Honors Biology Lecture note pack for

Unit 3: Cellular Energetics

Lesson 3.1, Energy Transformations
- In cells, energy-transforming reactions (aka metabolism) are
often coupled.
- An energy-releasing (exergonic or catabolic) reaction is coupled
to an energy-requiring (endergonic or anabolic) reaction.
o Exergonic/catabolic reactions break molecules down.
o Endergonic/anabolic reactions build molecules up.

- Cells have developed “energy taxis” – called coenzymes - to capture, transfer, and move energy around the cell.
- Common examples: ATP, GTP, NADH, FADH2, and NADPH (photosynthetic organisms).

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Energy Transformation: ATP

- Phosphate groups are negatively charged, so energy is required to get

them close enough to each other to create covalent bonds in the ATP
molecule.
- This energy is stored in the bond between the two phosphates. The bond
is easily broken, releasing that energy.
- Recall that ATP can be formed by substrate-level phosphorylation or
oxidative phosphorylation (we will review these methods in lesson 3.2).
- Side note: ATP is made up of an adenine + ribose + phosphate…sound
familiar? Yes – ATPs building blocks are the same as what makes up a
nucleotide!

- Remember that energy transformation is always paired.

- One molecule is receiving energy transferred rom another molecule.
This is called an oxidation–reduction or redox reaction.
o Reduction is the gain of one or more electrons (as the charge
of the molecule is being reduced; its becoming more negative
due to the addition of negatively charged electron).
o Oxidation is the loss of one or more electrons.
o “OIL RIG”

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CHECKPOINT QUESTIONS

1. In each of the following reactions, identify if it is anabolic or catabolic (endergonic or exergonic) and what kind
of coenzymes might be involved in the transfer of energy.
a. Glucose  glucose 6-phosphate (Hint: substrate-level phosphorylation is occurring)

b. Fatty acid  CO2 + H2O

2. A typical active young man requires 2,800 kilocalories of food energy a day to fuel metabolism, movement,
active transport, etc. the energy stored in the third phosphodiester bond of ATP is 0.0145 kcal/gram. If the
energy from the man’s food were all stored as ATP, he would need 2,800 kcal needed/0.0145 kcal/gram ATP per
day. However, the man only has about 50 grams of ATP at any one time. What does this mean in terms of ATP
hydrolysis and synthesis?

Lesson 3.2, Enzymes

- Metabolic reactions occur extremely fast (milliseconds) because of biological
catalysts.
- Catalysts (in general) are substances that speed up reactions without being
permanently altered.
- Our biological catalysts are called enzymes (specialized proteins).
- Recall that in any reaction, an input of energy (the activation energy or Ea) is
required to initiate that reaction.
- The Ea will put reactants into a transition state which is unstable.
- What role do enzymes play in a reaction?
o Enzymes lower the activation energy - they allow reactants to come
together and react more easily.
 Example: A molecule of sucrose in solution may hydrolyze in
about 15 days; with sucrase present, the same reaction
occurs in 1 second.
- Enzymes are highly specific - each one catalyzes only one chemical reaction.
o Review questions:
 Are enzymes used up in the reaction?
 Which molecule is the substrate?
 What is the active site and where is it located?
 Why do we need the addition of water?
- What keeps the enzyme and substrate together during the
reaction?
o The enzyme–substrate complex (ES) is held together by
hydrogen bonding, electrical attraction, or temporary
covalent bonding.

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 o Binding of substrate to enzyme is like a baseball in a catcher’s mitt. The enzyme changes shape to make
the binding tight - “induced fit.”
- Enzymes may use one or more mechanisms to catalyze a reaction:
o Inducing strain: bonds in the substrate are stretched, putting it in an unstable transition state.
o Substrate orientation: substrates are brought together so that bonds can form.
o Adding chemical groups: R groups may be directly involved in the reaction, forming or breaking bonds.
- Some enzymes require ions or other molecules to function. These molecules are referred to as cofactors.
o Cofactors are a nonprotein component of an enzyme and they can be:
 Coenzymes: organic molecule; relatively small size (e.g. ATP, NADH, NADPH, FADH2)
 Inorganic ions (e.g. Ca2+, Zn2+)
o Cofactors may be permanently or temporarily attached, depending on their type. (No, you do not need
to know this info.)

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- Can the rate of a catalyzed reaction be limited?

- Cells can regulate metabolism by controlling the amount of an active enzyme. How might this be done?
o One of two ways:
 Cells can control the synthesis of enzymes (we’ll discuss this in detail when we get to “control of
gene expression”).
 Chemical inhibitors can be used to slow reaction rates.
- Inhibitors:
o A competitive inhibitor competes with natural substrate for active site.
o A noncompetitive inhibitor binds at a site (allosteric site) distinct from the active site—this causes a
change in enzyme shape and function.
- Two types of inhibition:
o Irreversible inhibition: inhibitor covalently binds to a side
chain in the active site. The enzyme is permanently
inactivated.
 Poisons and toxins are often irreversible
o Reversible inhibition: more common and allows for flexibility
in enzyme control
- Allosteric regulation – can be both inhibitory or stimulatory
o When a non-substrate molecule binds to a site other than
the active site (the allosteric site).
o Enzyme changes shape, altering the chemical attraction (affinity) of the active site for the substrate.
o Allosteric regulation can activate or inactivate enzymes.
- Enzymes can also become inactive, or denatured, based on their environment.
o Denaturation is the alteration of a protein shape through some form of external stress, in such a way
that it will no longer be able to carry out its cellular function.
o The protein can return to normal when conditions return to normal.
o What conditions will cause denaturantion?
 Temperature (heat)
 Concentration of H+ (pH)
 High concentrations of polar substances
 Nonpolar substances
- Enzyme Control: pH
o All enzymes have an optimal pH for activity.
o The tertiary structure (and thus function) of a protein is very sensitive to the concentration of H + (pH) in
the environment.
o Alterations in the properties of the R groups can cause the protein shape to change and possibly
denature.
 Some amino acid side chains generate H+ and become anions (negatively charged ion).
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  Some amino acid side chains attract H+ and become cations (positively charged ion).
 Example: glutamic acid—COOH glutamic acid—COO– + H+
(non-ionized, hydrophobic) (anion, ionized, hydrophilic)

- Now you try: Imagine aspartic acid is at the active site of an enzyme. Normally this enzyme
is active at pH 7 but at pH 4, the enzyme is inactive. Explain these observations.

- Enzyme Control: Temperature

o All enzymes, like pH, have an optimal temperature for activity.
o General rule: warmer temperatures increase rates of chemical
reactions.
o However, if temperature is too high, enzymes will denature.
o (Again, the protein can return to normal when conditions
return to normal.)

Lesson 3.3, Cellular Respiration

- Cellular respiration is a major catabolic pathway.
o Glucose is oxidized
- Photosynthesis is a major anabolic pathway.
o Light energy is converted to chemical energy
- A lot of energy is released when reduced molecules with many C—
C and C—H bonds are fully oxidized to CO2.

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 - Oxidation occurs in a series of small steps in three pathways:
1. Glycolysis
2. Pyruvate oxidation
3. Citric acid cycle
- True or false: only animal cells perform cell respiration.

Glycolysis

- 10 enzyme-catalyzed reactions where glucose is partially oxidized and some energy is released.
- Occurs in the cytosol of the cell
- 2 main “stages”
o Endergonic: energy-consuming reactions
o Exergonic: energy-harvesting reactions
- Final products:
o 2 molecules of pyruvate (pyruvic acid)
o 2 molecules of ATP
o 2 molecules of NADH

Pyruvate Oxidation

- Each pyruvate produced from glycolysis is transported to the

mitochondrial matrix and is further oxidized producing:
o CO2 and acetate
o Acetate is then bound to coenzyme A (CoA) which is starting
molecule for the citric acid cycle.

Citric Acid Cycle

- Operates twice for every glucose molecule that enters glycolysis

o Why?
- Cycle starts with Acetyl CoA (and the 4C molecule, oxaloacetate)
o Note that oxaloacetate is regenerated in step 8
- Goal of cycle: oxidize the acetyl group into two CO2 molecules
- All 8 reactions in the C.A.C. are similar. Let’s focus on the final
reaction as an example (see image below).
o Notice the change that occurs in the blue highlighted region.
The hydrogen is removed from malate, reducing NAD+ into
NADH, which stores energy for later use.
o With four such reactions, the C.A.C. harvests a great deal of
chemical energy from the oxidation of acetyl CoA.

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Oxidative Phosphorylation

- Oxidative = oxidation event = NADH is oxidized to NAD+

- Phosphorylation = a phosphate group is added onto a molecule, in this case ADP, creating ATP
- Consists of two main events:
o Electron transport chain
o Chemiosmosis

- Electron transport chain (ETC)

o In this step, NADH is oxidized to NAD+ and O2 is reduced to H2O in a
series of steps.
o Note that the ETC only involves the transport of electrons. The
process of making ATP is a separate step (chemiosmosis).
o Two main events:
o Respiratory chain: a series of electron carrier proteins embedded in
the inner mitochondrial membrane. (Think respiratory because it
involved oxygen.)
o Electron transport: electrons from the oxidation of NADH and
FADH2 are pass from one carrier protein to the next in the respiratory chain.
o Remember that oxidation is always paired with reduction. When NADH is oxidized to NAD+, the
corresponding reduction reaction is:
 2H+ + 2e- + ½ O2  H2O
o So the key role of O2 in cells (and the reason we breath and have a blood system to deliver O2) is to act
as an electron acceptor, becoming reduced in the process.
o The oxidation reactions of the ETC are exergonic. This released energy is used to actively transport H+
ions from the mitochondrial matrix to the intermembrane space, setting up a H+ proton gradient.
 This proton gradient stores energy for later use – why?

o The enzyme ATP synthase (embedded in the mitochondrial inner membrane) uses the stored energy in
the H+ gradient to synthesize ATP by a mechanism called chemiosmosis.

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 - Chemiosmosis
o Chemiosmosis: The movement of ions (think “chemicals”) across a
semipermeable barrier from a region of high concentration to a region of
low concentration.
o This is just a form of facilitated diffusion.
o ~32 molecules of ATP are produced for each fully oxidized glucose.
o Four types of gradients are produced by chemiosmosis – can you name all
four?

Cell Respiration: Making the connection

- Ok so we now understand the steps of cellular respiration, but WHY such a long, complex stet of steps??
- Recall that energy is released in catabolism by oxidation. Released energy is then trapped by the reduction of
coenzymes such as NADH.
- However, cells use ATP energy for anabolic processes (building of macromolecules for example).
- In other words, most of the energy-releasing reactions produce NADH, but most energy-consuming reactions
require ATP.
- Cells need a way to connect these two coenzymes. That is, to transfer energy from NADH to ATP.

Energy Transformation

- This transfer of energy from NADH to ATP is achieved by oxidative phosphorylation.

o Energy released from NADH oxidation is used to actively transport protons (H+ ions) across the inner
mitochondrial membrane (ETC).
o This results in a high proton gradient. These protons then diffuse back across the membrane, powering
phosphorylation of ATP via chemiosmosis.
- These two paired events (ETC + chemiosmosis) transfer energy from NADH (which carried energy from
glycolysis and the CAC) to ATP (a form of energy the cell can use).

Connection

- Brown fat is
o a special type of tissue associated with the generation of heat and
o is more abundant in hibernating mammals and newborn infants.
- In brown fat,
o the cells are packed full of mitochondria,
o the inner mitochondrial membrane contains an uncoupling protein, which allows H+ to flow back down
its concentration gradient without generating ATP, and
o ongoing oxidation of stored fats generates additional heat.

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Effects of Poison on Oxidative Phosphorylation

1. Cyanide and CO bind to the fourth electron carrier protein. What would be the effect of these compounds on
the ETC?

2. The antibiotic oligomycin blocks the passage of H+ through the ATP synthase channel. How does oligomycin kill
fungal cells when applied to the skin? Why is it not lethal to humans?

3. Rotenone (poison to kill insects and fish) binds tightly to an electron carrier molecule in the first complex. What
would be the effect of this poison?

4. DNP is a poison called an “uncoupler.” It makes the membrane of the mitochondria leaky to H+ ions. How would
this affect a cell?

Cell Respiration: Fermentation

- Under anaerobic conditions, the respiratory chain cannot function as it required oxygen. In this situation, NADH
is oxidized by fermentation.
- There are many different types of fermentation, but all operate to regenerate NAD + (which feedback to be
reduced again in glycolysis).
- The overall yield of ATP during fermentation is two which are produced during glycolysis.

Lactic acid fermentation:

- End product is lactic acid (lactate).

- NADH is used to reduce pyruvate to lactic acid, thus regenerating NAD+.

Alcoholic fermentation:

- End product is ethyl alcohol (ethanol) and CO2.

- Pyruvate is converted to acetaldehyde, and CO2 is released.

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 - NADH is used to reduce acetaldehyde to ethanol, regenerating NAD+ for glycolysis.

Evolution Connection

- Glycolysis is generally considered the first method for producing energy….but why?!
- It’s an energy-harvesting process used by all life forms.
- It’s anaerobic, as was the early atmosphere on Earth around 3.8 MYA.
- Location within the cell, using pathways that do not involve any membrane-bounded organelles.

Lesson 3.4, Photosynthesis

- Photosynthesis involves two pathways:
o Light reactions convert light energy into chemical energy (in
ATP and the reduced electron carrier NADPH).
o Carbon-fixation reactions use the ATP and NADPH, along with
CO2, to produce carbohydrates.
- Light is a form of electromagnetic radiation, which travels as a wave
but also behaves as particles (photons).
- Photons can be absorbed by a molecule, adding energy to the
molecule and moving to an excited state.
- Pigments: molecules that absorb wavelengths in the visible spectrum.
- Most common pigment in plants: chlorophyll (absorbs blue and red
light)
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 - So why are most plants green?

- Absorption spectrum: plot of light energy absorbed against wavelength.

- Action spectrum: plot of the biological activity of an organism against the wavelengths to which it is exposed.
- Most plants absorb light energy using chlorophyll a and chlorophyll b.
- However, there are many accessory pigments which absorb wavelengths between red and blue. Why is it
beneficial for a plant to have these?

Light-Dependent Reaction

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- The first step in the light-dependent reaction is the absorption of a
photon of light by a chlorophyll pigment embedded in the
photosystem.
- The energy from this photon is passed from chlorophyll molecule to
the next until it reaches the primary electron acceptor.
- General steps:
o Photosystem II (PSII)
 Energy, in the form of electrons, is passed to the ETC
to actively pump H+ ions from stroma to thylakoid
lumen to produce ATP (more info on next slide)
 Electrons are replaced by the oxidization of water
molecules
o Photosystem I (PSI)
 Electrons arrive from the ETC in a low energy state.
 They are then reenergized (from sunlight) and then transferred to NADP+, reducing it to NADPH.
- Photophosphorylation
o Photo = photons = energy from the sun
o Phosphorylation = addition of a phosphate group
o Photophosphorylation is simply the production of ATP via energy from photons.
 ATP is produced chemiosmotically (movement of H+ ions down its concentration gradient) via
the ATPsynthase protein.
 The energy source to create the H+ gradient required for chemiosmosis was obtained from
photons, hence the name photophosphorylation.

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The Calvin Cycle (or Light Independent Cycle)
- Energy in ATP and NADPH is used to “fix” gaseous CO2 into a reduced form, converting it to a solid, organic
carbohydrate
- It occurs in the stroma of the chloroplast

- STEP 1: Fixation of CO2

o CO2 is added to the 5 carbon molecule, ribulose 1,5-bisphosphate (RuBP).
 Rubisco (ribulose bisphosphate carboxylase/oxygenase), an enzyme, catalyzes this reaction.
o Reaction produces a 6C molecule which immediately breaks down to two 3C molecules, called 3-
phosphoglycerate (3PG)

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- STEP 2: Reduction of 3PG to G3P
o 3PG is reduced to form glyceraldehyde 3-phosphate (G3P).
o Two step process which uses ATP and NADPH

- STEP 3: regeneration of RuBP

o The CO2 acceptor, RuBP, is regenerated from G3P.
o If there is extra G3P, it is..
 Exported to the cytosol and converted to hexoses (6C sugars such
as glucose and fructose).
 When glucose accumulates (later in the day), it is linked to form
starch (amylose), a storage carbohydrate.
 Starch then used at night when G3P levels have flat lined
or as an energy source for growth.

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