SHGenbio1

Biology
The exploration and understanding of the physical and chemical characteristics
defining all processes and principles that gives and identity to life as a holistic
and dynamic entity.
Branches of Biology
Mammalogy – study of mammals
Ornithology – study of birds
Herpetology – study of amphibians and reptiles
Ichthyology – study of fishes
Interdisiplinary Fields
• Genetics – Heredity and variation
• Molecular Biology – Biological molecules
• Taxonomy – Classification of organisms
• Systematics – Taxonomy with Genetics
• Anatomy – Structure
• Physiology – Function
• Morphology – Form
• Pathology – Disease
• Biogeography – Distribution
• Ecology – Interrelationships of organisms
• Environmental Science – environment as one dynamic

Theories on the Origin of Life

Biogenesis and Abiogenesis
• Biogenesis – life came from preexisting life forms; revolves around the concept
of the “mother
cell” – the source of all life
- Omne vivum ex vivo – “life came from life”
- Omnis cellula e cellula – “cells came from cells”
- Thomas Charlton Bastian
• Abiogenesis – life came from all non-living material
- Life supposedly came from the reaction of all inorganic matter which gave
rise to
the biomolecules, and eventually, the mother cell.
- Thomas Henry Huxley
Divine Creationism
• Life supposedly came from one “supreme being” or “higher state of consciousness”,
forming all life we see today.
The Philosophy of Eternity
• It upholds that there is an Alpha and an Omega – the first and the last.
• Plato, Boethius and St. Augustine of Hippo
Supporting Theories on the Origin of Life
Spontaneous Generation Theory
• Synthesized by Aristotle
• Life originated from an all-pure, non-living material through the catalysis of
pneuma
(Vital Heat)
• Disproved by John Needham (broth on flask), Francesco Redi (meat), Lazzaro
Spallanzani (broth on flask w/ cover), and ultimately by Louis Pasteur (swan neck)
in the 19th century.
Lamarckian Evolution
• Proposed by Jean Baptiste de Lamarck
• Concept of Transformism
• Life came from the agglutination of matter, which eventually acquired a form of
rudimentary nutrition, and then eventually the introduction of acquired
characteristics.
• Contradicted by Erasmus Darwin and eventually discarded by Charles Darwin
The Tree of Life and Darwinian Evolution
• First proposed by Erasmus Darwin and then expounded later by his son, Charles
Darwin, and his son’s colleague, Alfred Russell Wallace.Erasmus Darwin – in
ZoonomiaCharles Darwin and Alfred Wallace – in The Origin of Species
• Life came from an “primordial being”, believed as the “mother cell”
Haeckel’s Interpretation of Darwin’s “Tree of Life”
• It illustrates that life came from one “primordial being” that became complex
over time to form all species we see today.
• Ernst Haeckel expounded heavily on Darwin’s origin, generating a tree which
agrees much on Darwin’s ideas.
Big Bang Nucleosynthesis
• Proposed by Ralph Alpher and his disseration adviser, George Gamow in the 1940s,
and then added on by Hans Bethe.
• It proposes that the universe came from an entity called a “singularity”, whose
main characteristic is an unstable mass of isotopes.
• Due to constant collisions, this “singularity” exploded, and further collisions
and reactions formed the early universe, then the galaxies, stars, planets, and
eventually life.
Oparin - Haldane Theory and Miller-Urey Experiment
• Proposed by John Scott Haldane and Aleksandr Ivanovich Oparin in the 1920s, then
later proven by Stanley Miller and Harold Urey in the 1950s.
• Theory that suggested that life came from the violent reactions of the elements
existing from the Primordial Earth.
• It created a primordial “soup” from which the first mother cell came from
Panspermia (5th Century BC)
• Anaxagoras, then by J. J. Berzelius, H. von Helmholtz, S. Arrhenius, F. Hoyle and
C. Wickramasinghe, and recently by S. Hawking
• Life is everywhere, even outside of Earth; it is distributed by heavenly bodies
(asteroids, meteors, etc.)
Deep-Hot Biosphere Theory (1970s)
• Thomas Gold
• Proposed that life came from below the surface of the Earth
Deep-Sea Vent Theory (1988)
• Günter Wächtershäuser and Jeffrey L. Bada
• Life began deep under the sea, in the hydrothermal vents.
Characteristic of Life
• Growth – increase in size
• Development – changes that occur while an organism grows
• Reproduction – to ensure continuity
Asexual – without union of gametes
Sexual – with union of gametes
• Irritability / Excitability – responses
Tropism – plant response
Taxis – animals response
• Evolution and Adaption – change into meeting the demands of the environment
• Homeostasis – maintenance of the body; maintain constant, balanced state of the
body
(+) feedback – upon input of stimuli, response magnifies over time
(-) feedback – upon input of stimuli, response diminishes over time
Le Chatelier’s Principle – Shifting to a new balanced state once the previous
state has been disturbed.
• Metabolism and Energy Conservation – energy manipulation
Catabolism – breakdown
Anaphase – buildup
Adenosine Triphospate (ATP) – currency of energy
• Organization – organism hierarchy
Cells
The basic unit of life
Cell Theory
1. Cells are the basic unit of structure and function in an organism
2. All living things are made up of cells
3. Cells come from the reproduction of existing cells
History
• Zacharias Janssen – invented the compound optical microscope.
• Robert Hooke – observed a thin slice of cork from a bark of an oak tree;
described it as having a perforated and porous surface like honeycomb and called it
cellulae.
• Antoine van Leeuwenhoek – named the microscopic things he observed as
animalcules; devised his own microscope for biological specimens.
• Matthias Schleiden – German botanist who concluded that all plants were made up
of cells.
• Theodore Schwann – German zoologist who concluded that all animals were made of
cells.
• Rudolph Virchow – German physician who stated that all cells came from other
cells.

Cell Types
1. Nucleus
• Prokaryotes – cells that lack a nucleus; small in size with simple internal
structures
○ Nucleoid region - DNA
○ Cell wall (peptidoglycan) and have polysaccharide capsule
○ Ribosomes
○ Flagella, pili or fimbriae
• Eukaryotes – cells that has a nucleus; larger in size with complex internal
structures
○ Membrane bound nucleus - DNA
○ Membrane bound organelles
2. Nutrition
• Autotrophs – organism that produces complex organic compounds from simple
substances present in its surroundings, generally using energy from light or
inorganic chemical reactions.
• Heterotrophs – organism that ingests or absorbs organic carbon in order to be
able to produce energy and synthesize compounds to maintain its life.
• Chemotrophs – obtain their energy from chemicals (organic and inorganic
compounds)
3. Cellularity
• Unicellular – single-celled organism; consist of only one type of cell
• Multicellular – multi-celled organism; consist of more than one type of cell
Cell Structures
• Cell plasma /membrane
○ Thin barrier that forms the boundary separating an individual cell
○ Semi-permeable
○ Heads contain glycerol - Hydrophilic (attracts water)
○ Tails contain fatty acids - Hydrophobic (repel water) – make up a bilayer
Microvili – fingerlike projections where cells that specializes in absorption are
folded.

Molecule embedded within the phospholipid bilayer:

✓ Cholesterol
✓ Carbohydrates
✓ Membrane proteins

• Cell wall
○ Rigid layer for protection and shape to the cell
○ Plants & algae – Cellulose
○ Bacteria – Peptidoglycan
○ Fungi – Chitin
• Cytoplasm
○ Made up of organelles gel like cytosol (fluid portion consisting mainly water
(70-80
percent); made up of 80% water.
○ Where the metabolic process take place.

• Nucleus
○ Storehouse of genetic information and control center of the cell
○ Stores chromatin in a gel-like substance called the nucleoplasm
○ Nucleolus – condensed region of chromatin where ribosome synthesis occurs
○ Nuclear envelope – boundary of the nucleus; continuous with ER
○ Nuclear pores – allow substances to enter and exit the nucleus
• Ribosomes
○ Responsible for protein synthesis
○ Two subunits: Large and small subunits
○ Appear as clusters or single tiny dots
• Endomembrane System
○ Group of organelles and membranes that works together for manufacture, storage,
distribution and breakdown of lipids and proteins
○ Endoplasmic reticulum – modifies proteins and synthesis lipids; Lumen – interior
- Two parts: Rough (protein) and Smooth ER (lipids)
○ Golgi Apparatus – sorts, tags, packages, and distributes proteins and lipids
- receiving side – cis face; opposite side – trans face
○ Vesicles – membrane-bound sacs for transport, storage or secretory
○ Vacuoles – fluid-filled sac for storage of materials needed by the cell.
Central vacuole (plants) – regulates water concentration and supports expansion of
the cell
○ Lysosomes – round-shaped, membrane-bound structures that secrets digestive
chemicals; contains enzymes known as Lysozyme that defends cell from invading
bacteria and viruses.
○ Peroxisomes – contains digestive enzymes for breaking down toxic materials
• Mitochondria
○ Bean-shaped structure surrounded by two membranes: Inner and Outer
○ Supply energy to the cell by generating ATP by cellular respiration
○ Have ribosomes and DNA
• Chloroplasts
○ Only in plant cells
○ Structure for photosynthesis
○ Contains chlorophyll that captures light energy
○ Thylakoid – stacked fluid-filled membrane sacs
○ Granum / Grana – stack of thylakoids
○ Stroma – the fluid that surrounds the grana
• Endosymbiotic Theory – explains the origin of Mitochondria and Chloroplasts;
Eukaryotic cells
• Centrosome
○ Small dense region that serves as the main microtubule organizing center (MTOC)
○ Animal cells – Centrioles – aids in cell division
○ Organizes microtubules to form cilia and flagella
• Cilia and Flagella
○ Locomotory projections in eukaryotes
○ Both contain 9 microtubules doublets arranged in circle around 2 central
microtubules
○ Cilia – like a little hair with much shorter length
○ Flagella – like a whip or tail

• Cytoskeleton
○ Network of protein fibers that: help maintain shape of cell, secure some
organelles in specific positions, allow cytoplasm and vesicles to move within cell,
and enable cells within multicellular organisms to move.
Three Types of Fibers:
○ Microfilament – narrowest, functions in cellular movement, provide rigidity and
shape
○ Intermediate filaments – structural function, maintain shape, anchor the nucleus
and other organelles in place
○ Microtubules – widest, helps cell to resist compression, provide a track along
which vesicles move through, and pulls replicated chromosomes to opposite sides on
cell division.
Cell Division and Cell Cycle

Rudolph Virchow – Father of cell division

The cell cycle consists of:

Interphase – normal cell activity

• G1 (Primary Growth) – cells undergo majority of growth in size; organelles
duplicate
• S (DNA Synthesis) – each chromosome replicates to produce sister chromatids
(uncoiled)
- attached at centromeres
- contains attachment site( kinetochores)
• G2 (Secondary Growth) – duplicated DNA coils around histones – Chromatids;
chromatids form up into chromosomes
M-phase / Mitotic phase – cell division
Mitosis (Eukaryotes)
• Each new cell receives one copy of every chromosome that was present in the
original cell. Produces 2 new cells that are both genetically identical to the
original cell.
• Somatic cells only
• Division of the nucleus
• Also called Karyokinesis
Prophase – Nuclear envelope disappears, centrosomes produce centrioles, spindle
fibers are produced
- Centrioles migrate to the opposite ends of the cell
Metaphase – Spindle fibers become attached to the chromosome
- Chromosomes migrate and align at the center
Anaphase – Sister Chromatids migrate to the opposite ends of the cell
Telophase – cell invaginates or forms a dis-continuous plate at the middle and
separates into 2 new cells

Cytokinesis – cleavage of cell into two halves; animal – cleavage furrow; plant –
cell plate

Meiosis (Eukaryotes)
• A type of cell division that reduces the number of chromosomes in the parent cell
by half and produces four gamete cells. This process is required to produce egg and
sperm cells for sexual reproduction.

Binary Fission – asexual reproduction; cell division of prokaryotes

Checkpoints / Checkpoint Proteins:
Cyclin – master control protein
Cdk (Cyclin dependent kinase) – activator protein
CkI (Cyclin kinase Inhibitor) – inhibits Cdk
MPC (Maturation Promoter Complex) – ensures cell to reach maturity before going to
next phase
APC (Anaphase Promoter Complex) - promotes cyclin degradation and mitotic exit
G1 / S Checkpoint (Cell Growth Checkpoint) – checks whether the cell is big enough
and has made the proper proteins for the synthesis phase.
G2 / P or S / G2 (DNA Synthesis Checkpoint) – checks whether DNA has been
replicated successfully
M / A (Spindle Checkpoint) – prevents separation of the duplicated chromosomes
until each chromosome is properly attached to the spindle apparatus. In order to
preserve the cell's identity and proper function.
Functions of Cell Division:
• Reproduction
• Growth and Development
• Tissue Renewal
Cell Division – cells duplicate their genetic material which results in identical
daughter cells.
DNA – genetic information – genome
- packaged into chromosomes
Genome – the haploid set of chromosomes in a gamete or microorganism or in each
cell of a multicellular organism.
An average eukaryotic cell has about 1000 times more DNA than an average
prokaryotic cell.
Chromosomes - All eukaryotic cells store genetic information in chromosomes.
- Most eukaryotes have between 10 and 50 chromosomes in their body cells.
- Human cells have 46 chromosomes; 23 nearly-identical pairs
- composed of a complex of DNA and protein called
chromatin that condenses during cell
division
Parts of Chromosomes:
Chromonemata – coiled thread like filamentous structure
Chromomeres – bead-like enlargements
Centromere – clear zone that controls the movement of the chromosomes
Gametes – haploid cells – one set of chromosomes – 23 chromosomes
Somatic cells – diploid cells – two sets of chromosomes – 46 chromosomes
Centromere - a constricted region of the chromosome containing a specific DNA
sequence, to which is bound 2 discs of protein called kinetochores.
Kinetochores - serve as points of attachment for microtubules that move the
chromosomes during cell division:
Karyotype – a picture of the chromosomes from a human cell arranged in pairs by
size.
- First 22 pairs are called autosomes; last pair are the sex chromosomes
Homologous Chromosomes - The cell has two sets of each chromosome; one of the pair
is derived from the mother and the other from the father.
Spindle Fibers:
Mitotic spindle – form from the microtubules in plants and centrioles in animal
cells
Polar fibers – extends from one pole of the cell to the opposite pole
Kinetochore fibers – extend from the pole to the centromere of the chromosome to
which they attach
Asters – short fibers radiating from centrioles
Chiasmata – point of intersection between chromosomes
Polyploidy - cells and organisms are those containing more than two paired
(homologous) sets of chromosomes
Tetrads – pair of homologous chromosomes

Mitosis
Meiosis
# of cycle
1 – interphase
M –phase (PMAT)
1 – interphase,
M –phase (PMAT 1 & 2)
Cells
Somatic Cells
Germ Cells
Tetrads
Absent
Present - Interphase
Chiasmata and Crossing Over
Absent
Present –Interphase
Polyploidy
Diploid
Haploid

Metastasis – continuous cell division that results in malignancy and eventual tumor
formation.
Metastatic Suspension – Targeting of checkpoints
- suspension of cell division that allows continuous cell growth up
until it can no longer support itself and eventually dies by apoptosis (programmed
cell death)
If mitosis is not controlled, unlimited cell division occurs causing cancerous
tumors.
Oncogenes - specials proteins that increase the chance that a normal cell develops
into a tumor cell.
Replication – process of duplicating a chromosome
Sister Chromatids - replicated copies held together at centromere