Atoms and Elements

Subatomic Particles and Atomic Structure

Atoms are the fundamental units of matter, composed of three main subatomic particles: protons, neutrons, and electrons. Understanding atomic structure is essential for grasping chemical interactions in biological systems.

• Protons: Positively charged particles located in the nucleus.

• Neutrons: Neutral particles also found in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus in energy levels (shells).

The number of protons defines the atomic number and the element's identity. Electrons occupy various energy levels:

• 1st shell: up to 2 electrons

• 2nd shell: up to 8 electrons

• 3rd shell: up to 18 electrons (but is stable with 8)

Elements are arranged in the periodic table by increasing atomic number. Elements essential for life are classified as:

• Macroelements: Required in large amounts (e.g., C, H, O, N, Ca, P)

• Microelements (trace elements): Needed in small amounts (e.g., Fe, Zn, I)

Atomic Number and Mass Number

• Atomic Number: Number of protons in the nucleus.

• Mass Number: Total number of protons and neutrons.

To determine the number of neutrons:

• Subtract the atomic number from the mass number.

Chemical Bonds and Molecules

Types of Mixtures

• Suspension: Large particles, visible, will settle out (e.g., blood cells in plasma).

• Colloid: Intermediate particles, not visible, do not settle (e.g., cytoplasm).

• Solution: Small particles, not visible, do not settle, transparent (e.g., salt water).

Compounds and Molecules

• Compound: Two or more elements chemically combined.

• Molecule: Two or more atoms bonded together.

• Molecular formula: Shows the types and numbers of atoms (e.g., H2O).

• Molecular weight: Sum of atomic masses of all atoms in a molecule.

Formation of Chemical Bonds

Atoms form bonds to achieve stable electron configurations, often following the:

• Octet Rule: Atoms are most stable with 8 electrons in their outer shell.

• Duet Rule: Atoms with only one shell are stable with 2 electrons.

Inert atoms have full outer shells and are unreactive (e.g., Helium, Neon). Reactive atoms have incomplete outer shells and tend to form bonds (e.g., Hydrogen, Lithium).

Ions and Ionic Bonds

• Ion: Atom or molecule with a net charge due to loss or gain of electrons.

• Cation: Positively charged ion (lost electrons).

• Anion: Negatively charged ion (gained electrons).

Ionic bonds form when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other (e.g., NaCl).

Covalent Bonds

• Formed by sharing one or more pairs of electrons between atoms.

• Polar covalent bonds: Electrons are shared unequally, creating partial charges (e.g., H2O).

• Nonpolar covalent bonds: Electrons are shared equally (e.g., O2).

Hydrogen Bonds

• Weak attractions between a hydrogen atom (partially positive) and an electronegative atom (partially negative) in another molecule.

• Important in stabilizing the structure of water, proteins, and nucleic acids.

Chemical Reactions and Energy

Chemical Equations

Chemical equations represent the reactants and products in a chemical reaction. For example:

• Reactants: Starting substances.

• Products: Substances formed.

Types of Chemical Reactions

• Synthesis (Anabolism): Building larger molecules from smaller ones; energy required.

  • Example: Dehydration synthesis (removal of water to form bonds).

• Decomposition (Catabolism): Breaking down molecules; energy released.

  • Example: Hydrolysis (addition of water to break bonds).

• Exchange: Bonds are broken and new bonds are formed (e.g., acid-base reactions).

• Oxidation-Reduction (Redox): Transfer of electrons between atoms.

Energy in Biological Systems

• Potential energy: Stored energy (e.g., chemical bonds).

• Kinetic energy: Energy of motion.

• Chemical energy: Energy stored in chemical bonds.

• Electrical energy: Movement of charged particles.

• Mechanical energy: Directly involved in moving matter.

• Endergonic reaction: Absorbs energy.

• Exergonic reaction: Releases energy.

Enzymes and Reaction Rates

• Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Enzymes are specific to substrates and can be reused.

• Denaturation (loss of shape) can occur due to heat or pH changes, rendering enzymes inactive.

Inorganic Compounds: Water, Acids, Bases, and Salts

Properties of Water

• Excellent solvent (dissolves many substances).

• High heat capacity (absorbs and retains heat).

• High heat of vaporization (energy required to evaporate).

• Lubricates and cushions organs.

Water molecules are polar and can form hydrogen bonds, contributing to surface tension and other unique properties.

Acids, Bases, and pH

• Acids release H+ ions in solution; bases release OH- ions.

• pH scale measures H+ concentration (0-14):

  • pH < 7: Acidic

  • pH = 7: Neutral

  • pH > 7: Basic (alkaline)

• Buffers help maintain stable pH in the body.

Organic Compounds: Carbohydrates, Lipids, Proteins, and Nucleic Acids

General Features

• Organic molecules contain carbon, often bonded to hydrogen, oxygen, nitrogen, or other elements.

• Carbon forms the backbone of organic molecules, which may be straight chains, branched, or rings.

• Most organic compounds are polymers made from monomers.

• Polymers are built by dehydration synthesis and broken down by hydrolysis.

Carbohydrates

• Primary energy source for cells.

• Composed of carbon, hydrogen, and oxygen (CH2O).

• Types:

  • Monosaccharides: Simple sugars (e.g., glucose).

  • Disaccharides: Two monosaccharides joined (e.g., sucrose).

  • Polysaccharides: Long chains (e.g., glycogen, starch).

Lipids

• Hydrophobic molecules including fats, oils, and steroids.

• Types:

  • Glycerides: Composed of glycerol and fatty acids.

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

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

  • Phospholipids: Glycerol, two fatty acids, and a phosphate group; amphiphilic (hydrophilic head, hydrophobic tails); key component of cell membranes.

  • Steroids: Four fused carbon rings (e.g., cholesterol, hormones).

Proteins

• Polymers of amino acids joined by peptide bonds.

• Functions: Enzymes, structural support, transport, signaling, defense.

• Structure: Primary (sequence), secondary (folding), tertiary (3D shape), quaternary (multiple chains).

Nucleic Acids

• DNA and RNA store and transmit genetic information.

• Monomers: Nucleotides (sugar, phosphate, nitrogenous base).

Additional info: These foundational concepts in chemistry are essential for understanding physiological processes, including metabolism, cellular structure, and molecular interactions in the human body.