Module 5 Bio

Redox in the Overall Photosynthesis Equation

Overall formula:

6 CO2+6 H2O (light) →  C6H12O6 + 6O2

​Who loses electrons? Who gains electrons?Atoms thatloseelectrons (are oxidized):

• Oxygen atoms in water (H₂O) lose electrons.

• When water is split, electrons are stripped from H₂O → O₂, so oxygen goes from a reduced state to a more oxidized state.

✔ Molecule oxidized: H₂O
✔ Product formed from oxidation: O₂

Atoms that gain electrons (are reduced):

• Carbon atoms in CO₂ gain electrons.

• CO₂ is reduced to make glucose (C₆H₁₂O₆), which has high-energy C–H bonds.

✔ Molecule reduced: CO₂
✔ Product formed from reduction: Glucose

Energy consequences of these redox changes

Oxidation of water:

• Pulling electrons from water requires a massive energy input (sunlight).

• Water becomes low-energy O₂ gas, which stores very little chemical energy.

Reduction of CO₂:

• Adding electrons (and H⁺) to CO₂ creates energy-rich C–H and C–C bonds in glucose.

• Glucose stores the sunlight energy captured in the light reactions.

In short:

• Water → O₂ is an energy-requiring oxidation.

• CO₂ → glucose is an energy-storing reduction.

Summary Chart: PSII, PSI, Calvin Cycle

Inputs and outputs of the major stages

Process	Key Inputs	Key Outputs	What Happens?
PSII(Photosystem II)	H₂O, Light, ADP, Pi	O₂, e⁻, H⁺ gradient, ATP	Water is split (photolysis) → O₂ released, electrons sent to ETC; H⁺ gradient powers ATP synthesis
PSI(Photosystem I)	Light, e⁻ from PSII, NADP⁺ + H⁺	NADPH	Light re-excites electrons → high-energy electrons reduce NADP⁺ to NADPH
Calvin Cycle	CO₂, ATP, NADPH	Glucose precursor (G3P), ADP, Pi, NADP⁺	Uses ATP + NADPH to reduce CO₂ into carbohydrates; rubisco fixes CO₂

Energy Transformations Explained (PSII)

• Light (strong oxidizing agent) excites electrons in PSII.

• Takes electrons from H2O (splits into H+ ions and O₂)

• H₂O is oxidized

• Electron transport pumps H⁺ into the thylakoid → creates a gradient.

• ATP synthase uses the H⁺ gradient to make ATP.

Energy flow:
light → excited electrons → H⁺ gradient → ATP

Energy Transformations Explained (PSI)

• Electrons from PSII arrive with moderate energy (accepts electrons).

• PSI uses more light to boost them (light excite them).

• These electrons reduce NADP⁺ → NADPH

Energy flow:
light → excited electrons → NADPH

Energy Transformations Explained (Calvin Cycle)

• ATP gives energy.

• NADPH gives electrons.

• CO₂ is reduced into G3P, which becomes glucose.

Energy flow:
ATP + NADPH → C–C and C–H bonds in sugar (stored energy)

Chemical energy → Reduced carbon (sugar)

Role of Rubisco

Rubisco is the enzyme that captures CO₂ from the air and attaches it to a 5-carbon molecule (RuBP).

• It performs carbon fixation—the step that brings inorganic carbon into the biosphere.

• Without rubisco, plants could absorb light energy but could not turn CO₂ into sugar.

• It is the most abundant enzyme on Earth because every plant and photosynthetic organism depends on it.

Explaining CO₂ → Redwood Mass to an 8-year-old

The air has a tiny gas called CO₂ (carbon dioxide).
A tree breathes in CO₂ through its leaves.

Inside the leaf, the tree breaks the CO₂ apart and keeps the carbon.
The carbon gets stuck together into sugars.
The sugars get glued together into wood.

So:

• The carbon in CO₂ becomes the trunk,

• the branches,

• the needles,

• the roots,

• and even the “weight” of the whole tree.

The tree’s mass is mostly made of air.
A redwood is an air-tree!

General Role of ATP in the Cell

ATP is the cell’s immediate energy currency.
It provides usable energy by breaking the bond between the last two phosphate groups, forming ADP + Pi.

ATP is used to:

• power mechanical work (e.g., muscle contraction, motor proteins)

• power transport work (ion pumps, membrane transport)

• power chemical work (building molecules—polymerization, biosynthesis)

Main idea:
ATP stores energy in its high-energy, unstable phosphate bonds, and releasing one phosphate gives a controlled burst of usable energy.

What it Means for Two Chemical Reactions to Be Coupled

Two reactions are coupled when the cell links an endergonic (requires energy) reaction to an exergonic (releases energy) reaction so that the total process becomes favorable.

Example:
Endergonic:
A + B → AB (building molecules)

Exergonic:
ATP → ADP + Pi

Coupling:
ATP hydrolysis is directly linked to the reaction that needs energy, often by transferring the phosphate to a substrate or enzyme.

Key idea:
Exergonic ATP breakdown drives otherwise unfavorable reactions forward.

Why Phosphorylation Causes a Large Change in Free Energy

Phosphorylation = adding a phosphate group (PO₄³⁻) → adds two negative charges that are very close together.

Why this changes free energy:

1. Repelling negative charges increase instability
   —like pushing two magnets together.

2. Higher instability = higher potential energy
   —the molecule “wants” to release that tension.

3. Phosphorylated substrate is more reactive
   —easier to break bonds or undergo shape changes.

Bottom line:
Adding a phosphate raises the free energy of the molecule, making it more reactive and more likely to undergo the next step in the pathway.

Labeling a typical reaction-energy graph

A standard diagram includes:

• Reactants → left side baseline

• Activation Energy (EA) → the “hill” the reaction must climb

• Transition State → the peak (most unstable intermediate)

• Products → right side baseline

If the products are lower than the reactants → reaction is exergonic.
If they’re higher → endergonic.

How an Enzyme Affects the Energy Curve

Enzymes:

• lower the activation energy (EA)

• provide an easier pathway

• stabilize the transition state

• DO NOT change reactants or products

• DO NOT change the overall ΔG

On a graph:

• The “hill” becomes shorter.

• Start and end points remain the same.

Exergonic or Endergonic?

• Exergonic: products lower in free energy than reactants (ΔG < 0).

• Endergonic: products higher (ΔG > 0).

Why Enzymes Increase Rates but Do Not Change ΔG

Enzymes speed reactions by:

• lowering activation energy

• orienting substrates correctly

• straining bonds

• stabilizing transition states

BUT they do not:

• add energy to reactants

• change product energy

• change substrate energy

• alter equilibrium position

• change ΔG

Key idea:
Enzymes accelerate how fast equilibrium is reached, not where equilibrium lies.

If something needs energy input (endergonic), an enzyme cannot magically make it happen—it must be coupled to ATPor another energy source.

Model of How Plants “Fix” Carbon into Sugars (Step 1: Light Reactions (Thylakoid))

Location: Thylakoid membrane

• Sunlight energizes electrons.

• H₂O is split → O₂, electrons, H⁺.

• Electrons move through an ETC, generating:

  • ATP via a proton gradient

  • NADPH by powering reduction of NADP⁺

Outputs → ATP and NADPH
These drive the Calvin Cycle.

Model of How Plants “Fix” Carbon into Sugars (Step 2: Calvin Cycle)

Location: Stroma (fluid space around thylakoids)

1. Carbon Fixation

• CO₂ enters the stroma.

• uses ATP and NADPH to reduce carbon from CO2 to carbohydrates

• 6 ATP → 6 ADP

• Rubisco attaches CO₂ to RuBP (a 5-C molecule).
  → forms a 6-C molecule that splits into two 3-C molecules.

2. Reduction

• ATP provides energy.

• NADPH donates electrons → reduction of carbon (3-PGA) into G3P (a sugar precursor).

3. Regeneration

• ATP is used to rebuild RuBP so the cycle continues.

Some G3P is used to build:

• glucose

• starch

• cellulose

• other organic molecules

If PSII is damaged:

• No water splitting → fewer electrons

• No H⁺ gradient → less ATP

• Fewer electrons sent to PSI → less NADPH

• Calvin cycle slows or stops (no ATP + NADPH)

If PSI is damaged:

• NADPH production almost stops

• Calvin Cycle cannot perform the reduction step

• ATP may still be produced by PSII, but sugar production halts

If ATP synthase is impaired:

• H⁺ gradient builds up but cannot be used

• ATP production decreases sharply

• Calvin Cycle slows

• NADPH may accumulate because not enough ATP is available to use it

If rubisco is defective or slow (very common):

• CO₂ cannot be fixed into RuBP

• Calvin cycle stalls at step 1

• ATP and NADPH accumulate unused

• Plant growth slows dramatically

• Sugar production approaches zero

If CO₂ levels drop:

• Rubisco has less CO₂ to capture

• Photorespiration increases (wasteful)

• Calvin cycle efficiency falls

• Less glucose is produced → less biomass

If the thylakoid membrane leaks H⁺:

• H⁺ gradient collapses

• Dramatic drop in ATP synthesis

• NADPH might still form via PSI, but Calvin Cycle cannot function without ATP

Allosteric inhibition (noncompetitive)

inhibitor binds somewhere other than active site, causes shape of the active site to change

Competitive inhibitor

inhibitor competes with substrate to bind at active site

Isomerase

enzyme that changes the way atoms in a molecule are arranged
without adding or removing atoms (isomerization reaction)

allosteric activation

bind to locations on an enzyme away from active site, changes the shape of the active site so that it is more receptive to substrates, so its more efficient at its function

Glycolysis Stage 1:

• catalyzed by hexokinase (feedback inhibition)

  • phosphorylates glucose using ATP

  • G6P produced

• Glucose is trapped in the cell from negative charged (cannot bind to transporter)

*Regulatory step

Glycolysis Stage 2:

• isomerase converts glucose-6-phosphate into fructose-6-phosphate

• Oxygen binds to carbon 2 instead of 1

• spilts sugar into two 3-carbon molecules

Glycolysis Stage 3:

• phosphofructokinase phosphorylates of fructose-6-phosphate (used another pathways)

• ATP donates high-energy phosphate to fructose-6-phosphate → fructose-1,6,bisphosphate (continues in glycolysis)

• prepares for spilt

*Regulatory step

Glycolysis Stage 4:

• spilts into two three-carbon isomers: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.

Glycolysis Stage 5:

isomerase transforms the dihydroxyacetone-phosphate (DHAP) into its isomer, glyceraldehyde-3-phosphate (GAP)

Glycolysis Stage 6:

• oxidizes sugar glyceraldehyde-3-phosphate

• NAD+ is reduced to NADH

• Results in 2 NADH for each glyceraldehyde-3-phosphate

• Each glyceraldehyde-3-phosphate is phosphorylated → 1,3-bisphosphoglycerate (1,3-BPG).

• NADH is oxidized to NAD+ to continue reaction

• produces ATP

Glycolysis Stage 7:

• 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP

• energy is released from the carbohydrate and captured by the phosphorylation of ADP

• ADP is phosphorylated

• Substrate-level phosphorylation

• enzyme is a kinase

• 2 ATP per glucose

• 1,3 bisphosphoglycerate is oxidized → 3-phosphoglycerate

Glycolysis Stage 8:

• Phosphate group moves

• Isomerization catalyzed by an isomerase

Glycolysis Stage 9:

• H₂O is removed (dehydration)

• catalyzed by enolase

• double bond formed → increase potential energy

• PEP is produced

Glycolysis Stage 10:

• ADP is phosphorylated into ATP

• Pyruvate is produced

*Regulatory step

Kinases

Enzymes that add a phosphate group

Hexokinase dimerizes when concentrations of inhibitor are high enough

Reaction coupling

making an endergonic reaction proceed by pairing it with an exergonic reaction

Glycolysis Phase 1 (energy investment phase)

net of 2 ATP to breakdown one glucose molecule

lost 2 ATP and produced two 3 carbon sugar molecules

Glycolysis Phase 2 (Energy Harvesting Phase)

two ATP, two NADH, and Pyruvate produced

Fructose

• metabolized by fructokinase (an unregulated enzyme) into Glyceraldehyde-3-phosphate (G3P)

• G3P enter after step 4/5

• floods cells with too much pyruvate

Consequences of not regulating glycolysis

• metabolic dysregulation

• causing increases rates of diabetes

• high fructose corn syrup is bad

• cannot catabolized pyruvate → only 2 ATP are produced form one glucose

Substrate-level phosphorylation

A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP

Feedback inhibition

A product of a reaction inhibits of the enzyme that catalyzes the reaction that produces it.

prevents overproduction of final product

Feedforward stimulation

A molecule stimulates an enzyme that catalyzes a reaction that occurs later in the same metabolic pathway.

Pyruvate processing

• occurs in matrix of mitochondria

• hydroxyethyl is oxdizied to acetyl group

• NAD+ is reduced to NADH

• Top carbon on pyruvate is oxidized to from CO₂

• acetyl group transferred to CoA to produce acetyl CoA

Results: 4 carbons are in Acetyl CoA and 2 are in CO2

Citric Acid Cycle (TCA, Krebs) Summary

• occur in the matrix of mitochondria

• primary goal: To transfer high-energy electrons to electron carriers

• produce 2 CO₂, 1 GTP/ATP, reduced carriers NADH and FADH₂

  • all 6 original carbons are in CO₂

• does not directly consume oxygen

• releases energy from carbohydrates by oxidizing carbon

• Energy is captured as NADH, FADH₂ and ATP

• fatty acids enter

Citric Acid Cycle Step 1:

• Acetyl coA has 2 carbons

• It joins oxaloacetate, which is a 4-C molecule

• Makes citrate, a 6-C molecule

Citric Acid Cycle Step 2:

Acetyl coA has 2 carbons.
• -OH is moved to another citrate

isomerization

citrate → isocitrate

Citric Acid Cycle Step 3:

• isocitrate is oxidized

  • results 5 carbon molecule (alpha-ketoglutarate)

  • CO₂ produced

  • NAD+ → NADH

Citric Acid Cycle Step 4:

• Another carbon oxidized → CO₂ release

• Energy is released from the carbohydrate and captured by the formation of NADH

Citric Acid Cycle Step 5:

• Succinyl CoA transformed into Succinate

• CoA is released from the top carbon and replaced with an oxygen
  • Carbon was oxidized

• Energy is related by phosphorylation of ADP to create ATP

Citric Acid Cycle Step 6:

• Succinate is transformed into Fumarate

• New molecule: FADH2, another electron carrier (like NADH)
  • FAD is oxidized form
  (empty / not carrying
  electrons)
  • FADH2 is reduced form
  (Full / carrying electrons)

• Carbons are oxidized and energy is released from the carbohydrate and captured by the reduction of FAD to form FADH2

Citric Acid Cycle Step 7:

• water is added

• malate is oxidized

• fumarate is reduced

Citric Acid Cycle Step 8:

• Energy is released from
  carbohydrate -> NADH is
  produced

• Top circled carbon is
  oxidized

• We are back at the
  “beginning” of the cycle:
  Oxaloacetate is ready to
  bring to a new acetyl CoA

Cellular Respiration

breaking down glucose and releasing energy

Order:

1. pyruvate is produced

2. Acetyl CoA is oxidized

3. FADH₂ is produced

4. Electron form FADH₂ are donated

5. Water is produced

Electron Transport Chain (ETC)

• located in the inter-membrane space of mitochondria

• Uses NADH and FADH₂ from previous processes

• directly uses oxygen

• 4 complexes are used to pump H+ in and out to create the concentration gradient

• NADH has higher potential energy, results in high concentration of H+ in intermembrane space

• Q and Cytochrome C shuttle electrons

• Water is formed

• oxygen is the final electron acceptor

Complex I

• NADH (oxidized) donates its electrons and becomes NAD+

• Complex I pumps H+ into the intermembrane space powered by the transfer of high energy electrons

• Contains NADH dehydrogenase protein

• pumps 4 H+

Complex II

FADH2 donates its electrons at complex II and becomes FAD
• FADH2’s electrons are not high enough energy to be passed to complex I
Complex II does not pump H+
• Complex II is a peripheral membrane protein (not integral)
• The difference in energy level between FADH2 and Complex II is not sufficient to pump H+

Complex III

• Electrons move to lower energy level, Complex III harvests this energy to pump H+

• made of cytochrome b and c proteins

• pumps protons through the membrane and passes its electron to cytochrome c to transport to complex IV

Complex IV

• Electrons move to lower energy level, Complex IV harvests this energy to pump H+

• contains cytochrome proteins c, a, a3

• Complex IV gives these low- energy electrons to oxygen to create water

• This is why we need oxygen to breathe

Chemiosmosis

• movement of ions across a selectively permeable membrane, down their electrochemical gradient

• uses potential energy of the hydrogen ion gradient

• generate 90% of ATP during aerobic glucose catabolism

Q (ubiquinone)

• connects I and II

• delivers electrons to ETC

• receives NADH from complex I and FADH₂ from Complex II

• Q (uniquinone) is a small, non-polar molecule that shuttles electrons from Complexes I and II to Complex III

• fewer electrons are made from FADH₂

• # of ATP is directly proportional to # of H+ pumped

Oxidative Phosphorylation

production of ATP using the process of chemiosmosis in mitochondria

harness an electrochemical gradient to generate ATP

Effects of no oxygen on ETC and everything else

• all electron accepters will be full

  • Only NADH and FADH₂

• Glycolysis can’t happen without NAD+, only make ATP

Fermentation

extracts energy from glucose when oxygen is absent

• main function: regenerates NAD+ so glycolysis can occur

• 2 types

  • Lactic acid

  • Ethanol

Lactic Fermentation

• uses pyruvate as an electron acceptor to convert NADH → NAD+

• pyruvate is reduced

• generates lactate

• used in red blood cells

• Input: Pyruvic acid, NADH

• Outputs: lactic acid, NAD+

Ethanol fermentation

• pyruvate is converted into acetaldehyde (accepts electrons from NADH)

• pyruvate is reduced

• Generates ethanol

• Equation:

  • pyruvic acid + H⁺ → CO₂ + acetaldehyde + NADH + H⁺ → ethanol + NAD⁺