GENERAL BIOLOGY 1 REVIEWER

QUARTER 2 FIRST LAW OF THERMODYNAMICS

- law of conservation of energy
ENERGY FLOW AND RECYCLING - energy cannot be created nor destroyed; rather,
energy can be changed from one form to another
ENERGY
This means that the total amount of energy in
- defined as the ability to do work or bring about a
the universe is constant. Life is constantly converting
change
energy from one form to another
- allows organisms to carry out different life
processes, including growth, development,
SECOND LAW OF THERMODYNAMICS
metabolism, and reproduction. All organisms
- energy cannot be changed from one form to
perform a tremendous amount of work on a
another without a loss of usable energy
microscopic scale.

All energy transformations are inefficient

FORMS OF ENERGY
because every reaction loses a portion of the energy
Energy occurs in two forms, and they constitute input into the surroundings. This lost energy is in the
the total amount of energy in any object. form of heat.

These forms are the kinetic and potential ENTROPY

energy.
KINETIC ENERGY
- The energy due to the motion of an object.
- When water flows from a waterfall, a ball rolls
downhill, or a moose walks through a grassland,
kinetic energy is manifested.
- used to indicate the relative amount of
disorganization of a system
- It is the measure of randomness
- The more disordered a system is, the higher is its
entropy
ADENOSINE TRIPHOSPHATE

ATP is the common energy currency of cells—

POTENTIAL ENERGY
when cells require energy to drive their chemical
- The stored energy of an object whose capacity to
reactions, these cells use ATP
accomplish work is not being utilized at the
moment. The more active an organism is, the greater its
demand for ATP molecules. However, cells do not store
Food has chemical energy because it is composed large quantities of ATPs, rather, this molecule is
of organic molecules such as carbohydrates, proteins, constantly being generated from ADP (adenosine
and fat, which can be broken down to liberate energy. diphosphate) and a molecule of inorganic phosphate
When a person walks, he or she converts chemical (Pi).
energy into mechanical energy. Another form of energy
called thermal energy is a type of kinetic energy
associated with the random movement of atoms or
molecules. The thermal energy that is transferred from
one object to another is called heat.

LAW OF THERMODYNAMICS

The two laws of thermodynamics that are

formulated by early energy researchers explain why The ATP-ADP cycle in which ATP carries energy
energy flows through ecosystems and through cells. between exergonic and endergonic reactions. The
energy released from ATP is used to drive biochemical
functions.
STRUCTURE OF ATP
ATP is a nucleotide composed of the nitrogen-
containing base adenine, the 5-carbon sugar ribose, and
three phosphate groups.
MECHANISM OF ATP SYNTHASE
There are two ways to synthesize ATP. The first
one is mediated by a group of enzymes called kinases,
and the other one is through ATP synthases.
 SUBSTRATE-LEVEL PHOSPHORYLATION
- The process of producing ATP by combining ADP
and a phosphate group from a phosphorylated
molecule instead of an inorganic phosphate.
 OXIDATIVE PHOSPHORYLATION
- An ATP synthesizing mechanism that utilizes the
energy derived from the transfer of electrons in an
electron transport system to combine ADP and
inorganic phosphate.
 PHOTOPHOSPHORYLATION
- A process that is similar to oxidative
phosphorylation in several ways. The primary
difference is the source of energy for ATP synthesis
COUPLED REACTIONS
The ATP breakdown is coupled with energy-
requiring reactions. The energy-releasing reaction is
the hydrolysis of ATP.
Cells have two major ways to couple ATP
hydrolysis to an energy-requiring reaction—ATP is used
to energize a reactant, or ATP is used to change the
shape of a reactant. Both can be accomplished by
transferring phosphate groups to the reactant so that
the product is phosphorylated.
EXERGONIC AND ENDORGONIC REACTIONS
 EXERGONIC REACTIONS
- Spontaneous and release energy
- Begin with reactants whose covalent bonds
contain more potential energy than those in
products released to the surroundings
- An amount of energy equal to the difference in
potential energy between the reactants and the
products
 ENDERGONIC REACTIONS
- Require an input of energy to occur
- Starts with reactants that contain relatively little
potential energy
- Energy is absorbed from the surroundings as the
reaction occurs, so the products of an endergonic
reaction contain more chemical energy than the
reactants did.
ATP-ADP CYCLE
STRUCTURE OF ATP AND ADP
Adenosine triphosphate is a nucleotide with
three phosphate groups. It is particularly composed of
nitrogen-containing base adenine, five-carbon sugar
ribose, and three phosphate groups. High-energy bonds
link these phosphate groups together.
The transfer of a phosphate group to a
molecular is called phosphorylation. This is essential in
energizing ADP to synthesize ATP or another molecular
intermediate.
ADP has almost the same structural
components as the ATP, but ADP has only two
phosphate groups instead of three.
FUNCTIONS OF ATP
The triphosphate tail is the portion of ATP that
provides energy for cellular work. Each of these
phosphate groups is negatively charged, which makes
them repel each other. The crowding of negative
charges in the triphosphate tail contributes to the
potential energy of ATP.
ATP carries energy between exergonic reactions
and endergonic reactions.
MECHANISM OF ADP-ATP CYCLE
Adenosine triphosphate is unstable and has
high potential energy. ATP hydrolysis releases previously
stored energy, which allows the change in free energy to
perform various cellular processes.
The chemical composition and functions of
adenosine triphosphate
PHOTOSYNTHESIS AND THE ROLE OF PIGMENTS
PHOTOSYNTHESIS
- the process in which plants harness solar energy
and use it to synthesize high-energy organic
compounds in the form of sugars.
The process of photosynthesis in plants and
algae occurs in the membrane-bound organelle called
chloroplasts.
PHOTOSYNTHETIC PIGMENTS
Pigments are organic molecules that selectively
absorb light of specific wavelengths and are built into
the thylakoid membranes of the chloroplasts.
Photosynthetic pigments can be classified into
primary and accessory pigments based on their
contribution to light energy harvesting during
photosynthesis.
CHLOROPHYLL A
Chlorophyll a is the primary pigment during
photosynthesis. It is also the universal pigment in all
photosynthetic organisms. It participates directly in light
reactions and is the most common green photosynthetic
pigment in plants, algae, some protists, and
cyanobacteria. This pigment absorbs mainly blue, violet,
and red light, thus it appears green to us.
CHLOROPHYLL B
Chlorophyll b, an accessory pigment, absorbs
mainly blue and orange light but reflects olive green.
Although chlorophyll b does not participate directly in
light 8.1. Photosynthesis and the Role of Pigments 11
Unit 8: Photosynthesis reactions, it conveys absorbed
energy to chlorophyll a to work in the light reactions.
Other types of chlorophyll exist, particularly
chlorophylls c and d. These accessory pigments are
found in brown and red algae, respectively.
CAROTENOIDS
Carotenoids are accessory pigments consisting
of various shades of yellow and orange. These pigments
absorb mainly violet, blue, and green light. This pigment
is important in photoprotection. These pigments also
convey light energy harvest from other bands of the
visible light from the sun.
PHYCOBILINS
Phycobilins are also accessory pigments in red
algae and cyanobacteria that either give red or blue
coloration. They are especially important for deep-sea
red algae as they can utilize the blue light that can
penetrate into deeper waters.

Aside from the primary and accessory classification of
photosynthetic pigments, they can also be classified into
chlorophyll, carotenoids, and phycobilins.
LIGHT-DEPENDENT REACTION
LIGHT-DEPENDENT REACTION
The light-dependent reactions only occur when
solar energy is available. This process happens on the
thylakoid membrane of chloroplasts which converts
solar energy into chemical energy.
ELECTRON FLOW IN LIGHT-DEPENDENT REACTIONS
A photosystem consists of a number of light-
harvesting complexes (LHC) surrounding a reaction-
center complex. An LHC contains various pigment
molecules bound to proteins.
LIGHT STRIKING PHOTOSTEM 2 DRIVES ATP
PRODUCTION
Photosynthesis begins in the pigment molecules
of photosystem II, which absorb light energy and
transfer it to a chlorophyll a reaction center. This center
then excites two electrons.
As electrons move in the electron transport
chain, their energy is used to pump protons (H+) across
the membrane into the thylakoid space. The thylakoid
space will then have a high concentration of H+ and a
lower concentration in the stroma; thus, an H+ gradient
is established.
The H+ will diffuse through a protein in the
thylakoid membrane called ATP synthase. The diffusion
of H+ will rotate the ATP synthase to produce ATP.
PHOTOSYSTEM 1 ELECTRONS REDUCE NADP+
The second electron transport chain passes the
electrons from photosystem I to a molecule of NADP+,
forming the reduced NADPH. This NADPH is the electron
carrier that will reduce CO2 in the next phase, while ATP
will provide the energy.
THE NONCYCLIC PATHWAY
The noncyclic pathway is the linear mechanism
of electron transport from photosystem II to
photosystem I, including the electron transport chains.
This is the standard mechanism of light-dependent
reactions. Ultimately, it produces NADPH and ATP
molecules.
THE CYCLIC PATHWAY
The cyclic pathway involves only the
photosystem I and the electron transport proteins. The
electron chain in this pathway uses the electron’s
energy to move H+ into the thylakoid compartment. The
resulting H+ gradient drives ATP formation, just as it
does in the noncyclic pathway.
ATP GENERATION IN LIGHT-DEPENDENT REACTIONS
Cyclic photophosphorylation is important to
create ATP while maintaining NADPH
in the right proportion.
Graphical representation for light-dependent reactions

LIGHT INDEPENDENT REACTION (CALVIN CYCLE)
CALVIN CYCLE
The second stage of photosynthesis is known as
the Calvin cycle, which occurs in the stroma of the
chloroplast.
FIXATION
Carbon fixation is the process of incorporating
carbon atoms from an inorganic source into an organic
molecule.
During carbon fixation, the enzyme RuBisCo
catalyzes the reaction between ribulose bisphosphate
(RuBP) and CO2 to produce 3-phosphoglycerate (3-PGA).
REDUCTION
A series of two chemical reactions use the
energy from ATP and electrons donated from NADPH to
reduce molecules of 3-PGA into glyceraldehyde 3-
phosphate (G3P).
REGENERATION
For every three carbon dioxide molecules fixed,
one G3P molecule leaves the cycle as a product.
A series of chemical reactions must use energy
from the ATP to rearrange the atoms in the five G3P
molecules into three molecules of RuBP.
PRODUCTS OF CALVIN CYCLE
Overall, to produce one molecule of glucose, a
total of 18 ATP and 12 NADPH molecules are needed
while still replenishing the Calvin cycle with RuBP.
The Calvin cycle, which takes place in the
stroma, uses ATP and NADPH to fix atmospheric
CO2 to produce glucose, the primary energy
source for cell respiration.
CELLULAR RESPIRATION AND THE ROLE OF
MITOCHONDRION
CELLULAR RESPIRATION
Cellular respiration is a catabolic pathway that
uses glucose molecules to produce energy in the form of
ATP (adenosine triphosphate).
KINDS OF CELLULAR RESPIRATION:
Aerobic respiration is the process of producing
energy involving oxygen.
Anaerobic respiration is the process of
producing energy without the presence of oxygen.
AEROBIC RESPIRATION
Glycolysis, Krebs cycle, electron transport chain,
and chemiosmosis are the four stages of cellular
respiration.
Krebs cycle and electron transport chain
happens in the mitochondria of the cell.
Mitochondria has four main parts:
 outer membrane
 inner membrane and cristae
 intermembrane space
 matrix
REACTANTS AND PRODUCTS OF CELLULAR
RESPIRATION
Glucose and oxygen are the reactants while carbon
dioxide and water are the products of cellular
respiration.
The major processes involved in cellular respiration
AEROBIC RESPIRATION: GLYCOLYSIS
GLYCOLYSIS
Glycolysis is the process of breaking down
glucose molecules to generate energy and electron
carriers, which will be further utilized in the electron
transport chain in the mitochondria.
 OVERVIEW OF THE KREBS CYCLE
HANS KREBS
- He is a German-British scientist who discovered
Glycolysis can be divided into two phases: the Krebs Cycle in the 1930s. Thus, in honor of his
The energy-investment phase involves the use discovery and pioneering study, the pathway was
of ATP molecules. named after him.
The energy-harvesting phase involves the
production of ATP and NADH. KREBS CYCLE
Krebs cycle is the process of oxidizing and
THE PRODUCT OF GLYCOLYSIS further breaking down two pyruvate molecules to
The net products of glycolysis are 2 ATP, 2 produce energy.
NADH, and two pyruvate molecules. It is also known as the Citric Acid Cycle or
Tricarboxylic Acid Cycle because citric acid is its first
Pyruvate undergoes oxidation and becomes product, which is composed of three carboxyl groups
acetyl-CoA, which enters the Krebs cycle. (COO−).
In eukaryotic organisms, the Krebs cycle
TIPS occurs in the mitochondrion.
To memorize the correct order of enzymes
used during glycolysis, you may use the mnemonics TRANSITION REACTION
below: In the transition reaction before the Krebs cycle,
acetyl-CoA is formed from pyruvate through oxidation.
HE PUT THE CO2 and NADH are also produced in this stage.
PHONE AND
TRIED TO The series of redox reactions during the Krebs
GET cycle produces NADH, FADH2, CO2, and GTP. The CO2 is
THE PLASTIC released into the environment. NADH and FADH2 are
PLATE TO EAT used to produce more ATP in the electron transport
PIE. chain. GTP is used to drive chemical reactions similar to
how cells use ATP.
H- hexokinase
P-phosphoglucoisomerase
PHO- phosphofructokinase
P- phosphoglucoisomerase
PHO- phosphofructokinase
A- aldolase
TRI- triosephosphate isomerase
G- glyceraldehyde-3-phosphate
dehydrogenasedehydrogenase
P- phosphoglycerate kinase
P- phosphoglycerate mutase
P- phosphoglycerate kinase
P- phosphoglycerate mutase
E- enolase
P- pyruvate kinase

AEROBIC RESPIRATION: KREBS CYCLE

 AEROBIC RESPIRATION CHEMIOSMOSIS AND molecules to lactate through an enzyme called
ELECTRON TRANSPORT CHAIN lactate dehydrogenase.

ELECTRON TRANSPORT CHAIN AND PTOTON PUMPS
Electron transport chain is a series of four
multiprotein complexes embedded in the inner
membrane of the mitochondrion where NADH and
FADH2 are oxidized to release electrons.
The energy from the released electrons is used
to pump hydrogen ions from the matrix to the
intermembrane space. This pumping generates a proton
gradient.
Alcoholic fermentation involves the
conversion of pyruvate molecules into ethanol
through the help of pyruvate decarboxylase and
alcohol dehydrogenase.
The products of anaerobic respiration are 2
ATP, 2 NADH, and 2 pyruvate molecules. When
pyruvate molecules undergo fermentation the
products are either ethanol or lactate.

CHEMIOSMOSIS Fermentation is widely used in the

Chemiosmosis involves the downhill transport processing of dairy products and alcoholic
of hydrogen ions from the intermembrane space to the beverages.
matrix. This movement provides energy to ATP synthase
to phosphorylate ADP into ATP.

ATP YIELD
In terms of ATP synthesis, NADH is equivalent to
three ATP molecules because its electrons will move
through complexes I, III, and IV. By contrast, every
FADH2 is equivalent to two ATP molecules because its
electrons will only move through complexes III and IV.

A total of 34 ATP molecules are produced

through electron transport chain and chemiosmosis. The two main types of anaerobic respiration
The table below summarizes the net ATP yield for the
whole aerobic respiration process. COMPARING PHOTOSYNTHESIS AND CELLULAR
RESPIRATION
ANAEROBIC RESPIRATION
Photosynthesis and cellular respiration are
Anaerobic fermentation is the process by both energy-producing processes, which have several
which a glucose molecule is broken down to differences:
produce energy in the absence of oxygen.
Photosynthesis takes place in chloroplasts,
Fermentation is the process by which while cellular respiration takes place in mitochondria.
pyruvate is converted to either ethanol or lactate
which enables the oxidation of NADH to NAD+. The overall equation for photosynthesis is
shown below.
The two fermentation processes are:
Lactic acid fermentation is the process
involving the conversion of pyruvate

The overall equation of cellular respiration is
shown below.
The reactants of cellular respiration are the
products of photosynthesis and vice versa.
Photosynthesis is considered as endothermic,
whereas cellular respiration is exothermic.
Cellular respiration and photosynthesis are both
metabolic processes. However, cellular respiration is
considered as catabolic, while photosynthesis is
anabolic.
There are four stages involved in cellular
respiration, namely glycolysis, Krebs cycle, electron
transport chain, and chemiosmosis. By contrast,
photosynthesis involves two stages, namely the light-
dependent and light-independent reactions.
Photosynthesis and cellular respiration both
involve reduction-oxidation reactions and the ATP
synthesis that results from the flow of electrons
through the protein complexes and ADP
phosphorylation.
The nature of cellular respiration and photosynthesis
ATP COUNT IN PHOTOSYNTHESIS AND CELLULAR
RESPIRATION
Photosynthesis uses and produces ATP
molecules during its major phases.
Light-dependent reactions produce 18 ATPs
from 12 water molecules.
 The C3 Calvin pathway uses 18 ATP molecules.
 The C4 Calvin pathway uses 30 ATP molecules.
 The CAM Calvin pathway uses 39 ATP molecules.
Cellular respiration is the main process that
produces usable cellular energy in the form of ATP
molecules.
 Glycolysis uses 2 ATP molecules to prime the
cellular respiration and produces a net of 2 ATP
molecules.
 Krebs cycle produces 2 ATP/GTP molecules.
 In theory, the electron transport chain and
chemiosmosis produce 34 ATP molecules from
the oxidation of NADH (3 ATPs per NADH) and
FADH2 (2 ATPs per FADH2).
The actual ATP yield between prokaryotes and
eukaryotes varies. Factors that determine this variation
include the cytosolic NADH transport and experimental
results on the equivalence between the electron carriers
and ATP yield.
 The ATP yields from the oxidation of NADH and
FADH2 are 2.5 ATPs and 1.5 ATPs, respectively.
 The actual ATP yield for prokaryotes is 32
molecules. For eukaryotes, the actual yield is
30 or 32 molecules depending on the shuttle of
cytosolic NADH used.
ADVANTAGES AND DISADVANTAGES OF
FERMENTATION AND CELLULAR RESPIRATION
`Anaerobic respiration does not rely on the
presence of oxygen to produce ATP.
Fermentation is a catabolic reaction that occurs
in the cells whenever there is a scarcity in oxygen supply
to allow continuous production of ATP.
 In alcohol fermentation, the pyruvate produced
from glycolysis is converted into ethanol.
 In lactic acid fermentation, pyruvate is directly
reduced by using NADH to form lactate.
Given the differences between aerobic and
anaerobic respiration in terms of their reactants and
products, energy yield, rate of energy generation, and
degree of oxidation, they have their respective
advantages and disadvantages.
 Aerobic respiration is advantageous due to its
relatively greater energy yield due to the complete
oxidation of glucose molecules. However, it can only
do so when oxygen molecules are available as final
electron acceptors.

 Anaerobic respiration is advantageous for

organisms that thrive in oxygen-scarce
environments and tissues with temporarily low
levels of oxygen. However, its energy yield is
significantly lower. Thus, it cannot sustain the
energy requirements of cells of complex organisms.

ANAEROBIC RESPIRATION: PROS AND CONS

ADVANTAGES
- Continuous production of ATP in the absence of
oxygen. The difference in the fate of glucose molecules during
- Can serve as an adaptation in oxygen-depleted aerobic and anaerobic respiration
environments.
- No further energy investment for pyruvate
transport.
- Has the capacity to produce a significantly high GOODLUCK AND GOD BLESS
quantity of ATP.
- Can sufficiently support a wide range of biological
functions.
- Does not pose toxicity to cells even if it occurs at a
high rate.

DISADVANTAGES
- Significantly low ATP generation due to incomplete
oxidation.
- Can only occur in short periods of in some
organisms.
- May induce toxicity to some tissues when
excessive.
- Requires more time to complete glucose oxidation.
- Stops when an insufficient oxygen molecule is
present.
- Dangerous if an organism has no alternative
respiration pathway.