metabolic processes review

Question 1

The energy of life

Answer 1

The living cell generates thousands of different reactions
- Metabolism is the totality of an organism’s chemical reactions, which arises from interactions between molecules
- An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics

Question 2

Metabolic Pathways

Answer 2

• Biochemical pathways are organized units of metabolism 🡪 chemical reactions of an organism
• A metabolic pathway has many steps that begin with a specific molecule and end with a product, catalyzed by a specific enzyme
• The function of many metabolic pathways is to break down energy-rich compounds such
  as glucose and convert the energy into a form that the cell can use.
• Reactions that join small molecules together to form larger, more complex molecules are anabolic
• Reactions that break large molecules down into smaller subunits are catabolic
• A sequence of chemical reactions, where the product of one reaction serves as a substrate for the next; also called a biochemical pathway
• Most metabolic pathways take place in specific regions of the cell

Question 3

Bioenergetics and energy

Answer 3

• The study of how organisms manage their energy resources via metabolic pathways
• Catabolic pathways: release energy by breaking down complex molecules into simpler compounds
• Anabolic pathways: consume energy to build complex molecules from simpler ones
  (where are we allocating this energy and resources → we need good proportions of stuff → we need to balance the ctabaolic and anabolic pathways → what are we building and breaking )

Energy is the capacity to do work that is to cause change or move matter against an opposing force like gravity or friction. Any change in the universe requires energy.
2 forms:
- Potential energy is stored energy, including chemical energy stored in molecular structure. No change is currently taking place. (energy that available but not released)
- Kinetic energy is currently causing change. This always involves some type of motion. (energy of motion)

Energy can be converted from one form to another.

Kinetic energy and potential energy may themselves be classified as different types. For
example, the kinetic energy of particles moving in random directions is thermal energy.
An increase in the kinetic energy of particles of an object increases the temperature of the
object. Heat is the transfer of thermal energy from one object to another due to a temperature
difference between the objects. Chemical energy is potential energy stored in the arrangement
of the bonds in a compound.

Whenever a chemical bond forms between two atoms, energy is released. The amount of
energy needed to break a bond is the same as the amount of energy released when the bond
is formed. This amount of energy is called bond energy. Because energy is always released
when a bond forms, free (unbonded) atoms can be considered to have more chemical energy than any compound.

The energy released from chemical reactions in a laboratory is
usually in the form of thermal energy (heat). The energy released from chemical reactions in living cells can include thermal energy, but it can also be in the form of the movement of compounds across cell membranes, contraction of a muscle, or even the emission of light from compounds within specialized cells in certain organisms. In many cases, energy released from one reaction is used to make another reaction occur as part of a metabolic pathway.

Question 4

Laws of energy transform/Thermodynamics

Answer 4

All activities—those that are necessary to enable and sustain life processes as well as
those that occur in the non-living world and anywhere else in the universe—involve
changes in energy.
Thermodynamics is the study of energy changes

A system can be a whole
organism, a group of cells, or a set of substrates and products—whatever object or objects
are being studied. Surroundings are defined as everything in the universe outside of the system. In terms of thermodynamics, biological systems are considered to be open systems, meaning that the system and its surroundings can exchange matter and energy with each other. The laws of thermodynamics describe how a system can interact with its
surroundings and what can, and cannot, occur within a system.

The First Law of Thermodynamics:
Energy cannot be created or destroyed; it can only be transferred or transformed from one form to another and from one object to another. Thus, when a chemical reaction occurs and energy is released, some of the energy can be transformed into mechanical energy, such as the motion of a contracting muscle, and the rest can be transformed into heat or other forms of energy.

The Second Law of Thermodynamics:
Disorder (entropy) in the universe is continuously increasing; transformations proceed spontaneously to convert matter from a more ordered, but less stable form, to a less ordered, more stable form. (disorder is easy and is not done on purpose → organizing is done purposely
when organized it’s less stable since it’s not going to stay like that for long or requires lots of energy to stay like that whereas with disorder it can stay like that without doing anything so it’s stable) (According to the first thermodynamics law, the total amount of energy in the universe
remains constant. Despite this, however, the energy available to do work decreases as more
of it is progressively transformed into unusable heat. The second law of thermodynamics
concerns the transformation of potential energy into heat, or random molecular motion.
It states that the disorder in the universe—more formally called entropy—is continuously
increasing. Put more simply, disorder is more likely than order.) (When the universe
formed, it held all the potential energy it will ever have. It has become increasingly more
disordered ever since, with every energy exchange increasing the amount of entropy.)

Because organisms are highly ordered, it might seem that life is an exception to the laws
of thermodynamics. However, the second law applies only to closed systems. While they
are alive, organisms remain organized because they are not closed systems. They use inputs
of matter and energy to reduce randomness (decrease entropy) and thus stay alive. The
energy that keeps organisms alive comes ultimately from the Sun. That is, plants transform
light energy into the chemical bonds of carbohydrates, which humans and other organisms
temporarily store and later use as an energy source.

Second law of thermodynmaics: During each conversion, some energy dissipates into the environment as heat, and becomes unusable. Living cells unavoidably convert organized forms of energy to heat. Every energy transfer or transformation increases the entropy (disorder) of the universe.

Question 5

Biological Order and Disorder

Answer 5

Living systems:
-Increase the entropy of the universe
-Use energy to maintain order; free energy can do work under cellular conditions.

Free energy: portion of a system’s energy able to do work when temperature and pressure is uniform, as in a living cell; also refers to energy available to break and subsequently form other chemical bonds.

Gibbs’ free energy (G): in a cell; the energy contained in a molecule’s chemical bonds (constant T & P)

Change in free energy = ΔG

It takes energy to break the chemical bonds that hold atoms together. Heat, because it
increases the kinetic energy of atoms, makes it easier for the atoms to pull apart. Both
chemical bonding and heat have a significant influence on a molecule. Chemical bonding
reduces disorder; heat increases it. The net effect—the amount of energy actually available
to break and subsequently form other chemical bonds—is referred to as the free energy of
that molecule. In a more general sense, free energy is defined as the energy available to do
work in any system.
For a molecule within a cell, where pressure and volume usually do not change, the
free energy is denoted by the symbol G. G is equal to the energy contained in a molecule’s
chemical bonds, called enthalpy and designated H, together with the energy term related
to the degree of disorder in the system. This energy term is designated TS, where S is the
symbol for entropy and T is temperature. Thus:
G = H 2 TS
Chemical reactions break some bonds in the reactants and form new ones in the
products. As a result, reactions can produce changes in free energy. When a chemical
reaction occurs under conditions of constant temperature, pressure, and volume—as do
most biological reactions—the change in free energy (ΔG) is
ΔG = ΔH 2 TΔS

• Endergonic: any reaction requiring an input of energy
  -Exergonic: any reaction that releases free energy

Exergonic reactions:
- Reactants have more free energy than products
- Involve a net release of energy and/or an increase in entropy
- Occur spontaneously (without a net input of energy)
- (For other reactions, the ΔG is negative. In this case, the products of the reaction contain less free energy than the reactants. Thus, either the bond energy is lower, or the disorder is higher, or both. Such reactions tend to proceed spontaneously. These reactions release the excess free energy as heat and are said to be exergonic, which literally means “outward
energy.” Any chemical reaction tends to proceed spontaneously if the difference in disorder (TΔS) is greater than the difference in bond energies between reactants and products (ΔH).)

Endergonic reactions:
- Reactants have less free energy than products
- Involve a net input of energy and/or a decrease in entropy (so decrease in stability)
- Do not occur spontaneously
- (For some reactions, the ΔG is positive, which means that the products of the reaction contain more free energy than the reactants. Thus, the bond energy
(H) is higher, or the disorder (S) in the system is lower. Such reactions do not proceed spontaneously, because they require an input of energy. Any reaction that requires an input of energy is said to be endergonic, which literally means “inward energy.”)

Energy Coupling:
- Living organisms have the ability to couple exergonic and endergonic reactions
- Energy released by exergonic reactions is captured and used to make ATP from ADP and Pi
- ATP can be broken back down to ADP and Pi, releasing energy to power the cell’s endergonic reactions
- Energy is released from ATP when the terminal phosphate bond is broken (through hydrolysis)

A cell does three main kinds of work: Mechanical, transport and chemical
- Energy coupling is a key feature in the way cells manage their energy resources to do this work
- ATP powers cellular work by coupling exergonic reactions to endergonic reactions
- Releasing the third phosphate from ATP to make ADP generates energy (exergonic)
- Linking the phosphates together requires energy
- Catabolic pathways drive the regeneration of ATP from ADP and phosphate

Question 6

thermodynamic and metabolism

Answer 6

(similar to previous card)
In fact, most reactions require an input of energy to get started. This energy destabilizes existing chemical bonds and initiates the reaction. this input energy is called activation energy. An exergonic reaction may proceed very slowly if
the activation energy is quite large. One way that the activation energy of a reaction can be reduced is by using a catalyst. In metabolic pathways, biological catalysts—enzymes— decrease the activation energy of each reaction.
- In cells, energy from catabolic reactions is used to power anabolic reactions. The source of energy that links these sets of reactions is the molecule ATP, adenosine triphosphate. ATP is often called the energy currency of the cell, because so many cellular activities
depend on ATP. It is the major product of most catabolic pathways, and it is the major
source of energy for anabolic pathways.
Figure 3.6 shows the structure of ATP and the hydrolysis of the terminal (last)
phosphate group. The red tilde symbols (wavy lines) represent high-energy bonds that, when hydrolyzed, release energy. Each of the phosphate groups in an ATP molecule is negatively charged. The negative charges of the phosphate groups repel each other in
such a way that the phosphate groups strain away from each other like opposing teams in a tug-of-war contest. When one of the bonds between the phosphate groups is broken, ATP becomes ADP (adenosine diphosphate) plus an inorganic phosphate (Pi), and a large quantity of energy is released.

Cells use ATP to drive endergonic reactions. These reactions do not proceed spontaneously, because their products possess more free energy than their reactants. However, if the cleaving of ATP’s terminal high-energy bond releases more energy than the other reaction consumes, the two reactions can be coupled so that the energy released by the hydrolysis of ATP can be used to supply the endergonic reaction with energy. Coupled together, these reactions result in a net release of energy (−ΔG) and are therefore exergonic and proceed
spontaneously.
The use of ATP can be thought of as a cycle. Cells use exergonic reactions to provide the energy needed to synthesize ATP from ADP 1 Pi; they then use the hydrolysis of ATP to provide energy for endergonic reactions. Most cells typically have only a few seconds’ supply of ATP at any given time and continually produce more
from ADP and Pi.

Redox reactions are coupled reactions that play a key role in the flow of energy through
biological systems. Electrons that pass from one atom to another carry energy with them, so the reduced form of a molecule is always at a higher energy level than the oxidized form. Thus, electrons are said to carry reducing power. The amount of energy
they carry depends on the energy level they occupy in the atom donating the electrons. Electron carriers are compounds that pick up electrons from energy-rich compounds and then donate them to low-energy compounds. An electron carrier is recycled.
Two important electron carriers in metabolic reactions are NAD+ (nicotinamide
adenine dinucleotide) and FAD (flavin adenine dinucleotide). these electron carrier are used when creating atp in the ets

Question 7

how cells harvest chemical energy

Answer 7

glucose + oxygen –> carbon dioxide + water + ATP (energy)

cell matabolism involves glycolysis, aerobic cellular respiration (optimal o2 condition) and anaerobic cell repriation (low o2 condition)

Cellular metabolism how we harvest chemical energy
It consists of glycolysis, aerobic and anaerobic cellular respiration (depends on conditions → going from glucose to monosachardie reacts with o2 that is converted to energy where co2 and h2o is a byproduct and co2 is exhaled)

Question 8

Breathing and cellular respiration

Answer 8

sugar + o2 –> atp + co2 + H2o

Repriartion has to take place at the cellular level → u start by breathing bring o2 into ur lungs, then it goes under other processes to get the cell ?

muscle cells carry out cellular respiration

How our breathjing has to take place at a cellular level and the oxygen has ti do this because we need oxygen to go to our muscles because then the oxygen will help with our mobility

Question 9

efficency of cellular respiration

Answer 9

ellular Respiration uses oxygen and glucose to produce Carbon dioxide, water, and ATP.

Not that efficient → when u burn glucose it’s 100% efficient as the glucose is converted into light and heat energy → if we were to burn glucose in cellular respiration to lift weight, energy is released from the glucose banked in ATP, it’s inefficient as 40% is only directed to completing the task the other 60 is lost as heat, water loss production but mostly heat which is why we sweat, we produce energy in the form of sweat and heat → combustion of gasoline to move the car forward only 25 % relates to moving it, rest goes to the engine heating up and the sound coming fromthe car

Question 10

redox reaction in cellular respiration

Answer 10

gain or loss of e is often in the form of hydrogen

glucose losses hydrogen atoms to become co2 while o2 gains hydrogen atoms becoming h2o while energy/atp is also being produced

glucose gives off energy as it is oxidized –> Hydrogen is then passed to a coenzyme such as NAD+ (nicotinamide adenine dinucleotide). –> NAD+ and FAD (flavin adenine dinucleotide) are two important coenzymes. –> both receive hydrogen and become nadh + h and FADH2 –> NAD+ and FAD transfer high-energy electrons to the electron transport systems (ETS) during cell respiration. –> As the electrons move from carrier to carrier, energy is released in small quantities.

(The coenzyme is helpful as it work with fad → we need them because tehy work to transfer high energy e to the ets (improtant part of cellular respiration cause this is where u get more atp being produced, ex. U gotta spend money to make money, so u make atp to make even more atp (investing energy to get it started then it produces much more units of energy that we need but this all starts with the oxidation of glucose) in one step during cell respiration)

Question 11

Generation of atp

Answer 11

Two ways to generate ATP:
- Chemiosmosis: In chemiosmosis, cells use the energy released by “falling” electrons in the ETS to pump H+ ions across a membrane using an enzyme, ATP synthase.

• Substrate-Level Phosphorylation: ATP can also be made by transferring phosphate(that may come from food) groups from organic molecules to ADP

Question 12

general overview of cr

Answer 12

glucose undergoes glycolysis (the breaking of glucose) to form pyruvic acid
- with oxygen = aerobic –> goes under transition reaction, krebs cycle and gets and has a net production of 36 atp
- without oxygen = anaerobic –> goes under fermentation and has a net production of 2 atp

(Aerobic is ideal as it produces an efficient amount of atp
Fermentation isnt efficient and is slightly toxic
Human muscle cells also use fermentation. This occurs when muscle cells cannot get oxygen fast enough to meet their energy needs through aerobic respiration.
Humans undergo lactic acid fermentation when the body needs a lot of energy in a hurry. When you are sprinting full speed, your cells will only have enough ATP stored in them to last a few seconds. Once the stored ATP is used, your muscles will start producing ATP through lactic acid fermentation.)

Question 13

Glycolysis 1

Answer 13

first reaction in the metabolic pathway of cellular respiration

it takes places in the cytosol and it breaks down glucose into pyruvic acid or pyruvate acid

the glucose whihc is asymetrcial uses two atp, gets phosphorylates twice to become fructose with 2 phaspahets (symetrical) (2 phsopahte groups are tranferred to glucose via phosphorlation where atp is conevrted to adp and the product is fructose 1,6 bisphosphate). This fructose will get split/break/cleaves into DHAP and G3P which are isomers of eachother where DHAP will use an enzyme to convert into G3P. The G3P now gets phosphorylated into BPG with NAD which becomes NADH(x2)(attatches phosphate). The BPG converts into 3PG whihc produces 2 units of ATP (the phosphate transfered to adp creating atp) –> 3PG now undergoes a condensation reaction to become PEP and h2o is realesed. The PEP turns into pyruvate producing 2 atp (phosphtae transfered to adp making atp). The final products of glycolysis is 2 NADH and 2 ATP (net).

Question 14

Glycolysis 2 and Pyruvate oxidation

Answer 14

the glucose (6C) is split into 2 molecules of pyruvate (2 x 3C)
*Net production of ATP during glycolysis is 2 ATP
*Glycolysis is only around 2% efficient as there is still a lot of energy stored in pyruvate

pyruvic acid will now follow aerobic respiration metabolic pathway which includes transition reaction, krebs cycle and ets making 36atp if there enough oxygen. if there isnt enough or no oxygen then it undergoes fermentation, the anaerobic pathway which causes lactic acid, a toxic byproduct and only produces 2 atp.

in aerboic repriation after glyclysis, the pyruvic acid undergoes a transition reaction called pyruvate oxidation before it goes into the krebs cycle.

Pyruvate oxidation: Each pyruvic acid molecule is broken down to form 2 NADH, CO2 and a two-carbon acetyl group, acetyl CoA, a coenzyme which then enters the Krebs cycle.

Basically we take in nutrients, we break it down into glucose monomers, it undergoes glycolysis which creates 2 atp, it becomes pyruvate and nadh. pyruvate will undergo fermentation or it goes into the mitochondria undergoing pyruvate oxidation/transition reaction and becomes acetyl CoA which then will undergo the creb cycle producing 2atp and then the etc/s producing 26 atp as well as o2 and h2o.

Question 15

General overview of glycolysis

Answer 15

Step 1: ATP is used up and a
phosphate is added to glucose,
increasing the molecule’s energy.
In the first few steps of glycolysis, the
sugar molecule is energized, giving it
energy to start the glycolysis process.
The first 5 steps are called the
prepatory phase. Enzymes that use up or build ATP are often called kinases.

Step 2: Atoms are rearranged in the
glucose-6-phosphate molecule by the
enzyme to create a substrate
(fructose-6-phosphate) that the next
enzyme can use.

Step 3: ATP is used up and a
phosophate is added to
fructose-6-phosphate, creating a highly energized molecule called
fructose-1,6-bisphosphate. This
molecule is not stable and is easy to
“pull apart” in step 4. This step is the most important step in glycolysis because it is the rate limiting
step, the decision point. If the cell
decides to perform step 3 on a sugar
molecule, the rest of aerobic
respiration must happen afterwards.

Step 4: Fructose-1,6-bisphosphate is
broken apart into two smaller 3
carbon molecules, glyceraldehyde
3-phosphate and dihydroxyacetone
phosphate.

Step 5: The dihydroxyacetone
phosphate molecule’s atoms are
rearranged to create another
glyceraldehyde 3-phosphate, which is
the ideal substrate for the 6th enzyme. After step 5, because there are 2 three carbon sugars, each step happens twice, as shown with 2 arrows and 2 enzymes. Steps 6-10 are called the pay-off phase,
because the cell starts to harvest the
energy from the sugar. It stores the
energy in ATP.

Step 6: In this step, inorganic phosphate ions (phosphate groups not already attached to ATP) are added to the glyceraldehyde 3-phosphate molecules to create 1,3-bisphosphoglycerate. Also, some energy is released and stored
in an energy carrier molecule called
Nicotinamide Adenine Dinucleotide
(NAD). The energized form is called
NADH and the low energy form is
NAD+. These NADH molecules are
important later in aerobic respiration,
during the oxidative phosphorylation
process.

Step 7: In this step, high energy
phosphate groups are transferred to
ADP, creating the first 2 ATP
molecules to form during glycolysis.
1,3-bisphosphoglycerate becomes
glycerate 3-phosphate.

Step 8: In this step, the phosphate
group is rearranged to make the next
few reactions easier for the enzymes to perform. Glycerate 3-phosphate
becomes 2-phosphoglycerate.

Step 9: In this step, oxygen and
hydrogen (not shown) are rearranged
in the molecules to make the last step easier for the enzyme to perform. 2-phosphoglycerate becomes phosphoenolpyruvic acid (PEP).

Step 10: In this last step, high energy
phosphate groups are transferred to
ADP, creating the last 2 ATP
molecules to form during glycolysis.
Phosphoenolpyruvic acid becomes
pyruvate, the final sugar product of
glycolysis. Pyruvate is further processed and broken down in the Krebs Cycle (also called the Citric Acid Cycle).

Theres 10 steps in glycolysis. 6 c-c bonds are present in glucose. The two phases of glycolysis is prepatory phase (1-5) and payoff phase (6-10). 2 ATP is used up in the first phase while 4 ATP is built in the second phase. NADH is another molecule that stores energy harvested from the glucose and is involved in the payoff phase. Kinase eznymes are enxzymes that use up or build atp. In pyruvate molecule 3 c-c bonds exist. Glycolysis is an example of an enzymatic pathway as in each product t is a reactant for the next step in the pathway like a cellular assembly line.

Step 3 (phosphofructokinase’s reaction) is the decision point where the cell decides if it will carry out aerobic respiration to collect energy from that sugar molecule or not. Cells decide based on whether they already have enough ATP or not. If there is a lot of ATP around, the cell will not want to break down more sugar and will want to store the sugar
instead. ATP is an inhibitor of phosphofructokinase. ATP molecules can “stick” to the enzyme in allosteric sites (parts of the enzyme that are not directly involved in the chemical reaction) and cause the enzyme to stop “doing its job”, or catalyzing the reaction.

Other two possible “regulators” for phosphofructokinase: AMP and PEP. AMP is produced when the cell breaks down a lot of its ATP. The cell then breaks down a lot of ADP into AMP. AMP is often referred to as the cell’s “starvation signal”. High AMP would activate the phosphofructokinase as there is more energy/sugar needed since all of it has been broken down. PEP is produced at the end of step 9 in glycolysis. Since PEP is turned into pyruvate and creates 2 atp while doing this it means that if there is a high level of it lots of atp and sugar can be produced so it cause phosphofructokinase to slow down its reactions since there already is enough energy to be collected.

Question 16

Glycolysis review

Answer 16

Stages that occur in glycolysis:
It happens in the cytosol, anaerobic doesnt require oxygen, glucose (6c) broken down into 2 pyruvate molecules (3c), produces atp and nadh and the 10 reactions are divided into 2 phases glycolysis I and glycolysis II.

outline the key steps in glycolysis:
Glycolysis I is an energy investment. Involves 5 reactions. ATP helps power reactions in the cell by transferring its phosphate onto another substrate. Before any atp can be made, glucose needs to be activated by being phosphorylated by 2 atp molecules. Uses 2 atp: energy investment.

Glycolysis I:
- Glucose (phosphorylation - activation) glucose 6 phosphate (isomeraztion rearrangment) fructose 6 phosphate (phosphorylation activation) fructose 1,6 biphospahte (lysis cleavage) G3P and DHAP (isomerization rearrangement) 2 molecules of G3P

phosphorylation: glucose receives a phosphate from ATP to form glucose-6-phosphate
1 ATP used, 1 ADP produced
isomerization: glucose-6-phosphate rearranged to form fructose-6-phosphate
phosphorylation: fructose-6-phosphate receives a phosphate from another ATP to form fructose-1,6-bisphosphate
1 ATP used, 1 ADP produced
lysis: fructose-1,6-bisphosphate cleaved to form G3P and DHAP
isomerization: DHAP rearranged to form G3P
overall glycolysis I: glucose + 2 ATP 🡪 2 G3P + 2 ADP

Glycolysis II: energy payoff, 5 reactions, G3P are ready to release energy, ATP is made through substrate level phosphorylation: phosphate transferred directly form a molecule to aDP to form ATP, produces 4 atp and 2 NADH.
G3P (oxidation) 1,3 BPG (substrate level phosphorylation) 3PG (isomerzation) 2PG (oxidation) PEP (substrate level phosphorylation) pyruvate

oxidation: each G3P is oxidized by NAD+ and an inorganic phosphate is added (Pi) to form 1,3BPG
2 Pi and 2 NAD+ used, 2 NADH and 2 H+ produced
substrate-level phosphorylation: each 1,3BPG gives a phosphate to ADP to form 3PG and ATP
2 ADP used, 2 ATP produced
isomerization: each 3PG is rearranged to 2PG
oxidation: each 2PG is oxidized to form PEP
2 H2O produced (not counted overall)
substrate-level phosphorylation: each PEP gives a phosphate to ADP to form pyruvate and ATP
2 ADP used, 2 ATP produced
overall glycolysis II:
2 G3P + 4 ADP + 2 Pi + 2 NAD+ 🡪 2 pyruvate + 4 ATP + 2 NADH + 2 H+
overall glycolysis:
glucose + 2 ADP + 2 Pi + 2 NAD+ 🡪 2 pyruvate + 2 ATP + 2NADH + 2 H+

2 ATPs are used to prime glucose for splitting (glucose molecules are ‘phosphorylated’).
2 NADH are formed when G3P reduces NAD+ by adding an H.
4 ATP are formed by substrate-level phosphorylation:
Removing 2Pi from each 3 carbon intermediate
2 pyruvates are produced at the end of glycolysis.

identify the names of compounds formed in glycolysis:
G3P = glyceraldehyde 3-phosphate (G3P) molecules
DHAP = dihydroxide acidone phosphate
1,3 BPG = 1, 3 bi
3 PG - 3 phosphoglycerate
2 PG - 2 phosphoglycerate
PEP - phosphoenolpyruvate

identify the types of reactions that occur during glycolysis:
Phosphorylation, isomerization, lysis, oxidation, substrate level phosphorylation.

state the number of ATP/NADH used and produced in glycolysis:
2 ATP is used up, 4 ATP is produce and 2 NADH is produced in glycolysis.

state what steps are involved with ATP/NADH:
ATP is used in steps 1 and 3, NADH is produced in step 6 and ATP is produced in step 7 and 10.

Question 17

Krebs Cycle simple overview

Answer 17

recall: glycolysis occurs in the cytosol and it metabolzies glucose to yield 2 NADH, 2 ATP and 2 pyruvate. Pyruvate oxidation occurs in the mitochondrial matrix and it metabolizes the 2 pyruvate to yield 2 NADH, 2 CO2 and 2 Acetyl CoA.

Krebs cycle was named after hans adolf krebs (nobel winner) and it also sometimes called the citric acid cycle (CAC), it takes placed after pyruvate oxidation in the presence of oxygen so aerobic repiration/conditions

It occurs in mito matrix and it uses the 2 acetyl coa to make 2 atp, 6 NADH, 2 FADH2 and 4CO2

what happens in that the acetylcoa (2c) combines with (4c) oxalacetate to form (6c) citrate and becomes isomer isocitrate which decarboylzes into 2CO2 and oxidizes creating NADH twice becoming (4c) succinyl coA this becomes succinate (4c) as the GDP gets Pi added to become GTP which isomers or phospyls to ADP to become ATP and the succinate now dehydrate into fumarate (4c) while producing FADH2 and fumarate becomes (4c) oxaloacetate and produces NADH while doing that

so the final products were 2 FADH2, 2ATP and 6 NADH when u considered that it happened twice since there’s 2 acetyl coas

Question 18

Detailed steps of kreb cycle

Answer 18

in mitochondrial matrix
aerobic: requires oxygen
acetyl-CoA completely oxidized to produce CO2
also produces ATP, NADH and FADH2
8 steps
(Note, Two acetyl-Co A molecules enter, so the Krebs Cycle must happen twice for every one molecule of glucose that begins glycolysis.)

acetyl transfer, isomerization, oxidation + decarboxylation, oxidation + decarboxylation, CoA release + substrate-level, phosphorylation, oxidation, hydration, and last oxidation

(Oxidation is the loss of electrons during a reaction by a molecule, atom or ion
Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2)
H+ = Proton When the Hydrogen atom loses an electron all that is left is a proton. It becomes the positively charged hydrogen ion known as H+.)

1. acetyl transfer: each acetyl-CoA breaks: the CoA is recycled and the acetyl group (2C) joins with oxaloacetate (4C) to produce citrate (6C)
   - 1 water used (not counted in overall equation)
2. isomerization: each citrate is rearranged to form isocitrate
3. oxidation + decarboxylation: each isocitrate (6C) is oxidized by NAD+ and a carbon is released as CO2 to form α-ketoglutarate (5C)
   - 1 NAD+ used, 1 NADH, 1 H+ and 1 CO2 produced
4. oxidation + decarboxylation: each α-ketoglutarate (5C) is oxidized by NAD+, a carbon is released as CO2, and a CoA bonds to the compound to form succinyl-CoA (4C)
   - 1 NAD+ and 1 CoA used, 1 NADH, 1 H+ and 1 CO2 produced
5. substrate-level phosphorylation: each succinyl-CoA breaks: the CoA is recycled and succinate is left behind. The energy released is used to convert GDP and an inorganic phosphate (Pi) into GTP. GTP then phosphorylates ADP to create ATP.
   - 1 ADP and 1 Pi used, 1 ATP and 1 CoA produced
6. oxidation: each succinate is oxidized by FAD to form fumarate
   - 1 FAD used, 1 FADH2 produced
7. hydration: each fumarate has water added to form malate
   - 1 water used (not included in overall reaction)
8. oxidation: each malate is oxidized by NAD+ to form oxaloacetate
   - 1 NAD+ used, 1 NADH and 1 H+ produced

overall citric acid cycle for 1 acetyl-CoA:
1 acetyl-CoA + 3 NAD+ + FAD + ADP + Pi –> 2 CO2 + 3 NADH + 3 H+ + FADH2 + ATP + CoA

overall citric acid cycle for 2 acetyl-CoA (1 glucose):
2 acetyl-CoA + 6 NAD+ + 2 FAD + 2 ADP + 2 Pi –> 4 CO2 + 6 NADH + 6 H+ + 2 FADH2 + 2 ATP + 2 CoA

In step 1, acetyl-CoA combines with oxaloacetate to form citrate. NAD+ is reduced to NADH in steps 3, 4 and 8. FAD is reduced to FADH2 in step 6. ATP is formed in step 5 by substrate-level phosphorylation. In step 8, oxaloacetate is formed, which is used as a reactant in step 1. CO2 is released in steps 3 and 4

By the end of the Citric Acid Cycle, the original glucose molecule has been completely dismantled. Original carbon and oxygen atoms are in the form of CO2 and released as waste. All that remains is the hydrogen which are now carried by NADH and FDH2 - these electrons still hold large amount of chemical potential energy.

Question 19

General Ideas of Pyruvate oxidation and Krebs cycle

Answer 19

The goal of these two processes are to break down pyruvate and collect the energy released from the carbon-carbon bonds. This energy is stored in energy-carrier molecules called nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). The low energy forms of these are called NAD+ and FAD and the high energy forms are called NADH and FADH2.

Both the pyruvate oxidation step and the citric acid cycle take place in the mitochondrial matrix. Pyruvate is a product of glycolysis. Because glycolysis happens in the cytosol of the cell, pyruvate has to be transported inside the mitochondria through active transport.

In pyruvate oxidation, pyruvate is
transformed into acetyl-CoA. CoA is an abbreviation for coenzyme A. Coenzymes are large non-protein molecules that attach to enzymes and help them function. Carbon dioxide is released and one NADH is also produced. (for the 2 pyruvates that are produced from one glucose, 2 acetyl coa, 2 nadh and 2 co2 are technically produced)

In the first step of the citric acid cycle (see your diagram), acetyl-CoA reacts with oxaloacetate to form citrate. (coa is removed)

In steps 2-3, citrate is transformed into aconitate and then into isocitrate. Citrate and isocitrate are actually isomers; they look almost exactly alike except some of their oxygen atoms are rearranged.

In step 4, isocitrate is broken down into alpha-ketoglutarate and carbon dioxide. Energy from this reaction is released and collected by NAD+ to form NADH, an energy carrier molecule.

In step 5, a coenzyme A attaches to alpha-ketoglutarate and it is broken down into carbon dioxide and succinyl-CoA. In this step, energy again is released and collected by NAD+ to form another NADH. (sometimes step 4 and 5 are combined so it seems like isocitrate becomes succinyl-coA in one step and 2 NADH are produced)

In step 6, succinyl-CoA’s oxygen atoms are rearranged and coenzyme A is released to form succinate. This process releases energy and the energy is stored in a GTP (Guanosine triphosphate). This GTP (Guanosine triphosphate) is converted to ATP, the main energy-storage molecule or “battery” in the cell.(technically GDP to GTP and then GTP to ADP to ATP)

In step 7, succinate releases two hydrogens, forms a double bond between two of its carbons, and releases more energy to form fumarate. This energy is stored in FADH2, another energy carrier molecule.

In step 8, fumarate reacts with water to form malate. In step 9, malate’s oxygen atoms are rearranged to form
oxaloacetate. This reaction releases more energy, which is collected and used to form NADH.

Overall reaction of pyruvate oxidation of one pyruvate:
1 pyruvate + 1 NAD+ + CoA –> 1 Co2 + 1 NADH + 1 acetyl CoA

Overall reaction of pyruvate oxidation for one glucose:
2 pyruvate + 2NAD+ + 2 CoA –> 2Co2 + 2NADH + 2 acetyl CoA

Overall reaction of citric acid cycle for one acetylcoa:
1 acetyl CoA + 3NAD+ + 1GDP + Pi + FAD –> 1CoA + 2Co2 + 3NADH + 1FADH + 1 GTP

Overall reaction of cyrtic acid cycle for one glucose:
2 Acetyl CoA + 6NAD+ + 2GDP + 2Pi + 2FAD –> 2 CoA + 6 NADH + 2 GTP + 2 FADH

Overall reaction of glycolysis:
1 glucose + 2ADP + 2Pi + 2 NAD+ –> 2 Pyruvate + 2 ATP + 2 NADH ( + 2H+?)

When C is removed its called decarboxylation and the byproduct is usually CO2 (known as released as waste)

Hydrogen is removed by NAD+ or FAD

PRODUCTS OF KREB CYCLE:
CO2 is relased as waste
NADH and FADH2 move to the next stage of cellular respiration
Energy is released in form of ATP. A glucose molecule produces 2 molecules of ATP (from GDP/GTP) because two molecules of pyruvate are created from each molecule of glucose.

Question 20

ETS 1

Answer 20

The Electron Transport Chain, Oxidative Phosphorylation, and Chemiosmosis. –> end of aerobic stage. ets and oxidtative phorphyrlation and chemiosism are last steps of formation of atp → we start with glucose, krebs had side products, which all comes down to here → weve spent a couple of atp and gotten a few, our net is small but in this process we will get lots of a atp

Glycolysis: 2 NADH + 2 ATP
Pyruvate Oxidation: 2 NADH
Krebs Cycle: 6 NADH, 2 FADH2, 2 ATP

The NADHs and FADH2s are what we are interested in for the Electron Transport Chain. Electrons donated by them are transported through the chain, which provides energy for oxidative phosphorylation

The ets is a chain of protein complexes embedded in the inner mitochondrial membrane; site of oxidative phosphorylation –> produces many ATP. It transports e- by oxidizing NADH and FADH2; pumps H+ ions (protons) into intermembrane space –> creates a gradient

Key components are NADH dehydrogenase, Ubiquinone (Q), Cytochrome b-c1, Cytochrome c, Cytochrome oxidase

NADH produced in the cytoplasm by glycolysis: diffuses from the outer mitochondrial membrane to the intermembrane space, and then into the matrix. NADH produced from Krebs cycle: Already in the matrix

Question 21

ETS 2

Answer 21

(I) NADH dehydrogenase:
- NADH dehydrogenase oxidizes NADH back to NAD+
(NADH + H+ 🡪 NAD+ + 2H+ + 2e-)
- 2e- from NADH are passed to electron acceptors in ETS one at a time; then passed to ubiquinone (Q)
- H+ ions do not go with the 2e-; remain in solution in the matrix until after 2e- have completed passage through EACH complex of ETC; then they are actively pumped out of matrix and into the intermembrane space –> creates H+ gradient

(II) Ubiquinone (Q)
- A mobile electron carrier (carries e-)
- RECALL: FADH2 from Krebs is already in the matrix
- FADH2 embeds itself into the inner mitochondrial membrane and becomes oxidized:
(FADH2 🡪 FAD + 2e- )
- 2e- attach to Q (skips NADH hydrogenase) and move through remaining complexes in ETC

(III) cytochrome bc1
- Contains cytochrome b, cytochrome c1, and FeS (iron sulfide) proteins
- Q passes 2e- to cytochrome bc1; the energy generated from this passage actively pumps another H+ ion from the matrix into the intermembrane space

Cytochrome C (C)
- Another mobile electron carrier like Q that transports electrons from cytochrome bc1 to cytochrome oxidase complex

(IV) Cytochrome Oxidase Complex
- This is the end of the line for electrons from NADH and FADH2
- Oxygen breathed in is reduced and combines with these electrons to form WATER

For each glucose molecule that enters cellular respiration, chemiosmosis produces up to 38 ATP. (usually between 34-36 tho)

CHEMIOSMOSIS:
- Energy from reduced NADH and FADH2 produces an electrochemical H+ ion gradient in the intermembrane space
- Build up of positive charges in the intermembrane space relative to the matrix
- Electrical potential energy of the positive charges is converted to chemical potential energy of ATP by ATP synthase when H+ ions pass through the inner mitochondrial membrane via ATP synthase
- As H+ moves through the ATP synthase complex, the energy phosphorylates ADP to ATP

YIELD OF ATP = 36 or 38
- For each pair of e- from NADH or FADH2 that pass through one H+ pump, one ATP molecule can be formed. Therefore: 2e- from NADH go through 3 H+ pumps = 3 ATP. 2e- from FADH2 go through 2 H+ pumps(skipped dehydrogenase) = 2 ATP

Recall: Products from Processes
- Glycolysis: 2 NADH –> 4 or 6 ATP** (23)
- Pyruvate Oxidation: 2 NADH –> 6 ATP (23)
Krebs Cycle: 6 NADH, 2 FADH2 –> 18 ATP, 4 ATP(63 & 22)
Glycolysis and Krebs both produce 2 ATP each
* *Mitochondrial membrane is impermeable to NADH made in cytoplasm; 2e- need to be shuttled to either FAD or NAD+ molecule –> result is either 4 or 6 ATP

Question 22

Aerobic Respiration Overview

Answer 22

Cellular respiration includes the catabolic pathways that break down energy-rich compounds to produce ATP. Aerobic respiration refers to those pathways that require oxygen in order to proceed. The following summary reaction for this process represents more than two dozen reactions that take place in different parts of the cell.
C6H12O6(s) + 6O2(g) –> 6CO2(g) _ 6H2O(l) + energy

Although part of aerobic respiration, the first pathway, glycolysis, is not truly aerobic.
Glycolysis can proceed with or without oxygen. However, the products of glycolysis are
the starting materials for the metabolic pathways that follow, and they require oxygen.

Glycolysis occurs within the cytoplasm of cells. The starting material for glycolysis is glucose, a six-carbon sugar. Each glucose molecule is broken down, through a series of reactions, into two three-carbon compounds. Each of these compounds is converted into a three-carbon pyruvate molecule. Thus, the end products of glycolysis include two molecules of pyruvate for each molecule of glucose that enters glycolysis. The glycolytic pathway also converts two molecules of NAD+ into two molecules of NADH. The breakdown of glucose into pyruvate includes two reactions that consume ATP, as well as two reactions that produce ATP. Overall, the process consumes two molecules of ATP and produces four molecules of ATP. Thus, this pathway is responsible for a net production of two ATP molecules.
At various steps in the glycolytic pathway, a phosphate group is removed from a substrate molecule and combined with an ADP molecule to form ATP. This process is called substrate level phosphorylation. (Phosphorylation refers to any process that involves the combining of phosphate to an organic compound.)
When oxygen is available, pyruvate from glycolysis is transported across the outer and inner mitochondrial membranes into the mitochondrial matrix. There, the three-carbon pyruvate molecule undergoes oxidation. This produces a two-carbon molecule called acetyl-coenzyme A, abbreviated as acetyl-CoA, and releases one carbon atom in the form of carbon dioxide. In the process, one NAD+ molecule is reduced to form NADH. Since glycolysis produces two pyruvate molecules, pyruvate oxidation actually releases two molecules of carbon dioxide and reduces two molecules of NAD+ to form two molecules of NADH.
Each acetyl-CoA molecule then enters the Krebs cycle, which is also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. Tricarboxylic acid is a general name referring to an organic acid with three carboxyl groups. Citric acid is one example of a tricarboxylic acid. At physiological pH, citric acid exists in its ionized form, called citrate. Acetyl CoA combines with a four-carbon molecule in the Krebs cycle to form the six-carbon molecule, citrate. In each round of the Krebs cycle, one ATP molecule is formed, three NAD+ molecules are reduced to form three molecules of NADH, and one FAD molecule is reduced to form one molecule of FADH2. Since two molecules of acetyl CoA are produced for every molecule of glucose that enters glycolysis, the total yield from the Krebs cycle is two ATP molecules, six NADH molecules, and two FADH2 molecules.
The substrates, products, and enzymes of the Krebs cycle are in solution in the mitochondrial matrix.
The reduced NADH and FADH2 molecules diffuse to specific locations on the inner membrane of the mitochondrion and donate their electrons to a series of electron carriers that are embedded in the inner mitochondrial membrane. As each electron carrier passes an electron to the next carrier, some energy is released. This energy is used to pump protons, H+, across the inner mitochondrial membrane into the intermembrane space. This creates a proton gradient across the inner mitochondrial membrane, which provides the energy for the enzyme ATP synthase to phosphorylate (add Pi to) ADP molecules to make ATP.
Because this energy comes from the flow of electrons from NADH and FADH2 to oxygen, this process is called oxidative phosphorylation.
A maximum of 38 molecules of ATP can be generated by the breakdown of one molecule of glucose through the overall process of aerobic respiration. This includes ATP generated directly by glycolysis and the Krebs cycle, ATP generated from the two molecules of NADH produced during glycolysis, and ATP produced through oxidative phosphorylation, from reducing power generated during pyruvate oxidation and the Krebs cycle.

Although 36 or 38 ATP molecules per glucose molecule are theoretically possible,
experimental observations of the actual number of ATP molecules per glucose molecule are
much lower. There are several reasons to account for these lower values.
* Some protons leak through the inner mitochondrial membrane without passing through
an ATP synthase complex.
* Some of the energy from the hydrogen ion gradient in the mitochondria is used to
transport pyruvate molecules generated during glycolysis from the cytoplasm into the
mitochondria.
* Some energy is used to transport ATP out of the mitochondria for use in the cytoplasm.
Experimentally measured values are closer to 30 to 32 molecules of ATP produced per
glucose molecule.

most of a healthy diet is used for energy. Carbohydrates other than glucose, as well as fats and
proteins, are used for energy. Most carbohydrates can be broken down and converted into glucose. After the amino group has been removed from some amino acids, the remainder of the molecule is identical to some intermediate in either glycolysis or the Krebs cycle. Fat molecules are broken down into glycerol
and fatty acids. Glycerol can be converted into G3P, one of the intermediates in glycolysis. Fatty acids are transported into the mitochondria, where carbon atoms are removed two at a time and each two-carbon unit becomes an acetyl-CoA molecule, ready to enter the Krebs cycle.

How does the cell
determine and control the rate at which to generate ATP? The answer is feedback control.
- The enzyme phosphofructokinase is the main control point in glycolysis.
Phosphofructokinase has an allosteric binding site for ATP. Thus, when the cell has
sufficient ATP to supply energy for the endergonic reactions taking place at a given time, any excess ATP binds to the allosteric site of phosphofructokinase and inhibits the enzyme. Citrate, one of the intermediates in the Krebs cycle, can also inhibit phosphofructokinase. Thus, if there is an accumulation of citrate, pyruvate from glycolysis is not broken down into acetyl-CoA until some of the citrate is used up. In contrast, high levels of ADP activate phosphofructokinase.
- A second important control site in aerobic catabolic pathways is the conversion of pyruvate into acetyl-CoA and carbon dioxide. The enzyme that catalyzes this reaction, pyruvate dehydrogenase, is inhibited by excess NADH. Several Krebs cycle enzymes are also inhibited by excess ATP, NADH, and acetyl-CoA. When all of these control mechanisms are working together, the level of ATP remains constant within the cell.

Question 23

General Review Questions of the processes

Answer 23

In substrate-level phosphorylation, ATP is formed form transferring a phosphate group to ADP. In oxidative phosphorylation, the oxidation of NADH and FADH2 by the electron transport system is coupled with the synthesis of ATP by phosphorylation of ADP. (Substrate level phosphorylation is the conversion of ATP to ADP or vice versa on an enzyme. Oxidative phosphorylation is the use of electron transport chains to generate ATP chemiosmotically.)

The main function of glycolysis is to break down glucose in to 2 pyruvate molecules and generate side products like ATP and NADH. Water also is formed but not really counted in the equation. The role of the Krebs Cycle is to oxidize acetyl COA to Co2, regenerates a compound that connects to acetyl CoA so that the cycle can continue and create ATP, FADH2 and NADH. The side products of the Krebs Cycle are much more important as they actually move on to the next stage of respiration.

Why is oxidative phosphorylation an important process in aerobic respiration?
It effectively converts the energy stored in NADH and FADH2 to energy in the form of ATP. By oxidizing these two energy-rich compounds, it also forms NAD+ and FAD which are needed by the Krebs cycle, which will reduce them again while oxidizing carbon. Oxidative phosphorylation actually allows for the most ATP/energy to actually be produced.

The ETS is a series of e-carriers and proteins that are embedded in the inner membrane of the mitochondria. E- donated by NADH and FADH2 are transported through this chain which provides the energy needed for oxidative phosphorylation.

Chemiosomis is the process that uses energy in the hydrogen ion/proton gradient that was formed across the inner mitochondrial membrane by the ets/oxidative phosphorylation to drive the phosphorylation of ADP to form ATP. ATP synthase will catalyze the phosphorylation of ADP and most of the energy of cellular respiration is created by this.

The Krebs cycle requires NAD+ and FADH+ to reduce pyruvate. If there is no oxygen, the electron transport chain does not pass electrons to it to produce water. This means that electrons are not taken from the NADH and FADH2, and therefore NAD+ and FADH+ are not available.

If the electron transport chain is inhibited, very little ATP is produced, and human metabolism would not have enough energy to continue.

Question 24

Cell Respiration Summary

Answer 24

Cell respiration supplies energy for the functions of life. Cell respiration is the controlled release of energy from organic compounds to produce ATP.

The organic compounds used for cellular respiration are mostly glucose and fatty acids… but sometimes proteins.

Net equation for cellular reprition is glucose + 602 –> 6CO2 + 6H2O and energy (glucose is the organic molecule used to make atp, cells make more atp when oxygen is available, co2 is released as waste, water is a final product of preparation and atp is the energy currency of the cells)

In cells, energy is transferred in the form of adenosine triphosphate, ATP, which is immediately available for use. Cells will continuously produce and consume ATP. ATP is produced by the phosphorylation of ADP. Phosphorylation is the addition of a phosphate group to an organic molecule, either from inorganic (Pi) or organic sources.

Phosphorylation refers to the chemical reactions that make ATP. Phosphorylation takes place in two different kinds of reactions in cells:
Substrate-Level Phosphorylation and Oxidative Phosphorylation

Substrate-level phosphorylation: The formation of ATP in the cytoplasm occurs by substrate-level phosphorylation. Energy from a high-energy substrate (food molecule) is used to transfer a phosphate group to ADP to form ATP.

Oxidative phosphorylation: links an electron transport system, which creates a proton gradient, with ATP synthase, an enzyme that is activated by protons flowing through it, down the gradient. Chemiosmosis is a process that generates ATP by the movement of hydrogen ions across a biological membrane down an electrochemical (proton/concentration) gradient. In cell respiration, the gradient forms due to movement of electrons through the electron transport chain. In photosynthesis, the gradient forms due to electron transport and the photolysis of water. Oxidative phosphorylation occurs in mitochondria during the cell respiration. Electrons move by a series of redox reactions from one carrier protein to another along the inner membrane. This provides the energy to pump protons (H+) from the matrix to the intermembrane space, building up a concentration gradient. Protons flow back to the matrix by facilitated diffusion through the enzyme ATP synthase, which catalyzes phosphorylation of ADP. Photophosphorylation occurs in chloroplasts in the first stage of photosynthesis. Sunlight energy is used to pump hydrogen ions into the thylakoids. This creates a concentration gradient between the thylakoid and the stroma. Protons flow back to the stroma by facilitated diffusion through the enzyme ATP synthase, which catalyzes phosphorylation of ADP.

ATP is too unstable to be stored by cells. Instead, organisms store energy in polysaccharides and lipids. ATP is used for many things in the cell like active transport, DNA replication, muscle contraction, protein synthesis and cell signalling.

All of the processes that use ATP also generate heat. This means eventually, all energy becomes heat. This heat energy may be used to raise the organism’s body temperature, but is eventually lost to the environment.

Enzymes are used in metabolic pathways and cycles, which break down the release of energy from glucose and other food molecules into multiple small steps. Enzyme-catalyzed reactions are controlled by end-product inhibition.

Anaerobic cell respiration gives a small yield of ATP from glucose.

All cellular preparation begins with glycolysis. Glycolysis = “splitting glucose”. Glycolysis is an anaerobic process that occurs in the cytoplasm of all cells. . It is a multi-step pathway that produces 2 ATP and 2 molecules of pyruvate. And 2 molecules of NADH and H+

What happens to pyruvate in cells depends on the availability of oxygen: If sufficient oxygen is available, pyruvate is further broken down by Krebs cycle and the electron transport chain. If there is insufficient oxygen, a fermentation pathway allows glycolysis to continue forming ATP.

Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose. When cells have lots of oxygen available, pyruvate formed by glycolysis enters the mitochondria for aerobic respiration. Aerobic respiration consists of two processes in cells: Krebs cycle (a.k.a. citric acid cycle) produces carbon dioxide (waste) and a small amount of ATP. The electron transport chain (ETC) uses electrons released by glycolysis and Krebs cycle to generate a large amount of ATP.

Oxidation: addition of oxygen, removal of hydrogen, loss of e-, results in c-o bonds, and release of energy (lower potential energy). An oxidizing agent is a substance that oxidizes something else. Oxidizing agents give oxygen to another substance or remove hydrogen from it

Reduction: removal of oxygen, addition of hydrogen, gain of e-, reulst in many c-h bonds and uptake of energy (higher potential energy). A reducing agent is a substance that reduces something else. Reducing agents remove oxygen from another substance or give hydrogen to it.

During cellular respiration, the coenzyme NAD and FAD accepts hydrogen ions (and electrons), becoming reduced.

Thermodynamics:
- 1st Law: Energy cannot be created or destroyed. It can be converted from one form to another. The sum of the energy before the conversion is equal to the sum of the energy after the conversion.
- 2nd Law: During changes from one form of energy to another, some usable energy dissipates, usually as heat. The amount of usable energy therefore decreases.

In cells, energy is transferred in the form of adenosine triphosphate, ATP. Cells continuously produce & consume ATP.

Question 25

Anaerobic Respiration

Answer 25

Some organisms live in anoxic environments and thus cannot use oxygen as their final electron acceptor. Instead, they use inorganic compounds such as sulfate, nitrate, or carbon dioxide as electron acceptors. They are said to carry out anaerobic respiration.
In some organisms, anaerobic respiration is similar to aerobic respiration. For example, a few bacteria, including E. coli, carry out aerobic respiration when oxygen is available. When oxygen is not available but nitrate is, they synthesize an enzyme called nitrate reductase, which can accept electrons from the electron transport chain and pass them to nitrate according to the following equation: NO3-(aq) + 2e‒ + 2H+ → NO2‒(aq) + H2O(l)
Other organisms, such as methanogens, have different metabolic pathways. However, they use electron transport chains and generate hydrogen ion gradients that provide energy for phosphorylation. They use hydrogen that is synthesized by other organisms as an energy source and carbon dioxide as an electron acceptor. The summary equation for their metabolism is: 4H2(aq) + CO2(aq) → CH4(g) + 2H2O()
Some methanogens grow in swamps and marshes and are responsible for marsh gas, which is methane. Some of the prokaryotes that live in the stomachs of cows and other ruminants are methanogens, which are major sources of methane released into the environment.

Question 26

Fermentation

Answer 26

Fermentation allows the production of a small amount of ATP without oxygen. If no oxygen is available, cells can obtain energy through the process of anaerobic respiration.

A common anaerobic process is fermentation. Fermentation is not an efficient process and produces far fewer ATP molecules than aerobic respiration.

Many single-celled organisms such as yeasts and some bacteria, use only glycolysis for energy. Multicellular organisms use glycolysis as the first step in aerobic metabolism. During intense exercise, however, oxygen cannot be delivered to muscle cells rapidly
enough to supply the energy needs of the cells, so they rely on glycolysis for energy. The NADH that is reduced during glycolysis cannot be reoxidized by electron transport as fast as it is being reduced, and thus muscle cells will run out of oxidized NAD+ and glycolysis will cease unless another pathway is available. Different organisms and cell types have several different ways to reoxidize the reduced NADH, usually by reducing an organic molecule. These processes are called fermentation. Fermentation is much less efficient at supplying energy than aerobic respiration, because fermentation only produces the amount of ATP that is generated in glycolysis. Two common pathways are lactate fermentation and ethanol fermentation,

There are two primary fermentation processes: Lactic Acid Fermentation and Alcohol Fermentation

Occurs in the absence of O2 or insufficient O2. Requires NADH generated by glycolysis. Happens in the cytosol

What does it do?
- Yeasts convert sugar into carbon dioxide and ethanol (C6H12O6 🡪 2CO2 + 2CH3CH2OH)
- Muscle cells produce lactic acid from reduction of pyruvate (CH3COCOO− + 2H🡪 C3H6O3)

Only a few ATP are produced per glucose

Lactic acid fermentation: occurs when oxygen is not available. Example: in muscle tissues during rapid and vigorous exercise, muscle cells may become depleted of oxygen. They then switch from respiration to fermentation. In muscle cells under low O2 conditions, pyruvic acid formed during glycolysis is broken down to lactic acid and NAD+, and energy is released to form ATP.
Glucose → Pyruvic acid → Lactic acid + NAD+ + E

(The pyruvate generated by glycolysis reacts with NADH to reoxidize it to NAD+. In the reaction, pyruvate is converted into lactic acid. The reoxidized NAD+ allows glycolysis to continue. The lactate that is formed in bacteria is secreted into the surrounding medium, causing it to become acidic. The lactate that is generated in muscles must be reoxidized to protect the tissues from the acidic environment. Oxygen is ultimately needed to allow the lactate to return to the
oxidative pathways to be metabolized. The amount of oxygen required to eliminate the lactate is called the oxygen debt. The lactate produced in muscle cells is transported out of the cells into the bloodstream. there is evidence that the lactate is taken up by resting muscle cells. Some of the lactate is
converted back into pyruvate and oxidized, while some is converted into glycogen, which is stored in the muscle.

(as soon as u stop the strenuous activity adn rest your breathing and heart beat come back to normal and the oxygen demands can be met)

Lactic acid fermentation temporarily replaces aerobic respiration so that the cell can have a continual source of energy, even in the absence of oxygen or low oxygen. This shift is only temporary because cells need oxygen for sustained activity. When sufficient oxygen levels return, aerobic respiration resumes and removes the lactic acid build-up. (reps and stuff gets easier after training is because u build up ur body to that point where u delay lactic acid fermentation or anaerobic respiration due to ur increased endurance). Lactic acid that builds up in tissue causes a burning, painful sensation.

Alcohol Fermentation:
occurs in yeasts and some bacteria, often even when oxygen is present (preferred method of metabolism). Pyruvic acid formed during glycolysis is broken down to alcohol, CO2, and energy, which is used to form ATP. Glucose → Pyruvic acid → alcohol + CO2+ energy (in form of atp)

Yeast and some bacteria are able to function aerobically as well as anaerobically. These organisms are called facultative anaerobes. When they function anaerobically, they convert pyruvate to ethanol and carbon dioxide through ethanol fermentation.

Fermentation by brewer’s yeast (Saccharomyces cerevisiae) is used in industry to manufacture baked goods and alcoholic beverages. When used in brewing, a variety of
products can be made, depending on the substance being fermented, the variety of yeast used, and whether carbon dioxide is allowed to escape during the process. For example, yeast fermentation may be used to produce wine or champagne from grapes; a syrupy
drink, called mead, from honey; or cider from apples. Beer is brewed by fermenting sugars in grain such as barley, rice, or corn.

Fermentation has commercial uses –> () will ferment with other stuff to form certain products. ex. yogurt (lactobacillus)

Question 27

Extra Fermantion Info

Answer 27

Depending on the organism, fermentation can yield other substances besides lactate and ethanol.
Two other examples of fermentation products, acetone and butanol, were essential during World War I. The British needed butanol to make artificial rubber for tires and machinery; acetone was needed to make a smokeless gunpowder called cordite. When war broke out in 1917, the demand for acetone was great. A swift and efficient means for producing the chemical was needed. In 1915, Chaim Weizmann, a chemist, had developed a fermentation process using the anaerobic bacterium Clostridium acetobutylicum. Through this process, Weizmann converted 100 tonnes of molasses or grain into 12 tonnes of acetone and 24 tonnes of butanol. For the war effort, Weizmann modified the technique for large-scale production. Today, both acetone and butanol are produced more economically from petrochemicals.

Glucose is the main fuel for many organisms. However, much of the chemical energy of glucose remains in the compounds that form after glycolysis is complete. The process of fermentation does not remove much of this chemical energy. Therefore, the products of fermentation can still be used for fuel.
In organisms that carry out ethanol fermentation, the ethanol they produce is released as a waste product.
However, humans learned long ago that this “waste” can be burned. Ethanol was a common lamp fuel during the 1800s, and it was used for early internal combustion engines in cars and other machinery.
Historically, because gasoline costs less to produce than ethanol, the use of ethanol was limited to small-scale, specialized applications.
This situation changed in the late 1970s. At that time, rising oil prices, dwindling petroleum reserves, and environmental concerns caused some governments to invest in alternative energy resources such as ethanol fuels. When gas prices rise, some of these alternative resources become commercially viable sources of fuel. In cars, the use of a gasoline-ethanol fuel mixture has become common. Cars manufactured after 1980 can use this fuel mixture, called E-10, without any engine modification. Auto companies also design engines that can use fuels with ethanol percentages that are much higher than the 10 percent in gasohol.

In Canada, the most common source of ethanol is the fermentation of corn and wheat. First the grain is ground into a meal. Then it is mixed with water to form a slurry called “mash.” Enzymes added to the mash convert the starches into glucose. The mash is heated to destroy any bacteria, then cooled and placed in fermenters. In the fermenters, yeast is added to the mash. The yeast grows on the glucose under anaerobic conditions and releases the end products, ethanol and carbon dioxide. When the fermentation is complete, the resulting product, called “beer,” is approximately 10 percent ethanol and 90 percent water. Distilling the “beer” to eliminate as much of the water as possible yields nearly pure ethanol. A small amount of gasoline is added to make the ethanol unfit for human consumption. The solid residues from the grain and yeast are dried to produce a vitamin- and protein-rich product called Distiller’s Dried Grains and Solubles (DDGS) used as livestock feed.

Some single-celled organisms that live in conditions of very low oxygen can carry out anaerobic respiration by using an electron acceptor other than oxygen.
Some single-celled organisms and, during extreme exertion, some muscle cells, use only glycolysis for energy in a process called fermentation.
In lactate fermentation, pyruvate oxidizes NADH back to NAD+ and, in the process, is converted into lactate. In single-celled organisms, the lactate is released to the surroundings and in muscle cells, it is released into the bloodstream where it is carried to resting muscle cells and oxidized or converted to glycogen for storage.
In ethanol fermentation, pyruvate is converted into a two-carbon compound, acetaldehyde, and carbon dioxide. The acetaldehyde reoxidizes the NADH back to NAD+ for reuse and becomes ethanol.
Alcohol fermentation is a useful industrial process, used to generate ethanol for fuel. It is also the same process by which alcoholic beverages are produced.

Question 28

General Anaerobic Repriation notes

Answer 28

Anaerobic respiration is a metabolic pathway in which an inorganic molecule other than o2 is used as a final electron acceptor during the chemiosmotic synthesis of ATP. It occurs in the cytosol of bacteria, yeast and animal cells in the process of fermentation.

Fermentation is a form of anaerobic respiration. During anaerobic respiration, the final electron acceptor in bacteria can be nitrate or co2 but in fermentation NAD+ is regenerated by oxidizing NADH through an alternate method and there is no electron transport system involved.

Fermentation is less sufficient at supplying energy compared to aerobic respiration as it produces much less ATP. Since the ETC is where most ATP is produced in aerobic respiration and fermentation skips/doesnt go to the ETC as there is no oxygen to drive it, less ATP is produced. In fermentation all the energy comes from glycolysis and glucose can’t be completely oxidized.

Building up anaerobic threshold: It’s important to do this because when lactate fermentation occurs in the muscle cells, lactate acid will build up in the tissue which causes a buring and painful sensation which can last a while/ you need more time to recover and get the lactate acid out of the tissue.

Anaerobic and glycolysis: Both require NAD+ as an oxidizing agent, include the production of pyruvate, and don’t require oxygen. Glycolysis stops at the production of pyruvate. Anaerobic processes regenerate NAD+ but glycolysis itself does not. Anaerobic processes use electron acceptor other than oxygen to generate NAD+. (glycolysis is needed to actually allow anaerobic respiration to occur)

Question 29

Fermentation/Anaerobic Pathways Summary

Answer 29

If no oxygen is available, cells can obtain energy through the process of anaerobic respiration.

A common anaerobic process is fermentation. Fermentation is not an efficient process and produces far fewer ATP molecules than aerobic respiration.

There are two primary fermentation processes: Lactic Acid Fermentation
& Alcohol Fermentation

Fermentation allows the regeneration of NAD+ so that we can keep performing (NADH to NAD+). Start with glycolysis. Now we need the step to regenerate NAD+ (2 pyruvates will yield lactate) Lactate product - lactic acid

Lactic Acid Fermentation: occurs when oxygen is not available. in muscle tissues during rapid and vigorous exercise, muscle cells may become depleted of oxygen. They then switch from respiration to fermentation. Pyruvic acid formed during glycolysis is broken down to lactic acid, and energy is released to form ATP. Glucose → Pyruvic acid → 2 Lactic acid + energy (+ 2 NAD). Lactic acid fermentation temporarily replaces aerobic respiration so that the cell can have a continual source of energy, even in the absence of oxygen. This shift is only temporary because cells need oxygen for sustained activity. Lactic acid that builds up in tissue causes a burning, painful sensation.

Alcohol Fermentation: occurs in yeasts and some bacteria, often even when oxygen is present (preferred method of metabolism). Pyruvic acid formed during glycolysis is broken down to alcohol, CO2, and energy, which is used to form ATP. Glucose → Pyruvic acid → 2 alcohol + 2 CO2+ energy (+ 2NAD)

Anaerobic Pathways:
- tends to be less efficient: produces less ATP. for organisms that live in environments where oxygen is low or absent. e.g. inside gut, deep underground or underwater, wetlands
- found in some prokaryotes similar to aerobic cellular respiration. ETC takes place on specialized membranes. use another inorganic compound as a final electron acceptor instead of oxygen e.g. SO42-, NO3-, Fe3+

Fermentation:
- eukaryotes and some bacteria cannot undergo anaerobic cellular respiration
- can still undergo glycolysis: anaerobic
- produce 2 ATP and 2 NADH
- problem: will run out of NAD+
- solution: use fermentation after glycolysis to oxidize NADH back to NAD+ for use in glycolysis
- two kinds: lactate fermentation & alcohol fermentation

Lactate Fermentation:
- found in some bacteria and some eukaryotes, including human muscle cells
- pyruvate is reduced by NADH to create lactate (lactic acid) and NAD+
- lactate fermentation equation: 2 pyruvate + 2 NADH –> 2 lactate + 2 NAD+
- when oxygen is restored, the reaction is reversed: lactate is oxidized by NAD+ to recreate pyruvate and NADH

Alcohol Fermentation:
- found in some bacteria and yeasts
- pyruvate is decarboxylated, producing acetaldehyde and CO2
- acetaldehyde is reduced by NADH to create ethanol (alcohol) and NAD+
- alcohol fermentation equation: 2 pyruvate + 2 NADH –> 2 ethanol + 2 CO2 + 2 NAD+

Thinking question: why does yeast create fluffy bread? (think of products of fermentation) –> How light the bread is is a function of how much gas is in the dough. It’s the carbon dioxide that creates all the little bubbles that make the bread lighter and fluffier. Gas is created with the growth of the yeast. The more the yeast grows, the more gas in the dough

Question 30

Gizmo summary

Answer 30

• Glycolysis: Uses glucose and enzymes to break it down –> 2 pyruvate molecules are produced and a little ATP (makes 2 ATP)
• Krebs Cycle: Uses pyruvate to make a molecule of NADH and ATP–> makes ATP and NADH. CO2 is released as a waste product (makes 2 ATP)
• ETC: NADH is used, e- move in the chain while H+ ions move into the intermembrane. e- leave the chain by reacting with oxygen gas and H+ ions to create water –> Water is produced
• ATP Synthase: Hydrogen ions in the intermembrane space are used as they travel back to the matrix. They travel through ATP synthase and as it passes through it rotates and makes ATP –> ATP is made as the H+ passes through ATP synthase which rotates to make it. (makes 34 ATP)
• 2-deoxyglucose: It’s a poison that stops glycolysis. It attaches to the 1st enzyme in glycolysis. This stops glucose from being used by glycolysis so no pyruvate is made.
• arsenic: It’s a poison that stops the Krebs cycle. It attaches to the 1st enzyme in the Krebs cycle. This stops pyruvate from being used by the Krebs cycle so no NADH is made.
• cyanide: It’s a poison that stops the ETC. It attaches to the last enzyme in the ETC. This stops electrons from leaving the ETC, so new electrons cannot enter the ETC. Without new electrons, the ETC stops working and no H+ are moved into the intermembrane space.
• oligomycin: It’s a poison that stops ATP synthase. It attaches to the hole/pore in ATP synthase. This stops H+ from moving through ATP synthase and no ATP is made.

Cyanide stops the ETC. If the ETC was stopped that means pyruvate is being used and produced at a regular amount and NADH is not being used as the ETC stops working. This matches with the results from Jareds muscle cells. Also the intermembrane H+ ion concentration is decreased which correlates to cyanide being the poison as if the ETC stops working no H+ are moved into the intermembrane space.

Cyanide caused symptoms such as muscle weakness as it stopped the electron transport chain from working. This caused pyruvate to be produced and used normally, while there was an increase in NADH in the cells as it was not being used by the electron transport chain. Since the chain was not working this means the majority of the ATP that is made by cells was not being made therefore Jared had much less ATP/energy causing weakness in him.

The antidote helps Jared cells make ATP as it changes the cyanide molecule to thiocyanate. This can be removed from Jareds body easily. Since the cyanide is now removed the ETC can start to continue working and electrons can leave the chain by reacting with oxygen gas. Now the H+ protons can move into the intermembrane space and create a H+ gradient so when H+ moves through ATP synthase, ATP will be produced

Question 31

Basics of Photosynthesis

Answer 31

Anabolic: small molecules combine
Endergonic: stores energy
Requires carbon dioxide (CO2) → uses light energy, in the form of photons, and water (H2O) to produce glucose
Takes place in plants
plants are autotrophs, which means they make their own food (in the form of glucose)
More specifically, photosynthesis takes place in the leaves:
a. stoma: pores (which have guard cells for opening and closing)
b. mesophyll cells (the chloroplasts here is where it happens)

Stoma: The pores in a plant’s cuticle through which water vapour and gases (CO2 & O2) are exchanged between the plant and the atmosphere. Found on the underside of leaves

Photosyntheis hpannes in mesophyll cells of leaf which included the cell wall, nucleus, central vacuole and chloroplast

we have leaf → many different tissues → mesohpyll tissues have mysophyll cells which have chlorplasts → chrloplast has two membranes inner and outer → inside the inner memrbanes there are stroma in the stroma there are stacked discs celled grana → each disc called thylakoid → thylakoid has membrane and space (thylooikd in stac from a granum) → grana are connected together

Plants are green because of chlorophyll which is located in thylakoid membrane. hlorophyll pigments harvest energy (photons) by absorbing certain wavelengths (blue: 420 nm and red: 660 nm are most important). Plants are green because the green wavelength is reflected, not absorbed. In addition to the chlorophyll pigments, there are other pigments present. During the fall, the green chlorophyll pigments are greatly reduced due to shorter daylight hours, revealing other pigments. Carotenoids are pigments that are either red, orange, or yellow.

CO2 is reduced to glucose (gains e-).

Oxygen is produced through photolysis of water. photolysis is the splitting of water in the presence of light. the intended goal of photosynthesis is to produce glucose. Therefore, O2 is actually a waste product of photosynthesis
Rxn: 2H2O → 4e- + 4H+ + O2

three external factors affect the rate of photosynthesis:
- temperature
- light intensity
- carbon dioxide concentration
the factor furthest from optimal level is the limiting factor (varies throughout day, season, year, etc.)

Two reactions make up photosynthesis:
- Light Reaction or Light-Dependent Reaction: Produces energy from solar power (photons) in the form of ATP and NADPH.
- Calvin Cycle or Light-Independent Reaction: Also called Carbon Fixation. Uses energy (ATP and NADPH) from light reaction to make sugar (glucose).

Question 32

Light-dependent reactions

Answer 32

Photosynthesis transforms the radiant energy of sunlight into the chemical energy of high-energy compounds. Photosynthesis enables plants to produce structural and metabolic substances that aid in their survival.

6CO2(g) + 6H2O(l) + energy → C6H12O6(s) + 6O2(g)
numerous reactions occur between
the substrates on the left side of the equation to produce the products on the right side.

the process involves two sets of reactions. Photo refers to the reactions that capture light energy; synthesis refers to the reactions that produce a carbohydrate. The two sets of reactions that make up photosynthesis are called the light dependent reactions and the light independent reactions. In the light-dependent reactions, light energy is trapped and used to generate two high-energy compounds: ATP and NADPH. NADPH is similar in structure and function to NADH. In the light-independent reactions, the energy of ATP and the reducing power of NADPH are used to make a high-energy organic molecule.

Water enters plants through the roots and is transported to the leaves through the veins. Carbon dioxide enters through openings, called stomata, in the leaves. The carbon dioxide and water diffuse into the cells and then enter the chloroplasts, where photosynthesis takes place.

Thylakoids are central to photosynthesis, because the molecules that absorb the solar energy are embedded in the thylakoid membranes. Surrounding the grana in the chloroplasts is a fluid-filled interior called the stroma. The stroma contains the
enzymes that catalyze the conversion of the carbon dioxide and water into carbohydrates.

A compound that absorbs certain wavelengths of visible light is called a pigment. A photosynthetic pigment is a compound that traps
light energy and passes it on to other compounds. When sunlight is available, pigments embedded in the thylakoid membranes absorb light energy, initiating the light-dependent reactions. Eventually, the energy is used to synthesize high-energy compounds.

A chlorophyll solution absorbs red and blue light, and it transmits or reflects green light. An absorbance spectrum is a graph that shows the relative amounts of light of
different wavelengths that a compound absorbs. The carotenoids absorb blue
and green light, so they are yellow, orange, and red in colour.

photosystem: one of two protein-based complexes composed of clusters of pigments that absorb light energy. Embedded in thylakoid membrane. when chlorophyll molecules are associated with different proteins in a photosystem, they can absorb light energy of various wavelengths. When any pigment molecule absorbs a photon, the molecule passes the energy to a unique pair of chlorophyll a molecules associated with a specific group of proteins. This pair of chlorophyll a molecules, in combination with these proteins, is called the reaction centre. The antenna complex includes all the surrounding pigment molecules that gather the light energy. The antenna complex transfers light energy to the reaction centre much
as a funnel directs liquid into the mouth of a bottle. When a reaction centre has received the energy from the antenna complex, an electron in the reaction centre becomes “excited”—that is, the electron is raised to a higher energy level. The electron then has enough
energy to be passed to an electron-accepting molecule. Since this electron acceptor has received an electron, it becomes reduced and is a higher energy level. The reaction centre pigment molecule of photosystem I is called P700, and the reaction centre pigment molecule of photosystem II is called P680, based on the wavelengths (in nanometres) of light these molecules absorb.

Step 1: The P680 molecule in the reaction centre of photosystem II absorbs a light photon, exciting an electron. When the excited electron leaves P680 in photosystem II and goes to the electron acceptor, P680 is missing an electron. It is said to have a hole. The P680+, now positively charged, has a powerful attraction for electrons. Although water is very stable molecule, the attraction of P680+ pulls electrons from water. A water-splitting complex holds two water molecules in place as an enzyme strips four electrons from them, one at a time. P680+ accepts these electrons one at a time, and each is passed to another electron carrier. P680+ then absorbs another photon, becomes reduced, and passes on another electron. This process occurs a four times to form one oxygen molecule. The four hydrogen ions from the two water molecules remain in the thylakoid space. The oxygen atoms from the water molecules immediately form an oxygen molecule. This is the oxygen that is released by plants into the environment. Photosystem II can absorb photons, excite P680, and pass electrons to the electron acceptor more than 200 times a second.
Step 2: From the electron acceptor, the energized electrons are transferred, one by one, along a series of electron-carrying molecules. Together, these molecules are referred to as an electron transport system. This photosynthetic electron transport system is similar to the electron transport system in mitochondria that is used in cellular respiration. With each transfer of electrons along the system, a small amount of energy is released. The released energy is used by a protein complex called the b6-f complex to pump hydrogen ions from the stroma, across the thylakoid membrane, and into the thylakoid space. Eventually, there are many more hydrogen ions in the thylakoid space than there are in the stroma. This pumping of electrons generates a hydrogen ion concentration gradient across the thylakoid membrane. This is similar to the formation of a hydrogen ion concentration gradient across the inner mitochondrial membrane during cellular respiration.
Step 3: While the events of steps 1 and 2 are taking place, light energy is absorbed by photosystem I. This energy is transferred to the reaction centre P700 molecule, where electrons become excited. Once again, the excited electrons are passed to a high-energy electron acceptor. In photosystem I, the lost electrons are replaced by those that have reached the end of the electron transport system from photosystem II.
Step 4: The electrons that were received by the electron acceptor from photosystem I are used by the enzyme NADP reductase to reduce NADP+ to form NADPH. The reducing power of NADPH will be used in the light-independent reactions.

The movement of hydrogen ions is linked to the synthesis of ATP by chemiosmosis. Because the ultimate energy source is light photons, the process is called photophosphorylation. The hydrogen ions that are pumped from the stroma to the thylakoid space by the b6-f complex of the electron transport chain cannot diffuse back across the membrane, because the membrane is impermeable to these ions. As the hydrogen ions move down their concentration gradient through the ATP synthase molecule, the energy of the gradient is used to generate ATP molecules.

The production of ATP by the passing of electrons through the Z scheme is often called noncyclic photophosphorylation. It is considered noncyclical because the flow of electrons is unidirectional—that is, the electrons are transferred from photosystem II to NADP+ to form NADPH. The passage of one electron pair through this system generates 1 NADPH and slightly more than 1 ATP. However, this ratio of ATP to NADPH is not sufficient for the light-independent reactions. These require three ATP molecules to two NADPH molecules.

Chloroplasts are able to produce more ATP through cyclic photophosphorylation. excited electrons leave photosystem I and are passed to an electron acceptor. From the electron acceptor, they pass to the b6-f complex and back to photosystem I. The proton gradient is generated in the same manner as in noncyclic photophosphorylation, and ATP synthesis by chemiosmosis also occurs. Because the same electron that left the P700 chlorophyll molecule in photosystem I returns to fill the hole it left, the process is called cyclical. Notice, however, that neither NADPH nor oxygen is produced in cyclic photophosphorylation.

SUMMARY: Photosynthesis includes two distinct sets of reactions: the light-dependent reactions and the light-independent reactions. Enzymes and electron carriers responsible for the light-dependent reactions are embedded in the thylakoid membranes of the chloroplasts. Pigment molecules absorb photons from the radiant energy of sunlight and use it to energize electrons. The energy of the electrons in noncyclic photophosphorylation is used partially to pump hydrogen ions into the thylakoid space and partially to reduce NADP+. In cyclic photophosphorylation, the energy of the electrons is used only to generate a hydrogen ion gradient across the thylakoid membranes. The energy stored in the hydrogen ion gradient is used to phosphorylate ADP.

Question 33

LDR 2

Answer 33

Photosystems 1 and 2 are protein complexes of chlorophyll embedded in the thylakoid membranes of chloroplasts. they work together to capture photons and convert solar energy into chemical potential energy through “excitation” of electrons and electron transport.

Photosystem II (PSII):
Contains a reaction centre with a P680 molecule that absorbs light (~680nm) and “excites” electrons
The electrons leave the reaction centre and go to an electron acceptor 🡪 plastoquinone (PQ)
At the same time, H20 in the thylakoid space is split by a water-splitting enzyme to provide electrons that replace ones that have left
Electrons that have left the reaction centre transport through electron carriers and other protein complexes in an electron transport system (similar to mitochondrial ETS)

b6-f complex:
The next “stop” for electrons after PSII
Delivers electrons to photosystem I (PSI) via another electron carrier –> plastocyanin (PC)
Pumps an H+ ion from the stroma into the thylakoid space across the thylakoid membrane (similar to the mitochondrial matrix, intermembrane space and inner mitochondrial membrane in mitochondrial ETS)
Creates an electrochemical gradient in the thylakoid space (like in mitochondrial ETS)

Photosystem I (PSI):
Absorbs photons at the same time as PSII
Reaction centre has a P700 molecule which absorbs light at ~700nm and re-excites electrons from PSII
Electrons are passed to the final “stop” in the system via the electron acceptor called ferredoxin (FD)

NADP Reductase:
The final stop for electrons in the thylakoid ETS
Reduces NADP+ to form NADPH, which is used to power light-independent reactions

Chemiosmosis in Plants:
Similar to chemiosmosis in aerobic cellular respiration
H+ ions are pumped from the thylakoid space back into the stroma via ATP synthase
Energy released(from movement of ions from thylakoid back to stroma) generates ATP from ADP
Because photons are the energy source, this process is called photophosphorylation

Noncyclic:
Electron flow is unidirectional through Z scheme; transferred from PSII to NADP+ to form 1 NADPH, and slightly more than 1 ATP
This ratio of ATP to NADPH is not sufficient to power light-independent reactions

Cyclic:
Electrons leaving PSI are passed to an electron acceptor and carried back to the b6-f complex, pumping more H+ ions into the thylakoid space
This increases ATP production

(photons supply energy and excite the e- that came from water molecule splitting by enzyme. the e- move to e- acceptor pq then to b6-f where h+ ions are pumped into thylakoid space. e- continue to PC carrier then to ps1 where they are excited by the photon and go to fd acceptor and to nadp reductase to form nadph which go into indepenct cycle/reactions. h+ ions move out into stroma through synthase creating atp) (chlorophyll in the photosystems abrosb the photons/light)

The thylakoid membrane is composed of a phospholipid bilayer and photosystem I and photosystem II. The first and most important event in either system is the capturing of light energy by the pigments associated with each photosystem. Pigment 680 is associated with Photosystem II, and Pigment 700 is associated with Photosystem I. The numbers 680 and 700 refer to the wavelengths of light absorbed by the pigments.
When a photon of light strikes the reaction center of Photosystem II, it “excites” an electron. Two water molecules bind to an enzyme that splits water into hydrogen ions (aka protons) and releases an oxygen
atom. This process is called photolysis. Two electrons are released in this process, and these electrons can be traced through photosystem II and photosystem I. Two oxygen atoms will join together to create an oxygen molecule which is released from the plant as a byproduct of the entire reaction.

The primary electron acceptor for the light-energized electrons leaving photosystem II is plastoquinone. The reduced plastoquinone passes the excited electrons to a proton pump embedded in the membrane called the b6-f complex. This proton pump moves protons (H+) atoms across the
membrane against their concentration gradients, which eventually causes a build-up of protons in the thylakoid space. The thylakoid membrane is NOT permeable to protons, so they may only cross the membrane via transport proteins. The protons will exit the thylakoid space via a special channel provided by ATP Synthase. The protons move through the ATP synthase with the concentration gradient, which allows them to do work (namely, drive ATP synthesis). As protons pass through the ATP synthase, ADP is phosphorylated to ATP and released into the stroma. The process of making ATP is called photophosphorylation. This ATP is now on its way to the Calvin Cycle where it will be used to generate glucose.

But wait, there’s more! The electron that was used in Photosystem II is just sitting around, all de-energized
but its story is not finished. A small protein called plastocyanin carries the electron to Photosystem I. Light absorbed by photosystem I energizes this electron and passes it to another primary electron acceptor called ferredoxin. The enzyme NADP Reductase transfers these electrons to NADP to form NADPH. The electron is now on its way to the Calvin Cycle as part of an NADPH molecule. Electrons lost from photosystem I are replaced by electrons generated from
photosystem II.

Question 34

Light Dependent Reactions

Answer 34

Chloroplasts in plants contain enzymes in the stroma that, in conjunction with the energy supplied by ATP and NADPH, convert carbon dioxide to carbohydrates.
Since the reactions can take place in the presence or absence of light, the more accurate terminology is light-independent reactions.
The key initial step in the synthesis of carbohydrates in plants is conversion of carbon dioxide to organic compounds—a process called CO2 assimilation. The assimilation of carbon dioxide is carried out by a cyclical pathway that continually regenerates it’s intermediates. This pathway is called the Calvin cycle.
The Calvin cycle accomplishes the conversion of inorganic carbon, in the form of carbon dioxide from the atmosphere, into organic carbon, in the form of the three-carbon organic molecule glyceraldehyde-3- phosphate (G3P). This product of photosynthesis is then used as a starting substrate in many other metabolic pathways.
The reactions of the Calvin cycle can be grouped into three phases.
1. Fixing Carbon Dioxide: The first phase is carbon dioxide fixation. The key to this is the chemical bonding of the carbon atom in carbon dioxide to a pre-existing molecule in the stroma. This molecule is a five-carbon compound called ribulose- 1,5-bisphosphate, or RuBP for short. The resulting six-carbon compound is unstable and immediately breaks down into two identical three-carbon compounds called 3-phosphoglycerate (PGA). Because these three-carbon compounds are the first stable products of the process, plants that use this method for photosynthesis are called C3 plants, and the process is called C3 photosynthesis. The reaction that leads to these three-carbon compounds can be summarized as: CO2 + RuBP → unstable C6 → 2 PGA. This reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase, which is often called rubisco. Rubisco is possibly the most abundant protein on Earth.
2. Reduction: In the second phase, the newly formed three-carbon compounds are in a low-energy state. To convert them into a higher-energy state, they are first activated by ATP and then reduced by NADPH. The result of these reactions is two molecules of glyceraldehyde-3-phosphate (G3P). In their reduced (higher-energy) state, some of the G3P molecules leave the cycle and may be used to make glucose and other carbohydrates. The remaining G3P molecules move on to the third phase of the cycle, in which RuBP is replenished to keep the cycle going.
3. Regenerating RuBP: Most of the reduced G3P molecules are used to make more RuBP. Energy, supplied by ATP, is required to break and reform the chemical bonds to make the five-carbon RuBP from G3P. The Calvin cycle must be completed six times in order to synthesize one molecule of glucose. Of the 12 G3P molecules that are produced in six cycles, 10 are used to regenerate RuBP, and 2 are used to make one glucose molecule. The net equation for the Calvin cycle is: 6CO2 + 18 ATP + 12 NADPH + water → 2 G3P + 16 Pi + 18 ADP + 12 NADP+

The G3P that is produced can then be used for the synthesis of other molecules that plants require. A great deal of G3P is transported out of the chloroplasts and into the cytoplasm. There, G3P is used to produce a key sugar in plants, sucrose. In times of intensive photosynthesis, when G3P levels can rise quite high, the G3P is used to produce starch. G3P is also the starting substrate for cellulose. Plant oils such as corn oil, safflower oil, and olive oil are derived from G3P. As well, G3P and a source of nitrogen are used to synthesize the amino acids that are used to make proteins. Thus, G3P is a crucial molecule in plant metabolism.

Rubisco is a critical enzyme in light-independent reactions. However, it has an undesirable property.
Rubisco can use oxygen as a substrate as well as carbon dioxide. In fact, oxygen and carbon dioxide compete with each other for the same active site on the rubisco enzyme.
When oxygen reacts with ribulose-1,5-bisphosphate in the process called photorespiration, the products are a two-carbon compound called phosphoglycolate and one of the three-carbon compound, 3-phosphoglycerate. As a result of photorespiration, all of the energy used to regenerate the ribulose-1,5-bisphosphate is wasted, thus reducing the efficiency of photosynthesis.
Under normal conditions, when the temperature is near 25oC, C3 plants lose 20 percent of the energy used to fix one carbon dioxide molecule. Biologists estimate that the maximum possible efficiency of photosynthesis in C3 plants—assuming each photosystem absorbs the maximum amount of light—is 30 percent.
Some laboratory-grown plants, raised under controlled conditions, have reached efficiencies of 25 percent. In nature, however, photosynthetic efficiency ranges from 0.1 percent to 3 percent.
Atmospheric conditions influences the reduction of efficiency due to photorespiration.
For example, under hot, dry conditions, leaves begin to lose water through the stomata. In response to these conditions, the stomata close to prevent further loss of water. With the stomata closed, the oxygen formed in the light-dependent reactions accumulates inside the leaves and carbon dioxide cannot enter.
With the higher ratio of oxygen to carbon dioxide in the leaves, the amount of photorespiration increases significantly (which reduces the efficiency of photosynthesis).

Some plants that are native to regions in which the climate is normally hot and dry, typically above 28oC, have evolved mechanisms to reduce the amount of photorespiration. These plants fit into two categories: C4 plants and CAM plants. Both use the Calvin cycle; however, they have developed different mechanisms for the uptake and storage of carbon dioxide that increase the ratio of carbon dioxide to oxygen for the Calvin cycle reactions.

C4 plants have a structure that separates the initial uptake of carbon dioxide from the Calvin cycle into different types of cells. In the outer layer of mesophyll cells, carbon dioxide is fixed by addition to a three-carbon compound called phosphoenolpyruvate (PEP). The product is the four-carbon compound oxaloacetate, giving these plants the name C4. The oxaloacetate is converted to the four-carbon compound malate and transported into the bundle-sheath cells. There, the malate is decarboxylated.
The resulting three-carbon compound, pyruvate, is transported back into the mesophyll cells and converted into PEP. The bundle-sheath cells are impermeable to carbon dioxide. As a result, carbon dioxide is concentrated in the bundle-sheath cells where the Calvin cycle takes place. This high CO2 concentration makes the Calvin cycle much more efficient than in C3 plants.

CAM plants, which include succulent (water-storing) plants such as cacti and pineapples, use a biochemical pathway identical to the C4 plants, but the reactions take place in the same cell. Carbon dioxide fixation is separated from the Calvin cycle by time of day rather than by different cell types. Crassulaceae thrive in hot, arid desert conditions. To prevent water loss, their stomata remain closed during the day and open at night. Carbon dioxide is fixed at night while the stomata are open. The reactions proceed until malate is formed. It is then stored in a large vacuole until daytime, when the stomata close. When the light-dependent reactions have produced enough ATP and NADPH to support the Calvin cycle, the malate exists the vacuole and is decarboxylated, freeing the carbon dioxide which is then fixed again by rubisco and enters the Calvin cycle.

The reactions that capture light energy and convert it to organic material are closely related to the reactions of aerobic respiration reactions. Both of these processes occur in plants and represent a plant cell’s energy cycle. The products of aerobic respiration, carbon dioxide and water, are the starting substrates for photosynthesis. The products of photosynthesis, oxygen and glucose, are the starting substrates for aerobic respiration. For plant cells, an outside source of carbon dioxide and water is needed to produce glucose, leaving oxygen as a by-product. For animal cells, which lack chloroplasts, an outside source of glucose and oxygen are needed to generate energy, leaving carbon dioxide and water as by-products.

Respiration
Photosynthesis
Overall equation glucose
glucose + 6O2 → energy(ATP) + 6CO2+ 6H2O
energy(light) + 6CO2 + 6H2O → glucose 1 6O2

AEROBIC RESPIRATION (animal vs. plant):
Cell location: Mitochondrion, Chloroplasts
Starting substrates: Glucose and oxygen, Carbon dioxide and water
products: Carbon dioxide and water, Glucose and oxygen
Electron transport chain: yes, yes
Electron carriers: NADH and FADH2 , NADPH
ATP synthesis by chemiosmosis: yes, yes

The light-independent reactions use the energy from ATP and NADPH from the light-dependent reactions to assimilate carbon dioxide and synthesize high-energy organic compounds in a series of reactions called the Calvin cycle.
Plants that use only the Calvin cycle to assimilate carbon dioxide are called C3 plants.
Due to photorespiration, C3 plants are extremely inefficient in hot, dry climates.
Plants that thrive in these environments have evolved two mechanisms to increase their efficiency. C4 plants isolate carbon dioxide fixation from the Calvin cycle reactions by carrying out these reactions in two different cell types. CAM plants isolate dioxide fixation from the Calvin cycle reactions by fixing carbon dioxide at night and carrying out the Calvin cycle reactions in the daytime.

Question 35

Calvin cycle

Answer 35

fixing co2
light-independent reactions

RECALL: light-dependent reactions supply ATP and NADPH to drive light-independent reactions when light is not required
- LIR are also called dark reactions, but this is a misnomer because the reactions can take place both with or without the presence of light
- Ultimate goal of LIR: synthesize carbohydrates from CO2

RECALL: glyceraldehyde 3-phosphate (G3P) from glycolysis
- The Calvin Cycle: light-independent cyclical pathway in the stroma that converts CO2 to G3P → used to make glucose and other sugars, or continue through the cycle to keep it going

Carbon Fixation (light independent reaction)
C3 plants (80% of plants on earth)
Occurs in the stroma
Uses ATP and NADPH from light reaction as energy to drive them
Uses CO2
To produce glucose: it takes 6 turns and consumes 18 ATP and 12 NADPH.

happens in stroma of chloroplast

Start with co2 → one carbon bonds to RuBP which is a 5 carbon compound and this forms a 3 carbon pga (first into 6 6 carbon molecules then to 12 3 carbon molecules it’s converted by rubisco an enzyme) → the pga become g3p but that produces adp since it consumes ATP and also uses NADPH which gets oxidized to NADP+ → the 12 G3P, 10 of them converted to RuBP while consuming 6atp to become that (103c is 30c which is equal to the 65c RuBP) while 2 become glucose and other sugars (2 since 2*3 c becomes 6 c for glucose)
Does not porudce atp, it consumes atp but we produce glucose (stoarage molecule?) whihc is chemical potential enegry in the form of food, this glucose produces is used all over again to keep the plant alive
This is carbon fixation

pathway must happen 6 times to produce one molecule of glucose

6CO2 + 18ATP + 12NADPH + H2O –> 2G3P + 16Pi + 18ADP + 12NADP+

Question 36

General LIR question answers

Answer 36

The enzymes for the Calvin cycle are located in the stroma, in the chloroplast of the mesophyll cells.

The first step in which CO2 is assimilated into an organic compound is called carbon dioxide fixation reaction. It is catalyzed by rubisco. CO2 + RuBP → unstable C6 → 2 PGA

The reducation phase of the calvin cycle is to convert the PGA into high energy states/levels by converting them into G3P molecules.

Glycolysis will break down the glucose into 2 three carbon molecules producing one ATP and one NADPH so the first steps are to remove a phosphate group from ATP to form ADP and to oxidize an NADPH molecule to form NADP+.

Photorespiration is the reaction of oxygen with RuBP in a process that reverses carbon fixation and reduces the efficiency of photosynthesis. All the enegry that was used to make the RuBP becomes wastes which is why there is a reduction in the efficiency of photosynthesis.

In C3 plants when temperature increases the leaves lose water by evaporation through the stomata (opneing in the leaves) and to stop the water loss the stomata will close but as a result CO2 can not eneter the leaves as well as the oxygen produced by light dependent reactions remains in the cells and photorespiration will increase since the more oxygen is competing for sites on the rubisco enzyme.

Since C4 plants live in hot and dry climate they have evolved mechanisms to reduce the amount of photorepriation that occurs. They still have the calvin cycle but there are different mechanisms for the uptake and storage of CO2 that increases the ratio of it compared to oxygen for the cycles reactions. C4 plants have a layer of cells called bundle sheath cells, which C3 plants do not have. The Calvin cycle happens only in the bundle sheath cells. In C4 mesophyll cells, carbon dioxide is fixed to a compound called PEP, producing a 4-carbon compound called oxaloacetate. Oxaloacetate is converted into malate, which is then transported into the bundle sheath cells. Once there, it is converted/decarboxylized to pyruvate, and carbon dioxide is released into the Calvin cycle. When the climate is hot and dry, carbon dioxide levels normally decrease due to the stomata closing, and so photorespiration becomes more likely. However, the malate is pumped into the bundle sheath cells and so the carbon dioxide concentration inside the cell stays high enough for RuBP to bind with CO2 rather than oxygen. This decreases the amount of photorespiration. (calvin cycle happens in bundle sheath cells instead of calvin cycle.

CAM plants minimize photorespiration by separating carbon dioxide fixation from the Calvin cycle by time of day. At night, the stomata are open and carbon fixation happens, producing malate. It is then stored in a large vacuole. When the stomata are closed during the day, the carbon dioxide is removed from malate and enters the Calvin cycle.

The candle burned out because the combustion reaction used up all the available oxygen in the bell jar. During the 27 days, the plant photosynthesized. It used the carbon dioxide in the jar, some of which was a product of the candle’s combustion reaction, to produce glucose. The glucose was then used in cellular respiration. The by-products of cellular respiration are carbon dioxide and water. Photosynthesis must have happened at a higher rate than cellular respiration, so that oxygen unused in cellular respiration was released into the bell jar through the leaves. Enough oxygen accumulated to keep the combustion reaction going when the candle was re-lit.

Students will likely agree with the statement because the light-dependent reactions produce NADPH and ATP. The only source of these high-energy molecules are the light-dependent reactions. If the light-dependent reactions ceased to function, the light-independent reactions would also cease, once the NADPH and ATP were used up.

Question 37

Photosynthesis general

Answer 37

State when photosynthesis takes place:
Photosynthesis takes place in the presence of light (needed for the dependent reactions) it’s basically used to convert light energy into chemical energy.

Explain the two reactions of photosynthesis (light dependent and independent):
- When they happen → Light-dependent reactions will happen in the presence of light while independent happen in the presence or absence of light.
- How they happen → Light dependent reactions use the light energy it receives in the forms of photons and water molecules to produce ATP and NADPH. It uses the e- from water and the light energy to excite it and pass it through the electron transport system where at the end it’s passed to NADP+ reductase to form the NADPH and the H+ ion gradient that was formed by one of the complexes now produces ATP as the protons go through the synthase. The NADPH and ATP now go into the calvin cycle/independent reactions. The in the calvin cycle 6 CO2 will combine with RuBP by the use of the enzyme rubisco to form an unstable 6c compound which breaks into PGA. PGA will use up 12 atp to become 1,3 biphosphoglycerate and then use 12 NADPH to become 12 G3Ps two of which are used to become glucose and other sugars and 10 which use ATP to become the RuBP. The ADP and NADP+ are returned to the light reactions.
- Where they happen → light dependent reactions happen in the thylakoid membrane while the independent reactions happen in the stroma. Both are technically in the chloroplasts of mesophyll cells.

Overall reactions
6CO2 + 6H2O + energy → Glucose + 6O2
Two overall reactions in photosynthesis the light reactions which occur in the thylakoid membrane which involves the splitting of water into oxygen protons and e-. The protons and e- are transferred to the thylakoid membrane where they are used to create ATP and NADPH which go into the independent reactions. In there, co2 is converted into carbohydrates in the stroma.

List some important applications of photosynthesis
Photosynthesis fills our food requirements and needs for fibre (we eat the plants that use photosynthesis to create the high energy carbohydrates and when we eat it we use the glucose/starch to create energy). The energy in petroleum and natural gas comes from photosynthesis.

Light reactions:
* Are carried out by molecules in the
thylakoid membranes
* Convert light energy to the chemical
energy of ATP and NADPH
* Split H2O and release O2 to the
atmosphere

Calvin cycle reactions:
* Take place in the stroma
* Use ATP and NADPH to convert
CO2 to the sugar G3P
* Return ADP, inorganic phosphate, and
NADP+ to the light reactions

Question 38

c2,c3,c4 and cam

Answer 38

C3 Photosynthesis:
* Light reactions generate high energy molecules to run the dark reactions (Calvin cycle)
* The first step of the Calvin cycle is the fixation of carbon by RUBISCO using carbon dioxide and ribulose 1,5 bisphosphate as substrates

C2 Photosynthesis:
* RUBISCO is an ancient enzyme, and evolved when oxygenation was insignificant
* With oxygenic photosynthesis and higher O2 levels in the atmosphere, oxygenation by RUBISCO became significant

Problem is→ 2-Phosphoglycolate is toxic to plants, it inhibits distinct reactions in the Calvin Cycle. It also represents a significant loss of energy to the plant and is therefore at some cost returned to the Calvin cycle. It takes energy to return 2- phosphoglycolate to the Calvin cycle

The C4 and CAM pathways evolved to reduce the impact of oxidation by RUBISCO (photorespiration)

• The C4 photosynthetic pathway concentrates CO2 in the vascular bundle sheath cells of leaves to
  significantly reduce competition with O2 for the active site on RUBISCO
• The CAM photosynthetic pathway further separates absorption of CO2 in time from its incorporation in the Calvin cycle
• C4 & CAM are more efficient than C3 at yielding energy above about 85 degrees F–Rubisco favors oxygenation the higher the temp because the concentration of CO2
  in leaf tissue is less the higher the temp

At 86° F C4 becomes more efficient than C3 due to photorespiration. The starch rich chloroplasts of the Kranz anatomy lack grana, the site of the light reactions. They differ from the chloroplasts of the outer bundle sheath (dimorphic chloroplasts).

Some Grasses use the C3 photosynthetic pathway (cool season grasses) and some use the C4 pathway (warm season grasses)

CAM Photosynthesis: In addition to being more efficient like C4 at higher temperatures, CAM conserves water by allowing stomata to be closed during the heat of the day

“Since every CO2 molecule has to be
fixed twice, first by 4-carbon organic acid and second by RuBisCO, the C4 pathway uses more energy than the C3 pathway. The C3 pathway requires 18 molecules of ATP for the synthesis of one molecule of glucose, whereas the C4 pathway requires 30 molecules of ATP. This energy debt is more than paid for by avoiding losing more than half of photosynthetic carbon in photorespiration as occurs in some tropical plants, making it an adaptive mechanism for minimizing the loss.”