WHAT IS SCIENCE?

Characteristic of Life
 knowledge or a system of knowledge 1. Organization
covering general truths or the operation of 2. Metabolism
general laws especially as obtained and 3. Growth and development
tested through scientific method (Merriam- 4. Reproduction
Webster) 5. Responsiveness / irritability
 derived from the Latin word Scientia 6. Heredity
(knowledge based on demonstrable and 7. Homeostasis
reproducible data) 8. Adaptation through evolution

Scientific method Zoology and its Branches

1. Ask a question Taxonomic Divisions
2. Do your research  Acarology
3. Form a hypothesis  Mammalogy
4. Test your hypothesis  Herpetology
a. TYPES OF VARIABLES:  Ornithology
i.Independent Variable:  Ichthyology
 what you change in the experiment  Entomology
 Predictable change  Arachnology
 Graphed on the X-axis  Nematology
ii.Dependent Variable:  Helminthology
 what you measure in an experiment  Spongiology
 Unpredictable change  Malacology
 Graphed on the Y-axis  Carcinology
b. Must-haves before starting experiments: Basic Divisions
i. List of materials  Genetics
ii. Variables  Ecology
iii. Step-by-step instructions  Molecular Biology
iv. Data table to record results (or data  Evolution
notebook)  Anatomy
5. Analyze data
 Morphology
6. Draw your conclusions
 Cytology
7. Communicate the results
 Physiology
 Histology
Theory - “well-substantiated explanation of
some aspect of the natural world that can  Taxonomy
incorporate facts, laws, inferences, and tested  Ethology
hypotheses.” (National Academy of Sciences)  Embryology
 Explanation of a phenomenon; can be  Zoogeography
subject to revision  Pathology
 Parasitology
Law
 used to describe an action under certain
circumstances
 a description, usually mathematical, of some Classification and nomenclature of animals
aspect of the natural world. Aristotle: Scala Naturae
 Generalization about a phenomenon; not  Species are permanent, are perfect and do
subject to revision not evolve
 A concise summary of so many facts
1700s: Biology in Europe and America was
dominated by Natural Theology (a philosophy
Limitations of Science dedicated to discovering the Creator’s plan by
 Cannot make moral judgements studying nature)
Adaptations of organisms as evidence
 Cannot make value judgements
that the Creator had designed each and every
 As limited as the instruments we use
species for a particular purpose
 Limited by the knowledge we already have
 Limited by scientists
Carolus Linnaeus (1707 – 1778)

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  Swedish physician and botanist 5. If more than 1 scientific names are given, the
 Sought to discover order in the diversity of life first one that got published is adapted and the
“for the greater glory of God” others are considered synonyms.
 Systema Naturae (1735)
 Father of Taxonomy THE CELL
 Developed binomial nomenclature
Robert Hooke (1635-1703)
Basic taxa (singular: taxon-category)  the first person to see and name CELLS
Domain > Kingdom > Phylum > Class > Order >
Family > Genus > Species Robert Brown (1773-1858)
 Discovered and named the nucleus (1833)
Means of Classifying Organisms:
1. Means of obtaining energy (autotrophic vs. Matthias Jakob Schleiden (1804-1881)
heterotrophic)  studied plant tissues and concluded that all
2. Modes of reproduction (asexual vs. sexual) plants are aggregates of individual cells
3. Organization (unicellular vs. multicellular) which are fully independent (1838)
4. Type of cell (prokaryotic vs. eukaryotic)
5. Appearance Theodore Schwann (1810-1882)
 studied animal tissues and concluded that all
Three-domain system (Six-kingdom system) animals are aggregates of individual cells
1. Bacteria which are fully independent (1839)
2. Archaea
3. Eukarya Rudolf Virchow (1821-1902)
a. Protista  In 1858, he published “Omnis cellula e
b. Plantae cellula” ("every cell originates from another
c. Fungi existing cell like it")
d. Animalia
Schwann, Schleiden and Virchow are considered
More bases of Classification: the authors of the MODERN CELL THEORY
1. Evolutionary phylogeny (phylogenetic trees)
2. DNA and biochemical analysis Cell is the basic structural and functional unit in
3. Morphology any living thing and these cells arise from
4. Embryology preexisting cells

Basis of Classification General Attributes of the Cell

Evolutionary Phylogeny - believes that  A cell can eat, grow and move.
organisms descended from a common ancestor  A cell can perform necessary maintenance,
through the process of evolution recycle parts and dispose of wastes.
Phylogenetic trees - graphic depictions of the  Cell can adapt to changes in its environment.
evolutionary descent of organisms  It can replicate itself.
DNA and Biochemical Analysis - Comparisons of
DNA, enzymes, proteins, chemical reactions
between and among organisms
Morphology - based on superficial resemblances

Rules in Nomenclature:
1. Scientific name should be in Latin.
2. It is composed of the generic and the specific
names. (binomial)
3. It is written either in Italics or underlined
separately. The first letter of the genus name
is capitalized while the rest are in lower case.
(Homo sapiens ; Homo sapiens)
4. Only scientific names given after the
publication of Linnaeus’ Systema Naturae are
considered valid.

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Chemistry of the cell f. High specific heat
The CELL: Chemical Components
ESSENTIAL ELEMENTS

g. High heat of vaporization

h. Forms ice with decrease in temperature

2. Gases
3. Inorganic salts

MACROMOLECULES:
POLYMERIZATION

ORGANIC COMPOUNDS:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids

General formula: 1C:2H:1O

a. monosaccharides / simple sugars
 the basic building blocks of most
carbohydrates
 can be trioses, pentoses, hexoses…
ex: ribose
deoxyribose
glucose/dextrose
galactose/cerebrose C6H12O6
fructose

i. Hexoses
INORGANIC COMPOUNDS
1. Water
Unique Properties:
a. Cohesion - water molecules stick to each
other
b. Adhesion - water molecules stick to other
surfaces
c. Surface tension - the ability to support small ii. triose and pentoses
objects
d. Capillary action - the ability to “climb”
structures
e. Universal solvent

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b. disaccharides /double sugars
Biological Roles of Carbohydrates:
ex: maltose
sucrose 1. Energy storage (glycogen and starch)
lactose (C12H22O11) 2. Structural support (cellulose and chitin)
3. Biological recognition processes

LIPIDS – hydrophobic molecules

a. Triglycerides or Fats/Oils
b. Compound lipids
1) Phospholipids
2) Glycolipids
c. Steroids

a. Triglycerides or Fats/Oils
- composed of 3 fatty acids and glycerol

Types of fatty acids:

a. Saturated fatty acids – have only single H
bonds joining C atoms

b. unsaturated fatty acids – have a double

bond joining C atoms

c. POLYSACCHARIDES: large polymers of simple

sugars connected by covalent bonds
(glycosidic bonds)

c. Polyunsaturated fatty acids - have more

than 1 double bonds

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 Saturated (fats) : no double Unsaturated (oils): a double bond Polyunsaturated
bonds; saturated with ("kink") forms (loss of 2 hydrogens) (margarine, crisco) -
hydrogens. hydrogens are added
synthetically
Solid at room temperature - Liquids at room temperature - olive oil, Solids at room temperature -
animal fats (bacon, lard, butter, corn oil, cod liver oil, peanut oil, liquid oil converted to a solid
cheese, shortening, chocolate, almonds, mayo, sunflower oil. shortening - margarine or
coconut oil) semi-solid "soft" margarine

Biological Roles of Fats: Functions:

1) energy storage regulate metabolism, immune response,
2) insulation reproduction and other essential biological
3) padding processes

b. Compound lipids Proteins

1. Phospholipids  the most abundant organic compound in
 glycerol + 2 fatty acids + phosphate group the animal protoplasm
 Amphipathic molecule  monomers: amino acids (essential or
 basic structural component of cell non-essential)
membrane
types of proteins:
Biological roles: a. Simple proteins
1. Act as building blocks of the biological cell b. Conjugated proteins
membranes in virtually all organisms 1. glycoprotein – protein + carbohydrate
2. Participate in the transduction of biological 2. lipoprotein – protein + lipid
signals across the membrane 3. chromoprotein – protein + pigment
3. Act as efficient store of energy as with 4. phosphoprotein – protein + phosphate
triglycerides 5. flavoprotein – protein + FAD (flavin
4. Play an important role in the transport of fat adenine dinucleotide)
between gut and liver in mammalian
digestion Essential Amino acids:
5. An important source of acetylcholine (the 1. Isoleucine
most commonly occurring neurotransmitter 2. Leucine
substance occurring in mammals) 3. Lysine
4. Methionine
2. Glycolipids – lipid + carbohydrate 5. Phenylalanine
6. Threonine
Biological roles: 7. Tryptophan
1. provide energy 8. Valine
2. serve as markers for cellular recognition 9. Histidine
(ex: blood grouping)
Non-Essential Amino acids:
c. Steroids 1. Alanine
 no fatty acid component 2. Arginine
 contain the characteristic 4 cycloalkane rings 3. Aspartate
joined to each other 4. cysteine
5. Glutamate
6. Glutamine
7. Glycine
8. Proline
9. Serine
10. Tyrosine
11. Asparagine

Levels of Structure:

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 1. Primary structure - sequence of amino acids
forming a chain connected by peptide bonds

2. Secondary structure - spatial arrangement of

amino acids that are close to each other in the
peptide chain

Random Coil
Alpha helix

3. Tertiary structure - the 3D

relationship of the amino
acid segments that may be
ENZYMES - biological / organic catalysts
far apart from each other in
the linear sequence  catalyst - substance that accelerates
chemical reaction without undergoing
change
 substrate – substance that an enzyme acts
on

Mechanism of Enzyme Action:

a. Lock and key model

Chemical bonds contributing to protein’s tertiary

structure

4. Quaternary structure - arrangement of b. Induce fit model

protein subunits with complex proteins made
up of 2 or more subunits

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Factors affecting Enzyme Activity: e. inhibitors

a. Temperature

b. pH

Biological Roles of Proteins:

a. Catalyst
b. Structural
c. Transport
d. regulatory
e. Defense
f. Movement
g. Storage

Nucleic Acids
monomers:
 nucleotides
c. Concentration of substrate  nucleotide components:
o phosphate group
o pentose sugar
o nitrogenous base (purine:
adenine & guanine) (pyrimidine:
thymine, uracil, cytosine)

d. Concentration of enzyme

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Types of Nucleic Acids:
a. Deoxyribonucleic acid (DNA)
b. Ribonucleic acid (RNA)
Types of RNA:
1. messenger RNA (mRNA)
2. transfer RNA (tRNA)
3. ribosomal RNA (rRNA)
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Biological roles of Nucleic Acids:
a. Carry and transmit genetic information
b. Govern protein synthesis
Part 2: Cell Structure & Function
The basic structural and functional unit of all
living things.
TYPES OF CELL:
 Eukaryotes
o Animal Cell
o Plant Cell
 Prokaryote
o Bacterial Cell
most bacteria ▪ 1-10 microns
eukaryotic cells ▪ 10-100 microns
Note:
 micron = micrometer = 1/1,000,000 meter
 diameter of human hair = ~20 microns
Why do we need to study cells?
Cells → Tissues → Organs → Bodies
 bodies are made up of cells
 cells do all the work of life!
Functions of Cells:
1. Gas exchange
2. Take in and digest food
3. Energy production (ATP)
4. Build molecules (macromolecules)
5. Excretion/removes waste
6. Controls internal conditions
7. Respond to external environment
8. Make more cells
3 Main Jobs of Cells:
 Make energy to be used for all cellular
activities as well as to clean up wastes
produced during the making of energy
 Make a lot of proteins
 Make more cells for growth and
repair/replacement of damaged cells
Organelle - a specialized subunit within a cell Osmosis: the diffusion of a solvent (water) down
that has a specific function, and is usually its concentration gradient across a selectively
separately enclosed within its own lipid bilayer. permeable membrane
 Nucleus
 centrioles
 Nucleolus
 cilia
 Mitochondrion
 flagella
 Lysosome
 peroxisome
 Ribosome
 Endoplasmic reticulum
 Golgi apparatus

Organelles that are involved in making ENERGY

 Mitochondria
 Lysosome
 Plasma Membrane - a semi-permeable
membrane

 Vacuole

Fluid Mosaic Model - the cell membrane is a

phospholipid bilayer with chunks of proteins
attached to its inner or outer surfaces and some
even embedded in it (“like protein icebergs
floating on a sea of lipids”)

Functions of the Plasma Membrane:

 Separates cell from the outside
(protection)
 Regulates entry and exit of materials
(controls transport)
 Recognizes signal from other cells (allows
communication between cells)

Transport Mechanisms Across Plasma

Membrane:
1. Diffusion
1. osmosis
2. Dialysis
3. Facilitated diffusion
2. Active transport
3. Bulk transport (endocytosis, exocytosis)

Diffusion: net movement of a substance from a

region with high concentration to a region with
low concentration; does not require energy

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Dialysis: the diffusion of a solute (salt, glucose, b. Endocytosis
etc.) across a selectively permeable membrane.

Facilitated diffusion: passive diffusion down the

concentration gradient but involves channel
proteins (pores)

Transport Mechanisms

Active Transport: movement of substances

across the cell membrane against its
concentration gradient; requires energy and a
protein carrier

BULK TRANSPORT:
a. Exocytosis

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Cell Communication: controls adhesiveness Nuclear envelope: porous double-membrane
between cells that encloses it; protects nucleus and regulate
material exchange between nucleoplasm and
Cytoplasm: cytoplasm
 the portion of the cell that lies within the cell Nucleolus: spherical body within the nucleus
membrane which is responsible for the manufacture of
 holds many cellular constituents, including ribosomes
the organelles Chromosomes: threadlike organized structure
 exists in a colloidal state (thus the term of DNA and proteins
cytosol)
Endoplasmic reticulum (ER): extensive network
Vacuoles and Vesicles – membrane sacs of membranes arranged as tubules and sacs
Functions: separating the lumen from the cytoplasm;
1. storage of food and/or water (food vacuole) connected to the nucleus; 2 distinct regions:
2. Storage of waste (e.g. contractile vacuoles) rough/granular ER (RER) Smooth/agranularER
(SER)
Lysosomes – membrane sacs containing Functions:
hydrolytic (digestive) enzymes; “suicide bags” 1. Manufactures membranes and
Functions: secretoryproteins
1. Digestion of food 2. Plays a role in storage, synthesis and
2. Destroy foreign materials transport of proteins
3. Clean-up and recycle 3. Carbohydrate and lipid synthesis

Mitochondrion: double-membrane organelle Ribosomes: granular structures which are

present in all aerobic cells; “powerhouse of the clusters of proteins and nucleic acids assembled
cell” from components made in the nucleolus
Types:
1. Attached ribosomes
2. Free/soluble ribosomes
Function: protein synthesis

Function: Production of ATP through cellular

respiration

Organelles that are involved in making

PROTEINS:
 Nucleus
 Nucleolus involvement of ER and ribosomesin protein
 Ribosomes processing
 Golgi Apparatus
 Endoplasmic Reticulum Golgi apparatus
 membrane network arranged as parallel
Nucleus: a membrane-bounded region that flattened sacs (cisternae)
contains the cell's genetic information (genome)  secretory organ of the cell
within it; dark and usually spherical in stained  “post office of the cell”
specimens Functions:
Functions: 1. Manufactures, modifies and stores ER
1. Control center of the cell products
2. Cell reproduction 2. Transport of proteins in secretory vesicles

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Golgi apparatus
and cellular
secretion

Organelles that are involved in CELL Peroxisome: microbodies; membrane-bound

REPRODUCTION: organelle containing oxidative enzymes
 Centrioles FUNCTIONS:
 Nucleus 1. detoxification (of alcohol)
2. Bile acid formation
Centrioles: cylindrical structures that are 3. Oxidative breakdown of fats
composed of groupings of microtubules
arranged in a 9+3 pattern ; Found in animal cells Part 3: Cellular Respiration (extraction of
FUNCTIONS: energy from food)
1. help to organize the assembly of CELLULAR METABOLISM = catabolism +
microtubules during cell division anabolism
2. The mother centriole has a central role in Catabolism
making cilia and flagella.  Decomposition
 Degradation
Organelles that are involved in CELL MOTILITY:  Destructive metabolism
 Cilia (cilium)  Complex substances to simple materials
 Flagella (flagellum)  Exergonic process

Cilia and Flagella: protrusions from some cells

that are formed from specialized groupings of
microtubules called basal bodies

Adenosine triphosphate (ATP) - the chief

energy currency of the cell

Cytoskeleton

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 NAD – nicotinamide adenine dinucleotide

GLYCOLYSIS - conversion of glucose to pyruvic

acid
ATP formation occurs in 2 ways:
1. Oxidative phosphorylation

2. Substrate-level phosphorylation

Products: 2 NADH, 2 H2O, 2 ATP (net)

STEPS:
(1) Anaerobic Respiration: (cytoplasm)
1. Glycolysis

(2) Aerobic Respiration: (mitochondrion)

2. Citric Acid Cycle / Krebs Cycle
3. Electron Transport
System/Respiratory Chain

OVERVIEW OF CELLULAR RESPIRATION:

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What happens to PYRUVATE?
DECARBOXYLATION: removal of CO2
DEHYDROGENATION: removal of H2
OXIDATION: loss of electrons
REDUCTION: gain of electrons

Products/turn: 3 NADH, 1 FADH2, 1 ATP

Electron Transport Chain

fate of PYRUVATE in the presence of oxygen
Structure of the MITOCHONDRION
FMN – flavin mononucleotide
Cyt - cytochrome
Complex II
OXIDATION: loss of electrons
REDUCTION: gain of electrons

AEROBIC RESPIRATION

CITRIC ACID CYCLE or TRICARBOXYLIC ACID

CYCLE or KREBS CYCLE
Carrier molecules:
NAD – nicotinamide adenine dinucleotide
FAD – flavin adenine dinucleotide

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SUMMARY

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