General Biology 1

Module 6: Transport Mechanism/Cell Membrane

Structure and Composition of The Cell membrane to
its Function
Terms To Know
● Concentration – the amount of solute in a
solution.
● Solute – the dissolved substance in a solution.
A boundary that separates the living cell from
● Solution – a mixture in which two or more
its non-living surroundings.
substances are mixed evenly.
Phospholipid bilayer
● Concentration gradient - the gradual
Amphipathic - having both:
difference in the concentration of solutes in a
solution between two regions.
Cell Membrane and Cell Wall:
ALL cells have a cell membrane made
of proteins and lipids

~8 nm thick
Is a dynamic structure
Cell Membrane Structure:
A mosaic of lipids, proteins, and carbohydrate,
embedded in a fluid bilayer of phospholipids
SOME cells have cell membranes and cell walls –
Why is fluidity important?
ex: plants, fungi, and bacteria
The membrane must be fluid to work properly.
Solidification may result in permeability changes
Unsaturated hydrocarbon tails enhance membrane
fluidity because kinks at the carbon-to-carbon
double bonds hinder close packing of
phospholipids.

The function of the Cell Membrane:

The cell membrane separates the components of a
cell from its environment—surrounds the cell
“Gatekeeper” of the cell—regulates the flow of
materials into and out of the cell—selectively
permeable
Cell membrane helps cells
maintain homeostasis—stable internal balance
What else helps to keep membrane fluidity?
Cholesterol (Temperature Buffer)
Cholesterol allows the cell membrane to stay fluid
(esp. when the temp drops), while at the same time
keeping the cell from becoming too fluid (when the
temp rises) that it can no longer hold its shape.
 Since Symporter and antiporters allow multiple
molecules to pass through the membrane, it
doubles the rate of molecule transport. Symporter
and antiporters are commonly
called COTRANSPORTERS.
TRANSMEMBRANE TRANSPORTS
Different proteins allow the passage of materials in
the cell
THREE MAIN TYPES OF MEMBRANE TRANSPORT
PROTEINS (Gradients are indicated by triangles with
the tip pointing toward lower concentration,
electric potential, or both.)
1.CHANNELS/ CHANNEL PROTEINS - transport water,
3.ATP POWERED PUMPS - (or simply pumps) are
specific ions, or hydrophilic small molecules across
ATPases that use the energy of ATP hydrolysis to
membranes down their concentration or electric
move ions or small molecules across a membrane
potential gradients - Channels form a hydrophilic
against a chemical concentration gradient, an
“tube” or passageway across the membrane
electric potential, or both
through which multiple water molecules or ions
An example is ABC (ATP binding
move simultaneously, single file, at a very rapid rate
cassette) Transporter
● NONGATED CHANNELS - channels are open
much of the time
● GATED CHANNELS - open only in response to
specific chemical or electrical signals

Module 7: Passive Transport

● Refers to the passage of molecules within a
semi-permeable membrane.
● The movement of molecules is from an area of
2.TRANSPORTERS - (also called carriers) move a wide
higher concentration gradient to an area of a
variety of ions and molecules across cellular
lower concentration gradient. (moving down
membranes, but at a much slower rate than
the concentration gradient)
channels. - There are three types of transporters:
● A cell doesn’t use energy
a. Uniporter - transport a single type of molecule
Example of Passive Transport
down its concentration gradient. Glucose and
1. Diffusion
amino acids cross the plasma membrane into most
2. Osmosis
mammalian cells with the aid of uniporters.
3. Facilitated Diffusion
Collectively, channels and uniporters are sometimes
Diffusion is the movement of small particles across
called facilitated transporters, indicating movement
a selectively permeable membrane like the cell
down a concentration or electrochemical gradient.
membrane until equilibrium is reached.
b. Symporter – transports more than one type of
These particles move from an area of high
molecule against its concentration gradient in the
concentration to an area of low concentration.
same direction
Osmosis is the diffusion of water through a
c. Antiporter - transports more than one type of
selectively permeable membrane like the cell
molecule against its concentration gradient in the
membrane
opposite direction
Water diffuses across a membrane from an area
of high concentration to an area of low
concentration.
A semi-permeable membrane is permeable to
water, but not to sugar
The passage of water is dependent on the
concentration extra and intracellular.
There are 3 different solutions where a cell can be
submerged.
● Result: Water moves equally in both directions
and the cell remains the same size! (Dynamic
Equilibrium)
Facilitated Diffusion is the movement of larger
molecules like glucose through the cell membrane
– larger molecules must be “helped”
● Proteins in the cell membrane
form channels for large molecules to pass
through
● Proteins that form channels (pores) are
called protein channels

Different Concentration in a Solution

Hypotonic Solution
● The solution has a lower concentration of
solutes and a higher concentration of water
than inside the cell. (Low solute; High water)
● Result: Water moves from the solution to inside
the cell): Cell Swells and bursts open (cytolysis)!
Hypertonic Solution
● Hypertonic: The solution has a higher
concentration of solutes and a lower
concentration of water than inside the
cell. (High solute; Low water)
● Result: Water moves from inside the cell into the
solution: Cell shrinks (Plasmolysis)!
Module 8: Active Transport
Active and Bulk Transport
Active Transport
● Active transport is the movement of molecules
from LOW to HIGH concentration.
● Energy is required as molecules must
be pumped against the concentration
gradient.
● Proteins that work as pumps are called protein
pumps.
Example:
1. Body cells must pump carbon dioxide out into
the surrounding blood vessels to be carried to
the lungs for exhale. Blood vessels are high in
carbon dioxide compared to the cells, so
energy is required to move the carbon dioxide
across the cell membrane from LOW to
HIGH concentration.

Isotonic Solution
● The concentration of solutes in the solution is
equal to the concentration of solutes inside the
cell.
2. SODIUM-POTASSIUM PUMP In every 2 K+ that ● They are protein-derivatives thus made from
enters the cell there will be 3 Na+ moving out amino acids or polypeptide chains
expending 1 ATP molecule. ENZYME STRUCTURE
BULK TRANSPORT - Happens when large amount of
materials passes through the membrane.
● Endocytosis and Exocytosis is the mechanism by
which very large molecules (such as food and
wastes) get into and out of the cell.
● Food is moved into the cell by Endocytosis
● Wastes are moved out of the cell by Exocytosis

1. COENZYME/COFACTOR - It activates the

apoenzyme. A COENZYME is a vitamin derivative
while a COFACTOR is a mineral derivative
2. APOENZYME - inactive form of an enzyme. when
a cofactor or coenzyme activates the apoenzyme,
the complex is called a HOLOENZYME
3. ACTIVE SITE - the site where the substrate will bind.
4. SUBSTRATE - A molecule where an enzyme will act
upon. When a substrate is bonded in the active site,
we call it the Enzyme-Substrate complex
1. Endocytosis - Happens when large amount of
An enzyme acts upon a substrate by enhancing the
materials enters the cell.
capability of a chemical reaction to act. in a
Pinocytosis – Cell drinking. Liquid enters the cell
chemical reaction, the enzyme catalyzes the
Phagocytosis – Cell eating. Solids enter the cell
reaction but will not affect the chemical
Ex: White Blood Cells, which are part of the immune
composition of a chemical reaction just like a real
system, surround and engulf bacteria
inorganic catalyst.
by endocytosis.
How an enzyme acts in organic compounds and
biomolecules can be explained by two models:
MODELS OF ENZYME ACTION
1. Lock And Key Model
● Enzymes are specific. This high specificity of
enzymes can be explained by this lock and key
model.
● According to the lock and key model, enzymes
2. Exocytosis - Happens when large amount of will only act upon a specific substrate.
materials exits the cell.
Forces material out of cell in bulk.
● membrane surrounding the material fuses with
cell membrane
● Cell changes shape – requires energy
● EX: Hormones or wastes released from cell
2. Induced Fit Model
Module 9: Biomolecules
● When the active site on the enzyme contacts
Enzymes
the proper substrate, the enzyme molds itself to
● Are biological catalysts
the shape of the molecule
● They speed up the rate of chemical reactions
by lowering its activation energy
● This theory of enzyme-substrate interactions has
two advantages compared to the lock and key
model:
It explains how enzymes may exhibit broad
specificity (e.g., lipase can bind to a variety of
lipids)
It explains how catalysis may occur (the
conformational change stresses bonds in the
substrate, increasing reactivity)
Enzyme Reactions
ENZYMES AND ACTIVATION ENERGY
In order for a chemical reaction to move forward,
activation energy is required. Activation Energy is
the amount of energy that is required for chemical
energy to proceed.
The peak of the required activation energy for a
specific chemical reaction is called a Transition
State. The Transition State is very unstable in nature.
Because of its instability, reactant molecules don’t
stay there long but quickly proceed to the next step
of the chemical reaction.
The higher the transition state, more activation
energy will be required for a chemical reaction to
move forward.
The activation energy of a chemical reaction is
closely related to its rate. Specifically, the higher the
activation energy, the slower the chemical reaction
will be. This is because molecules can only start the
reaction once they have reached the transition
state. The higher the transition state is, the fewer
molecules that will have enough energy to make it
over at any given moment.
The role of catalysts is to lower the activation
energy of the chemical reaction without changing
the composition of the reactants. since there is no
change in the reactants, there will be no change in
the product. thus, making the chemical reaction
faster.
Factors Affecting Enzyme Activity
Enzymes work best under specific conditions.
sub-optimal conditions can cause an enzyme to
lose its ability to bind to a substrate.
Temperature
● Raising temperature generally speeds up a
reaction, and lowering temperature slows down
a reaction. However, extremely high
temperatures can cause an enzyme to lose its
shape (denature) and stop working.
● each enzyme has a certain temperature at
which it is more active. This point is called
the optimal temperature, which ranges from 37
to 40C°.
● The enzyme activity gradually lowers as the
temperature rises more than the optimal
temperature until it reaches a certain
temperature at which the enzyme activity stops
completely due to the change of its natural
composition.
● On the other hand, if the temperature lowers
below the optimal temperature, the enzyme
activity lowers until the enzyme reaches a
minimum temperature at which the enzyme
activity is the least. The enzyme activity stops
completely at 0°C but if the temperature rises
again, then the enzyme gets reactivated once
more.
 (ADENOSINE TRIPHOSPHATE) ATP is a nucleotide
consisting of adenine, ribose, and three phosphate
groups. it is quoted to be the energy currency of
the body. it is spent to acquire energy.

pH (Power of Hydrogen)
● Each enzyme has an optimum pH range.
Changing the pH outside of this range will slow
enzyme activity. Extreme pH values can cause
enzymes to denature, slowing and stopping the
enzyme activity
● For example, pepsin (a digestive enzyme that
breaks down proteins) works at a low pH, i.e., it
is highly acidic, while trypsin (a digestive
enzyme that digest proteins) that works at a
high pH, i.e., it is basic. Most enzymes work at
neutral pH 7.4.
This biochemical pathway (ATP-ADP Cycle)
happens when an ATP molecule
undergoes hydrolysis reaction. Hydrolysis happens
when a water molecule breaks the bond between
a phosphoanhydride (oxygen-phosphorus linkage)
linkage setting a free phosphate molecule forming
Adenosine diphosphate (ADP). An enzyme ATPase
will be used for this reaction

Substrate concentration
● Increasing substrate concentration also
increases the rate of reaction to a certain point.
Since this is a cyclic reaction, the ADP will
Once all of the enzymes have bound, any
undergo Phosphorylation, the linking of a free
substrate increase will not affect the rate of
inorganic phosphate to ADP to form ATP and
reaction, as the available enzymes will be
releasing water. An enzyme ATPSynthase will help
saturated and working at their maximum rate.
this chemical reaction to move forward
● In other words, the enzyme molecules are
saturated with substrate. The excess substrate
molecules cannot react until the substrate
already bound to the enzymes that have
reacted and been released (or been released
without reacting).

The Chloroplast
is a plant cell organelle that belongs to the family
of Plastids that holds the chlorophyll pigment and is
Module 10: Energy Transformation found inside the mesophyll layer of leaves. This
Adenosine Triphosphate (ATP) organelle is the site of photosynthesis
ATP - ADP CYCLE
The ATP - ADP Cycle is an energy-producing
process inside an organism. this involves two major
processes, Hydrolysis, and Phosphorylation.
Parts of a Chloroplasts
1. Double Membrane - the chloroplast is
enveloped by a bilipid layer where molecules
pass-through
2. Stroma - the spaces inside the chloroplast
where the light-independent reaction of
photosynthesis happens. it surrounds the grand
3. Thylakoid - it is the coin-like structure in the
chloroplast. The Thylakoid is site of the
light-dependent reactions and is where we can
find the chlorophyll. a stack of thylakoids is
called a granum (grana if plural). a granum is
composed of 10-20 thylakoids.
CHLOROPHYLL
are pigments that absorb light
from red to blue spectra. this is the main
photosynthetic pigment.
Chlorophyll consists of a porphyrin ring and
a hydrocarbon side chain. The porphyrin ring, with
a magnesium atom in its center, contains a system
of alternating double and single bonds; these
bonds are commonly found in molecules that
strongly absorb certain wavelengths of visible light
and reflect others (chlorophyll reflects green). Note
that at the top right corner of the figure 10.5,
the methyl group (—CH3) distinguishes chlorophyll
a from chlorophyll b, which has a carbonyl
group (—CHO) in this position. The hydrophobic
hydrocarbon side chain anchors chlorophyll to the
thylakoid membrane.
while chlorophyll a is the main photosynthetic
pigment that reflects green to yellow light, other
pigments found in the chloroplasts are
considered accessory pigments namely: (a)
Chlorophyll b and (b) Carotenoids (c) Lutein.
Accessory pigments absorb the light that cannot
be absorbed by Chlorophyll a. The energy
absorbed from these accessory pigments will be
passed to Chlorophyll a sufficing the limitations of
the pigment and broadening the energy absorbing
capacity of the plant
Module 11: Photosynthesis (Part 1)
Introduction to Photosynthesis
Photosynthesis – the process by which autotrophs
use light energy to convert carbon dioxide and
water to glucose and oxygen
Photons – light energy photons are very in the
process of photosynthesis
When a molecule absorbs a photon of light energy,
one of its electrons becomes energized, and one of
two things happen:
1. The atom may return to its lower-energy ground
state and energy dissipates as heat or
fluoresces
2. The energized electron may leave the atom
and be accepted by an electron acceptor
molecule (redox)
Photosynthesis is divided into two phases:
● Light-dependent reactions (photo part of
photosynthesis)
● Carbon fixation reactions (synthesis part of
photosynthesis)
The light-dependent reactions in the thylakoids
capture energy as ATP and NADPH, which power
the carbon fixation reactions in the stroma.
Non-cyclic Photophosphorylation
In the presence of light, there is a continuous,
one-way flow of electrons from H2O to NADP+
These are the steps for the Non-cyclic
Photophosphorylation:
1. A photon strikes chlorophyll from photosystem II.
Because of this, one electron jumps to a higher
energy level
2. This electron is then transferred to the primary
electron acceptor (plastoquinone)
Light-Dependent Reactions
3. An enzyme catalyzes and splits a water
Light-dependent reactions:
molecule into 2 electrons, 2 H+ and an Oxygen.
● Convert light energy to chemical energy
H+ is then transferred to the thylakoid space.
● Take place in thylakoids
The oxygen will combine with another Oxygen
● Begin as soon as chlorophyll captures light
to form O
energy
4. each electron passes from one electron
● Energized electron is transferred to an acceptor
acceptor to another.
molecule, and is replaced by an electron from
5. The passing of electron to a lower energy level,
H2O
it gives rise to the synthesis of ATP. H+ is pushed
● H2O is split and molecular oxygen is released
inside the thylakoid
● The energy of energized electrons is used to
6. Another photon will strike Photosystem I
phosphorylate ADP, forming ATP
7. The excited electron is being passed again to
● The coenzyme NADP+ becomes reduced,
another electron transport chain to the
forming NADPH
Ferredoxin. This does do no,5
● ATP and NADPH are used in the
8. The enzyme NADP+ Reductase catalyzes the
energy-requiring carbon fixation reactions
transfer of an electron from Ferredoxin to
PHOTOSYSTEMS
NADP+ then forms NADPH. NADPH will be used
● Composed of a reaction center complex
in the Calvin Cycle.
surrounded by several chlorophylls
● Two types of photosynthetic units are involved in
photosynthesis
o The reaction center of photosystem I (P700)
consists of two chlorophyll a molecule with
an absorption peak at 700 nm
o The reaction center of photosystem II
(P680) consists of two chlorophyll a molecule
with an absorption peak of 680 nm

CHEMIOSMOSIS
Energy from electrons passing through ETC is used
to pump protons from stroma into thylakoid lumen,
forming a proton gradient across the thylakoid
membrane
o Protons diffuse from thylakoid lumen to the
stroma, through channels formed by ATP
synthase
o ATP synthase catalyzes the
photophosphorylation of ADP to ATP
o The ATP Produced will be used in Calvin Cycle
To summarize Light-Dependent Reactions:
where:
NADP+ - Nicotinamide Adenine Dinucleotide
Phosphate
NADPH - the reduced form of NADP+
Pi - Free Inorganic Phosphate
Module 12: Photosynthesis (Part 2)
Photosynthesis II: Light-Independent Reaction
ALSO KNOWN AS CALVIN – BENSON CYCLE
● Carbon fixation occurs in the stroma through a
sequence of 13 reactions of the Calvin cycle.
● It is an anabolic pathway building
carbohydrates from smaller molecules and
consuming energy
● Carbon enters the Calvin cycle in the form of
CO2 and leaves in the form of sugar
● The product of Calvin-Benson cycle is not
glucose but the 3-carbon sugar
Glyceraldehyde-3-Phosphate (G3P)
There are 3 main stages in the Calvin – Benson
Cycle:
1. CO2 uptake
● CO2 reacts with 5-carbon ribulose bisphosphate
(RuBP)
● Catalyzed by ribulose bisphosphate
carboxylase/oxygenase (rubisco)
● The unstable 6-carbon product breaks down
into two molecules of 3-carbon
phosphoglycerate (PGA)
● The carbon of the CO2 molecule has been
“fixed” to a carbon skeleton
2. Carbon Reduction
● Energy from ATP and NADPH are used to
convert the PGA molecules to
glyceraldehyde-3-phosphate (G3P)
● Exergonic reaction of two molecules of G3P
leads to formation of a glucose or fructose
3. RuBP Regeneration
● 10 G3P molecules (30 carbons) remain in the
Calvin cycle
● Through a series of 10 reactions, these
molecules are rearranged into 6 molecules of
ribulose phosphate
● Ribulose phosphate is phosphorylated by ATP to
produce RuBP, which is used to restart the cycle
Summary of Photosynthesis
Here are the key points in photosynthesis:
● Photosynthesis converts inorganic carbon
dioxide to glucose
● it only occurs in plants, algae, and other
photosynthetic bacteria
● light energy triggers the reaction
● in the Light-dependent reaction, oxygen is
produced from the hydrolysis of H2O
● the products of Light-dependent reaction will
be used in the Light Independent Reaction and
vice versa
● the Light Dependent Reaction happens in the
thylakoid while Light Independent happens in
the stroma
● the end product of Photosynthesis is Glucose
Module 13: Respiration
Introduction to Cellular Respiration
CELLULAR RESPIRATION -the process by which a
reactant is used by the tissues is used to produce by
Adenosine Triphosphate.
-Cells use cellular respiration to obtain energy from percentage of oxygen was able to support life,
glucose: most organisms shifted to aerobic respiration. Now
let us look at the difference between these two
processes.
Anaerobic Respiration
This is a type of respiration utilized by old forms of life
on Earth, most organisms use this pathway to
harness the energy and to survive in the harsh
environment. It does not require oxygen as the last
electron acceptor and produces 2 mol adenosine
cellular respiration requires O2, and nutrients are
triphosphate very quickly. In today's time, humans
catabolized to CO2 and H2O
also make use of this process whenever the need
3 Phases of Cellular Respiration
arises such as lactic acid fermentation and alcohol
1. Glycolysis-breakdown of a glucose molecule into
fermentation for microbes.
2 pyruvates; it has two stages; the
Aerobic Respiration
energy-investment and energy-payoff phase
This is a type of respiration utilized by most
2. Kreb’s Cycle or Tricarboxylic acid Cycle - 2 acetyl
organisms today, we use this pathway to harness
CoA is converted into citrate, series of reactions
energy from the breakdown of glucose. It requires
such as oxidation-reduction reaction,
oxygen as the last electron acceptor and produces
decarboxylation, and phosphorylation and yields 6
32-36 adenosine triphosphate but in a slower
NADH, 2 FADH and ATP molecule from the initial
process. In today's time, humans also make use of
reactant acetyl CoA.
this process whenever the need arises such as lactic
3. Electron Transport Chain-series of chemical
acid fermentation and alcohol fermentation for
reactions where electrons carried by NADH and
microbes.
FADH from the Krebs Cycle is used to fuel this
process. These electrons are passed from one
electron acceptor to the another, oxygen is the
final electron acceptor in this process.
Overview of Cellular Respiration

Module 14: Cellular Respiration-Glycolysis

Glycolysis
● is the breakdown of glucose molecules to
produce pyruvic acid and ATP
● Happens in the cytosol
Aerobic Respiration vs Anaerobic Respiration
● Does not require oxygen
Organisms perform cellular respiration by breaking
● Glycolysis is subdivided into 2 phases:
down a molecule of glucose with either the
Investment and Pay-off phase
presence or absence of oxygen as the last electron
● The investment phase converts Glucose into
acceptor in the process. In Earth's early life,
two molecules of G3P
organisms utilize Anaerobic respiration due to the
(Glyceraldehyde-3-phosphate) with the use of
low percentage of oxygen in the atmosphere. As
two ATP
the atmosphere becomes more stable, and the
● The pay-off phase will convert the PGAL to
Pyruvic Acid-producing 4 molecules of ATP
Net PRODUCTS OF GLYCOLYSIS
● 2 ATP
● 2 PYRUVIC ACIDS
● 2 NADH
Below is a diagram which shows how glucose is
broken down into pyruvic acid:
Module 15: Cellular Respiration-Krebs’s Cycle
PYRUVIC ACID METABOLISM
● Pyruvic Acid cannot be directly used for Krebs’s
Cycle
● It is transformed to Acetyl Coenzyme A before
going to the Krebs’s Cycle
● The metabolism will produce NADH and CO2
KREB’S CYCLE
● the citric acid cycle takes place in the matrix of
mitochondria
● The eight steps of the cycle are a series of
redox, dehydration, hydration, and
decarboxylation reactions that produce two
carbon dioxide molecules, one GTP/ATP, and
reduced forms of NADH and FADH2
Total By-Products of Krebs’s Cycle:
● 6 NADH
● 4 CO2
● 2 ATP
● 2 FADH2
Module 16: Cellular Respiration-Electron Transport
Chain
-the last component of aerobic respiration and is
the only part of glucose metabolism that uses
atmospheric oxygen
-The ETC happens in the outer membrane of the
mitochondria
The ETC has 4 complexes:
● Complex I convert NADH to NAD+ + H+
● Complex II converts FADH2 to FAD
● Complex IV Converts 2H+ and ½ O2 to water
● The total ATP produced in ETC is 32 ATP
10. What are the 3 factors that affect enzyme
reaction?
-Temperature, pH level, substrate concentration

Review:
1. What is the outer boundary called on all cells that
controls what goes in and out of the cell?
-Cell Membrane
2. The cell membrane is described as a _______
mosaic model.
-Fluid
3. The polar head of the phospholipid ____ water
(loves or hates?)
-loves
4. Osmosis is a form of Passive Transport
-True
5. Facilitated diffusion uses the help of a transport
protein?
-True
6. What type of passive transport moves water
molecules from high concentration to low
concentration?
-Diffusion
7. The roots of a plant contain a high concentration
of minerals and the soil contains a lower
concentration. The roots absorb minerals from the
soil. This is an example of
-Active transport
8. What type of pump is typically present in most
vital organs of the body?
-Sodium-Potassium pump
9. What is the substance called if it speeds up a
chemical reaction?
-Enzymes