Exam 2 APK

What happens to ATP demand under aerobic circumstances? What happens to the NADH and pyruvate instead of doing anerobic respiration (producing lactate)

* The demand is low enough to be met with oxygen thus going into aerobic
* NADH and pyruvate get shuttled into the mitochondria

What happens to pyruvate when ATP demand is low

Pyruvate moves into the mitochondria with NADH instead of making lactate as if it were going through anerobic conditions

What is the purpose of a muscle fiber?

It tries to create a pathway for more ATP for meeting ATP demands in a certain cell.

When ATP demands are constantly shifting , what does it determine

The rate at which the system meets the demand

Give an example of what happens when ATP demand is low

When you move from a sitting position to walking, your muscle fibers:


1. contract causing calcium to elevate in muscle fibers, which causes a rise in epinephrine
2. A rise in epinephrine activates an enzyme that breaks glycogen into glucose-6-phate
3. ATP demand increases than the supply once you start walking
4. ADP accumulates by allosterically activating the rate-limiting enzyme of phosphofructokinase
5. Glycolysis increases significantly

Why do we need ADP to accumulate

It activates the pathway to go faster

What is the purpose of muscle fibers?

It tries to create a pathway for more ATP for meeting ATP demand in a certain cell

ATP demand is proportional to

the rate of glycolysis;

* if there is high atp demand the glycolysis rate will also increase integrating fast processes in order to make ATP as quickly as needed.
* If someone is sprinting and needs ATP immediately, the phosphagen system will be in place effectively then turn into anerobic conditions (since it is faster)

Why does low demand atp cause pyruvate and nadh to go into the mitochondria

pyruvate and NADH, which are intermediate products of glycolysis, have excess energy that needs to be efficiently utilized. Pyruvate and NADH enter the mitochondria to undergo further oxidation and maximize the extraction of energy from glucose

Where does pyruvate and NADH need to go into the mitochondria

The matrix past the inner and outer membrane; this is where enzymes exist to further breakdown pyruvate

What is also transported with pyruvate and NADH?

ADP and inorganic phosphate

What are the 3 driving forces that go into the cytosol to be diffused across the inner membrane into the matrix

* organic phosphate→ inorganic
* pyruvate
* adenine nucleotide →ADP

Why are ADP and inorganic phosphate trying to get past the inner membrane

they came from the usage of ATP (contraction of muscle fibers) which means its making ADP and inorganic phosphate→ ADP and inorganic phosphate have to get resynthesized as ATP

Why does Pyruvate need a pore and integral protein to get past the inner membrane vs inorganic phosphate

* Pyruvate is a charged molecule (negatively charged) and cannot freely diffuse across the lipid bilayer of the inner mitochondrial membrane, which is hydrophobic in nature


* Inorganic phosphate (Pi) is a small, negatively charged molecule that can cross the inner mitochondrial membrane more readily.

What is the significance of the Linking Step:

It converts pyruvate into acetyl-CoA, generating CO2 and NADH in the process. Acetyl-CoA then enters the citric acid cycle to continue the process of aerobic respiration, ultimately leading to the production of ATP and further energy extraction from glucose. It does this through 2 steps:


1. Pyruvate transport
2. Conversion of Acetyl- CoA

Where does the linking step occur

in the mitochondrial matrix

Where does the acetyl CoA go

the Krebs cycle

During the Linking Stage what happens during Pyruvate Transport

* After being produced in the cytoplasm through glycolysis, pyruvate molecules need to cross the mitochondrial membranes to reach the mitochondrial matrix, where the citric acid cycle (Krebs) takes place.
* Pyruvate is transported into the mitochondria through specific transporters located in the inner mitochondrial membrane.

During the Linking stage what happens after Pyruvate Transport

Conversion into Acetyl CoA

What happens in the Conversion into Acetyl CoA

Once inside the mitochondria, pyruvate undergoes decarboxylation. The enzyme pyruvate dehydrogenase complex (PDC) catalyzes this reaction in 3 steps

What are the steps of Conversion into Acetyl CoA

a. Decarboxylation

b. Oxidation

c. Coenzyme A Attachment

What happens during decarboxylation

a carboxyl group (COO-) is removed from pyruvate, releasing one molecule of CO2

What happens during oxidation

the remaining two-carbon molecule, called an acetyl group, undergoes oxidation. NAD+ is reduced to NADH by accepting a pair of high-energy electrons from the acetyl group. This oxidation reaction is an important step in energy extraction from glucose.

What happens during Coenzyme A Attachment

* oxidized two-carbon acetyl group now combines with coenzyme A (CoA) to form acetyl-CoA.
* Coenzyme A acts as a carrier molecule and facilitates the transfer of the acetyl group to the citric acid cycle. T
* he resulting acetyl-CoA carries the stored energy from the original glucose molecule.

Explain the main points in Aerobic Glycolysis

1. Linking Step


1. Pyruvate Decarboxylation:
2. Citric Acid Cycle (Krebs Cycle):
2. Electron Transport Chain (ETC)
3. Chemiosmosis and ATP Synthesis:
4. Oxygen as the Final Electron Acceptor: \\

What is the Krebs Cycle typically known for

being a series of oxidation reactions

What happens during the Krebs Cycle

\
a. Acetyl-CoA Entry

b. Citrate Isomerization

c. Isocitrate Oxidation

d. Succinyl-CoA Formation

e. Substrate-level Phosphorylation

f. Succinate Oxidation

g. Fumarate Conversion

h. Malate Oxidation

i. Regeneration of Oxaloacetate

What happens during acetyl coA entry

the two-carbon acetyl group from acetyl-CoA combines with a four-carbon molecule called oxaloacetate, forming a six-carbon molecule called citrate. The enzyme citrate synthase catalyzes this condensation reaction.

What happens during citrate isomeration

Citrate is then isomerized into its isomer, isocitrate, through a dehydration and rehydration process. The enzyme aconitase is responsible for this conversion.

What happens during isocitrate oxidation

Isocitrate is oxidized to α-ketoglutarate in two steps.

* oxidative decarboxylation of isocitrate, which generates NADH and releases a molecule of CO2. The enzyme isocitrate dehydrogenase carries out this reaction.
* The resulting molecule, α-ketoglutarate, undergoes a second oxidative decarboxylation, catalyzed by the enzyme α-ketoglutarate dehydrogenase complex, which generates another molecule of NADH and releases another molecule of CO2.

What happens during Succinyl CoA formation

α-ketoglutarate is then converted to succinyl-CoA. This conversion involves the release of a molecule of CO2 and the generation of NADH. The enzyme α-ketoglutarate dehydrogenase complex facilitates this reaction.

Substrate-level Phosphorylation

Succinyl-CoA undergoes a substrate-level phosphorylation reaction catalyzed by the enzyme succinyl-CoA synthetase. This process results in the direct transfer of a phosphate group from succinyl-CoA to guanosine diphosphate (GDP), producing guanosine triphosphate (GTP) and releasing CoA.

What happens during Succinate Formation:

Succinyl-CoA is converted into succinate. In this step, the high-energy phosphate group is transferred from succinyl-CoA to GDP, producing GTP, which can later be converted to ATP. The enzyme involved in this reaction is called succinyl-CoA synthetase.

What happens during Succinate Oxidation:

Succinate is oxidized to fumarate, and this reaction involves the transfer of electrons to an electron carrier called FAD (flavin adenine dinucleotide), converting it to FADH2. The enzyme succinate dehydrogenase, also known as complex II of the electron transport chain, catalyzes this reaction. Succinate dehydrogenase is unique among the enzymes of the citric acid cycle because it is embedded in the inner mitochondrial membrane.

What happens during Fumarate Conversion:

Fumarate is then converted to malate through the addition of water. The enzyme fumarase catalyzes this hydration reaction

What happens during Malate Oxidation

Malate is oxidized to oxaloacetate by the enzyme malate dehydrogenase. This reaction generates another molecule of NADH

What happens during Regeneration of Oxaloacetate

Oxaloacetate, the final product of the citric acid cycle, can then combine with another molecule of acetyl-CoA to begin the cycle again.

What is the significance of the citric acid cycle

It completes the breakdown of glucose, releasing CO2 and generating energy-rich molecules in the form of NADH, FADH2, and GTP. These energy carriers play a vital role in oxidative phosphorylation, the final step of aerobic respiration, where they transfer electrons to the electron transport chain, leading to the production of ATP. The citric acid cycle is a central hub of metabolism

What is the overall function of “The Linking Step”

* The pyruvate molecules produced in glycolysis move into the mitochondria, where they undergo decarboxylation. Each pyruvate molecule loses a carbon atom in the form of CO2, resulting in the formation of acetyl-CoA, a two-carbon molecule.


* This step generates NADH and occurs twice per glucose molecule (since two pyruvate molecules are produced in glycolysis).

What is the overall function of Citric Acid Cycle

Acetyl-CoA enters the citric acid cycle, also known as the Krebs cycle or tricarboxylic acid (TCA) cycle, which takes place in the mitochondrial matrix. In this cycle, the two-carbon acetyl group combines with a four-carbon molecule called oxaloacetate to form citrate. Through a series of enzymatic reactions, citrate is gradually converted back to oxaloacetate, releasing CO2 and generating ATP, NADH, and FADH2 (Flavin adenine dinucleotide)

What is the overall function of Electron Transport Chain

* To pump hydrogen ions into the matrix into the intermembrane space
* **The high-energy electrons carried by NADH and FADH2 from the previous steps enter the electron transport chain, which is located in the inner mitochondrial membrane. The ETC consists of a series of protein complexes (including NADH dehydrogenase, cytochrome b-c1 complex, and cytochrome c oxidase) and electron carriers (such as ubiquinone and cytochrome c). As electrons pass through the ETC, their energy is gradually released, and protons (H+) are pumped from the matrix to the intermembrane space, establishing an electrochemical gradient.**

What complexes help the electron transport chain

a. Complex 1

b. Ubinquinoine

c. Complex 2

d. Complex 3

e. Cytochrome C and Complex 4

f. ATP synthase

g. energy yield

\

Complex 1

The electron transport chain begins with NADH, a high-energy electron carrier produced in glycolysis, the pyruvate decarboxylation step, and the citric acid cycle. NADH donates its electrons to complex I, also known as NADH dehydrogenase. This complex accepts the electrons and transfers them to a molecule called ubiquinone (Q), also known as coenzyme Q.

Ubinquinoine

Ubiquinone (Q) is a mobile electron carrier embedded in the inner mitochondrial membrane. It accepts electrons from complex I and becomes reduced (QH2), carrying the electrons to the next component of the electron transport chain.

Complex 3

Complex III passes the electrons to cytochrome c, which is a mobile carrier located in the intermembrane space. Meanwhile, complex III pumps protons from the mitochondrial matrix into the intermembrane space, contributing to the establishment of a proton gradient.

Cytochrome C and Complex 4

Cytochrome c carries the electrons from complex III to complex IV, also known as cytochrome c oxidase. Complex IV facilitates the final transfer of electrons to molecular oxygen (O2), the ultimate electron acceptor. This reaction allows the reduction of molecular oxygen to water (H2O). At the same time, complex IV also pumps protons across the inner mitochondrial membrane, further contributing to the proton gradient.

ATP synthase

ATP synthase is an enzyme complex located in the inner mitochondrial membrane. It utilizes the proton gradient established by the electron transport chain to generate ATP. As protons flow back into the mitochondrial matrix through ATP synthase, the enzyme couples this flow with the synthesis of ATP from adenosine diphosphate (ADP) and inorganic phosphate (Pi).

Describe how and why a cell transitions between using only aerobic glycolysis to both aerobic and anaerobic glycolysis?

* the phsphogen system will run out super fast so its not much help but

When the ETC creates a gradient with a high concentration of electron ions in intermembrane space compared to the matrix what does this do to hydrogen ions

It causes hydrogen ions to move through ATP synthase back into the matrix to provide ATP synthase the energy needed to make more ATP

How can hydrogen ions come back into the matrix

* ATP synthase tunnel for hydrogen ions to come back into the matrix →
* The movement of hydrogen ions from intermembrane through ATP synthase to matrix is an energy producing process ( the movement of an ion through a protein requires energy) →
* Energy is used to rotate and recombine ADP and phosphate to make ATP which came from muscle contraction

What are 2 things that pull H ions back into the membrane space

* diffusion gradient- high concentration of H compared to ion concentration in the matrix
* negative matrix- pulls positive H ions back

What is the negative matrix also known as

electron driving force because its tempting for positive hydrogen atoms to get pulled into low concentrated area

What happens to the intermembrane space when there is an increase of hydrogen ions in the intermembrane area than in the matrix

the intermembrane space gets more positive than the matrix

What happens if you have a higher cncentration of ions that have a high positve charge in one location compared to another

the location that has a higher concentration of ions that are positively charged will be compared to the other location with low positivity and will have a negative charge → electrical driving force : that pulls it back into the matrix

What does a concentration of hydrogen ions in the intermembrane space and a lower concentration of hydrogen ions in the matrix result int

high concentration of molecules or atoms in one location and a lower concentration in those same molecules, the molecules and atoms will want to move to the low concentration via diffusion gradient

What is it when a series of oxidation reactions allow phosphorylation of ATP synthase to phosphorylate to ADP to ATP again

Oxidative Phosphorylation

What is also known as capturing energy by oxidative phosphorylation

ATP synthesis

Why is ATP synthesis an endergonic rxn

You need to put energy in rxn for it to occur because ADP and phosphate have less energy within them than ATP products

Where is the energy coming from for the endergonic reaction of ATP synthesis

the movement of hydrogen ions from intermembrane to the matrix

What happens when there is no oxygen in the cell

There is no ability for electrons to be removed from the complex and electrons will build up in the entire chain in the fourth complex→ traffic jam → stops electron transport chain

What happens when the ETC stops

H ions cant get pumped anymore which means no H ion gradient b/w the matrix and intracellular matrix forms

What happens when there is no H ion gradient

no energy for ATP synthase → no ATP→ no oxygen → cell death

Why does the ETC need oxygen

Oxygen is the final acceptor as it removes electrons from the 4th complex and by removing them, it allows for the the 4th complex to pump 2 more hydrogen ions into the intermembrane space, allowing electrons to continuously shuttle through complexes, further preventing traffic jam of electrons bc if oxygen is constantly taking away electrons from the 4th comp→ more electrons can be brought to the 4th comp by cytochrome c

What is the role of FADH in the ETC

1. created by comp 2
2. gives 2 elec from 2 H to coenzyme Q
3. coenzyme Q brings electrons to comp 3
4. cytochrome c takes 2 elec to comp 4 by oxidizing cytochrome c
5. oxygen is made through oxidizing comp 4
6. removal of 2 electrons allow from comp 4 to pump 2 H

What is the difference between NADH and FADH

* NADH contributes more to hydrogen ion gradient within the ETC than each FADH bc FADH pumps 10 H into the intermembrane space allowing more ATP creation
* for every 4 H ions one ATP is made so 10 hydrogen ions allows the creation of 2 . 5 ATP
* FADH has only 6 hydrogen ions pumped from the matrix into the intermembrane space bc electrons from FADH are never given to Comp 1 bc Comp 2 creates FADH
* for every 6 H into the intermembrane allows the creation of 1.5 ATP

Which system of glycolysis does high atp demand use

anerobic- lots of atp needs to be made in a short period ofo time

Which system of glycolysis does low atp demand use

aerobic - lots of atp over a slow period of time with a lot of step s

What is the ATP production in the 3 energy systems

* Phosphogen-
* Anerobic Glycolysis: 2 ATP
* Aerobic Glycolysis: 32 ATP

What are the limitations for aerobic glycolysis

although it makes a lot of atp over a short period of time, it is limited

Which stimulator activates all pathways; give an example

ADP

* when you start jogging from sitting, muscle cells contract more forcefully
* atp demand rises
* muscle celles make more adp which consumes more ATP A
* ADP allosterically activates enzymes for Krebs, ETC , and Glycolysis

What are the rate limiting enzymes in all pathways that are activated by ADP

* Phosphagen- creatine kinase
* Glycolysis- Phosphofructokinase
* Citric Acid Cycle - Isocitate Dehydrogenase
* ETC- Cytochrome oxidase

When ATP demand rises what happens

more atp is needed and the mitcochondria creates more

Why do we oxidize NADH to NAD and not let it continue to run infinitely fast; What happens to lactate

All NAD would become NADH and we wouldn’t have enough NADH to keep glycolysis running and lactate would increase in their blood stream

anerobic system does not need what

mitochondria

What is simple diffusion

when a molecule does not require an integral protein and can just pass through the membrane

What are molecules that can pass through the membrane through simple diffusion

nonpolar

* atmospheric oxygen

Why does slow aerobic dominates for ATP demand and the most efficient systemq

Oxygen needs to be brought to cells so they can be extracted from ATP to make more and meet ATP demands

Theoretically when a muscle fiber can be maxed out with the amount of oxygen that can be brought to it , but there’s an abundance of NADH, what happens

The muscle cell gets insufficient and the number of oxygen (limiting enzyme factor) electrons can’t get picked up by comp 4 causing there to be more NADH in the ETC than electrons →

What happens when there is a buildup of NAHD that can’t go through the ETC

There ill be les NAD bc NAD is the form of NADH which means there wont be enough NAD to turn into acetyl coA

Due to lack of oxygen what accumulates

Pyruvate and NADH

What do Pyruvate and NADH mostly use to get into the cytosol of mitochondria and stay in it

The diffusion gradient

What is an example of nonpolar molecule

* CO2
* high in cells to break up macro-nutrients

Why is there low oxygen in the matrix

it is used for ETC inside our cells

Why doesnt the nonpolar core in the membrane reject atmospheric oxygen

because atmospheric oxygen is nonpolar

Passive Diffusion through Channels happens when

charged and large molecules are able to diffuse through the plasma membrane through channels

Describe Osmosis

Diffusion of water from high to low

What are solutes

Anything in water that is NOT water

Water does water in osmosis use to move from high to low concentration

aquaporins

What is the most common pore/ channel that allows water to get in the plasma membrane intracellular

Aquaporins

What are the different types of Active Transport

* Primary and Secondary

What type of transport is it when the netflux is down the electrochemical gradient and MUST:

* move from high to low
* no energy is required to move it

Passive Transport

What are the different types of diffusion within passive transport

* simple diffusion
* facilitated diffusion
* diffusion through pores

which occurs within diffusion through channels?

osmosis

What has a netflux going up the electrochemical gradient along with:

* molecules that move from low to high against the gradient
* requires energy to move from high to low
* uses transmembrane proteins that use energy to drive molecules in a preferred direction

Active transport

What are the different types of active transport

Primary and Secondary

How are transmembrane (protein carriers) in active transport different from passive carriers in passive transport

* Passive carriers have equal affinity for molecules on either side of the membrane


* pumps have a greater affinity for a molecule on one side relative to the other side

What state is it when the concentration gradient offsets affinity

Steady state

What is the difference between PRIMARY and SECONDARY active transport

* Primary - The energy used is ALWAYS ATP to move from high to low
* Most ATP is used for the sodium-potassium pumps through resting membrane potential
* Secondary Active Transport- the energy source is the DIFFUSION OF SODIUM into a cell
* Uses symporters and antiporters
* Symporters- move two different molecules or ions in the same direction across the membrane
* Antiporter- These transporters move two different molecules or ions in opposite directions across the membrane
* Sodium is always high outside of the cell and low inside the cell → positively charged → the charged Na+ provides energy once it passes the integral protein to pump

What is an example of secondary active transport using glucose

1. You want to move glucose from a low to high which is going against the concentration gradient 9 (high to low)
2. The integral protein helps move the molecule (glucose) through energy given in the form of diffusion of a sodium ion as the energy source

What is it when molecules in the ECF are brought into the cell via the formation of an endosome

Endocytosis