GEN BIO 1: INTRODUCTION TO CELL
BIOLOGY
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 cell reflect the observable
characteristics of a living organism, and some even exist
as a singular living cell.
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 publish his
illustrations and observation of cells, which he called
“animalcules” on 1678.
Cell Theory and Spontaneous Generation.
Early people believed in the theory of “Spontaneous
Generation”, which states that non-living things can
produce living organism, 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
neck bottle experiment”.
•
Based on the spontaneous generation theory, what would be
the expected results from both flask after boiling?
• 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 organism 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 another 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 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 sub-units 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 shipped within the cell, or become lysosome. Shipping
outermost layer of the cell (for animal cells). Regulates out material via transport vesicles provides new layer
transportation of materials in and out of the cells. for the cytoplasm.
Mostly composed of phospholipid bilayer. Proteins can
Based on the cell parts and structure, there are two
be seen scattered and embedded to the plasma
distinguished groups of organisms.
membrane.
Prokaryotes: usually smaller in sized compared to
Extra Cellular Matrix: composed of collagen (protein)
eukaryotes. Prokaryotic cells do not have nucleus and
fibers and glycoprotein, which helps protect and
membrane bound organelles (Reece et. al, 2018).
support the plasma membrane. It is situated outside the
Eukaryotes: characterized with cell containing nucleus
cell and exist in animal cells.
and membrane bound organelles (Reece et. al, 2018).
Cell wall: protect and holds the cells in shape.
- Cell wall composition varies in different organisms: Currently, taxonomists use Three-domain system,
which uses molecular and genomic studies as basis for
- Plant cell wall: Cellulose
this grouping.
- Bacteria cell wall: Peptidoglycan
Domain Bacteria: Prokaryotes with peptidoglycan cell
- Fungi: Chitin
wall.
- Plant cell wall in fruits contain pectin layer, which
Domain Archaea: Prokaryotes that can survive in
degrades upon ripening.
extreme conditions.
- Holes in the plant cell wall (as shown in figure) are
Ex. Thermophiles: “heat lovers”, can survive in hot
called plasmodesmata, which allow water and other
temperature.
materials to move from cell to cell.
Methanogens: “Methane lovers”, lives in methane rich
Cilia: very small locomotory organ, covering the cell’s
environment.
exterior. The cilia are moving in an undulatory motion
Halophiles: “Salt lovers”, lives in very salty places.
(back and forth).
Domain Eukarya: contains all eukaryotic organisms.
Flagellum: long locomotory organ that moves in a
Major kingdoms and groups, Protist, Fungi, Animals and
propeller like motion.
Plants, are members of this domain.
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,

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.
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.

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)
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 or
RNA are biomolecules, involved in storing genetic
information in the form of “genes”. These genes are later
translated into the amino acid chains (primary structure)
by the ribosomes. This process is detailed on the Central
Dogma of Molecular Biology. These genes cab be also
passed from parents to their offspring (basis of heredity)
DNA means Deoxyribonucleic acid
RNA means Ribonucleic acid
Monomer Profile: Nucleotides. Nucleic acids are
composed of chains of nucleotides, connected by
phosphodiester bonds. As illustrated in figure 8,
nucleotides contain (1) phosphate group, (2) Pentose
sugar, (3) Nitrogenous base.
Nitrogenous bases, such as adenine (A), guanine (G),
cytosine (C), Thymine (T) and Uracil (U), may interact in
pairs in nucleic acids.
• Guanine to Cytosine
• Adenine to Thymine (thymine will change to uracil for
RNA).
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:
• Energy source. • Insulation/prevent heat loss.
• Prevent water loss (for skin and leaves).
• Cell membrane component. • Steroid hormone
production.
Some lipids, like triglycerides and phospholipids are
created from condensation reaction of glycerol and fatty
acids. These types of lipids can be saturated (solid in room
temperature) or unsaturated (liquid in room temperature).
Unsaturation refers to the presence of the double bonds in
the fatty acid chains (Reece et. al.,2018)
Carbohydrates: Energy Boosters.
Carbohydrates are biomolecules used by cells as (1) an
immediate source of energy; (2) structural support for
plant cells, fungi cells and exoskeleton of arthropods;
(3) component for other biomolecules such as nucleic
acids; and (4) for identification of biomolecules,
example for glycoproteins and glycolipids. Carbohydrate
monomers are bonded to form polymers (disaccharides
and polysaccharides) via glycosidic bonds.
Monomer Profile:
Monosaccharides. represent the monomer component
of other carbohydrates. Monosaccharides can be
characterized by following:
• Can be composed of multiple carbon, from 3 carbon
molecule (triose), to 6 carbon molecule (hexose).
• Some monosaccharides have the same molecular
formula (C6H12O6), but have different chemical
properties due to the different functional groups
present in the molecules. These organic molecules are
called isomers (Reece et.al, 2018). (see fig. 13)
Examples: Glucose, Galactose, Fructose, ribose (nucleic
acids)
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. . which they will work best. High temperatures can break the
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). Induce fit
model shows how enzyme change its shape, 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”
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.
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 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.