Chemistry and Molecules of Life

Definition of Matter: Matter is defined as any material that takes up space and possesses mass. The matter that constitutes every object is composed of one or more chemical elements.
- Element Definition: An element is a pure substance that cannot be decomposed into simpler substances through chemical means.

Overview: The periodic table is a systematic arrangement that lists all known chemical elements. It provides a way to organize information about the elements in a concise manner.
- Abbreviated Periodic Table: Highlights some of the most significant elements that are critical for life.

Element Boxes: Each box within the periodic table represents an element and displays:
- Full Name: The complete name of the element.
- Symbol: The one or two-letter abbreviation representing the element.
- Figure 2.1: Reference figure illustrating the layout of the periodic table.

Atomic Number: Represents the number of protons located in the nucleus of an atom.
Atomic Mass: The combined weight of protons and neutrons found within the atomic nucleus.
Atomic Weight: The average weight of all the isotopes of an element.
Ions: Atoms that have gained or lost electrons, resulting in a charge.
- Cations: Positively charged ions created when an atom loses electrons.
- Anions: Negatively charged ions formed when an atom gains electrons.
Isotopes: Variants of a particular chemical element that have the same number of protons but differ in the number of neutrons.
- Some isotopes are radioactive, while others remain stable and non-radioactive.

Atom Definition: An atom is the smallest unit of an element that retains its chemical properties.
Subatomic Particles:
- Protons: Positively charged particles found in the atomic nucleus.
- Neutrons: Particles with no charge, also located in the nucleus.
- Electrons: Negatively charged particles that orbit the nucleus at high speeds.

Chemical Bonds: These are the connections that link atoms to form molecules.
- Molecule Definition: A molecule consists of two or more atoms that are chemically bonded together.
Example of Molecules: Water molecules (H₂O) consist of two hydrogen atoms and one oxygen atom, whereas methane (CH₄) is a compound of one carbon atom and four hydrogen atoms.

Definition: Electronegativity is a measurement of an atom's ability to attract electrons in a chemical bond.
- Atoms with low electronegativity have a weak attraction for electrons, while atoms with high electronegativity have a strong attraction.
Example: In water (5H₂O), the oxygen atom possesses a higher electronegativity compared to hydrogen atoms, leading to an unequal sharing of electrons.

Partial Charges: Molecules may exhibit partial positive and negative charges due to unequal sharing of electrons. In water, the hydrogen atom has a slight positive charge that attracts the slight negative charge on the oxygen atom of neighboring water molecules, forming hydrogen bonds.
Importance: These hydrogen bonds contribute to the unique properties of water essential for life.

Unique Properties of Water:
- Adhesion: The tendency of water molecules to adhere to themselves and to other surfaces, contributing to high surface tension.
- Solvent Property: Water is known as an excellent solvent, especially for hydrophilic (water-loving) molecules, which include polar solutes and ions. This property allows water to dissolve many biologically relevant molecules due to its polarity.
- Expansion Upon Freezing: Water expands when it freezes because hydrogen bonds cause water molecules to spread further apart when in frozen form, making ice less dense than liquid water. This leads to ice floating, providing insulation for aquatic life below it during winter.
- Participation in Chemical Reactions: Water acts as a reactant in vital processes such as photosynthesis and respiration, facilitating chemical reactions crucial for living organisms.

Definition: The pH scale quantifies the acidity or basicity of a solution based on the concentration of hydrogen ions (H⁺).
- Acidic Solutions: Lower pH values (0-6) indicate acidic solutions, such as gastric acid (pH 0) and lemon juice (pH 2).
- Neutral Solution: A pH of 7 represents neutrality, like distilled water.
- Basic Solutions: Higher pH values (8-14) indicate basic solutions, such as baking soda (pH 9) or bleach (pH 12).

Organic Molecule Definition: Organic molecules are composed of carbon (C) and hydrogen (H). Methane is an example of a simple organic molecule.

Carbohydrates:
- Comprising simple and complex sugars. Examples include ribose, glucose, and fructose.
Proteins:
- Function as the “workers” of cells, performing various tasks such as forming cellular structures (collagen) and facilitating muscle contractions (actin and myosin).
Nucleic Acids:
- Include DNA and RNA, carrying genetic information and determining protein structure.
Lipids:
- Hydrophobic molecules that do not form chains like other organic molecules; include triglycerides (fats and oils) and steroids with various structural and functional roles.

Protein Synthesis and Breakdown:
- Proteins are formed by long chains of amino acids known as polypeptides.
- Dehydration Synthesis: The chemical process through which amino acids are linked together by peptide bonds to form polypeptides.
- Hydrolysis: The process by which proteins are broken down back into amino acids.

Primary Structure: The linear sequence of amino acids.
Secondary Structure: Formation of alpha helices and beta-pleated sheets due to hydrogen bonding.
Tertiary Structure: The final three-dimensional shape of the protein, crucial for its functionality.
Quaternary Structure: The arrangement of two or more folded proteins into a larger functional complex.

Denaturation: A process in which proteins lose their 3D shape, leading to loss of function.

Role: Nucleic acids (DNA and RNA) are responsible for carrying genetic information. The sequence of bases in nucleic acids determines the primary structure of proteins within a cell.

Hydrophobic Character: All lipids exhibit hydrophobic properties.
Classes of Lipids:
- Triglycerides: Utilized for long-term energy storage; consist of three fatty acids attached to glycerol.
- Steroids: Characterized by a four-ring structure; serve various biological functions in cells.

The fundamental properties of the organic molecules that compose living cells are intricately related to their atomic structure and the chemical bonds they form. Without the presence of these organic molecules, the manifestation of life as we know it would cease to exist.