to pass through against their gradient

Question 8

Where does Glycolysis occur in the cell?

Answer 8

Cytoplasm

Question 9

What are the options for pyruvate under anaerobic conditions? What do we make?

Answer 9

In humans, we make lactate (in muscles)

and generate NAD+ in the process

Question 10

Which process provides the primary source of ATP if no oxygen is present?

Answer 10

Glycolysis:
— Without oxygen, organisms can split glucose into just two molecules of pyruvate.
— This releases only enough energy to make two ATP molecules

or anaerobic respiration

Question 11

Where is the ATP produced in a cell if no oxygen is present?

Answer 11

Glycolysis in the cytoplasm

Question 12

What metabolite (small molecule) is produced as a result of anaerobic metabolism?

Answer 12

Lactate/Lactic acid
(low pH environment, repels immune system)

Question 13

Where does pyruvate go when oxygen is present?
remember pyruvate is the product of glycolysis!

Answer 13

—The pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are the sites of cellular respiration (The Citric Acid Cycle → ETC → ATP)
—There, pyruvate will be transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA).
—The resulting compound is called acetyl CoA.
—CoA is made from vitamin B5, pantothenic acid.

Question 14

What molecule is pyruvate converted to when oxygen is present?

Answer 14

Acetyl CoA

Question 15

Which tissues are likely to require aerobic metabolism on a regular basis?

Answer 15

Brain
Muscles
Heart

Question 16

What is the purpose of the Cori Cycle?
How many ATP required?
How many produced from Glycolysis?
Therefore, how much does the CC cost?

Answer 16

— To shift the metabolic burden from the muscles to the liver during intense exercise.

— Glucose → 2 lactate in the muscles → exported to the liver → turned into 2 pyruvate + 6 ATP → glucose
this is gluconeogenesis

— 6 ATP molecules are required for every cycle

— 2 ATP molecules are produced through glycolysis

— Therefore each iteration of the Cori cycle costs 4 ATP (net) which is fine temporarily when ATP needs are immediate

Question 17

Which tissues does it involve? (Cori Cycle)

Answer 17

Muscle tissues and liver

Question 18

What is the major regulatory enzyme in glycolysis? Which reaction does it catalyze?

Answer 18

Phosphofructokinase

It catalyzes the reaction of Fructose-6-phosphate → Fructose 1,6-bisphosphate

and, in the process, converts ATP to ADP

This is an irreversible reaction.

Question 19

Looking at the overall process, how can you determine the 3 points of regulation based on equilibrium?

Answer 19

The 3 points of regulation are irreversible and require ATP:
— Glucose → G6P (Hexokinase)
— F6P → F6B (PFK)
— Phosphoenolpyruvate → pyruvate (Pyruvate Kinase)

Question 20

What inhibits Phosphofructokinase (PKF), and what activates it?

Answer 20

ATP inhibits — If ATP is present, it means we have enough energy, don’t need more

AMP activates — this is the product of muscles using ADP + ADP desperately to make ATP so this signals we need ATP

Question 21

Explain how the activation and inhibition of PFK in the muscles is a competition between levels of AMP and ATP.

Answer 21

When ATP levels are low, muscles can combine two ADPs to make ATP and AMP:
ADP + ADP <> ATP + AMP
When ATP goes down, AMP goes up

When ATP is high, ATP will bind in the allosteric site of PFK and block the active site so F6P cannot bind at all.
= Turn OFF gycolysis

When AMP is high, AMP will bind in the allosteric site of PFK = Turn ON glycolysis

Non-competitive inhibition

Remember F6P in in the active site of PFK to turn it into F16BP

Question 22

How is PFK activated in the liver?

Answer 22

When sugar is high, the insulin hormone will increase protein phosphatase which activates the kinase site on PFK2 which stimulates F26BP which speeds PFK up and glycolysis

When sugar is low, the hormone glucagon will act on the GPCR which releases protein kinase A (PKA) which phosphorylates the kinase domain on PFK2, thus shutting it down, and activating the FBPase site, thus deactivating F26BP, thus sending F6P back to G6P and back to glucose. Glycolysis slows.

Note: the liver keeps enough ATP around to inactivate PFK but it differs when it needs to turn it back on. Muscle use AMP but the liver doesn’t have AMP because it’s not producing ATP.

When glucose goes up and the liver needs to turn PFK back on:
PFK2 (Kinase site) is activated which adds a phosphate to and activates F26BP → speeds up PFK

So F26BP activates PFK.
This is the AMP of the liver.

Question 23

What is the molecule that activates PFK in the liver?

Answer 23

F26BP activates PFK. This is the AMP of the liver

Question 24

Which enzyme synthesizes F26BP which activates PFK in the liver?

Answer 24

PFK2 kinase site

Question 25

Why can’t the liver use AMP the way the muscles do to activate PFK?

Answer 25

It doesn’t have enough ATP

Question 26

In the liver, explain how the kinase domain of Phosphofructokinase-2 (PFK2) is inhibited, thus activating the phosphatase domain.

Answer 26

High glucagon activating GPCR → Protein Kinase A → phosphorylates PFK2 Kinase site → increases the FBPase-2 function.

Question 27

the GPCR How does phosphorylation impact the activity of PFK2?

Answer 27

When the Kinase domain of PFK2 is phosphorylated by PKA (GPCR and signal transduction from the glucagon hormone) it shuts down the kinase and the FBPase is active, thus slowing down PFK

Question 28

Pentose Phosphate Pathway, purpose? Where does it take place

Answer 28

Produce NADPH Cytosol

Question 29

What molecules of glycolysis are made from Ribose-5 phosphate?

Answer 29

Fructose-6-phosphate (F6P) Glyceraldehyde-3-phosphate (G3P)

Question 30

Gluconeogenesis, how do you get from Pyruvate to Phosphoenolpyruvate

Answer 30

Use *pyruvate carboxylase* → **Oxaloacetate (2)** →*PEP carboxykinase* → **Phosphoenolpyruvate** **Oxaloacetate is the intermediary**

Question 31

What molecule is made between pyruvate and PEP?

Answer 31

Oxaloacetate

Question 32

What is the connection between the enzyme glucose-6 phosphatase and glycogen levels?

Answer 32

In liver, glucose-6-phosphatase catalyses the **terminal step of gluconeogenesis**. Glucose-6-phosphatase (G6Pase) is required for the hydrolysis of glucose-6-phosphate (G6P) into glucose and inorganic phosphate (Pi) It depends if you want the **glycogen to store or out into the blood to use**

Question 33

Glycogen metabolism: What is the role of glycogen phosphorylase (GP)?

Answer 33

Is the enzyme that catalyzses this reaction: Glycogen → G1P It is activated by phosphorylation (at Serine 14) GPb → GPa It has two states: GPa and GPb *Note: if we’re pulling out glucose from glycogen, sugar is low, and we’re not running glycolysis! Glycogen provides a rapid source of energy. It is highly branched, so it allows for rapid synthesis and degradation.*

Question 34

What are the two states of glycogen phosphorylase? Glycogen metabolism

Answer 34

**PKA** activates **phosphorylase kinase** which phosphorylates GP → **GPa (active)** Then we can make G1P → G6P → glucose → Get it out into blood **Phosphorylase Phosphatase** _removes_ the phosphate from GPa → **GPb (inactive)**

Question 35

In glycogen metabolism, which enzyme turns G1P to G6P (which then continues to glucose and shipped out to blood)

Answer 35

**Phosphoglucomutase** *mutases catalyze intramolecular group transfers.*

Question 36

How does Glycogen phosphorylase serve as a “glucose sensor” in the liver?

Answer 36

If glucose levels are low, this enzyme is going to ensure we’re pulling glucose out of glycogen and getting out into the blood by changing the state of GP from beta to alpha. It is the response to the glucagon that’s sensing the low sugar.

Question 37

How do the products of glycogen metabolism differ in the muscles in response to Epinephrine versus the liver in response to Glucagon?

Answer 37

in the **muscles** → run glycolysis to make pyruate → make **ATP** In the **liver** we’re going to make **glucose**

Question 38

Which protein is responsible for eliciting the cellular response at the end of signal transduction pathways?

Answer 38

**Protein Kinase A (PKA)** — starts the cascade of phosphorylation.

Question 39

What are the three GPCR hormones covered in class? And what conditions upregulates them?

Answer 39

Glucagon, insulin, and epinephrine Low sugar upregulates glucagon High sugar upregulates insulin Fight or flight upregulates epinephrine → run glycolysis

Question 40

What cellular response occurs with Glucagon?

Answer 40

Glucagon = sugar is gone! Don't run glycolysis! GPCR → PKA → phosphorylates the Kinase on PFK2 which slows down PFK if glucose is low ATP is in the allosteric site to inactivate PFK

Question 41

What cellular response occurs with insulin

Answer 41

Want to bring glucose into the cell Protein phosphatase **removes phosphate** so Kinase is active on PFK2 (FBPase is inactive) → F26BP → speeds up PFK

Question 42

What cellular response occurs with epinephrine

Answer 42

**Fight or flight — need ATP to muscles** Activate **glycogen phosphorylase** (glucogen metabolism with alpha and beta states) **GPa state → G1P → G6P** but from here, we’re not going to convert to glucose and pump it back into the blood, we need energy to fight the bear! So it’ll run down the **glycolysis pathway to pyruvate so the muscles get ATP** So in the liver: G6P → glucose If you’re in the muscles: G6P → glycolysis

Question 43

Where does the citric acid cycle occur in the cell?

Answer 43

In the mitochondrial matrix

Question 44

Walk through Pyruvate dehydrogenase protein What does it catalyse? What does it release?

Answer 44

They make electron carriers Pyruvate comes out of glycolysis, and **Pyruvate dehydrogenase converts it to Acetyl CoA** Releases **NADH and CO2**

Question 45

What molecule is contained within E1? What is released?

Answer 45

Pyruvate goes into a subunit called E1. Lose a CO2 E1 requires a **thiamine to pull the CO2 off**

Question 46

Where is Acetyl CoA made?

Answer 46

Acetyl-CoA is generated in the **mitochondria**. The **core of E2**

Question 47

What are the electron carriers involved with E3?

Answer 47

FADH2 & NADH

Question 48

What activates pyruvate dehydrogenase? (5)

Answer 48

**ADP** — Remember in the muscles we can mush two ADPs to make ATP and AMP in the cytoplasm. Here we are in the mitochondria, ADP is my precursor to ATP **Pyruvate** **Calcium** — Byproduct of muscle use so its a sign that this system needs to run **Magnesium** — ATP when it’s floating around will coordinate to Magnesium ions. At the centre of every kinase is a magnesium. Free floating magnesium means there is low ATP **Insulin** — Glucose levels are high so we want to generate as much ATP as possible. Run the system!

Question 49

What inhibits pyruvate dehydrogenase?

Answer 49

Inhibited by **ATP, Acetyl CoA, and NADH** if there’s a lot floating around, we don’t need to produce more!

Question 50

Control of E1 is based on phosphorylation – what is responsible for activating and inhibiting **PDH kinase**?

Answer 50

Pyruvate dehydrogenase kinase is a kinase enzyme which acts to **inactivate the enzyme pyruvate dehydrogenase** by phosphorylating it using ATP (so basically don’t run the citric acid cycle) _Pyruvate dehydrogenase kinase is_ Activated by ATP, NADH, and acetyl-CoA. It is inhibited by ADP, NAD+, and pyruvate.

Question 51

What activates PDH phosphatase?

Answer 51

**Pyruvate dehydrogenase phosphatases** catalyze the dephosphorylation and activation of the E1 component to reverse the effects of pyruvate dehydrogenase kinases (**meaning the citric acid cycle runs**). Insulin promotes the activation of PDH phosphatase. This makes sense because insulin is high when glucose is high so we want glycolysis and TCAC to run.

Question 52

What is the difference between passive and active transport across a membrane?

Answer 52

Active transport involves the movement of molecules from lower concentration to higher concentration with the use of energy. Passive transport involves the movement of molecules from higher concentration to lower concentration and no amount of energy is required.

Question 53

Simple diffusion example

Answer 53

GLUT transporters

Question 54

Facilitated diffusion example

Answer 54

Control open and close with a trigger, it's passive but **following a gradient**

Question 55

Active transport

Answer 55

Requires ATP!

Question 56

ETC: Trace the path of electrons from **NADH** through the chain to their endpoint in oxygen.

Answer 56

**Complex I** → Coenzyme Q → Complex III → Cytochrom c → Complex IV → Oxygen and water is released

Question 57

ETC: Trace the path of electrons from FADH2 through the chain to their endpoint in oxygen.

Answer 57

*skips complex I* **Complex II** → Coenzyme Q → Complex III → Cytochrom c → Complex IV → Oxygen and water is released

Question 58

Which complexes in the chain are responsible for pumping protons/generating the gradient?

Answer 58

All of them except complex II

Question 59

Why is NADH a more valuable electron carrier for ATP synthesis?

Answer 59

Because it can pump out protons. FADH2 enters complex II and doesn’t pump out protons

Question 60

In ATP synthesis, there are 3 steps (binding ADP/P, forming ATP, and releasing ATP) Which of these steps is dependent on the proton gradient?

Answer 60

Alpha and beta have three confirmations L: (loose) Bind ADP and phosphate, T: (tight) Smush together and make ATP **O: (open) Release ATP — this step is dependent on the proton gradient**