Unit 10: Metabolism Photosynthesis

Concept of Photosynthesis:

● Plants absorb molecules such as CO2, water, and minerals and organize
them into organic molecules, that could stabilize structures such as
○ Cells (cellulose) (made up of glucose units)
○ Tissues
○ organs (leaf)
● Photosynthesis is an example of an anabolic reaction (build up process of
metabolism wherein the simple organic molecules, a complex molecule is
produced.)
● Each plant carries photosynthesis with such precision
○ Photosynthesis is an efficient process. (ex.: light absorption, excitation
of electron)
● Death and decay increase entropy (disorder) of organisms
○ Inorganic molecules are released to the environment by a simple decay
process.
● Photoautotrophs and heterotrophs co-exist.
● Photosynthesis is a complex process

*pa-add dun sa difference of Photoautotroph & Heterotrophs table

Photoautotroph

● Produce their own food in the presence of light energy

 Ex: Green Algae, Brown Algae & Red Algae, Cyanobacteria bacteria (Nostoc,
Spirulina)

Heterotrophs

● Depend nutrients from other organisms

Ex: Plants that are non photosynthetic (Achlorophyllous)

Energy & Reducing Power

● Photosynthesis is a simple redox.

Energy Carriers in Photosynthesis:

● ATP (Adenosine triphosphate)

○ Composed of Adenine & Ribose (high carbon sugar) & 3 Phosphate
group
○ Carries high-energy phosphate bonds.
○ Three methods by which ADP can be phosphorylated
■ Photophosphorylation which is under substrate - level that involves
light energy in photosynthesis
■ Substrate-level phosphorylation
■ Oxidative phosphorylation

Reducing Power

● Oxidizing and reducing agents

○ NAD+ and NADP+ are oxidizing agents, take electrons from other
molecules
○ NADH (for respiration) and NADPH (for photosynthesis) are reducing
agents that have tendency to place electrons onto other neighboring
molecules
Other Electron Carriers:

* Fluorescence: electrons give off light energy.

*all electron carriers are found in the thylakoid.

Cytochromes

● Small proteins with co-factor heme, which holds an iron atom

● Intrinsic, parts of thylakoid membrane
● Carries electron only between sites that are extremely close together

Plastoquinone

● Transport electrons over short distance within the membrane

● Hydrophobic, long HC (hydrocarbon) tails (embedded in the thylakoid
membrane)
● Pick up two electrons and binds two protons
Plastocyanin

● Carries electron on a copper (RA)

● Oxidized is in the +2 oxidation state
● Reduced one level to the + 1 oxidation state after picking up electrons
● Loosely arranged with chloroplast membrane
● Only move short distance
Photosynthesis

● Is the process by which green plants and autotrophic organisms synthesize

food.
● Is the combination of carbon dioxide with water to form carbohydrates.

Chloroplast

● Major organelle involved in photosynthesis.

* Lumens where Hydrogen protons would accumulate in photosynthesis.

* Calvin cycle = AKA C3 Cycle, Dark reaction, light independent reaction

Photosynthesis has Light-dependent and Light-independent Reactions

* Light independent happens all throughout the day as long as there is enough ATP
& NADPH

FACTORS INVOLVED LIGHT DEPENDENT REACTION

1. The Nature of Light

a. Light is a small segment of electromagnetic radiation spectrum
(involves both short & long wavelengths of light)
b. Radiation is a set of particles called quanta (present in photons) or as
set of waves
c. Visible light is from 390 nm to 760 nm
d. Long wavelength has little energy
e. Short wavelength has large energy in each quantum

Wavelength

● distance between 2 consecutive peaks of waves

● measured/expressed in nanometers (nm)

Visible Light

● only portion that is used in photosynthesis

● found at the middle / near the middle
● region of electromagnetic radiation
● exemplifies the color of rainbow
● VIBGYOR (ROYGBIV) - Violet, Indigo, Blue, Green, Yellow, Orange,
Red
● Red - longest wavelength for visible light
● Violet - shortest wavelength for visible light
 ● Red & Blue - ONLY colors that can be used for photosynthesis
○ The other colors are NOT used because they are just reflected
back, not absorbed by the photosynthetic pigments
○ When colors are reflected back, it will be the color of the
organism/object
● Below 390 nm - short wavelength of light that includes UV Ray, X-ray,
& Gamma Ray
○ Short wavelength but contains too much energy
○ Cannot be used by plants for photosynthesis - destroys
chlorophyll structure
● Longer wavelength includes Infrared & Radio Waves
○ Cannot be used for photosynthesis because energy is very very
low to excite electrons from basal state to unexcited state

2. The Nature of Pigments

● Plant pigments transfer absorbed light energy to electrons

2 Main Pigments involved in Photosynthesis

● Main photosynthetic pigment - Chlorophyll a (Ch a)

○ Ch a absorbs only some red and some blue light
○ Needs helping pigments because it is inefficient
● Accessory pigments - Chlorophyll b (Ch b), Carotene, &
Xanthophyll
○ Helping pigments that absorb wavelengths of red & blue
light that are not absorbed by Chlorophyll a
○ Prevents photooxidation of Chlorophyll a (protects
Chlorophyll a from the harmful shorter wavelengths)
○ Increase the absorption spectrum of photosynthesis
● Chlorophyll does not use high energy quanta
● Bonds in chlorophyll ring system are double bonds alternating with
single bond

2 Major Parts of Chlorophyll Pigment

 ● Porphyrin Ring (head part)
○ Tetrapyrrole structure (4 pyrrole rings)
○ 4 pyrrole rings are joined together & sequestered at the
center by MAGNESIUM
○ Contains atoms of: Carbon, Hydrogen, Nitrogen,
Magnesium, Oxygen
● Phytol Tail (tail part)
○ Connected to the thylakoid membrane

● Chlorophyll a Chemical Formula: C₅₅H₇₂O₅N₄Mg

● Chlorophyll b Chemical Formula: C₅₅H₇₀O₆N₄Mg
○ Difference is that, the methyl group (CH₃) in Chlorophyll a is
transformed into an aldehyde (C, double bond O, H)

● Paper Chromatography / Chromatographic Separation - process of

separating pigments
 Separating the pigments in a plant using an alcohol extract.

● Done in a closed vessel to observe equilibrium

● Mobile phase
○ Solvent used to separate the pigments according
to polarity and affinity (both are directly
proportional with each other)
○ The more polar, the faster the rate migration
● Stationary phase
○ Filter / chromatographic paper
○ Interstitial airspaces present in the filter paper
exerts an effort for the migration of solvent system
together with the solute (pigments)
● Rf value - distance travelled by solute divided by distance
travelled by solvent
● Carotene - orange
● Xanthophyll - yellow
● Chlorophyll a - bluish green
● Chlorophyll b - grass green

2 Types of Carotenoid Pigment (involved in photosynthesis)

● Carotene - orange pigment

○ Antioxidant (no oxygen present)
○ Formula: C₄₀H₅₆
● Xanthophyll - yellow pigment
○ Oxidizing
○ Formula: C₄₀H₅₆O
● Fluorescence - release of light by a pigment
● Absorption Spectrum - graph that shows which wavelengths are most
strongly absorbed by a pigment
● Action Spectrum - shows which wavelengths are most effective at
powering a photochemical process
● Chlorophyll Absorbance and Photosynthetic spectrum MUST meet &
compliment each other
○ They meet at the blue & red region (shown in the image)

● Varigated - leaf having 2 colors/pigment

Pigments present in the image:

● Green pigment on the side

○ Contains the chlorophyll pigment
 ● Pink/reddish in the middle
○ Anthocyanin pigment (non-photosynthetic pigment)

Photosynthetic pigments: PHOTOSYSTEM

● Main photosynthetic pigment: Chlorophyll (Ch a)

● Accessory pigments: ch b and carotenoids

PHOTOSYSTEM

● Where Ch a & accessory pigments are arranged in a granule in the thylakoid

● A union / aggregation of the pigments & carriers in the thylakoid. (about 300
mol of ch a, b and carotenoids)
● Transfer of energy in the system is called resonance

2 types of Photosystem:

❖ Photosystem I
➢ A system having little ch b, has more ch a.
❖ Photosystem II
➢ A system having ch b & ch a in almost equal proportion.
● Transfer of energy in the system is called resonance
Photosynthetic units - 300 molecules of ch a & b & carotenoids
PHOTOSYSTEM I (dagdag sa table)

● It is in P700 because it maximally absorbs wavelengths of light having

700 nanometers
● Plastocyanin is a member of the electron carriers
● Iron-sulfur (Fe4S4)
● Strong Reducing Agent (NADPH)

PHOTOSYSTEM II (dagdag sa table)

● It is in P680 because it maximally absorbs wavelengths of light having

680 nanometers
● Quinone type - ung mga plastoquinone
● Involves photolysis of water, where oxygen is released via stomates.
● Strong oxidizing agent (NADP+)

PHOTOSYSTEM I STEPS

1. When sunlight strikes, energies will be absorbed by either ch b or

carotenoids. The light energy will travel from one molecule to another
until it reaches P700.
 ○ P700 is a special type of ch a and is not easily destroyed
2. When light energy excites, an electron in ch a becomes unstable that it
reacts with anything or it fluorescences (no absorbing molecules),
resulting for electrons to be lost, wasting energy. Which is why
electrons must react with proper molecules which are close enough for
a reaction to take place.
3. Due to the instability of the excited electrons, it leaves P700 and is
absorbed by Fx (Fe4S4) (a series of electron carriers). Making Fx a
powerful reducing agent.
4. The Fx immediately passes the electrons to the Ferredoxin ( a small
protein with 10,500-11K dalton).
5. As the electrons move from Ferredoxin, it creates energy strong
enough to add 2 H ion to the molecule of 2 NADP+, producing 2
NADPH
○ NADPH is stable enough to move away and move to stroma
regions where it can be used to power biochemical reactions.

PHOTOSYSTEM II

Remember: P700, loses an electron & becomes oxidized, so bonding

orbitals can be easily arranged which may destroy P700.

Meaning of Photosystem II: Adds electrons back to P700.

Important Concepts:

● Produce the reducing agent NADPH

 ● Synthesis of ATP by chemiosmotic phosphorylation (or non
cyclic)
● Breakdown of water into H+, O2

The procedure is like a backward reaction.

1. Once P700 is oxidized, plastocyanin (molecule with copper)

donates an electron to P700 making plastocyanin to lose its
electron.
2. Plastocyanin then receives an electron from the cytochrome
complex then the cytochrome complex loses an electron,
becoming an oxidized agent.
3. The cytochrome complex will then receive an electron from
plastoquinone.
● ATPs are produced by proton motive force
4. Once plastoquinone loses an electron, it will receive an electron
from pheophytin (ch a w/out magnesium). Pheophytin will
become oxidized.
5. Pheophytin will then get electrons from P680.
6. P680 will lose 4 electrons, becoming oxidizing agents. P680
then receives 4 electrons from water as it is present in the
thylakoid.
7. When water loses electrons, it will break down into protons and
oxygen & hydrogen will be discarded into stroma.

* The photosystems are known to be the Z-Scheme of Photosynthesis as electrons

are passed in Z-shaped.

Cyclic vs. Non-Cyclic Photophosphorylation

Non-Cyclic : electrons move smoothly from water to NADPH and generate small
amounts of ATP in the process.

* The generation of small amounts of ATP is problematic so there must be equal

balance in the production of NADPH & ATP to drive the next round of
photosynthesis.

Cyclic : Electrons flow from P700 to plastoquinone which carries the proton to the
lumen and it binds to electron to P700

* As the electrons from PQ are moving, for every electron, it will absorb 2 H ions
from stroma and will be forcefully placed in the thylakoid lumen.

As H ions increase, there will be a difference of protons between 2 regions. In the

thylakoid portion, it will move fast, creating energy which will be enough to add PI
(inorganic phosphate) to the ADP.

Production of NADP+ & NADPH used the process of simple reduction

Production of ADP & ATP used the process of chemiosmotic phosphorylation or

non-cyclic photophosphorylation

● Chemiosmosis is the movement of ions across a semipermeable membrane,

down their electrochemical gradient.
● An example of this would be the formation of adenosine triphosphate by the
movement of hydrogen ions across a membrane during photosynthesis

DARK REACTION

● If there will be enough ATPs & NADPH, the next round will be Dark Reaction
● Also known as Biochemical Reaction of Photosynthesis / C₃ Cycle / Light
Independent Reaction
○ It’s called as C₃ Cycle because the 1st stable product is 3-PGAL
● Stroma reaction - because it occurs in the stroma
● Calvin Benson Cycle - discovered by Biochemist tandem Calvin & Benson
● Chemistry: Conversion carbon dioxide to carbohydrates
○ Where glucose is produced in photosynthesis
● Carbon Dioxide Fixation
○ happens when leaves’ stomates are open
○ CO₂ from the atmosphere can easily diffused inside the leaf
○ CO₂ will enter the leaf > mesophyll > individual cell > chloroplast
● Once inside the chloroplast, CO₂ will be met by a 5-carbon compound called
RIBULOSE BIPHOSPHATE (RuBP)
○ Ribulose Bisphosphate (RuBP) - sugar having 5 carbons
○ 6C (6 carbon) - unstable & will simply breakdown into 2 parts (3C &
3C)
● 3C (3-Phosphoglycerate)
○ Compound having a phosphate attached at Carbon number 3
○ It will be phosphorylated (a phosphate group will be added, coming
from ATP)
● ATP has 3 phosphate groups
○ It will donate 1 of its phosphate to Carbon number 1
● ATP become ADP (Adenosine triphosphate > Adenosine diphosphate)
● 1, 3-Bisphosphoglycerate
○ It will be reduced by a good reducing agent, produced in the light
reaction
● NADPH - the reducing agent
○ Donates its H proton to 1, 3-Bisphosphoglycerate
○ It will now become NADP⁺ (becomes oxidized)
○ It will be reduced again in the light reaction photosynthesis
● When a molecule of 3-Bisphosphoglycerate is reduced by a molecule of
NADPH and the reduction is coupled to the loss of phosphate at Carbon
 number 1, it will form an aldehyde called Glyceraldehyde-3-phosphate
(3-PGAL)
● Glyceraldehyde-3-phosphate (3-PGAL)
○ 1st stable product of Calvin Cycle (Dark Reaction)
○ Each molecule of 3-PGAL has 3 carbons
○ It will react with another 3-PGAL molecules, because it needs
additional 2 carbon (5 carbon in all) from another 3-PGAL molecule
forming Ribulose 5-Phosphate (Ru5P)
● Ribulose 5-Phosphate (Ru5P)
○ Only 1 phosphate is attached to Carbon number 5
● The remaining carbon in the reaction of two 3-PGAL molecules will now form
Glucose (C₆H₁₂O₆)
● Ribulose 5-Phosphate (Ru5P) is phosphorylated again by a molecule of ATP
○ ATP will donate its phosphate to Carbon number 1 and will be RuBP
● Process will be repeated

RuBP Carboxylase (Rubisco)

● Ribulose-1,5-bisphosphate carboxylase
● Enzyme responsible for the Dark Reaction
● One of the largest & most complex enzymes
○ Has the highest quantity of protein in the Earth’s surface
● A giant complex of 2 protein subunits
● With 8 copies of large protein, each with a molecular wt of 14,000 - 15,000
daltons
● Total molecular weight of 480,000 daltons
● Low substrate specificity
○ Enzymes must be specific & loyal but RuBP is not loyal because it
does not only react with CO₂, it also reacts with oxygen
○ When oxygen is greater than CO₂, RuBP binds with oxygen instead of
CO₂ making it problematic and results to PHOTORESPIRATION
● When RuBP reacts with CO₂, it will go through C₃ Cycle and produce glucose
 ● But when it reacts with oxygen, it will produce 5 carbon compound splits into 2
(3C & 2C molecule)
● PHOSPHOGLYCOLATE (2C molecule) - transported from the chloroplast to
peroxisomes & mitochondria
○ Phosphoglycolates inside of each peroxisome & mitochondria will be
converted into useful amino acids known as GLYCINE & SERINE

PHOTORESPIRATION

● Energy wasting process

● Involves 3 organelles : chloroplast, peroxisome, mitochondrion
● Releases CO₂ in the end
○ CO₂ is not used in photosynthesis and just move out of the leaves,
released to the environment
● A good defense to remove the phosphoglycolic acid but an expensive process
because most ATP & NADPH are used in the process instead of using them
to produce sugar

ANABOLIC METABOLISM

● Anabolic - building up from simpler inorganic to organic

2 Important Anabolic pathways :

1. Synthetic pathway of polysaccharides and fats

2. Synthesis of ATPs and NADPH in photosynthesis

● Gluconeogenesis is the anabolic synthesis of glucose

* glucose-1-phosphate is acted upon by ADP-glucose phosphorylase.

Starch - polymer of glucose

2 forms of Starch: Amylose & Amylopectin

CAM PLANTS

● Crassulacean Acid Metabolism Plants

● Plants that fight off photorespiration and CO2 are stored in the form of an acid
before use in photosynthesis.
● First found in the plant family, Crassulaceae. Also found in Orchidaceae which
are found in warm, dry regions. It is also found in succulents such as cactuses
& agaves.
● Stomata open at night
● There are 2 major reactions that are separated temporarily. (Night time & day
time)
○ Night Time
■ Stomata is open, making CO2 to be easily diffused inside the
leaf.
■ Once inside, CO2 is converted to HCO3- and is met with 3C
PEP (Phosphoenolpyruvate)
■ 3C & 1C can produce PEPC that is further produced into C4
acid (Oxaloacetic acid, OAA) & Pi
■ OAA is stored in the vacuole wherein it is converted into malic
acid
○ Day Time
■ Stomata is closed to conserve water, forbidding CO2 to enter.
But it can be substituted by malic acid.
■ Malic acid undergoes decarboxylation, where it is broken down
into 2. One is CO2 and C3 acid.
● The continuous decarboxylation of Malic Acid inside the
chloroplast will ensure continuous supply of CO2 so that
Rubisco wouldn’t be confused and will fix it by conducting
the Calvin Cycle.
■ C3 acid goes back to the cycle and it becomes PEP.
C4 Metabolism in Monocot Plant Species

● Involved in 2 cells (Mesophyll cells & Bundle Sheath Cells

● In mesophyll region, doon ung C4 metabolism and in bundle sheath is

where Carbon Dioxide Fixation happens
● C4 metabolism happens in plants that has Kranz Anatomy
● Mesophyll cells enclose photosynthetic bundle sheath cells is an
adaptation against photorespiration.