Atoms, Macromolecules, and Biologically Important Molecules: Study Notes

Atoms to Macromolecules

Atomic Structure and Properties

This section introduces the basic building blocks of matter, focusing on atomic structure, subatomic particles, and the periodic table. Understanding these concepts is essential for studying the chemical basis of life in microbiology.

• Atom: The smallest unit of an element that retains its chemical properties.

• Subatomic particles:

  • Protons: Positively charged particles found in the nucleus.

  • Neutrons: Neutral particles found in the nucleus.

  • Electrons: Negatively charged particles orbiting the nucleus.

• Atomic number: Number of protons in an atom; determines the element.

• Atomic mass: Sum of protons and neutrons in the nucleus.

• Chemical symbol: One- or two-letter abbreviation for an element (e.g., H for hydrogen).

Ions and Isotopes

Ions and isotopes are variations of atoms that play important roles in biological systems and medical applications.

• Anion: An atom with a negative charge (gains electrons).

• Cation: An atom with a positive charge (loses electrons).

• Isotopes: Atoms of the same element with different numbers of neutrons. Some isotopes are radioactive and are used in medicine (e.g., radiotracers, cancer treatment).

Molecules, Compounds, and Isomers

Understanding the differences between molecules, compounds, and isomers is fundamental to studying chemical reactions in living organisms.

• Molecule: Two or more atoms bonded together.

• Compound: Molecules composed of different elements.

• Isomer: Molecules with the same molecular formula but different structures.

Organic vs. Inorganic Compounds

Organic and inorganic compounds differ in their composition and roles in biological systems.

• Organic compounds: Contain carbon and hydrogen; include carbohydrates, proteins, lipids, and nucleic acids.

• Inorganic compounds: May contain carbon but lack C-H bonds; include water, salts, acids, and bases.

Acids, Bases, and pH

Acids and bases are important in maintaining cellular homeostasis. Their strength is measured by the pH scale.

• Acids: Substances with pH less than 7; donate protons (H+).

• Bases: Substances with pH greater than 7; accept protons or donate hydroxide ions (OH-).

• pH scale: Measures hydrogen ion concentration; lower pH = more acidic, higher pH = more basic.

Chemical Bonds and Interactions

Ionic and Covalent Bonds

Chemical bonds hold atoms together in molecules and compounds. The type of bond affects molecular properties.

• Ionic bonds: Formed when electrons are transferred from one atom to another; result in charged ions that attract each other.

• Covalent bonds: Formed when atoms share electrons to fill their outermost shells.

Polar Covalent Bonds and Hydrogen Bonds

• Polar covalent bonds: Unequal sharing of electrons, leading to partial charges (e.g., in water molecules).

• Hydrogen bonds: Weak attractions between a hydrogen atom (attached to an electronegative atom) and another electronegative atom; important in stabilizing biological molecules.

Hydrophobic, Hydrophilic, and Amphipathic Molecules

• Hydrophobic: Repel water ("water-fearing").

• Hydrophilic: Attract water ("water-loving").

• Amphipathic: Contain both hydrophobic and hydrophilic regions (e.g., phospholipids in cell membranes).

Chemical Reactions

Reactants, Products, and Equations

Chemical reactions involve the transformation of reactants into products, often represented by chemical equations.

• Reactants: Substances present at the start of a reaction.

• Products: Substances formed as a result of the reaction.

• Chemical equation: Symbolic representation of a chemical reaction.

Catalysts and Enzymes

• Catalyst: Substance that speeds up a chemical reaction without being consumed.

• Enzyme: Biological catalyst, usually a protein, that accelerates biochemical reactions.

Dehydration Synthesis and Hydrolysis

• Dehydration synthesis: Reaction that joins two molecules by removing water.

• Hydrolysis: Reaction that breaks a bond by adding water.

Activation Energy and Reaction Types

• Activation energy: Minimum energy required to start a chemical reaction.

• Exergonic reactions: Release energy (e.g., cellular respiration).

• Endergonic reactions: Require energy input (e.g., photosynthesis).

Biologically Important Macromolecules

Major Classes and Building Blocks

Macromolecules are large, complex molecules essential for life. They are built from smaller subunits.

Macromolecule	Building Block	Example
Carbohydrates	Monosaccharides	Glucose, starch
Proteins	Amino acids	Enzymes, antibodies
Lipids	Fatty acids, glycerol	Fats, oils, phospholipids
Nucleic acids	Nucleotides	DNA, RNA

Bonds in Macromolecules

• Glycosidic bonds: Link monosaccharides in carbohydrates.

• Peptide bonds: Link amino acids in proteins.

• Phosphodiester bonds: Link nucleotides in nucleic acids.

Structural and Functional Characteristics

• Carbohydrates: Provide energy and structural support.

• Lipids: Store energy, form cell membranes, and act as signaling molecules.

• Nucleic acids: Store and transmit genetic information.

• Proteins: Perform a wide range of functions, including catalysis, transport, and structural support.

DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double-stranded	Single-stranded
Bases	A, T, C, G	A, U, C, G

Lipid Saturation

• Saturated fats: No double bonds; solid at room temperature.

• Unsaturated fats: One or more double bonds; liquid at room temperature.

Protein Structure

• Primary structure: Sequence of amino acids linked by peptide bonds.

• Secondary structure: Local folding (e.g., alpha helices, beta sheets) due to hydrogen bonding.

• Tertiary structure: Three-dimensional folding driven by interactions among side chains.

• Quaternary structure: Association of two or more polypeptide chains.

Key Equations and Concepts

• pH calculation: $pH = -\log_{10}[H^+]$

• General chemical reaction: $\text{Reactants} \rightarrow \text{Products}$

• Activation energy (Ea): $\text{Activation Energy} = E_a$

Example: The hydrolysis of ATP to ADP releases energy for cellular processes.

Additional info: Some explanations and examples have been expanded for clarity and completeness based on standard microbiology and biochemistry curricula.