BackChapter 2: The Chemical Context of Life – Study Notes
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IThe Chemical Context of Life.
Introduction to Chemistry in Biology "
All living organisms are composed of matter, which is anything that occupies space and has mass. Understanding the chemical basis of life is essential for studying biological processes, as the structure and behavior of atoms and molecules determine the properties of cells and organisms.
Elements and Compounds
Elements of Life
Elements are pure substances that cannot be broken down into other substances by chemical means. Of the 92 naturally occurring elements, about 20-25% are essential for life. These essential elements are required for an organism to survive, grow, and reproduce. Trace elements are needed only in minute quantities but are still vital for biological functions.
Example: Iodine is required for normal thyroid function in vertebrates; deficiency can cause goiter.
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Compounds
A compound is a substance consisting of two or more combined in a fixed ratio. Compounds have unique properties that are different from those of their constituent elements, a phenomenon known as emergent properties.
Example: Sodium (Na) and chlorine (Cl) combine to form sodium chloride (NaCl), or table salt, which has I properties distinct from either element alone.
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Adaptation to Toxic Elements
Some elements are toxic to organisms, but certain species have evolved mechanisms to tolerate or even utilize these elements. Phytoremediation is a process where plants, such as sunflowers, absorb heavy metals from contaminated soils, helping to detoxify the environment.
Example: Sunflowers were used to clean up soils contaminated with heavy metals after environmental disasters.
Atomic Structure and Properties
Subatomic Particles
Atoms are composed of three types of subatomic particles:
Protons: Positively charged, found in the nucleus
Neutrons: No charge, found in the nucleus
Electrons: Negatively charged, orbit the nucleus in electron shells
Atomic Number, Mass Number, and Isotopes
The atomic number of an element is the number of protons in its nucleus, which also equals the number of electrons in a neutral atom. The mass number is the sum of protons and neutrons. Isotopes are atoms of the same element with different numbers of neutrons.
Atomic Number (Z): Number of protons
Mass Number (A): Number of protons + neutrons
Isotopes: Atoms with the same number of protons but different numbers of neutrons
Formulas:
Atomic Number:
Mass Number:
Number of Neutrons:
Radioactive Isotopes
Radioactive isotopes have unstable nuclei that decay spontaneously, emitting particles and energy. They are used in dating fossils, tracing atoms in metabolic processes, and diagnosing medical disorders. However, radiation can damage cellular molecules and pose environmental hazards.
Example: PET scans use radioactive isotopes to detect cancerous tissues.
Energy Levels and Electron Shells
Energy and Electrons
Electrons have potential energy due to their position relative to the nucleus. They occupy specific energy levels or shells. Electrons can move to higher or lower energy shells by absorbing or releasing energy, respectively.
Chemical Bonds and Interactions
Covalent Bonds
Covalent bonds involve the sharing of pairs of valence electrons between atoms. Molecules are formed when two or more atoms are held together by covalent bonds. Covalent bonds can be single (one pair of electrons shared) or double (two pairs shared).
Polar Covalent Bonds: Electrons are shared unequally due to differences in electronegativity, resulting in partial charges (e.g., H2O).
Nonpolar Covalent Bonds: Electrons are shared equally between atoms.
Ionic Bonds
Ionic bonds are formed when one atom transfers electrons to another, resulting in oppositely charged ions (cations and anions) that attract each other. Ionic compounds are often called salts.
Cation: Positively charged ion (lost electron)
Anion: Negatively charged ion (gained electron)
Weak Chemical Interactions
Many biological molecules are stabilized by weak interactions, including hydrogen bonds and van der Waals interactions.
Hydrogen Bonds: Form between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom nearby. Important in water and biological macromolecules.
Van der Waals Interactions: Weak attractions due to transient local partial charges; significant when many such interactions occur together (e.g., gecko feet adhesion).
Chemical Reactions
Making and Breaking Bonds
Chemical reactions involve the making and breaking of chemical bonds. Reactants are the starting substances, and products are the resulting substances. Photosynthesis is a key example of a biological chemical reaction:
Water and Life
Hydrogen Bonding in Water
Water is a polar molecule, and hydrogen bonding between water molecules is responsible for many of its unique properties. These include cohesion, adhesion, high surface tension, moderation of temperature, expansion upon freezing, and versatility as a solvent.
Cohesion and Adhesion
Cohesion is the tendency of water molecules to stick together due to hydrogen bonding. Adhesion is the clinging of water molecules to other substances. Both are critical for water transport in plants, working with transpiration to move water against gravity.
Surface Tension
Surface tension is a measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension due to the ordered arrangement of hydrogen bonds at the surface, allowing small organisms to walk on water.
Moderation of Temperature
Water can absorb or release large amounts of heat with only slight changes in its own temperature, helping to stabilize environmental and organismal temperatures. This property is due to water's high specific heat capacity.
Floating of Ice on Liquid Water
Ice is less dense than liquid water because hydrogen bonds in ice are more ordered, creating a crystalline structure with more open space. This allows ice to float, insulating aquatic life in winter.
Water as a Solvent
Water is known as the "solvent of life" because it can dissolve a wide variety of substances, especially ionic and polar compounds. Solutions in which water is the solvent are called aqueous solutions. Hydrophilic substances have an affinity for water, while hydrophobic substances do not.
Acids, Bases, and pH
pH and Buffers
Acids increase the concentration of hydrogen ions (H+) in a solution (pH < 7), while bases decrease it (pH > 7). Most biological fluids have a pH between 6 and 8. Buffers are substances that minimize changes in pH by accepting or donating H+ ions as needed, maintaining homeostasis in living organisms.
Formula for pH:
