2general Biology 1 Learning Package Final Term

CATHOLIC SCHOOLS IN IFUGAO
GENERAL BIOLOGY 1
FIRST SEMESTER – FINALS A. Y. 2023 - 2024
LESSON 1. STRUCTURES AND FUNCTIONS OF BIOLOGICAL MOLECULES
INTRODUCTION
One of the common features of organisms here on earth is their biochemical composition. All organisms contain
a common set of chemicals such as Carbon, Oxygen, Nitrogen, Phosphorus, Sulfur and Hydrogen, which are the building
blocks of larger and more complex molecules like carbohydrates, lipids, proteins and nucleic acids.
BIOMOLECULES – organic molecules or macromolecules.

- serve as fuel for metabolic activities in organisms
- are of for major types:
I. CARBOHYDRATES – the most abundant of all organic compounds

- are composed of the elements C, H and O in a 1:2:1 ratio
- great sources of energy
Eg. Our brains function well and muscles work properly when powered by energy
TYPES OF CARBOHYDRATES
1. MONOSACHARIDES – the simple sugars since they are monomers; or the single structural units of some complex
carbohydrates
- can be classified
A. According to the placement of chemicals in the structure
a.) ALDOSES – characterized by the presence of an aldehyde ( -CHO ), usually at the terminal end or the
first carbon atom.
b.) KETOSES – are characterized by having a carbonyl ( C = O ) group or a ketone, which is usually located
at the second carbon atom of the molecules
B. According to the number of carbon atoms
a.) DIOSE – with two carbon atoms
b.) TRIOSE – with three carbon atoms
c.) PENTOSE – with 5 carbon atoms Eg. RIBOSE – found in ribonucleic acid and in some vitamins
d.) HEXOSE – with 6 carbon atoms
* GLUCOSE – a major source of energy for all organisms
* FRUCTOSE – found in most plants such as sugar cane, sugar beets and corn
* GALACTOSE
Monosaccharides ( HEXOSES ) Formula Common Name
Glucose C₆H₁₂O₆ Blood sugar
Fructose C₆H₁₂O₆ Fruit sugar
Galactose C₆H₁₂O₆ Brain sugar
DERIVATIVES OF MONOSACHARIDES
 Ascorbic Acid or Vitamin C is from glucose
 Sorbitol and Mannitol ( sugar alcohols ) – sweetening agents
* Monosaccharides provide immediate energy to the organism that takes them. Because monosaccharides are simple
sugars, they are smaller than other types of carbohydrates. Their size allows them to be absorbed immediately through
the digestive tract all the way to the blood stream. Sugary foods and fructose-rich fruits are the best sources of energy
for people who are drained or tired.
2. DISACCHARIDES – are composed of two monosaccharides joined together through a process called condensation
reaction
CONDENSATION REACTION
- in this process, dehydration synthesis takes place, wherein, water is extracted upon combining the two
molecules. The result of the condensation reaction is the formation of the glycosidic bond, a type of covalent
bond that links a carbohydrate molecule to another molecule.
Examples of Disaccharides
a.) SUCROSE ( table/cane sugar ) – a combination of glucose and fructose
- used in the food industry as sweeteners to make candies, ice cream, cookies, cakes, breads, sauces and
preserved goods
b.) LACTOSE ( milk sugar ) – a combination of glucose and galactose
- a great source of nutrients for infants; used in making processed dairy products
1 | GENERAL BIOLOGY 1
* WHEY – a by-product of dairy production that contains lactose and is used in making breads, cookies,
cakes, doughnuts and ice cream
* LACTASE – found in the body ; used to break down glucose
LACTOSE INTOLERANT – a condition that results when people do not produce enough lactase to
digest lactose.
People who are lactose intolerant experience nausea, diarrhea, bloating and abdominal cramps when
they take in dairy foods.
b.) MALTOSE ( malt or beer sugar ) – a combination of two glucose molecules; the least sweet among
the disaccharides
Disaccharides Composition Formula Common Name

Sucrose Fructose + glucose C₆H₁₂O₁₁ Cane/table sugar
Lactose Galactose + glucose C₆H₁₂O₁₁ Milk sugar
Maltose Glucose +glucose C₆H₁₂O₁₁ Malt/beer sugar
3. POLYSACCHARIDES- long chains of three or more monosaccharides.

- not sweet and do not form crystals when water molecules are removed.
- mostly used for energy storage
* BRANCHED POLYSACCHARIDES – soluble in water
* LINEAR POLYSACCHARIDE – forms a rigid structure; either branched or linear
Examples of Polysaccharides
a.) Starch
-Used for energy storage in plants
-Potatoes, pasta and rice are starches
-They provide a quick form of energy for the body i
b.) Chitin
– found in exoskeletons of arthropods (insects, spiders)
- found in cell wall of some fungi
- has stronger hydrogen bonds between bordering polymers which is why it is harder and more stable
than cellulose.
- has antibacterial and antiviral properties, making it useful in medicine and in making wound dressings,
suture materials, cosmetics and various food items.
c.) Glycogen
– as an energy storage in animals
d.) Cellulose
– provide structural support in plants
- cannot be digested by humans.
* RUMINANTS – animals that can digest cellulose because of the presence of special microorganisms in
their digestive tract
* FUNGI – can also digest cellulose into simpler sugars that can be absorbed through their cell walls
made of chitin. This allows the fungi to play an important role in decomposing wood and other plant materials
HEALTH BENEFITS OF POLYSACCHARIDES

A.) Serve as immediate energy reserves in the body
B.) Stabilize blood sugar and provide vitamins and minerals ( like the polysaccharides in mushrooms, berries, cereals
and grains, cabbages and carrots.
C.) Benefits the digestive system
PECTIN – a polysaccharide that is soluble fiber; found in apples, oranges, grapefruits, bananas
II. LIPIDS - biomolecules containing chains of hydrocarbons.

Hydrocarbons - organic compounds that are made up of carbon and hydrogen, and are insoluble in water.
* When lipids are metabolized, they release large amounts of energy, and thus they are useful to organisms. Aside from
functioning as long-term energy storage, they also serve as insulation.
- organisms with more lipids in the body can keep themselves warmer.
Eg. Animals that live in the polar regions, such as polar bears, reindeer, and penguins, have bodies with thick fat layers as
their form of adaptation to the freezing temperatures.
TYPES OF LIPIDS
1. TRIGLYCERIDES - generally known as fats
- contain a glycerol attached to three fatty acids.
FATTY ACID - composed of a long chain of carbon atoms connected to a carboxylic acid (-COOH).
TWO KINDS OF FATTY ACIDS: DEPENDING ON THEIR NATURE AND ORIGIN:
a.) SATURATED FATS - contain only single bonds in the fatty acid chain. Because of this, they are normally solid at
room temperature. They are found in animal fats such as those in pork and beef. They are also found in butter,
lard, cream, cheese, and some processed foods. Because saturated fats are solid in nature, they tend to clog the
lining of blood vessels and block the flow of blood when consumed in high amounts. Too much intake of food
rich in saturated fats is then associated with increased circulatory disorders, such as high blood pressure and
heart attack.
b.) UNSATURATED FATS - mostly known as oils, contain one or more double bonds in the fatty acid chain. Because
of this, they are normally liquid at room temperature. These unsaturated fats are commonly found in plants.
Examples are olive oil, coconut oil, and corn oil.
2. PHOSPHOLIPIDS - lipids with a phosphate group; have a structure similar to fats, but with additional properties.
* * Attached on one side of the glycerol backbone are the hydrophobic or nonpolar "tails," which are composed of two
chains of fatty acids.
** Attached on the other side of the glycerol backbone is the hydrophilic or polar "head, "which is composed of a
phosphate group.
When exposed to water, the hydrophilic heads are drawn toward the water, and the hydrophobic tails move away from
the water. Because of this orientation, the cell's plasma membrane contains a double layer of phospholipids, so that the
polar heads face outward and interact with water and also face the inside of the cell (in contact with the cytoplasm), and
the fatty acid tails face each other on the inside of the cell membrane. This arrangement is vital in keeping the cells and
their organelles separate from their biological components. The plasma membrane is essential to the structure and
function of the cell. Thus, the characteristics of the phospholipid bilayer are important in maintaining the function of the
plasma membrane.
3. STEROIDS – composed of four carbon rings

- help in regulating metabolism, immune response, reproduction and other essential biological processes.
EXAMPLES OF STEROIDS
(a.) CHOLESTEROL – a sterol or a steroid alcohol

- formation usually happens in major organs such as the brain and blood vessel where it gets deposited on the walls and
linings of these organs.
- major components in the formation of bile salts and gallstones
ATHEROSCLEROSIS – blood flow is hampered because of cholesterol that is deposited and hardens in the blood vessels.
(b.) TESTOSTERONE – a male hormone responsible for the development and maintenance of secondary male sex
characteristics
* PROGESTERONE AND ESTROGEN – control the ovulation cycle
(c.) ADRENOCORTICOID HORMONES – formed in the adrenal glands, released to achieve balance by responding to stress,
imbalances or threats to an organism´s body.
Eg. Aldosterone and Cortisol
(d.) WAXES – combined from certain alcohols and fatty acids.
- are extremely hydrophobic, they do not react with water.
- found in:
 leaves and stems of plants ; thereby preventing losing excess water
 furs and feathers of animals to repel water
 ear – CERUMEN; the earwax prevents the entry of some materials into the ear canal; repels and kills
insects
III. PROTEINS
Proteins are the most abundant biomolecules of the living system that is composed of carbon, hydrogen, oxygen,
nitrogen and sulfur (C H O N S). Chief sources of proteins are milk, cheese, pulses, peanuts, fish, meat, etc. They occur in
every part of the body and form the fundamental basis of structure and functions of life. They are also required for
growth and maintenance of body. The word protein is derived from Greek word, “proteios” which means primary or of
prime importance. All proteins are polymers of α-amino acids.
 Twenty percent of the human body is made up of proteins.

 Our body parts can be characterized by the proteins they contain or produce. For example, muscle cells contain
large amounts of actin and myosin proteins for contraction.
 The importance of proteins in organisms is diverse. Proteins play major roles as antibodies, enzymes, hormones
and other substances involved in digestion, respiration, reproduction and even normal vision.
 They are essential for the structure, function, and regulation of the body’s tissues and organs.
 Proteins are made up of smaller units called amino acids, which are building blocks of proteins. They are
attached to one another by peptide bonds forming a long chain of proteins.
All α-amino acids have trivial names, which usually reflect the property of that compound or its source. Glycine is so
named since it has sweet taste (in Greek glykos means sweet) and tyrosine was first obtained from cheese (in Greek,
tyros means cheese.) Amino acids are generally represented by a three letter symbol, sometimes one letter symbol is
also used.
Amino acids contain amino group (–NH2) and carboxyl group (–COOH). The third group is called an R group, which helps
distinguish the amino acid from others, because its specific name and function in the body will depend on the sets of
chemicals that are in this group. For example, Lysine, a protein, has an ionized R group with an ending of CH2-CH2-NH3.
Lysine is particularly important for the growth and repair of tissues.
Classification of amino acids

• There are 20 amino acids. Based on the nature of their ‘R’ group,
they are classified based on their polarity as:
 Plants are capable of making amino acids for themselves.

They convert nitrates that are available in the soil to amino acid groups that bond with the products of
photosynthesis.
 Animals, including humans, cannot make amino acids themselves so they must take in proteins as part of their
diet. Once consumed, these proteins are broken down into amino acids that can form other types of proteins.
CLASSIFICATION BASED ON ESSENTIALITY:

Amino acids are classified as acidic, basic or neutral depending upon the relative number of amino and carboxyl
groups in their molecule. Equal number of amino and carboxyl groups makes it neutral; more number of amino than
carboxyl groups makes it basic and more carboxyl groups as compared to amino groups makes it acidic. The amino acids,
which can be synthesized in the body, are known as nonessential amino acids. On the other hand, those which cannot
be synthesized in the body and must be obtained through diet, are known as essential amino acids
 Essential amino acids are the amino acids which you need through your diet because your body cannot make
them.
e.g. Valine, histidine, isoleucine, leucine, phenylalanine, threonine, tryptophan
 Non-essential amino acids are the amino acids which are not an essential part of your diet because they can be
synthesized by your body.
e.g. Alanine, Arginine, Aspartine, Cystine, Glutamic acid, Glycine, Ornithine, Proline, Serine, Tyrosine
Peptide bonds
Amino acids are linked together by ‘amide groups’ called peptide bonds.
During protein synthesis, the carboxyl group of amino acid at the end of the growing polypeptide chain reacts with the
amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between the amino acids is a
peptide bond.
STRUCTURE OF PROTEINS
Proteins can be classified into two types on the basis of their molecular shape.
(a) Fibrous proteins - When the polypeptide chains run parallel and are held together by hydrogen and disulfide
bonds, then fiber– like structure is formed. Such proteins are generally insoluble in water. Some common examples are
keratin (present in hair, wool, silk) and myosin (present in muscles), etc.
The sequence of a protein is determined by the DNA of the gene that encodes the protein (or that encodes a portion of
the protein, for multi-subunit proteins).
(b) Globular proteins This structure results when the chains of polypeptides coil around to give a spherical
shape. These are usually soluble in water. Insulin and albumins are the common examples of globular proteins. Structure
and shape of proteins can be studied at four different levels, i.e., primary, secondary, tertiary and quarternary, each
level being more complex than the previous one.
A change in the gene's DNA sequence may lead to a change in the amino acid sequence of the protein. Even changing
just one amino acid in a protein’s sequence can affect the protein’s overall structure and function.
To understand how a protein gets its final shape or conformation, we need to understand the four levels of protein
structure: primary, secondary, tertiary, and quaternary
SHAPES OF PROTEINS
1.Primary Structure
 The simplest structure of all the proteins. This is composed only of a linear sequence of amino acids in a peptide
chain. By just changing the sequence of 20 amino acids in polypeptide (which is composed of long, unbranched
peptide chains0, many different proteins are produced.
 Attached together by covalent or peptide bond
 Determined by gene (DNA)
2. Secondary Structure
 This is a three- dimensional shape created by several hydrogen bonds. The first two patterns of the secondary
structure were first predicted by Linus Pauling and Robert Corey in 1951. The called the coiling structure as
alpha helix because it was the first pattern they had discovered.
 The 2nd shape that was discovered was called the beta pleated sheet, which is wavelike in appearance.
3. Tertiary structure
 Refers to the comprehensive 3-D structure of the polypeptide chain of a protein.
4. Quaternary structure
 Formed by interactions between multiple polypeptide chains
 Often, the polypeptide chains will create hydrogen bonds with in another in unique patterns to achieve the
desired protein configuration.
1. Primary Structure 2. Secondary Structure
3.Tertiary structure 4. Quaternary Structure

FUNCTIONS:
1.STRUCTURE- Proteins comprise the skin, bones, hair and nails. Collagen and keratin are the main structural
components in animals and are the most important structural proteins. They form the scaffolding that gives animal cell
their shapes.
2.HORMONES- insulin are proteins that helps absorb glucose from the blood and prevents the body from using fat as
source of energy.
3. TRANSPORT- hemoglobin in the blood is an example of a transport protein. During cellular respiration, it carries
oxygen from the lungs to the cells, where it is used.
4.STORAGE- casein in milk stores nutrients for newborn mammals, as well as ovalbumin in eggs for birds.
5.CATALYSIS- enzymes are proteins that speed up chemical reactions that take place in organisms.
6.PROTECTION- when an antigen, a protein from an outside source enters the body, the body develops its own protein
called antibodies, to counteract the alien protein and fight disease. Fibrinogen is also a protein that facilitates blood
clotting.
7.MOVEMENT- the protein molecules in the muscles, myosin and actin are involved in muscle contraction and
relaxation.
8.REGULATION- some proteins not only and regulate the kind of proteins synthesized in a particular cell but also dictate
when such process takes place.
IV. NUCLEIC ACIDS

Nucleic acids are organic compounds composed of carbon, hydrogen, oxygen, and phosphates that functions for
the storage of genetic information, which is a transmitted from one generation to the next in all living organisms. It is the
physical carrier of inheritance that is passed from parents to offspring. Nucleic acids also function in protein synthesis, as
they carry the code needed in the formation of specific proteins.
There are two type of nucleic acids namely DNA (Deoxyribononucleic acid) and RNA (Ribonucleic acid). Both
types of nucleic acids are made up of the basic building blocks called nucleotide. A nucleotide is made up of a five carbon
sugar, phosphate group and nitrogenous base. The nitrogenous bases are either double- ringed purines, such as guanine
(G) and adenine (A), or singled- ringed pyrimidines such as cytosine (C) and thymine (T).
Organic Bases: There are two types of organic bases (amines)/NITROGENOUS BASES that are incorporated into nucleic
acids:
1) purines – adenine and guanine
2) 2 pyrimidines- cytosine, thymine, uracil
2 types of nucleic acid
STRUCTURE OF DNA:
The structure of DNA as a double-stranded helix molecule was first discovered by James Watson and Francis
Crick in 1953. The two strands strand that winds around each other, forming a double spiral molecule that resembles a
twisted ladder. The backbone of the helix consists of alternating sugars and phosphates, while the steps of the ladder
are made up of nitrogenous base pairs. According to Chargaff’s rule, the different nitrogenous bases from specific
pairs, such that A (Adenine) pairs with T (thymine) while C (cytosine) pairs with G (guanine).
As a result of this specific pairing, the double-stranded DNA molecule forms a uniform structure within the
entire length of a long helix. Hydrogen bonds connect nitrogenous base pairs together, making the double helix highly
stable. There are 3 and 2 hydrogen bonds between C-G and A-T. pairs respectively. Because of the base pairing rule, the
two strands of the double helix are said to be complementary bases. The same basic pairing rules exist in RNA except
that U is paired with A instead of T.
RNA: Ribonucleic acid

 The uses of RNA may range from encoding to decoding and regulating the expression of genes, depending on
the type of RNA present.
TYPES OF RNA:
1. Messenger RNA (mRNA ) serves as a temporary copy of gene in a DNA that directs the sequence of amino acids
during the protein synthesis.
2. Transfer RNA (tRNA ), Translates the sequence of nucleic acids in a gene to create the correct sequence of
amino acids during protein synthesis.
3. Ribosomal RNA (rRNA ) froms the peptide bonds between the amino acids in apolypeptide eaully important
functions within the cell.
SUMMARY OF THE DIFFERENCES BETWEEN DNA & RNA
DNA RNA
Sugar Deoxyribose Ribose
Strand Double-stranded with base pairing Single – stranded
Nitrogenous bases Adenine Adenine
Thymine Uracil
Cytosine Cytosine
Guanine Guanine
Helix Yes No
Location Mainly in nucleus, mitochondria and chloroplast Found in cytoplasm and nucleus
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FORMATIVE ASSESSMENT 1.1
Enumerate the four major biomolecules and differentiate them according to:
 Elemental composition
 Building blocks
 Functions
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Metabolism and Enzymes
All organisms on earth have cells that metabolize energy to support life. Thus, there is a need to have a constant
supply of energy around us. All biomolecules that make up the cell need energy for them to be useful in the body.
Cellular operations are accomplished through biochemical reactions that take place within the cell. These reactions are
switched on and off, or speed up and slowed down, depending on the cell's immediate needs and overall functions.
Metabolism
A series of chemical reactions in the body that converts food into energy. In the process of food conversion,
some forms of energy are released as by-products. Metabolism is important in maintaining the living state of the cells
and. Thus, of the organism. It helps us maintain the characteristics of life – growth, reproduction, repair of damaged
parts, and ability to respond to the environment.
Catabolism
This process involves the breakdown of molecules to release energy. For example carbohydrates, proteins, and
lipids). In catabolism reactions, these biomolecules are broken down to release energy. This energy is either used
immediately or stored for later use.
Some examples of catabolic reactions are the following:
 Breakdown of polysaccharides into monosaccharides to generate energy.
 Breakdown of nucleic acids into nucleotides for transmitting genetic information.
 Breakdown of proteins into amino acids, either to make new ones or to produce glucose in the blood.
 Breakdown of food in the stomach for the nutrients to be absorbed into the blood vessels.
The energy released in catabolic reactions is stored in ATP to be used in anabolic reactions.
Anabolism
Anabolism means “building things or substances in the body”. This process requires and consumes energy to
allow the building processes to proceed. In anabolic reactions, our Bodies us simple chemicals and molecules to
synthesize (or build) a vast array of products and substances, such as biomolecules, so they can serve important
functions.
Common Examples
 Building proteins (large, complex molecules) from amino acids (simple molecules)
 Cell reproduction, where cells multiply to increase tissue (or organ) size.
 Mineralization of bones from inorganic substances.
 Production of hormones necessary for certain organs to perform their functions.
As mentioned, anabolism is fueled by catabolism. Large molecules are broken down into smaller parts, releasing
several ATP molecules in the process. Many anabolic processes are powered by the use of these ATP molecules.
Anabolism and catabolism are both vital processes. Inside the human body, anabolism builds up substances. This
building up is balanced by catabolism, which breaks down the substances. Outside the human body, a person must
achieve and maintain an equal balance in everything that is taken in and excreted out of his or her body.
Enzymes
The chemical reactions that make up metabolism do not proceed by themselves. These reactions are switched
on and off, or sped up and slowed down, depending on the cell’s immediate needs ad overall functions. An Enzyme is a
molecule that helps speed up the process in a chemical reaction. Enzymes allow reactions to occur under mild
conditions, partly by eliminating nonspecific side reactions.
Components of an Enzyme
Enzymes are highly selective. They catalyze specific reactions only. This specific is due to their shapes. A typical
enzyme is composed of a protein called an apoenzyme and a nonprotein called a cofactor.
An Apoenzyme can be called as a Proenzyme when it is inactive, which means either it is not attached to any
substance or the enzyme is in its original form.
The Cofactor, on the other hand, assist apoenzymes in their biological activities.
Types of Cofactor
 Metal ion activators are not permanently bound to the apoenzymes. They supply positive charges to the
enzyme through covalent bonding. Examples of these metals are Magnesium (Mg +2), Zinc (Zn+2), Manganese
(Mn+2), Sodium (Na+1), Iron (Fe+2), Potassium (K+1), and Copper (Cu+2). These metals are actually the dietary
minerals that are part of your daily nutritional requirements.
 Coenzymes are organic molecules that usually come from the vitamins that you take in every day. Like the metal
ions activators, they temporarily bind to apoenzymes.
 Prosthetic cofactors can be either metal ions or organic molecules. The only difference is that they bind to
apoenzymes permanently.
Vitamins Function (s)

Part of coenzyme cocarboxylase; has several functions, including, the metabolism of
B1 (Thiamine)
pyruvate.
B2 (riboflavin) Coenzyme in flavoproteins; helps transfer electron
B6 (pyridoxine) Coenzyme in amino acid metabolism
Helps in the transfer of methyl groups (methyl cyanocobalamide); active in amino
B12 (cyanocobalamin)
acid metabolism.
Niacin (nicotinic acid) Part of the nicotinic acid dinucleotide (NAD) molecule; helps transfer electron.
Pantothenic acid Part of coenzyme A; metabolizes pyruvate and lipids
Biotin Helps in carbon dioxide fixation reactions and fatty acid synthesis
Folic acid Coenzyme involved in the synthesis of purines and pyrimidines
Vitamin E Coenzyme involved in cellular and molecular synthesis.
Vitamin K Coenzyme used in electron transport (naphthoquinones and quinones)
When the apoenzyme and the cofactors are bound, they form an enzyme complex called a holoenzyme. The
holoenzyme now becomes active and ready for any catalytic reactions.
Not all enzymes are proteins. Some enzymes are also made of RNA molecules. Examples, Ribozymes, which
synthesize the proteins in the ribosomes of cells. Ribozymes undergo catabolism to help build protein chains during
protein synthesis. This is why they are also called catalytic RNA.
Chemical reactions happen in an orderly manner through a series of linked reactions. Metabolic pathways start
with a particular reactant and end with a final product. The reactants in the first reaction are converted into products,
which may serve as reactions for another product, and so on. Enzymes are vital for one metabolic pathway to interact
with another metabolic pathway. This organized arrangement is also useful for releasing and capturing small increments
of molecular energy instead of releasing it all at once.
Activation Energy
Typically, molecules do not interact with one another unless they are triggered in some way. For example,
certain molecules do not get activated unless they are heated. In essence, the presence of energy is vital in causing a
reaction in these molecules. The amount of energy required to stimulate the reaction is called the activation energy.
This term was coined by the Swedish scientist Svante Arrhenius in 1889 to describe the minimum amount of energy
needed to start any chemical reaction.
Enzyme- Substrate Complex
The reactant in an enzymatic reaction are called the substrates for that enzyme. To illustrate this in a diagram, a
substrate combines with an enzyme to form an enzyme-substrate complex;
E (enzyme) + S (substrate) ES (Enzyme-substrate complex)
You have learned that enzymes only catalyze certain reactions. This means any slight change in the shape or the
condition of the substrate will stop the enzyme from catalyzing a chemical reaction.
Some enzymes have multiple functions. They do more than just form a complex with their substrate; they also take part
in the reaction. One example is trypsin, which digest proteins by breaking the peptide bonds. The active site of trypsin is
bound by three amino acids, with R groups interacting with the peptide bonds and introducing components of water.
Factors affecting Enzymatic Speed

The rate of reaction is the amount of product that is produced per unit of time. There are major factors that
affect the catalytic function of enzyme – temperature, substrate concentration, optimal pH, enzyme cofactors, and
enzyme inhibitors.
Temperature
As the temperature rises, molecules are more inclined to react because they have more kinetic energy. When
this temperature is elevated, the enzyme structure starts to undergo denaturation, or breakdown. The declines rapidly
because the change in the structure of an enzyme can no longer accommodate the shape of the substrate.
Endothermic (warm blooded) animals keep their internal heat in balance, allowing the enzymes to perform faster and
more effective.
Substrate Concentration
The substrate concentration refers to the amount of substrate molecules available for chemical reaction. For the
reaction to begin, molecules must collide. The substrate concentration increases the enzyme activity because more
collisions take place between the substrate molecules and the enzymes. There are more substrate molecules that fill the
active sites, and thus more results are produced per unit of time.
Optimal pH
Like two other two factors, each enzyme also has an optimal pH level for it to reach maximum reaction rate. If
the pH level continues to increase, the enzymatic reactions begin to decline. Each pH value has a specific structural
configuration for the enzyme. The globular structure of the proteins in the enzyme is dependent on certain interactions
of the enzyme such as the hydrogen bonding or the interactions between the R groups. Changing the pH level may affect
the ionization of the side chains and disrupt their interaction. When the pH Level is either lower or higher than the
optimal pH, the enzyme loses its structure and becomes inactive. No substrate will fit the altered active site, resulting in
disruption in the activity.
Enzyme Cofactors
Some are enzymes need the addition of inorganic ions or coenzymes to help speed up the rate of reaction.
These small organic molecules in trace amounts that can promote enzymatic activities. They help bind the substrate to
the active site or participate in the reaction at the active site. Vitamins either become part of the coenzyme’s molecular
structure or become coenzymes themselves, such that if vitamins are insufficient or deficient, certain vitamin disorders
occur. Riboflavin deficiency, for instance, resulting in cracks at the corners of the mouth.
Enzyme Inhibitors
There are instances when enzyme activity should be limited. The molecule that binds to the enzyme to decrease
its activity is called the enzyme inhibitor. The end product itself may be used as the inhibitor. Enzyme inhibition is
important in controlling enzymatic reactions because once the body has completed the necessary chemical processes,
enzymatic reactions have to stop. This is also beneficial in conserving raw materials and energy in the body.
When enzyme is inhibited, it is not capable of binding to any substrate. Metabolic pathways are inhibited until
conditions are altered to induce reactions to take place again. Enzyme inhibition may be reversible or irreversible,
depending on the type f enzyme. When inhibition is reversible, the enzymes do not allow for a reversal inhibition. In this
case, the inhibition permanently inactivates or destroys the enzyme.
Enzyme inhibitors are normally used in pharmaceutical industries, where certain chemicals or molecules block
the activity of the enzyme. For example, some antibiotics contain chemicals that may act as inhibitors to prevent
enzymatic activity of certain disease-causing bacteria. Thus, when an antibacterial medicine is taken in, it could kill those
bacteria. However, in some cases, these medicines may also inhibit or disrupt certain enzymatic activities in your body.
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FORMATIVE ASSESSMENT 1.2
Illustrate and explain the enzyme-substrate complex.
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LESSON II. ENERGY TRANSFORMATION
Energy is life. Living organisms will not be able to cope and proceed with the mechanisms of life if they do not
have energy. Plants process energy from the sun through photosynthesis to produce glucose. Animals feed on plants to
harvest glucose that contain energy. However, glucose lacks energy. Therefore, it has to be broken down from the
energy to be released and utilized by animals. This process is referred to as cellular respiration. This chapter focuses on
how plants harvest energy from the sun and change it into chemical energy stores in food. How energy in the form of
ATP is produced and how the cells of living things harvest, store and use it.
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I. ATP-ADP CYCLE
Autotrophs and heterotrophs share the same energy molecule to drive their cellular processes. Interestingly,
autotrophs have the capacity to release the energy from the same molecule that they created to power up the non-
photosynthetic parts of its system. Trapped light from the sun is processed by photosynthesis which produces energy.
This usable energy is stored as a chemical bond in a molecule known as Adenosine triphosphate (ATP). All organisms
then use this fuel molecule during cellular respiration as chemical source of energy. Metabolism of large molecules that
is carbohydrates by glycolysis and fats by β- oxidation produces substrates for cellular respiration. What are forms of
reactions that produce and consume ATP? How is ATP involved in energy coupling and transfer?
The “ATP/ADP cycle” is the continuously ongoing “energy recycling,” through oxidative phosphorylation of “low
energy” adenosine diphosphate (ADP) molecules, to “high energy” adenosine triphosphate (ATP) molecules (binding
energy), and the subsequent hydrolysis of ATP molecules back to ADP (releasing energy).
Adenosine triphosphate (ATP), energy-carrying molecule found in the cells of all living things. ATP captures chemical
energy obtained from the breakdown of food molecules and releases it to fuel other cellular processes.
1 adenine molecule
3 phosphates molecule
1 Ribose sugar molecule

Figure 1 CHEMICAL STRUCTURE OF ATP
ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups
(triphosphate). The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha (α),
beta (β), and gamma (γ) phosphates.
Functions of ATP
Adenosine triphosphate, also known as ATP, is a molecule that carries energy within cells. It is the main energy
currency of the cell, and it is an end product of the processes of photophosphorylation (adding a phosphate group to a
molecule using energy from light), cellular respiration, and fermentation.
ATP MECHANISM: Even when an organism is resting, ATP is still at work because certain cellular activities continue to
work and require energy input. Thus, ATP should be able to continuously meet all the energy demands of the organism.
How is energy released from an ATP molecule?
The bonds of adenosine triphosphate (ATP) can be broken through the addition of water, releasing one
phosphate group in an exergonic/exothermic process called hydrolysis. This reaction liberates the energy in the bonds
for use in the cell—for instance, to synthesize proteins from amino acids.
ATP + H2O + ATPase = energy *ATPase- energy user

How is ATP restored?
ADP phosphorylation is the addition of a phosphate group to ADP (adenosine diphosphate), converting it into
ATP. The covalent bonds binding phosphate groups to adenosine are energy rich bonds. Therefore, energy is required
for the formation of these bonds attaching phosphate group.
ADP is converted into ATP, whenever energy is available. This conversion of ADP into ATP is termed phosphorylation.
ADP + energy + ATP synthase = ATP *ATP synthase- energy builder

 The ATP-ADP cycle couples the cell’s energy
yielding processes to energy consuming process
 ATP regeneration happens very fast (10M
molecules of ATP used and regenerated per
second)
 If ATP could not be regenerated by
phosphorylation of ADP, HUMAN would use
nearly their body weight in ATP each day.
A BREATH OF HISTORY:
ATP was first discovered in 1929 by the German chemist
Karl Lohmann and its structure is established some years
later. In 1948, Alexander Todd from UK synthesized ATP
chemically while Vladimir Engelhart of Russia notes in
1953 that muscle contractions require ATP. Between 1939
and 1941 Fritz Lipmann of USA shows that ATP is the main
bearer of chemical energy in the cell thus he coins the
phrase “energy rich phosphate bonds
---------------------------------------------------------------------------------------------------------------------------------------------------------------
==================================================================================================
FA 2.1 Describe how ATP is formed from ADP
==================================================================================================
II. PHOTOSYNTHESIS
Key terms:
Terms Meaning
Photoautotroph An organism that produces its own food using light energy (like plants)
ATP Adenosine triphosphate, the primary energy carrier in living things
Chloroplast The plant cell structure where photosynthesis occurs.
Thylakoids Disc-like structures within a chloroplast that help absorb light
Grana Stacks of thylakoids in a chloroplast
Chlorophyll A pigment found in the thylakoid that absorbs light energy and uses it to produce carbohydrates.
Stroma Fluid filled space surrounding the grana.
A. Introduction: Photosynthesis comes from the Greek “PHOTO” meaning produced by light and
“SYNTHESIS” meaning a whole made of parts put together.
B. Definition: PHOTOSYNTHESIS is the process whereby green plants, algae, some bacteria, use the energy of the sun to
synthesize organic compounds (sugars) from inorganic compounds (CO2 and water).
WHY IS PHOTOSYNTHESIS SO IMPORTANT?
PHOTOSYNTHESIS is one of the most important biological process on earth!

 Provides the oxygen we breathe; Consumes much of the CO2; Food; Energy; Fibers and materials
BALANCED CHEMICAL EQUATION OF PHOTOSYNTHESIS:
SUNLIGHT
6CO2 + 6H2O C6H12O6 + 602
Carbon dioxide water glucose oxygen
THE BASICS OF PHOTOSYNTHESIS:
 Almost all plants are photosynthetic autotrophs, as are some bacteria and protists. Autotrophs generate their
own organic matter through photosynthesis. Photosynthesis takes place in the leaf of a plant.
LOCATION OF PHOTOSYNTHESIS:
 In most plants, photosynthesis occurs in the green areas of the plant. The internal structure of leaves includes
the mesophyll tissues, which contain cells that are specialized for photosynthesis. Carbon dioxide and water are
the materials necessary for photosynthesis to occur. First, water is absorbed by the plant’s roots. This is
distributed to the other parts of the plants through a vascular tissue called xylem. Finally, it makes its way to the
leaves through the leaf veins. Carbon dioxide likewise enters the leaf through small openings called the stomata.
When carbon dioxide makes its way through these openings, it goes through mesophyll tissues where, along
with water, it diffuses into the cell’s chloroplasts. This is the organelle where photosynthesis takes place. Each
mesophyll cell contain organelles called chloroplasts, which are specialized to carry out the reactions of
photosynthesis. Within each chloroplast, disc-like structure called thylakoids are arranged in piles likes stacks of
pancakes that are known as grana.
Figure 2 STRUCTURE OF CHLOROPLAST
INTERNAL STRUCTURE OF A LEAF
There are two main stages of photosynthesis: The Light-dependent reactions and the Calvin cycle.
Requires
Stage Location Events
sunlight?
Light- dependent reactions Thylakoid Light energy is captured by chloroplasts and stored as Yes
membrane ATP.
Calvin cycle Stroma ATP is used to create sugars that the plant will use to No
grow and live
A. Light Dependent Reaction
 Takes place in the presence of light.
 Light energy is converted to chemical energy during the first stage of photosynthesis, which involves a series of
chemical reactions known as the light-dependent reactions.
 The light-dependent reactions use light energy to make two molecules needed for the next stage of
photosynthesis: the energy storage molecule ATP and the reduced electron carrier NADPH. In plants, the light
reactions take place in the thylakoid membranes of organelles called chloroplasts.
 Photosystems, are large complexes of proteins and pigments (light-absorbing molecules) that are optimized to
harvest light and play a key role in the light reactions. There are two types of photosystems: Photosystem I
(P700) and Photosystem II (P680).
 Both photosystems contain many pigments that help collect light energy, as well as a special pair of chlorophyll
molecules found at the core of the photosystem. Photosynthetic pigments such as chlorophyll a, chlorophyll b
and carotenoids are light harvesting molecules found in the thylakoid membranes of the chloroplasts. When
pigment absorbs a photon, it is raised to an excited state.
In a process called non-cyclic photophosphorylation (the "standard" form of the light-dependent reactions),
electrons are removed from water and passed through PSII and PSI before ending up in NADPH. This process requires
light to be absorbed twice, once in each photosystem, and it makes ATP. In fact, it's called photophosphorylation
because it involves using light energy (photo) to make ATP from ADP (phosphorylation).
 Light absorption in PSII. When light is absorbed by one of the many pigments in photosystem II, energy is passed
inward from pigment to pigment until it reaches the reaction center. There, energy is transferred to P680,
boosting an electron to a high energy level. The high-energy electron is passed to an acceptor molecule and
replaced with an electron from water. This splitting of water releases the O2 we breathe.
 ATP synthesis. The high-energy electron travels down an electron transport chain, losing energy as it goes. Some
of the released energy drives pumping of H+ ions from the stroma into the thylakoid interior, building a
gradient. (H+ from the splitting of water also add to the gradient.) As H+ ions flow down their gradient and into
the stroma, they pass through ATP synthase, driving ATP production in a process known as chemiosmosis.
 Light absorption in PSI. The electron arrives at photosystem I and joins the P700 special pair of chlorophylls in
the reaction center. When light energy is absorbed by pigments and passed inward to the reaction center, the
electron in P700 is boosted to a very high energy level and transferred to an acceptor molecule. The special
pair's missing electron is replaced
by a new electron from PSII
(arriving via the electron
transport chain).
NADPH formation. The high-
energy electron travels down a
short second leg of the electron
transport chain. At the end of the
chain, the electron is passed to
NADP+ (along with a second
electron from the same pathway)
to make NADPH.
The net effect of these steps is to
convert light energy into chemical
energy in the form of ATP and
NADPH. The ATP and NADPH
from the light-dependent reactions are used to make sugars in the next stage of photosynthesis, the Calvin
cycle.
Some electrons flow cyclically
The pathway above is sometimes called linear photophosphorylation. That's because electrons travel in a line
from water through PSII and PSI to NADPH. (Photophosphorylation = light-driven synthesis of ATP.)
In some cases, electrons break this pattern and instead loop back to the first part of the electron transport chain,
repeatedly cycling through PSI instead of ending up in NADPH. This is called cyclic photophosphorylation.
After leaving PSI, cyclically flowing electrons travel back to the cytochrome complex (Cyt) or plastoquinone (Pq) in the
first leg of the electron transport chain. The electrons then flow down the chain to PSI as usual, driving proton pumping
and the production of ATP. The cyclic pathway does not make NADPH, since electrons are routed away from NADP+
reductase.
Why does the cyclic pathway exist?
At least in some cases, chloroplasts seem to switch from linear to cyclic electron flow when the ratio of NADPH to
NADP+ is too high (when too little NADP+ is available to accept electrons). In addition, cyclic electron flow may be
common in photosynthetic cell types with especially high ATP needs.
Summary of light dependent reaction:

1.Light reactions consist of two alternate electron
Light reaction: NON CYCLIC ELECTRON PATHWAY
pathways:
 Takes place in thylakoid membrane
 Noncyclic electron pathway  Uses two photosystems, PS-I and PS-II
 Cyclic electron pathway  PS II captures light energy
2. Capture light energy with photosystems  Causes an electron to be ejected from the reaction
3. Pigment complex helps collect solar energy like an center (chlorophyll a)
antenna  Electron travels down electron transport chain to PS-I
4. Occur in the thylakoid membranes  Replaced with an electron from water which causes
5. Both pathways produce ATP H+ to concentrate in thylakoid chambers
6. The noncyclic pathway also produces NADPH  Which causes ATP production
 PS-I captures light energy and ejects an electron
 Transferred permanently to a molecule of NADP+ 
Causes NADPH production
Light reaction: CYCLIC ELECTRON PATHWAY

 Uses only photosystem I (PS-I) Light reaction: CYCLIC ELECTRON PATHWAY
 Begins when PS I complex absorbs 1.PS II: Consists of a pigment complex and electron-
solar energy acceptors; Adjacent to an enzyme that oxidizes water;
 Electron ejected from reaction center Oxygen is released as a gas
*Travels down electron transport 2. Electron transport chain:
chain *Causes H+ to concentrate in  Consists of cytochrome complexes
thylakoid chambers  Carries electrons between PS II and PS I
*Which causes ATP production  Also pump H+ from the stroma into thylakoid
* Electron returns to PS-I (cyclic) space
 Pathway only results in ATP 3. PS I: Has a pigment complex and electron acceptors
production NADP+  Adjacent to enzyme that reduces NADP+ to
 Causes NADPH production NADPH
4. ATP synthase complex:
 Has a channel for H+ flow
 Which drives ATP synthase to join ADP and Pi
B. The Light Independent Reaction or Calvin Cycle)

 It is the second phase of photosynthesis in which CO2 is fixed or reduce to glucose. It takes place in the stroma
of the chloroplast.
 Calvin cycle was given by Melvin Calvin and Andrew Benson, hence also called as Calvin-Benson Cycle.
 In this cycle, phosphoglyceric acid (3 carbon compound) is produced as a first product and thus the called also as
C3 cycle or C3 photosynthesis.
 In plants, carbon dioxide enters the interior of a leaf via pores called stomata and diffuses into the stroma of the
chloroplast—the site of the Calvin cycle reactions, where sugar is synthesized. These reactions are also called
the light-independent reactions because they are not directly driven by light.
 In the Calvin cycle, carbon atoms from CO2 are fixed (incorporated into organic molecules) and used to build
three-carbon sugars. This process is fueled by, and dependent on, ATP and NADPH from the light reactions
Note: The Light and “Dark” or Carbon reactions happen at different sites in the chloroplast
 CALVIN CYCLE/ LIGHT REACTION/DARK REACTION / C3 PHOTOSYNTHESIS

o A cyclical series of reactions that utilizes atmospheric carbon dioxide to produce carbohydrates
o The Calvin cycle reactions can be divided into three main stages: carbon fixation, reduction, and
regeneration of the starting molecule.
Here is a general diagram of the cycle:

1. Carbon fixation.
 CO2 is attached to 5-carbon RuBP molecule
 Result in a 6-carbon molecule
 This splits into two 3-carbon molecules (3PG)
 Reaction accelerated by RuBP Carboxylase
(Rubisco)
 CO2 now “fixed” because it is part of a
carbohydrate
2. Reduction.
 ATP and NADPH are used to convert the 3-PGA
molecules into molecules of a three-carbon
sugar, glyceraldehyde-3-phosphate (G3P). This
stage gets its name because NADPH donates
electrons to, or reduces, a three-carbon
intermediate to make G3P.
3.Regeneration.
 RuBP used in CO2 fixation must be replaced
 Every three turns of Calvin Cycle, Five G3P (a 3-carbon molecule) used to remake three RuBP (a 5-carbon
molecule)
==================================================================================================
FORMATIVE ASSESSMENT 2.2 Identify the two main phases of Photosynthesis and describe each phase according to
place of occurrence, raw materials and end products
=================================================================================================
LESSON 3. CELLULAR RESPIRATION
 Cellular Respiration is a catabolic process in which digested glucose from food nutrients is broken down into
Adenosine triphosphate (ATP) with or without the presence of oxygen for use as energy by prokary otic and
eukaryotic organisms (except plants).
CHEMICAL EQUATION OF CELLULAR RESPIRATION:

C6H12O6 + 602 6CO2 + 6H2O + energy
glucose oxygen carbon dioxide water
Two types:
Aerobic Respiration Anaerobic Respiration
A. Aerobic Cellular Respiration- process by which glucose molecules are broken down to produce energy in the
presence of oxygen.
Phases of Complete Glucose Breakdown

1. Aerobic respiration includes metabolic pathways and one individual reaction:
a. Glycolysis is the breakdown of glucose to two molecules of pyruvate.
1) Enough energy is released for immediate buildup of two ATP.
2) Glycolysis takes place outside the mitochondria and does not utilize oxygen.
b. The transition reaction: pyruvate is oxidized to an acetyl group and CO2 is removed.
c. The Krebs cycle:

1) This series of reactions gives off CO2 and produces ATP.
2) Produces two immediate ATP molecules per glucose molecule.
d. The electron transport system:

1) Series of carriers accepts electrons from glucose; electrons are passed from carrier to carrier until received by
oxygen.
2) Electrons pass from higher to lower energy states, energy is released and stored for ATP production.
3) System accounts for 32 or 34 ATP depending on the cell.
2. Pyruvate is a pivotal metabolite in cellular respiration:
a. If O2 is not available to the cell, fermentation, an aerobic process, occur.
b. During fermentation, glucose is incompletely metabolized to lactate or CO 2 and alcohol.
c. Fermentation results in a net gain of only two ATP per glucose molecule.
Outside the Mitochondria: Glycolysis
A. Glycolysis
1. Occurs in the cytosol outside the mitochondria.
2. Is the breakdown of glucose to two pyruvate molecules.
3. Is universal in organisms; therefore, most likely evolved before Krebs cycle and electron transport system.
B. Energy Investment Steps

1. Glycolysis begins with addition of two phosphate groups activating glucose to react.
2. Two separate reactions use two ATP.
3. Glucose, a C6 molecule, splits into two C3 molecules, each with a phosphate group.
C. Energy Harvesting Steps

1. Two electrons and one hydrogen ion are accepted by NAD+ and result in two NADH.
2. Enough energy is released from breakdown of glucose to generate four ATP molecules.
3. Two to four ATP molecules produced are required to replace two ATP molecules used in the phosphorylation
of glucose.
4. There is a net gain of two ATP from glycolysis.
5. Pyruvate enters mitochondria if oxygen is available and aerobic respiration follows.
6. If oxygen is not available, glycolysis becomes a part of fermentation.
Inside the Mitochondria

A. Aerobic Respiration
1. Involves the transition reaction, the Krebs cycle, and the electron transport system.
2. Is process in which pyruvate from glycolysis is broken down completely to CO2 and H2O.
3. Takes place inside mitochondria.
B. Mitochondria
1. A mitochondrion has a double membrane with an intermembrane space between the outer and inner
membrane.
2. Cristae are the inner folds of membrane that jut into the matrix.
3. Matrix is the innermost compartment of a mitochondrion and is filled with gel-like fluid.
4. Transition reaction and Krebs cycle enzymes are in matrix; electrons transport system is in cristae.
5. Most ATP produced in cellular respiration is produced in mitochondria.
C. Transition Reaction
1. Transition reaction connects glycolysis to the Krebs cycle.
2. In this reaction, pyruvate is converted to a two-carbon acetyl group attached to coenzyme A.
3. This redox reaction removes electrons from pyruvate by dehydrogenase using NAD+ as coenzyme.
4. Reaction occurs twice for each original glucose molecule.
D. The Krebs Cycle

1. Krebs cycle reactions occur in matrix of mitochondria.
2. Cycle is named for Sir Hans Krebs, who received Noel Prize for identifying these reactions.
3. Cycle begins by adding C2 acetyl group to C4 molecule, forming citrate; also called the citric acid cycle.
4. The acetyl group is then oxidized to two molecules of CO2.
5. During the oxidation process, most electrons (e-) are accepted by NAD+ and NADH is formed.
6. In one instance, electrons are taken by FAD, forming FADH2.
7. NADH and FADH2 carry these electrons to electron transport system.
8. Some energy released is used to synthesize ATP by substrate-level phosphorylation, as in glycolysis.
9. One high-energy metabolite accepts a phosphate group and passes it on to convert ADP to ATP.
10. Krebs cycle turns twice for each original glucose molecule.
11. Products of the Krebs cycle per glucose molecule include 4 CO2, 2 ATP, 6 NADH and 2 FADH2
** In summary, each citric cycle produces 2 carbon dioxide molecules, 3 NADH molecules, an FADH2 molecule and an
ATP molecule. Because the citric cycle normally turns twice for every glucose molecule, the total amount of products
produced is as follows:
 2 acetyl CoA 4 CO2
 6 NAD+ 6 NADH
 2 FAD 2 FADH2
 A ADP + 2 phosphate 2 ATP
E. The Electron Transport System

1. Electron transport system is located in cristae of mitochondria; consists of carriers that pass electrons.
2. Some protein carriers are cytochrome molecules.
3. Electrons that enter the electron transport system are carried by NADH and FADH 2.
4. NADH gives up its electrons and becomes NAD+; next carrier gains electrons and is reduced.
5. At each sequential oxidation-reduction reaction, energy is released to form ATP molecules.
6. Oxygen serves as terminal electron acceptor and combines with hydrogen ions to form water.
7. Because O2 must be present for system to work, it is also called oxidative phosphorylation.
8. NADH delivers electrons to system; by the time electrons are received by O 2, 3 ATP are formed.
9. If FADH2 delivers electrons to system, by the time electrons are received by O2, 2 ATP are formed.
10. Coenzymes and ATP recycle
a. Cell needs a limited supply of coenzymes NAD+ and FAD because they constantly recycle.
b. Once NADH delivers electrons to electron transport system, it is free to pick up more hydrogen.
c. Components of ATP also recycle.
d. Efficiency of recycling NAD+, FAD and ADP eliminates need to synthesize them anew.
F. The Cristae of a Mitochondrion
1. Electron transport system consists of three protein complexes and two protein mobile carriers that transport
electrons between complexes.
2. Energy released from flow of electrons down electron transport chain is used to pump H+ ions, carried by
NADH
and FADH2, into intermembrane space.
3. Accumulation of H+ ions in this intermembrane space creates a significant electrochemical gradient.
4. ATP synthase complexes are channel proteins that also serve as enzymes for ATP synthesis.
5. As H+ ions flow from high to low concentration, ATP synthase synthesizes ATP; actual mechanism is still
unknown.
6. "Chemiosmosis" term used since ATP production tied to electrochemical (H+) gradient across a membrane.
7. Once formed, ATP molecules diffuse out of the mitochondrial matrix through channel proteins.
G. Energy Yield from Glucose Breakdown
1. Substrate-Level Phosphorylation
a. Per glucose molecule, there is a net gain of 2 ATP from glycolysis in cytosol.
b. The Krebs cycle in the matrix of the mitochondria produces 2 ATP per glucose.
c. Total of 4 ATP are formed outside of the electron transport system.
2. Oxidative Phosphorylation
a. Most ATP is produced by the electron transport system.
b. Per glucose, 10 NADH and 2 FADH2 molecules provide electrons and H+ ions to electron transport system.
c. For each NADH formed within the mitochondrion, 3 ATP are produced.
d. For each FADH2 formed by Krebs cycle, 2 ATP result since FADH2 delivers electrons after NADH.
e. For each NADH formed outside mitochondria by glycolysis, 2 ATP are produced as electrons are shuttled
across mitochondrial membrane by an organic molecule and delivered to FAD.
f. Heart and liver cells, which have high metabolic rates are exception; NADH results in production of 3 ATP.
g. Prokaryotes lack mitochondria; each NADH produces three ATP for total of 38 ATP.
3. Efficiency of Complete Glucose Breakdown
a. Energy difference between total reactants (glucose and O2) and products (CO2 and H2O) is 686 kcal.
b. ATP phosphate bond has energy of 7.3 kcal; 36 to 38 are produced during glucose breakdown for total of
atleast 263 kcal.
c. Efficiency is 263/686 or 39% of available energy in glucose is transferred to ATP.
B. Anaerobic Cellular Respiration- a type of respiration where oxygen is not used; instead, organic or inorganic
molecules are used as final electron acceptors.
==================================================================================================
Formative Assessment 3.1 Summarize, through an illustration, the important events that happen during Cellular
Respiration.
==================================================================================================
IMPORTANT NOTES ON CELLULAR RESPIRATION
 Cellular Respiration Includes Fermentation

1. Fermentation consists of glycolysis plus reduction of pyruvate to either lactate or alcohol and CO 2.
2. NADH passes its electrons to pyruvate instead of to an electron transport system; NAD+ is then free to return
and pick up more electrons during earlier reactions of glycolysis.
3. Examples:
a. Anaerobic bacteria produce lactic acid when we manufacture some cheeses. Lactic acid fermentation
Metabolic process by which glucose and other six-carbon sugars are converted into cellular energy
and the metabolite lactate, which is lactic acid in solution
Lactic acid fermentation converts the 3-carbon pyruvate to the 3-carbon lactic acid (C3H6O3) and
regenerates NAD + in the process, allowing glycolysis to continue to make ATP in low-oxygen
conditions. Since there is a limited supply of NAD + available in any given cell, this electron acceptor
must be regenerated to allow ATP production to continue. To achieve this, NADH donates its extra
electrons to the pyruvate molecules, regenerating NAD +. Lactic acid is formed by the reduction of
pyruvate.
b. Anaerobic bacteria produce industrial chemicals: isopropanol, butyric acid, propionic acid, and acetic
acid.
c. Yeasts use CO2 to make bread rise and produce ethyl alcohol in winemaking.
d. Animals reduce pyruvate to lactate when it is produced faster than it can be oxidized by Krebs cycle.
 Advantage and Disadvantage of Fermentation
1. Despite low yield of two ATP molecules, fermentation provides quick burst of ATP energy for muscular
activity.
2. Disadvantage is that lactate is toxic to cells.
a. When blood cannot remove all lactate from muscles, lactate change pH and causes muscles to fatigue.
b. Individual is in oxygen debt because oxygen is still needed after exercising.
c. Recovery occurs after lactate is sent to liver, converted into pyruvate; then respired or converted into
glucose.
 Efficiency of Fermentation
1. Two ATP produced per glucose molecule during fermentation is equivalent to 14.6 kcal.
2. Complete glucose breakdown to CO2 and H2O during cellular respiration results in 686 kcal of energy.
3. Efficiency of fermentation is 14.6/686 or about 2.1%; much less efficient than complete breakdown of glucose.
 Lactic Acid fermentation

 The pyruvate molecule from glycolysis is converted to lactic acid. In this process, NADH is oxidize into NAD+ to allow
glycolysis to continue.
 Lactic Acid fermentation happens in most bacteria, especially those used to make commercial food. Your body also carries
out this fermentation when you work muscles hard and fast. Because the capacity of your body to take in oxygen is limited,
your body resorts to lactic acid fermentation to produce more energy. Increased levels of lactic acid production make the
body’s active muscles.
 This effect is also considered a natural defense mechanism for the body to prevent any permanent damage during extreme
activities.
 When the body clears the lactic acid and other metabolites during the recovery period, oxygen becomes available again,
and lactic acid reverts back to pyruvate to resume aerobic metabolism for your body.
 Alcoholic Fermentation
 In this process, pyruvate changes to ethanol and releases carbon dioxide. NAD+ forms from NADH for glycolysis
to continue
 This type of fermentation is present in yeasts and some bacteria, most of which are used to make bread, wine
and biofuels.
 The pyruvate from glycolysis loses one carbon in the form of carbon dioxide to produce acetaldehyde. NADH is
oxidized into NAD+ and reduces the acetaldehyde to ethyl alcohol.
==================================================================================================
FORMATIVE ASSESSMENT 3.2. Answer the following questions:
1. What are the equations that summarize aerobic and anaerobic respiration?
2. What are the applications of aerobic and anaerobic cellular respiration
==================================================================================================
LESSON 4. A simple wine fermentation procedure via yeasts to correctly perform specific protocols demonstrating the
cellular processes that may lead to possible application in the production of commercial products using available local
raw materials.
==================================================================================================
FORMATIVE ASSESSMENT 4
A. Differentiate Lactic Acid Fermentation from Alcoholic Fermentation
B. In Alcoholic Fermentation, what microorganisms are used to promote wine fermentation

==================================================================================================

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CATHOLIC SCHOOLS IN IFUGAO

LESSON 1. STRUCTURES AND FUNCTIONS OF BIOLOGICAL MOLECULES

BIOMOLECULES – organic molecules or macromolecules.

I. CARBOHYDRATES – the most abundant of all organic compounds

Disaccharides Composition Formula Common Name

3. POLYSACCHARIDES- long chains of three or more monosaccharides.

HEALTH BENEFITS OF POLYSACCHARIDES

II. LIPIDS - biomolecules containing chains of hydrocarbons.

3. STEROIDS – composed of four carbon rings

(a.) CHOLESTEROL – a sterol or a steroid alcohol

 Twenty percent of the human body is made up of proteins.

Classification of amino acids

 Plants are capable of making amino acids for themselves.

CLASSIFICATION BASED ON ESSENTIALITY:

1. Primary Structure 2. Secondary Structure

3.Tertiary structure 4. Quaternary Structure

IV. NUCLEIC ACIDS

2 types of nucleic acid

RNA: Ribonucleic acid

Vitamins Function (s)

E (enzyme) + S (substrate) ES (Enzyme-substrate complex)

Factors affecting Enzymatic Speed

1 Ribose sugar molecule

ATP + H2O + ATPase = energy *ATPase- energy user

ADP + energy + ATP synthase = ATP *ATP synthase- energy builder

FA 2.1 Describe how ATP is formed from ADP

WHY IS PHOTOSYNTHESIS SO IMPORTANT?

PHOTOSYNTHESIS is one of the most important biological process on earth!

BALANCED CHEMICAL EQUATION OF PHOTOSYNTHESIS:

Figure 2 STRUCTURE OF CHLOROPLAST

INTERNAL STRUCTURE OF A LEAF

Summary of light dependent reaction:

Light reaction: CYCLIC ELECTRON PATHWAY

B. The Light Independent Reaction or Calvin Cycle)

 CALVIN CYCLE/ LIGHT REACTION/DARK REACTION / C3 PHOTOSYNTHESIS

Here is a general diagram of the cycle:

CHEMICAL EQUATION OF CELLULAR RESPIRATION:

Aerobic Respiration Anaerobic Respiration

Phases of Complete Glucose Breakdown

c. The Krebs cycle:

d. The electron transport system:

Outside the Mitochondria: Glycolysis

B. Energy Investment Steps

C. Energy Harvesting Steps

Inside the Mitochondria

D. The Krebs Cycle

E. The Electron Transport System

G. Energy Yield from Glucose Breakdown

IMPORTANT NOTES ON CELLULAR RESPIRATION

 Cellular Respiration Includes Fermentation

 Advantage and Disadvantage of Fermentation

 Lactic Acid fermentation

B. In Alcoholic Fermentation, what microorganisms are used to promote wine fermentation

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