LESSON 1 Introduction - systems biology, the exploration of a

Evolution- fundamental principle of biology biological system by analyzing the

Biology- the scientific study of life interac- tions among its parts

Properties of Life Structure and Function

1. Order- high order of complexity - Structure has a relation to function

2. Evolutionary adaptation- heritable traits
best suited for the environment The Cell: An Organism’s Basic Unit of Structure
3. Regulation- adjusting the body to the and Function
environment
4. Energy Processing- chemical energy in - Single celled: bacterium and archaea
food to do work - Eukaryotic cell: membrane-enclosed
5. Growth and Development- inherited organelles
genes control pattern of development - Prokaryotic cell: lacks nucleus and other
6. Response to environment- response to membrane-enclosed organelles
environmental stimulus
7. Reproduction

Five Unifying Themes

1. Organization
2. Information
3. Energy and Matter
4. Interactions
5. Evolution

Theme: New Properties Emerge at Successive

Levels of Biological Organization

1. Biosphere- consists of all life

2. Ecosystems- living things in a particular
area + nonliving
3. Communities- array of organisms
inhabiting in ecosystem; have many
species; set of populations
4. Populations- individuals of a species
5. Organisms- individual living things
6. Organs- a body part made up of tissues
with specific functions
7. Tissues- group of cells working together
8. Cells- life’s fundamental unit of structure
and function
9. Organelles- functional components
present in cells
10. Molecules- chemical structure w 2 or
more atoms
Emergent Properties
- due to the arrangement and interactions
of parts as complexity increases
Theme: Life’s Processes Involve Expression and
Transmission of Genetic Information
● chromosomes in cells contain DNA
● In cells preparing for division,
chromosomes are seen with a blue dye
when bound to the DNA
DNA, the Genetic Material
● Units of inheritance; universal genetic
language
● Encode the necessary information to
build molecules synthesized within the
cell; establishes cell’s identity and
function
● Made up of 2 long strands, arranged in
double helix
 ● Sequence as blueprint for making volume of data that results
protein from high-throughput methods
● RNA: through this, protein encoding ● Formation of interdisciplinary
genes control protein production research teams
indirectly ● DNA: double helix by
● Sequence of nucleotides transcribed into Watson-Crick
mRNA -> translated into amino acids -> ● Franklin- illustrated the DNA
protein with photograph
● Gene expression: process by which the ● DNA: 2 nucleotide chains
info info in a gene directs the (ribose, phosphate, base)
manufacture of a cellular product ● Nucleus - > chromosome ->
● Differences in nucleotide sequences DNA -> gene
reflects individual differences ● nucleoside: sugar, base
● Transcription -> translation (into amino ● nucleotides: chemical building
acids)-> protein building blocks (ATCG)
● Protein-encoding genes control protein ● Purines (2 rings)
production through RNA (mRNA) guanine, adenine
● pyrimidine: cytosine,
thiamine

Genomics: Large-Scale Analysis of DNA sequences

● genome: library of genetic instructions

inherited
● Each set of chromosome w 3 billion
nucleotide pairs of DNA
● genomics: studying a set of genes rather
than single Theme: Life Requires the Transfer and
● proteonomics: study of set of proteins; Transformation of Energy and Matter
proteome
● Highly throughput tenchnology ● use of energy to carry out activities
● bioinformatics: use of ● consumers: feed on others
computational tools to store,
organize, and analyze the huge
 ● Energy flows through an ecosystem
when energy is used and lost (entering
as light and exiting as heat)
● Chemicals, on the other hand, are
recycled; decomposers
● Photosynthesis
● Cell respiration
Theme: From Molecules to Ecosystems,
Interactions Are Important Biological Systems
● at any level of biological hierarchy,
interactions between components of the
system = smooth integration of parts;
functions as a whole
Molecules: Interactions Within Organisms
● interactions for smooth operation
● Feedback regulation: product of process
regulates the very process
● Negative feedback: most
common form of regulation;
response reduces initial
stimulus (e.g. insulin signaling)
● Positive feedback: product
speeds up own production (e.g.
blood clotting)
Ecosystems: An Organism’s Interactions with
Other Organisms and the Physical Environment
● interactions can either harm both
organisms, one of them, or could benefit
● Interaction regulate the functioning of
the ecosystem as a whole
● Climate change: can lead to extinction
C1.2
The Core Theme: Evolution accounts for the
unity and diversity of life
● evolution: the concept that the
organisms living on Earth today are the
modified descendants of common
ancestors
● Explains unity and diversity,
adaptation
Classifying the Diversity of Life
● genus: to which the species belong
● Second part: what is unique to that
species
● taxonomy: names and classifies
organisms
The Three Domains of Life
● Classified through qualities, structure,
function, DNA sequences
1. Bacteria and
2. Archaea (prokaryotic)
3. Eukarya: kingdom (by modes of
nutrition)
1. Plantae- photosynthesis
2. Fungi- absorb nutrients in
dissolved form from
surroundings
3. Animalia- eating and digesting
others
4. ** Protists- most numerous and
diverse; mostly single celled;
 recent DNA change that is why ○ Species are generally adapted
now into groups (dating to own environment
kingdom) ● Natural environment selects for the
propagation of certain traits

C1.3 Scientific Method

● science - from latin word meaning “to
know”
● Inquiry: a search for information and
explanations of natural phenomena
● Observations >collecting and analyzing
data > forming and testing hypotheses
(experiment)
● Data: recorded observations; on which
scientific inquiry is based
● Inductive reasoning- data to conclusion
● Deductive reasoning- general to specific;
if-then
● Hypothesis cannot be proven to be true;
must be testable; only limited to natural
phenomena and within the bounds of
science
● Control group (white mice in beach)
● Experimental group
● Controlled experiment- comparing
control with experimental group
● Variables- factors manipulated and
measured
● Theory- set of hypotheses that have
been thoroughly tested over time
● Dependent variable- measured
● Independent variable- manipulated
● Model organism
● Scientific study is limited to the area that
can be observed and measured
○ Cannot address all questions
○ Bound by practical limits
Charles Darwin and The Theory of Natural (temporal and spatial
Selection
● On the Origin of Species by Means of
Natural Selection
○ Descent with modification
○ Natural selection is the cause of
this ^
● From following observations:
○ Individuals in a population vary
in traits
○ A population can produce more
than can survive to produce
their own; competition from
indiv > support from
environment
conditions)

Notes on History of Biology
● Anaximander- theory that humans
evolved from fish
● Hippocrates- medicines, ethics and
ideals of a physician; Father of Medicine
● Aristotle & Pliny the Elder- collected
many facts about plants and animals;
Aris made first classification system for
all living things
** Middle Ages- interest in bio declined; focus on
religion and afterlife; Renaissance it went back
● Andreas Vesalius- Father of Anatomy
● William Harvey- human blood circulation
● Anton Van Leeuwenhoek- observed
bacteria and protozoa w own simple
microscope
● Robert Hooke- “cells walls of cork as tiny
boxes”
● Carolus Linnaeus- use of binomial
nomenclature; present day
● Baron Cuvier- compare anatomy of
animals and humans
● Matthias Schleiden & Theodore
Schwann- theory that cells make up all
living things
● Charles Darwin- Natural selection;
Theory of Evolution
● Gregor Johann Mendel- laws of heredity
with peas
● Louis Pasteur & Robert Koch- pioneered
bacteriology; debunked spontaneous
generation (pasteur); germ theory of
disease (Koch)
● Louis Agasizz- living and fossil forms of
fish
● Asa Gray- work on botany and
classification of plants, trees and flowers
● Ivan Petrovich Pavlov- breeding of wheat
resistant to disease by fungi
● Karl Landsteiner- main types of human
blood
● Herman Muller- “x-rays could produce
mutations”
● George Hutchinson- ecological studies
on lake; father of modern ecology
● Robert Whittaker- 5 kingdom scheme:
monerans, protists, fungi, plants, and
animals 1969
Late 19th century
● Gregor Mendel- basic principles of
heredity; peas
● Thomas Morgan- fruit fly; genes are
located in the chromosomes in linear
order
● James Watson and Francis Crick (1916)-
proposed DNA model;
● Rosalind Franklin- from x ray
crystallography and other info from
Maurice Wilkins and Linus Pauling
● Arthur Kornberg (artificial DNA) and
Severo Ochoa (artificial RNA)
● K.B. Mullis- amplified certain segments
of DNA strand with polymerase chain
reaction method
** Rudolph Virchow- spontaneous generation??
PH Biology
● Belief on spirits inhabiting all life forms
prevented propagation of scientific
explanations
● Spanish came- animalistic thinking to
empirical
● Father Manuel Blanco- book w
illustrations of plants in the ph
○ Antonio Llanos
○ Paul Klein
○ Trinidad Pardo de Tabera
○ Leon Maria Guerrero
○ Castro de Eleira
○ Manuel Viiches
○ Sebastian Vidal Y Soler
● Biological researches stopped during
american war
After:
● Dr. Gregorio Velasquez- phycology;
myxophyceae and blue algae; Father of
Phycology in the Ph
 ● Dr. Jose Vera Santos- taxonomy of
bamboo
● Dr. Flordeliz Uyenco- studies of fungi and
lichens

● Dr. Eduardo Quisimbing- medicinal

plants in the Ph
● Dr. Hilario Roxas- fishes
● Dr. Francisco Nemenzo Sr.- corals
● Dr. Dioscoro Rabor- Ph birds, bats, rats
● Dr. Agustin Rodolfo- physiologist and
cytogeneticist

Additional notes:
● Archaea- considered bacteria “archaea
bacteria” (ancient bacteria) bc appeared
prokaryotic
○ More closely related with
Eukarya
● Darwin- Galapagos Island; finches’ beaks
○ Artificial selection- choosing
specific characteristics to breed