Atomic Structure and Chemical Bonding

Atomic Number and Atomic Structure

The atomic number is a fundamental property of an element, representing the number of protons in the nucleus of an atom. Understanding atomic structure is essential for grasping how atoms interact and form molecules.

• Atomic Number: The number of protons in an atom; determines the element's identity.

• Atomic Structure: Atoms consist of a nucleus (protons and neutrons) surrounded by electrons in orbitals.

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

• Octet Rule: Atoms tend to gain, lose, or share electrons to achieve a stable configuration of eight valence electrons.

Example: Sodium (Na) loses one electron to achieve an octet, becoming Na+, while chlorine (Cl) gains one electron to become Cl-.

Organic Molecules and Bond Polarity

Organic molecules are primarily composed of carbon atoms bonded with hydrogen, oxygen, nitrogen, and other elements. The polarity of bonds affects molecular interactions and properties.

• Organic Molecule: A molecule containing carbon atoms bonded to hydrogen and often other elements.

• Polarity: A measure of how equally electrons are shared in a bond; polar bonds have unequal sharing, leading to partial charges.

Example: Water (H2O) is a polar molecule due to the difference in electronegativity between hydrogen and oxygen.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

• Common Functional Groups: Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4).

• Importance: Functional groups participate in chemical reactions and define the characteristics of organic molecules.

Example: The carboxyl group gives amino acids their acidic properties.

Macromolecules and Monomers

Structure of an Amino Acid

Amino acids are the building blocks of proteins, each consisting of a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group.

• General Structure:

• R Group: The side chain that determines the properties of each amino acid.

Example: Glycine has a hydrogen atom as its R group.

Monomer and Polymer Relationships

Macromolecules are large molecules formed by the polymerization of smaller subunits called monomers. The four major classes of macromolecules are carbohydrates, proteins, nucleic acids, and lipids.

• Monomer: A small molecule that can join with others to form a polymer.

• Polymer: A large molecule made up of repeating monomer units.

• Bonds: The type of bond linking monomers varies by macromolecule (e.g., peptide bonds in proteins, glycosidic bonds in carbohydrates).

Example: Glucose is the monomer of starch (a carbohydrate polymer).

Covalent Bonds in Macromolecules

Each class of macromolecule has a specific covalent bond that links its monomers:

• Carbohydrates: Glycosidic bonds

• Proteins: Peptide bonds

• Nucleic Acids: Phosphodiester bonds

• Lipids: Ester linkages (between glycerol and fatty acids)

Example: The ester linkage in triglycerides connects glycerol to fatty acids.

Dehydration Synthesis and Hydrolysis

Macromolecules are assembled and disassembled by two key reactions:

• Dehydration Synthesis: Joins monomers by removing a water molecule.

• Hydrolysis: Breaks polymers into monomers by adding a water molecule.

Example: Peptide bond formation between amino acids is a dehydration synthesis reaction.

DNA Structure and Cell Types

Structure of DNA

DNA is a double helix composed of two strands of nucleotides held together by hydrogen bonds between complementary bases.

• Phosphodiester Bonds: Link nucleotides within a single DNA strand.

• Hydrogen Bonds: Stabilize the double helix by connecting complementary bases (A-T, G-C).

Example: The DNA double helix is stabilized by hydrogen bonds between adenine and thymine, and between guanine and cytosine.

Prokaryotic vs. Eukaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on their structural features.

• Prokaryotic Cells: Lack a nucleus and membrane-bound organelles; include bacteria and archaea.

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles; include plants, animals, fungi, and protists.

Example: Escherichia coli is a prokaryotic bacterium; human cells are eukaryotic.

Organelles of Eukaryotic Cells

Eukaryotic cells contain specialized structures called organelles, each with distinct functions.

• Nucleus: Contains genetic material (DNA).

• Endoplasmic Reticulum (ER): Synthesizes proteins (rough ER) and lipids (smooth ER).

• Mitochondria: Site of cellular respiration and energy production.

Example: Mitochondria are often called the "powerhouse" of the cell.

Cytoskeleton

The cytoskeleton is a network of protein filaments that provides structural support, enables cell movement, and organizes organelles.

• Components: Microfilaments, intermediate filaments, and microtubules.

Example: Microtubules help separate chromosomes during cell division.

Plasma Membrane and Transport

Molecules of the Plasma Membrane

The plasma membrane is primarily composed of a phospholipid bilayer with embedded proteins, cholesterol, and carbohydrates.

• Phospholipids: Form the basic structure of the membrane.

• Proteins: Serve as channels, receptors, and enzymes.

Example: Integral membrane proteins span the bilayer and facilitate transport.

Selective Permeability

The plasma membrane is selectively permeable, allowing certain molecules to pass while restricting others.

• Freely Diffusing Molecules: Small, nonpolar molecules (e.g., O2, CO2).

• Restricted Molecules: Large or charged molecules require transport proteins.

Example: Water can cross the membrane via aquaporins (channel proteins).

Table: Comparison of Prokaryotic and Eukaryotic Cells