GENERAL BIOLOGY I & II

. LESSON 1: CHEMISTRY OF BIOLOGY .

BIOLOGY . 3. Energy and Matter
➢The scientific study of life that have 5 unifying ➔ Life requires the transfer and
themes: organization, information, energy transformation of energy and matter
and matter, interactions, and evolution ➔ Energy comes from the sun, making life
================================================ possible.
CHARACTERISTICS OF LIFE ➔ Energy flows one-way [ light to heat ], but
● Order chemical is cycled
● Homeostasis 4. Interactions
● Adaptation ➔ From molecules to ecosystems,
● Metabolism interactions are important in biosystems.
● Reproduction ➔ The environment affects the organism, and
● Response to Stimuli the organisms affect the environment.
● Growth and Development ● Feedback Regulation - the output or
================================================ product of a process regulates that very
Themes in Studying Biology . process.
○ Positive Feedback Loop - rarely happens,
1. Organization
the end product speeds up its own
➔ Life operates in biological organization.
production.
➔ This reveals the principle of reductionism. ○ Negative Feedback Loop - a loop in which
➔ As the complexity of life increases, the response reduces the initial stimulus.
emergent properties arise due to the 5. Evolution
interaction of different parts. ➔ The proposed core theme of biology.
◆ Systems biology is a field of life science that studies ● Evolution - a process of biological change
the interaction of biological systems in which species accumulate differences
➔ This complexity arises due to a series of from their ancestors as they adapt to
natural selection. different environments over time.
Level of Biological Organization: ➔ Evolution accounts for the unity (shared
Atom > Molecule > Macromolecule > Organelle > traits) and diversity (differences) of life.
Cell > Tissue > Organ > Organ System > Organism > ★ According to Theodosius Dobzhansky, a
Population > Community > Ecosystem > Biosphere
founder of modern evolutionary biology,
★ According to Cell Theory, developed in the “Nothing in biology makes sense except in the
1800s, the cell is the basic unit of life. light of evolution.”
○ Prokaryotic Cells lack membrane-bound
★ According to Charles Darwin, in his book On
organelle and nucleus
the Origin of Species by Means of Natural
○ Eukaryotic Cells have those qualities
Selection:
2. Information 1. Evolution is Descent with
➔ Life’s processes involve the expression Modification: Species accumulate
and transmission of genetic information. differences from ancestors
➔ Chromosomes are structures containing 2. Natural Selection causes Evolution:
genetic material in the form of DNA individuals with inherited traits that are
➔ A particular section of the DNA is called a better adapted are more likely to
gene that are the basic unit of inheritance survive and reproduce than less
➔ They encode the necessary information to adapted individuals.
build whatever the organism needs, and ★ Descent with modification implies that
they inherit characteristics from their common traits descend from one generation to
parents. the next, inheriting those characteristics.
➔ The sequences of genes serve as a ★ Fossils and other evidence corroborate
blueprint for making a protein. anatomical unity in supporting this view of
➔ The sequence of genes in one organism descent from a common ancestor.
essentially results in the same thing in
On the right is a
another.
phylogenetic tree that
● Genomics - a branch of biology that highlights the evolutionary
applies systems biology approach — it is relationships. A
the large-scale analysis of DNA sequence. phylogenetic tree is
○ Genome - the entire library of genetic composed of nodes and
instructions that an organism inherits. branches. The internal
○ Genome Sequence - the entire sequence nodes represent ancestors
of nucleotides for a representative member and are points in evolution
of a species when, based on scientific
● Proteomics - studies organism’s sets of evidence, an ancestor is
proteins and their properties thought to have diverged
○ Proteome - the entire library of proteins to form two new species.
that an organism expresses.
 GENERAL BIOLOGY I & II
WATER .
➢ Has many emergent properties
➢ Composed of 2 molecules of Hydrogen and 1
molecule of Oxygen
➢ Bent tetrahedral shape, shaped like V
➢ O is more electronegative than H, thus
attracting more electrons than H.
➢ A partial positive (𝝳+) charge forms in the
regions of hydrogen, partial negative (𝝳-)
charge in the regions of oxygen.
➢ Hydrogen bonds cause their interactions— the
reason for these emergent properties.
Properties of Water Contributing to Life Suitability .
1. Cohesion of Water Molecules
➔ Cohesion : Due to
hydrogen bonding, water
molecules are attracted to
each other.
➔ Surface Tension : Due to
cohesion, this results and the surface of the
liquid becomes hard to break or stretch.
★ The spider takes advantage of surface tension
to walk above water.
➔ It also contributes to the transport of
nutrients against gravity — capillary action
➔ Adhesion : water can hydrogen bond
extrinsically with other molecules. This
helps to transport nutrients in the body.
2. Thermoregulation Properties
● Kinetic Energy - energy acquired from
any movement of an object.
○ Thermal Energy - sum of kinetic energies
due to random atomic motions.
○ Temperature - average kinetic energies
due to random atomic motions.
● Heat - transfer of thermal energy in order
to reach equilibrium (m: calorie = 4.184 J).
➔ Specific heat is defined as the energy
required to raise the temperature of 1g of a
𝑐𝑎𝑙
substance by 1°C, in the case of water, 1 𝑔 · °𝐶
◆ It can be thought as how well a substance resists
temperature changes
➔ Water has relatively high specific heat.
➔ This allows the thermoregulation and
stabilization of environmental conditions
for marine life. Also, this is responsible for
sea and land breeze phenomena.
➔ At any temperature, some of the atoms in
liquids evaporate. Eventually, they will
vaporize completely.
● Heat of Vaporization - energy required to
convert 1g of a liquid into gas.
➔ By the same token, water has a relatively
high heat of vaporization, manifested thru:
a. Climate Moderation: high heat is
needed to evaporate surface water,
released, then condensed.
b. Steam Burns: steam can cause burns
when heat energy is released to the
skin when it condenses.
c. Evaporative Cooling: likewise, as heat
evaporates, it absorbs heat, leaving a
cold air and cools the environment.
3. Floating of Ice on Liquid
➔ Water is densest at 4°C, less dense as a
solid than a liquid.
➔ Due to hydrogen bonding, water expands
when cooled rather than heated.
➔ At 0°C, the molecules form crystalline
lattice structure, each water molecule
hydrogen bonded to four partners.
➔ Only a few inches are thawed, insulating
the water below and providing habitat for
both fishes, polar bears, etc.
➔ If this weren’t the case, all bodies of water
would eventually freeze.
4. Water: The Universal Solvent
➔ Because of water’s
polarity, water is a versatile
solvent.
➔ Oxygens are attracted
to the cation, while
hydrogens are attracted to
the anion.
➔ Water forms a shield
around the ions called
hydration shell, causing it
to be dissolved.
➔ If this weren’t the case, all bodies of water
would eventually freeze.
★ A material doesn’t need to be water-soluble to
be hydrophilic. It also has to do with atom size.
2 H2O ⇌ H3O + OH
★ The reaction shows the dissociation of Water
into hydronium and hydroxide.
★ It is in dynamic equilibrium and it is reversible.
★ In life, the concentrations of OH and H ions are
extremely important — changes can drastically
affect the conditions of chemistry.
● Acids - increase concentrations of H+ ions.
They have pH of <7
● Bases - reduces concentrations of H+ ions.
They have pH of >7
★ Once the concentrations of OH and H are equal
in a solution, they are said to be neutral.
★ Weak acids are acids that reversibly release
and accept back hydrogen ions, like:
2 H2CO3 ⇌ HCO3 + H
 GENERAL BIOLOGY I & II
The pH Scale .
➔ In any aqueous solution at
25°C, the product of the H+
and OH- concentrations is
constant at 10-14.

+ − −14
[𝐻 ][𝑂𝐻 ] = 10

➔ Particularly,
+ − −7
[𝐻 ], [𝑂𝐻 ] = 10 for neutral
solutions.

➔ If enough acid is added to a

solution to increase [H+] to 10-5 M, then the [OH-]
declines by 10-9 M.
➔ Similarly, if enough baseis added to a solution to
increase [OH-] to 10-4 M, then the [OH-] declines by
10-10 M.

+
𝑝𝐻 = − 𝑙𝑜𝑔[𝐻 ]

Buffers .
❖ The internal pH of most cells are close to 7
(blood pH is 7.4, which is slightly basic)
❖ If 0.01 mol of a strong acid is added to a liter of
pure water, the pH drops from 7.0 to 2.0.
❖ If the same amount of acid is added to a liter of
blood, however, the pH decrease is only from
7.4 to 7.3 due to existence of BUFFERS.
★ This is of great concern because carbonate ions
are required for calcification, the production of
calcium carbonate (CaCO3) by many marine
organisms, including reef-building corals and
animals that build shells.

BUFFERS .
➢ A substance that minimizes changes in the
concentrations of H+ and OH- in a solution.
➢ It does so by accepting hydrogen ions from
the solution when they are in excess and
donating hydrogen ions to the solution when
they have been depleted.
➢ Most buffer solutions contain:
○ A weak acid — serves as H+ donor
○ A base, — serves as H+ acceptor which
combines reversibly with hydrogen ions

2 H2CO3 (carbonic acid) ⇌ HCO3 (bicarbonate) + H

● Right reaction reduces pH, more acidic, > H+
● Left reaction increases pH, more basic, < H+
★ In the ocean, CO2 dissolves in water, forming
carbonic acid, making the pH more acidic.
★ This is called ocean acidification, fluctuating
the pH of the ocean and causing detrimental
effects to marine life.
 GENERAL BIOLOGY I & II
Characteristics of Carbon .
❖ Has 4 valence electrons Functional Group Properties Structure
❖ Has many allotropes and other forms Group
❖ Highly unreactive under normal conditions Hydroxyl (-OH) ● Polar
❖ Has ability to bond with multiple elements, ● Ampotheric
commonly with Hydrogen, Oxygen, and (can be both act
Nitrogen as acid / base)
● Forms Alcohols
★ The properties of a carbon-containing
molecule depend on the arrangement of its Carbonyl ● Polar
● Acidic
carbon skeleton and on its chemical groups. ● Can form either
Ketone,
Organic Chemistry is the Key to the Origin of Life . Aldehyde
❖ Compounds containing carbon are called
organic compounds (with a few exception) Carboxyl ● Polar
and their study is called organic chemistry. ● Acidic
STANLEY MILLER (1953) . ● Forms
Carboxylic
➔ Grad student under Harold Urey at
Acids
University of Chicago.
➔ Designed an experiment on the abiotic
synthesis of organic compounds — Amino ● Polar
compounds necessary for life’s existence ● Basic
➔ In his results, he ● Forms Amines
identified a variety of or Amides
organic molecules
common to
organisms Sulfhydryl ● Slightly Polar
● Basic
➔ He concluded that ● Forms Thiols
organic molecules are
the first step to the
origin of life, which
may have abiotically
been spontaneously Phosphate ● Ionic, Anion
synthesized in early ● [Strongly] Basic
Earth’s atmosphere ● Forms Organic
Phosphates
➔ Although results
● Releases
are viable, his
energy upon
replication was later reaction with
disproved since he fail water
to account for other (hydrolysis).
factors in the primeval
atmosphere.
➔ The overall
percentages of major
elements of life [ C, H, N , O , P , S] are quite uniform,
reflecting a common evolutionary origin of all life.

HYDROCARBONS .
➢ refers to an organic chemical compound that
is composed exclusively of hydrogen and
carbon.
FUNCTIONAL GROUPS .
➢ are specific groupings of atoms within
molecules that have their own characteristic
properties, regardless of the other atoms
present in a molecule.
 GENERAL BIOLOGY I & II
MACROMOLECULES .
➢ These are polymers that are built from
monomers.
➢ They are huge in size, hence macro.
➢ They can break down or be synthesized
through various mechanisms, facilitated by
enzymes.
● Dehydration Synthesis - aka
condensation synthesis, this is the
formation of polymers through the
combination of two units — monomers.
This reaction releases water, with the
release of one hydroxyl group from one
monomer and hydrogen ion from the
other. An enzyme is required for this to
function and it requires energy.
● Hydrolysis - this is the process by which a
polymer is broken down through the
addition of water. This releases energy in
the process. Requires enzymes as well.
★ The molecular logic of life is simple but
elegant: Small molecules common to all
organisms act as building blocks that are
ordered into unique macromolecules.
★ This is responsible for the diversity of
macromolecules
★ Despite this immense diversity, molecular
structure and function can still be grouped
roughly by class, having emergent properties as
well: carbohydrates, lipids, proteins, and
nucleic acids.
Classifications of Biological Macromolecules .
1. Carbohydrates
➔ They include sugars and their polymers
CARBOHYDRATES BASIC FACT SHEET
● ELEMENTS: C, H, O
● FUNCTIONAL GROUPS: Hydroxyls and
Carbonyls
● MONOMER: Monosaccharides
● POLYMER: Polysaccharides
● NAME CONVENTION: –ose
● FUNCTIONS: short-term energy storage
& building or structural materials
MONOSACCHARIDES .
➢ mono - one, sacchar - sweet
➢ These are simple sugars
➢ The aliphatic sugars cyclize in aqueous
solutions, forming ring structures containing
ether linkages.
➢ Generally have a molecular formula of (CH2O)n
➢ Aldose – monosaccharide w/ aldehyde group
➢ Ketose – monosaccharide w/ ketone group
➢ Can be named as diose… triose… pentose…
etc depending on the number of carbons.
1. Glucose
★ Most common and most important
monosaccharide in nature
★ aka blood sugar, an aldose and a hexose
★ Isomers of fructose & galactose
★ Functions as a major nutrient source for
cell in cellular respiration
★ When it forms a ring, the -OH group
attached in Carbon Number 1 is
positioned either below or above the
plane.
2. Fructose
★ aka fruit sugar, a ketose and a hexose
★ Naturally occurring found primarily in
fruits, but also in vegetables, honey,
sugar beets and sugar cane.
3. Galactose
★ aka brain sugar, an aldose and a hexose,
which is an enantiomer of glucose.
★ It supports the brain development of
infants. It helps trigger long-term
memory formation.
OLIGOSACCHARIDES .
➢ mono - one, sacchar - sweet
➢ This refers to any carbohydrate that consists of
2 to 10 units of monomers.
➢ Most of the few naturally occurring
oligosaccharides are found in plants.
○ Disaccharides - these are dimers that
are formed by bonding two
monosaccharides. They are connected
by a glycosidic bond or linkage by
dehydration synthesis.
1. Maltose
★ Glucose + Glucose = Maltose
★ aka Malt Sugar, this is an ingredient used
in brewing beer
 GENERAL BIOLOGY I & II
2. Sucrose
★ Glucose + Fructose = Sucrose
★ aka Table Sugar, this is the most
prevalent disaccharide,
★ Plants transport carbohydrates from
leaves to roots and other
nonphotosynthetic organs in the form of
sucrose.
3. Lactose
★ Glucose + Galactose = Lactose
★ This sugar is present in milk.
❖ Disaccharides must be broken down
into monosaccharides to be used for
energy by organisms.
❖ Lactose intolerance is caused when
humans can’t break it down thru the
enzyme lactase.
POLYSACCHARIDES .
➢ These are polymers of carbohydrates, having
a few hundred to a few thousand
monosaccharides joined by glycosidic
linkages
➢ They are known as complex sugars
Storage Polysaccharides
1. Starch
★ This is the sugar used by plants for their
short-term energy storage as granules
in cell structures called plastids.
★ This allows plants to “stockpile” surplus
glucose without consuming them.
★ Glucose is later withdrawn thru hydrolysis
★ All glucose monomers are in the α
configuration. This causes it to have a
largely helical structure, efficiently
storing glucose units.
★ Has two main composition, digestible:
○ Amylose — unbranched, soluble to
water, comprising 20% of starch. This
is the simplest form of starch. It has
1-4 glycosidic linkages
○ Amylopectin — somewhat branched,
soluble to water, comprising the other
80% of starch. It has 1-6 glycosidic
linkages.
2. Glycogen
★ This is the sugar used by animals that is
like amylopectin but more extensively
branched.
★ Vertebrates store this in liver and muscle
cells. It is broken down into glucose
when the demand for energy increases.
★ In humans, it depletes in a day unless
replenished by eating.
Structural Polysaccharides
1. Cellulose
★ It is the most abundant organic
compound on Earth
★ It has 1-4 glycosidic linkages
★ All glucose monomers are in the β
configuration.
○ α bond — formed when the OH
group on the carbon-1 of the first
glucose is below the ring plane
○ β bond — formed when the OH
group on the carbon-1 is above the
ring plane
★ It has straight, unbranched molecules.
★ Hydroxyl groups are free to hydrogen
bond with the hydroxyl groups of other
cellulose molecules lying parallel to it.
This structure is called MICROFIBRILS.
★ This parallel structure strengthens
plants’ cell walls, thus stabilizing them.
★ Cellulose is a major constituent of
paper, and the only component of
cotton.
★ It can’t be digested by humans and
most animals because we can’t break
down the glycosidic linkages.
★ If consumed, it abrades walls of the
alimentary canal and stimulates the
lining to secrete mucus, aiding the
smooth passage of food.
★ On food packages, insoluble fiber refers
mainly to cellulose.
2. Chitin
★ Many animals use it for their exoskeleton
★ Arthropods embed this in a layer of
protein, making it leathery and flexible at
first.
★ Insects have hardened this by
chemically-linking proteins with each
other
★ Crabs hardens this by
encrusting it with calcium
carbonate
★ It is also found in fungi—the
main material for their cell walls.
★ It is similar to cellulose with β
configuration, except that it has a
nitrogen-containing attachment
 GENERAL BIOLOGY I & II
2. Lipids WAXES .
➔ They are a diverse group of hydrophobic ➢ Main Function: Insulation
molecules. ➢ Structure: made up of long fatty acid chains
➔ They do not include a true polymer, and esterified to long-chain alcohols.
are generally not big enough to be ➢ They cover the feathers of some aquatic
macromolecules. birds and the leaf surfaces of some plants.
➔ It contains the elements C,H,O ➢ Hydrophobic, thus preventing water from
➔ Contains the functional group esters and sticking on the surface
alcohol groups, largely nonpolar in nature
➔ Has many functions depending on the
type of lipid and their composition.
FATS AND OILS .
➢ Main Function: Long-term Energy Storage
➢ Structure: consists of 3 glycerol (an alcohol
having 3 carbons that bears a terminal PHOSPHOLIPIDS .
hydroxyl) and a fatty acid that has a long ➢ Main Function: Cell
carbon skeleton of 16-18 carbons in length, Membrane Composition
usually having a carboxyl group, making it an ➢ Structure: hydrophilic
acid. head and hydrophobic
➢ If the glycerol mixes with fatty acids, they tail
form a triglyceride thru dehydration ➢ Similar to a fat molecule,
synthesis, forming an ester linkage (a bond but only has two fatty acid
between hydroxyl and carboxyl group). ➢ The third hydroxyl group of
glycerol is joined to a
phosphate group, which
has a negative electrical charge in the cell.
➢ The phospholipid bilayer in cells forms a
boundary between the cell and its external
environment.
STEROIDS .
➢ Main Function: growth, development,
sexual differentiation and reproduction
➢ Structure: carbon skeleton with four-fused
rings
➢ Different steroids are distinguished by the
particular chemical groups attached to this
ensemble of rings.
● Cholesterol
★ A type of steroid crucial in animals.
★ It is a common component of animal
cell membranes and is also the
precursor from which other steroids,
such as the vertebrate sex hormones, are
synthesized.
★ In vertebrates, cholesterol is
synthesized in the liver and is also
obtained from the diet.
★ A high level of cholesterol in the blood
may contribute to atherosclerosis.

➢ Fats separate from water (i.e. immiscible)

because the water molecules hydrogen-bond
to one another (cohesion) and exclude the fats
because they cannot hydrogen-bond with it
(due to nonpolarity).
1. Saturated Fats
★ They have a straight, flexible carbon
backbone, allowing them to pack tightly
★ Thus, they are solid in room temp.
★ Occurs for most animal fats, harmful
2. Unsaturated Fats
★ Has at least 1 kink or double bond,
forming a cis (same side H) kink.
★ Liquid in room temp, as w/ plant fats.
○ Hydrogenation — the process of
converting uns. Fat to sat. fat by
adding H, acquiring trans kinks.
 GENERAL BIOLOGY I & II
3. Proteins ★ The chemical nature of the side chain
➔ These are biologically functional determines the nature of the amino acid (acidic,
molecules made up of one or more basic, polar, nonpolar).
polypeptides, each folded and coiled into a ★ There are 20 amino acids that cells use to build
specific three-dimensional structure. their proteins. They exist typically in ionized form
➔ They include a diversity of structure, at the pH found in a cell.
resulting in a wide variety of functions.
➔ They are the most abundant organic
molecules in living systems
➔ They have the most diverse range of
functions of all macromolecules

PROTEINS BASIC FACT SHEET ○ Acidic Amino Acids - have

● ELEMENTS: C, H, O, N negatively-charged side change due to
● FUNCTIONAL GROUPS: Amine, presence of carboxyl group, which
Hydroxyl, Carboxyl, Alkyl / R- Group dissociates (ionizes) at cellular pH.
● MONOMER: Amino Acids ○ Basic Amino Acids - have
● POLYMER: Protein / Polypeptides positively-charged side change due to
presence of amino group.
FUNCTIONS OF PROTEINS .
1. Enzymatic Proteins
★ Function is to selectively accelerate The 20 Amino Acids of Proteins
chemical reactions by lowering the
Nonpolar Side Polar Side Electrically-char
activation energy.
Chains Chains ged Side Chains
2. Storage Proteins
★ Their function is the storage of amino ● Glycine [ Gly ] ● Serine [ Ser ] Acidic [ - charge ]
acids. ● Alanine [ Ala ] ● Threonine [ Thr ] ● Aspartic Acid
○ Casein, the protein of milk, is the ● Valine [ Val ] ● Cysteine [ Cys ] [ Asp ]
major source of amino acids for ● Leucine [ Leu ] ● Tyrosine [ Tyr ] ● Glutamic Acid
baby mammals. ● Isoleucine [ Ile ] ● Asparagine [ Glu ]
○ Plants have storage proteins in their ● Methionine [ Asn ] Basic [+ charge ]
seeds. [ Met ] ● Glutamine ● Lysine [ Lys ]
○ Ovalbumin is the protein of egg ● Phenylalanine [ Gln ] ● Arginine [ Arg ]
white, used as an amino acid source [ Phe ] ● Histidine [ His ]
for the developing embryo. ● Tryptophan
3. Hormonal Proteins [ Trp ]
★ Function is for the coordination and ● Proline [ Pro ]
regulation of the organism’s activities, as
with Insulin.
4. Contractile and Motor Proteins ★ Proline is an exception to the
★ Main function is for movement. standard structure of an animo
★ Motor proteins: Cilia and Flagella acid since its amino group is not
★ Contractile: Actin and Myosin separate from the side chain
5. Defensive Proteins
★ Function is protection against POLYPEPTIDES .
pathogens like the antibodies. ➢ These are the polymers of amino acids
6. Transport Proteins ➢ A bond between two monomers where the
★ Function is transport of substance carboxyl group is adjacent to the amino
★ Eg: Hemoglobin & Transport Protein group, can become joined by a dehydration
7. Receptor Proteins reaction held by a peptide bond.
★ Function is response of cell to chemical ➢ Once repeated, it yields a polypeptide that
stimuli, like with the synaptic may also be called a polypeptide backbone.
neurotransmission ➢ N-terminus is the
8. Structural Proteins end where it has a
★ Main function is for support free amino group.
★ Eg: Keratin - hair, horns, feather ➢ C-terminus is the
★ Eg: Collagen & Elastin - animal end where it has a
connective tissues
free carboxyl grp.
AMINO ACIDS . ➢ The nature of it is
➢ These are the monomers of determined by the
proteins kind and sequence
➢ It is an organic molecule with of the side chains,
both an amino group and a which determine
carboxyl group. how a polypeptide
➢ At the center of the amino acid is folds and thus its
an asymmetric carbon atom final shape and
called the α carbon chemical
➢ It also has a hydrogen atom and characteristics.
a side chain called the R
GROUP.
 GENERAL BIOLOGY I & II
STRUCTURES OF PROTEIN .
➢ A functional protein is not just a
polypeptide chain, but one or more
polypeptides precisely twisted, folded, and
coiled into a molecule of unique shape,
which can be shown in several different types
of models.
➢ When a cell synthesizes a polypeptide, the
chain may fold spontaneously because of
intermolecular bonds between the chains.
➢ Thus, the amino acid sequence of each
polypeptide determines what 3D structure
the protein will have under normal cellular
conditions.
○ Globular Proteins - roughly spherical
○ Fibrous Proteins - long fiber shape.
➢ The function depends on its shape.
1. Primary Structure
★ This is a linear sequence of amino acids,
having amino end / N-terminus and
carboxyl end / C-terminus
2. Secondary Structure
★ Here, there are regions that stabilize by
hydrogen bonds (due to H,O,N) between
atoms of a polypeptide backbone.
★ The constituents of the polypeptide
backbone coil (called α helix) and / or
fold (called β pleated sheets)
○ α helix — coil held by hydrogen bond
between every 4th amino acid.
○ β pleated sheets — two or more
segments of the polypeptide chain
lying side by side (called β strands)
are connected by hydrogen bonds
between parts of the two parallel
segments.
3. Ternary Structure
★ These are 3D Shapes — the overall
shape stabilized by interactions
between the side chains.
★ Hydrophobic interactions contribute to
this structure, with nonpolar side chains
clustering up at the core of the protein.
★ Van der Waals interactions hold them
together once amino acids are close
together
★ Hydrogen bonds hold the polar side
chains and Ionic Bonds hold charged
side chains.
★ Sometimes, covalent disulfide bridges
may further reinforce the structure from
two sulfhydryl groups.
4. Quaternary Structure
★ In some proteins, they even have this
structure occurring with the association
of two or more polypeptide subunits.
★ Some proteins have nonpolypeptide
components called heme (other fnctn).
DENATURATION .
➢ Even a slight change in the primary structure
can affect a protein’s shape and ability to
function.
➢ This refers to changes in the aspects of a
protein’s environment that could alter the
chemical bonds and interactions within a
protein, causing it to be destroyed and lose its
shape:
○ pH
○ salt concentration
○ temperature
○ Other aspects (polarity, charge, etc)
➢ When a protein in a test-tube solution has
been denatured by heat or chemicals, it can
sometimes return to its functional shape
when the denaturing agent is removed in a
process called renaturation.
★ Misfolding of polypeptides in cells is a serious
problem, as with cystic fibrosis, Alzheimer’s,
Parkinson’s, and mad cow disease, associated
with an accumulation of misfolded proteins.
○ X-ray Crystallography - the most common
method to determine 3D structure of
proteins, depending on the diffraction of
an X-ray beam by the
atoms of a crystallized
molecule. Using this
technique, scientists
can build a 3-D model
that shows the exact
position of every atom
in a protein molecule.
★ Alternatives for XRC: Nuclear
magnetic resonance (NMR)
spectroscopy, cryo-electron
microscopy and
bioinformatics.
 GENERAL BIOLOGY I & II
4. Nucleic Acids
➔ They store, transmit, and help express
hereditary information.
➔ It consists the elements: C,H,N,O,P
ROLES OF NUCLEIC ACIDS .
➢ Primarily, DNA carries the genetic information
and RNAs help in carrying-out protein
synthesis.
➢ Protein synthesis works through the process
of central dogma [DNA->RNA->Proteins].
COMPONENTS OF NUCLEIC ACIDS .
➢ They exists as polymers called
polynucleotides, and their monomers are
called nucleotides.
➢ Each nucleotide consists of:
○ Five-carbon Sugar (Pentose)
■ Deoxyribose [lacks an oxygen
atom in C2] for DNA and Ribose for END OF CHAPTER 1.
RNA
■ A nitrogenous base + pentose is
called a nucleoside, like adenosine
○ Nitrogenous Base
■ Purines - larger, six-membered,
fused with a five-membered ring.
Includes Guanine, Adenine
■ Pyrimidines - six-membered
carbon ring. Include Cytosine,
Thymine, and Uracil
○ One to Three Phosphate groups
■ These phosphate groups attach to
the 5’ carbon of sugar
➢ Not only DNA and RNA, there are also
nucleotides that do not carry-out these
functions such as:
○ Adenosine Triphosphate (ATP)
○ Cyclic Adenosine Monophosphate (cAMP)
○ Cyclic Guanosine Monophosphate (cGMP)
○ Nicotinamide Adenine Dinucleotide
(NAD+)
○ Nicotinamide Adenine Dinucleotide
Phosphate (NADP+)
○ Flavin Adenine Dinucleotide (FAD)
STRUCTURES OF DNA .
➢ Adjacent nucloetides are joined by
phosphodiester bonds, consisting of covalent
bonds through phosphate groups.
➢ This forms a repeating called the
sugar-phosphate backbone in DNAs and
RNAs
○ 5’ end - this is an end with an attached
phosphate at the 5’ carbon.
○ 3’ end - this is an end with a hydroxyl
group on a 3’ carbon.
➢ DNA Replication starts from 5’ to 3’
➢ DNA has two polynucleotide chains that
wind around an imaginary axis, forming a
double helix structure.
➢ The first one has a direction 5’->3’, while the
other runs from 3’->5’, and thus they are
termed as having an antiparallel structure.

DNA
● Stores genetic info
● Double helix structure
● Sugar is deoxyribose
● Bases are GCAT
● Found in nucleus and
mitochondria
RNA
● Transmits and copies
● Single-stranded
● Sugar is ribose
● Bases are GCAU
● Found in cytoplasm
 GENERAL BIOLOGY I & II

. LESSON 2: CELL BIOLOGY AND CYTOLOGY .

CELL THEORY . 3. Glycocalyx – this may be another network of
➢ Contributions: polysaccharides that project from cellular
○ Antony van Leeuwenhoek: a shoekeeper surfaces of bacteria, made up of a capsule
that crafts lenses, observed movements of 4. Cytosol – a jellylike semifluid substance in
unicellular organisms he called which organelles are suspended
animalcules. 5. Cell Wall – the rigid structure outside the
○ Robert Hooke: coined the term cell in his plasma membrane present in all prokaryotes
publication called Micrographia (1665), to 6. Plasma Membrane – aka cell membrane, the
which he observed plant cells thru cork membrane enclosing the protoplasm
tissues. 7. Ribosomes – these are complex proteins that
➢ Final ver. was developed by the late 1830s by also synthesize other proteins.
Matthias Schleiden [botanist], Theodor
Schwann [zoologist], and Rudolf Virchow. EUKARYOTES .
➢ Propositions: ➢ From the Greek eu – “true” and karyon –
1. All living things are composed of one “kernel / nucleus”; literally meaning true
or more cells nucleus
2. The cell is the basic unit of life ➢ These are cells that have a clearly-defined
3. Cells arise from preexisting cells nucleus and other membrane-bound
organelles
★ All cells share 4 common characteristics: ➢ They have several, rod-shaped chromosomes
A. Plasma membrane and more complex structures than prokaryotic
B. Cytoplasm cells
C. DNA [particularly, chromosomes]
D. Ribosomes

PROKARYOTES .
➢ These are simple, unicellular organisms,
lacking a nucleus or any membrane-bound
organelle
➢ In prokaryotes, the DNA is concentrated in the
center region called the nucleoid.

★ Cells keep their size small to optimize the

surface area — which determines the rate of
exchange of nutrients and wastes.
★ Sometimes, microvilli are present that increase
surface area without any appreciable increase
in the volume

Parts of a Prokaryotic Cell .

1. Fimbriae, Pilus, and Flagella – these are
hairlike appendages that help cells adhere to
other cells, move, and to be motile.
2. Nucleoid – this is the region where the cell’s
DNA is located / concentrated
○ Typically, circular chromosomes are
accompanied by ring-like DNA called
plasmids — a coiled DNA.
 GENERAL BIOLOGY I & II
The Compartments of Eukaryotic Cells . 6. Nucleoplasm
1. The Structural Support System ★ aka Karyoplasm
➔ Includes the Plasma Membrane, ★ Like the cytosol, it is the semi-solid fluid
inside the nucleus, where we find the
Cytoplasm, and Cell Wall (for some).
chromatin and the nucleolus.
➔ This is a set of structures that allow the
ORGANIZATION OF GENETIC MATERIAL .
existence of the structure of cells.
➢ The DNA is packaged into discrete packets
PLASMA MEMBRANE . called chromosomes that carry these genetic
➢ A phospholipid bilayer embedded with
information.
protein that separates internal content and
➢ Each chromosome contains one long DNA
environment of cells.
molecule associated with many proteins like
➢ It also controls the passage and leave of
histones that help DNA coil to reduce its
nutrients and wastes to and from the cell.
length and fit into the nucleus.
➢ May contain microvilli that are fingerlike
➢ The complex of DNA and proteins making up
projections that increase surface area.
the chromosomes is called the chromatin.
NUCLEOLUS .
➢ This is a prominent structure within the
nondividing nucleus that allows the synthesis
of ribosomal RNA (rRNA), used in synthesis of
ribosomes from the genes in DNA.
➢ Proteins are imported here from the
cytoplasm, assembled with rRNA into large
CYTOPLASM .
subunits of ribosomes, exiting thru pores.
➢ It is the entire region between plasma
➢ The nucleoli may also play a role in controlling
membrane and the nuclear envelope
cell division and the lifespan of a cell.
➢ It is made up of organelles suspended in the
gel-like cytosol, the cytoskeleton, and various
chemicals
➢ 70% to 80% water, having semi-solid
consistency due to proteins and others
2. The Nucleus
➔ This is the control center of the cell,
housing the cell's genetic material.
➔ It regulates gene expression, controls
cellular activities, and is responsible for
the replication and transcription
processes.
➔ Contains most of the genes and usually
the most conspicuous organelle
PARTS OF NUCLEUS .
1. Nuclear Envelope
★ Envelopes the nucleus, separating it from
the plasma membrane
2. Nuclear Pores
★ aka Pore Complex
★ These are structures that perforate the
nuclear membrane that allows the
passage of proteins and RNAs in and
out of the cell. RIBOSOME .
3. Nuclear Lamina ➢ These are protein-rRNA complexes that carry
★ These are netlike array of protein out protein synthesis.
filaments that lines the nuclear side of ➢ Cells with high rates of protein synthesis
the nuclear membrane
have particularly large numbers of
★ It is responsible for maintaining the
shape of the nucleus by mechanically ribosomes as well as prominent nucleoli.
supporting the nuclear envelope. ○ mRNA, tRNA, and microRNA in cytop.
4. Nuclear Matrix ○ rRNA in nucleolus
★ Although it has evidences, it hasn’t been ➢ Ribosomes carry protein synthesis out in 2 regions
confirmed yet in the cytoplasm:
★ It is a framework of protein fibers ○ Free ribosomes – suspended in cytosol; they
extending throughout the nuclear typically create ribosomes that function
interior within the cytosol themselves.
★ The nuclear lamina and matrix may help organize ○ Bound ribosomes – attached outside the
the genetic material so it functions efficiently. rough ER or the nuclear envelope; they
5. Perinuclear Space synthesize proteins destined for insertion
★ The nuclear envelope is a double into other membranes, packaging, or export
membrane of phospholipid bilayer. ➢ Has a large subunit and small subunit that
★ In between the two layers is a space together function as an interactive workbench,
called the perinuclear space. occurring as a catalyst to facilitate protein
★ aka perinuclear cistern synthesis.
 GENERAL BIOLOGY I & II
3. The Endomembrane System
➔ This is a network of membranous
structures within the cell that work
together to modify, package, and
transport lipids and proteins.
➔ They are responsible for the metabolic
functions inside the cell.
VESICLES .
➢ These are small, membrane-bound sacs that
transport and store substances within a cell.
➢ They are formed from segments of
membranes in the endomembrane system
and play crucial roles in various cellular
processes.
ENDOPLASMIC RETICULUM .
➢ From the word endoplasmic – “within the
cytoplasm” and reticulum – “L. little neck”
➢ The cisternal space of the nuclear membrane
is continuous with the lumen of the ER
➢ Have 3 main parts:
○ Cisternae – membranous tubules and
sacs; flattened for rough ER and curvy
for smooth ER
○ ER Membrane – separates internal
compartment of ER from the cytosol
○ ER Lumen – aka cisternal space, this is
the internal compartment or cavity of
ER.
1. Smooth Endoplasmic Reticulum
★ Termed as smooth because it does not
have any attached ribosomes
★ They are included in the synthesis of
carbohydrates, cholesterol, lipids, and
steroid hormones, as well as the
detoxification of some drugs and toxins
★ Termed as smooth because it does not
have any attached ribosomes
★ In muscle cells, they are specialized SER
are presented and they are called the
Sarcoplasmic Reticulum with functions:
○ Sequesters and releases calcium
ions in muscle cells
○ Regulates muscle contraction
and relaxation
2. Rough Endoplasmic Reticulum
★ Termed as rough because of ribosome
attachments on the surface
★ Many cells secrete proteins that are
produced by ribosomes attached in RER.
★ Their cytoplasmic surface of RER
possesses receptor molecules:
○ Ribophorins — for ribosomes and
○ Docking Proteins — for signal
recognition particles (SRPs)
(known
★ It also functions in the synthesis and
modification of proteins that are to be
packaged, as well as in the synthesis of
lipids and proteins found in the plasma
membrane of cells.
======================================================
SEQUENCE OF RER PROTEIN SYNTHESIS
I. As a polypeptide chain grows from a bound
ribosome, the chain is threaded into the ER lumen
through a pore formed by a protein complex in the
ER membrane and anchored there by their
hydrophobic portions.
II. The new polypeptide folds into its functional shape
as it enters the ER lumen. Enzymes built in the ER
membrane allow the modification of these proteins.
III. The proteins can either be incorporated in ER
membrane or secreted out of the cell (secretory
proteins)
IV. After secretory proteins are formed, the ER
membrane keeps them separate from proteins in the
cytosol, which are produced by free ribosomes.
● Transitional ER – this is a specialized region to
which secretory proteins depart from the ER.
The proteins are wrapped in the membranes of
vesicles that bud like bubbles called transport
vesicles.
V. After leaving the ER, transport vesicles travel to the
Golgi Apparatus (warehouse for manufacturing and
modifying proteins) or directly to their destination.
======================================================
GOLGI APPARATUS .
➢ aka Golgi Bodies, these are a series of
flattened membranes (the cisternae)
responsible for modifying, sorting, tagging,
packaging, and distributing proteins and
lipids.
○ cis Face – receiving side
○ trans Face – opposite, shipping side
★ Acc. to Cisternal Maturation Model, the cisternae
of Golgi progress forward from cis to trans face,
carrying and modifying the cargo as they move.
LYSOSOMES .
➢ These are membranous sacs of hydrolytic
enzymes that cells use to digest / hydrolyze
macromolecules
➢ Their enzymes work best in acidic
environment, found in lysosomes, which are
synthesized in RER and altered in GA.
➢ These organelles are formed by the utilization
of late endosomes as an intermediary
compartment, and some arise by budding
from the trans face of the Golgi apparatus.
1. Phagocytosis
★ Lysosomes carry out intracellular
digestion in a variety of circumstances.
I. When cells engulf smaller organisms
or molecules, this process is called
phagocytosis.
II. These substances fuse with the
lysosome, hydrolyzing them.
 GENERAL BIOLOGY I & II
III. The waste products pass / exit into
the cytosol and become nutrients for
the cell.
2. Autophagy
★ This is a process where lysosomes use
their hydrolytic enzymes to recycle the
cell’s own organic material.
★ It starts because of signals like nutrient
deprivation, stress, or damage.
I. In response to these, a small portion
of the ER, the Golgi, or the Plasma
membrane elongates and curves to
form a double-membrane structure
called the phagophore or isolation
membrane.
II. The phagophore expands and
engulfs a portion of the cytoplasm,
including organelles or other cellular
components targeted for degradation
to form an autophagosome.
III. The autophagosome undergoes a
series of maturation steps, including ENDOSOMES .
fusion with endosomes and ➢ These are intermediate compartments used
lysosomes, to form an autolysosome. for the destruction of endocytosed,
IV. The contents of the autolysosome are
phagocytosed, or autophagocytosed
degraded by lysosomal enzymes..
V. The degraded components are
materials or formation of lysosomes.
recycled back to the cytosol. ➢ They possess proton pumps which acidify
the interior compartment.
○ Early Endosomes — found at the
periphery of cell; contain receptor-ligand
complexes
○ Late Endosomes — found deeper within
the cytoplasm
➢ Receptors allow more concentration to be
endocytosed in a process called
receptor-mediated endocytosis that involves
formation of a clathrin-coated vesicle that
sheds its coat once inside and fuses with an
early endosome.
➢ Receptors are carried into a system of tubular
vesicles, recycling endosomes, from which
the receptors are returned to the
plasmalemma, whereas the ligands are
translocated to late endosomes.

VACUOLES .
➢ These are large vesicles derived from ER and
Golgi Bodies
➢ Its membrane is selectively permeable for
transporting solutes and its interior has a
solution of different composition than cytosol
called the cell sap.
○ Food Vacuoles — formed by
phagocytosis, it allows the storage of food
by the cell
○ Contractile Vacuoles — they pump excess
water out of the cell that maintains ion
balance, used by many unicellular
freshwater protists
○ Plant and Fungal Vacuoles — carry out
enzymatic hydrolysis, hold reserves of
organic compounds, store defensive
poisons against herbivores, and even
pigments to attract pollinating insects
○ Central Vacuoles — typically large in plant
cells which develop by the coalescence of
smaller vacuoles.
★ Vesicles can fuse with other organelles,
while Vacuoles cannot fuse with other
components.
 GENERAL BIOLOGY I & II
4. The Metabolic Organelles
➔ They are responsible for generating the
energy required for various cellular
processes.
ENDOSYMBIONT THEORY .
➢ States that an early ancestor of eukaryotic
cells engulfed an oxygen-using non
photosynthetic prokaryotic cell.
➢ They endosymbiosed, merging into one single
organism that later became mitochondrion.
➢ By the same virtue, one ancestor has taken up
a photosynthetic prokaryote, becoming the
ancestor of chloroplasts.
===================================================
EVIDENCES FOR ENDOSYMBIOTIC THEORY
1. Similarity with bacteria
★ Chloroplasts and Mitochondria are the same size
as prokaryotic cells
★ They divide by binary fission, and have Fts
proteins at their division plane.
★ They replicate autonomously in the cell.
2. Presence of Plastids
★ Mitochondria and chloroplasts have their own
DNA that is circular, not linear.
3. Presence of Ribosomes
★ Mitochondria and chloroplasts have their own
ribosomes that have 30S and 50S subunits, not
40S and 60S.
4. Double-membrane Structure
★ Unlike the single-membraned endomembrane
system, they have a double membrane.
★ This implies invagination by ancestral eukaryotes
as with endocytosis.
5. Evolutionary Systematics
★ Several more primitive eukaryotic microbes, such
as Giardia and Trichomonas have a nuclear
membrane but no mitochondria.
===================================================
MITOCHONDRIA .
➢ Mitochondria are the sites of cellular
respiration, hence they are called the
“powerhouses” or “energy factories” of
a cell since they are responsible for
making adenosine triphosphate (ATP),
the cell’s main energy-carrying molecule.
➢ Cells with higher demand for energy
have more mitochondria to produce
ATP, like muscles, through chemiosmotic
coupling mechanisms because of the
enzymes in their cristae.
➢ They generate heat in brown fat instead
of producing ATP, assisting in the
synthesis of certain lipids and proteins
★ When your cells don’t get enough
oxygen, they do not make a lot of
ATP. They carry-out anaerobic
respiration, accompanied by the
production of lactic acid.
○ Cristae — the inner folds of the
mitochondrial membrane
○ Mitchondrial Matrix — the area
surrounded by the folds of the cristae.
CHLOROPLAST .
➢ It is a type of plastid found in plants and
algae as sites of photosynthesis.
➢ It has a very narrow intermembrane
space, housed by a double membrane.
○ Chlorophyll — green pigment that
captures sunlight for photosynthesis.
○ Thylakoid — these are flattened,
interconnected sacs stacked like
pancakes where light-dependent
photosynthesis takes place.
○ Granum — the term used to describe a
stack of thylakoids
○ Stroma — this is a fluid similar to
cytosol that fills the chloroplast.
 GENERAL BIOLOGY I & II
PEROXISOMES .
➢ These are specialized metabolic
compartments bounded by a single
membrane that houses oxidative enzymes
such as urate oxidase, D-amino acid
oxidase, and catalase.
➢ Peroxisomes contain enzymes that perform
OXIDATION — they remove hydrogen atoms
from various substrates and transfer them to
oxygen, producing hydrogen peroxide as a
by-product.
➢ Peroxisomes themselves are toxic, but
contain catalase that convert H2O2 to water.
➢ Most of the proteins intended for inclusions
into peroxisomes are synthesized in the
cytosol rather than on the RER.
➢ All peroxisomes are formed by fission from
preexisting peroxisomes
1. Peroxisomes break fatty acids
★ Some peroxisomes use oxygen to break
fatty acids down into smaller molecules
that are transported to mitochondria
and used as fuel for cellular respiration.
2. Peroxisomes detoxify alcohol
★ Peroxisomes in the LIVER detoxify alcohol
and other harmful compounds by
transferring hydrogen from the
poisonous compounds to oxygen.
3. Peroxisomes can store fats
★ Specialized peroxisomes called
GLYOXYSOMES are found in the
fat-storing tissues of plant seeds.
★ They contain enzymes that initiate the
conversion of fatty acids to sugar, which
the emerging seedling uses as a source
of energy and carbon until it can
produce its own sugar by photosynthesis.
PROTEASOMES .
➢ These are small, barrel-shaped organelles that
function in the degradation of cytosolic
proteins.
➢ The practice of cytosolic proteolysis is highly
regulated, and the candidate protein must be
TAGGED by several UBIQUITIN molecules
before it is permitted to be destroyed.
○ 26S Proteasome System — the larger
protease that “splits” the proteins into
smaller subunits.
○ 20S Proteasome System — the smaller
protease that consumes the splitted
protein subunits. It also degrades proteins
that are oxidized by reactive oxygen
species to form protein carbonyls.
5. The Cytoskeleton
➔ This is a dynamic network of protein fibers
that provide structural support to the cell,
maintain its shape, and facilitate
movement.
➔ It is involved in various cellular functions,
including intracellular transport, cell
division, and cell signaling.
● Cell Motility – this is the movement
and change in location of cell parts. It
generally requires interaction of the
cytoskeleton with motor proteins.
MICROTUBULES .
➢ These are hollow rods of 25 nm with 15 nm
lumen in diameter.
➢ It is a protein polymer made up of globular
proteins called tubulin dimers. Their walls
consist of 13 polymerized α- and β-tubulin
monomers.
➢ They grow in length by adding tubulin
dimers that can be disassembled and built
elsewhere.
○ Plus end — mobile end of MT.
○ Minus end — anchored on centrosom.
➢ It functions in:
○ Maintenance of cell shape
○ Cell motility – they serve as tracks along
which organelles equipped with motor
proteins can move
○ Chromosome movements / separation
during cell division
○ Organelle movements – microtubules
guide vesicles from the ER to the Golgi
apparatus and from the Golgi to the
plasma membrane
===================================================
AFFILIATED ORGANELLES OF MICROTUBULES
1. Centrosomes
★ Present in Animal Cells, these
are structures to which
microtubules grow out from,
located near the nucleus.
★ The microtubules function as
compression-resisting girders
of the cytoskeleton.
★ Inside them is a pair of
CENTRIOLES composed of 9 sets
of triplet microtubules arranged
in a ring.
★ Centrosomes with centrioles is
the microtubule organizing
center (MTOC) that helps
organize microtubule assembly
in animal cells.
 GENERAL BIOLOGY I & II
2. Cilia and Flagella
★ Present in some eukaryotes, a specialized
arrangement of microtubules is responsible for
the beating of these structures.
★ Their primary functions are for locomotion and
movement through fluids.
★ Motile cilia appear numerously on cell’s surfaces,
having alternating power and recovery strokes,
much like the oars of a racing crew boat.
★ Non Motile cilium may also act as a
signal-receiving “antenna” for the cell, limited to
only one per cell.
★ Flagella only appears limitedly, has an
undulating motion like the tail of a fish.
★ All have a group of microtubules sheathed in an
extension of the plasma membrane.
★ It has 9 doublets arranged in a ring with 2 single
microtubules in the center, called the 9+2
pattern found in eukaryotic flagella and motile
cilia.
★ 9+0 pattern is observed in nonmotile cilia,
lacking a pair of microtubules.
● Basal Body – this is where the MTOC of a
cilium or flagellum is anchored in the
cell. It is structurally very similar to a
centriole, with microtubule triplets in a
“9 + 0” pattern. In fact, in many animals,
the basal body of the fertilizing sperm’s
flagellum enters the egg and becomes a
centriole.
★ Bending involves large motor proteins called
DYNEINS that are attached along each outer
microtubule doublet.
★ The outer doublets and two central
microtubules are held together by flexible
cross-linking proteins; the walking movement is
coordinated so that it happens on one side of the
circle at a time.
★ If the doublets were not held in place, the walking
action would make them slide past each other.
★ Instead, the movements of the dynein feet cause
the microtubules—and the organelle as a
whole—to bend.
===================================================
MICROFILAMENTS .
➢ aka Actin Filaments
➢ These are thin solid rods made of two
intertwined strands of actin (a globular
protein), of 7 nm diameter.
➢ It functions in the maintenance of cell shape,
changes in cell shape, muscle contraction,
cytoplasmic streaming in plant cells, cell
motility, and cell division in animal cells.
➢ They can have a linear or branched structure
when protein binds along in the side,
extending as a new network of filaments.
➢ Their role is to bear tension to support shape
and their role for cellular motility:
○ Cortical Microfilaments – a 3D network
formed by microfilaments inside,
adjacent to the plasma membrane to
help support the cell’s shape.
○ Microvilli – microfilaments make up its
core that increases its SA, allowing it to
absorb more nutrients.
○ Actin and Myosin – thousands of actin
filaments and thicker filaments made of
a protein called MYOSIN interact to cause
contraction of muscle cells.
 GENERAL BIOLOGY I & II
○ Pseudopodia – these are extensions that
cells use to crawl along a surface. It is
especially prominent with unicellular
protist Amoeba and some of our white
blood cells. Localized contractions
brought by actin and myosin are involved
in the amoeboid (crawling) movement.

6. The Extracellular Matrix

➔ This is a complex network
of proteins and
polysaccharides outside
the cell that provides
structural support,
segregates tissues and
regulates intercellular
communication.
➔ It plays a crucial role in tissue
development, wound healing,
maintaining the physical properties of
tissues, and even cell differentiation.
○ Cytoplasmic Streaming – this is a circular ➔ Collagen fibers are interwoven with
flow of cytoplasm within (large plant) carbohydrate-containing protein
cells. It is brought by actin-protein molecules called proteoglycans.
interactions, speeds up the movement of ★ Cells have protein receptors on their plasma
organelles and the distribution of
membrane, changing its molecular structure
materials within the cell.
when a molecule binds within the matrix.
★ The receptor, in turn, changes the
conformation of the microfilaments
positioned just inside the plasma membrane.
★ These conformational changes induce
chemical signals inside the cell that reach the
nucleus and turn “on” or “off” the transcription
of specific sections of DNA, which affects the
production of associated proteins, thus
changing the activities within the cell.

INTERMEDIATE FILAMENTS .
➢ These are fibrous proteins coiled into cable
shapes of 8–12 nm found in only animal cells.
➢ They are specialized for bearing tension, and
have a diverse class of cytoskeleton.
➢ Each type is constructed from a particular
molecular subunit belonging to a family of
proteins whose members include the keratins.
➢ It functions in the maintenance of cell shape,
anchorage of nucleus and certain, other
organelles, and formation of nuclear lamina
○ The nucleus typically sits within a cage
made of intermediate filaments.
○ Other intermediate filaments make up ○ Intercellular Junctions – allow plant cells
the nuclear lamina. to communicate through direct contact.
○ In general, the various kinds of ★ Plasmodesmata are junctions between plant
intermediate filaments seem to function cells, whereas animal cell contacts include tight
together as the permanent framework of junctions, gap junctions, and desmosomes.
the entire cell.
 GENERAL BIOLOGY I & II
CELL WALL .
➢ It is a rigid covering that protects the cell,
provides structural support, gives shape to
the cell, and prevents excessive uptake of
water.
➢ At the level of the whole plant, the strong
walls of specialized cells hold the plant up
against the force of gravity.
○ Prokaryotic cell walls are made of
peptidoglycan
○ Plant cell walls are made of cellulose
○ Fungal cell walls are made of chitin
○ Protistan cell walls are made of other
sugars and proteins, not having a fixed
composition
PARTS OF PLANT EXTRACELLULAR MATRIX
1. Microfibrils
★ They are made of cellulose, synthesized by
an enzyme called cellulose synthase and
secreted to the extracellular space, where
they become embedded in a matrix of
other polysaccharides and proteins.
★ Hydroxyl groups are free to hydrogen bond
with the hydroxyl groups of other cellulose
molecules lying parallel to it.
2. Ground Substance
★ It is an amorphous gel-like substance in the
extracellular space of animals that contains
all components of the extracellular matrix
(ECM) except for fibrous materials such as
collagen and elastin.
3. Primary Cell Wall
★ It is the flexible wall that young plant cells
first secrete.
★ It is relatively thin, whose main functions are
to protect the plasma membrane, maintain
turgor pressure, and allow for growth.
4. Middle Lamella
★ A thin layer between the adjacent primary
cell walls; it is rich is sticky polysaccharide
called pectin.
★ It glues adjacent cells together,
strengthening the plant once it stops grow.
5. Secondary Cell Wall
★ Some cells strengthen middle lamella, while
some add a secondary cell wall.
★ It is deposited in several laminated layers,
has a strong and durable matrix that affords
cell protection and support.
★ The primary function of the secondary cell
wall is to strengthen the cell and prevent it
from bursting under high water pressure.
ANIMAL EXTRACELLULAR MATRIX .
➢ The main ingredients of the ECM are
glycoproteins and other
carbohydrate-containing molecules secreted
by the cells.
COMPONENTS OF ANIMAL ECM
★ Collagen forms strong fibers
extracellularly
★ Large proteoglycan complexes can form
when many proteoglycan molecules
become noncovalently attached to a
single long polysaccharide molecule.
INTEGRINS .
★ These are surface receptor proteins to
which fibronectins and other ECM proteins
bind.
★ They span the membrane and bind on their
cytoplasmic side to associated proteins
attached to microfilaments in the
cytoskeleton.
★ Integrins are in a position to transmit
signals between the ECM and the
cytoskeleton and thus to integrate changes
occurring outside and inside the cell.
➔ Current research on fibronectin, other ECM
molecules, and integrins reveals the influential
role of the ECM in the lives of cells.
➔ By communicating with a cell through
integrins, the ECM can regulate a cell’s behavior.
➔ Researchers have also learned that the
extracellular matrix around a cell can influence
the activity of genes in the nucleus.
➔ Information about the ECM probably reaches the
nucleus by a combination of mechanical and
chemical signaling pathways.
CELL JUNCTIONS .
➢ These are sites of physical contacts to which
cells communicate upon.
1. Plasmodesmata
★ Plant cell walls are perforated with
plasmodesmata — channels that
connect cells, lined with membranes.
★ Although not connected directly,
plants use vascular tissues and
plasmodesmata to transport
materials, with aid from cytoskeleton,
cell-to-cell and throughout the plant.
★ They are continuous and they unify
most of the plants in a one continuum.
 GENERAL BIOLOGY I & II
2. Tight Junctions
★ In these junctions, the plasma
membranes are very tightly pressed,
bound together by proteins, primarily
claudins and occludins.
★ They form continuous seals around cells
that establish a barrier preventing the
leakage of extracellular fluid across a
layer of epithelial cells.

FORMATION OF GAP JUNCTIONS .

★ They develop when a set of six proteins called
CONNEXINS in the plasma membrane arrange
themselves in an elongated donut-like
configuration called a CONNEXON.
★ When the pores of connexons in adjacent animal
cells align, a channel between the two cells forms.

3. Desmosomes
★ Is a type of an ANCHORING junction
★ aka Adhesion Junctions
★ It functions like rivets that fasten cells
together into strong sheets.
★ Sturdy keratin protein called cadherins
typically allow this anchoring by
connecting the intermediate filaments
of adjacent cells..

END OF LECTURE 1.

4. Gap Junctions
★ aka Communicating Junctions
★ They provide cytoplasmic channels from
two adjacent cells, functioning similar to
plasmodesmata in plants.
★ Membrane proteins extend to two
membranes that create pores through
which small molecules may pass.
★ They are necessary for communication
of cells
 GENERAL BIOLOGY I & II
PLASMALEMMA .
➢ A common term for cell membrane
➢ It is the selective, structural barrier between the
cell and outside world composed of a
phospholipid bilayer with embedded proteins
and other lipids.
History of Membrane Models .
1. Gorter–Grendel Model (1925)
➔ Proposed that plasmalemma is composed
of lipid bilayers.
➔ The cell membrane has a phospholipid
with hydrophobic tails facing inward and
hydrophilic heads facing outward.
2. Davson–Danielli Model (1935)
➔ aka Sandwich Model of the plasmalemma
➔ Basically, the lipid bilayer is coated on both
sides by a layer of hydrophilic proteins.
➔ The model could not explain the fluidity of
the membrane and the diversity of
membrane proteins observed.
3. Robertson Model (1957)
➔ aka Unit Membrane Model
➔ TEMs suggested that all membranes have
the same structure — a trilaminar model.
➔ It suggested that there is a central lipid
bilayer flanked by two layers of proteins.
➔ The model implied that the protein layers are
tightly associated with the lipid bilayer.
➔ This did not fully address the mobility and
variability of proteins within the
membrane.
4. Singer–Nicolson Model (1972)
➔ Proposed the Fluid Mosaic Model
➔ It suggested a dynamic structure where
lipids and proteins can move laterally
within the layer.
➔ It is a 2D fluid embedded with proteins
The Fluid-Mosaic Model .
❖ Phospholipids and most membrane proteins
are amphipathic, implying that they have a
hydrophilic and a hydrophobic region.
❖ Although fluid, they are not randomly
distributed.
Components of the Cell Membrane .
1. Lipids
❖ Phospholipids – held by hydrophobic
interactions
❖ Cholesterol and sterols – contributes to
membrane fluidity
2. Proteins
❖ A study by Larry Frye and Michael Edidin
at Johns Hopkins University revealed that
membrane proteins are mobile.
❖ Integral proteins – proteins integrated
completely into the membrane structure;
they have transmembrane hydrophobic
segment
➢ G-Proteins – these are signaling
molecules embedded within the cell
membrane
❖ Peripheral proteins – these are proteins
that are found on the interior and exterior
membranes attached either to integral
proteins or phospholipids
3. Carbohydrates
❖ They can either be glycoproteins or
glycolipids
❖ They play an essential role in cell-to-cell
recognition
❖ They are collectively called glycocalyx as a
combination of sugar “coatings”
❖ They are hydrophilic and aid in the
interaction of the cell with its watery
environment and in the cell’s ability to
obtain substances dissolved in the water.
The Fluidity of Plasma Membranes .
★ Similar to an actual mosaic, the plasma
membrane has various classes of lipids,
proteins, and carbohydrates moving with
respect to one another.
★ It CAN’T contract or expand; it is fairly rigid
and can burst.
★ Membranes are NOT STATIC! They are held by
hydrophobic interactions rather than CB.
Thus, they can move around sideways or
flip-flop across by switching phosp. layers.
★ In some evolutionary adaptations, variations
in plasmalemma composition occurred under
specific environmental conditions.
★ Some even have the ability to modify their
plasmalemma composition on their own — all
in order to maintain the appropriate
membrane fluidity for them to function
efficiently.
 GENERAL BIOLOGY I & II
Factors Affecting Plasmalemma Permeability .
1. Membrane Composition
A. Saturation
➔ Saturated phospholipids have relatively
straight tails, resulting in compressed form.
❖ Lower temp. means more compressed,
dense, and rigid structure.
➔ Unsaturated phospholipids have bent kinks
of about 30 degrees.
❖ Kinks help to push phospholipids away
to maintain them fluid even at low
temp.
B. Length of Fatty Acids
➔ Shorter fatty acid chains reduce van der
Waals forces, increasing fluidity.
➔ Longer fatty acid chains increase
interactions, decreasing fluidity.
C. Cholesterol Content
➔ They lie alongside phospholipids in the
membrane which tends to dampen the
effects of temperature on the membrane.
➔ It acts like a buffer that prevents fluid
inhibition at lower temperature.
➔ It also is important in organizing
transmembrane protein clusters into lipid
rafts.
2. Sideway Movement of Phospholipids
➔ Their rapid sideway movement allows
phospholipids to change positions about
107 s-1.
➔ Proteins are larger than lipids and move
more slowly; many of them are immobile
because they are attached to the
cytoskeleton or ECM; some of the move
highly directed and some simply drift.
3. Temperature
➔ + temperatures = + KE = + movement = +
fluidity
4. Hydrostatic Pressure
➔ + pressure = + compress = - fluidity
5. Environmental Factors
➔ pH and concentration of ions affect
proteins & other macromolecules, and
thus the fluidity, indirectly.
Cell-to-Cell Recognition .
❖ A protein can carry-out on or more functions:
➢ Transport
➢ Enzymatic Activity
➢ Signal Transduction
➢ Cell-Cell Recognition
➢ Intercellular Joining
➢ Attachment to cytoskeleton or ECM
❖ Proteins on a cell’s surface are important in the
medical field.
❖ Carbohydrates are important for cell-cell
recognition, cell sorting for animal embryos,
and rejection of foreign cells or molecules.
❖ Membrane proteins are short which can be
glycolipids or glycoproteins, like the antigens
in RBCs.
Synthesis and Sidedness of Membranes .
❖ Membrane surfaces have asymmetry: different
characteristics on the two sides.
❖ There are differences in lipid composition
between the sides of a membrane.
❖ The mechanism for generating this sidedness is
unknown. Different enzymes appear on the
two sides of membranes.
Selective Permeability of Plasma Membrane .
❖ The plasmalemma exhibits selective
permeability, meaning it allows some
substances to cross more easily than others.
❖ Nonpolar, small, and uncharged molecules
can easily pass through because they are
hydrophobic and dissolve in the bilayer w/o aid.
❖ Ionic and polar molecules are hydrophilic, and
thus impeded by the hydrophobic interior to
traverse the lipid bilayer.
❖ Proteins built into the membrane also play key
roles in regulating transport.
● Channel proteins help the molecules to be
transported via passive transport.
★ Aquaporins - channel proteins that
allow passage of water molecules.
● Carrier proteins help the molecules to be
transported via active transport. They have an
open and closed configuration. They are aka
pumps.
★ Glucose transporter - only permits
glucose passage, esp. in RBCs
★ Sodium-potassium pump -
maintains resting potential in many
cells to balance the membrane
potential.
 GENERAL BIOLOGY I & II
Cell Transport System .
1. Passive Transport
➔ These are cellular transport mechanisms
that occur spontaneously without
requiring any energy input.
================================================
CONCENTRATION GRADIENT
➢ It is a form of chemical potential energy
➢ This is a region of space over which the
concentration of a substance changes
○ Moving against and up the concentration
gradient means moving from an area of
lower to higher concentration.
○ Moving down, with, and along the
concentration gradient means moving from
an area of higher to lower concentration.
================================================
A. Diffusion
➔ This is the movement of particles to spread
out into the available space.
➔ Each molecule moves randomly but a
population of molecules moves
directionally.
➔ Simple Rule Diffusion: in absence of other
forces, the substance will diffuse down its
concentration gradient, regardless of the
concentration of other substances.
➔ Most of cell traffic occurs by diffusion; they
will move with their C.G. if they are
permeable.
❖ Filtration – this is a variation of diffusion
where materials move according to its
CG, which is enhanced by pressure
allowing substances to pass through a
membrane .
======================================================
FACTORS AFFECTING THE RATE OF DIFFUSION
1. Pressure – + P = + KE = + Movement = + Diff
2. Extent of CG – more net concentration = rapid diff. ;
less net concentration = slow diffusion
3. Mass of Solute – heavier = slower ; lighter = faster
4. Temperature – more temp. = more energy = more
movement = higher rate of diffusion
5. Solvent Density – higher solvent density = lower diff.
6. Solubility – nonpolar = faster diffusion
7. SA & Thickness of Plasmalemma – + SA & thic = + diff
8. Distance to be Travelled – + distance = - diff ;
9. pH – neutral pH or optimal pH allow functionality
======================================================
B. Osmosis
➔ This is the diffusion of water through a
semipermeable membrane according to
the CG of WATER — inversely proportional
to the CG of solutes.
➔ It occurs when solutes are impermeable
with the membrane.
================================================
CELL-WATER BALANCE
● Tonicity – capability of a solution to affect the volume
of a cell by affecting osmosis.
○ Hypotonic: ECF lower osmolarity
○ Hypertonic: ECM has higher osmolarity
○ Isotonic: same osmolarity
● Osmolarity – describes the total osmoles
concentration of the solution
○ Osmotic P.: prevents inward flow
○ Turgor P.: pushes PM against CW
● Osmoregulation – homeostasis of conc.
○ Lysis: bursting due to hypotonic sol.
○ Crenation: shrinking / swelling, hypert.
================================================
C. Facilitated Diffusion
➔ aka Facilitated Transport, hydrophilic
molecules diffuse through membrane
proteins by their concentration gradient.
================================================
CHANNEL PROTEINS
➔ These provide corridors that allow specific
molecules or ions to cross the membrane
➔ They may be open all the time or gated.
CARRIER PROTEINS
➔ aka PUMPS, these proteins have open and closed
states which can be configured by the substance
binding into ligands.
➔ It is typically only for a specific substance and allows
the substance to move against its concentration
gradient.
★ Channel proteins transport much more quickly than do
carrier proteins
Classifications of channels / carriers :
❖ Uniporter – carries 1 specific ion or molecule
❖ Symporter – 2 same. ions / molec., same directions
❖ Antiporter – 2 diff. ions / molec., diff. directions
================================================
2. Active Transport
➔ This type of transport requires energy
because it requires the transport of
substances against their conc. Gradient in
order to balance the ECG.
================================================
ELECTROCHEMICAL GRADIENT
➔ This is the combination of electrical and chemical
gradients that affects ionic movement.
➔ EG & CG drive Na+ inward, while EG due to negatively
charged proteins drive K+ into while the CG drives K+
outside the cell.
● Electrogenic Pump – a transport protein that
generates voltage across a membrane,
================================================
A. Primary Active Transport
➔ A form of active transport that uses energy
from ATP Phosphorylation in order to
change the configuration of pumps.
================================================
SODIUM-POTASSIUM PUMP
➔ Animal cells have higher [K+] and lower [Na+], making
the cell more electrically negative than the
extracellular fluid.
➔ It helps to maintain the resting potential of a cell
================================================
 GENERAL BIOLOGY I & II
B. Secondary Active Transport ★ Transcytosis – a variation of potocytosis by
➔ aka Cotransport, it uses the stored PE from which smaller substances are used to
the electrochemical gradient of Na+ in transport molecules to be released on the
order to actively pump other materials other side of the cell after processing.
against their concentration gradient. ★ Receptor-mediated Endocytosis – aided
================================================ with receptors, this type of pinocytosis by
which bulk quantities of solutes attach to
COTRANSPORT
solutes. After attachment, these receptors
➔ Using the potential energy stored from the ECG of
gather around coated pits where they are
Na+, the sodium-glucose cotransporter facilitates
invaginated, and the receptors recycle after.
the transfer of glucose actively.
======================================================
FAMILIAL HYPERCHOLESTEROLEMIA
➔ In this genetic disease, the LDL receptors are
defective or missing entirely.
➔ This causes atherosclerosis because LDL (bad
cholesterol) is removed from the blood by
receptor-mediated endocytosis.
★ If uptake of a compound is dependent on
receptor-mediated endocytosis and the process is
ineffective, the material will not be removed from the
tissue fluids or blood.
======================================================

================================================
C. Bulk Transport
➔ This is a form of active transport that allows
the transport of more than one molecule
[especially macromolecules] at once in or
out of the cell where they are packaged in
vesicles.
◆ Exocytosis – it allows the export of waste materials by
enveloping them in transport vesicles until it fuses with
the plasma membrane where they are expelled.

END OF LECTURE 2.

◆ Endocytosis – a reverse of exocytosis where the plasma

membrane invaginates and pinches out that causes it to
form a vesicle that would transport the molecules inside.
○ Phagocytosis – a process of “cell eating” where it
engulfs large molecules by forming pseudopodia
and storing them in endosomes or food vacuoles.
I. Clathrin coats inner pseudopodia to stabilize it.
II. The pseudopodia engulfs the molecule, forming an
endosome or food vacuole.
III. The vesicle fuses with lysosome to be broken down
IV. Remaining waste particles are excreted to ECF
○ Pinocytosis – a process of “cell drinking” where the
cell engulfs water and other smaller particles from
ECF. Rather than pseudopodia, it invaginates.
Moreover, it happens in areas called coated pits
made of clathrin.
★ Potocytosis – a form of pinocytosis that uses
caveolin rather than clathrin also made of
lipid rafts & receptors, forming smaller
cavities than pinocytosis.