Study Guide Flashcards
What does “favorable” mean in terms of ΔG (aka: free energy)?
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
Explain the process of reaction coupling to ATP
Reaction coupling can make an overall process spontaneous.
The individual Delta Gs are unchanged
How does reaction coupling drive an unfavorable process or reaction?
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)
Is ATP the only molecule in the cell considered to be a “high energy phosphate compound?”
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?
In general, what does it mean to have high “phosphotransfer” potential energy?
A means of comparing the tendency of organic molecules to transfer a phosphoryl group to an acceptor molecule. For example transferring a phosphate
Name the two major electron carrier molecules in the cell
NADH → NAD+ (mostly people)
FADH2 → FAD
Explain how coupling to an electron carrier can drive an unfavorable reaction
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
Where does Glycolysis occur in the cell?
Cytoplasm
What are the options for pyruvate under anaerobic conditions? What do we make?
In humans, we make lactate (in muscles)
and generate NAD+ in the process
Which process provides the primary source of ATP if no oxygen is present?
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
Where is the ATP produced in a cell if no oxygen is present?
Glycolysis in the cytoplasm
What metabolite (small molecule) is produced as a result of anaerobic metabolism?
Lactate/Lactic acid
(low pH environment, repels immune system)
Where does pyruvate go when oxygen is present?
remember pyruvate is the product of glycolysis!
—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.
What molecule is pyruvate converted to when oxygen is present?
Acetyl CoA
Which tissues are likely to require aerobic metabolism on a regular basis?
Brain
Muscles
Heart
What is the purpose of the Cori Cycle?
How many ATP required?
How many produced from Glycolysis?
Therefore, how much does the CC cost?
— 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
Which tissues does it involve? (Cori Cycle)
Muscle tissues and liver
What is the major regulatory enzyme in glycolysis? Which reaction does it catalyze?
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.
Looking at the overall process, how can you determine the 3 points of regulation based on equilibrium?
The 3 points of regulation are irreversible and require ATP:
— Glucose → G6P (Hexokinase)
— F6P → F6B (PFK)
— Phosphoenolpyruvate → pyruvate (Pyruvate Kinase)
What inhibits Phosphofructokinase (PKF), and what activates it?
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
Explain how the activation and inhibition of PFK in the muscles is a competition between levels of AMP and ATP.
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
How is PFK activated in the liver?
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.
What is the molecule that activates PFK in the liver?
F26BP activates PFK. This is the AMP of the liver
Which enzyme synthesizes F26BP which activates PFK in the liver?
PFK2 kinase site
Why can’t the liver use AMP the way the muscles do to activate PFK?
It doesn’t have enough ATP
In the liver, explain how the kinase domain of Phosphofructokinase-2 (PFK2) is inhibited, thus activating the phosphatase domain.
High glucagon activating GPCR → Protein Kinase A → phosphorylates PFK2 Kinase site → increases the FBPase-2 function.
the GPCR
How does phosphorylation impact the activity of PFK2?
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
Pentose Phosphate Pathway, purpose? Where does it take place
Produce NADPH
Cytosol
What molecules of glycolysis are made from Ribose-5 phosphate?
Fructose-6-phosphate (F6P)
Glyceraldehyde-3-phosphate (G3P)
Gluconeogenesis, how do you get from Pyruvate to Phosphoenolpyruvate
Use pyruvate carboxylase → Oxaloacetate (2) →PEP carboxykinase → Phosphoenolpyruvate
Oxaloacetate is the intermediary
What molecule is made between pyruvate and PEP?
Oxaloacetate
What is the connection between the enzyme glucose-6 phosphatase and glycogen levels?
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
Glycogen metabolism: What is the role of glycogen phosphorylase (GP)?
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.
What are the two states of glycogen phosphorylase?
Glycogen metabolism
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)
In glycogen metabolism, which enzyme turns G1P to G6P
(which then continues to glucose and shipped out to blood)
Phosphoglucomutase
mutases catalyze intramolecular group transfers.
How does Glycogen phosphorylase serve as a “glucose sensor” in the liver?
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.
How do the products of glycogen metabolism differ in the muscles in response to Epinephrine versus the liver in response to Glucagon?
in the muscles → run glycolysis to make pyruate → make ATP
In the liver we’re going to make glucose
Which protein is responsible for eliciting the cellular response at the end of signal transduction pathways?
Protein Kinase A (PKA) — starts the cascade of phosphorylation.
What are the three GPCR hormones covered in class? And what conditions upregulates them?
Glucagon, insulin, and epinephrine
Low sugar upregulates glucagon
High sugar upregulates insulin
Fight or flight upregulates epinephrine → run glycolysis
What cellular response occurs with Glucagon?
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
What cellular response occurs with insulin
Want to bring glucose into the cell
Protein phosphatase removes phosphate so Kinase is active on PFK2 (FBPase is inactive) → F26BP → speeds up PFK
What cellular response occurs with epinephrine
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
Where does the citric acid cycle occur in the cell?
In the mitochondrial matrix
Walk through Pyruvate dehydrogenase protein
What does it catalyse?
What does it release?
They make electron carriers
Pyruvate comes out of glycolysis, and Pyruvate dehydrogenase converts it to Acetyl CoA
Releases NADH and CO2
What molecule is contained within E1?
What is released?
Pyruvate goes into a subunit called E1.
Lose a CO2
E1 requires a thiamine to pull the CO2 off
Where is Acetyl CoA made?
Acetyl-CoA is generated in the mitochondria.
The core of E2
What are the electron carriers involved with E3?
FADH2 & NADH
What activates pyruvate dehydrogenase? (5)
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!
What inhibits pyruvate dehydrogenase?
Inhibited by ATP, Acetyl CoA, and NADH if there’s a lot floating around, we don’t need to produce more!
Control of E1 is based on phosphorylation – what is responsible for activating and inhibiting PDH kinase?
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.
What activates PDH phosphatase?
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.
What is the difference between passive and active transport across a membrane?
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.
Simple diffusion example
GLUT transporters
Facilitated diffusion example
Control open and close with a trigger, it’s passive but following a gradient
Active transport
Requires ATP!
ETC: Trace the path of electrons from NADH through the chain to their endpoint in oxygen.
Complex I → Coenzyme Q → Complex III → Cytochrom c → Complex IV → Oxygen and water is released
ETC: Trace the path of electrons from FADH2 through the chain to their endpoint in oxygen.
skips complex I
Complex II → Coenzyme Q → Complex III → Cytochrom c → Complex IV → Oxygen and water is released
Which complexes in the chain are responsible for pumping protons/generating the gradient?
All of them except complex II
Why is NADH a more valuable electron carrier for ATP synthesis?
Because it can pump out protons.
FADH2 enters complex II and doesn’t pump out protons
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?
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
