History of Philippine Biology
Regulation = homeostasis/balance regulation
Prehistoric times = all forms of life are sacred
Spanish conquistadores = shift from animistic
thinking to a more empirical one
o Father Manuel Blanco = author of Flora de
Filipinas Segun al Systema Sexual de Linnaco
(illustrations of plants found in Philippines)
o Together with: Antonio Llanos, Fr. Paul
Klein, Fr. Manuel Viiches, Sebastian Vidal y
Soler, Trinidad Pardo de Tavera, Dr. Leon
Maria Guerrero and Castro de Eleira
Biological researches = halted during Spanish-
American
o Dr. Gregorio T. Velasquez = father of
phycology in the Philippines (myxophycea
and blue-green algae)
o Dr. Jose Vera Santos taxonomy of grasses
(bamboo)
o Dr. Flordeliz R. Uyenco fungi and lichens
o Dr. Eduardo Quisumbing medicinal plants
in Philippines
Zoologists
o Dr. Hilario Roxas = fishes
o Dr. Leopoldo S. Clemente = geneticist
o Dr. Francisco Nemenzo, Sr. = corals
o Dr. Dioscoro Rabor = Philippine birds, bats
and rats
o Dr. Agustin Rodolfo = physiologist and
cytogeneticist
Concepts of Life, the Cell Theory and the
Scientific Method
Biology = scientific study of life
Life is recognized by what living things do.
Manifestations and properties
Manifestations of Life:
1. High degree of complexity & order = based on
hierarchy of structural levels with each
building on the levels below it
2. Reproduction = organisms reproduce their own
kind, asexually and sexually (biogenesis)
3. Growth and Development = heritable programs
stored in DNA
4. Energy Processing/ Utilization = organizing
take in and transform energy to do work,
including the maintenance of their
ordered state (use of light energy
during photosynthesis (Light E. ->
Chemical E. in the form of glucose
5. Response to Environment
6.
of internal environment to maintain a steady
state, even in the face of fluctuating external
environment
7. Evolutionary adaptation = interaction between
organisms
5 Unifying Themes
1. Organization = new properties energy at
successive levels of biological organization.
Life can be studied at different levels from
molecules:
i. Biosphere = sum of all the planet's ecosystems
ii. Biome = large scale ecosystem, predominant
vegetation type
iii. Ecosystem = energy processing system
including abiotic factors
iv. Community = group of diff. species
v. Population = group of same species
vi. Organism
vii. Organ and organ system
viii. Tissue
ix. Cell
x. Organelle
xi. Molecule
Emergent Properties = result from the arrangement
and interaction of parts within a system
= characterize non biological entities as well
Structure & Function = correlation between
structure and function
E.g. hummingbird's anatomy = wings are able to
rotate which allow them to fly backward or hover
in place
Cell = lowest level - can perform all activities
required for life
= basic unit of structure and function
Types of cell:
Eukaryotic cell
Prokaryotic cell
2. Information - expression and transmission
of genetic information
Chromosomes contain DNA -
deoxyribonucleic acid
Cell - Nucleus - chromosomes - DNA -
genes
DNA = genetic material that encode
information for building molecules or proteins and
it is made up of 2 long chains arranged in a double
helix. Each chain is made up of four kinds of
chemical building blocks called nucleotides
(AGCT)
3. Energy and matter - life requires the transfer and
transformation of energy and matter
i. The input of energy from the sun
and the transformation of energy from one form to
another make life possible
ii. Some energy is lost to the
surroundings as heat
4. Interactions - important to ensure smooth
integration of all parts between the components of
the system
Ecosystem = each organisms interact
continuously with other organisms. These
interactions can be beneficial or harmful which
also include interactions with physical factors
(abiotic)
Cells are able to coordinate various chemical
pathways through a mechanism called feedback.
Feedback regulation = many biological processes
are self regulating
Negative feedback = slows/stops processes, the
response reduces the initial stimulus
Positive Feedback = speeds a process up
5. Evolution (core theme of biology) - evolutionary
mechanisms account for the unity and diversity of
all species on Earth. Same species share the same
characteristics.
Classifying diversity of life
Approximately 1.8 M species have been
identified and named.
Taxonomy= group species based on their
common characteristics. Classifies species into
groups of increasing breadth
Domains= followed by kingdoms, are the
broadest units of classification
Domain - Kingdom - Phylum - Class - Order
- Family - Genus - Species
Organisms divided into three domains =
bacteria, archaea(extremophiles), eukarya
Domain bacteria and domain Archaea
compose the prokaryotes.
Classification is based on how they acquire
food.
Domain Eukarya (3 multicellular kingdoms)
Plants, Fungi
Unity = DNA is the universal genetic
language common to all organisms. Unity is
evident in many features of cell structure
Charles Darwin = theory of natural selection
1. Species showed evidence of descent with
modification from common ancestors
2. Natural selection is the mechanism behind
descent with modification
Species who have characteristics or traits
that enable them to survive will remain. Those who
don't acquire these characteristics go through
extinction. Those who survive reproduce and
passed their genes to their offspring. The
environment selects for the propagation of
beneficial traits. Natural selection results in the
adaptation of organisms to their environment.
Natural selection gives rise to two or more
descendent species.
Scientific Method - science = derived from Latin
that means to know. Includes observations,
forming logical hypotheses and testing them
Inquiry - search for information
Data - recorded observations
Qualitative = take the form of descriptions
Quantitative = expressed as numerical
measurements, organized tables and graphs
Controlled experiment = experimental group is
compared with a control group
Ideally, experimental and control differ in only one
factor
Without controls, the researchers would not be able
to rule out others factors that might have affected
the results.
Theory = broader in scope than a hypothesis. It can
lead to new testable hypotheses. It is supported by
a large body of evidence in comparison to
hypotheses.
Cell Structures
Discovery of cells arose from invention and
improvement of microscope in the 17th century
Robert Hooke - first to discover cells (1665)
Anton van Leeuwenheok - observed sperm,
bacteria cells.
Matthias Schleiden (plant tissue) and Theodor
Schwann composed the cell theory:
1. Cell is the unit of structure, physiology
and organization in living things.
2. The cell retains a dual existence
 3. Cells form by free cell formation, similar
to formation of crystals.

Rudolph Virchow - "all cells only arise from pre-

existing cells" not through spontaneous generation
of cells.
Minimum resolution of light microscope - 2
microns (size of small bacterium)

All known living things are made up of cells. All

cells come from pre-existing cells. Cells contain
hereditary information which is passed from cell to
cell during cell division. Cells are basically the
same in chemical composition. Energy flow
(metabolism and biochemistry) of life occurs
within cells.

All cells are surrounded by a plasma membrane.

Cytosol = all cells have this semi-fluid substance
within the membrane containing the organelles
Chromosomes = all cells have genes in the form of
DNA
Ribosomes = all cells have tiny organelles that
make proteins using instructions contained in
genes

In eukaryotic cells, chromosomes are contained

within a membranous nuclear envelope.
Region between nucleus and plasma membrane =
cytoplasm
Plasma membrane = functions as a selective barrier
that allows passage of oxygen, nutrients, and
wastes for the whole volume of the cell.
*structure of the plasma membrane*
Hydrophilic - water-loving (head)
Hydrophobic- tails
Amphipathic = because of presence of hydrophilic
and hydrophobic

Nucleus = contains most of the genes in a

Prokaryotic cell = simple structure, lacks nucleus
(nucleoid)
eukaryotic cell, some genes are located in
mitochondria and chloroplasts
= averages about 5 microns in diameter
= separated from the cytoplasm by a double
membrane
= when double membranes are fused, a pore allows
large macromolecules and particles to pass through
= directs protein synthesis by synthesizing mRNA
which is then transported to the cytoplasm via the
nuclear pores.
Ribosomes = transport the mRNA's genetic
message into the primary structure of a specific
polypeptide (polymer of linked amino acids -
which are building blocks of proteins). This is
where translation occurs. Free to move around the
cytoplasm
mRNA - complementary of A is U instead of T
For every triplet codon = corresponds to a
particular amino acid
Nuclear lamina = network of intermediate
filaments that maintain the shape of the nucleus by
mechanically supporting the nuclear membrane
DNA and associated proteins (histones) organized
into chromatin- appear as diffused mass. When cell
prepares to divide through mitosis, chromatin
fibers coil up, seen as separate structures
(chromosomes)
Nucleolus = mass of densely stained fibers and
granules
Where ribosomal RNA (rRNA) is synthesized
which combines with proteins in the cytoplasm to
form the ribosomal subunit.
Ribosome = composed of 2 subunits that combine
for protein synthesis
Free ribosomes - suspended in the cytosol and
synthesize proteins that function within the cytosol
Bound ribosomes - attached outside the
endoplasmic reticulum
These synthesize proteins that are either included
into membranes or for export from the cell.
The Endomembrane System
= internal membranes in a eukaryotic cell can
either be in contact or connected via transfer of
vesicles, sacs of membrane with this system
= Includes:
Nuclear envelope
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vacuoles/vesicles
Plasma membrane
*structure*
= plays a key role in synthesis and hydrolysis of
macromolecules in the cell
ER = includes tubules, and internal fluid filled
spaces, cisternae
Smooth ER = lacks ribosomes
= for synthesis of lipids, oils phospholipids and
steroids and metabolism of carbohydrates
= catalyzes a key step in the mobilization of
glucose from stored glycogen in the liver
= Other enzymes in SER of the liver help detoxify
drugs and poisons which include alcohol.
Rough ER = contain bound ribosomes attached on
the outside
= abundant in cells that secrete proteins e.g.
pancreatic cells that synthesize protein insulin on
the ER
= a polypeptide is synthesized by ribosome,
threaded in to space through a pore formed by a
protein in the ER membrane
=many of these polypeptides are glycoproteins
These secretory proteins are packaged in transport
vesicles that carry them to their next stage.
= is a membrane factory
Membrane-bound proteins are synthesized
directly into the ER membrane
Enzymes in the rough ER also synthesize
phospholipid from precursors in the cytosol
Golgi Apparatus = many transport vesicles from
the ER travel to Golgi for modification of their
contents = center of warehousing, sorting and
shipping
= usually extensive in cells specialized for
glycoprotein
= contains of flattened membranous sacs, cisternae
which separate its internal space form the cytosol
= 2 sides of Golgi = cis side (receiving side, fuses
with vesicles), trans side (buds off vesicles that
travel to other sites)
Lysosomes = digestive components
= membrane bound sac of hydrolytic enzymes that
digests macromolecules
= can hydrolyze proteins fats polysaccharides and
nucleic acids
= work best at pH 5
= rupturing one or few lysosomes has little impact
on a cell, massive leakage from lysosomes can
destroy an entire cell by autodigestion
= creates a space where the cell can digest
macromolecules safely
= synthesized by RER and then transferred to
Golgi
= arise from budding from the trans face of the
Golgi
= can fuse with other organelles = process called
autophagy
 Vacuoles/vesicles
Food vacuoles = form from phagocytosis, fuse
with lysosomes
Contractile vacuoles = found in freshwater protists,
pump excess water out of the cell
Central vacuoles = found in many mature plant
cells
Tonoplast = selective in transport of solutes into
the central vacuole
= contains glycolipids not phospholipids
Other Membraneous Organelles
Perixosomes contain enzymes that transfer
hydrogen from various substrates to oxygen
An intermediate product of this process is
h202, a poison but the perixosome has another
enzyme that converts h2o2 to water
Some perixosomes break fatty acids down
to smaller molecules that are transported to
mitochondria for fuel
Others detoxify alcohol and other harmful
compounds
Perixosomes are bounded by a single
membrane
Formed by incorporation of proteins and
lipids from cytosol
They split into two when they reach a
certain size
Mitochondria and chloroplasts
These are the organelles that convert
energy into forms calls can use for work
Mito are sites of cellular respiration,
generates ATP from the catabolism of sugars, fats
and other fuels in the presence of oxygen
Grow and reproduce as semiautonomous
organelles
Have small quantities of DNA that direct
synthesis of proteins
Chloroplasts
Sites of photosynthesis
Found in plants and eukaryotic algae
Convert solar energy to chemical energy
and synthesize new organic compounds from co2
and h2o
One of several members of a generalized
class of plant structures called plastids
Amyloplasts = store starch in roots and
tubers
Chromoplasts = store pigments for fruits
and flowers
Produces sugar via photosynthesis.
Measures about 2 microns x 5 microns
Found in leaves and other green structures
of plants and in eukaryotic algae.
Mitochondria
Have smooth outer membrane and a highly
folded inner membrane, the cristae
- Creates a fluid filled space between them
intermembrane space
- Cristae present ample surface area for the
enzymes that synthesize ATP
Inner membrane encloses the mitochondrial
matrix, a fluid-filled space with DNA, ribosomes
and enzymes
The processes in the chloroplast are separated from
the cytosol by two membranes
Inside the innermost membrane is a fluid filled
space, the stroma in which float membranous sacs,
the thylakoids
- Stroma contains DNA, ribosomes and
enzymes for part of photosynthesis
- Thylakoids, flatted sacs are stacked into
grana(sing. Granum) and are critical for converting
light to chemical energy
Cytoskeleton
- Network of fibers extending throughout the
cytoplasm
- Organizes the structures and activities of
the cell

- Provides mechanical
structural support and
maintains shape of the cell
- Functions in cell motility
and regulation
- Provides anchorage for
many organelles and cytosol
- Interacts with motor
proteins, in cilia and flagella.
Motor proteins pull compo
Motor molecules carry vesicles
or organelles to various
destinations along monorails
provided by the cytoskeleton
Microtubules move chromosomes during cell
division.
- Are the central structural supports in cilia
and flagella
Microfilaments, thinnest class of the cytoskeletal
fibers, are solid rods of globular protein actin.
Muscle cells, thousands of actin filaments are
arranged parallel to one another.
Cell surfaces and junctions
Cell wall - found in prokaryotes, fungi and some
protists
Protects the cell, maintains shape and
prevents uptake/leakage of water
Basic component are microfibrils of
cellulose embedded in a matrix of proteins and
other polysaccharides
Middle lamella with sticky
polysaccharides(calcium pectate) that holds cell
together
Lignin - secondary cell wall
Extracellular matrix (ECM) of animal cells
functions in support, adhesion, movement and
regulation
Plasmodesmata = allow cytosol to pass between
cells
3 main intercellular links = tight junctions (prevent
leakage), desmosomes(anchoring) and gap
junctions (communication)
Plant Crystals= wastes or excretory products of the
protoplasts, calcium oxalate and calcium
carbonate, druse, prismatic, styloid, raphide,
cystolith, lithocyst contains cystolith
Typical components of prokaryotic and eukaryotic
cells
Cell wall - protection; structural support -
prokaryotic(moneran), eukaryotic(protistan,
fungus, plant, animalia
Chromosomes - bearers of hereditary units(only
animalia)
Plasma membrane - regulation of the movement of
substances in and out of cells - moneral, protistan
fungus, plant, Animalia
Membrane Structure and Function
Plasma membrane = lipid bilayer with proteins and
carbohydrates forming the fluid mosaic model
= separates living cell from its surroundings
= selective permeability
Phospholipids = most abundant lipid
= amphipathic molecules
Fluidity of membranes
o Lateral movement (107 times per second)
o Flip-flop (once per month)
o Fluid = unsaturated hydrocarbon tails with
kinks
o Viscous = saturated hydrocarbon tails
o Cholesterol within the animal cell membrane
o Warm temp (37) restrains movement
o Cool temp maintains fluidity, prevents tight
packing
Proteins = in the membrane determines
membranes specific functions
o Peripheral bound to the surface
o Integral penetrate hydrophobic core
o Transmembrane integral proteins that span
the membrane
6 major functions of membrane proteins
o Transport
o Enzymatic activity
o Signal transduction
o Cell-cell recognition
o Intercellular joining
o Attachment to the cytoskeleton
Cell-cell recognition(carbohydrates)
o Cells recognize each other by binding to
surface molecules
o Covalently bonded to lipids, glycolipids or to
proteins, glycoproteins
o Carbs vary among species, individuals and
even cell types of an individual
Permeability of membrane
o Selective regulates cells molecular traffic
o Non polar can dissolve in the lipid bilayer and
pass thru membrane rapidly
o Polar molecules do not cross easily
Transport proteins
o Allows transport of polar substances
o Channel proteins = has hydrophilic channel
that certain ions or molecules can use
o E.g. aquaporins for water
o Carrier proteins = bind to molecules and
change shape
o Specific for the substance it moves
Passive Transport
o Substance diffuses down their concentration
gradient
Osmosis = water diffuses across a membrane from
the region of low solute conc to a region of high
solute conc.
Tonicity = ability of a soln to cause cell to gain or
lose water
Isotonic = solute conc equal
o Plant = flaccid; animal = normal
Hypertonic solute conc higher outside the cell
o Plant = plasmolysed; animal =
crenate/shrivered
Hypotonic solute conc lower outside the cell
o Plant = turgid; animal = burst/lysed
Osmoregulation = control of water balance
= contractile vacuole when full, the canals and
vacuole contract expelling fluid from the cell
Facilitated Diffusion
o channel proteins = provide corridors
e.g. aquaporins; ion channels = open or close
in response to a stimulus (gated channels)
o carrier proteins = change shape that translocate
the solute-binding site across the membrane
Active Transport = moves molecules against their
concentration gradient
= requires energy (ATP)
= performed by specific proteins embedded in the
membranes
= Sodium-potassium pump
cystoplasmic Na+ binds to the Na-K pump
Na+ binding stimulates phosphorylation by
ATP
Phosphorylation cause protein to change
shape, Na+ expelled outside
K+ released, cycle repeats
Loss of phosphate group restores proteins
original shape
K+ binds on the extracellular side and
triggers release of PO4 group
Membrane potential = voltage difference across a
membrane cause by the differences in distribution
of + and ions
Electrochemical gradient = drives the diffusion of
ions across a membrane
- Chemical force = ions conc gradient
- Electrical force = effect of the membrane
potential on the ions movement
Electrogenic pump = transport protein that
generates voltage across a membrane
Sodium-potassium pump = major electrogenic
pump of animal cells
Proton pump = plants, fungi and bacteria
= occurs when active transport of a solute
indirectly drives transport of another solute
= plants use the gradient of hydrogen ions
generated by hydrogen ions generated by proton
pumps to drive active transport of nutrients into the
cell
Bulk transport = large molecules via vesicles
= requires energy
= exo and endocytosis
Exocytosis = transport vesicles migrate to
membrane, fuse with it and release their contents
Endo = takes in macromolecules by forming
vesicles from the plasma membrane
- Phago cell engulfs a particle in a vacuole,
vacuole fused with a lysosome to digest the
particle
- Pino molecules taken up when extracellular
fluid is gulped into tiny vesicles
- - Receptor-mediated endo binding of ligands
to receptors triggers vesicle formation; ligand
is any molecule that binds specifically to a
receptor site of another molecules