BackAtoms, Ions, Molecules, and Water: Foundations of General Biology
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Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution
Major Elements in Living Organisms
Living organisms are primarily composed of four elements: Hydrogen (H), Carbon (C), Nitrogen (N), and Oxygen (O). These elements form the basis of biological molecules essential for life.
Basic Atomic Structure
Atoms are the smallest units of matter that retain the properties of an element. Each atom consists of:
Protons: Positively charged particles found in the nucleus.
Neutrons: Neutral particles found in the nucleus.
Electrons: Negatively charged particles orbiting the nucleus.
The atomic number is the number of protons in an atom, which defines the element. The mass number is the sum of protons and neutrons.
Isotopes
Isotopes are atoms of the same element that have different numbers of neutrons, and thus different mass numbers. For example, an oxygen atom with 8 protons and 8 neutrons has a mass number of 16.
Electron Shells and Valence Electrons
Electrons are arranged in shells around the nucleus. The innermost shell can hold up to 2 electrons, and the second shell can hold up to 8 electrons. The electrons in the outermost shell are called valence electrons and determine the atom's chemical properties.
Valence shell: The outermost electron shell of an atom.
Valence electrons: Electrons in the valence shell; involved in chemical bonding.
Unpaired electrons: The number of unpaired electrons in the valence shell determines how many covalent bonds an atom can form.
For example, carbon has 4 unpaired electrons in its valence shell, allowing it to form 4 covalent bonds.
Characteristics of Bonds Between Atoms
Chemical bonds form when atoms share or transfer electrons. The main types of bonds are:
Covalent bond: A type of chemical bond in which two atoms share one or more pairs of electrons.
Ionic bond: A bond formed when one atom transfers electrons completely to another atom, resulting in oppositely charged ions that attract each other.
Cation: An atom that has lost electrons and has a net positive charge. Anion: An atom that has gained electrons and has a net negative charge.
Electronegativity and Bond Polarity
Electronegativity is the amount of strength an element has in pulling the shared electron toward itself in a bond. It varies among elements and determines bond polarity.
Nonpolar covalent bond: Electrons are shared equally between atoms.
Polar covalent bond: Electrons are shared unequally, resulting in partial charges on atoms.
In a polar covalent bond, the atom with higher electronegativity attracts the electrons more strongly, creating a partial negative charge, while the other atom has a partial positive charge.
Comparison of Covalent and Ionic Bonds
Bond Type | Electron Sharing/Transfer | Resulting Particles |
|---|---|---|
Covalent | Electrons are shared between atoms | Molecules |
Ionic | Electrons are transferred from one atom to another | Ions (cations and anions) |
Simple Molecules Important to Life
The number of covalent bonds an atom can form is determined by the number of unpaired electrons in its valence shell. For example, carbon can form 4 covalent bonds due to its 4 unpaired valence electrons. Molecules can have different shapes based on the arrangement of bonds and electron pairs (e.g., CO2 is linear, CH4 is tetrahedral).
Properties of Water and the Early Oceans
Structure and Polarity of Water
Water (H2O) is a polar molecule due to the difference in electronegativity between oxygen and hydrogen. Oxygen has a partial negative charge, while hydrogens have partial positive charges. This polarity allows water molecules to form hydrogen bonds with each other.
Hydrophilic and Hydrophobic Substances
Hydrophilic: Substances that interact readily with water; typically polar or charged compounds.
Hydrophobic: Substances that do not interact readily with water; typically nonpolar molecules.
Hydrophilic molecules have partial or full charges, while hydrophobic molecules generally do not.
Unique Properties of Water
Water's unique properties arise from its structure and hydrogen bonding. These properties are essential for life.
Property | Description |
|---|---|
Adhesion | The tendency of water molecules to stick to other substances. |
Cohesion | The tendency of water molecules to stick to each other. |
Surface tension | The cohesive force at the surface of water, making it behave like a stretched elastic membrane. |
Density as liquid and solid | Water is less dense as a solid (ice) than as a liquid, so ice floats on water. |
High specific heat | Water can absorb a lot of heat before its temperature rises significantly. |
High heat of vaporization | Water requires a lot of energy to change from liquid to gas. |
Chemical Reactions and Acids/Bases
Chemical reactions involve the rearrangement of atoms to form new substances. For example, the reaction of carbon and oxygen to form carbon dioxide:
Acids are substances that give up protons (H+), while bases accept protons. The pH scale measures the concentration of H+ ions in a solution:
A solution with a high pH is basic (low concentration of H+).
A solution with a low pH is acidic (high concentration of H+).
Life is Carbon-Based
Organic molecules contain carbon atoms bonded to other atoms. Carbon's ability to form four covalent bonds makes it uniquely suited to form the backbone of biological molecules.
Functional Groups in Organic Molecules
Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity. Two important functional groups are:
Functional Group | Structure | Properties |
|---|---|---|
Amino group | -NH2 | Acts as a base; can pick up a proton (H+). |
Carboxyl group | -COOH | Acts as an acid; can donate a proton (H+). |
Example: All proteins have amino and carboxyl groups as part of their structure.
Additional info: Functional groups such as hydroxyl (-OH), phosphate (-PO4), and sulfhydryl (-SH) are also important in biological molecules, affecting their solubility and reactivity.