Module 9: active site, we call it the

Enzyme-Substrate complex
ENZYMES
MODELS OF ENZYME ACTION
 Are biological catalysts
 They speed up the rate of chemical 1. LOCK AND KEY MODEL
reactions by lowering its activation
energy - Enzymes are specific. This high
 They are protein-derivatives thus made specificity of enzymes can be
from amino acids or polypeptide chains explained by this lock and key
 An enzyme acts upon a substrate by model.
enhancing the capability of a chemical - According to the lock and key
reaction to act. model, enzymes will only act upon a
 In a chemical reaction, the enzyme specific substrate.
catalyzes the reaction but will not affect
the chemical composition of a chemical
reaction just like a real inorganic
catalyst.

2. INDUCED FIT MODEL

3. When the active site on the enzyme

makes contact with the proper
substrate, the enzyme molds itself to
the shape of the molecule
4. This theory of enzyme-substrate
1. COENZYME/COFACTOR interactions has two advantages
- It activates the apoenzyme. compared to the lock and key
A COENZYME is a vitamin model:
derivative while a
COFACTOR is a mineral It explains how enzymes may exhibit broad
derivative specificity (e.g. lipase can bind to a variety
2. APOENZYME of lipids)
- inactive form of an enzyme. It explains how catalysis may occur (the
when a cofactor or conformational change stresses bonds in
coenzyme activates the the substrate, increasing reactivity)
apoenzyme, the complex is
called a HOLOENZYME
3. ACTIVE SITE
- the site where the
substrate will bind.
4. SUBSTRATE
- A molecule where an
enzyme will act upon. When
a substrate is bonded in the ENZYME REACTIONS
 Free Energy (∆𝐺) − The energy - each enzyme has a certain
associated with a chemical reaction temperature at which it is more
that can be used to do work active. This point is called the
Activation Energy optimal temperature, which ranges
- Amount of energy required to start from 37 to 40C°.
a chemical reaction - enzyme activity gradually lowers as
- The activation energy of a chemical the temperature rises more than the
reaction is closely related to its rate. optimal temperature until it reaches
Specifically, the higher the activation a certain temperature at which the
energy, the slower the chemical enzyme activity stops completely
reaction will be due to the change of its natural
Transition State - The peak of the composition.
required activation energy for a - if the temperature lowers below the
specific chemical reaction optimal temperature, the enzyme
The role of catalysts is to lower the activity lowers until the enzyme
activation energy of the chemical reaches a minimum temperature at
reaction without changing the which the enzyme activity is the
composition of the reactants. since least. The enzyme activity stops
there is no change in the reactants, completely at 0°C but if the
there will be no change in the temperature rises again, then the
product. thus making the chemical enzyme gets reactivated once more
reaction faster. POWER OF HYDROGEN(pH)
- Each enzyme has an optimum pH
range. Changing the pH outside of
this range will slow enzyme activity.
Extreme pH values can cause
enzymes to denature, slowing and
stopping the enzyme activity
SUBSTRATE CONCETRATION
- • Increasing substrate concentration
also increases the rate of reaction to
a certain point. Once all of the
enzymes have bound, any substrate
increase will not affect the rate of
reaction, as the available enzymes
will be saturated and working at their
FACTORS AFFECTING ENZYME REACTIONS maximum rate.
- the enzyme molecules are saturated
TEMPERATURE
with substrate. The excess substrate
- generally speeds up a reaction, and
molecules cannot react until the
lowering temperature slows down a
substrate already bound to the
reaction. However, extremely high
enzymes that have reacted and
temperatures can cause an enzyme
been released (or been released
to lose its shape (denature) and stop
without reacting)
working.
Module 10
ENERGY TRANSFORMATIONS IN LIVING
THINGS

ATP-ADP CYCLE
- an energy-
producing process inside an
organism. PLASTIDS
this involves two major processes, - Plastids are the site of manufacture
Hydrolysis, and Phosphorylation. and storage of
1. Adenosine Triphosphate important chemical compounds
- ATP is a nucleotide consisting of used by the cells of
adenine, ribose, and three autotrophic eukaryotes. They often
phosphate groups. it is quoted to be contain pigments used
the energy currency of the body. it in photosynthesis, and the types of
is spent in order to acquire energy. pigments in a plastid
HYDROLYSIS REACTION IN ATP-ADP determine the cell's color.
- Hydrolysis happens when a water - A Proplastid is a primary plastid that
molecule breaks the bond between can be seen in
a phosphoanhydride (oxygen- meristematic cells that give rise to a
phosphorus linkage) linkage setting a specific plastid
free phosphate molecule forming
COMMON KINDS OF PLASTIDS
Adenosine diphosphate (ADP).
- An enzyme ATPase will be used for 1. CHOROPLAST
this - Contain chlorophyll that absorbs
reaction sunlight in photosynthesis
PHOSPHORYLATION - Produce and store glucose
- the linking of a free inorganic 2. CHROMOPLAST
phosphate to ADP to form ATP and - Contain carotenoids )red, orange,
releasing water. An enzyme and yellow pigment)
ATPSynthase will help this chemical 3. LEUCOPLAST
reaction to move forward - Contain no pigment
- Used to store starch
PLANTS CHLOROPLAST
AUTOTROPHS - a plant cell
- Self-produces organelle that belongs to
the family of Plastids
LOCATION:
that holds the
1. LEAVES chlorophyll pigment and i s
A. STOMA found inside the mesophyll
B. MESOPHYLL CELLS layer of leaves.
STOMATA (STOMA) - This organelle is the site
- Pores in a plant’s cuticle through of photosynthesis
which water and gases are - Organelle where photosynthesis
exchanged between the plant takes place
and the atmosphere. 1. DOUBLE MEMBRANE
- the chloroplast is chlorophyll b, which has a carbonyl
enveloped by a bilipid layer where group (—CHO) in this position. The
molecules pass-through hydrophobic hydrocarbon side
2. STROMA chain anchors chlorophyll to the
- the spaces inside the chloroplast thylakoid
where the light-independent membrane.
reaction of
photosynthesis happens. it surrounds WAVELENGTH OF LIGHT
the
SHORT WAVE
grand
- More energy
3. THYLAKOID
LONG WAVE
- it is the coin-like structure in
- Less energy
the chloroplast. The Thylakoid is site
 Plants are green because the green
of the
wavelength is reflected, not
light-dependent reactions and is
absorbed.
where we
FALL COLORS
can find the chlorophyll. a stack of
- In addition to the chlorophyll
thylakoids is called a granum (grana
pigments, there are other
if
pigments present.
plural). a granum is composed of 10-
- During the fall, the green chlorophyll
20
pigments are
thylakoids.
greatly reduced revealing the other
CHLOROPHYLL MOLECULES
pigments.
- Located in the thylakoid
- Carotenoids are pigments that are
membranes.
either red or yellow.
• Chlorophyll have Mg+ in the
PIGMENT
center.
- any chemical compound which
• Chlorophyll pigments harvest
absorbs visible radiation
energy (photons)
between about 380 nm (violet) and
by absorbing certain wavelengths
760 nm (ruby-red)
(blue-420
1. ACCESORY PIGMENTS
nm and red-660 nm are most
- Absorb the light that cannot be
important).
absorbed by Chlorophyll a.
- Chlorophyll consists of a porphyrin
The energy absorbed from these
ring and a hydrocarbon side chain.
accessory pigments will be
The porphyrin ring, with a
passed to Chlorophyll a sufficing the
magnesium atom in its center,
limitations of the pigment
contains a
and broadening the energy
system of alternating double and
absorbing capacity of the plant
single bonds; these bonds are
- CHLOROPHYLL B, CARETENOIDS,
commonly found in molecules
LUTEIN
that strongly absorb certain
wavelengths of visible light and MODULE 11
reflect others (chlorophyll
reflects green). the methyl group (— PHOTOSYNTHESIS (PART 1)
CH3) distinguishes chlorophyll a from
 PHOTOSYNTHESIS
- An anabolic, endergonic,
carbon dioxide (CO2) requiring
process that uses light energy
(photons) and water (H2O) to
produce organic
macromolecules (glucose).

B. NONCYCLING ELECTRON FLOW

CALVIN CYCLE (LIGHT INDEPENDENT
REACTION/CARBON FIXATION)
- Uses energy (ATP and NADPH)
from light rxn to make sugar
(glucose).
- Occurs in the thylakoid membrane
REDOX REACTION
• Uses PS II and PS I
- The transfer of one or more
• P680 rxn center (PSII) - chlorophyll a
electrons from one reactant to
• P700 rxn center (PS I) - chlorophyll a
another.
• Uses Electron Transport Chain (ETC)
• Two types:
• Generates O2, ATP and NADPH
1. Oxidation
• one-way flow of electrons from
- The loss of electrons from a
H2O to NADP
substance or the gain of oxygen
2. Reduction
- The gain of electrons to a substance
or the loss of oxygen

BREAKDROWN OF PHOSTOSYNTHESIS

LIGHT DEPENDENT REACTION (LIGHT

REACTION)
- Produces energy from solar power
(photons) in the form of ATP and
NADPH.
- Occurs in the Thylakoid membranes
- During the light reaction, there are
two possible routes for electron flow.
A. CYCLIC ELECTRON FLOW
- Occurs in the thylakoid membrane.
• Uses Photosystem I only
• P700 reaction center- chlorophyll a
• Uses Electron Transport Chain
(ETC)
• Generates ATP only
ADP + P ATP
 CHEMIOSMOSIS CO2 UPTAKE
- Power ATP synthesis - CO2 reacts with 5-carbon ribulose
- Located in the thylakoid membranes bisphosphate (RuBP)
- Uses ETC and ATP synthase (enzyme) - Catalyzed by ribulose bisphosphate
to make ATP carboxylase/oxygenase
- Photophosphorylation: (rubisco)
addition of phosphate to ADP to - The unstable 6-carbon product
make ATP. breaks down into two molecules of
3-
carbon phosphoglycerate (PGA)
- The carbon of the CO2 molecule has
been ―fixed‖ to a carbon skeleton
CARBON REDUCTION
- Energy from ATP and NADPH are
used to convert the PGA molecules
to
glyceraldehyde-3-phosphate (G3P)
- Exergonic reaction of two molecules
MODULE 12: PHOTOSYNTHESIS (PART 2) of G3P leads to formation of a
glucose or fructose
LIGHT INDEPENDENT REACTION
RuBP Regeneration
(CALVIN CYCLE)
- 10 G3P molecules (30 carbons)
- Carbon fixation occurs in the stroma
remain in the Calvin cycle
through a sequence of 13 reactions
- Through a series of 10 reactions,
of
these molecules are rearranged into
the Calvin cycle.
6 molecules of ribulose phosphate
- It is an anabolic pathway building
- Ribulose phosphate is
carbohydrates from smaller
phosphorylated by ATP to produce
molecules and consuming energy.
RuBP, which
- Carbon enters the calvin cycle in
is used to restart the cycle
the form of CO2 and leaves in the
form of
sugar
- The product of calvin-benson cycle
is not glucose but the 3-carbon sugar
Glyceraldehyde-3-Phosphate (G3P)

 RuBisCO has a down side, it is not

exclusive in catalyzing CO2 but it
also reacts with O2when this
3 MAIN STAGES IN CALVIN CYCLE
 happens, instead of Calvin happening in specialized plants. The
Cycle,Photorespiration happens. most common that we have
discussed is also called C3 PATHWAY
C4 PLANTS
- Hot, moist environments.
- 15% of plants (grasses, corn,
sugarcane).
- Divides photosynthesis spatially.
- Light rxn - mesophyll cells.
- Calvin cycle - bundle sheath cells.
C4 PATHWAY
- The C4 pathway is designed to
efficiently fix CO2 at low
concentrations and plants that use
this pathway are known as C4 plants.
- These plants fix CO2 into a four
carbon compound (C4) called
oxaloacetate. This occurs in cells
called mesophyll cells

PHOTORESPIRATION
- Occurs on hot, dry, bright days.
Stomates close.
- Fixation of O2 instead of CO2 .
- Produces 2-C molecules instead of 3-
C sugar molecules.
- Produces no sugar molecules or no
ATP.
 Photorespiration Reduces
Photosynthetic Efficiency
- Photorespiration does not produce
ATP On hot, dry days, C3 plants, i.e.
soybeans and wheat, close stomata
to conserve water
 Photosynthesis rapidly uses up CO2 in
the leaf and O2 accumulates in the CAM PLANTS
chloroplasts O2 binds to rubisco, - Hot, dry environments. 5% of plants
which then acts as an oxygenase (cactus and ice plants).
and degrades certain molecules to - Stomates closed during day.
CO2 and H2O - Stomates open during the night.
Light rxn - occurs during the day.
PHOTOSYNTHETIC PATHWAYS
- Calvin Cycle - occurs when CO2 is
- In order to reduce photorespiration, present.
other photosynthetic pathways are
 - the Light Dependent
Reactionhappens in thethylakoid
while Light Independent happens in
the stroma
- the end product of Photosynthesis is
Glucose

CAM PATHWAY
- the Acid Metabolism separates the
carbon fixation and calvin cycle by
time. MODULE 13, 14 & 15: CELLULAR RESPIRATION
- This is evident in plants that has very
CELLULAR RESPIRATION
minimal water source since the
- It is a set of metabolic pathways that
stomata are closed during the day.
converts Glucose to Adenosine
Triphosphate
- The main goal of Cellular Respiration
is to manufacture the most number
of ATP out of a single molecule of
Glucose

2 TYPES OF RESPIRATION
AEROBIC RESPIRATION
- The use of Oxygen in the respiration
process. Cellular Respiration is a kind
of Aerobic Respiration
-----REACTIONS INVOLVED IN
AEROBIC RESPIRATION------
 Dehydrogenations: two
hydrogen atoms are
NOTES: removed from the substrate
and transferred to NAD+ or
- Photosynthesis converts inorganic
FAD
carbon dioxide to glucose
 Decarboxylations: part of a
- it only occurs in plants, algae, and
carboxyl group (COOH) is
other photosynthetic bacteria
removed from the substrate
- light energy triggers the reaction
as a molecule of CO2
- in the Light-dependent reaction,
 Preparation reactions:
oxygen is produced from the
molecules are rearranged so
hydrolysis of H2O
they can undergo further
- the productsof Light-dependent
dehydrogenations or
reaction will be used in the Light
decarboxylations
Independent Reaction and vice
ANAEROBIC RESPIRATION
versa
 - respiration process that does not use - Kreb’s Cycle and ETC takes place in
oxygen. Ethyl alcohol fermentation is the mitochondria
an example
 EXERGONIC REACTION
(ERGON=WORK)
- A spontaneous chemical reaction in
which there is a net release of free
energy.
 ENDERGONIC REACTION
- A non spontaneous chemical
reaction, in which free energy is
absorbed from the surroundings to
form the products of the reaction.

MITOCHONDRIA
- are membrane-boundcell organelles
----3 MAJOR METABOLIC PATHWAYS-----
(mitochondrion, singular) that generate
GLYCOLYSIS most of the chemical energy needed to
- – Converts Glucose to Pyruvic Acid power the cell's biochemical reactions
KREB’S CYCLE - Chemical energy produced by the
- makes use of Acetyl CoA to produce mitochondria is stored in a small
coenzymes required for Electron molecule called adenosine triphosphate
Transport Chain (ATP).
ELECTRON TRANSPORT CHAIN
- contain their own small chromosomes.
- the ATP producing pathway,
Generally, mitochondria, and therefore
electrons transport to several
electron acceptor complexes to
mitochondrial DNA, are inherited only
enable a chemiosmosis from the mother

----STRUCTURE OF MITOCHONDRIA----
 OUTER MEMBRANE
- Contains porins that enable passage of
 WHERE DOES CELLULAR RESPIRATION molecules
TAKE PLACE?  CRISTAE
- Glycolysis occurs in the cytoplasm
- – fluid filled spaces in the mitochondria MODULE 16: CELLULAR RESPIRATION –
where Krebs’ Cycle happens ELECTRON TRANSPORT CHAIN
 MATRIX
PYRUVIC ACID METABOLISM
- it expands the surface area of the inner
-THE BY-PRODUCT OF GLYCOLYSIS IS
membrane. Where ETC happens
PYRUVIC ACID AND THE MOLECULE
GLYCOLYSIS
THAT WILL REACT WITH KREB CYCLE IS
- Is a metabolic pathway that converts
ACETYL COENZYME-A
glucose molecule to pyruvic acid
 PYRUVATE IS CONVERTED TO ACETYL
- Happens in the cytosol
CoA
- Does not require oxygen
- Undergoes oxidative decarboxylation
- A carboxyl group is removed as CO2 ,
which diffuses out of the cell
- Occurs in mitochondria of eukaryotes
- The two-carbon fragment is oxidized
and is attached to coenzyme A, yielding
acetyl coenzyme A (acetyl CoA)

KREB’S CYCLE
----HISTORY---
- Discovered by Hans Krebs in 1937
- He received the Nobel Prize in
physiology or medicine in 1953 for his
discovery
- Forced to leave Germany prior to
WWII because he was Jewish
 Kreb’s Cycle / Tricarboxylic Acid
- the citric acid cycle takes place in the
matrix of mitochondria
- The eight steps of the cycle are a series
of redox, dehydration, hydration, and
decarboxylation reactions that produce
 two carbon dioxide molecules, one - 4 CO2
GTP/ATP, and reduced forms of NADH - 2 ATP
and FADH2 - A FADH2
- Begins when acetyl CoA transfers its
two-carbon acetyl group to the four-
carbon acceptor compound
oxaloacetate, forming citrate, a six-
carbon compound:

 THE CITRIC ACID CYCLE

- Citrate goes through a series of
chemical transformations, losing two
carboxyl group as CO2 OXIDATIVE PHOSPHORYLATION
- One ATP is formed (per acetyl group) by - Most ATP production occurs by
substrate- level phosphorylation oxidative phosphorylation
- Most of the oxidative energy is - involves electron transport and
transferred to NAD+ , forming 3 NADH chemiosmosis and requires an
- Electrons are also transferred to FAD, adequate supply of oxygen
forming FADH2  ELECTRON TRANSPORT CHAIN
- The mitochondria has two membranes--
the outer one and the inner membrane
- The H+ which are brought to
mitochondria accumulate between
these two membranes.
o the last component of aerobic
respiration and is the only part of
glucose metabolism that uses
NOTE: atmospheric oxygen
o The ETC happens in the outer
In a single turn of the cycle,
membrane of the mitochondria
- two carbonsenterfrom acetyl CoA and o The ETC has 4 complexes:
two molecules of carbon dioxide are o Complex I converts NADH to NAD+
released; + H+
- three molecules of NADH and one o Complex II converts FADH2 to FAD
molecule of FADH2 are generated; and o Complex IV Converts 2H+ and ½ O2
- one molecule of ATP or GTP produced. to water
 TOTAL BY-PRODUCTS OF KREB’S CYCLE o The total ATP produced in ETC is 32
- 6 NADH ATP
 o The electrons are passed back and CHEMIOSMOSIS
forth across the membrane where - the H+ diffuses back across the inner
their energy is gradually decreased membrane through ATP synthase
and used to transport H+ through complexes, driving the synthesis of ATP
the membrane.
o Oxygen is the final electron
acceptor and it joins with the H + to
produce H2O. (If there is no oxygen,
the electron chain cannot continue
because there is no way to release
electrons)
- Electrons from NADH and FADH2 travel
down the electron transport chain to
O2
- Oxygen picks up H+ to form water.
- Energy released by these redox
reactions is used to pump H+ from the ----SUMMARY-----
mitochondrial matrix into the
intermembrane space.

GARCIA, DANIELLE RAVEN V.

12STEMA2