1930s - identified the intermediates of the citric acid cycle and

of urea biosynthesis

1940s - determined the essential roles of certain

vitamin-derived cofactors or “coenzymes” such as
thiamin pyrophosphate, riboflavin, and ultimately coenzyme A,
coenzyme Q, and cobamide coenzymes

1950s - how complex carbohydrates are synthesized from, and

broken down to simple sugars, and delineated the pathways for
biosynthesis of pentoses and the breakdown of amino acids and
lipids

Animal models, perfused intact organs, tissue slices, cell

homogenates and their subfractions, and purified enzymes all
were used to isolate and identify metabolites and enzymes.

1. Discovery of enzyme’s role as catalysts for biochemical

reactions.

WHAT?
★ The systematic study of the chemicals of living systems,
their organization into cells, and the principles of their
chemical interactions as they participate in the process
of life

WHY?
★ Humanity is continuously challenged to seek
understanding of the most fundamental processes of
life at the molecular level.

Louis Pasteur – a French microbiologist who stated that

the process of fermentation could ONLY occur in intact cells (in
wine making and brewing)
2. Discovery of DNA as the carrier of genetic information.

Büchner (1899) – discovered that fermentation can indeed

occur in cell-free extracts
Early years of the 20th century
- vital roles of inorganic phosphate, ADP, ATP, and NAD(H).
- identification of phosphorylated sugars and chemical
reactions and enzymes (Gk “in yeast”) that convert
glucose to pyruvate (glycolysis) or to ethanol and CO2
(fermentation).
 ★ illuminates many aspects of health and diseases

★ has significant contributions to the fields of cell biology,

physiology, immunology, microbiology, pharmacology,
and toxicology, as well as the fields of inflammation, cell
injury, and cancer.

Refers to the variety of life on Earth at all its levels, from genes to
ecosystems, and can encompass the evolutionary, ecological, and
★ Investigates genetic and molecular basis of familial cultural processes that sustain life.
hypercholesterolemia, a disease that results in early
onset atherosclerosis.

★ Provides a deeper understanding of cell receptors and Compounds that make up living systems obey the fundamental
mechanisms of uptake, not only of cholesterol, but of laws of chemistry – THERE ARE NO NEW PRINCIPLES.
how other molecules’ cross cell membranes.

★ Studies of oncogenes and molecular mechanisms

involved in control of normal cell growth.

Omics - focuses on comprehensive study of the structures and

functions of molecules with which each is concerned.
1. BIOCHEMICAL STRUCTURES

Transcriptomics – deals with RNA molecules. ● Chemical and 3D structures

● Physical and chemical properties
Proteomics – deals with proteins. ●

●
Interaction, organization and coordination
Synthesis and degradation
Other fields - glycomics, lipidomics, metabolomics,
nutrigenomics, and pharmacogenomics.

Bioinformatics - uses computer technology to collect, store,

analyze and disseminate biological data and information, such as
DNA and amino acid sequences or annotations about those
sequences.

Nanotechnology - provide novel methods of diagnosis and

treatment for cancer and other disorders.

Gene therapy - aims to fix a faulty gene or replace it with a

healthy gene to try to cure disease or make the body better able
to fight disease

Synthetic biology - a multidisciplinary field of biotechnology

that involves engineering the genetic material of
organisms—such as viruses, bacteria, yeast, plants, or animals—to
have new characteristics
 ● METABOLIC PATHWAYS

- SERIES of chemical reactions occurring within a

cell
- Metabolic pathways are linked together by a
common intermediate
- Linked metabolic pathways = Metabolic
Network

2. METABOLISM

● Describesall chemical reactions by which

complex molecules taken into an organism are
broken down to produce energy and by which
build up
that energy is in turn used to complex
molecules.
● Energy production, utilization and
conservation
● CATABOLISM (breaking down)
● ANABOLISM (building up)
3. GENETIC INFORMATION

● Transmission, expression and storage of

genetic information
Why is Life Based on the Element Carbon?
- There are two important properties of carbon that make
it a suitable element to form the compounds in living
things:
● Firstly, carbon atoms can link together to form
stable chains of great length.

● Carbon atoms bind strongly to each other and

form very large molecules which are built
around this carbon 'backbone'.

● The covalent bond between two carbon atoms

is strong so that the backbones are stable. In
all of these compounds simple sub-units called
monomers are linked together by
condensation reactions.
● One carbon chain may contain hundreds of carbon
atoms.
What Makes Carbon so special?
- It has a “central” role in all living organisms.
● A very large carbon-based molecule made of repeating

- It has 4 valence electrons. It makes

polymer
units is called a .

4 covalent bonds.
● Each unit of a polymer is called a monomer.
- It can bond with any element, but really loves to bond
● Polymers can be thousands of atoms long
with other carbon atoms and make long chains.

● Carbon-based molecules also can be shaped like rings.

5 6
Most carbon rings contain or carbon atoms.

● One of the most important carbon rings is benzene.

● It has 6 carbons & 6 hydrogens , with alternating double
bonds.

● Many compounds are based on benzene. They often have

very strong smells or aromas, so they are calledaromatic
compounds.
● An example of one aromatic compound is a molecule
called naphthalene.
 Atoms will bind to other atoms to form molecules to fill their
● The alkanes make up a series of saturated hydrocarbons, outer shells with electrons and be more stable.
called a homologous series because they have similar
TYPES OF BONDS:
properties and have the same general formula:
● Covalent Bond – very stable bond often formed by
carbon atoms; occurs when two or more atoms share
CnH2n+2
electrons to fill their outer shells

● The first four members of the series are gases at room ● Ionic Bond – two or more atoms bind to form a
temperature and are called: molecule by giving up or receiving electrons from each
methane, CH4 other to fill their outer shells
ethane, C2H6
propane, C3H8 IONS - atoms with a charge; attracted to each other because of
butane, C4H10 their opposite charges, forming a bond resulting in an
electrically neutral molecule
- When placed in water, ionically bonded molecules
separate into their individual ions. These ions in
solutions, called electrolytes , are capable of conducting
electricity.
- Electrolyte balance is a very important concept in
homeostasis, as it can mean life or death.

HYDROGEN BOND - a weak bond that occurs between a

positively charged hydrogen atom and a negatively charged
oxygen or nitrogen atom
- Hydrogen bonds are responsible for holding water
molecules together.

ACID – molecule that releases H+ ions when added to water

BASE – a molecule that will accept H+, often by releasing OH-

when added to water

● An atom or group of atoms within a molecule that has
similar chemical properties whenever it appears in The strength of acids and bases is measured using a pH scale.
various compounds

● Serves as the basis for naming organic compounds and

as the units by which we classify organic compounds
into families

The sum of all the chemical reactions that take place in the human
body is called METABOLISM.

To speed up the reactions:

1. Increase the concentration of the reactants
2. Increase the speed of the reactants
3. Use a catalyst
( Catalyst: a substance that increases the rate of a chemical reaction
without itself undergoing any permanent chemical change.)
(To balance the reaction, count the number of atoms of each
element on each side of the reaction.)

Cellular respiration is performed in cells (to deliver glucose, to

deliver oxygen). The reason our cells perform such is to release
energy within the bonds of the glucose molecule. The energy
should be converted into a usable form (ATP).

part to ng cells nilagay ko lang here para di sayang sa bond paper :]

 ➔ CHEMICAL
➔ ORGANELLE
➔ CELLULAR
➔ TISSUE
➔ ORGAN
➔ ORGAN SYSTEM
➔ ORGANISM

Why do we need to review the cell structure?

● Cellular components are made up of biomolecules.

● The turnover (biosynthesis and degradation) of

biomolecules happens inside the cell.

● Biochemical reactions are taking place inside the various Eukaryotic Cell
cellular components

What is a cell?
● Basic building block of life

● Smallest living unit of an organism

● Capable of growth, reproduction, energy adaptation, and

response to the environment

● A cell may be an entire organism or it may be one of

billions of cells that make up an organism.
(The nucleoid region is the irregularly-shaped section of a prokaryotic cell where DNA is housed.)

An Escherichia coli cell:

Prokaryotic Cell
A Typical ANIMAL CELL:

A Typical PLANT CELL:

(Cellular respiration is a metabolic pathway that breaks down glucose and produces
ATP.)

Only plant cells have this.)

(
Only plant cells have this.)
(

Only plant cells have this.)

(
 Sulfur-containing:

Phosphorus-containing:

(most commonly found in biomolecules)

(most commonly found in biomolecules)

Hydrocarbons:

Organic Derivatives of Water:

Carbonyl Compounds:

Acyl compounds:

Amines:
 ★ Hydrogen bonds are attractions of electrostatic
force caused by the difference in charge between
slightly positive hydrogen ions and other, slightly
negative ions. In the case of water, hydrogen bonds
form between neighboring hydrogen and oxygen atoms
of adjacent water molecules.

Thanks to their polarity, water molecules happily attract each

other. The plus end of one—a hydrogen atom—associates with
the minus end of another—an oxygen atom.

These attractions are an example of hydrogen bonds, weak

interactions that form between a hydrogen with a partial
positive charge and a more electronegative atom, such as
● Molecular Geometry: bent/V-shaped
oxygen. The hydrogen atoms involved in hydrogen bonding must
● Has four electron groups around oxygen: nearly be attached to electronegative atoms, such as O,N, or F.
tetrahedral in arrangement.

● A polar molecule

Water molecules are also attracted to other polar molecules

and to ions. A charged or polar substance that interacts
with and dissolves in water is said to be hydrophilic: hydro
means "water," and philic means "loving."

In contrast, nonpolar molecules like oils and fats do not

interact well with water. They separate from it rather than
Note: A polar molecule is a molecule in which one end of the molecule is slightly
positive, while the other end is slightly negative. dissolve in it and are called hydrophobic: phobic means
"fearing." You may have noticed this as a not-so-handy feature
of oil and vinegar salad dressings. Vinegar is basically just
water with a bit of acid.
 Adhesion Vs Cohesion
ADHESION COHESION

Adhesion happens between two When two similar substances or

● Cohesion and Adhesion of Water Molecules dissimilar molecules or molecules face the force of
substances. attraction, this force is known
● Moderation of Temperature by Water as the cohesion force.

● Floating of Ice on Water Adhesion is generally the force Cohesion force is unrestrained
of attraction present between among water molecules.
● Water as medium for biochemical processes the water molecules and the
walls of xylem vessels.

Capillary action and meniscus Surface tension, meniscus and

(the curved surface which is capillary action are the effects
formed by any liquid in a of cohesion.
★ Cohesion and adhesion allows water to be transported cylinder) are the effects of
adhesion.
inside a tall tree even if the direction is against the pull
of gravity.
Adhesion is caused by Cohesion is caused by hydrogen
electrostatic or mechanical bonding and Van der Waals
forces that exist among two forces.
kinds of different substances.

A strong adhesion force causes A strong force of cohesion

the liquid to spread all over the forms water droplets on any
surface. surface.

Note: Van der Waals forces are weak intermolecular forces that are
dependent on the distance between atoms or molecules. These forces
arise from the interactions between uncharged atoms/molecules.

★ A measure of the resistance of a substance to

increase its surface area

★ According to the definition of surface tension, it is

the phenomenon that occurs when the surface of a
liquid is in contact with another phase (it can be a liquid
as well). Liquids tend to acquire the least surface area
possible. The surface of the liquid behaves like an
elastic sheet.

★ “Surface tension is the tension of the surface film

of a liquid caused by the attraction of the particles
in the surface layer by the bulk of the liquid, which
tends to minimize surface area”.

● By absorbing heat from warmer air and releasing that

heat to cooler air

● Water has high specific heat:

1 cal/g·°C
● 1 cal of heat applied to 1 g of H2O causes a
relatively small change in T
➢ Much heat is used to disrupt
H-bonds before H2O molecules begin
Note: In summary, cohesion keeps molecules of the same substance together, while
adhesion causes them to stick to different substances.
moving faster

➢ Comparison: Ethyl alcohol has a

specific heat of 0.6 cal/g·°C
EVAPORATIVE COOLING This behavior can be explained through the concepts of density,
molecular structure, and hydrogen bonding.
★ Water has high heat of vaporization: 580 cal/g at 25°C Molecular Structure and Hydrogen Bonding
➔ Water molecules (H₂O) are made up of two hydrogen
★ As a liquid evaporates, the liquid surface that remains atoms bonded to one oxygen atom. The oxygen atom is
behind cools down. more electronegative, meaning it pulls the shared
Examples: electrons closer to itself, creating a polar molecule
- evaporation of water on the surface of with a slightly negative charge near the oxygen and a
leaves slightly positive charge near the hydrogens.
- sweating
➔ In liquid water, these polar molecules are constantly
moving, and the hydrogen bonds between them are
continuously forming and breaking. This dynamic
nature allows the molecules to pack closely together,
making liquid water relatively dense.

➔ However, as water cools and approaches freezing, the

movement of water molecules slows down, and the
hydrogen bonds become more stable. When water
freezes into ice, these stable hydrogen bonds cause
the molecules to arrange themselves in a hexagonal
lattice structure. This structure holds the water
molecules further apart than in the liquid state,
creating a solid form (ice) that is less dense than liquid
water.

● Ice crystal is spacious as it has fewer molecules than Density and Buoyancy
in an equal volume of liquid water. ➔ Density is defined as mass per unit volume. Since the
hexagonal lattice structure of ice is less dense than
● Ice is less dense than water. the more tightly packed molecules in liquid water, ice
has a lower density.

➔ When an object is placed in a fluid (such as water),

whether it sinks or floats depends on its density
relative to the fluid. Since ice is less dense than liquid
water, it floats. The principle of buoyancy, which states
that an object will float if it is less dense than the fluid
it is placed in, governs this behavior.

Weak Interactions in the aqueous system

- Influence structure, function and specificity of
biomolecules

Water and its ionization products H3O+ and −OH

- Influence structure, self-assembly and properties of
all cellular components

Weak acid-base equilibria/physiological buffers

- Maintain optimum pH of biochemical reactions

Water plays a fundamental role in supporting life, primarily

serving as the medium in which biochemical processes occur.
Due to its unique properties, water is essential in facilitating
the chemical reactions that sustain living organisms.
Hydrogen Bonding: A type of weak bond that occurs when a
hydrogen atom, covalently bonded to an electronegative atom
(like oxygen or nitrogen), is attracted to another
electronegative atom nearby. This is common in water and gives
rise to many of its unique properties.

Ionic Interactions: These are strong electrostatic

attractions between oppositely charged ions (e.g., Na⁺ and Cl⁻ in
salt). Ionic interactions play a critical role in the structure and
function of biomolecules, like proteins and nucleic acids.

Hydrophobic Interactions: These occur when nonpolar

molecules (or parts of molecules) come together in water. Since
water is polar, nonpolar substances minimize their contact with
water, leading to the clustering of hydrophobic molecules. This
is key in forming cell membranes and protein folding.

Van der Waals Forces: Weak, short-range forces between

molecules due to temporary fluctuations in electron
distribution. These include attractions between nonpolar
molecules and play a role in stabilizing molecular structures,
such as the stacking of DNA base pairs.
Hydrogen bonds (H-bonds) are crucial for the structure and
function of various biological molecules. Here’s a quick overview
of their roles:

DNA Structure: H-bonds hold the two strands of DNA together

by connecting complementary nitrogenous bases. Adenine pairs
with thymine (A-T) through two hydrogen bonds, and cytosine
pairs with guanine (C-G) through three hydrogen bonds. These
bonds are strong enough to maintain the DNA structure but
weak enough to allow strand separation during replication and
transcription.

Protein Structure: Hydrogen bonds are vital in stabilizing the

secondary (α-helices and β-sheets) and tertiary structures of
proteins. In α-helices, H-bonds form between the carbonyl
oxygen of one amino acid and the amide hydrogen of another,
several residues ahead. In β-sheets, H-bonds connect adjacent
strands, providing stability to the overall structure.

Enzyme-Substrate Interaction: H-bonds contribute to the

binding of substrates to enzymes' active sites, enhancing the
specificity and efficiency of catalysis. These bonds help position
the substrate correctly for the chemical reaction to occur.

Water as a Solvent: Water’s ability to form hydrogen bonds

makes it an excellent solvent for biological molecules. The
H-bonds between water molecules contribute to the solubility
of polar substances, facilitating biochemical reactions in
aqueous environments.

Stabilizing Macromolecular Structures: H-bonds help

maintain the integrity of large biomolecules, such as nucleic
acids and proteins, by contributing to their three-dimensional
structure, which is essential for their biological function.

● Electrostatic interactions are forces between

charged particles. These forces can be attractive or
repulsive, depending on the charges of the particles
involved.
The hydrophobic effect refers to the tendency of nonpolar
substances to aggregate in aqueous solutions and
exclude water molecules. This phenomenon is driven by the
way water molecules interact with each other and with
nonpolar substances. Here’s a breakdown of the key points:

1. Nonpolar Molecules: Nonpolar molecules, like oils and

fats, do not interact favorably with water because
they don’t have charged regions to form hydrogen
bonds. Instead, they are more likely to clump together
to minimize their exposure to water.

2. Water’s Structure: Water is a polar molecule with a

partial positive charge on the hydrogen atoms and a
partial negative charge on the oxygen atom. This
polarity allows water molecules to form hydrogen
bonds with each other.

3. Entropy Considerations: When nonpolar molecules

are dispersed in water, they disrupt the
hydrogen-bond network of water. To minimize this
disruption, water molecules surround nonpolar
molecules, forming a structured “cage” around them.
This organization decreases the entropy (or disorder)
of the system. By clustering together, nonpolar
molecules minimize their exposure to water and
reduce the ordered structure of water around them,
leading to an increase in entropy.

4. Biological Implications: The hydrophobic effect is

crucial in biology. It drives the folding of proteins,
where hydrophobic amino acids tend to be buried in
the interior away from water, while hydrophilic ones
are exposed to the aqueous environment. It also plays
a role in the formation of cell membranes, where
hydrophobic tails of phospholipids face inward,
shielded from water, while hydrophilic heads face
outward towards the water.

5. Micelle Formation: In detergents, the hydrophobic

effect helps form micelles, where the hydrophobic
tails of detergent molecules cluster together in the
center of the micelle, away from water, while the
hydrophilic heads face outward, interacting with the
water.

Osmotic pressure - measure of the tendency of water

molecules to migrate from a dilute to a concentrated solution
through a semipermeable membrane

Osmosis – migration of water molecules

these properties are important in estimating solute

concentrations in biological fluids
● The ionization of water refers to the process by
which water molecules dissociate into ions. This is a
fundamental concept in chemistry and helps explain
water's role as a solvent and its behavior in various
chemical reactions.

The Henderson-Hasselbalch equation is a mathematical formula

used to estimate the pH of a buffer solution. It relates the pH of
the solution to the concentration of an acid and its conjugate
base, providing insight into the buffer’s capacity to maintain a
stable pH.

● The pH scale is important for several reasons, as it

provides a measure of the acidity or alkalinity of a
solution, which is crucial in many fields.
 PHOSPHATE BUFFER SYSTEM
● Buffers the extracellular fluids and cytoplasmic
components (pH ≈ 6.9 to 7.4)

● pKa = 6.86
● Buffering region = 5.9 to 7.9

BICARBONATE BUFFER SYSTEM

● Partially buffers human blood plasma
(pH ≈ 7.4)

● When blood pH falls to 6.8 or below (as in the case of

Buffering Region (blue area) - pH range in which the buffer is severe uncontrolled diabetes where metabolic acids
effectively resisting drastic pH changes pH = pKa ± 1 are largely produced), irreparable cell damage and
death may occur.

Many therapeutic agents are weak acids or bases.

Condensation - formation of ATP from ADP and inorganic Types:
phosphate, wherein the elements of water are eliminated
● Electrolytes: These are ions such as sodium (Na⁺),
potassium (K⁺), calcium (Ca²⁺), and chloride (Cl⁻). They
help regulate fluid balance, nerve function, and muscle
contraction.
● Nutrients: Glucose, amino acids, and fatty acids are
examples of nutrients found extracellularly that are
transported to cells for energy and growth.
Hydrolysis - cleavage accompanied by the addition of the ● Waste Products: Metabolic waste products, such as
elements of water urea and carbon dioxide, are also present in
extracellular fluids and need to be removed from the
- responsible for the enzymatic depolymerization of body.
proteins, carbohydrates, and nucleic acids
Function: Extracellular solutes play crucial roles in maintaining
- catalyzed by hydrolases
osmotic balance, regulating blood pressure, and facilitating
communication between cells. They help in transporting
nutrients to cells and removing waste products.

Oxidation – produces water and carbon dioxide

Types:

● Electrolytes: Potassium (K⁺) and phosphate (PO₄³⁻)

are prevalent in the intracellular fluid. They are vital
for maintaining the cell’s membrane potential and
enabling cellular processes.
● Nutrients: Intracellular nutrients include glucose,
amino acids, and fatty acids that are utilized in cellular
● Water forms hydrogen-bonded clusters with itself and metabolism and energy production.
with other proton donors or acceptors. Hydrogen ● Macromolecules: Proteins, nucleic acids (DNA and
bonds account for the surface tension, viscosity, liquid RNA), and polysaccharides are also found inside cells
state at room temperature, and solvent power of and are essential for cellular structure and function.
water.
Function: Intracellular solutes are critical for various cellular
● pH is the negative log of [H+]. A low pH characterizes an processes, including metabolism, signal transduction, and
acidic solution, and a high pH denotes a basic solution. maintaining cellular structure. They help regulate cell volume,
intracellular pH, and are involved in energy production and
● The strength of weak acids is expressed by pKa, the storage.
negative log of the acid dissociation constant. Strong
acids have low pKa values and weak acids have high pKa
values.

● Buffers resist a change in pH when protons are

produced or consumed. Maximum buffering capacity
occurs plus or minus 1 pH unit on either side of pKa.

● Physiologic buffers include bicarbonate,

orthophosphate, and proteins.

● Water is both the solvent in which metabolic reactions

occur and a reactant in many biochemical processes,
including hydrolysis, condensation, and
oxidation-reduction reactions.

● In cells and tissues, buffer systems maintain

intracellular and extracellular fluids at their optimum
(physiological) pH, which is usually close to pH 7.
Enzymes generally work optimally at this pH.
Serine (N-terminal residue) → glycine → phenylalanine → alanine
→ leucine (C-terminal residue)
Construction of a STANDARD CURVE