BSN - 1st Year (2nd Trimester)

Dannah Louise O. Palanca

Dannah
Biochemistry
 Chemica Bond
● Chemical bonds are interactions that hold atoms together to form molecules or compounds.
● These bonds play a crucial role in determining the physical and chemical properties of substances. The strength and type of bond depend on
factors like electronegativity, atomic structure, and the arrangement of atoms in a molecule.
● There are three main types of chemical bonds:
1. Ionic Bonds
2. Covalent Bonds
3. Metallic Bonds

Ionic Bonds

● Formed by the transfer of electrons between a metal and a non-metal. The metal loses electrons (cation), and the non-metal gains them
(anion), resulting in electrostatic attraction between the oppositely charged ions.
● lonic bonds form when electrons are transferred between a metal and a non-metal. Metals, with few electrons in their outer shell, tend to
lose electrons, becoming positively charged ions (cations). Non-metals, with a tendency to gain electrons, become negatively charged ions
(anions). The electrostatic attraction between oppositely charged ions results in the formation of an ionic bond.

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● Characteristics of ionic bonds include:
1. Electron Transfer: The metal donates electrons to the non-metal, achieving a full outer electron shell for both ions.
2. Ionic Compounds: The resulting combination of ions forms an ionic compound, typically having a crystalline structure.
3. High Melting and Boiling Points: lonic compounds often have high melting and boiling points due to the strong electrostatic
forces holding ions together.
4. Solubility in Water: Many ionic compounds dissolve in water because water molecules surround and stabilize individual ions,
allowing them to separate.
5. Conductivity: In the molten or dissolved state, ionic compounds can conduct electricity as ions are free to move.
● Example: Sodium Chloride (NaCI)
● Explanation: Sodium (Na), a metal, transfers an electron to chlorine (Cl), a non-metal. This results in the formation of positively charged
sodium ions (Na+) and negatively charged chloride ions (Cl-), leading to the ionic compound NaCl.

Covalent Bonds

● Involves the sharing of electrons between two non-metal atoms. This sharing allows each atom to achieve a more stable electron
configuration, forming molecules. Covalent bonds can be polar or nonpolar, depending on the electronegativity di erence between the
atoms.
● Covalent bonds form when two non-metal atoms share electrons to achieve a more stable electron configuration. This type of bonding is
common in molecular substances, where atoms are held together by the shared electrons.
● Key features of covalent bonds:
1. Electron Sharing: Non-metal atoms share electrons to achieve a full outer electron shell. Each shared pair of electrons
constitutes a covalent bond.
2. Molecules: Covalent bonds lead to the formation of molecules, discrete units composed of atoms held together by covalent
interactions.

Dannah Louise O. Palanca

 3. Single, Double, and Triple Bonds: Depending on the number of shared electron pairs, covalent bonds can be single (one pair),
double (two pairs), or triple (three pairs).
4. Polarity: Covalent bonds can be polar or nonpolar based on the electronegativity di erence between the atoms. Unequal sharing
results in a polar covalent bond, while equal sharing creates a nonpolar covalent bond.
5. Low Melting and Boiling Points: Generally, covalent compounds have lower melting and boiling points compared to ionic
compounds because the forces holding molecules together are weaker.
● Covalent bonds are primarily classified based on the electronegativity di erence between the atoms involved. The two main types are:
1. Polar Covalent Bond: Occurs when there is an unequal sharing of electrons between atoms due to di erences in
electronegativity. The more electronegative atom attracts the shared electrons more strongly, leading to a partial negative charge
on that atom and a partial positive charge on the other.
2. Nonpolar Covalent Bond: Forms when there is an equal sharing of electrons between atoms, usually involving atoms with
similar electronegativities. In this case, the electrons are shared evenly, and there is no significant charge separation within the
molecule.
● Example: Water (H20)
● Explanation: Oxygen and hydrogen, both non-metals, share electrons to achieve a stable electron configuration. Each hydrogen atom
shares one electron with the oxygen atom, forming a covalent bond. The resulting molecule is water.

Metallic Bonds

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● Common in metals, where electrons are delocalized and move freely between metal ions. This creates a "sea of electrons" that contributes
to the characteristic properties of metals, such as conductivity and malleability.
● Metallic bonds are the type of bonds that occur between metal atoms. Key features of metallic bonds include:
1. Electron Delocalization: In metallic bonds, electrons are not confined to individual atoms but are free to move throughout the
entire metal structure. This creates a "sea of electrons" that holds the metal atoms together.
2. Cation Formation: Metal atoms lose their outer-shell electrons, becoming positively charged cations. These electrons then move
freely, forming a shared electron cloud.
3. Electrical Conductivity: The delocalized electrons allow metals to conduct electricity because they can move in response to an
electric field.
4. Malleability and Ductility: Metals are typically malleable and ductile due to the ability of the metal cations to slide past each
other without the repulsion that would occur with fixed electron positions.
5. Luster: The free movement of electrons also contributes to the characteristic luster or shine of metals by allowing the
absorption and re-emission of light.
● Example: Copper (Cu)
● Explanation: In a copper metal lattice, copper atoms lose their outer-shell electrons, creating a sea of delocalized electrons. The positive
copper ions (Cu+) are held together by the shared electron cloud, forming a metallic bond. This characteristic gives copper its conductivity
and malleability.

Dannah Louise O. Palanca

Intramolecular Forces

Intramolecular forces refer to interactions within a molecule. Intramolecular forces are the forces that hold atoms together within a molecule.
Intermolecular forces are forces that exist between molecules

1. Ion-Dipole Interactions:

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○ Occur between an ion and a polar molecule.
○ The charged ion attracts the partially charged end of the polar molecule.
○ Common in solutions where ionic compounds are dissolved in polar solvents.
2. Hydrogen Bond:
○ A specific type of dipole-dipole interaction.
○ Involves a hydrogen atom bonded to a highly electronegative atom (usually N, 0, or F) and another electronegative atom with lone
pairs.
○ Stronger than typical dipole-dipole interactions and plays a crucial role in the properties of water and biological molecules.
3. Dipole-Dipole Interactions:
○ Occur between polar molecules.
○ Result from the attraction between the positive end of one polar molecule and the negative end of another.
○ Weaker than ion-dipole interactions and hydrogen bonds.
4. Van der Waals Forces:
○ Collective term for weak intermolecular forces, including London dispersion forces and dipole-dipole interactions.
○ London dispersion forces arise from temporary shifts in electron density, creating temporary dipoles.
○ These forces are generally weaker than the other intramolecular forces.

Hydrogen Bonds

● Hydrogen bonds are a type of intermolecular force that occurs when hydrogen is bonded to a highly electronegative atom (typically
nitrogen, oxygen, or fluorine) and is attracted to another electronegative atom nearby. Key points about hydrogen bonds include:
1. Nature of Bonding: Hydrogen bonds are a special type of dipole-dipole interaction. The hydrogen atom involved is
partially positively charged, and the electronegative atom is partially negatively charged.

Dannah Louise O. Palanca

 2. Stronger than Typical Dipole Forces: Hydrogen bonds are stronger than regular dipole-dipole interactions,
contributing to their unique properties.
3. Common Examples: Common examples of hydrogen bonding occur in water molecules (H20), where the hydrogen
atoms are attracted to the oxygen atoms of neighboring water molecules.
This contributes to water's high boiling point, surface tension, and other unique properties.
4. Biological Significance: Hydrogen bonds play a crucial role in biological systems. They are involved in the structure
of proteins and DNA, influencing the three-dimensional shapes and functions of these biomolecules.
5. Directionality: Hydrogen bonds exhibit directionality, meaning they have a specific orientation.
This directional nature contributes to the stability of certain molecular structures.
● Understanding hydrogen bonds is essential for explaining the behavior of molecules in various contexts, from the physical properties of
substances to the intricacies of biological macromolecules.
● Example:
○ A classic example of hydrogen bonding is found in water molecules (H₂O). In a water molecule, the oxygen atom is more
electronegative than the hydrogen atoms, creating a partial negative charge (δ-) on the oxygen and partial positive charges (δ+)
on the hydrogens.
○ Adjacent water molecules then form hydrogen bonds due to the attraction between the δ- oxygen of one water molecule and the
δ+ hydrogen of another. This interaction results in a network of hydrogen bonds between water molecules.
○ The hydrogen bonds in water contribute to its unique properties, such as high boiling and melting points, surface tension, and the

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ability to dissolve a wide range of substances. This example illustrates how hydrogen bonding influences the behavior and
characteristics of a substance at the molecular level.

Vander Waals Forces

● Van der Waals forces refer to the weak attractive forces that exist between molecules. These forces play a significant role in determining
the physical properties of substances. There are three main types of van der Waals forces:
1. London Dispersion Forces (Dispersion Forces or Induced Dipole Forces):
■ Nature: Temporary fluctuations in electron distribution can create temporary dipoles in molecules.
■ E ect: These temporary dipoles induce dipoles in nearby molecules, leading to weak attractive forces.
■ Strength: Weakest of the van der Waals forces.
2. Dipole-Dipole Interactions:
■ Nature: Occur between polar molecules where there is a permanent dipole moment.
■ E ect: The positive end of one molecule is attracted to the negative end of another.
■ Strength: Stronger than London dispersion forces.
3. Hydrogen Bonding:
■ Nature: A specific type of dipole-dipole interaction.
■ Requirement: Hydrogen must be bonded to a highly electronegative atom (0, N, or F).
■ E ect: Results in a particularly strong dipole-dipole interaction.
■ Strength: Stronger than regular dipole-dipole interactions.
● Van der Waals forces are crucial in explaining various properties of gases, liquids, and solids.
● They influence boiling points, melting points, and solubility, among other characteristics, contributing to the behavior of molecules in
di erent states of matter.

Dannah Louise O. Palanca

Intramolecular Forces:

● Involve interactions within a molecule.

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● Include forces like ion-dipole interactions, hydrogen bonds, dipole-dipole interactions, and van der Waals forces.
● These forces influence the physical properties of substances, such as boiling points, melting points, and solubility.
● They are weaker than chemical bonds and do not involve the formation or breaking of actual chemical bonds.

Chemical Bonds:

● Involve the sharing, transfer, or overlap of electrons between atoms to achieve a stable electronic configuration.
● Types of chemical bonds include covalent bonds (sharing electrons), ionic bonds (transfer of electrons), and metallic bonds (delocalized
electrons in metals).
● Chemical bonds are much stronger than intramolecular forces.
● They are responsible for holding atoms together to form molecules or compounds.

Dannah Louise O. Palanca

 Introductio t Biomolecule
Biochemistry Levels of Structural Organization
● See all the living or once living things around you? The
processes that allow them to grow, multiply, age, and die are
all biochemical in nature.

What is Biochemistry and Where does it take place?

● Biochemistry is the chemistry of living organisms.

● Biochemists - study the chemical reactions that occur at the
molecular level of organisms.
● Biochemistry really combines aspects of all the fields of
chemistry.
● And biochemistry is also similar to molecular biology: both
fields study living systems at the molecular level, but
biochemists concentrate on the chemical reactions that
occur.
Types of Living Cells

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Biochemical Substances
● Is a chemical substance found within a living organism
● Biochemical substance are divided into two groups:
1. Bioinorganic substances - includes water and
inorganic salts. (with carbon)
2. Bioorganic substances - include carbohydrates,
lipids, proteins, and nucleic acid.
The Beginnings of Biology: Origins of Life
● Cells come in two types: prokaryotes and eukaryotes.
(Viruses also bear some similarities to cells, but these are
limited. In fact, many scientists don't consider viruses
"living.")
● Prokaryotic cells are the simplest type of cells. Many
one-celled organisms are prokaryotes.
● “The simplest way to distinguish between these two types of
cells is that a prokaryotic celll contains no well-defines
nucleus, whereas the opposite is true for a eukaryotic cell.

● The most widely accepted cosmological theory for the origin
of the universe is the BIG BANG, a cataclysmic explosion.
● According to big-bang cosmology, all the matter in the
universe was originally contained to a comparatively small
amount of space.
The Rest of the Chemical Elements are thought to have been
formed in three ways:
Prokaryotes
● Prokaryotes are mostly bacteria. Besides the Lack of a
nucleus, a prokaryotic cell has few well-defined structures.
● The PROKARYOTIC CELL has three components: a cell wall,
an outer membrane, and a plasma membrane.
● This wall allows a controlled passage of material into and out
of the cell.

1. by thermonuclear reactions that normally take place in stars, Eukaryotes

2. In explosion of stars,
3. By the action of the cosmic rays outside the stars since the ● Eukaryotes are animals, plants, fungi and;
formation of the galaxy. ● In addition to having a nucleus, eukaryotic cells have a
number of membrane-enclosed components known as
organelles.

Dannah Louise O. Palanca

 Anima Cell Mitochondria

● All animal cells (which, as you now know, are eukaryotic
cells) have a number of components, most of which are
considered to be organelles.
Primary components of Animal Cells
Plasma membrane
● This separates the material inade the cell from everything
outside the cell. The plasma or cytoplasm is the fluid inside
the cell, For the sake of the cell's health, this fluid shouldn't
leak out.
● Transport through the membrane may be active or passive,
Active transport requires that a price be paid for a ticket to
enter (or leave) the cell.
● The cost of the ticket is energy. Passive transport doesn't
require a ticket. Passive transport methods include di usion,
osmosis, and filtration.
● These structures are the cell's power plants, where the cell
produces energy, Mitochondria (ringular mitochondrion) use
food, primarily the carbohydrate glucose, to produce energy,
which comes mainly from breaking down adenosine
triphosphate (or ATP).
Nucleus/nucleolus
● Each cell has a nucleus and, inside it, a nucleolus. These
serve as the cell's control center and are the root from which
all future generations originate. A double layer known as the
nuclear membrane surrounds the nucleus Usually the
nucleus contains a mass of material called chromatin. If the
cell is entering a stage leading to reproducing itself through
cell division, the chromatin separates into chromosomes.
Ribosomes
● These contain protein and ribonucleic acid subunits, In the

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ribosomes, the amino acids are assembled into proteins.
Centrioles Many of these proteins are enzymes, which are part of nearly
every process that occurs in the organism.
● These behave as the cell's "train conductors." They organize
structural components of the cell like microtubules, which Small vacuoles
help move the cell's parts during cell division.
● Also known as simply vacuoles, these serve a variety of
Endoplasmic reticulum functions, including storage and transport of materials. The
stored materials may be for later use or may be waste
● The coll can be thought of as a smoothly running factory. The
material that the cell no longer needs.
endoplasmic reticulum is the main part of the cell factory.
This structure has two basic region, known as the rough
endoplasmic reticulum, Which contains ribosomes, and the
smooth endoplasmic reticulum, which does not.

Golgi apparatus

● This structure serves as the cells postal system. It looks a

bit like a mane. and within it, materials produced by the coll
are packaged in vesicles small, membrane-enclosed sacs.

Lysosomes

● These are the cells landfills. They contain digestive enzymes

that break down substances that may harm the cell.

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 Plan Cell
● Plant cells contain the same components as animal cells,
plus a cell wall, a large vacuole, and, in the case of green
plants, chloroplasts.
Parts of a Plant Cell
● The cell wall is composed of cellulose. Cellulose, like starch,
is a polymer of glucose. The cell wall provides structure and
rigidity.
● The large vacuole serves as a warehouse for large starch
molecules. Glucose, which is produced by photosynthesis, is
converted to starch, a polymer of glucose. At some later
time, this starch is available as an energy source.
● Chloroplasts, present in green plants, are specialized
chemical factories.
● Ribosomes - particle that is present in large numbers in all
living cells and serves as the site of protein synthesis.
● Endoplasmic reticulum - important particularly in the
● Vacuoles - are essential cytoplasmic organs (organelles),
performing functions such as storage, ingestion, digestion,
excretion, and expulsion of excess water.
● Nuclear pore - is a protein-lined channel in the nuclear
envelope that regulates the transportation of molecules
between the nucleus and the cytoplasm.
● Chloroplast - structure within the cells of plants and green
algae that is the site of photosynthesis, the process by which
light energy is converted to chemical energy, resulting in the
production of oxygen and energy-rich organic compounds.
● Mitochondrion, membrane-bound organelle found in the
cytoplasm of almost all eukaryotic cells (cells with clearly
defined nuclei), the primary function of which is to generate
large quantities of energy in the form of adenosine
triphosphate (ATP).
Chemical Composition of Living Matter
● Every living cell contains, in addition to water and salts or
minerals, a large number of organic compounds, substances
composed of carbon combined with varying amounts of

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synthesis, folding, modification, and transport of proteins.
hydrogen and usually also of oxygen.
● Chromosomes - is a long DNA molecule with part or all of
● Nitrogen, phosphorus, and sulfur are likewise common
the genetic material of an organism.
constituents.
● Nucleolus - known as the site of ribosome biogenesis,
which is the synthesis of ribosomes. The nucleolus also
Significance of Biomolecules in Nature and
participates in the formation of signal recognition particles
and plays a role in the cell's response to stress. Nucleoli are
Science
made of proteins, DNA and RNA.
● Biomolecules are the essence and currency of life and health
● Nucleus - controls and regulates the activities of the cell
processes lying at the heart of the simplest to the most
(e.g., growth and metabolism) and carries the genes,
complex system.
structures that contain the hereditary information. Nucieoli
● Understanding the fundamental nature of biomolecules, their
are small bodies often seen within the nucleus. The gel-like
structure, location, behavior and function, is critical to
matrix in which the nuclear components are suspended is
knowledge and understanding of health, the development of
the nucleoplasm.
disease and appropriate therapeutic intervention.
● Nuclear membrane - also called the nuclear envelope, is a
● When considering biomolecules it is thus important to
double membrane laver that separates the contents of the
include structural variants or anomalies that may arise
nucleus from the rest of the cell.
either spontaneously or as a result of some interaction that
● Leucoplast - only found in plant cells. As such, they can be
can alter functionality.
used to distinguish between a plant and animal cell.
● Cell membrane - (also known as the plasma membrane or
cytoplasmic membrane, and historically referred to as the
plasmalemma) is a biological membrane that separates and
protects the interior of a cell from the outside environment
(the extracellular space):
● Golgi complex - The Golgi apparatus is responsible for
transporting, modifying, and packaging proteins and lipids
into vesicles for delivery to targeted destinations.

Dannah Louise O. Palanca

 Chemica Bondin ● Electronegativity - The measure of the attraction an atom
has for electrons, which can determine the polarity of bonds
formed with that atom.
● Chemical bonding provides the energy necessary to hold two
di erent atoms together as part of a chemical compound.
A Comparison in the Properties of Organic
● Strength of the bond depends on the molecules or atoms
involved in the process of bond formation.
and Inorganic Compounds
ORGANIC COMPOUNDS

● Bonding is almost entirely covalent

● Compounds may be gases, liquids, or solids with low melting
points (< 360 degree Celsius)
● Mostly insoluble in water
● Mostly soluble in organic solvents such as gasoline, benzene,
carbon tetrachloride.
● Solutions in water or any other solvent do not conduct
electricity.
● Almost all burn.
● Reactions are usually slow

INORGANIC COMPOUNDS

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Atomic Structure ● Many compounds have ionic bonds
● Mostly high melting solids (>360)
● Many soluble in water
● Almost entirely insoluble in organic solvents.
● Water solutions conduct electricity.
● Very few bum.
● Reactions are often very fast.

MOLECULES - are tightly bound clusters of atom. What holds atoms

together are powerful attractions called CHEMICAL BONDS.

Two Types of Chemical Bond

1. ionic bond
2. covalent bond

IONIC BONDS

Definition of Terms
● Polarity - The measure of electrical di erence within a
molecule, bond, or structure.
● Non-polar Molecule - A molecules make of
electronegativity similar atoms, which distributes electrons
equally.
● Amphiphilic Molecule - Some large molecules which have
both polar and nonpolar regions, such as the phospholipids
used to create cell membranes.
● An atom that loses one or more electrons becomes an ION. It
now has a positive charge. Positive ion are called CATIONS.
● An IONIC BOND is the attraction between positive and
negative ions.
● Positive ions are called cations.
● If an atom gains one or more electrons, it becomes an ion
that contains more electrons than protons.
● It now has a negative charge because it has extra electrons.
NEGATIVE IONS are called ANIONS.

Dannah Louise O. Palanca

Di erence Between Cation and Anion

Covalent Bonds
● lonic Bonds - An lonic bond is when an electron leaves one
● A covalent bond is one in which two atoms share a pair of
atom and exothermically enters into orbit around another.
electrons.
These two oppositely charged ions now attract each other.
● Would a fluorine atom take an electron from another fluorine
● IONIC BOND is the attraction between positive and negative
atom?
ions.
● NO: FLOURINE atom do not have to take electrons from each
● lonic bonds are generally formed between metals and

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other. They can and do share electrons to form a covalent
nonmetals
bond. When they do this, both atoms have a complete octet.
● A classic example of ionic bonding is between Na and Cl. Na
is a silvery metal. It has 1 valence electron. Cl is a Single, Double, and Triple Covalent Bond
yellow-green gas, and it needs 1 electron to fill its valence
shell. If you put the gas and the metal together, then they
will burn as electrons are exchanged.
● The metal dissolves and the gas disappears. The ions now
have opposite charges and are attracted to each other by
electrostatic forces. They form a crystal with the rock salt
structure.

Ionic Bond Examples

The Octet Rule

● Is there any way to predict which ions are stable?

● We use the principle that ATOMS AND IONS are MOST
STABLE when they have a COMPLETE OUTER SHELL
of ELECTRONS.

Dannah Louise O. Palanca

Electron Clouds
● Another way to look at it is to remember that the electrons
of Fluorine (and all other) atoms are in orbitals, which are
clouds of electrons.
● The orbital with the lowest energy is called the 1s orbital.
● The next orbitals, with higher energy, are the 2s and 2p
orbitals, respectively.
● The s orbitals are spherical; all p orbitals look like dumbbells
and come in sets of three.
1S, 2S, and 2P Orbitals
Polarity
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● Polar Molecule - A polar molecule is a chemical species in
which the distribution of electrons between the covalently
bonded atoms is not even.
● Polarity, in chemical bonding, the distribution of electrical
charge over the atoms joined by the bond.
EXAMPLES OF POLAR MOLECULE
● Water: The most important polar molecule on Earth is water.
● Ammonia: The chemical formula of ammonia is NH3
The existence of equal but opposite partial charges on the atoms at
each end of a heteronuclear bond (i.e., a bond between atoms of
di erent elements) gives rise to an electric dipole.
Hydrogen Bonding
● A hydrogen bond is an intermolecular force (IMF) that forms
a special type of dipole-dipole attraction when a hydrogen
atom bonded to a strongly electronegative atom exists in the
vicinity of another electronegative atom with a lone pair of
electrons.
● Dipole Moment
● When two electrical charges, of opposite sign and equal
magnitude, are separated by a distance, an electric dipole is
established. The size of a dipole is measured by its dipole
moment.
● A hydrogen bond is the attractive force between the
hydrogen attached to an electronegative atom of one
molecule and an electronegative atom of a di erent
molecule.
● Usually the electronegative atom is oxygen, nitrogen, or
fluorine, which has a partial negative charge.
● Water is an ideal example of hydrogen bonding. Notice that
each water molecule can potentially form four hydrogen
bonds with surrounding water molecules: two with the
hydrogen atoms and two with the with the oxygen atoms.
There are exactly the right numbers of + hydrogens and lone
pairs for every one of them to be involved in hydrogen
bonding.
Non-Covalent Interactions
non-covalent interaction di ers from a covalent bond in that
●
it does not involve the sharing of electrons, [1] but rather
involves more dispersed variations of electromagnetic
interactions between molecules or within a molecule.
Electrostatic Interactions
● lonic interactions involve the attraction of ions or molecules
with full permanent charges of opposite signs.
● A hydrogen bond (H-bond), is a specific type of interaction
that involves dipole dipole attraction between a partially
positive hydrogen atom and a highly electronegative,
partially negative oxygen, nitrogen, sulfur, or fluorine atom
not covalently bound to said hydrogen atom). It is not a
covalent bond, but instead is classified as a strong
non-covalent interaction.
● Halogen bonding is a type of non-covalent interaction which
does not involve the formation nor breaking of actual bonds,
but rather is similar to the dipole dipole interaction known
as hydrogen bonding.
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 Aci , Base an Buffer
Acids and Bases
● The terms acid and base have been defined in di erent ways,
depending on the particular way of looking at the properties
of acidity and basicity.
● Arrhenius first defined acids as compounds which ionize to
produce hydrogen ions, and bases as compounds which
ionize to produce hydroxide ions.
● According to the Lowry-Bronsted definition, an acid is a
proton donor and a base is a proton acceptor.
● According to the Lewis definition, acids are molecules or
ions capable of coordinating with unshared electron pairs,
and bases are molecules or ions having unshared electron
pairs available for sharing with acids. To be acidic in the
Lewis sense, a molecule must be electron deficient. This is
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the most general acid base concept.
● All Lowery Bronstead acids are Lewis acids but, in addition,
the Lewis definition includes many other reagents such as
boron trifluoride, aluminum chloride, etc.
Theories of Acids and Bases
● Three di erent theories have been put forth in order to
define acids and bases. These theories include the Arrhenius
theory, the Bronsted-Lowry theory, and the Lewis theory of
acids and bases. A brief description of each of these theories
is provided in this subsection. Acids and bases can be
defined via three di erent theories.
1. The Arrhenius theory of acids and bases states
that "an acid generates H+ ions in a solution
whereas a base produces an OH- ion in its
solution".
2. The Bronsted-Lowry theory defines "an acid as a
proton donor and a base as a proton acceptor"
3. Finally, the Lewis definition of acids and bases
describes "acids as electron-pair acceptors and
bases as electron-pair donors".
Properties of Acids and Bases
1. Properties of Acids
● Acids are corrosive in nature. They are good conductors of
electricity.
● Their pH values are always less than 7. When reacted with
metals, these substances produce hydrogen gas. Acids are
sour in taste.
● Examples: Sulfuric acid [H204], Hydrochloric acid [HC],
Acetic acid [СНЗСООН].
● Physical Properties of Acids
○ Sour in taste in aqueous solution
○ Mineral acid (HCI,HNO3,H2S04) Are highly
corrosive
○ Turns blue litmus red.
● Chemical Properties of Acids
○ Acid neutralize bases to give salt and water only
○ Acid react with active metals to liberate hydrogen.
2. Properties of Bases
● Some properties, like a bitter taste, are owned by all bases.
The bases feel slippery, too. Dream on what slippery soap
looks like. And this is a foundation. Furthermore, when
immersed in water, bases conduct electricity because they
consist of charged particles in the solution.
● They are found to have a soapy texture when touched. These
substances release hydroxide ions (OH- ions) when dissolved
in water. In their aqueous solutions, bases act as good
conductors of ectricity. The pH values corresponding to
bases are always greater than 7. Bases are bitter-tasting
substances which have the ability to turn red litmus paper
blue.
● Examples: Sodium hydroxide [NaOH], milk of magnesia
[Mg(OH)2], calcium hydroxide [Са (ОН)2].
● Physical Properties of Bases
○ Bitter in taste in Aqueous solution.
○ Caustic alkalis (KOH, NaOH) are highly corrosive.
○ Turns red litmus blue.
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 ● Chemical Properties of Bases
○ Alkalis react with ammonium salts on heating to
liberate ammonia.
○ Alkalis react with certain metallic salt solutions to
precipitate insoluble hydroxides.
3. Neutral Substances
● The neutral substance is a substance which is not acidic or
basic, has the same amount of hydrogen and hydroxyl ions,
and does not alter the colour of the litmus surface. These
substances do not display any acidic or basic characteristics.
Their pH values approximate to 7. Neutral substances have
no e ect on red or blue litmus paper. 1 ne pH of pure water
is exactly 7.
● Examples: Water, Common salt (NaCI)
pH of Acids and Bases
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● In order to find the numeric value of the level of acidity or
basicity of a substance, the pH scale (wherein pH stands for
'potential of hydrogen') can be used. The pH scale is the most
common and trusted way to measure how acidic or basic a
substance is. A pH scale measure can vary from 0 to 14,
where 0 is the most acidic and 14 is the most basic a
substance can be.
● Another way to check if a substance is acidic or basic is to
use litmus paper.
● There are two types of litmus paper available that can be
used to identify acids and bases - red litmus paper and blue
litmus paper. Blue litmus paper turns red under acidic
conditions and red litmus paper turns blue under basic or
alkaline conditions.
Buffers
● A bu er is a solution that can resist pH change upon the
addition of an acidic or basic components. It is able to
neutralize small amounts of added acid or base, thus
maintaining the pH of the solution relatively stable. This is
important for processes and/or reactions which require
specific and stable pH ranges.
● Bu er solutions have a working pH range and capacity which
dictate how much acid/base can be neutralized before pH
changes, and the amount by which it will change.
What is a Bu er composed of?
● To e ectively maintain a pH range, a bu er must consist of a
weak conjugate acid-base pair, meaning either a. a weak acid
and its conjugate base, or b. a weak base and its conjugate
acid. The use of one or the other will simply depend upon the
desired pH when preparing the bu er.
● For example, the following could function as bu ers when
together in solution: Acetic acid (weak organic acid w/
formula CH3C00H) and a salt containing its conjugate base,
the acetate anion (CH3C00-), such as sodium acetate
(CH3COONa) Pyridine (weak base w/ formula C5H5N) and a
salt containing its conjugate acid, the pyridinium cation
(C5H5NH+), such as Pyridinius Chloride. Ammonia (weak
base w/ formula NH3) and a salt containing its conjugate
acid, the ammonium cation, such as Ammonium Hydroxide
(NH40H
What Is a Bu er Solution?
● The bu er solution is a solution able to maintain its
hydrogen ion concentration (pH) with only minor changes in
the dilution or addition of a small amount of either acid or
base.
● Bu er solutions are used in fermentation, food preservatives,
drug delivery, electroplating, printing and the activity of
enzymes, and the blood oxygen-carrying capacity needs
specific hydrogen ion concentration (pH).
● Solutions of a weak acid and its conjugate base or weak base
and its conjugate acid are able to maintain pH and are bu er
solutions.
Dannah Louise O. Palanca
Types of Buffer Solutions ● To understand the mechanism of bu er action, we can take
the example of an acidic bu er that is made up of a weak
The two primary types into which bu er solutions are broadly acid like acetic acid and its sodium salt, sodium acetate. In
classified are acidic and alkaline bu ers. this acidic bu er, the solution contains equimolar amounts
of acetic acid and sodium acetate. Usually, a large number of
● Acidic Bu ers - As the name suggests, these solutions are
sodium ions (Na+), acetate ions (CH3C0O-) and
used to maintain acidic environments. Acid bu er has acidic
undissociated acetic acid molecules are present. The salt
pH and is prepared by mixing a weak acid and its salt with a
exists completely as ions
strong base. An aqueous solution of an equal concentration
of acetic acid and sodium acetate has a pH of 4.74. The pH of
these solutions is below seven. These solutions consist of a
weak acid and a salt of a weak acid. An example of an acidic
bu er solution is a mixture of sodium acetate and acetic
acid (pH = 4.75).
● Alkaline Bu ers - These bu er solutions are used to
maintain basic conditions. A basic bu er has a basic pH and
is prepared by mixing a weak base and its salt with strong
acid. The aqueous solution of an equal concentration of

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ammonium hydroxide and ammonium chloride has a pH of
9.25. The pH of these solutions is above seven. They contain
a weak base and a salt of the weak base. An example of an
alkaline bu er solution is a mixture of ammonium hydroxide
and ammonium chloride (pH = 9.25).

Buffer Composition and its Mechanism

● Bu er Solution A bu er solution is a water solvent-based

solution which consists of a mixture containing a weak acid
and the conjugate base of the weak acid or a weak base and
the conjugate acid of the weak base. They resist a change in
pH upon dilution, or upon the addition of small amounts of
acid/alkali to them. The pH of bu er solutions shows
minimal change upon the addition of a very small quantity of
strong acid or strong base. They are therefore used to keep
the pH at a constant value.

Mechanism of Buffering Action

● When generating a bu er solution, its pH is adjusted to

bring it within the proper operating range. A strong acid, like
hydrochloric acid (HCI), is frequently added to lower the ph
of acidic bu ers. A strong base like NaOH solution will be
added to raise the pH of the alkaline bu ers.

Dannah Louise O. Palanca

Finals
Dannah

Dannah Louise O. Palanca

 Organi Chemistr
What is Organic Chemistry?
● Organic chemistry is the branch of chemistry that focuses
on the study of carbon-containing compounds, playing a vital
role in understanding the structures, properties, reactions,
and synthesis of these compounds.
● Within organic chemistry, various classes of hydrocarbons
serve as foundational components.

Definition of Terms:
● Alkanes: Alkanes are saturated hydrocarbons consisting of
single bonds between carbon atoms.
● Alkenes: Alkenes are unsaturated hydrocarbons containing
at least one carbon-carbon double bond.
Three Types of Alkanes:
● Alkynes: Alkynes are unsaturated hydrocarbons
characterized by at least one carbon-carbon triple bond. ● Linear or normal alkanes:

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● Aromatic: Aromatic compounds contain a unique ring these have all the carbon
structure with alternating single and double bonds. atoms arranged in a straight
● Hydrocarbons: They are the simplest organic molecules chain. Examples include
and can be classified as aliphatic (alkanes, alkenes, alkynes) methane (CH4), ethane
or aromatic based on their structure. (C2H6), and propane (с3н8).

ALKANES
● Alkanes are the simplest and most fundamental category of ● Branched alkanes: these
organic molecules. They are acyclic (non-cyclic) saturated have one or more carbon
hydrocarbons, meaning they contain only single bonds atoms branching o the
between carbon atoms and are solely composed of hydrogen main chain. Examples
and carbon atoms. include 2-methylbutane.
● General Formula: Alkanes follow the general formula
CnH2n+2, where: C represents the number of carbon atoms
in the molecule. H represents the number of hydrogen atoms ● Cyclic alkanes: these have the carbon atoms arranged in a
in the molecule. n is the number of carbon atoms. This ring. Although not
formula allows you to quickly determine the number of technically alkanes
hydrogen atoms in any alkane. according to IUPAC
● Example: definition, they share similar
○ Ethane (C2H6): n=2, so there are 2*2+2=6 properties and are often
hydrogen atoms. studied alongside them.
○ Propane (C3H8): n=3, so there are 3*2+2=8 Examples include
hydrogen atoms. cyclopropane.

Dannah Louise O. Palanca

ALKENES ALKYNES
● Alkenes is any of the series of unsaturated hydrocarbons ● Alkynes are hydrocarbons which contain carbon-carbon
containing a double bond, including ethylene and triple bonds.
propylene.Alkenes are more reactive than alkanes due to the ● Their general formula is CnH2n-2 for molecules with one
presence of the double bond. Nomenclature of Alkenes. The triple bond (and no rings). Alkynes undergo many of the
characteristic name ending is -ene. same reactions as alkenes, but can react twice because of
● Alkenes, a type of hydrocarbon with carbon-carbon double the presence of the two p-bonds in the triple bond.
bonds, don't have a direct purpose in the human body.
However, some compounds derived from alkenes, like fatty
acids, play crucial roles. For instance, omega-3 and omega-6
fatty acids, which contain double bonds, are essential
components of cell membranes and are involved in various
physiological processes.
● Alkenes also called an olefin.
● Formula of Alkenes: their general formula is CnH2n for
molecules with one double bond (and no rings).

AROMATIC

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● The term aromatics is derived from the Greek word
aromatikos meaning pleasant smell Aromatics is the study of
the chemistry of compounds containing aromatic rings.
Benzene is the most important member with a molecular
formula C6H6.
● Aromatic compounds contain a special stability associated
with a cyclic arrangement of electrons.
● Aromaticity is not just about pleasant odors; it's a key
concept in organic chemistry.

Properties of Alkenes

● Physical Properties: Alkenes are typically colorless gases

● Benzene Ring: Central to aromatic chemistry, benzene has
or liquids with varying degrees of odor. Their physical
a hexagonal structure.
properties depend on factors such as molecular size and
● Resonance structures show delocalized n-electrons,
branching.
contributing to stability.
● Chemical Properties: Alkenes undergo addition reactions
● Benzene is a versatile building block in organic synthesis.
due to the presence of the double bond. This reactivity
makes them valuable in organic synthesis for the production
of diverse compounds.

Dannah Louise O. Palanca

 ● Most of the benzene used commercially comes from
petroleum. It is employed as a starting material for the
production of detergents, drugs, dyes, insecticides, and
plastics. once widely used as an organic solvent, benzene is
now known to have both short- and long-term toxic e ects.
HYDROCARBONS
Applications
● Widely present in nature: DNA bases (adenine, guanine) and
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amino acids (tyrosine, phenylalanine).
● Essential in pharmaceuticals: Many drugs, such as aspirin
and antibiotics, contain aromatic rings.
● Aromatic compounds play crucial roles in various biological
processes, such as in the structure of amino acids, nucleic
acids (Like DNA and RNA), and many other biomolecules.
● Aromaticity in Biochemistry
○ Aromatic compounds are prevalent in
biomolecules.
○ DNA bases (adenine, guanine), amino acids
(tyrosine, phenylalanine).
● Aromatic Compounds in Medicine
○ Pharmaceuticals of ten contain aromatic rings.
○ Aspirin, paracetamol, and many antibiotics.
Aromatic rings are a common feature in drugs
● Hydrocarbon, any of a class of organic chemical compounds
composed only of the elements carbon (c) and hydrogen (H).
the carbon atoms join together to form the framework of the
compound, and the hydrogen atoms attach to them in many
di erent configurations.
● Hydrocarbons are the principal constituents of petroleum
and natural gas. They serve as fuels and lubricants as well as
raw materials for the production of plastics, fibers, rubbers,
solvents, explosives, and industrial chemicals.
● Hydrocarbons, particularly in the form of organic
compounds, play a significant role in medicine. Many
pharmaceuticals and therapeutic agents are derived from
hydrocarbons. For example, aspirin is synthesized from
salicylic acid, which itself is derived from benzene, a
hydrocarbon. Additionally, hydrocarbons are crucial in the
development of various medical devices and imaging
technologies used in diagnostics and treatment.
● Medical applications of hydrocarbons:
○ Halogenated hydrocarbons are used in medicine to
make anesthetics like halothane, propellants for
inhalers, and sedatives like chloral hydrate. Freon
and other halogenated hydrocarbons are used as
refrigerants.
Dannah Louise O. Palanca
 Hydrocarbo Derivative Wit
Phenol
an Withou Carbony Carbo
● Phenol is a specific type of hydrocarbon derivative that
Hydrocarbon Derivatives contains a hydroxyl (-OH) group attached to a benzene ring.
It is aromatic and is distinct from other hydrocarbons.
● Compounds that are made primarily of carbon and hydrogen ● Phenols are more acidic than alcohols due to resonance
atoms with specific groups of atoms attached. delocalization of the negative charge in the phenoxide
● Hydrocarbon Derivatives are formed from hydrocarbons, but conjugate base.
at least one of the hydrogen atoms in a hydrocarbon ● Phenols are widely used as antiseptic and as disinfectants.
derivative is substituted with a di erent atom. The first widely used antiseptic was phenol.
● used to produce several di erent products such as fuel,
Alkanes
perfumes, and flavor extracts.

● These are saturated hydrocarbons

Hydrocarbon WITHOUT Carbonyl containing only single bonds between
carbon atoms. An example is methane
Alcohol (CH4).

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● Derived by replacing a hydrogen atom in a hydrocarbon with Alkenes
a hydroxyl (-OH) group.
● Alcohols have the general formula R-OH, where R represents ● These are unsaturated hydrocarbons
an alky group containing at least one carbon-carbon
● Alcohols are more general and can be classified as primary, double bond. An example is ethene
secondary, or tertiary based on the number of carbon atoms (C2H4).
directly bonded to the carbon bearing the hydroxyl group.
Alkynes
● Base chain name + change ending to -ol

Classification of Alcohols: ● These are unsaturated hydrocarbons

containing at least one carbon-carbon
● Primary Alcohol (-OH triple bond. An example is ethyne
group attached to carbon (C2H2).
with single carbon.
Ether

● Ethers are organic compounds characterized by an oxygen

● Secondary Alcohol (the atom bonded to two alkyl or aryl groups.
hydroxyl group is ● The general formula for ethers is R-O-R', where R and R'
attached to carbon with represent alkyl or aryl groups.
two more carbon) ● Contain a lone oxygen atom with hydrocarbons bonded to
each side.
● Ether is an extremely flammable chemical and was one of
the first anesthetics.
● Tertiary Alcohol (the
hydroxyl group is attached
to carbon with three more
carbon)

Dannah Louise O. Palanca

 Hydrocarbon WITH Carbonyl
● A hydrocarbon with a carbonyl group refers to an organic
compound that combines the basic structure of a
hydrocarbon (composed of hydrogen and carbon atoms) with
the presence of a carbonyl functional group (C=0).

Aldehydes and Ketones

● Both organic compounds that contain a carbonyl group,

which is a carbon atom double-bonded to an oxygen atom.
● Aldehydes
○ Always located at the end of carbon chain
○ Ends with -al
○ Ex: Propanal
● Ketones
Amines ○ Positioned within the carbon chain
○ Ends with -one
● Amines are organic compounds that contain a nitrogen atom ○ Ex: Propanone
bonded to hydrogen atoms and/or alkyl or aryl groups.

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● They are classified based on the number of alkyl or aryl
groups attached to the nitrogen atom.
● Primary amines have one alkyl or aryl group attached to
nitrogen, secondary amines have two, and tertiary amines
have three.

Carboxylic Acids

● A Carboxylic Acid is an organic compound containing a

carboxyl functional group.
● They occur widely in nature and are also synthetically
manufactured by humans. Upon deprotonation, carboxylic
acids yield a carboxylate anion with the general formula
R-COO-, which can form a variety of useful salts such as
soaps.

Physical Properties of Carboxylic Acids

● Carboxylic acid molecules are polar due to the presence of

two electronegative oxygen atoms.
● They also participate in hydrogen bonding due to the
presence of the carbony! group (C=0) and the hydroxyl
group.
● When placed in nonpolar solvents, these compounds form
dimers via hydrogen bonding between the hydroxyl group of
one carboxylic acid and the carbonyl group of the other.

Dannah Louise O. Palanca

Chemical Properties of Carboxylic Acids

● The a-carbon belonging to a carboxylic acid can easily be

halogenated via the Hell-Volhard-Zelinsky reaction.
● These compounds can be converted into amines using the
Schmidt reaction. " A carboxylic acid can be reduced to an
alcohol by treating it with hydrogen to cause a
hydrogenation reaction.
● Upon reaction with alcohols, these compounds yield esters.

Esters

● An ester is a chemical compound derived from an acid

(organic or inorganic) in which at least one -OH hydroxyl
group is replaced by an -O- alkyl (alkoxy) group. To put it in
simple terms, esters are a
group of chemical
compounds which are
formed by bonding of an
alcohol group with a group

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of organic acids, by losing
water molecules.

Amides

● Amides are compounds that have a carbonyl group (C=O)

bonded to a nitrogen atom (N), which is also bonded to a
hydrogen atom.

Dannah Louise O. Palanca

 ● Characteristics: Multiple sugar units linked together. Serve

Carbohydrate functions like energy storage (starch, glycogen) and

structural support (cellulose).

Functions and Classifications of

Key functions of carbohydrates:
Carbohydrates
● Energy Source
Carbohydrates ○ The body uses carbs primarily as an energy source.
After being ingested, carbohydrates are converted
● are sugar molecules along with proteins and fats
by the body into glucose and other simple sugars,
● You can found carbohydrates in foods and drinks
which are then utilized by cells for cellular
● Your body breaks carbohydrates into glucose or blood sugar
respiration, a process that produces energy.
is the main source of energy that your body cells, tissues
● Energy Storage
and organs need
○ Glucose surplus is frequently stored as starch in
● They are composed of carbon, hydrogen, and oxygen atoms
plants and as glycogen in the muscles and liver of
● Three Main Types of Carbohydrates
mammals. When the body needs more energy, it
1. Monosaccharides
can convert these forms that have been stored into
2. Disaccharides
glucose.
3. Polysaccharides

Sugars or Monosaccharides Chirality Enantiomers

Dannah
● These are also called simple carbohydrates because they are Isomers
the most basic form. They can added to foods such as the
sugar in candy, desserts, processed foods, and regular soda. ● Molecules or ions that has identical molecular formula
They also include the kinds of sugar that are found naturally di erent chemical structures
in fruits, vegetables, and milk
● Examples: Glucose, fructose, and galactose. Types of Isomers:
● Characteristics: unable to be divided into simpler sugars.
● Structural Isomers - molecules with same molecular formula
Starches or Disaccharides with di erent connectivity

● are complex carbohydrates that are made of lots of simple

sugars strung together. Your body needs to break starches
into sugar to use them for energy.
Starches include bread, cereal, and pasta.
● They also include certain vegetables like potatoes, peas and
corn.
● Examples: Sucrose (glucose + fructose), lactose (glucose +
galactose), and maltose (glucose + glucose).
● Stereoisomers - compounds with same molecular formula
● Characteristics: Double sugars composed of two
and the same connectivity. Same atoms connected in the
monosaccharide units.
same way but di ers in the way they are connected in 3
Fibers or Polysaccharides dimensional spaces.

● It has also a complex carbohydrate. your body cannot break

down most fibers, so eating foods with fibers can help you
feel full and make you less likely to overeat. They may also
help lower cholesterol and blood sugar.
● Examples: Starch, glycogen, cellulose.

Dannah Louise O. Palanca

Enantiomers 5. Formation of Glycosides, N-glycosides, and O-glycosides:

● Type of stereoisomeric relationship ● Monosaccharides can react with alcohols or amines to form
● Molecules that are non-superimposable mirror images glycosides. For example, glucose can react with methanol to
of one another world as we knew it is gone. The dead have form methyl glucoside.

I
risen and taken over. It's up to us to survive and fight for our
lives.
6. Glycosidic Bond Formation:

● Monosaccharides can react with each other to form

disaccharides and polysaccharides. This involves the
formation of a glycosidic bond between the anomeric carbon
of one monosaccharide and a hydroxyl group of another. For
example, glucose molecules can link together to form
maltose or cellulose.

Digestion of Carbohydrates
Digestion in MOUTH

Reaction of Monosaccharides ● Digestion of carbohydrates starts at the mouth.

● In mouth, food undergoes mastication,during mastication,
1. Oxidation-Reduction (Redox) Reactions:

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food comes in contact with saliva (secreted by salivary
gland)
● Monosaccharides can be oxidized, where they lose electrons,
● saliva contain salivary amylase (ptyalin).
or reduced, where they gain electrons. For example, glucose
can be oxidized to gluconic acid or reduced to sorbitol. Digestion in STOMACH

2. Isomerization Reactions: ● digestion of carbohydrates temporarily stops in the stomach

● the action of salivary amylase stops in stomach because of
● Monosaccharides can rearrange their atoms to form isomers.
high acidity of stomach
For example, glucose can isomerize to fructose in a process
● no carbohydrates splitting enzymes available in gastric juice
called mutarotation.
Digestion in INTESTINE
3. Glycosidic Bond Formation:
● further digestion of carbohydrates occurs in small intestine
● Monosaccharides can react with each other to form
by pancreatic enzyme
disaccharides and polysaccharides. This involves the
● food bolus reaches the small intestine from stomach where
formation of a glycosidic bond between the anomeric carbon
it meets the pancreatic juice
of one monosaccharide and a hydroxyl group. For example,
● pancreatic juice contains enzyme called pancreatic amylase
glucose molecules can link together to form maltose or
(amylopsin) similar to salivary amylase
cellulose.
● Two phase of intestinal digestion:
○ Digestion due to pancreatic amylase
4. Esterification:
○ Digestion due to intestinal brush border enzyme
● Action of pancreatic amylase
● Monosaccharides can react with acids to form esters. For
○ it hydrolyzes the dextrins to mixture of maltose,
example, glucose can react with acetic acid to form glucose
isomaltose, limit dextrin action of intestinal brush
pentaacetate.
border enzymes
○ These enzymes are responsible for final digestion
of carbohydrates

Dannah Louise O. Palanca


Metabolic Control of Carbohydrates
● Carbohydrate metabolism in liver is regulated by
glucoregulatory hormones of the body to maintain
circulating glucose concentration in a relatively narrow
range.
● The glucoregulatory hormones includes:
○ Insulin
○ Glucagon
○ Amylin
○ Epinephrine
○ Cortisol
● Insulin and Glucagon
○ Insulin and glucagon are two hormones that play a
crucial role in carbohydrate metabolism and
maintaining blood sugar levels in the body. They
work together in a balance to ensure that the body
has a constant supply of energy while preventing
damage from excessive or insu cient blood sugar
glucose from the liver, delaying the emptying of
the stomach to regulate the absorption of sugar,
and influencing feelings of fullness after eating.
○ Amylin plays a crucial role in managing blood
sugar levels and overall metabolism.
● Epinephrine
○ also known as adrenaline, plays a significant role
in carbohydrate metabolism. It increases h glucose
production by stimulating glycogenolysis and
gluconeogenesis.
○ This leads to a prompt increase in blo glucose
concentration, particularly in the postabsorptive
state.
○ Additionally, epinephrine contributes to the
mobilization of energy stores in the form of
glucose, making it available for use during
situations of increa energy demand, such as stress
or physical activity.
● Cortisol

Dannah
○ Cortisol is a steroid hormone that plays a crucial
levels. role in various metabolic processes in the body,
including carbohydrate metabolism.
Glucoregulatory Hormones:
Here are some keyways in which cortisol
● Insulin:
○ Secreted by pancreatic ß-cells in response to high
influences carbohydrate metabolism:
blood sugar levels
● Gluconeogenesis: Cortisol stimulates gluconeogenesis,
○ Promotes the uptake of glucose from the
which is the process of synthesizing glucose from
bloodstream into cells, where it is used for energy
non-carbohydrate sources, such as amino acids and glycerol.
production.
This helps increase blood glucose levels, especially during
○ Inhibits the release of glucose from the liver,
periods of fasting or stress.
reducing endogenous glucose production.
● Inhibition of glucose uptake: Cortisol can inhibit the
○ Enhances the storage of glucose as glycogen in
uptake of glucose by peripheral tissues, such as muscles and
the liver and muscles.
adipose tissue. This helps to conserve glucose for vital
● Glucagon:
organs, particularly the brain, during times of stress.
○ Secreted by pancreatic a-cells in response to low
● Insulin antagonism: Cortisol opposes the e ects of insulin,
blood sugar levels.
the hormone responsible for promoting glucose uptake by
○ Promotes the breakdown of glycogen in the liver
cells. In situations where cortisol levels are elevated, such as
into glucose, which is released into the
stress, it can counteract the actions of insulin, leading to
bloodstream.
increased blood glucose levels.
○ Stimulates the liver to produce glucose from
non-carbohydrate sources, such as amino acids
and fatty acids
● Amylin
○ Amylin is a hormone that helps control the level of
sugar (glucose) in your blood, working alongside
insulin. It does this by slowing down the release of

Dannah Louise O. Palanca

 ● This process occurs in the cytoplasm of the cell and does not
necessarily require the presence of oxygen that is why it is a
Metabolic Control of Carbohydrate common process in both the aerobic respiration and the
Metabolism anaerobic pathway.

● Carbohydrates metabolism - It is a fundamental

biochemical process that ensures a constant supply of
energy to living cells. Just as an oil furnace uses oil (its fuel)
to produce heat, the cells of the body use carbohydrates as
their cellular energy (ATP).
● The most important carbohydrate is glucose, Glucose, also
known as blood sugar, is the major breakdown product of
carbohydrate digestion. Glucose is also the major fuel used
for making АТР.
● The liver is an exemption; it routinely uses fats as well, thus
saving glucose for other body cells.
● Essentially, glucose is broken apart piece by piece, and some
of the chemical energy released when its bond is broken is
captured and used to bind phosphate to molecules to make
ATP.

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● The carbon atoms released from glucose leave the cells as
carbon dioxide, and the hydrogen atoms removed (which
contain energy-rich electrons) are eventually combined with
oxygen to form water. These oxygen-using events are
referred to collectively as cellular respiration.
○ Cellular respiration - is a metabolic pathway
that breaks down glucose and produces ATP.
● The three main metabolic pathways involved in cellular
respiration are glycolysis, the citric acid Cycle, and the
electron transport chain.
○ The citric acid Cycle - occurs in the
mitochondria and produce virtually all the carbon
dioxide that results during cell respiration.
○ The electron transport chain - is where the
action is for ATP production.

Glycolysis
● Process of breaking down Glucose to form energy.
● Product: Two molecules of pyruvate, 2 ATP, NADH, and
Water
● Location: Cytoplasm
● Does not necessarily require oxygen
● Glycolysis is a series of reactions that extract energy from
glucose by splitting it into two three-carbon molecules
called pyruvates.
● As the word itself indicates, this a splitting (lysis) of sugar
or some other carbohydrate (glyco).

Dannah Louise O. Palanca

 ● A-U, C-G

Nuclei Acid ● RNA, containing a ribose sugar, is more reactive than DNA
and is not stable in alkaline conditions. RNA's larger helical
● The two main types of nucleic acids are deoxyribonucleic grooves mean it is more easily subject to attack by enzymes.
acid (DNA) and ribonucleic acid (RNA). DNA is the genetic
What are the three types of RNA?
material found in all living organisms, ranging from
single-celled bacteria to multicellular mammals. It is found ● Messenger RNA (mRNA) copies portions of genetic code,
in the nucleus of eukaryotes and in the chloroplasts and a process called transcription, and transports these copies
mitochondria. to ribosomes, which are the cellular factories that facilitate
● In prokaryotes, the DNA is not enclosed in a membranous the production of proteins from this code.
envelope, but rather free-floating within the cytoplasm. ● Transfer RNA (tRNA) is responsible for bringing amino
● Both DNA and RNA are made from nucleotides, each acids, basic protein building blocks, to these protein
containing a five-carbon sugar backbone, a phosphate group, factories, in response to the coded instructions introduced
and a nitrogen base. by the mRNA. This protein-building process is called
translation.
Components of Nucleic Acids ● Finally, Ribosomal RNA (rRNA) is a component of the
ribosome factory itself without which protein production
1. Phosphate
would not occur1.
2. Five-carbon sugar
3. Nitrogenous Base Biosynthesis and Degradition

Dannah
○ Each nucleotide in DNA contains one of four
possible nitrogenous bases: adenine (A), guanine ● Degradation of nucleic acids is a catabolic reaction and the
(G) cytosine (C), and thymine (T). resulting parts of the nucleotides or nucleobases can be
○ Each nucleotide in RNA contains one of four salvaged to recreate new nucleotides. Both synthesis and
possible nitrogenous bases: adenine (A), guanine degradation reactions require multiple enzymes facilitate
(G) cytosine (C), and Uracil (U). the event.
● Degradation - Nucleases function in Many Processes that
Structure are Important for Life. Nucleases are enzymes that degrade
nucleic acids, either DNA or RNA. DNases degrade DNA and
Depxyribonucleic Acids (DNA)
RNases degrade RNA.
● Biosynthesis - DNA biosynthesis occurs when a cell divides,
● DNA replicates and stores genetic information. It is a
in a process called replication. It involves separation of the
blueprint for all genetic information contained within an
DNA double helix and subsequent synthesis of
organism.
complementary DNA strand, using the parent DNA chain as a
● The sugar in DNA is deoxyribose, which contains one less
template
hydroxyl group than RNA's ribose.
● A-T,C-G
DNA Replication
● Due to its deoxyribose sugar, which contains one less
oxygen-containing hydroxyl group, DNA is a more stable
molecule than RNA, which is useful for a molecule which has
the task of keeping genetic information safe.

Ribonucleic Acids (RNA)

● RNA converts the genetic information contained within DNA

to a format used to build proteins, and then moves it to
ribosomal protein factories.
● RNA contains ribose sugar molecules, without the hydroxyl
modifications of deoxyribose.

Dannah Louise O. Palanca

Genetic Code TERMS
Code Functions ● Plasmid - circular self-replicating form of DNA found in
bacteria.
● The genetic code is a set of three-letter combinations of ● Enzymes - Used to cut a specific DNA sequence often called
nucleotides called codons, each of which corresponds to a as digestion. Example: Escherichia Coli (EcoR1)
specific amino acid or stop signal. The concept of codons
was first described by Francis Crick and his colleagues in History of insulin:
1961.
A story of recombinant DNA
Flow of genetic information
● Animal source insulin was the only type available until 1977
● The flow of genetic information in cells is therefore from when...
DNA to RNA to protein ● The first genetically-engineered insulin was produced in a
laboratory using E. coli by Dr.
Riggs, Dr. Itakura and Dr. Boyer.
● The vast majority of insulin used today is produced by using
recombinant DNA

Mutation

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● is a change to a gene's DNA sequence to produce something
di erent. It creates a permanent change to that gene's DNA
sequence. Genetic variations are important for humans to
evolve, which is the process of change over generations.
REMEMBER!

1. Universal
2. Recundant
3. Not ambiguous

Recombinant DNA
● DNA molecules formed by laboratory methods of genetic
recombination (sucb as molecular cloning).
○ Bringing together genetic material from multiple
sources.
○ Creating sequences would not be found in other
biological organisms.

Dannah Louise O. Palanca

Technologies
1. DNA isolation
2. Restriction Enzyme
3. Amplifying of DNA
4. DNA ligase
5. Insertion into a host

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6. Replication

Techniques
1. Microinjection
2. Biolistics or gene gun
3. Cooling and heating
4. Calcium ion usage

Benefits
● Recombinant DNA technology has been widely used in
medical science, industries, animal husbandry, and
agriculture.

Dannah Louise O. Palanca

 Protein amide and participate in hydrogen bonding of protein
structure. The simple amino acid glycine (where R = H) is
also considered in this category. The amino acids in this
Amino Acids group are - glycine, serine, threonine, cysteine, glutamine,
asparagine and tyrosine.
● Amino acids are the monomers that make up proteins.
3. Polar amino acids with positive 'R' group: The three
Specifically, a protein is made up of one or more linear
amino acids lysine, arginine, and histidine are included in
chains of amino acids, each of which is called a polypeptide.
this group.
● Amino acids are a group of organic compounds containing
4. Polar amino acids with negative 'R' group: The
two functional groups - amino and carboxyl. The amino
dicarboxylic monoamino acids - aspartic acid and glutamic
group (-NH2) is basic while the carboxyl group (-COOH) is
acid are considered in this group.
acidic in nature.
● General structure of amino acids
○ The amino acids are termed as D-amino acids, if
both the carboxyl and amino groups are attached
to the same carbon atom.
● Amino acids are organic compounds that are the building
blocks of proteins. They contain both an amino group
(-NH2) and a carboxyl group (-COOH), which are
attached to a central carbon atom. The remaining side
chain of each amino acid is unique and determines its

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properties 1234.
● There are 20 di erent types of amino acids that can be
found in proteins. They can be classified based on the nature
of their side chains into three categories: nonpolar, polar,
and charged 24. Nonpolar amino acids have hydrophobic side
chains, while polar amino acids have hydrophilic side chains.
Charged amino acids have either a positive or negative
charge on their side chains 24.
● The properties of amino acids are determined by the nature
of their side chains. For example, nonpolar amino acids tend
to be hydrophobic and are often found in the interior of
proteins, while polar and charged amino acids tend to be
hydrophilic and are often found on the surface of proteins
24.

Classification of Amino Acids based on

Polarity
Polarity is important for protein structure.

1. Non-polar amino acids: These amino acids are also

referred to as hydrophobic (water hating). They have no
charge on the 'R' group. The amino acids included in this
group are - alanine, leucine, isoleucine, valine, methionine,
phenylalanine, tryptophan and proline.
2. Polar amino acids with no charge on 'R' group: These
amino acids, as such, carry no charge on the 'R' group. They
however possess groups such as hydroxyl, sulfhydryl and

Dannah Louise O. Palanca

 Classification of Amino Acids
Amino acids can classified according to the properties of their side
chains, that is, whether they are nonpolar (have an even distribution of
electrons) or polar have an uneven distribution of electrons, such as
acids and bases

1. Nonpolar (Hydrophobic) And Uncharged

● Each of these amino acids has a nonpolar side chain that

does not gain or lose protons or participate in hydrogen or
ionic bonds.
Each amino acid consists of a central carbon atom connected to a side
● The side chains of these amino acids can be thought of as
chain (R), a hydrogen, a nitrogen-containing amino group (-NH2), a
"oily" or lipid-like, a property that promotes hydrophobic
carboxyl group (-COOH)-hence the name "amino acid." Amino acids
interaction (water fearing or repelling).
di er from each other by which specific side chain (or the R group) is
● In proteins found in aqueous solutions a polar environment),
bonded to the carbon center.
the side chains of the nonpolar amino acids tend to cluster
together in the interior of the protein due to the
Nutritional Classification
hydrophobic e ect or nature of the nonpolar side chains
Non-Essential (R-groups).
● Nonpolar amino acids are commonly found in the

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● Your nonessential amino acids are the amino acids your body transmembrane domains of integral membrane proteins,
can create on its own as a byproduct of normal functioning. where they help anchor the protein in the lipid bilayer.
There are 11 of these amino acids, and they include the ● These amino acids play a critical role in maintaining the
following: structural integrity of proteins and providing stability to
1. Alanine (ala) protein cores or to its structure.
2. Arginine (arg)
3. Asparagine (asn) 2. Polar (Hydrophilic) And Uncharged
4. Aspartic acid (asp)
● Unlike nonpolar amino acids, polar uncharged amino have
5. Cysteine (cys)
hydrophilic (water loving) side chains,
6. Glutamic acid (glu)
which allows them to interact with water and form
7. Glutamine (gIn)
hydrogen bonds.
8. Glycine (gly)
● Serine, threonine, and tyrosine each contain a polar hydroxyl
9. Proline (pro)
group that can participate in hydrogen bond formation.
Essential ● Asparagine and glutamine each contain a carbonyl group and
an amide group, both of which can also participate in
● Your essential amino acids are the ones you need but cannot hydrogen bonding
produce yourself, and so must be gained either from your ● Found on the surface of proteins
diet or via supplementation. ● These amino acids can form hydrogen bonds and engage in
1. Histidine (his) interactions with water molecules, making them important
2. Isoleucine (ile) for the solubility, protein-protein, and protein-solvent
3. Leucine (leu) interactions.
4. Lysine (lys)
5. Methionine (met)
6. Phenylalanine (phe)
7. Threonine (thr)
8. Tryptophan (typ)
9. Valine (val)

Dannah Louise O. Palanca

3. Acidic (Polar And Charged)
● The amino acids aspartic and glutamic acid are proton
donors.
● At physiologic pH, the side chains of these acidic amino
acids are fully ionized, forming a negatively charged
carboxylate group (-COO-).
● These amino acids are often involved in the ionic
interactions and binding of metal ions within proteins.
● They also play essential roles in enzyme catalysis, signal
transduction, and protein-protein interactions.
4. Basic (Polar And Charged)
● The side chains of the basic amino acids accept protons.
● At physiologic pH, the basic amino acids, lysine, arginine,
and histidine, contain side chains with amino groups that are
positively charged.
● Their positive charges enable them to interact with
negatively charged molecules and surfaces, influencing
various biochemical processes (vise versa.)
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● These amino acids are essential for various biological
functions, including DNA binding, enzyme catalysis, and
maintaining the overall charge balance within proteins.
Properties of Amino Acids
Isomerism:
● Two types of isomerism are shown by amino acids basically
due to the presence of asymmetric carbon atom. Glycine has
no asymmetric carbon atom in its structure hence is
optically inactive
Stereoisomerism:
● Stereoisomerism means that the molecules have the same
molecular formula and the same structural formula but have
a di erent three dimensional arrangement in space.
Optical Isomerism
● The optical isomers are called enantiomers
● Enantiomers are any pair of stereoisomers that are
non-superimposable mirror images of each other.
● Enantiomers are said to be Chiral.
● Example: Alanine
Amphoteric Nature
● Means something can act as both an acid and a base
depending on the situation. For example, amino acids can
donate or accept protons depending on the pH of the
solution they're in.
Physical Properties
● Proteins are colourless and usually tasteless.
● Shape and Size.
○ Globular proteins: Round proteins mainly found
in plants, like in seeds and leaf cells.
○ Fibrillar proteins: Thread-like or oval-shaped
proteins mostly found in animal muscles.
Types of Chemical Reactions given by Amino
Acids
Chemical Reactions due to...
-СООН group
● 1. Amino acids forms salts (-COONa) with bases and esters
(COOR) with alcohols.
● A. Formation of Salts with Basess
○ Amino acids contain both acidie (carboxyl group,
-COOH and basie (amino group, - NH2) functional
groups. The acidic -COOH group can react with a
base to form a salt
○ The amino acid donates a proton (E1+) from the
-COOIl group, forminga carboxylate
ion (-COO-). The base accepts the proton to
become a positively charged ion.
○ The resulting salt is formed between the
carboxylate ion of the amino acid and the
positively charged ion of the base.
● B. Formation of Esters with Alcohols
○ The -COOH group of an amino acid can also react
with an alcohol to form an ester
○ In this reaction, the -OH group of the alcohol
reacts with the -COOH group of the
amino acid in the presence of an acid catalyst.
This reaction is known as
esteri fication.
○ The result is the formation of an ester and water,
as the -COOH group loses a hydroxyl (OH) group,
and the -OH group of the alcohol loses a hydrogen
atom
Dannah Louise O. Palanca
 ● 2. Decarboxylation: Amino acids undergo decarboxylation to
produce corresponding amines.
○ The -COOH group undergo decarboxy lation,
wherein it loses a carbon dioxide molecule. This
results to the formation of a new functional group.
● 3. Reaction with ammonia: The carboxyl group of
dicarboxylie amino acids react with
○ NH3 to form amide.
○ The amino acid and ammonia engage in a reaction
known as deamination. In this interaction, the
amino group of the amino acid bids farewell. It
doesn't just vanish; instead, it combines with the
ammonia, forming an ammonium fon
-NH2 group
● 1. Amino Groups behave as bases and combine with acids to
form salts.
○ The amino group has a lone pair of elections on
the nitrogen atom, which can accept a proton (E)
from an acid through a process called protonation.
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● 2. Reaction with ninhydrin: The amino acifs react with
ninhydrin to form a purple, blue or pink color complex
(Ruhemann's purple)
○ The mechanism of the reaction involves the
interaction of ninhydrin with the amino group of
amino acids, leading to the formation of a colored
product. The specific color can vary, but typically,
a purple or blue color is observed.
● 3. Transamination: The transfer of an amino group from an
amino acid to a keto acid to form a new amino acid.
○ Transamination is a biochemical process where an
amino group (NiE12) is transferred from one amino
acid to another, facilitated by enymes called
transaminases. This leads to the creation of a new
amino acid and a new keto acid. It plays a crucial
role in amino acid mctabolism, allowing for tho
synthes's and breakdown of amino acids..
● 4. Oxidative deamination: Amino acids undergo oxidative
deamination to liberate ammonia.
○ Oxidative deamination is a process where an amino
group (NER) is removed from an amino acid,
resulting in the formation ofa keto acid. This
reaction is catalyzed by Enzymes, and ammonia
(NE3) is rcleased as a byproduct Oxidative
deamination is a key step in the breakdown of
amino acids and is important for climinating
excess nitrogen from the body.
Protein Separation Methods
Methods of Protein Seperation depends on their characterestics
These characterestics are;
● Solubility
● Tonic Charge
● Polarity
● Molecular Size
● Binding Specificity
Depending On Solubility
1. Salting In
● Prepare Protein Solution: Start with a protein solution in
water, where the proteins are surrounded by water
molecules.
● Gradual Salt Addition: Add a neutral salt (og, ammonium
sulfate) gradually to the protein solution.
● Monitor Solubility: As salt is added, the ionic strength of the
solution increases.
● Ion Shielding: The salt ions shield the charges on the surface
of the proteins, reducing repulsive forces between proteins.
● Complete Solubilization: The shielding e ect ofions allows
hydrophobic interactions between proteins to dominate,
leading to increased solubility.
● Further Processing: Solubilized proteins can undergo
additional processing steps, such as chromatography, to
isolate and purify specific proteins.
2. Salting Outs
● Prepare Protein Solution: Begin with a protein solution in
water, where the proteins are sumounded by water
molecules.
● Gradual Salt Addition: Add a neutral salt (og» ammonium
sulfate) gradually to the protein solution.
● Monitor Precipitation: As salt concentration increases, water
molecules are disrupted, and the water structure around
proteins is disturbed.
● Complete Precipitation: Proteins, now less solvated due to
disrupted water structure, aggregate and precipitate out of
the solution.
● Centrifugation: Centrifuge the solution to separate the
precipitated proteins from the liquid phase.
● Resuspend and Further Processings: Resuspend the protein
pellet in a chosen bu er. Additional processing steps may
include purification techniques.
Dannah Louise O. Palanca
 Depending on Ionic Charge 7. Reverse-Phase Chromatography:

3. Electrophoresiss ● Prepare Column: Use a column with a hydrophobic stationary

phase.
● Gel Preparation: Prepare a gel (agarose or polyacry lamide)
● Sample Loading: Load the protcin mixture onto the column.
with wells for sample loading.
● Elution: Flute protcins by changing the polarity of the mobile
● Sample Loading: Load protein or nucleic acid samples into
phase.
the wells.
● Separation: Proteins are separated based on hydrophobic
● Electrophoresis: Apply an clectric field. Charged molecules
interactions.
migrate through the gel based on size and charge
● Visualization: Stain or label molecules for visualization under 8. Hydrophobic Interaction Chromatography (HIC):
UV light or specific dyes.
● Separation: Molecules are separated based on size and ● Prepare Column: Use a column with a material that dislikes
charge. water (hydrophobic).
● Sample Loading: Put proteins into the column.
4. Isoelectric Focusing: ● Hydrophobic Interaction: Proteins with hydrophobic parts
stick to the material in the column
● Prepare Gel: Set up a gel with a pH gradient
● Elution: Change the solution to release proteins; less
● Sample Loading: Load the protein mixture.
hydrophobie ones come out first.
● Isoclectric Focusing: Apply an clectric field. Proteins migrate
● Separation: Proteins separate based on how much they
to their isoclectric point (pI.
dislike water.

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● Visualization: Stain or label proteins for visualization.
● Separation: Proteins are separated based on their pI. Depending on Molecular Size

Depending on Polarity 9. Dialysis and Ultrafiltration:

5. Adsorption Chromatographys ● Sample Containment: Place the protein sample in a dialysis

bag or ultrafiltration device.
● Prepare Column: Set up a column with a solid matrix coated
● Solvent Exchange: Dialyze or ultrafilter the sample against a
with an adsorbent.
bu er to exchange solvents.
● Sample Loading: Load the protein mixture onto the column.
● Concentration: Concentrate the sample by removing excess
● Adsorption: Proteins bind to the adsorbent based on
solvent.
interactions like hydrogen bonding or hydrophobicity.
● Separation: Larger molecules are retained, while smaller
● Elution: Flute proteins by changing conditions like pEl or salt
molecules pass through.
concentration.
● Separation: Proteins are separated based on their a nity for 10. Gel Electrophoresis:
the adsorbent.
● Gel Preparation: Prepare a gel (agarose or polyacry lamide)
6. Paper Chromatographys with wells for sample loading.
● Sample Loading: Load protein or nucleie acid samples into
● Prepare Paper: Apply a small spot of the protein sample on
the wells.
chromatography paper.
● Electrophoresis: Apply an clectric ficld Charged molecules
● Solvent Migrations: Allow a solvent to migrate through the
migrate through the gel based on size.
paper
● Visualization: Stain or label molecules for visualization under
● Separation: Di erent proteins move at di erent rates based
UV light or specific dyes.
on their a nities for the paper and solvent
● Separation: Molecules are separated based on size.
● Visualization: Stain or label proteins for visualization.

Dannah Louise O. Palanca

11. Gel Filtration Chromatographys Dipeptide

● Prepare Column: Set up a column with a porous gel matrix
● Sample Loading: Load the protein mixture onto the column.
● Elution: Flute proteins based on their size. Larger molecules
pass through the gel more quickly.
● Separation: Proteins are separated based on their size.
12. Ultracentrifugation:
● A dipeptide contains 2 amino acid molecules linked by a
single peptide bond.
● Dipeptides help to maintain the pH of cells or act as
antioxidants.
● Some examples of dipeptides include carnosine, anserine,
and homoanserine.

● Sample Loading: Load the protein sample into

ultracentrifuge tubes.
● Centrifugation: Centrifuge at high speeds to separate
components based on density.
● Separation: Components separate into layers or pellets
based on their densities.

Depending on Binding Specificity

13. A nity Chromatographys

Prepare Column: Set up a column with a matris containing

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●
ligands specific to the target protein.
● Sample Loading: Load the protein mixture onto the column.
● A nity Binding: Target protcins sclectively bind to the
ligands.
● Elution: Flute the target proteins by changing conditions like
pH or adding a competitive ligand
● Separation: Target proteins are separated based on their
a nity for the ligands.

Peptides
● A Combination of Amino Acids
● Peptides makes proteins like Collagen, Elastin & Keratin.
● Crucial for maintaining the texture, firmness, & elasticity of
our skin.

Dannah Louise O. Palanca

Tripeptide Polypeptide

● Tripeptides contain 3 amino acid molecules linked by
● 2 peptide bonds.
● Tripeptide helps improve muscle growth and strength, as
well as to reduce fatigue and improve overall health.
● Example of tripeptides are Glutathione
● A polypeptide contains more than 20 amino acid molecules,
and up to 100 residues.
● Some examples of polypeptides are natriuretic peptides (a
component of snake venom), some antibiotics, and peptide
hormones.

Oligopeptide
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● Oligopeptides are protein sequences ranging from 2 to 20
amino acids.
● Oligopeptide has been found to help improve digestion,
reduce inflammation, boost the immune system, and even
help with weight loss.

Dannah Louise O. Palanca

 E yme ● Material Transport: Enzymes facilitate the movement of
molecules across cell membranes. For instance, enzymes
embedded in the cell membrane, such as ATP-powered
What are Enzymes? pumps, actively transport ions and nutrients into or out of
the cell. maintaining the cell's internal environment and
● Enzymes speed up (catalyze) chemical reactions in cells.
enabling cellular communication.
More specifically, they lower the threshold necessary to
● Respiration: Enzymes play a crucial role in cellular
start the intended reaction. They do this by binding to
respiration, the process by which cells generate energy in
another substance known as a substrate.
the form of ATP. Enzymes in the mitochondria, such as the
● The majority of enzymes are proteins, though some are
enzymes involved in the citric acid cycle and the electron
Ribonucleic acid (RNA) molecules. RNA molecules translate
transport chain, catalyze the oxidation of glucose and other
information from DNA and create proteins.
fuel molecules to produce ATP through oxidative
● Each cell contains thousands of enzymes, providing specific
phosphorylation.
help throughout the body.
● Signal Transduction: Enzymes participate in signal
● Enzymes help with specific functions that are vital to the
transduction pathways, which allow cells to respond to
operation and overall health of the body.
external stimuli. For example, enzymes like adenylate
● They help speed up chemical reactions in the human body.
cyclase and phospholipase C are involved in converting
● They are essential for respiration, digesting food, muscle and
extracellular signals, such as hormones or
nerve function. and more.
neurotransmitters, into intracellular signals that regulate
gene expression, metabolism. and other cellular responses.
Enzymes function in…

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● Digestive System: Enzymes help the body break down Lock and Key Model
larger complex molecules into smaller molecules, such as
● In the lock and key model, enzymes are like keys that fit into
glucose, so that the body can use them as fuel.
specific locks, which are molecules. When they fit together,
● DNA Replication: Each cell in the body contains DNA. Each
enzymes trigger chemical reactions, changing the molecules.
time a cell divides, the cell needs to copy its DNA. Enzymes
Then, the enzymes release the transformed molecules and
help in this process by unwinding the DNA coils.
can move on to interact with others.
● Liver Enzymes: The liver breaks down toxins in the body. To
do this, it uses a range of enzymes the facilitate the process
of destroying the toxins.
● Hormone Production: Enzymes help convert precursor
molecules into hormones that regulate various bodily
functions. For example, enzymes in the endocrine glands
facilitate the synthesis of hormones like insulin, which
controls blood sugar levels, and adrenaline, which regulates
the body's response to stress.
● Cell Regulation: Enzymes regulate cellular processes by
controlling the speed and specificity of biochemical
reactions. For instance, enzymes called kinases add
phosphate groups to proteins, altering their activity and Four Steps of Enzyme Action
regulating cell signaling pathways involved in growth,
STEP 1: Recognition:
metabolism, and di erentiation.
● Muscle Contractions: Enzymes called ATPases provide the
● The enzyme recognizes and binds to its specific substrate,
energy needed for muscle contraction. These enzymes
which is the molecule it acts upon. This binding occurs at
hydrolyze Adenosine Triphosphate (ATP) into Adenosine
the enzyme's active site, which is like a precise docking
Diphosphate (ADP) and inorganic phosphate, releasing
station for the substrate.
energy that powers the movement of muscle fibers.

Dannah Louise O. Palanca

STEP 2: Catalysis:
● Once the enzyme and substrate are bound together, the
enzyme catalyzes the chemical reaction by lowering the
activation energy required for the reaction to occur. In other
words, it makes it easier and faster for the reaction to
happen.
STEP 3: Transformation:
● During the catalytic process, the enzyme facilitates the
transformation of the substrate into one or more products.
This transformation can involve breaking chemical bonds,
rearranging atoms, or combining molecules to form new
compounds.
STEP 4: Release:
● After the reaction is complete, the enzyme releases the
products of the reaction. It's now free to bind with another
substrate molecule and repeat the process. The enzyme
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itself remains unchanged and can continue its role as a
catalyst in multiple rounds of reactions.
Factors Affecting Enzyme Activity
● Temperature: Enzymes work best within a certain
temperature range. Too low temperatures slow down enzyme
activity, while too high temperatures can denature (unfold)
the enzyme, rendering it nonfunctional.
● Potential of Hydrogen: Enzymes have an optimal pH at
which they function most e ectively. Changes in pH can
alter the charge distribution on the enzyme's active site,
a ecting its ability to bind with the substrate.
● Substrate Concentration : As the concentration of
substrate molecules increases, the rate of enzyme activity
also increases, up to a point. However, once all the enzyme's
active sites are saturated with substrate, further increases
in substrate concentration won't increase the rate of
reaction.
● Enzyme Concentration : Higher concentrations of enzymes
typically lead to faster reaction rates, assuming there are
enough substrates available. More enzymes mean more
active sites available for substrate binding.
● Cofactors and Coenzymes: Enzymes may require
additional non-protein molecules called cofactors or
coenzymes to function properly. These molecules can help
activate the enzyme or assist in substrate binding.
● Inhibitors: Inhibitors are molecules that decrease enzyme
activity by either blocking the enzyme's active site
(competitive inhibitors) or altering the enzyme's shape
(non-competitive inhibitors).
● Activators: Activators are molecules that increase enzyme
activity by binding to the enzyme and stabilizing its active
conformation or by promoting substrate binding.
Classification of Enzymes
Oxireductases
● These enzymes catalyze oxidation-reduction reactions,
involving the transfer of electrons between molecules.
● Examples:
○ Dehydrogenases: Catalyze the transfer of
hydrogen atoms (and their electrons) between
molecules.
○ Cytochromes: Participate in electron transport
chains. transferring electrons between molecules.
Transferases
● Transferases catalyze the transfer of functional groups (such
as amino, methyl, or phosphate groups) from one molecule
to another.
● Examples:
○ Kinases: Transfer phosphate groups from ATP to
other molecules.
○ Transaminases: Transfer amino groups between
amino acids and keto acids.
Hydrolases
● Hydrolases catalyze hydrolysis reactions, breaking chemical
bonds by adding water molecules.
● Examples:
○ Lipases: Hydrolyze ester bonds in lipids to release
fatty acids and glycerol.
○ Proteases: Break peptide bonds in proteins to
degrade them into amino acids.
Lyases
● Lyases catalyze the removal or addition of groups to double
bonds or the breaking down of a chemical compound into
smaller parts without hydrolysis or oxidation.
● Examples
○ Decarboxylases: Remove carboxyl groups from
molecules, releasing carbon dioxide.
Dannah Louise O. Palanca
 ○ Synthases: Catalyze the formation of new bonds 3. "Translocases for Small Molecules": These
between molecules. enzymes facilitate the movement of small
molecules across membranes. Examples include:
Isomerases ■ Glucose transporters: Facilitate the
transport of glucose across cell
● Isomerases catalyze the rearrangement of atoms within a
membranes, maintaining glucose
molecule to form isomeric forms.
homeostasis in the body.
● Examples
■ Aquaporins: Facilitate the movement of
○ Isomerases: Catalyze the conversion of one
water molecules across membranes,
isomer into another, such as converting
ensuring proper water balance within
glucose-6-phosphate into fructose-6-phosphate.
cells and tissues.
Ligases 4. “Protein Translocases": These enzymes are
involved in the translocation of proteins across
● Ligases, also known as synthetases, catalyze the joining of membranes, such as:
two molecules, often with the input of ATP. ■ Sec translocase: Facilitates the
● Examples translocation of proteins across the
○ DNA ligase: Joins DNA strands together during bacterial plasma membrane or the
DNA replication and repair. endoplasmic reticulum membrane
○ ATP synthase: Catalyzes the synthesis of ATP during protein synthesis.
from ADP and inorganic phosphate during cellular ■ Mitochondrial translocase complexes:

Dannah
respiration. Facilitate the import of proteins into
mitochondria, where they play essential
Translocases roles in mitochondrial function.

● Translocases are a type of enzyme that facilitate the

movement of molecules or ions across biological
membranes. They are often classified as a subgroup of Uses of Enzymes in Medical Diagnosis
transport proteins.
● Translocases can be further categorized based on the ELISA (Enzyme Linked Immunosorbent Assay)
specific molecules they transport and the mechanism of
transport. ● ELISA is a widely used diagnostic technique that employs
● Examples: enzymes to detect the presence of specific antibodies or
1. “lon Translocases": These enzymes transport ions antigens in patient samples. Enzyme-labeled antibodies or
across membranes, maintaining ion gradients antigens bind to the target molecule, and the enzyme
essential for various cellular processes. Examples catalyzes a colorimetric or fluorescent reaction, allowing for
include: the detection and quantification of the target substance.
■ Sodium-potassium ATPase: Transports
sodium ions out of cells and potassium Enzyme Based Biosensors
ions into cells against their
● Enzyme-based biosensors are devices that utilize enzymes to
concentration gradients, using ATP as
detect specific analytes in patient samples, such as glucose,
energy.
cholesterol, or biomarkers indicative of disease. These
■ Calcium ATPase: Transports calcium ions
biosensors can provide rapid and sensitive measurements,
out of the cytoplasm, helping regulate
making them valuable tools for point-of-care diagnostics.
intracellular calcium levels.
2. “ATP Synthases" : While ATP synthases are often
classified as ligases, they can also be considered
translocases because they facilitate the
translocation of protons across membranes,
generating ATP in the process.

Dannah Louise O. Palanca

Enzyme Activity Assays Hypertension Medications

● Measurement of enzyme activity levels in patient samples
can provide valuable diagnostic information.
● Abnormal enzyme activity levels may indicate the presence
of certain diseases or disorders. For example, elevated levels
of liver enzymes (e.g.. alanine transaminase, aspartate
transaminase) in blood serum may indicate liver damage or
disease.
● ACE inhibitors, work by relaxing and widening blood vessels.
They do this by blocking an enzyme called ACE, which
normally makes a substance that narrows blood vessels and
raises blood pressure. When ACE is blocked, blood vessels
relax, allowing blood to flow more easily, and blood pressure
decreases. This helps your heart work more e ciently and
reduces the risk of heart problems.

Genetic Testing

● Enzymes are used in various molecular diagnostic

techniques, including polymerase chain reaction (PCR) and
DNA sequencing, to detect genetic mutations associated
with inherited diseases or genetic predispositions to certain
conditions. Enzymes like DNA polymerases and restriction
endonucleases play key roles in these techniques.

Enzyme Based Immunoassays

Dannah
● Enzyme-based immunoassays, such as Western blotting and
immunohistochemistry, utilize enzymes to detect and
visualize specific proteins in patient samples. These
techniques are widely used in research and clinical settings
for protein expression analysis and disease diagnosis.

Enzyme Deficiency Screening

● Enzyme assays can be used to screen for enzyme

deficiencies associated with metabolic disorders, such as
phenylketonuria (PKU) or lysosomal storage diseases.
Measurement of enzyme activity levels in patient samples
can help diagnose these conditions and guide treatment
decisions.

Other Enzyme-Related Medications

Pain Reliever Medicines

● Nonsteroidal anti-inflammatory drugs (NSAIDs), work by

inhibiting enzymes involved in the production of
inflammatory mediators called prostaglandins.
Prostaglandins are lipid compounds derived from fatty acids
and are involved in various physiological processes. including
inflammation, fever, and pain perception. Simply, they work
by inhibiting enzymes involved in the production of
inflammatory prostaglandins, thereby reducing pain,
inflammation, and fever.

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 Lipid an Fatt Acid ●
●
transport fat-soluble nutrients.
storage of energy.
● absorbing vitamins
What are Lipids? ● making hormones

● Lipids are fatty, waxy, or oily compounds that are essential

How Lipids React
to many body functions and serve as the building blocks for
all living cells. Lipids help regulate hormones, transmit nerve ● Lipid molecules of all classes undergo some degree of
impulses, cushion organs, and store energy in the form of chemical reaction, especially in the presence of heat.
body fat. Hydrolysis, hydrogenation, and oxidation represent the major
types of chemical reactions occurring fo food lipids.
Kinds of Lipids
● Crude emulsions of lipids enter the duodenum as fine lipid
droplets and then mix with bile and pancreatic juice to
● PHOSPHOLIPIDS: major membrane lipids that consist of
undergo marked changes in chemical and physical form.
lipid bilayers. his basic cellular structure acts as a barrier to
Emulsification continues in the duodenum along with
protect the cell against various environmental insults and
hydrolysis and micellization in preparation for absorption
more importantly, enables multiple cellular processes to
across the intestinal wall.
occur in subcellular compartments.
● fatty compounds that perform a variety of functions in your
● TRIGLYCERIDES: a type of fat, called lipid, that circulate in
body. They're part of your cell membranes and help control
your blood. They are the most common type of fat in your
what goes in and out of your cells. They help with moving
body. Triglycerides come from foods, especially butter, oils,
and storing energy, absorbing vitamins and making

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and other fats you eat.
hormones. But, having too much of some lipids is harmful.
● CHOLESTEROL: a waxy, fat-like substance that your body
needs for good health, but in the right amounts. Unhealthy
Reaction of Lipids With…
levels of cholesterol can lead to a condition called high blood
cholesterol. Cholesterol in your blood is carried on Hydrolysis
lipoproteins: Low-density lipoprotein (LDL), sometimes called
"bad" cholesterol. ● The reaction can be catalyzed by acid, base, or lipase, but it
● WAXES: Esters made of long-chain alcohol and a fatty acid. also occurs as an un-catalyzed reaction between fats and
They provide protection, especially to plants in which wax water dissolved in the fat phase at suitable temperatures
covers the leaves of plants. In humans, cerumen, also known and pressures
as earwax, helps protect the skin of the ear canal.
● STEROL: regulate biological processes and sustain the
domain structure of cell membranes where they are
considered as membrane reinforcers [2]. While cholesterol
(CHO) is the major sterol of vertebrates, ergosterol (ERG)
plays a key role in fungi
● GLYCEROL: a naturally occurring alcohol. It is an odorless
liquid that is used as a solvent, sweetening agent, and also
as medicine. When glycerol is in the intestines, it attracts
water into the gut, softening stools and relieving Hydrogenation
constipation.
● the process by which hydrogen atoms are added to
Main Function of Lipids in the Body unsaturated fats and oils. Unsaturated molecules are those
that contain double bonds, while saturated fats and oils
● as an energy reserve
contain only single bonds. These double bonds have the
● regulate hormones
potential to accept hydrogens and thus become
● transmit nerve impulses,
hydrogenated.
● cushion vital organs

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Oxidation
● Lipid oxidation is a series of reactions that has a negative
impact on food quality and shelf life. During lipid oxidation,
unsaturated fatty acids react with oxygen to form lipid
hydroperoxides, which are later degraded into small, volatile
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molecules such as aldehydes and ketones
Fatty Acids
● are energy sources and membrane constituents. They have
biological activities that act to influence cell and tissue
metabolism, function, and responsiveness to hormonal and
other signals.
● are carboxylic acids that are the structural components of
many lipids. They may be saturated or unsaturated.
Unsaturated fatty acids have lower melting points, saturated
fatty acids containing the same number of carbon atoms
● Types of Fats:
1. Saturated - If there are only single bonds
between neighboring carbons in the hydrocarbon
chain, a fatty acid is said to be saturated.
2. Unsaturated - contain one or more double or
triple bonds between the molecules. These fats are
liquid at room temperature in oil form,
unsaturated.
● Characteristics of Fatty Acids: fatty acid consists of a
straight chain of an even number of carbon atoms, with
hydrogen atoms along the length of the chain and at one end
of the chain and a carboxyl group (-COOH) at the other end.
It is that carboxyl group that makes it an acid (carboxylic
acid).
Sphingolipids
● are a class of lipids containing a backbone of spingoid bases,
which are a set of aliphatic amino alcohols that includes
sphingosine
● are found throughout the body. Primarily located in nerve
cell membranes, they make up approximately 25% of the
lipids in the myelin sheath. First identified in brain tissue,
some sphingolipid sub-classes can be found in other parts of
the body including the spleen and blood
● Involved in diverse cellular processes, including apoptosis,
cell adhesion, and cell signaling.
● Cellular Processes of Sphingolipids
1. Sphingolipids play an important role in both
extrinsic and intrinsic apoptotic pathways
depending on the stimuli, cell type and cellular
response to the stress.
2. Sphingolipid play an important role in cell
adhesion as they regulate actin-binding proteins
such as the ezrin, radixin, and moesin protein
families
3. signal transduction pathways that involve
sphingolipids include the regulation of cell growth,
di erentiation, di erentiated cell functions (such
as responses to cytokines), and programmed cell
death (apoptosis). Recent reviews of sphingolipid
metabolism, transport, and cell regulation can be
found in Refs.
Dannah Louise O. Palanca
Phosphoglycerides
● esters of only two fatty acids, phosphoric acid and a
trifunctional alcohol - glycerol
● hey are the main component of biological membranes in
eukaryotic cells. They are a type of lipid, of which its
composition a ects membrane structure and properties
● also known as glycerophospholipids
● Phosphoglycerates is always made up of a saturated or
unsaturated fatty acid esterified to a glycerol molecule to
which a phosphate group is also attached.

Steroids
● are a man-made version of hormones normally produced by
the adrenal glands which are 2 small glands found above the
kidneys. Steroids reduce redness and swelling
(inflammation). This can help with inflammatory conditions
such as asthma and eczema.
● The steroid cholesterol is an essential component of animal
cell membranes, where it maintains membrane structure and

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fluidity. Most steroids function as signaling molecules, such
as hormones [6]. Animal steroid hormones include
estrogens, androgens, glucocorticoids, mineralocorticoids,
and progestogens
● Purpose of Steroids:
○ Reduce redness and swelling
○ cellular signaling or modulation of the lipid
membrane structure and dynamics.
○ Can help with inflammatory conditions
○ increase in muscle strength very quickly.
○ maintains the membrane fluidity and they are also
precursors of vitamin (for example vitamin D)

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 Bod Fluid
What are Considered Body Fluids?
● Body fluids are the fluids that are produced, intaked,
created, formed, and the byproducts of the body while
maintaining homeostasis.
● The body fluid or the physiologic fluid is essential for various
physiological processes and the maintenance of body
homeostasis.
○ Temperature regulation
○ Moistening of tissues
○ Transportation of essential nutrients
○ Elimination of waste from the body ● The body fluid content of the body changes with the body's
○ Lubricating di erent joints and tissues development. The maximum body fluid is present at the fetal
development stage (approximately 95%), which goes down
Body Fluid Compartments to about 75% for an infant and eventually to about 50-60%
in the adult stage.

Kinds of Body Fluids

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● Body fluids can be discussed in terms of their specific fluid
compartment, a location that is largely separate from
another compartment by some form of a physical barrier.
● The intracellular fluid (ICE) compartment is the system that
includes all fluid enclosed in cells by their plasma
membranes.
● Extracellular fluid (ECE) surrounds all cells in the body.
Extracellular fluid has two primary constituents: Plasma the
fluid component of the blood
● Interstitial fluid (LE) that surrounds all cells not in the blood.
Interstitial fluid (the fluid filling up the spaces between
cells) is the major constituent.
● Intravascular fluid
● Transcellular fluid the fluid filling up the spaces of chambers
formed from the linings of the epithelial cells) is the least in
terms of the amount.
● Non-Infectious Body Fluids: These are fluids that are
created by the body naturally and biologically for
maintaining homeostasis. This kind of body fluid is produced
by the body to ensure proper functioning.
● Infectious body fluids: These are fluids that are
transferred by second or third-party contributors. This kind
of body fluid is obtained by the body and it a ects proper
functioning, due to it disrupting the proper flow of body
fluids.
● Special body fluids: These are fluids that are produced by
the body to protect against infections, either internally or
externally. This kind of body fluid is provided and created to
protect, isolate, and eliminate from the body the unknown
organisms that can enter the body.
Types of Body Fluids

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Dannah Louise O. Palanca

Body Fluid Mechanism:
● The body maintains tight control over total body water and
total body osmolarity, thus ingestion and excretion of water
are regulated. The water in di erent components of the
compartment is maintained to match total body osmolarity,
and in the process of maintaining a steady-state,
redistribution of water from the di erent compartments of
the body can occur.
● Osmotic pressure is the force created by the fluid. Part of
the osmotic pressure is the oncotic pressure (i.e., which is
the osmotic pressure created by the large molecules
(colloids).
● Hydrostatic pressure is the force that drives the movement
of fluid; it is the pressure that blood exerts against the
vessel walls.
● While osmotic pressure pulls the fluid (water and the
dissolved substances) back into the capillary, hydrostatic
pressure drives fluid out of the capillary and into the
interstitial fluid. This process is referred to as filtration.

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Dannah Louise O. Palanca