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 (C 6 H 12 O 6 ) 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.