Chemical Elements and Bonding in Biological Systems: Study Notes

Chapter 2: Chemical Elements in Pure Form and in Combinations

Concept 2.1: Matter Consists of Chemical Elements in Pure Form and in Combinations Called Compounds

This section introduces the basic building blocks of matter—elements and compounds—and their relevance to living organisms.

• Matter: Anything that takes up space and has mass. Examples: rocks, metals, oils, gases, and humans.

• Element: A substance that cannot be broken down into other substances by chemical reactions. Examples: gold, copper, carbon, oxygen.

• Compound: A substance consisting of two or more different elements combined in a fixed ratio. Examples: sodium chloride (NaCl), water (H2O).

• Essential elements: Elements required by an organism to live a healthy life and reproduce. Examples: Oxygen, carbon, hydrogen, nitrogen (make up ~96% of living matter).

• Trace elements: Elements required in minute quantities, such as iodine (I) for vertebrates.

Concept 2.2: An Element's Properties Depend on the Structure of Its Atoms

The properties of elements are determined by the structure of their atoms, including the number and arrangement of subatomic particles.

• Atom: The smallest unit of an element, retaining its properties.

• Subatomic particles:

  • Neutron: Electrically neutral particle.

  • Proton: Particle with a positive charge.

  • Electron: Particle with a negative charge.

• Atomic nucleus: Dense core of protons and neutrons.

• Atomic number: Number of protons in the nucleus; defines the element.

• Mass number: Total number of protons and neutrons.

• Isotope: Atoms of the same element with different numbers of neutrons. Example: Carbon-12, Carbon-13, Carbon-14.

• Radioactive isotope: Isotope with an unstable nucleus that decays, emitting particles and energy. Applications: PET scans, radiometric dating.

• Electron shells: Energy levels where electrons are found; shells farther from the nucleus have higher energy.

• Potential energy: Energy due to location or structure. Example: Electrons in higher shells have more potential energy.

• Valence electrons: Electrons in the outermost shell; determine chemical behavior.

Concept 2.3: The Formation and Function of Molecules Depend on Chemical Bonding Between Atoms

Chemical bonds form between atoms to create molecules and compounds, which are essential for biological structure and function.

• Covalent bond: Sharing of a pair of valence electrons between two atoms.

• Molecule: Two or more atoms held together by covalent bonds.

• Valence: The bonding capacity of an atom, usually equal to the number of unpaired electrons in the outer shell. Examples: Hydrogen (1), Oxygen (2), Nitrogen (3), Carbon (4).

Table: Common Molecules and Compounds

Name	Molecule?	Compound?	Molecular Formula	Structural Formula
Water	Yes	Yes	H2O	H–O–H
Carbon dioxide	Yes	Yes	CO2	O=C=O
Methane	Yes	Yes	CH4	H–C–H (tetrahedral)
Oxygen	Yes	No	O2	O=O

• Double covalent bond: Two pairs of shared electrons (e.g., O2 molecule).

• Electronegativity: The tendency of an atom to attract electrons in a covalent bond.

• Nonpolar covalent bond: Electrons are shared equally between atoms of similar electronegativity.

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges (e.g., water molecule).

• Ionic bond: Attraction between oppositely charged ions, formed when electrons are transferred from one atom to another (e.g., NaCl).

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

Concept 2.4: Chemical Reactions Make and Break Chemical Bonds

Chemical reactions involve the making and breaking of chemical bonds, leading to changes in the composition of matter.

• Hydrogen bond: Weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom. Example: Water molecules.

• Van der Waals interactions: Weak attractions between molecules or parts of molecules due to transient local partial charges.

Table: Types of Chemical Bonds

Bond Type	Strength	Example
Covalent	Strong	H2O, CH4
Ionic	Strong (in dry conditions)	NaCl
Hydrogen	Weak	Between water molecules
Van der Waals	Very weak	Between nonpolar molecules

Concept 2.5: Hydrogen Bonding Gives Water Properties That Help Make Life Possible on Earth

Hydrogen bonds between water molecules give water its unique properties, which are essential for life.

• Cohesion: Water molecules stick together due to hydrogen bonding.

• Adhesion: Water molecules stick to other substances.

• High specific heat: Water can absorb or release large amounts of heat with little temperature change.

• Solvent properties: Water dissolves many substances, facilitating chemical reactions in cells.

Key Equations and Concepts

• Atomic number: $\text{Atomic number} = \text{Number of protons}$

• Mass number: $\text{Mass number} = \text{Number of protons} + \text{Number of neutrons}$

• Electron shells: $\text{First shell: 2 electrons; Second shell: 8 electrons}$

Summary Table: Essential Elements in Living Matter

Element	Symbol	Approximate % of Living Matter
Oxygen	O	65%
Carbon	C	18%
Hydrogen	H	10%
Nitrogen	N	3%

Additional info: These notes expand on the original content by providing definitions, examples, and tables for clarity. The structure follows the logical progression of the chapter, covering all major concepts and subtopics relevant to General Biology.