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 • From figure 3, how can Pasteur disprove spontaneous
the 1600’s led to the first observation of cork plant cells generation theory?
under microscope by Robert Hooke. He first used the Based on the spontaneous generation, both flasks should
word “cells”, as he described those cells as “chamber show signs of living cells in the broth. But due to the
like” structures (Rea et. al, 2020). Later shape of the flask’s neck, living cells cannot pass directly
on, Anton van Leuwenhoek published his illustrations inside the flask, making the broth inside sterile or free
and observation of cells, which he called “animalcules” with living cells. This experiment supports one of the
in 1678. statements in our cell theory, “living cells arise from
Cell Theory and Spontaneous Generation. another living cells” (Reece et. al, 2018). On the
succeeding years, development in the cell biology
Early people believed in the theory of “Spontaneous reached out to the accepted statements in the cell
Generation”, which states that non-living things can theory.
produce living organisms, such as maggots from rotten
meat or fishes from mud (Reece et. al, 2018). 1.Cell is the fundamental structural unit of life (Reece
Several scientists in the past tried to disprove and et. al, 2018)
support spontaneous generation. One scientist, Louis 2. Living organisms are composed of cells-combined
Pasteur, disproved this theory by his famous “Swan
 subunits.
from the conclusion of Matthias Schleiden for plants
and Theodor Schwann for animals (Rea et. al, 2020). - They can be free floating in cytoplasm or attached in
3.Living cells arise from other living cells. -Derived the rough endoplasmic reticulum.
from the research of Rudolf Virchow and Robert Rough Endoplasmic Reticulum (rough ER): Site of
Remak. protein synthesis, due to the presence of the attached
ribosomes. It is also responsible with the attachment of
glycoproteins.
Review: Parts of the Cell. In a far away city called Grant Smooth Endoplasmic Reticulum (smooth ER): site for
City, the main export and production product is the steel lipid production, steroid hormone production. It is also
widget. Everyone in the town has something to do with responsible to metabolism of drugs, alcohol and other
steel widget making and the entire town is designed to harmful substances (very important in the liver cells). -
build and export widgets. The town hall has the Sarcoplasmic reticulum: in muscle cells, smooth ER can
instructions for widget making, widgets come in all store calcium ions. Calcium ions are important for the
shapes and sizes and any citizen of Grant can get the contraction and relaxation in the muscle cells.
instructions and begin making their own widgets. Golgi Bodies (Golgi Apparatus / Golgi Complex):
Widgets are generally produced in small shops around Packaging center of the cells. It receives proteins from
the city, these small shops can be built by the carpenter's rough ER and modifies proteins for distribution outside
union (whose headquarters are in town hall). After the and within the cells.
widget is constructed, they are placed on special carts Lysosome: Filled with enzymes, lysosomes break down
which can deliver the widget anywhere in the city. In damaged organelles, food material and pathogens. Can
order for a widget to be exported, the carts take the be only found in animal cells.
widget to the postal office, where the widgets are Vacuole: A membrane bound organelle with specialized
packaged and labeled for export. Sometimes widgets functions.
don't turn out right, and the "rejects" are sent to the - Central Vacuole: largest organelle in plant cells. Can
scrap yard where they are broken down for parts or store food, pigments, water, waste and poisonous
destroyed altogether. The town powers the widget shops substances (that can deter plant eaters). It is also acidic,
and carts from a hydraulic dam that is in the city. The similar to lysosomes in animal cells.
entire city is enclosed by a large wooden fence, only the - Food Vacuole: use to deliver ingested materials from
postal trucks (and citizens with proper passports) are outside the cell (see lysosome figure).
allowed outside the city. - Contractile Vacuole: can be found in some freshwater
protist. Use to collect water (osmoregulation).
Cell Parts and Function
Nucleus- a region in the cell where the DNA was stored. Peroxisome: helps break down lipids and hydrogen
It serves as the command center in the cell. It has three peroxide.
distinguishable features. (town hall) Chloroplast: site of photosynthesis (production of food
- It was encased in a phospholipid bilayer sheet called in the form of carbohydrates), and can be only found in
nuclear envelope. The nuclear envelope has pores plant cells. Due to its role in photosynthesis, it also
which selectively allow the passage of materials in and stores chlorophyll pigments. It has double layered
out of the nucleus. membrane, and has its own genetic material (DNA and
- The “cloudy” or the light and dark regions (pink in the RNA) and ribosomes.
drawing) inside the nucleus are composed of different Mitochondria (sing. Mitochondrion): a double
complexes of DNA and proteins called chromatin. membraned organelle, which produces ATP via aerobic
- The large dark blob in the nucleus is the nucleolus. respiration. Same as chloroplast, with its own DNA, RNA
This is where ribosomal RNA is produced, and RNA and ribosomes.
subunits are assembled.
Cytoskeleton: provides support, anchorage and aid
- Prokaryotes do not have a nucleus. Instead, their DNA
movement for the cell.
is clumped in one area, called the nucleoid region.
- Microtubule: - Largest cytoskeleton element. Consist
Ribosomes: responsible for production of protein
of two subunits of tubulin(protein), forming a hollow
(protein synthesis).
tube. - Guide movement of cellular component.
- Composed of 2 subunits, large subunits and small
- Main component of locomotory organelles cilia and the steps on how proteins like insulin is produced in this
flagellum. system.
- Intermediate Filament: - Cable like. Composed of 1. The nucleus will give the “instruction” (in the form of
different fibrous proteins. messenger RNA) to the ribosome attached to the rough
- Helps in anchorage of different cell parts. ER.
- Microfilament: - Smallest among the cytoskeleton 2. Attached ribosomes will synthesize the amino acid
element. - Twisted, double chain of actin proteins. sequence (primary structure of the protein) from the
- Supports the cell’s shape. - Movement in muscle cells. messenger RNA. (see fig. 3)
Centrosome: organelle found only in animal cell. It has 3. The protein will undergo major changes in rough ER.
two centrioles, which produces microtubules (mitotic This will include protein folding and attachment of
spindles/spindle fibers) during cell division. glycoprotein (molecular marker). (see fig. 3)
Cytoplasm: The region between the plasma membrane 4. The protein will be shipped out of the rough ER and
and nucleus. transferred to Golgi bodies using transport vesicles.
- Cytosol: fluid in the cytoplasm. 5. The protein will undergo more modification while it
passes each lumen of the Golgi bodies.
Plasma Membrane: also known as cell membrane, is the
6. The proteins either be shipped out to the cells,
outermost layer of the cell (for animal cells). Regulates
shipped within the cell, or become lysosome. Shipping
transportation of materials in and out of the cells. Mostly
out material via transport vesicles provides new layer
composed of phospholipid bilayer. Proteins can be seen
for the cytoplasm.
scattered and embedded to the plasma membrane.
Extracellular Matrix: composed of collagen (protein) Based on the cell parts and structure, there are two
fibers and glycoprotein, which helps protect and support distinguished groups of organisms.
the plasma membrane. It is situated outside the cell and Prokaryotes: usually smaller in sized compared to
exist in animal cells. eukaryotes. Prokaryotic cells do not have nucleus and
membrane bound organelles (Reece et. al, 2018).
Cell wall: protect and holds the cells in shape.
Eukaryotes: characterized with cell containing nucleus
- Cell wall composition varies in different organisms:
and membrane bound organelles (Reece et. al, 2018).
- Plant cell wall: Cellulose
Currently, taxonomists use Three-domain system,
- Bacteria cell wall: Peptidoglycan
which uses molecular and genomic studies as basis for
- Fungi: Chitin
this grouping.
- Plant cell wall in fruits contain pectin layer, which
Domain Bacteria: Prokaryotes with peptidoglycan cell
degrades upon ripening.
wall.
- Holes in the plant cell wall (as shown in figure) are
Domain Archaea: Prokaryotes that can survive in
called plasmodesmata, which allow water and other
extreme conditions.
materials to move from cell to cell.
Ex. Thermophiles: “heat lovers”, can survive in hot
Cilia: very small locomotory organ, covering the cell’s temperature.
exterior. The cilia are moving in an undulatory motion Methanogens: “Methane lovers”, lives in methane rich
(back and forth). environment.
Flagellum: long locomotory organ that moves in a Halophiles: “Salt lovers”, lives in very salty places.
propeller like motion. Domain Eukarya: contains all eukaryotic organisms.
Both of them are composed of nine pairs of Major kingdoms and groups, Protist, Fungi, Animals and
microtubules and 2 central microtubules (9+2). Plants, are members of this domain.

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
 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
GEN BIO 2: PLASMA MEMBRANE AND CELL TRANSPORT that pass the membrane. Selective permeability means
that, in a certain membrane, some molecule can pass
Plasma membrane or cell membrane is one of the very easily than other substances (Freeman et. al, 2017).
important structure in our cells because it helps Based on figure 4, gases/non-polar molecules and
regulate movement of materials and waste (inward or small polar molecules can pass easily the bilayer. Large
outward). In animal cells, plasma membrane keeps the polar molecules (like glucose) and ions may have a
cellular content inside the cell. difficulty passing the bilayer. To compensate the low
Properties of the Cell Membrane: “Fluid Mosaic permeability of some substances, carrier proteins are
Model”. needed to transport these substances across the
membrane.
Membrane fluidity: phospholipids and other • Symporter: both molecules transported in same
component of the plasma membrane can move around, direction (ex. Sodium-Glucose transporter).
due to the spaces provided by the “bents” in the • Antiporter: transport two molecules in opposite
phospholipid tails. (see fig. 5). According to Freeman et. directions (ex. Na+/K+ pump).
al (2017), phospholipid bilayer increases permeability in IV. Glycoproteins and Glycolipids:
high temperature, but in return can weaken the Glycolipids: lipids with carbohydrates attached to them.
bilayer*. The presence of cholesterol helps strengthen Glycoproteins: proteins with carbohydrates attached
the phospholipid bilayer, especially in high from them. Both glycolipids and glycoproteins are
temperatures important for cell-to-cell recognition and signaling
III. Membrane Proteins: (Freeman et. al, 2017).
Membrane proteins can be found around the plasma
Passive Transport: Diffusion and Facilitative Diffusion.
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. in a membrane system, like plasma membrane,
- Transport molecules across membrane. diffusion is always described as movement of
- Attachment of cells to other cells (see junction molecules from higher concentration to lower
proteins). Peripheral Membrane Proteins: membrane concentration, until it reaches equilibrium. But, as we
proteins that are located at the surface of the plasma discussed earlier, some molecules (such as ions and
membrane (inside or outside the cell), interacting with large polar substances) cannot pass easily across the
the hydrophilic heads of the phospholipid bilayer. plasma membrane. Diffusion would be possible for
Trans-membrane/Integral Membrane Proteins: these molecules with the help of different membrane
membrane proteins that are embedded across the protein. This type of diffusion is called facilitated
membrane. diffusion. One of the examples of this is the transport of
Specialized Integral Membrane Proteins: water molecules using a membrane protein called
- Channels: proteins that allows the passage of certain aquaporins. Aquaporins are very important to plant
molecules freely. cells, kidney cells (Reece et. al, 2018) and large intestine
Ex. Ion channels: responsible for transport of ions (Ma & Verkman, 1999) for water absorption.
across membrane. * Concentration Gradient: describes the difference of
Aquaporins: type of channel which help transport water concentration of molecules on the both side of the
molecules. membrane system.
- Carrier Proteins: unlike channels, carrier proteins need Passive Transport: Osmosis.
to change their shape to transport their molecules
successfully.
Ex. Sodium-Potassium Pump (Na+ /K+ Pump) Sodium-
Glucose transporter

- Uniporter: transport one molecule only. Osmosis is defined as movement of water from low
- Co-transporter: transport two molecules. 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 On the other hand, active transport is movement of
membrane and interact with the solute from the other molecules from low concentration to higher
side, until it reaches equilibrium. In this case, we can concentration, which would require energy (in form of
also describe osmosis as movement of free water ATP) for this transport. According to Freeman et. al.
molecules from solution with higher free water (2017), there are two types of active transport.
molecules to solution with lower free water molecules. Primary Active Transport: Directly uses energy (ATP)
Osmosis can also affect cells in many ways, with plasma for transport.
membrane as the “semi-permeable membrane”. We Secondary Active transport: indirectly uses ATP. The
can describe solutions based on their tonicity, which transport was driven on the changes of electrochemical
describes as the ability of the surrounding solutions to gradient* by another primary active transporter inside
make the cell loose or gain water. the cell.
Osmosis happens in two solutions, separated by semi- * Electrochemical Gradient forms due to the difference
permeable membrane. of the ion concentration, creating a partial charge inside
Solution = Solute + Solvent (Water) and outside the cell
Here is the summary of tonicity of solution and their
*Sodium-Glucose Transporter/SGLUT: Found in
effect on cells.
intestine and kidney cells. This transporter is used to
Hypotonic: If the solution has less solute than the other
absorb glucose from digested food and urine.
solution. This solution tends to lose “free” water,
favoring the water movement towards solution with Bulk Transport: Exocytosis and Endocytosis.
more solute. For transport of larger molecules (such as complex
Hypertonic: If the solution has more solute than the carbohydrates, proteins, fats), they will be enclosed in a
other solution. This solution tends to gain “free” water membrane bound sac composed of materials, as similar
from the solution with less solute. as the plasma membrane. This transport is called
Isotonic: The solution has equal solute concentration to vesicle-mediated transport (Rea et. al, 2020) or bulk
other solution. Since both solutions are in equilibrium, transport. The transport works with molecules going in
free water passes through in and out of the cell, (endocytosis) or going out (exocytosis) of the cell.
describing as “no net water movement”. Exocytosis usually involves with the transport of
*Note: the following description on the figure describes proteins and hormones from the cell (via
solution outside the cell (environment). endomembrane system). Vesicles used for exocytosis
Any cellular transport that does not require energy are will merge with the plasma membrane.
called passive transport. Passive transport is also Endocytosis can be classified into three types.
characterized with movement of molecules from high - Phagocytosis: “cell-eating”. It is used to transport
concentration to lower concentration. large food materials.
Passive Transport: Diffusion, Facilitative Diffusion, - Pinocytosis: “cell-drinking”. It is used to transport
Osmosis. liquid substances in large amount.
* Plant cell needed to maintain a turgid state for - Receptor-mediated endocytosis: It is used to transport
support, otherwise water loss causes the plant cell to specific type of molecules. Vesicles contains receptors
plasmolyze (and the plant looked wilted). inside to bind specific molecules, while vesicles outside
Active Transport. have surrounding coated proteins.
* Bulk transport needs energy to transport molecules,
just like active transport. 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.
GEN BIO 3: THE WORLD OF BIOMOLECULES • Primary structure: formed from amino acid sequence
in the polypeptide chain.
According to Merriam-Webster dictionary, biomolecules • Secondary structure: formed from the oxygen-
are substances that are produced by living organisms. hydrogen interactions (called hydrogen bonds) of the
Most of our food we eat are composed of different peptide backbone. These structures can be categorized
biomolecules, which we can read on their food label. In into two types, alpha helix and beta sheet.
today’s lesson, we will learn in this module that
different biomolecules have different roles and Note: peptide backbone composed of everything in the
functions in our cell. Forming and Breaking amino acid chain (primary structure) except the residual
Macromolecules. Biomolecules in our body can exist in group (check figure 2).
big amounts. One of those biomolecules in our body are • Tertiary Structure: formed from the different
called macromolecules, a type of nutrients which we interaction of the residual groups of the amino acids
need in large amounts. Cell our body may (1) creates (hydrophobic interactions, interactions with ions/ionic
these macromolecules by combining small units (called bonds, hydrogen bonding, disulfide bonds).
monomers) via dehydration/condensation reaction (to • Quaternary Structure: formed from the interaction of
form a polymer) or (2) break down these two or more tertiary structures/sub-units.
macromolecules into individual monomers via
Protein structure and function can be greatly affected
hydrolysis.
depending on the level of structure it was
* Unsaturated fats, like vegetable oil, are liquid in room altered/changed. An example happened to people with
temperature (more or less 20℃). Sickle cell anemia.

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