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GEN BIO

BY IRISH P.
PLASMA MEMBRANE AND TRANSPORT MECHANISM
PLASMA MEMBRANE
• Serves as the boundary between the cell’s internal
and external environments. Regulates all substances
that enter and exits the cell
Figure 1.1. Plasma Membrane Components
• Exhibits selective permeability, which is why it is The model shows how the components of the plasma
referred to as a semi-permeable membrane membrane are placed in relation to each other.
The structures, which can either be found superficially
A.1. Structure and Organization attached to the outside layer of the membrane
The main body of the plasma membrane is composed of
(peripheral) or found embedded within the bilayer
an amphipathic molecule known as a Phospholipid.
(integral), have specific functions in the plasma
Amphipathic molecules are those that exhibit the unique
membrane. These components can be divided into three
characteristic of having both hydrophilic (water-loving)
(3) categories based on their function:
and hydrophobic (water- fearing) parts. Below you can see
• Cell-surface markers
the parts of a phospholipid:
These are responsible for the recognition of foreign
and local (self) cells and tissues. These markers are
crucial for histocompatibility of the immune
system. The markers responsible are glycoproteins
and glycolipids.

A.3 Proteins and Protein Complexes


The diverse composition of a cell’s plasma membrane aids
its function as a selectively permeable barrier, determine
Phospholipid the overall shape of the cell, and also ensure the stability
The left model shows the structural formula of the and fluidity of the membrane. One (1) of the most crucial
molecule. You can see the individual elements and their
arrangement and how they contribute to the shape of the molecules in the plasma membrane are proteins. Proteins
molecule. The right image shows how the molecule and protein complexes are responsible for the majority of
occupies space.
internal and external interactions. There are six (6) classes
A.2. Structures of the Membrane of membrane proteins, and each serves a specific
The plasma membrane is represented using a model
function:
known as the fluid mosaic. Its name is derived from the
• Transporters (channels/carriers)
diverse proteins and other macromolecules embedded • Enzymes
• Cell-surface receptors
within the membrane, which causes the membrane to
• cell-surface identity markers
appear like a mosaic. The embedded macromolecules are
• Cell-to-cell adhesion proteins
able to move along and across the membrane regularly, • Attachment to the Cytoskeleton
which is why it is referred to as “fluid.” B. TRANSPORT MECHANISMS
• Molecules and solutes constantly pass through the Channel vs. Carrier Proteins
cell as chemical reactions occur (e.g., respiration As mentioned earlier, facilitated diffusion makes
requires oxygen to enter cells and carbon dioxide to use of either channel proteins or carrier proteins.
move out). Channel proteins provide a small, hydrophilic
Transport mechanisms are broadly categorized into three (3) passageway for specific molecules and ions. Some
types. Each category has subcategories depending on the
channels can remain open most of the time (leak
characteristic of the protein and the solute being transported
channels), while others can be opened or closed
B.1 Passive Transport
depending on the presence of a stimulus
This type of transport relies on the concentration
(something that triggers a reaction in the cell). The
gradient of solutes to move them across the plasma
latter is referred to as gated channels and can react
membrane. No energy will be spent to move the
to a chemical or electrical stimulus.
solutes across. Passive transport can be further
subdivided into the following categories:
. Water is the solvent, while the molecules and ions
• Simple Diffusion
are the solutes. Osmosis is the movement of water
The movement of ions and molecules from high
from high concentration of solutes to low
concentrations to low concentrations is known as
concentration across membranes. This movement
diffusion. This applies to lipid soluble molecules
is influenced by the presence of solutes and their
and ions that can pass freely through the
ability to pass through the membrane.
membrane. No proteins or energy is involved in this
Water molecules interact with solutes by bonding with
mechanism.
them and creating a hydrogen shell. If a solute cannot
Simple diffusion applies to small, non-polar
freely pass through a membrane, the bonded water
molecules such as oxygen and hormones. Once the
molecules are no longer considered as free and cannot
concentration gradient has been equalized, the
pass through as well. Due to the concentration of solutes
molecules will still move however there will be no
on one (1) side of the membrane, there is now a
net change in their direction.
concentration gradient among the free water molecules.
• Facilitated Diffusion
This causes water to move in the direction of the solutes
Some small molecules may still be unable to pass
until the number of free water molecules is equal, known
due to their charge. These small, charged
as osmotic balance
molecules, such as K+, are repelled by the interior
Tonicity
non-polar tails of the plasma membrane. To combat
In cells, the difference in osmotic concentration which
this, integral proteins (specifically called ion
leads to the movement of water is known as tonicity.
channels) that are lined with hydrophilic molecules
The solution which has a higher concentration of
inside aid the charged ions to move across. Proteins
solutes is described as hypertonic, while the solution
manage and assist the movement of solutes across
with low concentration of solutes is hypotonic. If there
the membrane, which is why this is referred to as
is no difference in osmotic concentration, then both
facilitated diffusion.
solutions are described as isotonic.
Active transport makes use of protein transporters
Hypertonicity: If animal cells were placed in hypertonic
similar to facilitated diffusion in the sense that the
solutions, the water inside the cell would rush out to
molecule needs to bind with the protein receptor via
try and balance the concentration gradient. This
the active site. Active transport proteins can vary in
causes the cells to shrivel and “dry.”
their direction of transport and where they get their
energy.
Hypotonicity: If animal cells were placed in hypotonic
solutions, the concentration gradient formed by the solutes
Active Transport According to Direction
inside the cell would cause water from the environment to
• Coupled/Co-transport
rush inside. This causes the cell to swell and eventually burts,
This method of transport is when one (1) protein shuttles
or lyse two (2) different molecules across the membrane in the
same direction. Most often, the movement is initiated by
Plant cells are affected differently with tonicity. Since the one (1) of the molecules, and the second molecule simply
inside of the cell is naturally hypertonic due to the large attaches to the same transport protein and joins the
movement. Both molecules must have an affinity for the
amount of solutes located in the central vacuole, constant
transport protein, which is now referred to as a symporter
osmotic pressure is being exerted onto the plasma membrane
• Counter-transport
causing it to be pushed firmly against the cell wall. This
This method of transport occurs when one
internal pressure is known as turgor pressure and provides (1) transporter moves two (2) different molecules across
the membrane in different directions. Counter-transport is
plant cells their normal turgid appearance
often a combination of primary and secondary active
If plants are not placed in hypotonic solutions, they will not transport (as seen in the sodium-potassium pump).
Movement may be simultaneous (both molecules may move
appear as turgid. If placed in an isotonic solution, the at the same time) or in sequence (one (1) molecule is
lowered turgor pressure causes the plant to appear flaccid. transported first, then the next one (1) follows after). Both
molecules must have an affinity for the transport protein,
However, if placed in a hypertonic solution, the plasma which is now referred to as an antiporter. A protein may
membrane shrinks away from the cell wall transport a single molecule against its concentration gradient.
In this case, the protein is referred to as a uniporter regardless
Aquaporins of the direction it moves the molecule
Water is an example of a polar molecule that is able to cross
the plasma membrane in small quantities. However, since our DEFINITIONS BOX
cells are suspended in an aqueous environment, it is expected
Plasma Membrane Hydrophilic
that water should be able to pass through the cell freely. This
is facilitated by specialized protein channels known as Hydrophobic Fluid-mosaic
aquaporins. These channels allow water molecules to move Transmembrane Carriers
across the membrane in large quantities
Channels Receptor Transporter
B.1 Active Transport Solute
Passive Transport Facilitated
This type of transport mechanism relies on the Diffusion Concentration Active Transport
expense of cell energy, Adenosine triphosphate Gradient ATP Gated Channels
(ATP). This expenditure is needed to move molecules Conformation
Osmosis
against their concentration gradient to maintain Tonicity
Antiporter Symporter
internal conditions. The most common example of
active transport is the Sodium- Potassium pump. Uniporter
transformed and affected.
In writing a chemical equation, the
reactants are written on the left-hand side

while the products are written on the right-hand side. The


two (2) are separated by an arrow which shows the
direction of the reaction. An arrow pointing to the right is
known as a forward reaction, while an arrow pointing to the
left is known as a reverse reaction. If two (2) arrows (⇋) are
placed between the reactants and products, this shows that
the reaction is reversible. Some reactions include a word or
symbol above the arrow. This indicates a condition or
influencing factor is being added to execute the reaction.

Things to Remember when Writing Reactions


• Use subscripts to indicate the state of the compound. If
solid (s), if liquid (l), if gas (g), and if in an aqueous
solution (aq).
• Be mindful of capitalization in elements. NI (Nitrogen
iodide) is different from Ni (Nickle).
• Don’t forget to add all the compounds and elements
involved in the reaction.
• Coefficients indicate how much of that compound is
involved in the reaction. Subscripts indicate the charge.
𝐶𝑂2(𝑔) + 𝐻2𝑂(𝑙) 𝐶6𝐻12𝑂62(𝑠) + 𝑂2(𝑔)

Equation 1.0 Sample Chemical Equation Photosynthesis


involves the interaction of carbon dioxide (in gaseous)
form and water to synthesize glucose (in solid form) and
oxygen (in gaseous form). The elements in red are the
reactants, while those in blue are the products.

Types of Reactions
The products formed will depend on the type of
The Organizational Chart Of Matter reaction occurring. Generally speaking, there are four (4)
The Periodic Table of Elements
main types of chemical reactions:
The periodic table is divided mainly by Families. • Composition/Synthesis Reactions
Families are the elements in a column in the periodic table. These are reactions where multiple reactants, such as
The older International Union of Pure and Applied Chemistry element A and B
(IUPAC) system would use Roman numerals and letters to interact with each other to form element a single
differentiate the families; however the modern IUPAC product, compound AB. Energy is required for
makes use of Arabic numbers which simply numbers the composition reactions to occur. The general formula for
columns 1 to 18. composition reactions is: A + B = AB.
Biochemical Reactions 𝑁𝑎(𝑙) + 𝐶𝑙(𝑙) 𝑁𝑎𝐶𝑙(𝑔)
New compounds are formed through a chemical Equation 1.1 Example of a Composition Reaction Used in
reaction. To understand how the reaction took place, a various industries, salt (NaCl) is a common example of a
chemical equation is written to see which elements were composition reaction. The elements sodium and chlorine are
present in both liquid forms when they interact. Once they carbohydrates. These can be in ring structure or chain
interact, they form salt in an aqueous solution. Salt farms, formation. Examples of these include Glyceraldehyde (3
such as those seen in Pampanga or Parañaque, use this to carbon), Ribose and deoxyribose (5 carbon), and Glucose,
create salt. As the salt farm dries, the salt suspended in the fructose, and galactose (6 carbon).
aqueous solution is left behind while the water evaporates. Disaccharides are simply combinations of
monosaccharides linked together by their fused -OH
• Decomposition Reactions compounds, forming the glycosidic linkage. Examples
These are reactions where one (1) compound include Sucrose (glucose and fructose), Lactose (glucose and
undergoes changes due to an external factor that galactose), and Maltose (glucose and glucose).
initiates the reaction (temperature, Ph). It is broken Polysaccharides are simply chains of disaccharides.
down into its constituents and releases energy as the These differ in the level of branching chains. Examples
bonds are broken. include Glycogen (seen in animals, formed from amylose
CATEGORY CARBOHYDRATES
𝐻2𝑂2(𝑙) 𝐻2𝑂(𝑙) + 𝑂2(𝑔) Macromolecule Subunit Function
(example)
Equation 2.0 Sample Chemical Equation Starch, Glycogen Glucose Energy storage
Cellulose Glucose Structural
Hydrogen peroxide is used as a disinfectant for minor support
wounds and is usually stored in a tinted bottle. This is to (plants)
prevent the compound to decompose into water (H2O) and Chitin Modifie Structura
air (O2). d l support
Glucose (animals)
Functional Groups CATEGORY LIPIDS
Functional groups are specific groups of molecules that Macromolecule Subunit Function
are responsible for the varying molecular properties and (example)
interactions. These molecules have unique characteristics Triglycerides (Fat, Glycerol and Energy storage
and personalities, regardless of the individual atoms that Oil) three (3)
compose them. Below are the main functional groups fatty acids
involved in Organic and Biochemistry. Phospholipids Glycerol, two Cell
Biological Molecules (2) fatty acids, membranes
Biological molecules are essential macromolecules phosphate,
and non-polar
that are composed of smaller organic molecules. Since all
R group
biomolecules are organic, their common factor is the
Prostaglandins Five (5) Chemical
presence of Carbon.
carbon rings messengers
Biomolecules are polymers, meaning they are
with two (2)
formed from the combination of monomers (single subunit
non-polar tails
molecules) via dehydration synthesis. This process describes Steroids Four (4) fused Membranes,
the synthesis of new compounds while losing water. carbon rings hormones
Dehydration synthesis is the opposite of hydrolysis. Terpenes Long carbon Pigments,
Organic molecules are also capable of existing in chains Structura
more than one (1) form. Organic molecules which have the l
same molecular formula but exists in different forms are support
called isomers. Stereoisomers are a form of isomers whose CATEGORY PROTEINS
skeletal Macromolecule Subunit Function
(example)
Carbohydrates Functional Amino acids Catalysis,
transport
Carbohydrates are composed of carbon, hydrogen, Structural Amino acids Support
and oxygen with a ratio of 1:2:1. They differ in the number CATEGORY NUCLEIC ACIDS
of carbon atoms present. Their main function is storage due Macromolecule Subunit Function
to the large amounts of C-H bonds, which can store large (example)
amounts of energy. Categories of carbohydrates depend on DNA Nucleotides Encodes genes
the complexity of their constituents. RNA Nucleotides Needed
for gene
Monosaccharides are the simplest unit of
expression
chains), Amylopectin (seen in plants), and Amylose (seen in
plants, formed from glucose). Lipids

acid. However, if the carbons form double bonds and


thereby reducing the number of hydrogen atoms
attached, it is now known as an unsaturated fatty acid.
In an unsaturated fatty acid, the double C-C bonds
form kinks in the tails which prevent it from aligning
with itself. Which is why these lipids are known as
oils (those that stay liquid at room temperature), while
saturated lipids are known as fats (those that become
solid at room temperature). Lipids can also have an
additional group attached to the glycerol head. These
additional groups cause the many variations of lipids. If a
phosphate group is attached, it becomes a
phospholipid. As mentioned before, due to the
hydrophobic nature of the fatty acids and the
hydrophilic nature of the phosphate group, these
phospholipids are responsible for the fluid structure
of the cell membrane.

Nucleic Acid
There are only two (2) variants of nucleic acids:
Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
Their main function is the storage and synthesis of genetic
information of cells. Nuclei

acids are composed of repeating subunits called Nucleotides


(polynucleotides are therefore chains of nucleotides). Each
nucleotide is composed of three
(3) main parts: the 5-carbon sugar, an organic nitrogen
base, and a phosphate group. The 5-carbon sugar for DNA is
deoxyribose, while in RNA it is simply ribose. Their main
difference is the presence of an attached -OH group to the
2nd Carbon of RNA. The nitrogen bases in DNA are Adenine
(A), Guanine, (G), Cytosine (C), and Thymine (T). The
former two (2) are known as purines due to their two
(2) ringed structure. The latter two (2) are known as
pyrimidines due to their single ring structure.
RNA has a similar set of nitrogen bases to DNA.
Except that instead of Thymine, it has Uracil (U).
Proteins
Proteins are composed of amino acids linked
together by peptide bonds. Polypeptides are chains of
multiple amino acids. Proteins are multiple chains of
polypeptides. A protein can have up to 20 or more
polypeptide chains. If a protein is composed of only one (1)
chain, it can also be referred to as a polypeptide.
3. Lipids
Categories of proteins depend on their function.
• Spot Test
Refer to the table below for the list of functions and some
This test relies on the non-volatile nature of lipids.
examples.
Using water as a control, the spot test determines that
Chemical Tests to Identify Biomolecules lipids are less volatile than water. Because of this, the
1. Carbohydrates lipids that get absorbed in the paper are not able to
• Benedict’s Test conduct enough heat for it to evaporate. This leaves a
This test is meant to identify reducing sugars. Reducing translucent spot on the paper.
sugars are those that have a free aldehyde or ketone group to
transfer hydrogen atoms as part of the reduction process.
Benedict’s reagent is composed of Copper (II) sulfate
(CuSO4) and Sodium citrate (Na3C6H5O7). The copper (II) in
the solution gets reduced and forms copper (I), which results
in the brick red color.
• Emulsion Test
The emulsion test requires a mixture of fat/oil with
water. Sudan IV, which is a lipophilic molecule, acts as
an indicator that forms micelles/droplets when added
to the solution. If the solution contains lipids, the lipid
molecules will congregate at the top layer due to the
difference in density and will be stained red by the
2. Proteins indicator. If the solution is free of lipids, the indicator
• Biuret Test will disperse throughout the solution evenly.
This test identifies the presence of peptide
bonds. A sample that has high amounts of peptide
bonds (long chains) will give off a light to deep
purple color. Meanwhile, samples that have short
peptide bonds or amino acids will give off a pink
color. If no peptide bonds are present, no color
change will occur. The biuret reagent is composed
mainly of Copper (II) sulfate (CuSO4) and potassium
sodium tartrate (KNaC4H4O6·H2O). Unlike the
Benedict’s Test, Copper (II) sulfate reacts with
peptide bonds to form a chelate complex (wherein
a metal atom is bound between two [2] non-
metals). The potassium sodium tartrate is meant to
stabilize the chelate complex.
1. Nucleic Acids
• Dische Test
This is also referred to as the Diphenylamine test. This test
identifies the presence of DNA based on the reaction The Cell Cycle
between the Dische reagent (mainly diphenylamine) and the The cell cycle is the ordered series of events
2-deoxypentose sugar of DNA. The redox reaction forms a involving cell growth and division to produce new cells
blue colored complex upon conversion of the pentose sugar. (daughter cells). An overview of the cell cycle shows two (2)
The concentration of DNA is proportional to the intensity of major phases: interphase and mitotic phase. These two (2)
the blue color. Since RNA has a different sugar base, ribose, the are further subdivided into different phases. Interphase is
reaction will not form a blue complex. Rather a green- divided into four (4) phases, while mitotic phase is divided
colored complex will be shown. A clear result indicates the into five
(5) phases.
absence of DNA.
Although eukaryotes and prokaryotes have similar cell
cycles, the processes to be discussed are specific to
eukaryotes. This is because eukaryotic cells are more
complex, and the cell cycle of prokaryotes are simplified
versions of the former

Interphase

This phase is dedicated to the growth, preparations,


DNA synthesis, and replication. It is subdivided into three
(3) phases: Gap 0 (G0), Gap 1 (G1), Synthesis (S), and Gap 2
How Does a Cell Know What Cell to Become? (G2).
To ensure that the new cells being formed are the
same as its progenitor, it refers to an internal blueprint on
• G0
how to construct itself. This blueprint is referred to as DNA, This phase is where the cell spends the longest
which, as established, consists of sequenced nitrogen bases, amount of time. It is the normal state of the cell where
phosphate groups, and sugar backbones. it undergoes standard levels of growth, metabolism,
DNA in its uncondensed form can span thousands of and no active division. Cells can stay in this state for
kilometers, which is why it is condensed by being wrapped minutes to years. It is also referred to as the resting
around a histone. This new structure is referred to as a state.
nucleosome. Then, nucleosomes are further condensed by
coiling and forming a chromatin fiber. Condensed groups of • G1
chromatin fibers form a single chromatid. When two (2) This phase is directly associated with G1 and is the
chromatids are linked at the centromere by a kinetochore, it second-longest phase of the
forms a chromosome, which is the most condensed form of cell cycle. Although visually similar to G0, the
genetic material biochemical aspect of the cell is much more active.
Proteins, building blocks for DNA, and energy are
being accumulated by the cell in preparation for the
following phases.

• S
Once the cell has accumulated enough building
blocks and energy, it beings the process of replicating and Anaphase B. Anaphase A can be observed once the
DNA. Genetic material is normally observed as semi- kinetochores (and in relation the chromatids) are pulled
condensed chromatids. The centrosome will be toward the opposite poles. The “pulling” is not caused
duplicated to form the mitotic spindle, which will be by the microtubules contracting, rather the subunits of
important in the separation of chromatids. the microtubule directly attached to the kinetochore
are removed, resulting in the chromatid to draw closer.
• G2 Anaphase B is observed when the poles themselves
Significant changes to the organelles and cell move apart. This causes the chromatids to move away
structure occur during this phase. The cytoskeleton is from the center of the cell, allowing a clear separation.
dismantled, organelles are duplicated, proteins The cell membrane will be visibly elongated at this
needed to separate chromosomes are synthesized, point.
and large amounts of energy are stored. Once anaphase is complete, the accurate division
Mitotic Phase and separation of the cell’s genome have been
After the preparations done during interphase are accomplished.
completed, the cell begins the process of aligning genetic
material, separating them, dividing the cell, and forming the
• Telophase
two (2) new daughter cells. The M phase can be subdivided
The second to the last phase is initiated once the
five (5) phases: prophase, metaphase, anaphase, telophase, separated chromosomes are clearly located on
and cytokinesis opposite poles of the cell. Microtubules and centrioles
• Prophase disassemble to construct the new cytoskeleton of the
Condensed chromosomes must be identified to daughter cells. A nuclear envelope will form around the
differentiate prophase with the end of interphase. DNA chromosomes. Once enclosed, these will uncoil and
replication has ended at this point and is being condensed begin replication for gene expression.
into thick, bulky structures called chromosomes. During late telophase, two (2) new nucleoli can be
Protein structures called centrioles begin to form and seen in the daughter cells. Daughter cells are either
migrate toward opposite ends of the cell. The centrioles diploid (denoted as 2n) or haploid (denoted as n). 2n
then organize an array of microtubules (spindle fibers), indicates that the cell contains two (2) sets of matching
which will later be sued to attach and pull the chromosomes from the original cell, while n indicates
chromosomes. Another set of microtubules will connect that the cell contains only one (1) set of chromosomes.
the centriole to the cell membrane, which is referred to as Human cells that are not involved in reproduction
an aster. (known as somatic cells) are diploid, while those that
The disintegration of the nuclear envelope signifies the are involved in reproduction (known as gametes) are
late phase of prophase and the transition to metaphase haploid.
known as prometaphase. • Cytokinesis
• Metaphase Once the chromatids have been separated, the
After the nuclear envelope is removed, the microtubule spindle will form an actin ring in between
microtubules attach to the kinetochore of the the two (2) new daughter cells. For animal cells, this is
chromosomes. Each chromosome has two (2) known as a cleavage furrow, while in plant cells it is
kinetochores, and each kinetochore will be connected a known as the cell plate. This results in the splitting of the
microtubule from one (1) of the centrioles. This results in cell membrane, hence the name cyto – cells, and kinesis
the chromosome being pulled into the center of the cell. – movement. Cytokinesis is different from karyokinesis
Once the microtubules have pulled all the - which is the overall movement of genetic material.
chromosomes, they will align at an imaginary equator Checkpoints and Regulation of the Cell Cycle
known as the metaphase plate. Metaphase ends when all The cell cycle requires specific indicators before
chromosomes have been neatly aligned at the plate. proceeding with each phase. To limit the errors that may
• Anaphase occur during each phase, three (3) main checkpoints are
This phase is the shortest, most crucial, and visually established. Each checkpoint is found in between critical
active phases of the M phase. The initiation of anaphase phases that may require regulation.
starts with the removal of cohesion proteins • G1 Checkpoint
(responsible for the presence of the centromere). This During Gap 1, the cell is focused on increasing
results in the two (2) chromatids of a chromosome cell size and accumulating proteins and energy. The
(sister chromatids) to separate. G1 checkpoint therefore evaluates if the necessary
Anaphase is divided into two (2) parts: Anaphase A conditions for DNA replication have been met. If
the G1 checkpoint has not been met, the cell will
either remedy the necessary conditions or revert
back into Gap 0 and wait until additional signals
indicate that the cell is ready for division.

• G2 Checkpoint
Similar to the G1 checkpoint, the G2
checkpoint asses the cell size and protein reserves
of the cell. However, the main feature of G2
checkpoint is that it evaluates the DNA replicated.
If the amount of DNA replicated is not enough or if
there is damage detected, the cell will not proceed
until the necessary changes have been made. The
G2 checkpoint is the last checkpoint before
proceeding with M phase.

• M Checkpoint
The M Checkpoint is also referred to as the
spindle checkpoint. It checks if all sister chromatids
are attached to their corresponding microtubules.
If the M Checkpoint is not met, the cycle will not
continue. This is crucial because Meta-anaphase
will determine the number of chromosomes found
in each cell.

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