GENERAL BIOLOGY I

SEMESTER 1: QUARTER 2 REVIEWER

PHOTOSYNTHESIS
6CO2 + 6H2O → C6H12O6 + 6O2
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By dela Cruz, O., (in pain) & Corpuz, L. (reese’s puffs reese’s puffs) 2023

INTRODUCTION
Photosynthetic autotrophs capture light energy from the sun and absorb carbon
dioxide and water from their environment. Using light energy, they combine the reactants
to produce glucose and oxygen. They store glucose, usually as starch, and release oxygen into
the atmosphere.

Re: Photosynthesis is the process by which plants capture energy from the sun to build
carbohydrates through chemical pathways, which is used to make glucose.
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Types of Organisms

There are two types of organisms:

➔ Autotrophs
◆ Organisms that make their own food. They are producers and the basis of the
food chain. Includes:
● plants
● algae
● certain bacteria
➔ Heterotrophs
◆ Living things that cannot make their own food. They are consumers.

Energy Molecules: Glucose and ATP

➔ Glucose (6 Carbon Sugar)

◆ The end product of photosynthesis. Chemical formula: C6H12O6
◆ It is the simplest sugar. It stores chemical energy in a concentrated, stable form.
◆ Universal food for nearly all life.
● This includes you. Glucose is the energy carried in your blood and taken
up by each of your cells.

➔ ATP (Adenosine TriPhosphate)

◆ The energy-carrying molecule that is used for energy by cells for most other
cellular processes.
● Energy is released when ATP gives up one of its three phosphate groups
and changes to ADP (Adenosine DiPhosphate).
◆ Made during the first half of photosynthesis and then used for energy during
the second half of photosynthesis when glucose is made.

Why are both ATP and Glucose needed?

➔ Glucose is better than ATP for storing and transporting energy yet still contains more
chemical energy in a smaller "package" than ATP. However, glucose is too powerful
for cells to use, while ATP contains just the right amount of energy to power life
processes within cells.
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Photosynthesis

Where does it take place? In autotrophs, it happens in leaves, where there are:

➔ Stomata (singular: Stoma)

◆ Pores in a plant’s cuticle through which water and gases enter and exit.
➔ Mesophyll Cells
◆ It is the internal ground tissue present in leaves.
◆ Contain the organelle chloroplast, which is where photosynthesis specifically
occurs.
● Chloroplasts contain pigments within thylakoid membranes, one of
which is chlorophyll.
● Pigments harvest energy (photons) by absorbing certain wavelengths.
Plants are green because the green wavelength is reflected, not absorbed.

6CO2 + 6H2O + Light Energy → C6H12O6 + 6O2

This is the formula for photosynthesis. If you read it, it would be 6 Carbon Dioxide plus
6 Water is converted to 1 Glucose and 6 Oxygen through Light Energy.

2 Stages of Photosynthesis

➔ Light Reaction “Photo”

◆ An energy fixing reaction where light is absorbed and transformed into chemical
energy in the bonds of NADPH and ATP by the thylakoids of the chloroplast,
used to drive the next stage.

◆ Re: The first stage of photosynthesis requires light to generate energy.

➔ Dark Reaction “Synthesis”

◆ Occur without light, so they can be called light-independent or dark reactions.
◆ Takes place in the stroma (not to be confused with stoma) surrounding the
thylakoid membranes of the chloroplast.
◆ Chemical energy in NADPH and ATP from the Light Reactions are used to
make glucose.
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First Stage: The Light Reactions

Water + Photons of light → Oxygen + ATP + NADPH

3 Parts Of Light Reactions

➔ Photoexcitation
◆ Absorption of light photons whose energy is used to split water releasing
electrons
➔ Electron Transport Chain (ETC)
◆ Harnessing the energy in electrons to form an electrochemical gradient (pump
hydrogen ions against its concentration gradient)
➔ Photophosphorylation (Chemiosmosis)
◆ ATP synthesis due to electrochemical gradient and the proton motive force

Photoexcitation

➔ When atoms absorb energy from the sun, the electrons gain energy and become
excited on the reaction-center (containing chlorophyll a)
➔ Primary electron acceptor traps the high energy electron before it can return to the
ground state. Excited electrons will fall back to the ground state if it isn’t transferred to
an electron acceptor.

Photosystems

➔ A cluster of pigments
➔ Embedded in the transmembrane proteins of the thylakoid membrane

Photosystem Structure

➔ Consists of a few hundred pigment molecules

➔ Reaction center contains a chlorophyll a that is located next to a primary electron
acceptor
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Photosystem Mechanism

➔ Photosystem I:
◆ Reaction-centre chlorophyll is P700

➔ Photosystem II:
◆ Reaction-centre chlorophyll is P680

Note: Numbers indicate optimal wavelength for absorption.

Electron Transport: Thylakoid Proteins

1. PSII (P680)

a. PSII absorbs light

b. Excited electron in the reaction center chlorophyll (P680) is captured by the
primary electron acceptor
c. P680 now “missing” an electron. To replace the missing electrons on P680,
electrons are extracted from water (in the lumen).
d. As a result, water is split into oxygen and hydrogen ions.
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2. Plastoquinone (Pq)

a. The electron captured by the primary electron acceptor of PSII (pheophytin) will
now be passed through an electron transport chain
b. The electron is first transferred to plastoquinone (Pq)
c. Pq is a mobile component within the thylakoid membrane

3. Cytochrome Complex
a. Electrons are transferred from Pq to cytochrome complex
b. Protons are pumped against its concentration gradient (the gradual change in
the concentration of solutes in a solution) from stroma across the thylakoid
membrane to the lumen.

4. Plastocyanin (Pc)
a. Electrons are transferred to plastocyanin (Pc)
b. Pc is a movable component on lumen side of the thylakoid membrane

5. PSI (P700)
a. Electrons on P700 is excited by light and captured by the PEA
b. Electrons transferred from Pc to P700 replaces the electrons that were lost

6. Ferredoxin (Fd)
a. Electrons undergo a second transport chain
b. Electrons are transferred to ferredoxin (Fd)
c. Fd is an iron containing mobile component on the stromal side of the
thylakoid membrane

7. NADP+ Reductase
a. Electrons are transferred by enzyme NADP+ reductase to the final electron
acceptor NADP+
b. NADP+ is reduced to NADPH due to the electron being accepted

8. ATP Synthase
a. Protons pumped into the lumen pass through ATP Synthase
b. ATP is produced in the stroma
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Phosphorylation
➔ light-dependent formation of ATP by chemiosmosis
➔ ETC provides energy for photosystems to pump H+ (hydrogen) from stroma to the
lumen

Types of Electron Transport Mechanisms

➔ Non-cyclic Electron Flow (Z Scheme)

◆ H2O is split to produce O2 (released from cell) and H+ ions (released into the
lumen)
◆ Electron transport chain helps establish electrochemical proton gradient
◆ NADP+ is the final electron acceptor and produces NADPH

➔ Cyclic Electron Flow

◆ Only involves Photosystem I (P700)

◆ Ferredoxin returns electrons back to Cytochrome Complex
◆ Protons pumped into lumen to produce more ATP through chemiosmosis
◆ No NADPH produced

● Purpose of Cyclic Electron Flow

○ Non-cyclic electron flow produces roughly equal quantities of

ATP and NADPH
○ In the Calvin cycle, more ATP is consumed than NADPH
○ Need for a method to increase ATP production without affecting
NADPH
○ When ATP runs low, NADPH will accumulate because the Calvin
cycle slows down
○ A rise in NADPH levels stimulate a temporary shift to cyclic
electron flow

Second Stage: Dark Reaction

Carbon dioxide enters a leaf via stomata and goes into the stroma of the chloroplast.
Carbon atoms from CO2 are fixed (incorporated into organic molecules) and used to build
three-carbon sugars. It’s not directly driven by light, but powered by the energy made from the
light reactions (NADPH and ATP).
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3 stages of Dark Reaction:

➔ Carbon Fixation

◆ An enzyme nicknamed Rubisco (RuBPcarboxylase-oxygenase) catalyzes

attachment of CO2 to a five-carbon sugar called ribulose bisphosphate (RuBP) is
the resulting 6-carbon molecule is unstable and quickly splits into two molecules
of a three-carbon compound called 3-phosphoglycerate (3-PGA).

● Re: RuBP (5C) gains 1 carbon, and the product is unstable. It splits.

➔ Reduction

◆ 3-PGA receives a phosphate group from ATP, turning into a doubly

phosphorylated molecule called 1,3-bisphosphoglycerate.

◆ Each molecule receives two electrons from NADPH and loses one of its
phosphate groups, turning into glyceraldehyde 3-phosphate (G3P).
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➔ Regeneration

◆ One of the 6 G3P molecules goes on to form glucose while the rest (5) of the
G3P molecules are used to regenerate the RuBP. Three more molecules of ATP
are used in the regeneration reactions.

You can observe that one of the end products, RuBP, is also the starting molecule. Using carbon
dioxide and the energy we have from the light reactions, we are able to make 1 glucose after 6
cycles of Dark Reaction.

Photosynthesis: Recap
Whether you read all that or you didn’t read all that, this section exists to help you grasp
photosynthesis in a wider view.

Photosynthesis is how plants make food (glucose). Plants need 3 things to make food:
Sunlight, water (H2O), and carbon dioxide (CO2).

They don’t need everything from these 3, so after they’re done with them, they spit it out.
What they spit out is oxygen (O2). So you are breathing in plant spit, think about that.
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Getting into it technically, photosynthesis is split into 2 major parts: the Light and the Dark.

The light part uses sunlight and water, and with these, it can make energy. During the energy
making process, it realizes that it doesn’t need the oxygen in the water, so it spits it out.

The dark uses carbon dioxide and the energy made from light. The dark is where plant food is
made. It’s not a very good way to make food, so materials need to go through the dark 6 times.

But hey, if I could feed myself just by basking in the sun, drinking water, and breathing, you will
not see me complaining. Goodluck in exams you crammer.

Trivia and Extras

◆ Chlorophyll has Mg+ in the center.

◆ Blue-420 nm and red-660 nm are the most important wavelengths.
◆ Dark Reaction is also known as the Calvin Cycle because its reactions were
discovered by a scientist named Melvin Calvin.
◆ Endergonic - a reaction that absorbs (heat) energy from its environment
◆ Exergonic - a reaction that releases (heat) energy from its environment.
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CELLULAR
RESPIRATION
C6H12O6 + 6O2 → 6CO2 + 6H2O

INTRODUCTION
Aerobic cellular respiration is the process wherein cells break down the nutrients in
food and turn them into ATP. This process uses molecular oxygen in a series of catabolic
reactions that break down large molecules to release energy.

Re: Cellular respiration is the process that breaks down food molecules, usually in the form of
glucose, to turn into carbon dioxide and water, making ATP.
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Two types of Respiration

Aerobic Respiration

◆ requires oxygen in order to produce ATP. It is the characteristic of eukaryotic

cells when there is enough oxygen and most of it occurs in the mitochondria.
◆ Re: this is what people usually mean when they say “cellular respiration”.

Anaerobic Respiration

◆ the release of a relatively small amount of energy in cells by the breakdown of

food (undigested food) in the absence of oxygen.
● Fermentation - process where the hydrogen atoms generated by
glycolysis are donated to organic molecules.

Aerobic Respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + 36 ATP

There are 3 parts in Aerobic cellular respiration:

Glycolysis (Glucose-Splitting)

◆ Involves the splitting of six-carbon sugars (usually glucose) into two

molecules of pyruvate, a three-carbon molecule.
◆ Occurs in the cytoplasm (cytosol).

Krebs Cycle/Citric Acid Cycle

◆ Pyruvate oxidation takes place before Krebs Cycle.

● 2 pyruvate is oxidized into 2 acetyl CoA
● Pyruvate oxidation and Citric Acid cycle occurs in the matrix, the
innermost space within a mitochondrion.
◆ Acetyl CoA (2C) joins with oxaloacetate (4C) to make a 6-carbon molecule, then
is oxidized to make NADH, ATP, and FADH2.

Electron Transport Chain

◆ Energy from NADH and FADH2 is transferred to ADP, making ATP.

◆ Occurs within the cristae, a fold in the inner membrane of a mitochondrion.
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First Stage: Glycolysis

Glucose → 2 Pyruvate + 2 ATP + 2 NADH

2 Phases of Glycolysis

➔ Energy Investment
◆ Energy-requiring phase, uses 2 ATP.
● Phosphorylation - attachment of a phosphate group to a molecule.
➔ Energy Harvesting
◆ Energy-releasing phase, releases 4 ATP, 2 NADH, and 2 pyruvate.
● Since 2 ATP was used in the first phase, we will deduct that from the net
gain, which will then be a total of 2 ATP for one molecule of glucose.

Energy Investment

Looking at the diagram, we can see that 1 molecule of glucose is split into 2 different
molecules. This is done in 2 major steps.

1. Glucose Priming

Three reactions``prime” glucose by changing it into a compound that can be cleaved readily
into two 3-carbon phosphorylated molecules.

Re: Glucose is prepared to be split into 2 molecules.

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2. Cleavage and Rearrangement

In the first of the remaining pair of reactions, the six-carbon product of step A is split into 2
different three-carbon molecules. Only one of the molecules can proceed to the next phase, so
the unneeded molecule will be transformed into a needed molecule.

Re: The “primed glucose” is then split into 2 molecules.

Did you know?

We still advise you to look at other sources of information. Reading text on your own is not
helpful, if we write all of the processes, we know you wouldn’t read them anyway. Keep slaying.

Energy Harvesting

From the first phase, we now have 2 “needed molecules”. In turn, energy harvesting will occur
twice. More enzymes will react with our molecules, producing 2 NADH (1*2) and 4 ATP (2*2).

1. Oxidation
Two electrons and one proton are transferred from G3P to NAD+, forming NADH. Again, energy
harvesting happens twice, so our end product will be 2 NADH.
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2. ATP Generation
Four reactions convert G3P into another three-carbon molecule, pyruvate. This process
generates 2 ATP molecules. 2 multiplied by 2 is 4 ATP.

After all of this, we would have used 2 ATP, generated 2 NADH, 4 ATP, and our end product,
2 pyruvate. Our net gain from 1 molecule of glucose under glycolysis would then be:

2 pyruvate, 2 NADH, and 2 ATP

Prep Stage: Pyruvate Oxidation

Pyruvate, the end product from glycolysis, is converted into carbon dioxide and a two-carbon
molecule called Acetyl CoA. For each molecule of pyruvate converted, one molecule of NAD+ is
reduced to NADH. It takes place in the mitochondrial matrix

Pyruvate + NAD+ + CoA → Acetyl-CoA + NADH + CO2

What happens?
A carboxyl group (CO2 and hydrogen) is
removed from pyruvate with the help of
pyruvate dehydrogenase, turning it into an
acetyl group. A carrier protein, Co-A then
attaches to the acetyl group in order to carry
it into the Krebs cycle, becoming Acetyl
Co-A.

*Net yield of 2 NADH

Second Stage: Krebs Cycle

Chain of reactions occurring in the mitochondrial matrix, through which most living cells
produce energy in aerobic respiration. Named after its discoverer, Hans Krebs.
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Overview of Krebs. Follow along with the diagram.

➔ Step 1
◆ Catalyzed by the enzyme Citrate synthase, Acetyl CoA (2 carbon-molecule or 2c)
joins with Oxaloacetate (4c), releasing the CoA group and forming the molecule
citrate (6c). Co-A detaches from the acetyl group because it's no longer needed.

➔ Step 2
◆ Catalyzed by the enzyme aconitase, citrate is converted into cis-aconitase before
the addition of water, turning it into one of its isomers, isocitrate. (However
most diagrams move directly to isocitrate from citrate.)

➔ Step 3
◆ Isocitrate (6c) is catalyzed by isocitrate dehydrogenase, and with that is the
removal of hydrogen (turning NAD to NADH) and the release of CO2, producing
α-ketoglutarate (5c).

➔ Step 4
◆ α-ketoglutarate is oxidized by α-ketoglutarate dehydrogenase, reducing NAD to
NADH in the process once again. At the same time, another carbon molecule is
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released, turning our 5c molecule into a 4c molecule. This produces succinyl

Co-A.

➔ Step 5
◆ Succinyl Co-A is then catalyzed by succinyl Co-A synthase, releasing 1 phosphate
group and donating it to GDP, making it GTP. This GTP is then converted into
ATP for energy use. This produced succinate.

➔ Step 6
◆ Succinate is catalyzed by succinate dehydrogenase, producing fumarate.
Dehydrogenase means another hydrogen is donated, this time to FAD, turning it
into FADH2, once again for energy source.

➔ Step 7
◆ The enzyme fumarase gives off H20 to fumarate producing malate.

➔ Step 8
◆ Oxaloacetate – the starting four-carbon compound is regenerated by oxidation of
malate in a reaction catalyzed by malate dehydrogenase. Another molecule of
NAD+ is reduced to NADH in the process.

PRODUCTS OF KREBS CYCLE

★ In a single turn of the cycle: 3 molecules of NADH, 1 molecule of FADH2, and 1 molecule
of ATP are produced.
★ Krebs Cycle normally turns twice for every glucose molecule, therefore 6 molecules of
NADH, 2 molecules of FADH2 and 2 molecules of ATP are the net yield.

Third Stage: Electron Transport Chain (ETC)

A series of proteins and organic molecules that are found in the inner membrane of
the mitochondria. Electrons are passed from one member of the transport chain to another
in a series of redox reactions, wherein, energy from NADH and FADH2 is transferred to ATP,
most being synthesized. In ETC, oxygen is our final electron acceptor.
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Overview of ETC

Visuals Steps
Step 1: NADH Dehydrogenase

➔ Reduced electron carriers (NADH

and FADH2) from other steps of
cellular respiration (Glycolysis and
Krebs) transfer their electrons to
molecules near the beginning of the
transport chain to Complex 1 or
NADH Dehydrogenase, wherein the
hydrogen and electrons are
removed from NADH.
➔ In the process, NADH and FADH2
turn back into NAD+ and FAD,
which can be reused in other steps of
cellular respiration.
➔ As electrons are passed down the
chain, they move from a higher to a
lower energy level, because they
release energy.
➔ Some of this energy is used to pump
H+ ions, moving them out of the
matrix and into the intermembrane
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space. This pumping establishes an

electrochemical gradient.

Step 2: Ubiquinone, Cytochrome BC1 and

Succinate Dehydrogenase

➔ The electrons from NADH

dehydrogenase are accepted by a
mobile electron carried called
ubiquinone and taken to Complex
III or cytochrome BC1.
➔ At the same time, below ubiquinone,
Complex II or succinate
dehydrogenase takes in FADH2
from glycolysis and Krebs, reducing
it and taking away its hydrogen. This
H+ (hydrogen) then joins the
electrons through the chain.

Step 3: Cytochrome C and Cytochrome C

Oxidase

➔ Cytochrome C, another mobile

carrier, will then take the electrons
from Complex III and bring it to
Complex IV or cytochrome C
oxidase. Within this complex
electrons are transferred to
molecular oxygen, which splits in
half and takes up H+ to form water.
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Step 4: Gradient-driven Synthesis of ATP

➔ H+ ions are now free flowing in the

intermembrane space as it is
pumped out of the ETC proteins. This
has a higher concentration of positive
charge compared to the matrix’s
negative charge, causing the H+ ions
to go against the electrochemical
gradient. So as H+ ions flow down
their gradient and back into the
matrix, they pass through an
enzyme called ATP Synthase, which
harnesses the flow of protons (+) to
synthesize ATP.

Anaerobic Respiration: Fermentation

This process is the release of a relatively small amount of energy in cells through the
breakdown of food substances in the absence of oxygen. Under these conditions, the
hydrogen atoms generated by glycolysis are donated to organic molecules in a process
called fermentation.

➔ Fermentation
◆ Bacteria carry out more than a dozen kinds of fermentation, all using some form
of organic molecule to accept the hydrogen atom from NADH and thus
recycle NAD+. There are two kinds of fermentation:

● 1. ETHANOL FERMENTATION
○ It occurs in single-celled fungi called yeast.
○ Yeast enzymes remove a terminal CO2 group from pyruvate
through decarboxylation, producing a two-carbon molecule called
acetaldehyde.
○ The acetaldehyde then accepts a hydrogen atom from NADH
(through a reduction), producing NAD+ and ethanol (ethyl
alcohol).

● 2. LACTIC ACID FERMENTATION

○ Regeneration of NAD+ without decarboxylation.
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○ Muscle cells use an enzyme called lactase dehydrogenase to

transfer a hydrogen atom from NADH back to the pyruvate that is
produced by glycolysis.
○ This reaction converts pyruvate into lactic acid and regenerates
NAD+ from NADH.

Cellular Respiration: Recap

If you want me to compress the whole process in 1 paragraph, you are screwed, but I will try.

Since we’re helpless and can’t make food out of sunlight, we eat what plants work hard for. Very
humane. Anyway, you remember photosynthesis right? Cellular respiration is just a reversal of
that process. So: plants use energy to make food, and we use food to make energy. That’s it.

The picture above is aerobic cellular respiration by the way, aerobic for oxygen, it needs oxygen.

The other type is anaerobic, which, surprise, does not need oxygen. Our body does it when
there’s food we can’t digest by aerobic-ing. Please read the whole file if you want to pass genbio.