BIOLOGY
PHOTOAUTOTROPHS
PHOTOSYNTHESIS
● is essential to all life on Earth; both plants
and animals depend on it.
● it is the only biological process that can
capture energy that originates in outer space
(sunlight) and convert it into chemical
compounds (carbohydrates) that every
organism organisms uses to power its
metabolism.
● the energy of sunlight is captured and used
to energize electrons, which are then stored
in the covalent bonds of sugar molecules.
● is vital because it evolved as a way to store
the energy in solar radiation (the “photo-“
part) as high-energy electrons in the
carbon-carbon bonds of carbohydrate
molecules (the “-synthesis” part).
● those carbohydrates are the energy source
that heterotrophs use to power synthesis of
ATP (adenosine triphosphate) via
RESPIRATION.
● photosynthesis powers 99% of Earth’s
ecosystems.
● is a multi-step process that requires sunlight,
carbon dioxide (which is low in
● energy), and water as substrates.
● after the process is complete, it releases
OXYGEN (generated as a waste product of
photosynthesis) and produces
Glyceraldehyde-3-phosphate (GA3P),
● simple carbohydrate molecules (which are
high in energy) that can be subsequently be
converted into glucose, sucrose, or any
dozens of other sugar molecules.
● these sugar molecules contain energy and
the energized carbon that all living things
need to survive.
● the chemical equation for photosynthesis has
many steps that takes place and are actually
quite complex.
● before learning the details of how
photoautotrophs turn sunlight into food, it is
important to become familiar with the
structures involved.
● literally, “self-feeders using light”, use light
to manufacture their own food.
● Plants, algae, and a group of bacteria called
cyanobacteria are the only organisms
capable of performing photosynthesis.
HETEROTROPHS
● “other feeders”, they must rely on the sugars
produced by photosynthetic organisms for
their energy needs (e.g., animals, fungi, and
most other bacteria).
CHEMOAUTOTROPHS
● synthesize sugars, not by using sunlight’s
energy, but by extracting energy from
inorganic chemical compounds.
LAYERS OF CELL
Mesophyll
● the process of photosynthesis occurs in a
middle layer.
Stomata (singular: stoma)
● small, regulated openings where the gas
exchange of carbon dioxide and oxygen
occurs.
● also plays roles in the regulation of gas
exchange and water balance.
● it is typically located on the underside of the
leaf, which helps minimize water loss.
Chloroplast
● an organelles where photosynthesis of
autotrophic eukaryotes takes place.
● it has a double membrane; the outer
membrane and inner membrane.
Thylakoids
● stacked and disc-shaped structure within the
chloroplast.
● embedded in the thylakoid membrane is
chlorophyll, a pigment (molecule that
absorbs light).
● the thylakoid membrane encloses an internal
space called the thylakoid lumen.
Granum
● a stack of thylakoids
Stroma or “bed”
● the liquid-filled space surrounding the
granum

TWO PARTS OF PHOTOSYNTHESIS
LIGHT-DEPENDENT REACTIONS
● energy from sunlight is absorbed by
chlorophyll and that energy is converted into
stored chemical energy.
LIGHT-INDEPENDENT REACTIONS
● the chemical energy harvested during the
light-dependent reactions drive the assembly
of sugar molecules from carbon dioxide.
LIGHT ENERGY
● sun emits an enormous amount of
electromagnetic radiation (solar energy).
● visible light is the only portion of the
fraction of energy which human can only
see.
● the manner in which solar energy travels is
described as waves.
● scientist can determine the amount of energy
of a wave by measuring its wavelength, the
distance between consecutive points of a
wave.
● a single wave is measured from two
consecutive points, such as from crest to
crest or from trough to trough.
● light energy initiates the process of
photosynthesis when pigments absorb the
light.
● Organic pigments like the chloroplast
thylakoid have a narrow range of energy
levels that they can absorb.
● plants pigment molecules absorb only light
in the wavelength range of 700nm to 400nm.
● lower energy levels represented by red light
are insufficient to raise an orbital electron to
a populatable, excited (quantum) state.
● Higher energy levels represented by blue
light will physically tear the molecules
apart, called bleaching.
TWO MAJOR CLASSES OF PIGMENT
CHLOROPHYLLS
● there are five major chlorophylls: a, b, c, d
and a related molecule found in prokaryotes
called bacteriochlorophyll.
CAROTENOIDS
● are much larger group of pigments. (e.g.,
found in fruit – such as the red tomato
(lycopene), the yellow of corn seeds
(zeaxanthin), or the orange peel
(B-carotene).
SPECTROPHOTOMETER
● is an instrument that can differentiate which
wavelength of light a substance can absorb.
● it measures transmitted light and compute
from it the absorption.

ELECTROMAGNETIC SPECTRUM
● is the range of all possible frequencies of
radiation.
● the difference between wavelengths relates
to the amount of energy carried by them.
● the longer the wavelength, the less energy is
carried. The shorter the wavelength, the
most energy is carried.
● the higher-energy waves can penetrate
tissues and damage cells and DNA,
explaining why X-rays and UV rays can be
harmful to living organisms.
 HOW LIGHT-DEPENDENT REACTION
WORK
● the overall function of light-independent
reactions is to convert solar energy into
chemical energy in the form of NADPH and
ATP. This chemical energy supports the
light-independen reactions and fuels the
assembly of sugar molecules.
● protein complexes and pigment molecules
work together to produce NADPH and ATP.
● both photosystem have the same basic
structure; a number of antenna proteins to
which the chlorophyll molecules are bound
surround the reaction center where the
photochemistry takes place.
● each photosystem is serviced by the
light-harvesting complex, which passes
energy from sunlight to the reaction center;
it consists of multiple antenna proteins that
contain a mixture of 300-400 chlorophyll a
and b, as well as other pigments like
carotenoids.
● the absorption of a single photon or distinct
quantity or “packed” of light by any of the
chlorophylls pushes that molecule into an
excited state.
● the energy is transmitted from chlorophyll to
chlorophyll until eventually (after a
millionth of a second), it is delivered to the
reaction center.
PHOTOSYSTEM
● a multiprotein complex where the actual step
that converts light energy into chemical
energy takes place.
● Two types of photosystem are embedded in
the thylakoid membrane, photosystem II
(PSII) and photosystem I (PSI).
REACTION CENTER
● where the photochemistry takes place.
● center contains a pair of chlorophyll a
molecules with a special property.
PHOTOACT
● two chlorophylls can undergo oxidation
upon excitation; they can actually give up an
electron in this process.
CYTOCHROME COMPLEX
● is an enzyme composed of two protein
complexes, transfers the electrons from the
carrier molecule plastoquinone (Pq) to the
protein plastocyanin (Pc), thus enabling both
the transfer of protons across the thylakoid
membrane and the transfer of electrons from
PSII to PSI.
TWO MAJOR COMPONENTS OF ELECTRON
TRANSPORT CHAIN
PHOTOSYSTEM I (P700)
● delivers its high-energy electrons, one at the
time, to the primary electron acceptor, and
through the electron transport chain.
PHOTOSYSTEM II (P680)
● is oxidized and sends a high-energy electron
to NADP+ to form NADPH (Nicotinamide
adenine dinucleotide phosphate).
● thus, PSII captures the energy to create
proton gradients to make ATP, and PSI
captures the energy to reduce NADP+ into
NADPH.
HOW LIGHT-INDEPENDENT REACTION
WORK
● the products of light-dependent reactions,
ATP and NADPH, have life spans in the
range of millionths of seconds, whereas the
product of light-independent reactions
(carbohydrates and other forms of reduced
carbon) can survive for hundreds of millions
of years.
● also called the Calvin Cycle discovered by
Dr.Marvin Calvin
THREE BASIC STAGES OF CALVIN CYCLE
● Fixation
● Reduction
● Regeneration
Stage 1: Carbon Fixation
● in the stroma, carbon dioxide and two other
components are present to initiate the
light-independent reactions: an enzyme
called ribulose bisphosphate carboxylase
(RuBisCO), and three molecules of ribulose
bisphosphate (RuBP), have a five atoms of
carbon and flanked by two phosphates.
● RuBisCO catalyzes a reaction between CO2
and RuBP. For each CO2 molecule that
reacts with one RuBP, two molecules of
another compound (3-PGA) form.
● this process is called carbon fixation,
because carbon dioxide is “fixed” from an CELLULAR RESPIRATION
inorganic form in organic molecules.
● is a series of metabolic pathways that
Stage 2: Reduction extracts energy from the bonds in glucose
● ATP and NADPH are used to convert the six and converts it into a form that living things
molecules of 3-PGA into six molecules of a can use- both producers like plants, animals,
chemical called glyceraldehyde 3-phosphate and consumers.
(G3P). That is a reduction reaction because ● Cellular respiration is the process on how
it involves the gain of electrons by 3-PGA. we derive energy or fuel energy from what
Six molecules of both ATP and NADPH are we eat or specifically, from glucose.
used.
● for ATP, energy is released with the loss of STAGES OF CELLULAR RESPIRATION
the terminal phosphate atom, converting it
into ADP; for NADPH, both energy and a
hydrogen atom are lost, converting it into
NADP+. Both of these molecules return to
the nearby light-dependent reactions to be
reused and reenergized.

Stage 3: Regeneration
● at this point, only one of the G3P molecules
leaves the Calvin Cycle and is sent to the
cytoplasm to contribute to the formation of
other compounds needed by the plant. It
takes three “turns” of Calvin Cycle to fix
enough net carbon to export one G3P. GLYCOLYSIS
● one is exported while the remaining five ● is the first step in the breakdown of glucose
molecules of G3P are remain in the cycle to extract energy for cellular metabolism.
and is used to regenerate RuBP, which ● Nearly all living organisms carry out
enables the system to prepare for more CO2 glycolysis as part of their metabolism.
to be fixed. ● The process does not use oxygen and is
therefore anaerobic (processes that use
oxygen are called aerobic).
DARK REACTIONS ● Glycolysis takes place in the cytoplasm of
● the most outdated name both prokaryotic and eukaryotic cells.
● can be misleading because it implies
incorrectly that the reaction only occurs at
night or is independent of light, which is
why most scientists and instructors no
longer use it.

BREAKDOWN OF PYRUVATE
Glycolysis begins with the six carbon ring-shaped
structure of a single glucose molecule and ends with
two molecules of a three-carbon sugar called
pyruvate.
GLUCOSE ENTERS HETEROTROPHIC
CELLS IN TWO WAYS:
● through secondary active transport.
● through a group of integral proteins called
GLUT proteins, also known as glucose
transporter proteins.
GLYCOLYSIS CONSISTS OF TWO DISTINCT
PHASES:
First Half of Glycolysis (Energy-Requiring Steps)
● the first part of the glycolysis pathway traps
the glucose molecule in the cell and uses
energy to modify it so that the six-carbon
sugar molecule can be split evenly into the
two three-carbon molecules.
Second Half of Glycolysis (Energy-Releasing
Steps)
● the second part of glycolysis extracts energy
from the molecules and stores it in the form
of ATP and NADH, the reduced form of
NAD.
OUTCOMES OF GLYCOLYSIS
● glycolysis starts with a 6-carbon structure
glucose molecule and ends with two
molecules of a 3-carbon sugar called
pyruvate.
● two ATP molecules were used in the first
half of the pathway to prepare the six-carbon
ring for cleavage, so the cell has a net gain
of two ATP molecules and 2 NADH
molecules for its use.
● the last step in glycolysis will not occur if
pyruvate kinase, the enzyme that catalyzes
the formation of pyruvate is not available in
sufficient quantities.
● in this situation, the entire glycolysis
pathway will proceed,but only two ATP
molecules will be made in the second half.
● in order for the pyruvate from glycolysis to
enter the Krebs cycle, it must be converted
to Acetyl CoA (2-carbon).
● a carboxyl group is removed from pyruvate,
releasing CO2 into the surrounding.
● NAD+ is reduced to NADH
● an acetyl group is transferred to coenzyme
A, resulting in acetyl CoA.
CITRIC ACID OR KREBS CYCLE
● Hans Kreb
● like conversion of pyruvate to acetyl CoA,
the Citric Acid Cycle takes place in
the matrix of Mitochondria.
● almost all the enzymes of the Citric Acid
Cycle are soluble, with the single exception
of the enzyme Succinate Dehydrogenase,
which is embedded in the inner membrane
of Mitochondria.
● unlike glycolysis, the Citric Acid Cycle is a
closed loop: the last part of the pathway
regenerates the compounds used in the first
step.
● the 8 steps of the cycle are a series of redox,
dehydration, hydration and decarboxylation
reactions that produce two carbon dioxide
molecules the GTP/ATP and reduced NADH
and FADH. This is considered an aerobic
pathway because the NADH and FADH2
produced must transfer their electrons to the
next pathway in the system, which will use
oxygen.
ENZYMES INVOLVED IN EACH STEP:
Step 1: Citrate synthase
Step 2: Aconitase
Step 3: Isocitrate dehydrogenase
Step 4: α-ketoglutarate dehydrogenase
Step 5: Succinyl-CoA dehydrogenase
Step 6: Succinate dehydrogenase
Step 7: Fumarase
Step 8: Malate dehydrogenase
PRODUCTS OF THE CITRIC ACID CYCLE:
2 - CO2
3 – NADH
1 – FADH
1 – GTP or ATP
ELECTRON TRANSPORT CHAIN
● the electron transport chain is the last
component of aerobic respiration and is the
only part of glucose metabolism that uses
atmospheric oxygen.
● Oxygen continuously diffuses into plants,
● animals.
● It enters the body through the respiratory
system.
● Electron transport is a series of redox
reactions that resemble a relay race or
bucket brigade in that electrons are passed
rapidly from one component to the next.
● It is present in multiple copies in the inner
● mitochondrial membrane of eukaryotes and
the plasma membrane of prokaryotes.
CHEMIOSMOSIS
● chemiosmosis is the movement of ions
across a selectively permeable membrane,
down their electrochemical gradient.
● during chemiosmosis, the free energy from
the series of reactions that make up the
electron transport chain is used to pump
hydrogen ions across the membrane,
establishing an electrochemical gradient.
● the uneven distribution of H+ ions across the
membrane establishes both concentration
and electrical gradients, owing to the
hydrogen ions' positive charge and their
aggregation on one side of the membrane.
● hydrogen ions in the matrix space can only
pass through the inner mitochondrial
membrane through a membrane protein
called ATP synthase.
● as protons move through ATP synthase,
ADP is turned into ATP.
● the production of ATP using the process of
chemiosmosis in mitochondria iscalled
oxidative phosphorylation.
ATP YIELD ● various methods of fermentation are used by
● the amount of energy (as ATP) gained from assorted organisms to ensure adequate
glucose catabolism varies across species and supply of NAD+ for the sixth step of
depends on other related cellular processes. glycolysis.
● while glucose catabolism always produces ● without these pathways, that step would not
energy, the amount of energy (in terms of occur and no ATP would be harvested from
ATP equivalents) produced can the breakdown of glucose.
vary,especially across different species.
● the number of hydrogen ions that the
electron transport chain complexes can
pump through the membrane varies between
species.
● NAD+ - in the liver
● FAD+ - in the brain.
● the use of intermediates from glucose
catabolism in other biosynthetic pathways,
such as amino acid synthesis, can lower the
yield of ATP.
● overall, these pathways of glucose
metabolism extract about 34% of the energy
contained in glucose.

CELLULAR RESPIRATION EQUATION

ANAEROBIC RESPIRATION
● is the type of respiration through which cells
can break down sugars to generate energy in
the absence of oxygen.

OTHER TYPES OF FERMENTATION:

● other fermentation methods occur in
bacteria.
● many prokaryotes are Facultatively
Anaerobic, meaning that they can switch
between aerobic respiration and
fermentation, depending on the availability
of oxygen.
● certain prokaryotes, like Clostridia, are
obligate anaerobes.
● obligate anaerobes live and grow in the
absence of molecular oxygen.
● oxygen is a poison to these microorganisms
and kills them from exposure.
● should be noted that all forms of
fermentation, except lactic acid
fermentation, produce gas.
● the production of particular types of gas is
used as an indicator of the fermentation of
specific carbohydrates, which plays a role in
laboratory identification of the bacteria.