GEN BIO 1: INTRODUCTION TO CELL BIOLOGY neck bottle experiment”.

What do plants, animals, protozoans and bacteria have

in common?

-This question can be answered in the field of cell

biology. Cell biology deals with the study of cellular
structure and activity. For this term, we will be discussing
some topics in Cell Biology such as (1) Structure and
parts, (2) Cellular Transport, (3) Metabolism, and (4) Cell
Cycle.

Cell was defined as “a structural and functional unit of

life” (Reece et. al, 2018), as cells reflect the observable
characteristics of a living organism, and some even exist
as a singular living cell

• Based on the spontaneous generation theory, what

would be the expected results from both flasks after
boiling?

The invention of the simple compound microscope in
the 1600’s led to the first observation of cork plant cells
under microscope by Robert Hooke. He first used the
word “cells”, as he described those cells as “chamber
like” structures (Rea et. al, 2020). Later
on, Anton van Leuwenhoek published his illustrations
and observation of cells, which he called “animalcules”
in 1678.
Cell Theory and Spontaneous Generation.
Early people believed in the theory of “Spontaneous
Generation”, which states that non-living things can
produce living organisms, such as maggots from rotten
meat or fishes from mud (Reece et. al, 2018).
Several scientists in the past tried to disprove and
support spontaneous generation. One scientist, Louis
Pasteur, disproved this theory by his famous “Swan
• From figure 3, how can Pasteur disprove spontaneous
generation theory?
Based on the spontaneous generation, both flasks should
show signs of living cells in the broth. But due to the
shape of the flask’s neck, living cells cannot pass directly
inside the flask, making the broth inside sterile or free
with living cells. This experiment supports one of the
statements in our cell theory, “living cells arise from
another living cells” (Reece et. al, 2018). On the
succeeding years, development in the cell biology
reached out to the accepted statements in the cell
theory.
1.Cell is the fundamental structural unit of life (Reece
et. al, 2018)
2. Living organisms are composed of cells-combined

from the conclusion of Matthias Schleiden for plants
and Theodor Schwann for animals (Rea et. al, 2020).
3.Living cells arise from other living cells. -Derived
from the research of Rudolf Virchow and Robert
Remak.
Review: Parts of the Cell. In a far away city called Grant
City, the main export and production product is the steel
widget. Everyone in the town has something to do with
steel widget making and the entire town is designed to
build and export widgets. The town hall has the
instructions for widget making, widgets come in all
shapes and sizes and any citizen of Grant can get the
instructions and begin making their own widgets.
Widgets are generally produced in small shops around
the city, these small shops can be built by the carpenter's
union (whose headquarters are in town hall). After the
widget is constructed, they are placed on special carts
which can deliver the widget anywhere in the city. In
order for a widget to be exported, the carts take the
widget to the postal office, where the widgets are
packaged and labeled for export. Sometimes widgets
don't turn out right, and the "rejects" are sent to the
scrap yard where they are broken down for parts or
destroyed altogether. The town powers the widget shops
and carts from a hydraulic dam that is in the city. The
entire city is enclosed by a large wooden fence, only the
postal trucks (and citizens with proper passports) are
allowed outside the city.
Cell Parts and Function
Nucleus- a region in the cell where the DNA was stored.
It serves as the command center in the cell. It has three
distinguishable features. (town hall)
- It was encased in a phospholipid bilayer sheet called
nuclear envelope. The nuclear envelope has pores
which selectively allow the passage of materials in and
out of the nucleus.
- The “cloudy” or the light and dark regions (pink in the
drawing) inside the nucleus are composed of different
complexes of DNA and proteins called chromatin.
- The large dark blob in the nucleus is the nucleolus.
This is where ribosomal RNA is produced, and RNA
subunits are assembled.
- Prokaryotes do not have a nucleus. Instead, their DNA
is clumped in one area, called the nucleoid region.
Ribosomes: responsible for production of protein
(protein synthesis).
- Composed of 2 subunits, large subunits and small
subunits.
- They can be free floating in cytoplasm or attached in
the rough endoplasmic reticulum.
Rough Endoplasmic Reticulum (rough ER): Site of
protein synthesis, due to the presence of the attached
ribosomes. It is also responsible with the attachment of
glycoproteins.
Smooth Endoplasmic Reticulum (smooth ER): site for
lipid production, steroid hormone production. It is also
responsible to metabolism of drugs, alcohol and other
harmful substances (very important in the liver cells). -
Sarcoplasmic reticulum: in muscle cells, smooth ER can
store calcium ions. Calcium ions are important for the
contraction and relaxation in the muscle cells.
Golgi Bodies (Golgi Apparatus / Golgi Complex):
Packaging center of the cells. It receives proteins from
rough ER and modifies proteins for distribution outside
and within the cells.
Lysosome: Filled with enzymes, lysosomes break down
damaged organelles, food material and pathogens. Can
be only found in animal cells.
Vacuole: A membrane bound organelle with specialized
functions.
- Central Vacuole: largest organelle in plant cells. Can
store food, pigments, water, waste and poisonous
substances (that can deter plant eaters). It is also acidic,
similar to lysosomes in animal cells.
- Food Vacuole: use to deliver ingested materials from
outside the cell (see lysosome figure).
- Contractile Vacuole: can be found in some freshwater
protist. Use to collect water (osmoregulation).
Peroxisome: helps break down lipids and hydrogen
peroxide.
Chloroplast: site of photosynthesis (production of food
in the form of carbohydrates), and can be only found in
plant cells. Due to its role in photosynthesis, it also
stores chlorophyll pigments. It has double layered
membrane, and has its own genetic material (DNA and
RNA) and ribosomes.
Mitochondria (sing. Mitochondrion): a double
membraned organelle, which produces ATP via aerobic
respiration. Same as chloroplast, with its own DNA, RNA
and ribosomes.
Cytoskeleton: provides support, anchorage and aid
movement for the cell.
- Microtubule: - Largest cytoskeleton element. Consist
of two subunits of tubulin(protein), forming a hollow
tube. - Guide movement of cellular component.
- Main component of locomotory organelles cilia and
flagellum.
- Intermediate Filament: - Cable like. Composed of
different fibrous proteins.
- Helps in anchorage of different cell parts.
- Microfilament: - Smallest among the cytoskeleton
element. - Twisted, double chain of actin proteins.
- Supports the cell’s shape. - Movement in muscle cells.
Centrosome: organelle found only in animal cell. It has
two centrioles, which produces microtubules (mitotic
spindles/spindle fibers) during cell division.
Cytoplasm: The region between the plasma membrane
and nucleus.
- Cytosol: fluid in the cytoplasm.
Plasma Membrane: also known as cell membrane, is the
outermost layer of the cell (for animal cells). Regulates
transportation of materials in and out of the cells. Mostly
composed of phospholipid bilayer. Proteins can be seen
scattered and embedded to the plasma membrane.
Extracellular Matrix: composed of collagen (protein)
fibers and glycoprotein, which helps protect and support
the plasma membrane. It is situated outside the cell and
exist in animal cells.
Cell wall: protect and holds the cells in shape.
- Cell wall composition varies in different organisms:
- Plant cell wall: Cellulose
- Bacteria cell wall: Peptidoglycan
- Fungi: Chitin
- Plant cell wall in fruits contain pectin layer, which
degrades upon ripening.
- Holes in the plant cell wall (as shown in figure) are
called plasmodesmata, which allow water and other
materials to move from cell to cell.
Cilia: very small locomotory organ, covering the cell’s
exterior. The cilia are moving in an undulatory motion
(back and forth).
Flagellum: long locomotory organ that moves in a
propeller like motion.
Both of them are composed of nine pairs of
microtubules and 2 central microtubules (9+2).
Endomembrane System To answer the question above,
we will discuss one of the important systems in our cell,
called endomembrane system. This system consists of
the following organelles (1) nuclear envelope, (2)
Endoplasmic Reticulum, (3) Golgi bodies, (4) Lysosome,
(5) vesicles and vacuoles, and (6) cytoplasm. Here are
the steps on how proteins like insulin is produced in this
system.
1. The nucleus will give the “instruction” (in the form of
messenger RNA) to the ribosome attached to the rough
ER.
2. Attached ribosomes will synthesize the amino acid
sequence (primary structure of the protein) from the
messenger RNA. (see fig. 3)
3. The protein will undergo major changes in rough ER.
This will include protein folding and attachment of
glycoprotein (molecular marker). (see fig. 3)
4. The protein will be shipped out of the rough ER and
transferred to Golgi bodies using transport vesicles.
5. The protein will undergo more modification while it
passes each lumen of the Golgi bodies.
6. The proteins either be shipped out to the cells,
shipped within the cell, or become lysosome. Shipping
out material via transport vesicles provides new layer
for the cytoplasm.
Based on the cell parts and structure, there are two
distinguished groups of organisms.
Prokaryotes: usually smaller in sized compared to
eukaryotes. Prokaryotic cells do not have nucleus and
membrane bound organelles (Reece et. al, 2018).
Eukaryotes: characterized with cell containing nucleus
and membrane bound organelles (Reece et. al, 2018).
Currently, taxonomists use Three-domain system,
which uses molecular and genomic studies as basis for
this grouping.
Domain Bacteria: Prokaryotes with peptidoglycan cell
wall.
Domain Archaea: Prokaryotes that can survive in
extreme conditions.
Ex. Thermophiles: “heat lovers”, can survive in hot
temperature.
Methanogens: “Methane lovers”, lives in methane rich
environment.
Halophiles: “Salt lovers”, lives in very salty places.
Domain Eukarya: contains all eukaryotic organisms.
Major kingdoms and groups, Protist, Fungi, Animals and
Plants, are members of this domain.

GEN BIO 2: PLASMA MEMBRANE AND CELL TRANSPORT
Plasma membrane or cell membrane is one of the very
important structure in our cells because it helps
regulate movement of materials and waste (inward or
outward). In animal cells, plasma membrane keeps the
cellular content inside the cell.
Properties of the Cell Membrane: “Fluid Mosaic
Model”.
Plasma membrane was characterized with (1) the
mixture of different biomolecules (mosaic), (2) which
are constantly moving (property of a fluid).
I. Phospholipid Bilayer
One of the major components of the plasma membrane
is the phospholipids bilayer. As shown in figure two, it
has two major parts
Hydrophilic (“water-loving”) Head – with phosphate
ion, which makes the “polar” part of the phospholipid.
Two Hydrophobic (“water-hating”) Tails- with long
chains of hydrocarbons, this comprises the “non-polar”
part of phospholipids. Sometime, it may contain an
unsaturated fatty acid chain (fatty acid with double
bonds in its carbon chain). This unsaturated fatty acid
forms a “bent” or “kink” in the hydrophobic tail.
Polar molecules are molecules that exhibit “partial
charges”, which can interact with ions and other polar
molecules. On the other hand, non-polar molecules do
not exhibit partial charges. Non-polar molecules attract
other nonpolar molecules via London dispersion forces.
As we see in figure 3, the hydrophilic heads are oriented
outside while the hydrophobic tails are oriented within
the membrane. This arrangement of phospholipids
affects the how molecules passes through the
membrane.
II. Membrane permeability and fluidity. Due to the
nature of the phospholipid bilayer, the cell membrane
has “selective permeability” over different molecules
that pass the membrane. Selective permeability means
that, in a certain membrane, some molecule can pass
easily than other substances (Freeman et. al, 2017).
Based on figure 4, gases/non-polar molecules and
small polar molecules can pass easily the bilayer. Large
polar molecules (like glucose) and ions may have a
difficulty passing the bilayer. To compensate the low
permeability of some substances, carrier proteins are
needed to transport these substances across the
membrane.
Membrane fluidity: phospholipids and other
component of the plasma membrane can move around,
due to the spaces provided by the “bents” in the
phospholipid tails. (see fig. 5). According to Freeman et.
al (2017), phospholipid bilayer increases permeability in
high temperature, but in return can weaken the
bilayer*. The presence of cholesterol helps strengthen
the phospholipid bilayer, especially in high
temperatures
III. Membrane Proteins:
Membrane proteins can be found around the plasma
membrane, and they can be classified based on their
function and their location. According to Reece et. al.
(2018), functions of membrane protein are the
following (but not limited to):
- Provide support via attachment to cytoskeletal
elements.
- Act as receptor for cellular recognition and
transmission of messages (via hormones).
- Perform enzymatic reactions.
- Transport molecules across membrane.
- Attachment of cells to other cells (see junction
proteins). Peripheral Membrane Proteins: membrane
proteins that are located at the surface of the plasma
membrane (inside or outside the cell), interacting with
the hydrophilic heads of the phospholipid bilayer.
Trans-membrane/Integral Membrane Proteins:
membrane proteins that are embedded across the
membrane.
Specialized Integral Membrane Proteins:
- Channels: proteins that allows the passage of certain
molecules freely.
Ex. Ion channels: responsible for transport of ions
across membrane.
Aquaporins: type of channel which help transport water
molecules.
- Carrier Proteins: unlike channels, carrier proteins need
to change their shape to transport their molecules
successfully.
Ex. Sodium-Potassium Pump (Na+ /K+ Pump) Sodium-
Glucose transporter
- Uniporter: transport one molecule only.
- Co-transporter: transport two molecules.
• Symporter: both molecules transported in same
direction (ex. Sodium-Glucose transporter).
• Antiporter: transport two molecules in opposite
directions (ex. Na+/K+ pump).
IV. Glycoproteins and Glycolipids:
Glycolipids: lipids with carbohydrates attached to them.
Glycoproteins: proteins with carbohydrates attached
from them. Both glycolipids and glycoproteins are
important for cell-to-cell recognition and signaling
(Freeman et. al, 2017).
Passive Transport: Diffusion and Facilitative Diffusion.
in a membrane system, like plasma membrane,
diffusion is always described as movement of
molecules from higher concentration to lower
concentration, until it reaches equilibrium. But, as we
discussed earlier, some molecules (such as ions and
large polar substances) cannot pass easily across the
plasma membrane. Diffusion would be possible for
these molecules with the help of different membrane
protein. This type of diffusion is called facilitated
diffusion. One of the examples of this is the transport of
water molecules using a membrane protein called
aquaporins. Aquaporins are very important to plant
cells, kidney cells (Reece et. al, 2018) and large intestine
(Ma & Verkman, 1999) for water absorption.
* Concentration Gradient: describes the difference of
concentration of molecules on the both side of the
membrane system.
Passive Transport: Osmosis.
Osmosis is defined as movement of water from low
solute concentration to high solute concentration,
across a semi-permeable membrane (Reece et. al.,
2018). The cause of this movement is the tendency of
water molecules to achieve equilibrium in terms of
solute concentration on both side of the membrane.
As the figure 10 shows, water molecules in solution
tends to interact with the solute, making them too big
to pass through the semipermeable membrane. In this
case, free water molecules may pass freely through the
membrane and interact with the solute from the other
side, until it reaches equilibrium. In this case, we can
also describe osmosis as movement of free water
molecules from solution with higher free water
molecules to solution with lower free water molecules.
Osmosis can also affect cells in many ways, with plasma
membrane as the “semi-permeable membrane”. We
can describe solutions based on their tonicity, which
describes as the ability of the surrounding solutions to
make the cell loose or gain water.
Osmosis happens in two solutions, separated by semi-
permeable membrane.
Solution = Solute + Solvent (Water)
Here is the summary of tonicity of solution and their
effect on cells.
Hypotonic: If the solution has less solute than the other
solution. This solution tends to lose “free” water,
favoring the water movement towards solution with
more solute.
Hypertonic: If the solution has more solute than the
other solution. This solution tends to gain “free” water
from the solution with less solute.
Isotonic: The solution has equal solute concentration to
other solution. Since both solutions are in equilibrium,
free water passes through in and out of the cell,
describing as “no net water movement”.
*Note: the following description on the figure describes
solution outside the cell (environment).
Any cellular transport that does not require energy are
called passive transport. Passive transport is also
characterized with movement of molecules from high
concentration to lower concentration.
Passive Transport: Diffusion, Facilitative Diffusion,
Osmosis.
* Plant cell needed to maintain a turgid state for
support, otherwise water loss causes the plant cell to
plasmolyze (and the plant looked wilted).
Active Transport.
On the other hand, active transport is movement of
molecules from low concentration to higher
concentration, which would require energy (in form of
ATP) for this transport. According to Freeman et. al.
(2017), there are two types of active transport.
Primary Active Transport: Directly uses energy (ATP)
for transport.
Secondary Active transport: indirectly uses ATP. The
transport was driven on the changes of electrochemical
gradient* by another primary active transporter inside
the cell.
* Electrochemical Gradient forms due to the difference
of the ion concentration, creating a partial charge inside
and outside the cell
*Sodium-Glucose Transporter/SGLUT: Found in
intestine and kidney cells. This transporter is used to
absorb glucose from digested food and urine.
Bulk Transport: Exocytosis and Endocytosis.
For transport of larger molecules (such as complex
carbohydrates, proteins, fats), they will be enclosed in a
membrane bound sac composed of materials, as similar
as the plasma membrane. This transport is called
vesicle-mediated transport (Rea et. al, 2020) or bulk
transport. The transport works with molecules going in
(endocytosis) or going out (exocytosis) of the cell.
Exocytosis usually involves with the transport of
proteins and hormones from the cell (via
endomembrane system). Vesicles used for exocytosis
will merge with the plasma membrane.
Endocytosis can be classified into three types.
- Phagocytosis: “cell-eating”. It is used to transport
large food materials.
- Pinocytosis: “cell-drinking”. It is used to transport
liquid substances in large amount.
- Receptor-mediated endocytosis: It is used to transport
specific type of molecules. Vesicles contains receptors
inside to bind specific molecules, while vesicles outside
have surrounding coated proteins.
* Bulk transport needs energy to transport molecules,
just like active transport.
GEN BIO 3: THE WORLD OF BIOMOLECULES
According to Merriam-Webster dictionary, biomolecules
are substances that are produced by living organisms.
Most of our food we eat are composed of different
biomolecules, which we can read on their food label. In
today’s lesson, we will learn in this module that
different biomolecules have different roles and
functions in our cell. Forming and Breaking
Macromolecules. Biomolecules in our body can exist in
big amounts. One of those biomolecules in our body are
called macromolecules, a type of nutrients which we
need in large amounts. Cell our body may (1) creates
these macromolecules by combining small units (called
monomers) via dehydration/condensation reaction (to
form a polymer) or (2) break down these
macromolecules into individual monomers via
hydrolysis.
* Unsaturated fats, like vegetable oil, are liquid in room
temperature (more or less 20℃).
Proteins: The Versatile One
Proteins are macromolecules, formed from the complex
arrangements of its monomers, amino acids, liked by
peptide bonds. As we discussed in our previous lesson,
proteins have various types depending on its functions:
• Structural- found in different connective tissues, skin,
nails and hair (eg. Collagen for connective tissues and
keratin for nails).
• Contractile proteins- for muscular movement (actin
and myosin proteins in muscles).
• Storage Protein- albumin in egg white
• Defense Proteins- such as antibodies, involve in
protection against foreign bodies.
• Signal Proteins- such as protein-based hormones,
which help bodies coordinate with cell to body
activities.
• Enzymes- serve as catalyst that speed up chemical
reaction.
Monomer Profile: Amino Acids.
Amino acids have three distinct parts (see fig. 2), there
are amino group, carboxyl group and residual group
(the “R” in the figure). Peptide bonds are created via
dehydration reaction of the amino-carboxyl group of
two amino acids. There are 20 amino acids, which can
be differentiate based on their residual group.
Four Structures of Proteins According to Reece et. al.
(2018), protein structures can be identified into 4
layers.
• Primary structure: formed from amino acid sequence
in the polypeptide chain.
• Secondary structure: formed from the oxygen-
hydrogen interactions (called hydrogen bonds) of the
peptide backbone. These structures can be categorized
into two types, alpha helix and beta sheet.
Note: peptide backbone composed of everything in the
amino acid chain (primary structure) except the residual
group (check figure 2).
• Tertiary Structure: formed from the different
interaction of the residual groups of the amino acids
(hydrophobic interactions, interactions with ions/ionic
bonds, hydrogen bonding, disulfide bonds).
• Quaternary Structure: formed from the interaction of
two or more tertiary structures/sub-units.
Protein structure and function can be greatly affected
depending on the level of structure it was
altered/changed. An example happened to people with
Sickle cell anemia.
Based on the figure, the drastic change in the shape of
the blood cell was cause by the change in the amino acid
sequence of the protein hemoglobin. Here are the
mechanisms on how sickle cell affects blood circulation:
1. In low oxygen areas, such as capillaries, red blood cells
with the mutation/changed amino acid sequence will
change their shape from normal to sickle shape.
2. Due to its shape, sickle red blood cells block the
bloodstream, which can affect the oxygen delivery.
3. In severe cases, the clogged sickle cells were destroyed
by white blood cells, which can lower the amount of red
blood cells (anemia).
Nucleic Acid: The Book of Life Nucleic acids, like DNA • Energy source. • Insulation/prevent heat loss.
or RNA are biomolecules, involved in storing genetic • Prevent water loss (for skin and leaves).
information in the form of “genes”. These genes are • Cell membrane component. • Steroid hormone
later translated into the production.
amino acid chains Some lipids, like triglycerides and phospholipids are
(primary structure) by created from condensation reaction of glycerol and
the ribosomes. This fatty acids. These types of lipids can be saturated (solid
process is detailed on in room temperature) or unsaturated (liquid in room
the Central Dogma of temperature). Unsaturation refers to the presence of
Molecular Biology. the double bonds in the fatty acid chains (Reece et.
These genes cab be also al.,2018)
passed from parents to
Carbohydrates: Energy Boosters.
their offspring (basis of
Carbohydrates are biomolecules used by cells as (1) an
heredity)
immediate source of energy; (2) structural support for
DNA means plant cells, fungi cells and exoskeleton of arthropods;
Deoxyribonucleic acid (3) component for other biomolecules such as nucleic
RNA means Ribonucleic acid acids; and (4) for identification of biomolecules,
example for glycoproteins and glycolipids. Carbohydrate
Monomer Profile: Nucleotides. Nucleic acids are
monomers are bonded to form polymers (disaccharides
composed of chains of nucleotides, connected by
and polysaccharides) via glycosidic bonds.
phosphodiester bonds. As illustrated in figure 8,
nucleotides contain (1) phosphate group, (2) Pentose Monomer Profile:
sugar, (3) Nitrogenous base. Monosaccharides. represent the monomer component
of other carbohydrates. Monosaccharides can be
characterized by following:
Nitrogenous bases, such as adenine (A), guanine (G), • Can be composed of multiple carbon, from 3 carbon
cytosine (C), Thymine (T) and Uracil (U), may interact molecule (triose), to 6 carbon molecule (hexose).
in pairs in nucleic acids. • Some monosaccharides have the same molecular
• Guanine to Cytosine formula (C6H12O6), but have different chemical
• Adenine to Thymine (thymine will change to uracil for properties due to the different functional groups
RNA). present in the molecules. These organic molecules are
called isomers (Reece et.al, 2018). (see fig. 13)
Examples: Glucose, Galactose, Fructose, ribose (nucleic
acids)

Lipids: Energy Reservoirs

Lipids or Fats are very hydrophobic substances, which
are composed of long chains of carbon and hydrogen.
Some fats like cholesterol and other steroid hormones
are cyclic (planar shape) instead of chains. Lipid have
different roles in our cells. These are:
Disaccharides are carbohydrates formed from
dehydration/condensation reaction of two
monosaccharides (see figure 14). The common isomer
of disaccharides has the molecular formula of
(C12H22O11). According to Rea et. al (2020), here are
some examples of disaccharides:
• Maltose (Malt sugar): from combination of two
glucose. Can be found in sprouting grains.
• Sucrose (Table sugar): from combination of glucose
and fructose. Found in carrots, sugar cane and fruits.
• Lactose (Milk sugars): from combination of glucose
and galactose.
Polysaccharides: Polysaccharides are complex
carbohydrates, which consist of hundreds to thousand
sugar (monosaccharide) units. They function as storage
molecules or structural component for cells (Reece et.
al, 2018). Here are the following examples of
polysaccharides:
• Starch/Amylose: plants store glucose by forming long
chains of polysaccharide molecule (starch). Plants later
breaks down glucose from starch for energy production.
• Glycogen: A storage carbohydrate for animal cell, with
similar function to starch. Usually stored in liver and
muscle cells.
• Cellulose: a polysaccharide, which is the main
material of plan cell wall.
• Chitin: a structural polysaccharide, which is the main
component of arthropods exoskeleton and fungi cell
walls.
GEN BIO 3: ENZYMES AND ENZYMATIC REACTIONS
One of the very important biomolecules existed are
enzymes. Enzymes are biomolecules (mostly proteins)
that can speed up chemical reaction. In our pre-activity
earlier, the decomposition of hydrogen peroxide was
sped up by an enzyme called catalase. Many of
chemical reactions in our body are speed up by an
enzyme.
Enzymes usually ends with a suffix “-ase”.
Activation energy: is the minimum energy required to
proceed the reaction.
Enzymes are an example of a “catalyst”, made by living
organisms (biocatalyst). In chemistry, catalyst are any
substances that can speed up chemical reaction by
lowering its activation energy
Enzymatic Reactions. are chemical reaction which a
certain enzyme is involved. . Induce fit model shows how enzyme change its shape,
Reactants (the substances/molecules that are needed in
the reaction) are called substrates, which interact with
the enzyme. Take note that enzymes are substrate
specific, which means enzymes only works and interact
with specific substrates. Eventually enzyme will speed up
the chemical reaction, and producing the product.
Different reaction may show enzyme breaking or binding
substrates to form a new product/s.
Enzyme activity happens in three stages:
1. Attachment of the substrate to the active site of the
enzyme. Active site is the region in the enzyme where
the substrate bind sand undergoes chemical reaction.
2.Formation of “Enzyme-Substrate Complex”. This
complex is the reaction intermediate (temporary).
3.Formation of product and released from the enzyme.
Co-factor: Inorganic substances that helps enzymes in
the reaction.
Co-enzymes: organic substances that helps enzymes in
the reaction.
Substrate Specificity of Enzyme in Enzymatic Reaction:
Scientist describes the specificity of enzyme to its
substrate using two models:
1. Lock-and-Key model: proposed by Emil Fischer (Rea
et. al., 2020). According to the model, the specificity
relies on the geometry/shape of both active site of
enzyme and the substrate. The enzyme should match
the substrate in a complementary manner, like jigsaw
puzzle pieces (Farrell & Campbell, 2015).
Lock-and-key mode shows complementary matching of
shape of both enzyme and substrate (jigsaw).
2.Induced Fit model: proposed by Daniel Koshland (Rea
et. al., 2020). The model suggest that the enzyme
changes its shape to fit and temporarily bind with the
substrate (Farrell & Campbell, 2015). This is currently
accepted model because it was able to explain how
different inhibitors affect enzymes (Rea et. al., 2020).
fitting to the shape of the substrate (gloves).
Factors affecting Enzymatic Reactions.
1.Substrate concentration: due to the limited amount
of enzyme in the reaction, the enzyme activity will
increase until it reaches “saturation point”, where the
reaction rate remains the same
.2. Temperature: enzymes have “optimum
temperature” which they will work best. High
temperatures can break the bonds holding the enzyme
structure. Protein based enzymes may have an
irreversible denaturation and permanently inactivate
the enzyme (Rea et. al., 2020).
3. pH: enzymes have “optimal pH”, which they will
work the best. Enzyme outside their optimal pH may
denature, affecting their function and enzymatic
reaction. 4. Presence
of inhibitors: these are substances that can affect
enzyme activity by interacting with the enzymes. The
interaction may be reversible or irreversible.
Denaturation happens for proteins and nucleic acids.
Denaturation loosens some of the bonds that hold the
structure of the biomolecules. Denaturation may be
reversible or irreversible.
How Inhibitors affects Enzymatic reaction:
Inhibitors work in three ways (Reece et. al., 2020):
1. Competitive inhibitor (type of inhibitor) will block the
interaction of enzyme to substrate by interacting itself
to the active site of the enzyme. Ex. Disulfiram as inhibit
or to acetaldehyde dehydrogenase.
2. Non-competitive inhibitor (type of inhibitor) will
prevent the formation of enzyme-substrate complex by
binding to a certain part of the enzyme (but not on the
active site). The binding of the non-competitive
inhibitor will cause to change the shape of active site.
3.Feedback inhibition: cells using feedback inhibition to
regulate the production of a certain substances. The
series of enzymatic reaction (as shown in the figure) will
produced a product that will inhibit one of the enzymes
in the series.
Catalase is a very important enzyme in our body
because it helps degrade hydrogen peroxide in our
body. Hydrogen peroxide is one of the side products in
cellular respiration (specifically aerobic respiration).
Hydrogen peroxide reacts with different substances in
our body, which will produce “reactive oxygen species”
(a type of free radicals). Free radicals damage our cell
by reacting to different biomolecules. Catalase helps
decomposing hydrogen peroxide, reducing the
production of these free radicals.
Free radicals are very reactive molecules which consist
of one or more unpaired electrons.
GEN BIO 5: INTRODUCTION TO CELLULAR METABOLISM
As humans, we get our nutrients and energy from the
food we eat. From food digestion, we absorb nutrients
(especially biomolecules) in our food for the daily activity
of our cells, such as energy production, protein
production, cell repair and many more. These activities
can be summarized in a simple word called metabolism.
According to Reece et. al. (2018), Metabolism describes
the overall reactions happening in a living organism.
Most of these reactions involve breaking and forming
different biomolecules, as we discussed from Course
Material 3. These reactions/ processes can be
interconnected to each other in our body, forming
different metabolic pathways. Today we will discuss how
energy is being produced and consumed in our body via
different types of metabolism.
Anabolism and Catabolism. Metabolism happens in two
ways: 1. Anabolism: refers to the formation of complex
molecules from its small molecular components. The
reaction needed energy to form bonds between these
small molecules (endergonic).
Ex. Photosynthesis for Carbohydrates, ATP synthesis.
Anabolism: forming complex molecules from simple
molecules, needs/absorb energy (endergonic).
2. Catabolism: refers to the reaction involving breaking
down of complex molecules into simple molecules. This
reaction releases energy from the breaking of the bonds
of the complex molecules (exergonic). Ex. Cellular
Respiration for Carbohydrates, ATP hydrolysis.
Catabolism: break down complex to simple molecules,
releases energy (exergonic).
ATP as Energy Currency of the Cell Humans like us need
energy to do work, so do the cells in our body. Many of
the metabolic processes in our body need/produce
energy. With the study of these processes, we will
encounter a very familiar acronym of a certain chemical
called ATP.
ATP means Adenosine triphosphate.
The combination of adenine and ribose is called
adenosine.
ATP has 3 major structure: 1.
Three phosphate groups (triphosphate tail).
2. Adenine (nitrogenous base).
3. Ribose (pentose sugar)
Due to the crowded negative charges, the triphosphate
tail is very unstable, and can be easily hydrolyzed.
Hydrolysis of produces ADP (adenosine diphosphate)
and phosphate ion. This reaction is an example of
catabolic reaction/catabolism, due to the release of
energy.
Energy from ATP hydrolysis couples/partner with
different endergonic reactions (require energy) by
transferring its phosphate to another molecule. This
process is called phosphorylation. shows different cell
activities that requires phosphorylation.
down as we grow older (Shimokata & Kuzuya, 1993).
• Diseases: metabolic rates may change due to
endocrine related disease such as
hypothyroidism/hyperthyroidism. It is recommended by
the experts to eat a balance diet and have an active
lifestyle. Moreover, always consult medical and fitness
professional for specialized fitness activities and diet
suitable for you.

ATP Synthesis , cell in our body uses and recycle 10

million ATP molecules each second. This is possible due
to different mechanism of recycling ATP, by adding back
the lost phosphate to ADP to reform ATP. There are three
processes to reform back ATP from ADP.

1. Substrate-level phosphorylation: ATP is regenerated

by transferring phosphate from a phosphorylated
(phosphate containing) molecule (substrate). This
reaction is accompanied by enzymes (see fig. 6) and
energy for ATP regeneration came from the enzymatic
reaction.

2. Oxidative level phosphorylation: ATP is regenerated

by the movement of electrons. Energy was controllably
released from the moving electrons, which will be used
to regenerate ATP

In redox reaction, Gain Electrons: Reduction (GER)

Loose Electrons: Oxidation (LEO)
NAD: nicotinamide adenine dinucleotide (oxidized
state)
FAD: flavin adenine dinucleotide (oxidized state)

3. Photophosphorylation: This process also involved

ATP regeneration from the movement of electrons,
except electrons were energize first with light energy in
the pigment molecule.

Implications of Metabolism in Health.

The term “fast/slow metabolism” is commonly used to
describe how fast your body uses energy from the food
we eat. People with fast metabolism tend have fast
metabolic rate, consuming much energy in the process.
People with slow metabolism tend to store energy in the
form of fats, since their body uses less energy in its
metabolic processes (Harvard Men's Health Watch,
2018). There are different factors that can affect people’s
metabolic rate:
• Genetics/Hereditary: people have predisposed
metabolic rate based on their genetic make-up.
• Age: based on different studies, our metabolism slows