Chapter 1: Exploring life

A. Biologist explores life from the microscopic to global scale.

The study of life extends from the microscopic scale (molecules and cells) to
macroscopic scale (ecology, biosphere).

1. A hierarchy of biological organization

Levels of biological organization:

Levels definition
Molecules - A chemical structure consists of two or more small chemical units call atoms
(an electrically neutral group of at least two atoms)
- Ex: chlorophyll is a pigment molecule that makes the leaf green. Chlorophylls
absorb sunlight in the first step of photosynthesis. In chloroplast, chlorophylls
and other molecules are organized into equipment to convert light into energy.
Organelles A specialized subunit within a cell that has a specific function, and is usually
separately enclosed within its own lipid bilayer.
Cells Life’s functional unit of structure and function
Amoebas and bacteria are single cells.
Other organisms, including plants and animals are multicellular
A multicellular organism has the division of labor among specialized cells
Tissues Tissue is a cellular organizational level intermediate between cells and a
complete organism
A tissue is an ensemble of cells, not necessarily identical, but from the same
origin, that together carry out a specific function
Animal tissues can be grouped into four basic types: connective, muscle,
nervous, and epithelial.
Plant tissues are categorized broadly into three tissue systems: the epidermis,
the ground tissue, and the vascular tissue. Together they are often referred to as
biomass.
Organs and A body part consisting of two or more tissues which are serving the same
organ function
system Humans and other complex animals have organs organized into organ system
team of organs that cooperates in a certain function.
Circulatory System (heart, blood, vessels)
Respiratory System (nose, trachea, lungs)
Immune System (many types of protein, cells, organs, tissues)
Skeletal System (bones)
Excretory System (lungs, large intestine, kidneys)
Urinary System (bladder, kidneys)
Muscular System (muscles)
Endocrine System (glands)
Digestive System (mouth, esophagus, stomach, intestines)
Nervous System (brain, spinal cord, nerves)
Reproductive System (male and female reproductive organs)
Organism An organism is any contiguous living system
All organisms are capable of response to stimuli, reproduction, growth and
development, and maintenance of homoeostasis as a stable whole. An organism
may either be unicellular (single-celled) or be composed of, as in humans, many
trillions of cells grouped into specialized tissues and organs. The term
multicellular (many-celled) describes any organism made up of more than one
cell.
Population A population consists of all the individuals of a species living within the bounds of
a specified area
Communitie The entire array of organisms inhabiting a particular ecosystem is called a
s biological community
A species is one of the basic units of biological classification and a taxonomic
rank. A species is often defined as a group of organisms capable of interbreeding
and producing fertile offspring. While in many cases this definition is adequate,
more precise or differing measures are often used, such as similarity of DNA,
morphology or ecological niche
Ecosystems An ecosystem consists of all the living things in a particular area, along with all
the non-living components of the environment which the life interact with such
as water, soil, atmospheric gas and light.
All of earth’s ecosystems combined make up the biosphere
The The biosphere, which consists of all the environments on earth that are
biosphere inhabited by life. The biosphere include most regions of land; most bodies of
water, such as oceans, lakes, and rivers; and the atmosphere to an altitude of
several kilometers

2. A closer look at ecosystems

 Life does not exist in vacuum.
 Each organism interacts with its environment, which includes other organisms and nonliving
factors
 Both organism and environment are affected by the interactions between them. Plants also
interact with other life, including soil organisms associated with its roots and animals that eat
leaves and fruits.
a. Ecosystem dynamics
 The dynamics of any ecosystem include two major processes:
 The cycling of nutrients: ex: the minerals acquired by plants will be eventually
returned to soil by organisms that decompose dead body parts of plants.
 The flow of energy from sun light to producers to consumers : producers: organisms
that convert light energy into chemical energy. Consumers: any organisms that feed
on producers and other consumers.
b. Energy conversion
 Moving, growing, reproducing, and any other activities of life require organisms to
perform work. Thus, organism needs a source of energy.
 The exchange of energy between an organism and its surroundings involves the
transformation of energy from one form to another.
  Contrast to chemical nutrients, which recycle within an ecosystem, energy flows
through an ecosystem, entering as light and exiting as heat.

3. A closer look at cells

 Cell: lowest level of organization that can perform all activities required for life
a. The cell’s heritable information
 At the center of every cell is the chromosomes (stained with blue-glowing dye)
 Chromosomes are made of deoxyribonucleic acid (DNA). Each DNA molecule is made
up of two long chains arranged into what is called double helix. Each link in the chain is
one of four kinds of chemical called nucleotides
 DNA is the substance of genes, the units of inheritance that transmit information from
parents to offspring
 DNA replicate as the cell prepares to divide; thus, each offspring cell inherits a complete
set of genes.
 DNA directs the development and maintenance of the entire organism
 Specific sequential arrangement of four kinds of nucleotides encodes the inheritable
information in genes
 Most genes program for the production of proteins in cells. The sequence of
nucleotides along each gene codes for the specific protein with a unique shape and
function in the cell.
 Almost all cellular activities involve the action of one or more proteins.
 DNA provides the blueprints, but proteins actually build and maintain the cell.
 Differences between organisms reflect the differences in between their nucleotides
sequences. The genetic code is universal  it is possible to engineer cells to produce a
protein that is normally found in other organism. Ex: using this technology, Human
insulin is produced by bacteria whose gene was inserted by human genes that direct
insulin production.
 The entire library of genetic instructions that an organism inherits : genome
 Chromosomes of each human cell pack a genome that is about 3 billion nucleotides long
and coding for more than 75,000 different kinds of proteins

b. Two main forms of cell

 Prokaryotic cells: including two groups of microorganisms called bacteria and archaea.
In prokaryotic cell, DNA is not separated from the rest of the cell by a membrane.
Prokaryote also lack many kinds of organelle that characterize in eukaryotic cells
 Eukaryotic cells: including all other forms of life. The cell is subdivided by internal
membranes into various membrane-enclosed organelles. The largest organelle is
nucleus, which contains DNA. Other organelle is located in cytoplasm
B. Biological systems are much more than the sum of their part
1. The emergent properties of systems
 With each step upward in the hierarchy of biological order, novel properties emerge
that are not present at the level just below.
The emergent properties are due to the arrangement and interactions as parts of
complexity increases
2. The power and limitations of reductionism.
 The properties of life emerge from complex organization. We can’t understand the higher
level of order by breaking it down into its parts.
 Reductionism: reducing complex systems to simpler components that are more manageable
to study.

3. Systems biology
 The ultimate goal of systems biology is to model the dynamic behavior of whole biological
systems. Accurate models will enable biologists to predict how a change in one or more
variables will impact other components and the whole system
 System biology is relevant to study of life at all levels
 System biology is now taking hold in study of life at the cellular and molecular levels, driven
partly by the deluge of data from the sequence of genomes and the growing catalog of known
protein functions.
 3 key research developments:
 High-throughput technology: is the method that can analyze biological materials very
rapidly and produce enormous volumes of data. This is mega-data-collection methods
 Bioinformatics: the huge data that results from high-throughput methods need computer
software and mathematic models to process and integrate all this biological information.
 Interdisciplinary research teams: including engineers, medical scientists, chemists,
physicists, mathematician, computer scientists and biologists.

4. Feedback regulation in biological system:

 The ability of many biological processes to self-regulate by a mechanism called feedback
 In feedback regulation, the output (product) of a process regulates that very process. There are
two kinds of regulation.
 Negative feedback: in which the accumulation of an end product of a process slows that
process.
 Positive feedback: in which an end product speeds up its production. Example: when the blood
vessels is damaged, platelets begins to aggregate at the site. Positive feedback occurs when the
chemical released by platelets attract more platelets

C. Biologists explore life across its great diversity of species.

1. Grouping species
Taxonomy: the branch of biology that names and classifies species, formalizes this ordering
of species into series of groups of increasing breadth.
 In biology, a species is one of the basic units of biological classification and a taxonomic
rank. A species is often defined as a group of organisms capable of interbreeding and
producing fertile offspring. While in many cases this definition is adequate, more precise or
differing measures are often used, such as similarity of DNA, morphology or ecological niche.
Presence of specific locally adapted traits may further subdivide species into subspecies.

2. The three domains of life

 Even though there is always a debate at the kingdom level, there is more of a consensus
that the kingdoms of life can grouped into three even higher of levels of classification called
domains.
 Three domains: domain bacteria, domain archaea (both are prokaryotic), and domain
eukarya.
 In five kingdom system: bacteria and archaea were combined in a single kingdom, called
kingdom Monera. Domain Eukarya is divided into 4 kingdoms which are Protists, fungi,
plantae, and animalia.
 Archaea: many of the prokaryotes known as archaea live in Earth’s extreme environments,
such as salty lakes and boiling hot spring. There are also many evidences that archaea are at
least as closely related to eukaryotic organisms as they are to bacteria.
 Protists: are unicellular eukaryotes and their simple multicellular relatives (ex: seaweeds).
Organisms are called protists such as protozoans. The recent taxonomic trend has been to
split the protists into several kingdoms
 Kingdoms Plantae, Fungi and Animalia are distinguished by their modes of nutrition.
  Plants produce their own sugars and other foods by photosynthesis
 Fungi are mostly decomposers that absorb nutrients by breaking down dead
organisms and organic wastes such as leaf litter and feces.
 Animals obtain food by ingestion, which is eating and digesting of other organisms.

3. Unity in the diversity of life.

The universal genetic language of DNA which is common to organisms as different as
bacteria and animals
Among Eukaryotes, unity is evident in many features of cell structure

D. Evolution account for life’s unity and diversity

- The evolutionary view of life came into sharp focus in November 1859, When Charles Darwin
publish one of the most important book, entitled On the Origin of Species by Natural
selection.
- Darwinism is almost synonymous with the concept of evolution.
- Two main points of Darwinism:
 Temporary species arose from a succession of ancestors. Darwin called this
evolutionary history of species “descent with modification.” It captured the duality of
life, unity in the kinship among species that descended from a common ancestors,
diversity in the modifications that evolved as species branched from their common
ancestors
 The mechanism for descent with modification is natural selection.
1. Natural selection
 Individual variation: population with species which vary in many inherited traits
 Overproduction and competition: competition which leads to elimination of
individuals with certain traits
 Unequal reproductive success: those survived individuals are best suited to
environment. Those survivors will reproduce large number of healthy, fertile offspring.
 Evolutionary adaption: over generations, the traits (inheritable) that enhance survival
and reproductive success are passed down to offspring and tend to increase in
frequency among a population’s individuals.  the population evolves
Darwin called this natural selection because natural environment selects for the propagation
of certain favorable traits.

2. The tree of life

E. Biologists use various forms of inquiry to explore life

1. Discovery science
 Discovery science = descriptive science, which describes natural structures and processes
through careful observation and analysis of data.
a) Types of data
- Recorded observations are called data (items of information on which scientific inquiry is
based)
- Qualitative data: recorded description rather than numerical measurement.
- Quantitative data: data are recorded as measurements

b) Induction in discovery science

2. Hypothesis-based science
F. A set of themes connects the concepts of biology