Intro to Biology and The Chemical
Nature of Life
• Biology (the study of life) is based on the systems approach to science
whereby each system belongs to a larger system based on a hierarchical
structure.
– Biosphere - Ecosystem - Communities - Populations - Organisms Organs & Organ systems - Tissues - Cells - Organelles - Molecules
• The emergent properties of the system are based on the arrangement and
interactions of the parts as complexity increases.
Reductionism
• The understanding of the larger systems is based on a process known as
reductionism. Reductionism therefore states that in order to understand
the complexity of a system one must break it into its smallest parts.
Watson and Crick had this view as they described the nature of the double
helix of DNA and how it related to heritable traits.
• What are some emergent properties that you
can identify moving from DNA to system?
– From organism to ecosystem?
• Could a scientist describe an
ecosystem without knowing the
communities present?
Systems Approach
• Through the systems approach to science and reductionism it is possible to
pool knowledge from multiple sources to increase the knowledge of the
larger systems. The systems approach has been enhanced with the
emergence of 3 main research developments:
– 1. High-throughput technology - Example is DNA sequencing machine (PCR)
developed in the mid to late 80s.
– 2. Bioinformatics - includes data bases that store and organize the data
obtained through high-throughput technology
– 3. Interdisciplinary research teams - biologists teaming with chemists,
engineers, physicists, ... to expand their knowledge of events.
Taxonomy
• The ordering of organisms is known as the study of taxonomy. The
study of taxonomy divides organisms based on similarity of traits.
Although scientists had originally (up until about 10 years ago)
classified things into 5 kingdoms, the study of phylogenetics
(relatedness due to gene sequences) now has all organisms placed
into 3 main domains at the top of the chart based on their genetic
makeup.
– 1. Bacteria - prokaryote formerly
of kingdom Monera
– 2. Archaea - prokaryote formerly
of kingdom Monera
– 3. Eukarya - contains the 4 other
previous kingdoms: Protista,
Fungi, Plantae, Animalia
– How are each group taxonomically related?
– How could you verify your hypothesis using the
systems approach and phylogenomics?
Chemical Foundations of Biology
• Everything that is made of matter. That matter is made
of elements. There are currently 92 naturally occurring
elements. Of the 92, 4 (C, H, O, & N) make up roughly
96% of your body's mass. Another 4% can be made
from adding only P, S, Ca, & K. Similar make-ups are
found in other living organisms lending additional
evidence for relatedness.
CHEMISTRY REVIEW!
• Atoms are made of subatomic particles
– Protons (+) & neutrons (+&-) are found in the nucleus
and determine the functional mass. Proton
determines the chemical identity of the atom.
Differing amounts of neutrons form isotopes. All that
differ from the one found most commonly in nature
are radioactive. (ex: C-12, C-13, & C-14)
– Electrons (-) exists in electron cloud densities around
the nucleus. Can be gained or lost forming ions and
add to the atoms overall charge. The arrangement of
electrons in valence (bonding) orbitals of atoms in a
compound of molecule leads to polarity.
• Most organisms are made of covalent bonds.
– Covalent bonds are formed by the sharing of
electrons between 2 atoms. 2 or more covalent
bonded atoms form a molecule.
– Molecular formulas list only the #s of atoms
present (C6H12O6) while the structural formula
shows how they are attached.
– The electronegativity difference between the
atoms determines the amount of polarity.
• The transfer of electrons between metals and
non-metals creates ionic bonds
– The atom that loses and electron becomes a cation
(positively charged) and the one that gains becomes
an anion (negatively charged).
– The product formed is a salt.
• Other bonds
– Hydrogen bonds gives water its unique properties.
Formed between O & H or N & H
– Van der Waals Interactions (temporary dipoles)
created by the temporary rearrangement of electron
cloud densities.
• Molecular geometry determines function and
is called the molecule's confirmation.
– Determined by the organization of the s & p
hybrid orbitals (review: linear, bent, tetrahedral,
pyramidal, & trigonal planar)
– The confirmation is critical in biology because it
determines how molecules bind and interact in
nature.