GENERAL BIOLOGY I

ENERGY TRANSFORMATION

LESSON 1. ATP AND ADP CYCLE

• Even exergonic, energy-releasing reactions require a small amount of activation

energy in order to proceed. However, consider endergonic reactions, which require

much more energy input, because their products have more free energy than their

reactants. Within the cell, where does energy to power such reactions come from?

The answer lies with an energy-supplying molecule called adenosine triphosphate,

or ATP. ATP is a small, relatively simple molecule, but within some of its bonds, it

contains the potential for a quick burst of energy that can be harnessed to perform

cellular work. This molecule can be thought of as the primary energy currency of

cells in much the same way that money is the currency that people exchange for

things they need. ATP is used to power the majority of energy-requiring cellular

reactions.

• As its name suggests, adenosine triphosphate is comprised of adenosine bound to

three phosphate groups (Figure 6.4.1). Adenosine is a nucleoside consisting of the

nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate

groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta,

and gamma. Together, these chemical groups constitute an energy powerhouse.

However, not all bonds within this molecule exist in a particularly high-energy state.

Both bonds that link the phosphates are equally high-energy bonds

(phosphoanhydride bonds) that, when broken, release sufficient energy to power a

variety of cellular reactions and processes. These high-energy bonds are the bonds

between the second and third (or beta and gamma) phosphate groups and
 between the first and second phosphate groups. The reason that these bonds are

considered “high-energy” is because the products of such bond breaking—

adenosine diphosphate (ADP) and one inorganic phosphate group (P i)—have

considerably lower free energy than the reactants: ATP and a water molecule.

Because this reaction takes place with the use of a water molecule, it is considered

a hydrolysis reaction. In other words, ATP is hydrolyzed into ADP in the following

reaction: ATP+H2O→ADP+Pi+free energy

• Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse

reaction regenerates ATP from ADP + Pi. Indeed, cells rely on the regeneration of ATP

just as people rely on the regeneration of spent money through some sort of income.

Since ATP hydrolysis releases energy, ATP regeneration must require an input of free

energy. The formation of ATP is expressed in this equation:

ADP+Pi+freeenergy→ATP+H2O

• Two prominent questions remain with regard to the use of ATP as an energy source.

Exactly how much free energy is released with the hydrolysis of ATP, and how is that

free energy used to do cellular work? The calculated ∆G for the hydrolysis of one

mole of ATP into ADP and Piis −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is

true under standard conditions, it would be expected that a different value exists

under cellular conditions. In fact, the ∆G for the hydrolysis of one mole of ATP in a

living cell is almost double the value at standard conditions: 14 kcal/mol (−57

kJ/mol).

• ATP is a highly unstable molecule. Unless quickly used to perform work, ATP

spontaneously dissociates into ADP + Pi, and the free energy released during this

process is lost as heat. The second question posed above, that is, how the energy

released by ATP hydrolysis is used to perform work inside the cell, depends on a

strategy called energy coupling. Cells couple the exergonic reaction of ATP

hydrolysis with endergonic reactions, allowing them to proceed. One example of

energy coupling using ATP involves a transmembrane ion pump that is extremely

important for cellular function. This sodium-potassium pump (Na+/K+ pump) drives

sodium out of the cell and potassium into the cell (Figure 6.4.2). A large percentage

of a cell’s ATP is spent powering this pump, because cellular processes bring a great
 deal of sodium into the cell and potassium out of the cell. The pump works

constantly to stabilize cellular concentrations of sodium and potassium. In order for

the pump to turn one cycle (exporting three Na + ions and importing two K+ ions), one

molecule of ATP must be hydrolyzed. When ATP is hydrolyzed, its gamma phosphate

doesn’t simply float away, but is actually transferred onto the pump protein. This

process of a phosphate group binding to a molecule is called phosphorylation. As

with most cases of ATP hydrolysis, a phosphate from ATP is transferred onto another

molecule. In a phosphorylated state, the Na +/K+ pump has more free energy and is

triggered to undergo a conformational change. This change allows it to release

Na+ to the outside of the cell. It then binds extracellular K +, which, through another

conformational change, causes the phosphate to detach from the pump. This

release of phosphate triggers the K+ to be released to the inside of the cell.

Essentially, the energy released from the hydrolysis of ATP is coupled with the energy

required to power the pump and transport Na + and K+ ions. ATP performs cellular

work using this basic form of energy coupling through phosphorylation.

• Often during cellular metabolic reactions, such as the synthesis and breakdown of

nutrients, certain molecules must be altered slightly in their conformation to

become substrates for the next step in the reaction series. One example is during

the very first steps of cellular respiration, when a molecule of the sugar glucose is

broken down in the process of glycolysis. In the first step of this process, ATP is

required for the phosphorylation of glucose, creating a high-energy but unstable

intermediate. This phosphorylation reaction powers a conformational change that

sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward.

Here, the exergonic reaction of ATP hydrolysis is coupled with the endergonic

reaction of converting glucose into a phosphorylated intermediate in the pathway.

Once again, the energy released by breaking a phosphate bond within ATP was used

for the phosphorylation of another molecule, creating an unstable intermediate and

powering an important conformational change.

SUMMARY

• ATP is the primary energy-supplying molecule for living cells. ATP is made up of a

nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that

connect the phosphates (phosphoanhydride bonds) have high-energy content.

The energy released from the hydrolysis of ATP into ADP + Pi is used to perform

cellular work. Cells use ATP to perform work by coupling the exergonic reaction of

ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to

another molecule via a process known as phosphorylation. The phosphorylated

molecule is at a higher-energy state and is less stable than its unphosphorylated

form, and this added energy from the addition of the phosphate allows the molecule

to undergo its endergonic reaction.

LESSON 2. PHOTOSYNTHESIS

DESCRIPTION OF PHOTOSYNTHESIS

• Among all the living organisms, only plants are capable of producing their own food

and obtaining energy from it. By producing energy, plants supply all the necessary

nutrients and energy, directly or indirectly, to all other living organisms.

HOW DO PLANTS PRODUCE THEIR OWN FOOD?

• The process of photosynthesis allows plants to capture the energy found in sunlight

and use that energy to convert carbon dioxide and water into glucose. Glucose

provides a form of chemical energy which plants use to grow and function. Oxygen

is also released during this process. Photosynthesis makes life possible.

• Photosynthesis is the process by which the energy in sunlight is converted into

chemical energy. Photosynthesis in plants takes place in the chloroplasts. The green

color of a leaf comes from chlorophyll, a pigment found inside chloroplasts. A double

membrane surrounds the chloroplast. The dense fluid found within the chloroplast

is called stroma. Thylakoids are an elaborate system of interconnected membrane

sacs. It is here, in the thylakoid membrane, where chlorophyll is found and

photosynthesis takes place.

2 STAGES OF PHOTOSYNTHESIS

• Photosynthesis can be summarized by the following equation:

• The process of photosynthesis is actually 2 processes:

and NADPH).

o Calvin Cycle (Light Independent Reactions): incorporates carbon dioxide

from the air into organic molecules, which are converted to sugar.

• Chlorophyll and the other molecules involved in the light reactions are built into the

thylakoid membranes. The enzymes that catalyze the Calvin Cycle are located in

the stroma of the chloroplast. Light reactions convert sunlight energy into chemical

energy in the form of ATP and NADPH. This process starts when sunlight is absorbed

by chlorophyll. The ATP and NADPH made by the light reactions are then used by the

Calvin Cycle to convert cardbon dioxide to sugar. The ATP provides the energy and

the NADPH supplies electrons needed during the Calvin Cycle. The ADP and NADP+

that are leftover from the Calvin Cycle are shuttled back to the light reactions to

regenerate ATP and NADPH.

LIGHT REACTIONS

• Sunlight is used to produce ATP and NADPH in the light reactions. The molecules

involved in the light reactions are found in the thylakoid membrane.

• Photosystem I (PSI) & Photosystem II (PSII): contain chlorophyll molecules as well

as other proteins and are responsible for moving electrons from water to NADP+ to

form NADPH.

• Electron transport chain: generates a store of potential energy in the form of a

hydrogen ion gradient in the thylakoid space, with the H+ concentration in the

thylakoid being higher than that found in the stroma.

• ATP synthase: uses the energy generated by the hydrogen ion gradient to produce

ATP.

THE LIGHT-DEPENDENT REACTIONS TAKE PLACE IN 5 STAGES:

1. Capturing light: Pigment molecules (chlorophyll) are anchored into place within the

photosystem complexes by a lattice of proteins. The precise positioning of the

pigment molecules allows them to capture photons (little packets of energy).

2. Exciting an electron: The position of the chlorophyll molecules within the

photosystem is such that when a photon of light strikes any chlorophyll molecule in

the photosytem, the excitation passes from one chlorophyll to another. Eventually,

the energy arrives at a key chlorophyll molecule that is touching a membrane

bound protein. The excited electron is then tranferred from that key chlorophyll

molecule to an acceptor molecule in the membrane.

3. Electron Transport: The excited electron is then shuttled along a series of electron-

carrier molecules embedded in the membrane. This is called the electron transport

system. The energy from the electron is released in small amounts as the electron
 passes along the electron transport system. This energy is used to pump hydrogen

ions (protons, H+) across the membrane, creating a high concentration of protons

on one side of the membrane.

4. Making ATP: The high concentration of protons can be used as an energy source to

make ATP molecules. Protons are restricted from crossing the membrane and are

only able to move back across the membrane in special channels. The movement

of protons as they pass through the ATP synthase drives the conversion of ADP to

ATP. This process is called chemiosmosis and makes the ATP that will be used in the

Calvin Cycle to make carbohydrates.

5. Making NADPH: Once the electron leaves the transport system, it enters another

photosystem where it is re-energized by the absorption of another photon of light.

The newly energized electron enters another electron transport system where it is

again passed along a series of electron-carrier molecules. The electron is eventually

transferred to a molecule of NADP+ and with the addition of a hydrogen ion, is used

to create a molecule of NADPH. Both ATP and NADPH are important for the synthesis

of carbohydrates in the Calvin Cycle.

CALVIN CYCLE

• The Calvin Cycle uses the ATP and NADPH produced by the light reactions to

convert three molecules of carbon dioxide to one molecule of a 3-carbon sugar.

The plant can then utilize this small sugar to make larger sugars such as glucose

and other organic compounds.

• Phase 1: Carbon Fixation: Carbon dioxide comes into the stroma of the chloroplast.

The enzyme rubisco catalyzes the bonding of carbon dioxide to Ribulose

two 3-carbon molecules of 3-phosphoglycerate.

• Phase 2: Reduction: Each 3-phosphoglycerate molecule is phosphorylated by ATP

to create 1,3-bisphosphoglycerate. NADPH donates a pair of electrons and reduces

1,3-bisphosphoglycerate, which loses a phosphate group and becomes

glyceraldehyde 3-phophate (G3P).

• Phase 3: Regeneration: For every six molecules of G3P created, five molecules

continue on to phase 3, while one leaves to be used for the production of organic

compounds. ATP is needed to phosphorylate G3P to regenerate Ribulose

bisphosphate.

LESSON 3. CELLULAR RESPIRATION

• Inside every cell of all living things, energy is needed to carry out life processes.

Energy is required to break down and build up molecules and to transport many

molecules across plasma membranes. All of life’s work needs energy. A lot of

energy is also simply lost to the environment as heat. The story of life is a story of
 energy flow — its capture, its change of form, its use for work, and its loss as heat.

Energy, unlike matter, cannot be recycled, so organisms require a constant input of

energy. Life runs on chemical energy. Where do living organisms get this chemical

energy?

WHERE DO ORGANISMS GET ENERGY FROM?

• The chemical energy that organisms need comes from food. Food consists of

organic molecules that store energy in their chemical bonds. Glucose is a simple

carbohydrate with the chemical formula C6H12O6.

• It stores chemical energy in a concentrated, stable form. In your body, glucose is

the form of energy that is carried in your blood and taken up by each of your

trillions of cells. Cells do cellular respiration to extract energy from the bonds of

glucose and other food molecules. Cells can store the extracted energy in the form

of ATP (adenosine triphosphate).

What is ATP?

• Let’s take a closer look at a molecule of ATP, shown in the figure 5.9.2. Although it

carries less energy than glucose, its structure is more complex. “A” in ATP refers to

the majority of the molecule – adenosine – a combination of a nitrogenous base

and a five-carbon sugar. “T” and “P” indicate the three phosphates, linked by bonds

that hold the energy actually used by cells. Usually, only the outermost bond breaks

to release or spend energy for cellular work.

• An ATP Molecule is like a rechargeable battery: its energy can be used by the cell

when it breaks apart into ADP (adenosine diphosphate) and phosphate, and then

the “worn-out battery” ADP can be recharged using new energy to attach a new

phosphate and rebuild ATP. The materials are recyclable, but recall that energy is

not! ADP can be further reduced to AMP (adenosine monophosphate and

phosphate, releasing additional energy. As with ADT "recharged" to ATP, AMP can be

recharged to ADP.
 • How much energy does it cost to do your body’s work? A single cell uses about 10

million ATP molecules per second and recycles all of its ATP molecules about every

20-30 seconds.

WHAT IS CELLULAR RESPIRATION?

• Some organisms can make their own food, whereas others cannot. An autotroph is

an organism that can produce its own food. The Greek roots of the word autotroph

mean “self” (auto) “feeder” (troph). Plants are the best-known autotrophs, but

others exist, including certain types of bacteria and algae. Oceanic algae contribute

enormous quantities of food and oxygen to global food chains. Plants are

also photoautotrophs, a type of autotroph that uses sunlight and carbon from

carbon dioxide to synthesize chemical energy in the form of

carbohydrates. Heterotrophs are organisms incapable of photosynthesis that must

therefore obtain energy and carbon from food by consuming other organisms. The

Greek roots of the word heterotroph mean “other” (hetero) “feeder” (troph),

meaning that their food comes from other organisms. Even if the food organism is

another animal, this food traces its origins back to autotrophs and the process

of photosynthesis. Humans are heterotrophs, as are all animals. Heterotrophs

depend on autotrophs, either directly or indirectly.

• Cellular respiration is the process by which individual cells break down food

molecules, such as glucose and release energy. The process is similar to burning,

although it doesn’t produce light or intense heat as a campfire does. This is

because cellular respiration releases the energy in glucose slowly, in many small
 steps. It uses the energy that is released to form molecules of ATP, the energy-

carrying molecules that cells use to power biochemical processes.

• Cellular respiration involves many chemical reactions, but they can all be summed

up with this chemical equation: C6H12O6+6O2⟶6CO2+6H2O+

• Energy where the energy that is released is in chemical energy in ATP (vs.

thermal energy as heat). The equation above shows that glucose (C6H12O6) and

oxygen (O2) react to form carbon dioxide (CO2) and water H2O, releasing energy in

the process. Because oxygen is required for cellular respiration, it is an aerobic

process.

• Cellular respiration occurs in the cells of all living things, both autotrophs and

heterotrophs. All of them catabolize glucose to form ATP. The reactions of cellular

respiration can be grouped into three main stages and an intermediate

stage: glycolysis, Transformation of pyruvate, the Krebs cycle (also called the

citric acid cycle), and Oxidative Phosphorylation.

• The first stage of cellular respiration is glycolysis. This process is shown a 6-carbon

molecule being broken down into two 3-carbon pyruvate molecules. ATP is

produced in this process which takes place in the cytosol of the cytoplasm.

SPLITTING GLUCOSE

• The word glycolysis means “glucose splitting,” which is exactly what happens in this

stage. Enzymes split a molecule of glucose into two molecules of pyruvate (also

known as pyruvic acid). This occurs in several steps. Glucose is first split into

glyceraldehyde 3-phosphate (a molecule containing 3 carbons and a phosphate

group). This process uses 2 ATP. Next, each glyceraldehyde 3-phosphate is

converted into pyruvate (a 3-carbon molecule). this produces two 4 ATP and 2

NADH.

RESULTS OF GLYCOLYSIS

• Energy is needed at the start of glycolysis to split the glucose molecule into two

pyruvate molecules. These two molecules go on to stage II of cellular respiration.

proceeds, energy is released, and the energy is used to make four molecules of

ATP. As a result, there is a net gain of two ATP molecules during glycolysis. high-

energy electrons are also transferred to energy-carrying molecules called electron

carriers through the process known as reduction. The electron carrier of glycolysis

is NAD+(nicotinamide adenine diphosphate). Electrons are transferred to 2 NAD+

to produce two molecules of NADH. The energy stored in NADH is used in stage III of

cellular respiration to make more ATP. At the end of glycolysis, the following has

been produced:

o 2 molecules of NADH

o 2 net molecules of ATP

TRANSFORMATION OF PYRUVATE INTO ACETYL-COA

• In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are

transported into mitochondria, which are sites of cellular respiration. If oxygen is

available, aerobic respiration will go forward. In mitochondria, pyruvate will be

transformed into a two-carbon acetyl group (by removing a molecule of carbon

dioxide) that will be picked up by a carrier compound called coenzyme A (CoA),

which is made from vitamin B5. The resulting compound is called acetyl CoA and

its production is frequently called the oxidation or the Transformation of Pyruvate.

Acetyl CoA can be used in a variety of ways by the cell, but its major function is to

deliver the acetyl group derived from pyruvate to the next pathway step, the Citric

Acid Cycle.
CITRIC ACID CYCLE

• Before you read about the last two stages of cellular respiration, you need to

review the structure of the mitochondrion, where these two stages take place. A

mitochondrion has an inner and outer membrane. The space between the inner

and outer membrane is called the intermembrane space. The space enclosed by

the inner membrane is called the matrix. The second stage of cellular respiration,

the Krebs cycle, takes place in the matrix. The third stage, electron transport, takes

place on the inner membrane.

• Recall that glycolysis produces two molecules of pyruvate (pyruvic acid). Pyruvate,

which has three carbon atoms, is split apart and combined with CoA, which stands

for coenzyme A. The product of this reaction is acetyl-CoA. These molecules enter

the matrix of a mitochondrion, where they start the Citric Acid Cycle. The third

carbon from pyruvate combines with oxygen to form carbon dioxide, which is

released as a waste product. High-energy electrons are also released and

captured in NADH.

STEPS OF THE CITRIC ACID (KREBS) CYCLE

• The Citric Acid Cycle begins when acetyl-CoA combines with a four-carbon

molecule called OAA (oxaloacetate). This produces citric acid, which has six

carbon atoms. This is why the Krebs cycle is also called the citric acid cycle. After

citric acid forms, it goes through a series of reactions that release energy. This
energy is captured in molecules of ATP and electron carriers. The Krebs cycle has

two types of energy-carrying electron carriers: NAD+ and FAD. The transfer of

electrons to FAD during the Kreb’s Cycle produces a molecule of FADH2. Carbon

dioxide is also released as a waste product of these reactions. The final step of the

Krebs cycle regenerates OAA, the molecule that began the Krebs cycle. This

molecule is needed for the next turn through the cycle. Two turns are needed

because glycolysis produces two pyruvate molecules when it splits glucose.

• After the second turn through the Citric Acid Cycle, the original glucose molecule

has been broken down completely. All six of its carbon atoms have combined with

oxygen to form carbon dioxide. The energy from its chemical bonds has been

stored in a total of 16 energy-carrier molecules. These molecules are:

o 2 ATP

o 8 NADH

o 2 FADH2

o 6 CO2: 2 CO2 from Transformation of Acetyl CoA and 4 CO2 from

Citric Acid Cycle.

OXIDATIVE PHOSPHORYLATION

• Oxidative phosphorylation is the final stage of aerobic cellular respiration. There are

two substages of oxidative phosphorylation, Electron transport chain and

Chemiosmosis. In these stages, energy from NADH and FADH2, which result from the

previous stages of cellular respiration, is used to create ATP.

• During this stage, high-energy electrons are released from NADH and FADH2, and

they move along electron-transport chains found in the inner membrane of the

mitochondrion. An electron-transport chain is a series of molecules that transfer

electrons from molecule to molecule by chemical reactions. These molecules are

found making up the three complexes of the electron transport chain. As electrons

flow through these molecules, some of the energy from the electrons is used to

pump hydrogen ions (H+) across the inner membrane, from the matrix into the

intermembrane space. This ion transfer creates an electrochemical gradient that

drives the synthesis of ATP. The electrons from the final protein of the ETC are gained

by the oxygen molecule, and it is reduced to water in the matrix of the

mitochondrion.

CHEMIOSMOSIS

• The pumping of hydrogen ions across the inner membrane creates a greater

concentration of these ions in the intermembrane space than in the matrix –

producing an electrochemical gradient. This gradient causes the ions to flow back

across the membrane into the matrix, where their concentration is lower. The flow of

these ions occurs through a protein complex, known as the ATP synthase complex.

The ATP synthase acts as a channel protein, helping the hydrogen ions across the

membrane. The flow of protons through ATP synthase is considered chemiosmosis.

ATP synthase also acts as an enzyme, forming ATP from ADP and inorganic

phosphate. It is the flow of hydrogen ions through ATP synthase that gives the energy

for ATP synthesis. After passing through the electron-transport chain, the low-

energy electrons combine with oxygen to form water.

HOW MUCH ATP?

• You have seen how the three stages of aerobic respiration use the energy in glucose

to make ATP. How much ATP is produced in all three stages combined? Glycolysis

produces 2 ATP molecules, and the Krebs cycle produces 2 more. Electron transport
from the molecules of NADH and FADH2 made from glycolysis, the transformation of

pyruvate, and the Krebs cycle creates as many as 32 more ATP molecules. Therefore,

a total of up to 36 molecules of ATP can be made from just one molecule of glucose

in the process of cellular respiration.