Lesson 1: Water

Water is an inorganic compound made up of two hydrogen atoms and one oxygen
atom covalently bonded. It is the most abundant form of compound in living organisms.
It makes up 60-80% of organisms’ body weight. Without water, life would not be
possible.

Figure 1.1 Water Molecule

Chemical Properties of Water and their Functions

Water is a universal solvent. It can dissolve almost any substance except fats and
oils. This property makes possible chemical reactions in cells such as in plant
photosynthesis (anabolism). It helps partial digestion of food in the mouth, transport
dissolved substances or nutrients that we obtain from our food, excrete waste products
of metabolism in the form of sweat and urine, and eliminate waste products of digestion.

Figure 1.2 Water as Medium of Biochemical Reactions in Photosynthesis

Water is cohesive and adhesive. The attractive force between water molecules
is cohesion, while adhesion is the attractive force between a water molecule and
another substance. Adhesion and cohesion make possible the transport of water and
minerals from the soil via the roots in plants. It also facilitates the transport of nutrients
and wastes through the blood plasma within internal vessels.
 Figure 1.3 Cohesion and Adhesion in Plant Transport

Water has high specific heat capacity and high heat of evaporation. In high heat
capacity, the hydrogen bonds of water can absorb a great amount of heat without
increasing temperature. The high heat of vaporization is the capacity of water to be
converted to gas or water vapor. These two properties are important because they
regulate the temperatures of ecosystems and the body of organisms. Vaporization cools
body surfaces as a result of dispensing body heat.

Figure 1.4 Heat Capacity and Vaporization Property of Water

Water is less dense as ice. This property of water is why ice floats in water. As water
freezes, the hydrogen bonds hold the molecules apart, increasing the intermolecular
space and resulting in expansion. This makes ice less dense than water. Why is this
property important? In parts of the Earth where the temperature becomes too low,
bodies of water like lakes, rivers, and oceans freeze into ice. Will these bodies of water
solidify to the bottom? It is only the surface that forms into ice. This is important for the
organisms living in these ecosystems to survive and not be frozen to death. What will be
the impact on the environment if these organisms will freeze to death?

Figure 1.5 Water being less Dense as Ice

There are other physiological functions of water in the body aside from what was
mentioned with the chemical properties. It also moistens surfaces such as the lungs and
skin of aquatic organisms to facilitate the diffusion of gases. It is important in the
functioning of sense organs such as the eyes, nose, and ears. It lubricates joints,
preventing friction, and cushions vital organs such as the brain, lungs, and heart. So,
are you drinking enough water daily? Let’s drink to that!

Lesson 2: Carbohydrates
Carbohydrates are organic compounds that contain molecules of carbon, hydrogen,
and oxygen. It has a fixed 1:2:1 ratio of C:H:O for monosaccharides or a 2:1 ratio for
hydrogen and oxygen molecules. They are the primary products of photosynthesis in
green plants and a source of energy for cells.

Classification of Carbohydrates

Carbohydrates are known as sugars or saccharides. Sugars are sweet and soluble in
water. Sugars are classified into simple sugars or monosaccharides, double sugars
or disaccharides, and complex sugars or polysaccharides.

Monosaccharides are the smallest carbohydrates, hence known as simple sugars.

They are the building blocks for the other types of sugars. Common examples of simple
sugars include glucose, fructose, and galactose.

Glucose is a hexose sugar that forms the base unit of many polymers. It is also known
as blood sugar and the first option of our cells to extract energy during cellular
respiration.
Fructose is a pentose sugar that is considered the sweetest naturally occurring
carbohydrate in fruits and honey.

Galactose is also a hexose sugar that is less sweet, most commonly found in milk and
cereals. These three simple sugars have the same chemical formula of C6H12O6, but
they differ in their structure.

Figure 2.1 The Monosaccharides

Disaccharides are formed by condensation reactions of two simple sugars that are
bonded together. Hence, known as double sugars. Its molecular formula
is C12H22O11. It tastes sweet and is soluble in water. Double sugars are broken down by
hydrolysis with the help of enzymes. Examples of disaccharides
include maltose, sucrose, and lactose.

Maltose, also known as malt sugar, is formed by condensation reactions of two

molecules of glucose. It is used in breweries and extends the shelf life of certain food
products. It is found in germinating grains.

Sucrose is formed by the condensation of glucose and fructose. It is the sugar found in
sugar canes and beets. It is commonly used as a sweetener.

Lactose is formed by reactions of glucose and galactose. It is naturally found in dairy

products and milk of all mammals.

Figure 2. 2 The Formation of Disaccharides

Polysaccharides are known as complex sugars because they are made from many
units of monosaccharides. This results in their having a large molecular size, hence,
insoluble in water. These sugars do not taste sweet and do not crystallize. Examples of
complex sugars include starch, glycogen, cellulose, and chitin.

Starch is the storage form of carbohydrates in plants. They are stored in plant organs
such as leaves, stems, fruits, seeds, and grains.

Glycogen is the storage form of carbohydrates in animals. Excess glucose units in the
blood are converted into glycogen and stored in the liver and muscles of animals.

Figure 2.3 Starch and Glycogen Structure

Cellulose is the structural form of carbohydrates found in the cell walls of plant cells. It
is an important source of dietary fibers which help maintain the regular elimination of
wastes.

Chitin is a polysaccharide found in the exoskeleton of crabs, lobsters, insects and is a

structural component of the cell walls of fungi. Its primary function is protection.
 Figure 2.4 Cell wall and Chitin

Functions of Carbohydrates

Carbohydrates serve as the body's chief energy source since glucose is used as a
substrate for cellular respiration. It forms the supporting structure of cells such as
cellulose and the backbone of nucleic acids. It combines with other compounds such as
proteins and lipids, forming glycoproteins and glycolipids for structural components of
living cells. It is a source of carbon, hydrogen, and oxygen for the biosynthesis of other
inorganic compounds.

Figure 2.5 Some of the Functions of Carbohydrates

Lesson 3: Proteins
Proteins are large and complex molecules composing of carbon, hydrogen, oxygen,
nitrogen, and sometimes sulfur. These are made up of small organic molecules
called amino acids, known as the basic units or building blocks of proteins. There are
20 different amino acids that are bound together, forming a polypeptide chain.

Figure 3.1 Amino Acids Build Proteins

Eleven (11) of the 20 amino acids are non-essential because our body cells can make
them, while nine (9) are essential and need to be obtained from our diet because our
body cannot synthesize them. So, what are food sources for proteins? Proteins can be
found in both animal and plant foods. Milk, eggs, seafood, and meat such as chicken
and lean beef are animal foods rich in proteins. Plant foods rich in proteins include soya
beans, nuts, grains, and vegetables such as French beans.

Proteins containing all the nine essential amino acids are complete proteins, while
proteins that do not contain all the essential amino acids are incomplete proteins.

Figure 3.2 Sources of Complete Proteins (Left) and Incomplete Proteins (Right)

Functions of Proteins

Proteins contribute to the structure and function of the cell membrane. They are
components of the cell membrane, and they also serve as transport and channel
proteins, assisting the flow of molecules across the cell membrane. Cytoskeleton, which
is near the cell membrane, are also proteins that support the cell.

Figure 3.3 Proteins as Cell Membrane Structure

Proteins function for support. Structural proteins that perform this function
are keratin and collagen. Keratin support and protect hairs, nails, hoofs, horn, and
feathers. Collagen fibers are found in the dermis of the skin, tendons, and ligaments.
and support these tissues.

Figure 3.4 Collagen and Keratin

Proteins function in metabolism. Metabolism such as cell respiration and

photosynthesis involves complex chemical reactions. Enzymes are proteins that hasten
or speed up the chemical reactions of these processes. The breakdown of proteins,
carbohydrates, and lipids also requires enzymes in the process of digestion.
 Figure 3.5 Enzymes in Chemical Reactions

Proteins are used for transport. Carrier and channel proteins move specific
substances into and out of the cell through the cell membrane.
The hemoglobin molecule is a protein component of red blood cells and enables the
transport of oxygen and carbon dioxide to and from the body's cells.

Figure 3.6 Transport Proteins

Proteins are used for defense. When foreign bodies such as viruses and other
disease-causing agents invade the body, our immune cells produce proteins to fight
these infectious agents. The proteins for defense are called antibodies. Antibodies bind
with these agents and prevent them from destroying cells.

Figure 3.7 Antibodies Against Antigens

Proteins regulate bodily functions and processes. Hormones are regulatory
proteins that are produced by cells of endocrine glands. They act as intercellular
messengers in plants and animals that influence metabolism, growth, development,
sexuality, reproduction, and other functions and processes.

Figure 3.8 Hormones as Regulatory Proteins

Proteins are used in motion or movement. Have you ever wondered why our hearts
bet continuously? Why are we able to move? Well, these actions are the works of
contractile proteins, called actin and myosin. These contractile proteins enable
muscles to contract, shorten, and act. The action produced by our muscles such as
heartbeat, walking, running, etc., are the functions of the actin and myosin filaments in
our muscle cells.

Figure 3.9 Actin and Myosin in Muscle Cells

Lesson 4: Lipids
Like other organic compounds, lipids are composed primarily of Carbon, Hydrogen,
and Oxygen, but with less oxygen than in
carbohydrates. Phosphorus and Nitrogen may also be present. All lipids dissolve in
organic solvents like ether and kerosene but not in water. It is insoluble in water
because of its long hydrocarbon chains. The building blocks or monomers are lipids
are fatty acids and glycerol.
 Figure 4.1 Monomer of Lipids

Fats and Oils

These are the most familiar lipids that are made up of fatty acids and glycerol. Fats and
oils maybe classified based on the structure of the fatty acid tails. The three fatty acid
tails are also known as triglycerides. Each fatty acid is composed of a long chain of
hydrocarbon.

When fatty acids of fats and oils have one or more double bonds between their carbon
atoms, they are classified as monounsaturated (1 double bond)
or polyunsaturated (2 or more double bonds). Generally, unsaturated fats, because of
their structure, do not solidify at room temperatures. This is the reason why they are
healthier to consume. Sources are usually plant oils, such as corn, olive, and sunflower,
and sesame.

Figure 4.2 Types of Fatty Acids

Fatty acids of fats and oils that do not have double bonds between their carbon atoms
are classified saturated. Saturated fats and oils tend to solidify at room temperature,
and their source are animal fats. Saturated fats are linked to cardiovascular diseases
such as atherosclerosis because of plaque buildup in the walls of blood vessels.

Trans fats have partially hydrogenated fatty acids, making them more saturated and
more solid. Did you know that most of your favorite foods contain trans fats? These
include burgers, fries, nuggets, and other fried foods.
 Figure 4.3 Fatty Acids and Their Sources

Other Kinds of Lipids

Phospholipids are the most important molecules of the cell because they form the cell
membrane. A phospholipid molecule is composed of glycerol, 2 fatty acid tails, and
a phosphate head. The phosphate heads are hydrophilic, while the tails are
hydrophobic. Hence, the arrangement in the cell membrane has the heads directed to
the cytoplasm and the extracellular fluid, which are mostly water.

Figure 4.4 Phospholipid Structure Cell Membrane

Steroids do not contain fatty acids but are similar to lipids because they are insoluble in
water. Steroid cholesterol is an important component of the cell membrane because it
maintains the cell membrane’s fluidity. This aids the flow of materials in and out of the
cell. Further, steroid cholesterol is also involved in the formation of bile salts and
Vitamin D.

Sex hormones, such as testosterone and progesterone play roles in the development
of secondary sex characteristics of humans and other animals.
 Figure 4.5 Steroids

Terpenes are long-chain lipids that are components of chlorophyll pigments and the
visual retinal pigment of the eyes. Terpenes are also found in the aroma oils extracted
from plants such as cinnamon, lemon, lavender, and cedarwood.

Figure 4.6 Terpenes in Aromatic Oils

Waxes are lipids found in the cuticles of fruits, leaves, seeds, stems, and beehives.
They prevent the entry of air and unnecessary water loss in plants. Animals also
produce this kind of lipids in the form of cerumen or ear wax. It protects the middle and
inner ears from the entry of small animals such as insects.
 Figure 4.7 Waxes in Plants and Animals

Functions of Lipids

 Lipids contribute to the structure and the function of the cell

membranes by forming the phospholipid bilayer.
 It is a long-term storage and source of energy, containing more
energy per gram compared to carbohydrates.
 It provides thermal insulation under the skin and around body
organs. Hence, it serves to regulate body temperature.
 It provides protection from traumatic injury or shock to the kidneys.
 It supplies the body with fat-soluble vitamins such as Vitamin D,
making our food more palatable or tastier.

The chart below shows the sources, applications, and functions of lipids.

Lesson 5: Nucleic Acids

Nucleic acids are organic compounds composed
of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorous. The monomers or
building blocks of these compounds are the nucleotides. A nucleotide is composed of a
pentose sugar, which maybe a ribose or deoxyribose, a nitrogen base, and phosphoric
acid. Series of nucleotides form these compounds. How many nucleotides can you see
in the figure on the right below?
 Figure 5.1 A Nucleotide and a Nucleic Acid

The nitrogenous bases of nucleic acids are classified into two

types, purines and pyrimidines. Purines are large, double-ring molecules found in
both DNA and RNA. It includes adenine (A) and guanine (G). On the other
hand, pyrimidines are smaller, single ring molecules that include cytosine
(C), thymine (T), and uracil (U).

Figure 5.2 Nitrogenous Bases in Nucleic Acids

Two Types of Nucleic Acids

Deoxyribonucleic acid (DNA) is double-stranded molecule which is shaped like a

helix. The backbone of each strand is made up of phosphates that are bonded to
deoxyribose sugar. The bases project to the inside, where complementary base pairing
is observed. Purine base complements with pyrimidine base. So, guanine always pairs
with cytosine, and adenine always pair with thymine.
 Figure 5.3 DNA Double Helix Molecule

Ribonucleic Acid (RNA) is a single-stranded molecule with a pentose ribose

sugar and phosphate backbone. Its nucleotide bases are cytosine that pairs
with guanine and adenine that pairs with uracil instead of thymine.

Figure 5.4 RNA Structure

Functions of Nucleic Acids

There are two main functions of DNA. First, it is a heredity material. It is the chemical
component of chromosomes, hence, the genetic material containing traits passed from
parent to offspring. Second, it contains information or codes needed for an organism to
develop, survive, and reproduce. These are found in the DNA sequences converted into
messages, used to build specific proteins that determine a particular trait.

The RNA molecule is the one involved in protein synthesis. It is the one that translates
the codes from the DNA into proteins.
 Figure 5.5 The Flow of Information From the DNA
Module 4
Lesson 1: Structure of ATP
ATP Structure

ATP is the primary carrier of energy in cells. It consists of three main structures:
adenine, ribose sugar, and three phosphates.

Figure 1.1 ATP Structure

ATP-ADP Cycle

The bonds between the phosphate groups store the energy. The said energy is
released for cellular work as the phosphates are broken through a process called
hydrolysis (addition of a water molecule). In this process, the outer phosphate detaches
from the ATP and will form adenosine diphosphate (ADP), a nucleotide with two
phosphates.

The ATPs in the cell are being used up continuously. This means that the ATP’s break
down continuously to yield energy and produce ADPs. By adding a phosphate group
back to the ADP, ATP is being synthesized. This becomes possible with the aid of the
energy from sunlight or food obtained by an organism, as shown in the figure below.
There will be a transfer of energy from the obtained energy by undergoing various
processes, and the cycle continues as the ATP loses a phosphate group to release
energy for cellular work, and a phosphate group from obtained energy attaches to ADP
again and so on.

Figure 1.2 ATP-ADP Cycle

Lesson 2: Photosynthesis
Photosynthesis is an anabolic phase of metabolism. The process converts light energy
into usable chemical energy of carbohydrates. This process takes place in plants,
photosynthetic protists, and cyanobacteria. These organisms, which can convert light
energy to chemical energy, are collectively called autotrophs.

Figure 2.1 Photosynthetic Organisms

For photosynthesis to efficiently take place in autotrophs, there should be adequate

amount of solar energy from the sun, chlorophyll, and accessory pigments should be
present in their cells, carbon dioxide and water are available in their environments, and
the temperature should be suitable, meaning not too cold or too warm.

Sunlight or solar energy is made of photons and electromagnetic waves.

The visible spectrum is a portion of the electromagnetic waves visible to the human
eye, which is used by autotrophs as an energy source. Photons are captured by
pigments molecules contained in chloroplasts of plant and protist cells.

Chlorophyll is the most common and important photosynthetic pigments in plants and
algae. It can absorb red, blue, and violet light. It reflects and transmits green light.
Hence, plants appear green.
 Figure 2.2 Photon Absorption of Photosynthetic Pigments

Aside from chlorophyll pigments, other pigments can also absorb light during
photosynthesis. These are called accessory pigments, which include beta-
carotene (orange) in carrots, zeaxanthin (yellow) in corn, lycopene (red) in tomatoes,
and anthocyanin (blue, red, or purple) in fruits and vegetables.

Chloroplasts are cytoplasmic organelles in eukaryotic autotrophs such as plants and

algae. It is a double-walled organelle with outer and inner membranes. Between the
outer and inner membranes is the intermembrane space. Within the inner membrane is
a fluid-filled space called the stroma, which contains compounds such as ribulose
bisphosphate (RuBP), and RuBisCO (Ribulose Bisphosphate carboxylase
oxygenase). Suspended in the stroma are the stacks of thylakoids called grana. Each
granum connects with another through the lamella.

Figure 2. 3 Structure and Function of a Chloroplast

The Phases of Photosynthesis

Photosynthesis is a series of chemical reactions that occurs in two stages, the light-
dependent and light-independent reactions. Below is a figure which shows the reactants
and products of the two stages.
 Figure 2.4 Reactants and Products of the Two Phases of Photosynthesis

Light-dependent Phase

This is the “photo” phase of photosynthesis, which means that the reactions require
light energy from the sun to proceed. The reactions take place in the thylakoid
membrane, where light energy is converted to chemical energy of ATP and
NADPH. The steps in this stage are summarized and enumerated below.

 First, CO2 and H2O enter the leaf.

 As light energy hits the chlorophyll pigments in the membrane of a
thylakoid (Photosystem II), H2O is split into O2 and H+.
 The electrons move down to enzymes of the electron transport
chain, then
 sunlight hits the second pigment molecule (Photosystem
I) allowing the enzymes to convert ADP to ATP and NADP+ gets
converted to NADPH.

Figure 2.5 Steps of Light-dependent Reaction

Light-independent Phase

The second stage, which is the “synthesis” phase of photosynthesis, occurs in the
chloroplast's stroma. It is also known as the Calvin cycle, as it was first discovered by
Melvin Calvin and Andrew Benson at the University of California. The reactions in this
phase make use of the energy of ATP and NADPH produced in the first stage. This
stage is divided into four steps: carbon fixation, reduction phase, carbohydrate
formation, and regeneration phase.

 In carbon fixation, a 5-C molecule, RuBP, incorporates CO2 with

the help of the enzyme RuBisCO, forming a 6-C molecule
called phosphoglyceric acid (PGA).
 In the reduction phase, PGA, an unstable molecule, is
immediately reduced into phosphoglyceraldehyde
(PGAL) or glyceraldehyde-3-phosphate (G3P).
 Carbohydrate if formed in the form of glucose with 1 PGAL
molecule, and
 Regeneration of RuBP using 5 molecules of PGAL. The cycle
continues as RuBP is used at the start of the cycle.

Figure 2.6 Steps of Light-independent Phase

Lesson 3: Cellular Respiration

Cellular respiration is a catabolic phase of metabolism that involves the breakdown of

glucose into chemical energy of ATP. In this process, carbon dioxide and water are
released by the cell as waste products.

Figure 3.1 General Equation of Cell Respiration

Types of Cell Respiration

There are two ways by which organisms extract energy from carbohydrates. One way is
through anaerobic respiration. This type of respiration releases energy from food in
the absence of oxygen. Organisms that extract energy through this process are
called anaerobes.

Anaerobic respiration can be classified as alcoholic fermentation or lactate

fermentation. Both anaerobic fermentation pathways begin with glycolysis and end in
the cytoplasm.

In alcoholic fermentation, ATP, ethyl alcohol, and CO2 are produced after glycolysis.
Yeasts and few other microorganisms undergo this process. Since the organism is
single-celled, the amount of ATP produced is enough to sustain its needs. Alcoholic
fermentation as a process has its application in the food industry. It is used to produce
alcoholic beverages, and it also causes bread dough to rise.

The other type of aerobic respiration is lactic acid fermentation. This type is carried
out by most organisms, including humans. After glycolysis, the products include lactic
acid, ATP, and CO2. This process is used by bacteria to make sour cream, yogurt,
cheese, and buttermilk.

Figure 3.2 Anaerobic Respiration Pathways

Figure 3.3 Application of Anaerobic Respiration in Food Industry

Aerobic Cellular Respiration

This process requires oxygen to extract ATP molecules from glucose. It is a more
efficient pathway of cell respiration since more ATP molecules are extracted from
glucose. It involves three stages, namely; glycolysis, Krebs cycle and oxidative
phosphorylation.

In glycolysis, glucose is broken down into a 3-carbon compound called pyruvate or

pyruvic acid. To initially break down glucose, it requires an energy input of 2ATP
molecules and the NAD+ enzyme. This stage takes place in the cytosol or cytoplasm of
the cell. The net gain in this chemical reaction is 2ATP molecules and 2 NADH.

Figure 3.4 Reactants and Products of Glycolysis

In the presence of oxygen, cell respiration continues with the next stage, which
is Krebs Cycle. The two pyruvate molecules from glycolysis are transported to
the mitochondrial matrix. With oxygen, the 3-C pyruvate molecule is converted to 2-C
acetyl-CoA and CO2 is released with the help of Coenzyme A. Each pyruvate produces
acetyl-CoA, and each one enters the Krebs cycle.

Figure 3.5 Acetyl-CoA Formation

Krebs cycle a series of enzyme-assisted reactions. It is also known as

the Tricarboxylic acid cycle or Citric acid cycle. Acetyl-CoA combines with
oxaloacetic acid forming citric acid. Each turn of the cycle will produce: 3 NADH, 1
FADH2, 1 ATP, 2 CO2. Electron carriers NADH and FADH₂ temporarily store chemical
energy that was previously stored in glucose and pyruvate. These will be used to create
ATP in the next stage of aerobic respiration.
 Figure 3.6 Krebs Cycle

igure 3.7 Summary of the Products of Krebs Cycle

The 3rd stage of aerobic respiration is the electron transport chain or electron
transport phosphorylation. This is a series of carrier molecules that are, in turn,
oxidized and reduced as electrons are passed down the chain. It allows the release of a
large amount of chemical energy stored in reduced NAD+ (NADH) and reduced FAD
(FADH2). The energy released is captured in the form of ATP (3 ATP per NADH and 2
ATP per FADH2). This stage takes place in the inner mitochondrial membrane. The
steps of the electron transport chain are shown in the figure below.

1. NADH and FADH2 deliver electrons to electron transfer chains in the inner
mitochondrial membrane.
 2. Electron flow through the chains causes hydrogen ions (H+) to be pumped from
the matrix to the intermembrane spaces.
3. The activity of the electron transfer chains causes a hydrogen ion gradient to
form across the inner mitochondrial membrane.
4. Hydrogen ion flow back to the matrix through ATP synthases drives the formation
of ATP from ADP and phosphate (Pi).
5. Oxygen (O2) accepts electrons and hydrogen ions at the end of mitochondrial
electron transfer chains, so water forms.

Overall, aerobic respiration typically yields 36 ATP for each glucose molecule 32 ATP
typically forms in the third stage, but yield varies. The typical yield of aerobic respiration
in the brain and skeletal muscle cells is 38 ATP, not 36.

Figure 3.8 Summary of Energy Harvest from a Glucose Molecule

Our body cells have alternative sources of organic compounds that enter aerobic
respiration. These organic compounds are first converted into their monomers or
building blocks before they are oxidized by our cells to extract the energy of ATP. Their
breakdown into their subunits involves the digestive system. For example, proteins are
converted into amino acids, or fats are converted into fatty acids and glycerol first before
they are broken down and transformed into chemical energy of ATP. The figure below
shows alternative pathways of aerobic respiration.
Figure 3.9 Alternative Pathways of Aerobic Respiration